gew 2.3

Jonathan Bell [2012-02-15 15:38:25]
gew 2.3
Filename
create.sql
genspace-common/src/org/geworkbench/components/genspace/entity/Tool.java
genspace-common/src/org/geworkbench/components/genspace/server/stubs/UserFacade.java
genspace-common/src/org/geworkbench/components/genspace/server/stubs/WorkflowRepository.java
genspace-ejb/build/classes/META-INF/persistence.xml
genspace-ejb/ejbModule/META-INF/persistence.xml
genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/GenericUsageInformation.java
genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/WorkflowRepository.java
genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/task/WorkflowStatisticsMaintainer.java
geworkbench-core/.settings/.svn/entries
geworkbench-core/.svn/all-wcprops
geworkbench-core/.svn/entries
geworkbench-core/_all/.svn/entries
geworkbench-core/annotation/.svn/entries
geworkbench-core/bin/.svn/entries
geworkbench-core/bin/matrixreduce/.svn/entries
geworkbench-core/cascripts/.svn/entries
geworkbench-core/classes/.svn/entries
geworkbench-core/classes/cruisecontrol/.svn/entries
geworkbench-core/classes/images/.svn/entries
geworkbench-core/classes/org/.svn/all-wcprops
geworkbench-core/classes/org/.svn/entries
geworkbench-core/classes/org/geworkbench/.svn/all-wcprops
geworkbench-core/classes/org/geworkbench/.svn/entries
geworkbench-core/classes/org/geworkbench/analysis/.svn/all-wcprops
geworkbench-core/classes/org/geworkbench/analysis/.svn/entries
geworkbench-core/classes/org/geworkbench/analysis/.svn/text-base/AbstractAnalysis.java.svn-base
geworkbench-core/classes/org/geworkbench/bison/.svn/all-wcprops
geworkbench-core/classes/org/geworkbench/bison/.svn/entries
geworkbench-core/classes/org/geworkbench/bison/algorithm/.svn/entries
geworkbench-core/classes/org/geworkbench/bison/algorithm/classification/.svn/entries
geworkbench-core/classes/org/geworkbench/bison/annotation/.svn/entries
geworkbench-core/classes/org/geworkbench/bison/datastructure/.svn/all-wcprops
geworkbench-core/classes/org/geworkbench/bison/datastructure/.svn/entries
geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/.svn/all-wcprops
geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/.svn/entries
geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/gsea/.svn/entries
geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/medusa/.svn/entries
geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/microarrays/.svn/all-wcprops
geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/microarrays/.svn/entries
geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/microarrays/.svn/text-base/CSMicroarraySet.java.svn-base
geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/pca/.svn/entries
geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/sequences/.svn/entries
geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/views/.svn/entries
geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/.svn/all-wcprops
geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/.svn/entries
geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/markers/.svn/all-wcprops
geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/markers/.svn/entries
geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/markers/annotationparser/.svn/entries
geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/markers/goterms/.svn/all-wcprops
geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/markers/goterms/.svn/entries
geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/markers/goterms/.svn/text-base/GeneOntologyTree.java.svn-base
geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/microarray/.svn/entries
geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/sequence/.svn/entries
geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/structure/.svn/entries
geworkbench-core/classes/org/geworkbench/bison/datastructure/complex/.svn/entries
geworkbench-core/classes/org/geworkbench/bison/datastructure/complex/panels/.svn/entries
geworkbench-core/classes/org/geworkbench/bison/datastructure/complex/pattern/.svn/entries
geworkbench-core/classes/org/geworkbench/bison/datastructure/complex/pattern/matrix/.svn/entries
geworkbench-core/classes/org/geworkbench/bison/datastructure/complex/pattern/sequence/.svn/entries
geworkbench-core/classes/org/geworkbench/bison/datastructure/properties/.svn/entries
geworkbench-core/classes/org/geworkbench/bison/model/.svn/entries
geworkbench-core/classes/org/geworkbench/bison/model/analysis/.svn/entries
geworkbench-core/classes/org/geworkbench/bison/model/clusters/.svn/entries
geworkbench-core/classes/org/geworkbench/bison/parsers/.svn/entries
geworkbench-core/classes/org/geworkbench/bison/parsers/resources/.svn/entries
geworkbench-core/classes/org/geworkbench/bison/util/.svn/all-wcprops
geworkbench-core/classes/org/geworkbench/bison/util/.svn/entries
geworkbench-core/classes/org/geworkbench/bison/util/colorcontext/.svn/all-wcprops
geworkbench-core/classes/org/geworkbench/bison/util/colorcontext/.svn/entries
geworkbench-core/classes/org/geworkbench/bison/util/colorcontext/.svn/text-base/ExpressionPValueColorContext.java.svn-base
geworkbench-core/classes/org/geworkbench/builtin/.svn/all-wcprops
geworkbench-core/classes/org/geworkbench/builtin/.svn/entries
geworkbench-core/classes/org/geworkbench/builtin/projects/.svn/all-wcprops
geworkbench-core/classes/org/geworkbench/builtin/projects/.svn/entries
geworkbench-core/classes/org/geworkbench/builtin/projects/.svn/text-base/FileOpenHandler.java.svn-base
geworkbench-core/classes/org/geworkbench/builtin/projects/comments/.svn/entries
geworkbench-core/classes/org/geworkbench/builtin/projects/comments/help/.svn/entries
geworkbench-core/classes/org/geworkbench/builtin/projects/comments/help/Dataset annotation_files/.svn/entries
geworkbench-core/classes/org/geworkbench/builtin/projects/experimentinformation/.svn/entries
geworkbench-core/classes/org/geworkbench/builtin/projects/experimentinformation/help/.svn/entries
geworkbench-core/classes/org/geworkbench/builtin/projects/experimentinformation/help/infoPanel_files/.svn/entries
geworkbench-core/classes/org/geworkbench/builtin/projects/help/.svn/entries
geworkbench-core/classes/org/geworkbench/builtin/projects/help/Manage_workspace_files/.svn/entries
geworkbench-core/classes/org/geworkbench/builtin/projects/help/delete_dataset_files/.svn/entries
geworkbench-core/classes/org/geworkbench/builtin/projects/help/manage_projected_files/.svn/entries
geworkbench-core/classes/org/geworkbench/builtin/projects/help/merge_dataset_files/.svn/entries
geworkbench-core/classes/org/geworkbench/builtin/projects/help/open_dataset_files/.svn/entries
geworkbench-core/classes/org/geworkbench/builtin/projects/help/projects area_overviewed_files/.svn/entries
geworkbench-core/classes/org/geworkbench/builtin/projects/help/remote_files/.svn/entries
geworkbench-core/classes/org/geworkbench/builtin/projects/help/rename_dataset_files/.svn/entries
geworkbench-core/classes/org/geworkbench/builtin/projects/help/user preference_files/.svn/entries
geworkbench-core/classes/org/geworkbench/builtin/projects/history/.svn/entries
geworkbench-core/classes/org/geworkbench/builtin/projects/history/help/.svn/entries
geworkbench-core/classes/org/geworkbench/builtin/projects/history/help/historyPanel_files/.svn/entries
geworkbench-core/classes/org/geworkbench/builtin/projects/history/help/images/.svn/entries
geworkbench-core/classes/org/geworkbench/builtin/projects/remoteresources/.svn/entries
geworkbench-core/classes/org/geworkbench/builtin/projects/remoteresources/carraydata/.svn/entries
geworkbench-core/classes/org/geworkbench/builtin/projects/target/.svn/entries
geworkbench-core/classes/org/geworkbench/builtin/projects/util/.svn/all-wcprops
geworkbench-core/classes/org/geworkbench/builtin/projects/util/.svn/entries
geworkbench-core/classes/org/geworkbench/builtin/projects/util/.svn/text-base/CaARRAYPanel.java.svn-base
geworkbench-core/classes/org/geworkbench/components/.svn/entries
geworkbench-core/classes/org/geworkbench/components/caarray/.svn/all-wcprops
geworkbench-core/classes/org/geworkbench/components/caarray/.svn/entries
geworkbench-core/classes/org/geworkbench/components/caarray/arraydata/.svn/all-wcprops
geworkbench-core/classes/org/geworkbench/components/caarray/arraydata/.svn/entries
geworkbench-core/classes/org/geworkbench/components/caarray/arraydata/.svn/text-base/CaArray2Component.java.svn-base
geworkbench-core/classes/org/geworkbench/components/genspace/.svn/all-wcprops
geworkbench-core/classes/org/geworkbench/components/genspace/.svn/entries
geworkbench-core/classes/org/geworkbench/components/genspace/.svn/text-base/GenSpaceServerFactory.java.svn-base
geworkbench-core/classes/org/geworkbench/components/genspace/bean/.svn/entries
geworkbench-core/classes/org/geworkbench/components/genspace/chat/.svn/all-wcprops
geworkbench-core/classes/org/geworkbench/components/genspace/chat/.svn/entries
geworkbench-core/classes/org/geworkbench/components/genspace/chat/.svn/text-base/ChatReceiver.java.svn-base
geworkbench-core/classes/org/geworkbench/components/genspace/help/.svn/entries
geworkbench-core/classes/org/geworkbench/components/genspace/help/genspace_files/.svn/entries
geworkbench-core/classes/org/geworkbench/components/genspace/rating/.svn/entries
geworkbench-core/classes/org/geworkbench/components/genspace/server/.svn/all-wcprops
geworkbench-core/classes/org/geworkbench/components/genspace/server/.svn/entries
geworkbench-core/classes/org/geworkbench/components/genspace/server/wrapper/.svn/all-wcprops
geworkbench-core/classes/org/geworkbench/components/genspace/server/wrapper/.svn/entries
geworkbench-core/classes/org/geworkbench/components/genspace/server/wrapper/.svn/text-base/WorkflowWrapper.java.svn-base
geworkbench-core/classes/org/geworkbench/components/genspace/ui/.svn/all-wcprops
geworkbench-core/classes/org/geworkbench/components/genspace/ui/.svn/entries
geworkbench-core/classes/org/geworkbench/components/genspace/ui/.svn/text-base/WorkflowVisualizationPanel.java.svn-base
geworkbench-core/classes/org/geworkbench/components/genspace/ui/chat/.svn/entries
geworkbench-core/classes/org/geworkbench/components/genspace/ui/graph/.svn/all-wcprops
geworkbench-core/classes/org/geworkbench/components/genspace/ui/graph/.svn/entries
geworkbench-core/classes/org/geworkbench/components/genspace/ui/graph/.svn/text-base/myStackLayout.java.svn-base
geworkbench-core/classes/org/geworkbench/components/genspace/workflowRepository/.svn/all-wcprops
geworkbench-core/classes/org/geworkbench/components/genspace/workflowRepository/.svn/entries
geworkbench-core/classes/org/geworkbench/components/genspace/workflowRepository/.svn/text-base/WorkflowCommentsPanel.java.svn-base
geworkbench-core/classes/org/geworkbench/engine/.svn/all-wcprops
geworkbench-core/classes/org/geworkbench/engine/.svn/entries
geworkbench-core/classes/org/geworkbench/engine/ccm/.svn/entries
geworkbench-core/classes/org/geworkbench/engine/config/.svn/entries
geworkbench-core/classes/org/geworkbench/engine/config/events/.svn/entries
geworkbench-core/classes/org/geworkbench/engine/config/rules/.svn/entries
geworkbench-core/classes/org/geworkbench/engine/help/.svn/entries
geworkbench-core/classes/org/geworkbench/engine/help/caWorkbench introduction_files/.svn/entries
geworkbench-core/classes/org/geworkbench/engine/help/ccm_files/.svn/entries
geworkbench-core/classes/org/geworkbench/engine/help/images/.svn/entries
geworkbench-core/classes/org/geworkbench/engine/management/.svn/entries
geworkbench-core/classes/org/geworkbench/engine/preferences/.svn/entries
geworkbench-core/classes/org/geworkbench/engine/properties/.svn/entries
geworkbench-core/classes/org/geworkbench/engine/skin/.svn/all-wcprops
geworkbench-core/classes/org/geworkbench/engine/skin/.svn/entries
geworkbench-core/classes/org/geworkbench/engine/skin/.svn/text-base/Skin.java.svn-base
geworkbench-core/classes/org/geworkbench/events/.svn/entries
geworkbench-core/classes/org/geworkbench/events/listeners/.svn/entries
geworkbench-core/classes/org/geworkbench/parsers/.svn/all-wcprops
geworkbench-core/classes/org/geworkbench/parsers/.svn/entries
geworkbench-core/classes/org/geworkbench/parsers/.svn/text-base/MageTabFileFormat.java.svn-base
geworkbench-core/classes/org/geworkbench/parsers/.svn/text-base/MicroarraySetParser.java.svn-base
geworkbench-core/classes/org/geworkbench/parsers/.svn/text-base/SOFTFileFormat.java.svn-base
geworkbench-core/classes/org/geworkbench/parsers/.svn/text-base/SampleFileParser.java.svn-base
geworkbench-core/classes/org/geworkbench/parsers/.svn/text-base/TabDelimitedDataMatrixFileFormat.java.svn-base
geworkbench-core/classes/org/geworkbench/parsers/sequences/.svn/all-wcprops
geworkbench-core/classes/org/geworkbench/parsers/sequences/.svn/entries
geworkbench-core/classes/org/geworkbench/parsers/sequences/.svn/text-base/SequenceFileFormat.java.svn-base
geworkbench-core/classes/org/geworkbench/util/.svn/all-wcprops
geworkbench-core/classes/org/geworkbench/util/.svn/entries
geworkbench-core/classes/org/geworkbench/util/.svn/text-base/splashscreen.png.svn-base
geworkbench-core/classes/org/geworkbench/util/annotation/.svn/entries
geworkbench-core/classes/org/geworkbench/util/associationdiscovery/.svn/entries
geworkbench-core/classes/org/geworkbench/util/associationdiscovery/cluster/.svn/entries
geworkbench-core/classes/org/geworkbench/util/associationdiscovery/statistics/.svn/entries
geworkbench-core/classes/org/geworkbench/util/microarrayutils/.svn/entries
geworkbench-core/classes/org/geworkbench/util/network/.svn/entries
geworkbench-core/classes/org/geworkbench/util/pathwaydecoder/.svn/entries
geworkbench-core/classes/org/geworkbench/util/pathwaydecoder/mutualinformation/.svn/entries
geworkbench-core/classes/org/geworkbench/util/patterns/.svn/entries
geworkbench-core/classes/org/geworkbench/util/sequences/.svn/entries
geworkbench-core/classes/org/geworkbench/util/splashscreen.png
geworkbench-core/classes/org/geworkbench/util/visualproperties/.svn/entries
geworkbench-core/components/.svn/all-wcprops
geworkbench-core/components/.svn/entries
geworkbench-core/components/alignment/.svn/all-wcprops
geworkbench-core/components/alignment/.svn/entries
geworkbench-core/components/alignment/lib/.svn/entries
geworkbench-core/components/alignment/src/.svn/all-wcprops
geworkbench-core/components/alignment/src/.svn/entries
geworkbench-core/components/alignment/src/org/.svn/all-wcprops
geworkbench-core/components/alignment/src/org/.svn/entries
geworkbench-core/components/alignment/src/org/geworkbench/.svn/all-wcprops
geworkbench-core/components/alignment/src/org/geworkbench/.svn/entries
geworkbench-core/components/alignment/src/org/geworkbench/components/.svn/all-wcprops
geworkbench-core/components/alignment/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/.svn/all-wcprops
geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/.svn/entries
geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/.svn/all-wcprops
geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/.svn/entries
geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/.svn/text-base/AlgorithmMatcher.java.svn-base
geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/.svn/text-base/BlastAnalysis.java.svn-base
geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/.svn/text-base/BlastAnalysisPanel.java.svn-base
geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/.svn/text-base/NCBIBlastParser.java.svn-base
geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/AlgorithmMatcher.java
geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/BlastAnalysis.java
geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/BlastAnalysisPanel.java
geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/NCBIBlastParser.java
geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/help/.svn/entries
geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/help/blast_files/.svn/entries
geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/.svn/entries
geworkbench-core/components/analysis/.classpath
geworkbench-core/components/analysis/.svn/all-wcprops
geworkbench-core/components/analysis/.svn/entries
geworkbench-core/components/analysis/.svn/text-base/.classpath.svn-base
geworkbench-core/components/analysis/lib/.svn/all-wcprops
geworkbench-core/components/analysis/lib/.svn/entries
geworkbench-core/components/analysis/lib/.svn/text-base/Dispatcher-client.jar.svn-base
geworkbench-core/components/analysis/lib/.svn/text-base/Dispatcher-common.jar.svn-base
geworkbench-core/components/analysis/lib/.svn/text-base/Dispatcher-stubs.jar.svn-base
geworkbench-core/components/analysis/lib/Dispatcher-client.jar
geworkbench-core/components/analysis/lib/Dispatcher-common.jar
geworkbench-core/components/analysis/lib/Dispatcher-stubs.jar
geworkbench-core/components/analysis/src/.svn/all-wcprops
geworkbench-core/components/analysis/src/.svn/entries
geworkbench-core/components/analysis/src/edu/.svn/entries
geworkbench-core/components/analysis/src/edu/columbia/.svn/entries
geworkbench-core/components/analysis/src/edu/columbia/geworkbench/.svn/entries
geworkbench-core/components/analysis/src/edu/columbia/geworkbench/cagrid/.svn/entries
geworkbench-core/components/analysis/src/edu/columbia/geworkbench/cagrid/discovery/.svn/entries
geworkbench-core/components/analysis/src/edu/columbia/geworkbench/cagrid/discovery/client/.svn/entries
geworkbench-core/components/analysis/src/org/.svn/all-wcprops
geworkbench-core/components/analysis/src/org/.svn/entries
geworkbench-core/components/analysis/src/org/geworkbench/.svn/all-wcprops
geworkbench-core/components/analysis/src/org/geworkbench/.svn/entries
geworkbench-core/components/analysis/src/org/geworkbench/components/.svn/all-wcprops
geworkbench-core/components/analysis/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/.svn/all-wcprops
geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/.svn/entries
geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/.svn/text-base/AnalysisPanel.java.svn-base
geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/.svn/text-base/PollingThread.java.svn-base
geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/AnalysisPanel.java
geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/PollingThread.java
geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/.svn/entries
geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/Pattern Discovery/.svn/entries
geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/Pattern Discovery/DiscoveryOverviewed_files/.svn/entries
geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/Pattern Discovery/Pattern Discovery Parameter Settings_files/.svn/entries
geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/clustering/.svn/entries
geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/clustering/Hierarchical Clusteringed_files/.svn/entries
geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/clustering/SOMCluster_files/.svn/entries
geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/clustering/images/.svn/entries
geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/normalizers/.svn/entries
geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/normalizers/Housekeeping%20Gene%20Normalization[2]_files/.svn/entries
geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/normalizers/Housekeeping_files/.svn/entries
geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/normalizers/MarkerMean Normalizered_files/.svn/entries
geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/normalizers/Normalizers Overviewed_files/.svn/entries
geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/normalizers/Quantile_files/.svn/entries
geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/normalizers/images/.svn/entries
geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/ttest/.svn/entries
geworkbench-core/components/analysis/src/org/geworkbench/components/cagrid/.svn/entries
geworkbench-core/components/analysis/src/org/geworkbench/components/cagrid/gui/.svn/entries
geworkbench-core/components/annotations/.classpath
geworkbench-core/components/annotations/.svn/all-wcprops
geworkbench-core/components/annotations/.svn/entries
geworkbench-core/components/annotations/.svn/text-base/.classpath.svn-base
geworkbench-core/components/annotations/conf/.svn/entries
geworkbench-core/components/annotations/lib/.svn/entries
geworkbench-core/components/annotations/src/.svn/entries
geworkbench-core/components/annotations/src/org/.svn/entries
geworkbench-core/components/annotations/src/org/geworkbench/.svn/entries
geworkbench-core/components/annotations/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/annotations/src/org/geworkbench/components/annotations/.svn/entries
geworkbench-core/components/annotations/src/org/geworkbench/components/annotations/help/.svn/entries
geworkbench-core/components/annotations/src/org/geworkbench/components/annotations/help/annotationspanel/.svn/entries
geworkbench-core/components/annotations/src/org/geworkbench/components/annotations/help/annotationspanel/images/.svn/entries
geworkbench-core/components/annotations/src/org/geworkbench/components/annotations/help/annotationspanel/markerannotationsed_final_files/.svn/entries
geworkbench-core/components/annotations/src/org/geworkbench/components/annotations/help/pathwaypanel/.svn/entries
geworkbench-core/components/annotations/src/org/geworkbench/components/annotations/help/pathwaypanel/pathwaysed_files/.svn/entries
geworkbench-core/components/anova/.settings/.svn/entries
geworkbench-core/components/anova/.svn/entries
geworkbench-core/components/anova/conf/.svn/entries
geworkbench-core/components/anova/lib/.svn/entries
geworkbench-core/components/anova/src/.svn/entries
geworkbench-core/components/anova/src/org/.svn/entries
geworkbench-core/components/anova/src/org/geworkbench/.svn/entries
geworkbench-core/components/anova/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/anova/src/org/geworkbench/components/anova/.svn/entries
geworkbench-core/components/anova/src/org/geworkbench/components/anova/gui/.svn/entries
geworkbench-core/components/anova/src/org/geworkbench/components/anova/help/.svn/entries
geworkbench-core/components/anova/src/org/geworkbench/components/anova/help/anova_files/.svn/entries
geworkbench-core/components/aracne-java/.svn/all-wcprops
geworkbench-core/components/aracne-java/.svn/entries
geworkbench-core/components/aracne-java/lib/.svn/entries
geworkbench-core/components/aracne-java/src/.svn/all-wcprops
geworkbench-core/components/aracne-java/src/.svn/entries
geworkbench-core/components/aracne-java/src/org/.svn/all-wcprops
geworkbench-core/components/aracne-java/src/org/.svn/entries
geworkbench-core/components/aracne-java/src/org/geworkbench/.svn/all-wcprops
geworkbench-core/components/aracne-java/src/org/geworkbench/.svn/entries
geworkbench-core/components/aracne-java/src/org/geworkbench/components/.svn/all-wcprops
geworkbench-core/components/aracne-java/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/aracne-java/src/org/geworkbench/components/aracne/.svn/all-wcprops
geworkbench-core/components/aracne-java/src/org/geworkbench/components/aracne/.svn/entries
geworkbench-core/components/aracne-java/src/org/geworkbench/components/aracne/.svn/text-base/AracneAnalysis.java.svn-base
geworkbench-core/components/aracne-java/src/org/geworkbench/components/aracne/AracneAnalysis.java
geworkbench-core/components/aracne-java/src/org/geworkbench/components/aracne/help/.svn/entries
geworkbench-core/components/aracne-java/src/org/geworkbench/components/aracne/help/aracne_files/.svn/entries
geworkbench-core/components/caarray/.svn/all-wcprops
geworkbench-core/components/caarray/.svn/entries
geworkbench-core/components/caarray/lib/.svn/entries
geworkbench-core/components/caarray/src/.svn/all-wcprops
geworkbench-core/components/caarray/src/.svn/entries
geworkbench-core/components/caarray/src/org/.svn/all-wcprops
geworkbench-core/components/caarray/src/org/.svn/entries
geworkbench-core/components/caarray/src/org/geworkbench/.svn/all-wcprops
geworkbench-core/components/caarray/src/org/geworkbench/.svn/entries
geworkbench-core/components/caarray/src/org/geworkbench/components/.svn/all-wcprops
geworkbench-core/components/caarray/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/caarray/src/org/geworkbench/components/caarray/.svn/all-wcprops
geworkbench-core/components/caarray/src/org/geworkbench/components/caarray/.svn/entries
geworkbench-core/components/caarray/src/org/geworkbench/components/caarray/arraydata/.svn/all-wcprops
geworkbench-core/components/caarray/src/org/geworkbench/components/caarray/arraydata/.svn/entries
geworkbench-core/components/caarray/src/org/geworkbench/components/caarray/arraydata/.svn/text-base/CaArray2Component.java.svn-base
geworkbench-core/components/caarray/src/org/geworkbench/components/caarray/arraydata/CaArray2Component.java
geworkbench-core/components/celprocessing/.svn/entries
geworkbench-core/components/celprocessing/src/.svn/entries
geworkbench-core/components/celprocessing/src/org/.svn/entries
geworkbench-core/components/celprocessing/src/org/geworkbench/.svn/entries
geworkbench-core/components/celprocessing/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/celprocessing/src/org/geworkbench/components/celprocessing/.svn/entries
geworkbench-core/components/celprocessing/src/org/geworkbench/components/celprocessing/help/.svn/entries
geworkbench-core/components/celprocessing/src/org/geworkbench/components/celprocessing/help/open_dataset_files/.svn/entries
geworkbench-core/components/cgems/.svn/entries
geworkbench-core/components/cgems/conf/.svn/entries
geworkbench-core/components/cgems/lib/.svn/entries
geworkbench-core/components/cgems/src/.svn/entries
geworkbench-core/components/cgems/src/gov/.svn/entries
geworkbench-core/components/cgems/src/gov/nih/.svn/entries
geworkbench-core/components/cgems/src/gov/nih/nci/.svn/entries
geworkbench-core/components/cgems/src/gov/nih/nci/system/.svn/entries
geworkbench-core/components/cgems/src/gov/nih/nci/system/comm/.svn/entries
geworkbench-core/components/cgems/src/gov/nih/nci/system/comm/client/.svn/entries
geworkbench-core/components/cgems/src/org/.svn/entries
geworkbench-core/components/cgems/src/org/geworkbench/.svn/entries
geworkbench-core/components/cgems/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/cgems/src/org/geworkbench/components/cgems/.svn/entries
geworkbench-core/components/colormosaic/.svn/all-wcprops
geworkbench-core/components/colormosaic/.svn/entries
geworkbench-core/components/colormosaic/classes/org/geworkbench/components/colormosaic/ColorMosaicPanel.cwb.xml
geworkbench-core/components/colormosaic/src/.svn/all-wcprops
geworkbench-core/components/colormosaic/src/.svn/entries
geworkbench-core/components/colormosaic/src/org/.svn/all-wcprops
geworkbench-core/components/colormosaic/src/org/.svn/entries
geworkbench-core/components/colormosaic/src/org/geworkbench/.svn/all-wcprops
geworkbench-core/components/colormosaic/src/org/geworkbench/.svn/entries
geworkbench-core/components/colormosaic/src/org/geworkbench/components/.svn/all-wcprops
geworkbench-core/components/colormosaic/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/colormosaic/src/org/geworkbench/components/colormosaic/.svn/all-wcprops
geworkbench-core/components/colormosaic/src/org/geworkbench/components/colormosaic/.svn/entries
geworkbench-core/components/colormosaic/src/org/geworkbench/components/colormosaic/.svn/text-base/CMVRuler.java.svn-base
geworkbench-core/components/colormosaic/src/org/geworkbench/components/colormosaic/.svn/text-base/ColorMosaicImage.java.svn-base
geworkbench-core/components/colormosaic/src/org/geworkbench/components/colormosaic/.svn/text-base/ColorMosaicPanel.cwb.xml.svn-base
geworkbench-core/components/colormosaic/src/org/geworkbench/components/colormosaic/.svn/text-base/ColorMosaicPanel.java.svn-base
geworkbench-core/components/colormosaic/src/org/geworkbench/components/colormosaic/CMVRuler.java
geworkbench-core/components/colormosaic/src/org/geworkbench/components/colormosaic/ColorMosaicImage.java
geworkbench-core/components/colormosaic/src/org/geworkbench/components/colormosaic/ColorMosaicPanel.cwb.xml
geworkbench-core/components/colormosaic/src/org/geworkbench/components/colormosaic/ColorMosaicPanel.java
geworkbench-core/components/colormosaic/src/org/geworkbench/components/colormosaic/help/.svn/entries
geworkbench-core/components/colormosaic/src/org/geworkbench/components/colormosaic/help/ColorMosaic View_files/.svn/entries
geworkbench-core/components/cupid/.settings/.svn/entries
geworkbench-core/components/cupid/.svn/entries
geworkbench-core/components/cupid/src/.svn/entries
geworkbench-core/components/cupid/src/org/.svn/entries
geworkbench-core/components/cupid/src/org/geworkbench/.svn/entries
geworkbench-core/components/cupid/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/cupid/src/org/geworkbench/components/cupid/.svn/entries
geworkbench-core/components/cutenet/.svn/entries
geworkbench-core/components/cutenet/lib/.svn/entries
geworkbench-core/components/cutenet/lib/kodo/.svn/entries
geworkbench-core/components/cutenet/src/.svn/entries
geworkbench-core/components/cutenet/src/org/.svn/entries
geworkbench-core/components/cutenet/src/org/geworkbench/.svn/entries
geworkbench-core/components/cutenet/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/cutenet/src/org/geworkbench/components/cutenet/.svn/entries
geworkbench-core/components/cutenet/src/org/geworkbench/components/cytoscape_v2_4/.svn/entries
geworkbench-core/components/cutenet/src/org/geworkbench/components/cytoscape_v2_4/help/.svn/entries
geworkbench-core/components/cutenet/src/org/geworkbench/components/cytoscape_v2_4/help/cytoscape_files/.svn/entries
geworkbench-core/components/cytoscape/.svn/all-wcprops
geworkbench-core/components/cytoscape/.svn/entries
geworkbench-core/components/cytoscape/classes/org/geworkbench/components/cytoscape/CytoscapeWidget.cwb.xml
geworkbench-core/components/cytoscape/lib/.svn/all-wcprops
geworkbench-core/components/cytoscape/lib/.svn/entries
geworkbench-core/components/cytoscape/lib/.svn/text-base/biopax-2.8.2-jar-with-dependencies.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/cpath2-2.8.2-jar-with-dependencies.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/table-import-2.8.2-jar-with-dependencies.jar.svn-base
geworkbench-core/components/cytoscape/lib/biopax-2.8.2-jar-with-dependencies.jar
geworkbench-core/components/cytoscape/lib/cpath2-2.8.2-jar-with-dependencies.jar
geworkbench-core/components/cytoscape/lib/table-import-2.8.2-jar-with-dependencies.jar
geworkbench-core/components/cytoscape/src/.svn/all-wcprops
geworkbench-core/components/cytoscape/src/.svn/entries
geworkbench-core/components/cytoscape/src/org/.svn/all-wcprops
geworkbench-core/components/cytoscape/src/org/.svn/entries
geworkbench-core/components/cytoscape/src/org/geworkbench/.svn/all-wcprops
geworkbench-core/components/cytoscape/src/org/geworkbench/.svn/entries
geworkbench-core/components/cytoscape/src/org/geworkbench/components/.svn/all-wcprops
geworkbench-core/components/cytoscape/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/cytoscape/src/org/geworkbench/components/cytoscape/.svn/all-wcprops
geworkbench-core/components/cytoscape/src/org/geworkbench/components/cytoscape/.svn/entries
geworkbench-core/components/cytoscape/src/org/geworkbench/components/cytoscape/.svn/text-base/CytoscapeWidget.java.svn-base
geworkbench-core/components/cytoscape/src/org/geworkbench/components/cytoscape/CytoscapeWidget.java
geworkbench-core/components/cytoscape/src/org/geworkbench/components/cytoscape/help/.svn/entries
geworkbench-core/components/cytoscape/src/org/geworkbench/components/cytoscape/help/Cytoscape_files/.svn/entries
geworkbench-core/components/discovery/.svn/all-wcprops
geworkbench-core/components/discovery/.svn/entries
geworkbench-core/components/discovery/lib/.svn/entries
geworkbench-core/components/discovery/src/.svn/all-wcprops
geworkbench-core/components/discovery/src/.svn/entries
geworkbench-core/components/discovery/src/org/.svn/all-wcprops
geworkbench-core/components/discovery/src/org/.svn/entries
geworkbench-core/components/discovery/src/org/geworkbench/.svn/all-wcprops
geworkbench-core/components/discovery/src/org/geworkbench/.svn/entries
geworkbench-core/components/discovery/src/org/geworkbench/components/.svn/all-wcprops
geworkbench-core/components/discovery/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/.svn/all-wcprops
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/.svn/entries
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/.svn/text-base/PatternDiscoveryParamPanel.java.svn-base
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/PatternDiscoveryParamPanel.java
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/help/.svn/entries
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/help/patternDiscovery_files/.svn/entries
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/session/.svn/entries
geworkbench-core/components/evidenceintegration/.svn/entries
geworkbench-core/components/evidenceintegration/lib/.svn/entries
geworkbench-core/components/evidenceintegration/src/.svn/entries
geworkbench-core/components/evidenceintegration/src/org/.svn/entries
geworkbench-core/components/evidenceintegration/src/org/geworkbench/.svn/entries
geworkbench-core/components/evidenceintegration/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/evidenceintegration/src/org/geworkbench/components/ei/.svn/entries
geworkbench-core/components/example/.svn/entries
geworkbench-core/components/example/src/.svn/entries
geworkbench-core/components/example/src/org/.svn/entries
geworkbench-core/components/example/src/org/geworkbench/.svn/entries
geworkbench-core/components/example/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/example/src/org/geworkbench/components/example/.svn/entries
geworkbench-core/components/filtering/.svn/entries
geworkbench-core/components/filtering/src/.svn/entries
geworkbench-core/components/filtering/src/org/.svn/entries
geworkbench-core/components/filtering/src/org/geworkbench/.svn/entries
geworkbench-core/components/filtering/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/filtering/src/org/geworkbench/components/filtering/.svn/entries
geworkbench-core/components/filtering/src/org/geworkbench/components/filtering/help/.svn/entries
geworkbench-core/components/filtering/src/org/geworkbench/components/filtering/help/Filtering_files/.svn/entries
geworkbench-core/components/foldchange/.settings/.svn/entries
geworkbench-core/components/foldchange/.svn/entries
geworkbench-core/components/foldchange/classes/org/geworkbench/components/foldchange/FoldChangeAnalysis.cwb.xml
geworkbench-core/components/foldchange/classes/org/geworkbench/components/foldchange/FoldChangeViewer.cwb.xml
geworkbench-core/components/foldchange/src/.svn/entries
geworkbench-core/components/foldchange/src/org/.svn/entries
geworkbench-core/components/foldchange/src/org/geworkbench/.svn/entries
geworkbench-core/components/foldchange/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/foldchange/src/org/geworkbench/components/foldchange/.svn/entries
geworkbench-core/components/geneontology2/.svn/all-wcprops
geworkbench-core/components/geneontology2/.svn/entries
geworkbench-core/components/geneontology2/lib/.svn/entries
geworkbench-core/components/geneontology2/src/.svn/all-wcprops
geworkbench-core/components/geneontology2/src/.svn/entries
geworkbench-core/components/geneontology2/src/org/.svn/all-wcprops
geworkbench-core/components/geneontology2/src/org/.svn/entries
geworkbench-core/components/geneontology2/src/org/geworkbench/.svn/all-wcprops
geworkbench-core/components/geneontology2/src/org/geworkbench/.svn/entries
geworkbench-core/components/geneontology2/src/org/geworkbench/components/.svn/all-wcprops
geworkbench-core/components/geneontology2/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/geneontology2/src/org/geworkbench/components/geneontology2/.svn/all-wcprops
geworkbench-core/components/geneontology2/src/org/geworkbench/components/geneontology2/.svn/entries
geworkbench-core/components/geneontology2/src/org/geworkbench/components/geneontology2/.svn/text-base/GoAnalysisParameterPanel.java.svn-base
geworkbench-core/components/geneontology2/src/org/geworkbench/components/geneontology2/.svn/text-base/GoAnalysisResultView.java.svn-base
geworkbench-core/components/geneontology2/src/org/geworkbench/components/geneontology2/GoAnalysisParameterPanel.java
geworkbench-core/components/geneontology2/src/org/geworkbench/components/geneontology2/GoAnalysisResultView.java
geworkbench-core/components/genspace/.svn/all-wcprops
geworkbench-core/components/genspace/.svn/entries
geworkbench-core/components/genspace/lib/.svn/all-wcprops
geworkbench-core/components/genspace/lib/.svn/entries
geworkbench-core/components/genspace/lib/.svn/text-base/genspace-common.jar.svn-base
geworkbench-core/components/genspace/lib/genspace-common.jar
geworkbench-core/components/genspace/src/.svn/all-wcprops
geworkbench-core/components/genspace/src/.svn/entries
geworkbench-core/components/genspace/src/org/.svn/all-wcprops
geworkbench-core/components/genspace/src/org/.svn/entries
geworkbench-core/components/genspace/src/org/geworkbench/.svn/all-wcprops
geworkbench-core/components/genspace/src/org/geworkbench/.svn/entries
geworkbench-core/components/genspace/src/org/geworkbench/components/.svn/all-wcprops
geworkbench-core/components/genspace/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/genspace/src/org/geworkbench/components/genspace/.svn/all-wcprops
geworkbench-core/components/genspace/src/org/geworkbench/components/genspace/.svn/entries
geworkbench-core/components/genspace/src/org/geworkbench/components/genspace/.svn/text-base/GenSpaceServerFactory.java.svn-base
geworkbench-core/components/genspace/src/org/geworkbench/components/genspace/GenSpaceServerFactory.java
geworkbench-core/components/genspace/src/org/geworkbench/components/genspace/bean/.svn/entries
geworkbench-core/components/genspace/src/org/geworkbench/components/genspace/chat/.svn/all-wcprops
geworkbench-core/components/genspace/src/org/geworkbench/components/genspace/chat/.svn/entries
geworkbench-core/components/genspace/src/org/geworkbench/components/genspace/chat/.svn/text-base/ChatReceiver.java.svn-base
geworkbench-core/components/genspace/src/org/geworkbench/components/genspace/chat/ChatReceiver.java
geworkbench-core/components/genspace/src/org/geworkbench/components/genspace/help/.svn/entries
geworkbench-core/components/genspace/src/org/geworkbench/components/genspace/help/genspace_files/.svn/entries
geworkbench-core/components/genspace/src/org/geworkbench/components/genspace/rating/.svn/all-wcprops
geworkbench-core/components/genspace/src/org/geworkbench/components/genspace/rating/.svn/entries
geworkbench-core/components/genspace/src/org/geworkbench/components/genspace/rating/.svn/text-base/Star.java.svn-base
geworkbench-core/components/genspace/src/org/geworkbench/components/genspace/rating/Star.java
geworkbench-core/components/genspace/src/org/geworkbench/components/genspace/server/.svn/all-wcprops
geworkbench-core/components/genspace/src/org/geworkbench/components/genspace/server/.svn/entries
geworkbench-core/components/genspace/src/org/geworkbench/components/genspace/server/wrapper/.svn/all-wcprops
geworkbench-core/components/genspace/src/org/geworkbench/components/genspace/server/wrapper/.svn/entries
geworkbench-core/components/genspace/src/org/geworkbench/components/genspace/ui/.svn/all-wcprops
geworkbench-core/components/genspace/src/org/geworkbench/components/genspace/ui/.svn/entries
geworkbench-core/components/genspace/src/org/geworkbench/components/genspace/ui/chat/.svn/entries
geworkbench-core/components/genspace/src/org/geworkbench/components/genspace/ui/graph/.svn/all-wcprops
geworkbench-core/components/genspace/src/org/geworkbench/components/genspace/ui/graph/.svn/entries
geworkbench-core/components/genspace/src/org/geworkbench/components/genspace/workflowRepository/.svn/all-wcprops
geworkbench-core/components/genspace/src/org/geworkbench/components/genspace/workflowRepository/.svn/entries
geworkbench-core/components/genspace/src/org/geworkbench/components/genspace/workflowRepository/.svn/text-base/WorkflowCommentsPanel.java.svn-base
geworkbench-core/components/genspace/src/org/geworkbench/components/genspace/workflowRepository/WorkflowCommentsPanel.java
geworkbench-core/components/genspace/src/org/geworkbench/events/.svn/entries
geworkbench-core/components/gpmodule_v3_0/.svn/all-wcprops
geworkbench-core/components/gpmodule_v3_0/.svn/entries
geworkbench-core/components/gpmodule_v3_0/lib/.svn/entries
geworkbench-core/components/gpmodule_v3_0/src/.svn/all-wcprops
geworkbench-core/components/gpmodule_v3_0/src/.svn/entries
geworkbench-core/components/gpmodule_v3_0/src/org/.svn/all-wcprops
geworkbench-core/components/gpmodule_v3_0/src/org/.svn/entries
geworkbench-core/components/gpmodule_v3_0/src/org/geworkbench/.svn/all-wcprops
geworkbench-core/components/gpmodule_v3_0/src/org/geworkbench/.svn/entries
geworkbench-core/components/gpmodule_v3_0/src/org/geworkbench/components/.svn/all-wcprops
geworkbench-core/components/gpmodule_v3_0/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/gpmodule_v3_0/src/org/geworkbench/components/gpmodule/.svn/all-wcprops
geworkbench-core/components/gpmodule_v3_0/src/org/geworkbench/components/gpmodule/.svn/entries
geworkbench-core/components/gpmodule_v3_0/src/org/geworkbench/components/gpmodule/classification/.svn/all-wcprops
geworkbench-core/components/gpmodule_v3_0/src/org/geworkbench/components/gpmodule/classification/.svn/entries
geworkbench-core/components/gpmodule_v3_0/src/org/geworkbench/components/gpmodule/classification/.svn/text-base/AbstractTrainingPanel.java.svn-base
geworkbench-core/components/gpmodule_v3_0/src/org/geworkbench/components/gpmodule/classification/.svn/text-base/GPTrainingPanel.java.svn-base
geworkbench-core/components/gpmodule_v3_0/src/org/geworkbench/components/gpmodule/classification/AbstractTrainingPanel.java
geworkbench-core/components/gpmodule_v3_0/src/org/geworkbench/components/gpmodule/classification/GPTrainingPanel.java
geworkbench-core/components/gpmodule_v3_0/src/org/geworkbench/components/gpmodule/classification/cart/.svn/entries
geworkbench-core/components/gpmodule_v3_0/src/org/geworkbench/components/gpmodule/classification/gui/.svn/entries
geworkbench-core/components/gpmodule_v3_0/src/org/geworkbench/components/gpmodule/classification/gui/images/.svn/entries
geworkbench-core/components/gpmodule_v3_0/src/org/geworkbench/components/gpmodule/classification/images/.svn/entries
geworkbench-core/components/gpmodule_v3_0/src/org/geworkbench/components/gpmodule/classification/knn/.svn/entries
geworkbench-core/components/gpmodule_v3_0/src/org/geworkbench/components/gpmodule/classification/svm/.svn/entries
geworkbench-core/components/gpmodule_v3_0/src/org/geworkbench/components/gpmodule/classification/svm/gui/.svn/entries
geworkbench-core/components/gpmodule_v3_0/src/org/geworkbench/components/gpmodule/classification/wv/.svn/entries
geworkbench-core/components/gpmodule_v3_0/src/org/geworkbench/components/gpmodule/event/.svn/entries
geworkbench-core/components/gpmodule_v3_0/src/org/geworkbench/components/gpmodule/gsea/.svn/entries
geworkbench-core/components/gpmodule_v3_0/src/org/geworkbench/components/gpmodule/gsea/browser/.svn/entries
geworkbench-core/components/gpmodule_v3_0/src/org/geworkbench/components/gpmodule/images/.svn/entries
geworkbench-core/components/gpmodule_v3_0/src/org/geworkbench/components/gpmodule/kmeans/.svn/entries
geworkbench-core/components/gpmodule_v3_0/src/org/geworkbench/components/gpmodule/listener/.svn/entries
geworkbench-core/components/gpmodule_v3_0/src/org/geworkbench/components/gpmodule/pca/.svn/entries
geworkbench-core/components/gpmodule_v3_0/src/org/geworkbench/components/gpmodule/pca/viewer/.svn/entries
geworkbench-core/components/hierarchicalclustering/.svn/all-wcprops
geworkbench-core/components/hierarchicalclustering/.svn/entries
geworkbench-core/components/hierarchicalclustering/classes/org/geworkbench/components/hierarchicalclustering/FastHierClustAnalysis.cwb.xml
geworkbench-core/components/hierarchicalclustering/classes/org/geworkbench/components/hierarchicalclustering/HierClusterViewAppComponent.cwb.xml
geworkbench-core/components/hierarchicalclustering/src/.svn/all-wcprops
geworkbench-core/components/hierarchicalclustering/src/.svn/entries
geworkbench-core/components/hierarchicalclustering/src/org/.svn/all-wcprops
geworkbench-core/components/hierarchicalclustering/src/org/.svn/entries
geworkbench-core/components/hierarchicalclustering/src/org/geworkbench/.svn/all-wcprops
geworkbench-core/components/hierarchicalclustering/src/org/geworkbench/.svn/entries
geworkbench-core/components/hierarchicalclustering/src/org/geworkbench/components/.svn/all-wcprops
geworkbench-core/components/hierarchicalclustering/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/hierarchicalclustering/src/org/geworkbench/components/hierarchicalclustering/.svn/all-wcprops
geworkbench-core/components/hierarchicalclustering/src/org/geworkbench/components/hierarchicalclustering/.svn/entries
geworkbench-core/components/hierarchicalclustering/src/org/geworkbench/components/hierarchicalclustering/.svn/text-base/FastHierClustAnalysis.cwb.xml.svn-base
geworkbench-core/components/hierarchicalclustering/src/org/geworkbench/components/hierarchicalclustering/.svn/text-base/HierClusterViewAppComponent.cwb.xml.svn-base
geworkbench-core/components/hierarchicalclustering/src/org/geworkbench/components/hierarchicalclustering/.svn/text-base/HierClusterViewAppComponent.java.svn-base
geworkbench-core/components/hierarchicalclustering/src/org/geworkbench/components/hierarchicalclustering/.svn/text-base/HierClusterViewWidget.java.svn-base
geworkbench-core/components/hierarchicalclustering/src/org/geworkbench/components/hierarchicalclustering/FastHierClustAnalysis.cwb.xml
geworkbench-core/components/hierarchicalclustering/src/org/geworkbench/components/hierarchicalclustering/HierClusterViewAppComponent.cwb.xml
geworkbench-core/components/hierarchicalclustering/src/org/geworkbench/components/hierarchicalclustering/HierClusterViewAppComponent.java
geworkbench-core/components/hierarchicalclustering/src/org/geworkbench/components/hierarchicalclustering/HierClusterViewWidget.java
geworkbench-core/components/hierarchicalclustering/src/org/geworkbench/components/hierarchicalclustering/help/.svn/entries
geworkbench-core/components/idea/.settings/.svn/entries
geworkbench-core/components/idea/.svn/all-wcprops
geworkbench-core/components/idea/.svn/entries
geworkbench-core/components/idea/lib/.svn/entries
geworkbench-core/components/idea/src/.svn/all-wcprops
geworkbench-core/components/idea/src/.svn/entries
geworkbench-core/components/idea/src/org/.svn/all-wcprops
geworkbench-core/components/idea/src/org/.svn/entries
geworkbench-core/components/idea/src/org/geworkbench/.svn/all-wcprops
geworkbench-core/components/idea/src/org/geworkbench/.svn/entries
geworkbench-core/components/idea/src/org/geworkbench/components/.svn/all-wcprops
geworkbench-core/components/idea/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/idea/src/org/geworkbench/components/idea/.svn/all-wcprops
geworkbench-core/components/idea/src/org/geworkbench/components/idea/.svn/entries
geworkbench-core/components/idea/src/org/geworkbench/components/idea/.svn/text-base/IDEAAnalysis.java.svn-base
geworkbench-core/components/idea/src/org/geworkbench/components/idea/.svn/text-base/IDEAPanel.java.svn-base
geworkbench-core/components/idea/src/org/geworkbench/components/idea/.svn/text-base/IDEAViewer.java.svn-base
geworkbench-core/components/idea/src/org/geworkbench/components/idea/.svn/text-base/IdeaNetworkEdge.java.svn-base
geworkbench-core/components/idea/src/org/geworkbench/components/idea/.svn/text-base/Phenotype.java.svn-base
geworkbench-core/components/idea/src/org/geworkbench/components/idea/IDEAAnalysis.java
geworkbench-core/components/idea/src/org/geworkbench/components/idea/IDEAPanel.java
geworkbench-core/components/idea/src/org/geworkbench/components/idea/IDEAViewer.java
geworkbench-core/components/idea/src/org/geworkbench/components/idea/IdeaNetworkEdge.java
geworkbench-core/components/idea/src/org/geworkbench/components/idea/Phenotype.java
geworkbench-core/components/idea/test_data/.svn/entries
geworkbench-core/components/interactions/.svn/all-wcprops
geworkbench-core/components/interactions/.svn/entries
geworkbench-core/components/interactions/lib/.svn/entries
geworkbench-core/components/interactions/src/.svn/all-wcprops
geworkbench-core/components/interactions/src/.svn/entries
geworkbench-core/components/interactions/src/org/.svn/all-wcprops
geworkbench-core/components/interactions/src/org/.svn/entries
geworkbench-core/components/interactions/src/org/geworkbench/.svn/all-wcprops
geworkbench-core/components/interactions/src/org/geworkbench/.svn/entries
geworkbench-core/components/interactions/src/org/geworkbench/components/.svn/all-wcprops
geworkbench-core/components/interactions/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/interactions/src/org/geworkbench/components/interactions/.svn/all-wcprops
geworkbench-core/components/interactions/src/org/geworkbench/components/interactions/.svn/entries
geworkbench-core/components/interactions/src/org/geworkbench/components/interactions/cellularnetwork/.svn/all-wcprops
geworkbench-core/components/interactions/src/org/geworkbench/components/interactions/cellularnetwork/.svn/entries
geworkbench-core/components/interactions/src/org/geworkbench/components/interactions/cellularnetwork/.svn/text-base/ExportSelectionPanel.java.svn-base
geworkbench-core/components/interactions/src/org/geworkbench/components/interactions/cellularnetwork/ExportSelectionPanel.java
geworkbench-core/components/interactions/src/org/geworkbench/components/interactions/cellularnetwork/help/.svn/entries
geworkbench-core/components/interactions/src/org/geworkbench/components/interactions/cellularnetwork/help/CNKB_files/.svn/entries
geworkbench-core/components/jmol/.svn/entries
geworkbench-core/components/jmol/lib/.svn/entries
geworkbench-core/components/jmol/src/.svn/entries
geworkbench-core/components/jmol/src/org/.svn/entries
geworkbench-core/components/jmol/src/org/geworkbench/.svn/entries
geworkbench-core/components/jmol/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/jmol/src/org/geworkbench/components/jmol/.svn/entries
geworkbench-core/components/jmol/src/org/geworkbench/components/jmol/help/.svn/entries
geworkbench-core/components/jmol/src/org/geworkbench/components/jmol/help/jmol_files/.svn/entries
geworkbench-core/components/markus/.svn/entries
geworkbench-core/components/markus/lib/.svn/entries
geworkbench-core/components/markus/src/.svn/entries
geworkbench-core/components/markus/src/org/.svn/entries
geworkbench-core/components/markus/src/org/geworkbench/.svn/entries
geworkbench-core/components/markus/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/markus/src/org/geworkbench/components/markus/.svn/entries
geworkbench-core/components/markus/src/org/geworkbench/components/markus/help/.svn/entries
geworkbench-core/components/markus/src/org/geworkbench/components/markus/help/MarkUs_files/.svn/entries
geworkbench-core/components/masterregulator/.svn/all-wcprops
geworkbench-core/components/masterregulator/.svn/entries
geworkbench-core/components/masterregulator/lib/.svn/entries
geworkbench-core/components/masterregulator/src/.svn/all-wcprops
geworkbench-core/components/masterregulator/src/.svn/entries
geworkbench-core/components/masterregulator/src/org/.svn/all-wcprops
geworkbench-core/components/masterregulator/src/org/.svn/entries
geworkbench-core/components/masterregulator/src/org/geworkbench/.svn/all-wcprops
geworkbench-core/components/masterregulator/src/org/geworkbench/.svn/entries
geworkbench-core/components/masterregulator/src/org/geworkbench/components/.svn/all-wcprops
geworkbench-core/components/masterregulator/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/masterregulator/src/org/geworkbench/components/masterregulator/.svn/all-wcprops
geworkbench-core/components/masterregulator/src/org/geworkbench/components/masterregulator/.svn/entries
geworkbench-core/components/masterregulator/src/org/geworkbench/components/masterregulator/.svn/text-base/CSVFileFilter.java.svn-base
geworkbench-core/components/masterregulator/src/org/geworkbench/components/masterregulator/.svn/text-base/MasterRegulatorAnalysis.java.svn-base
geworkbench-core/components/masterregulator/src/org/geworkbench/components/masterregulator/.svn/text-base/MasterRegulatorPanel.java.svn-base
geworkbench-core/components/masterregulator/src/org/geworkbench/components/masterregulator/.svn/text-base/MasterRegulatorViewer.java.svn-base
geworkbench-core/components/masterregulator/src/org/geworkbench/components/masterregulator/.svn/text-base/TableViewer.java.svn-base
geworkbench-core/components/masterregulator/src/org/geworkbench/components/masterregulator/CSVFileFilter.java
geworkbench-core/components/masterregulator/src/org/geworkbench/components/masterregulator/MasterRegulatorAnalysis.java
geworkbench-core/components/masterregulator/src/org/geworkbench/components/masterregulator/MasterRegulatorPanel.java
geworkbench-core/components/masterregulator/src/org/geworkbench/components/masterregulator/MasterRegulatorViewer.java
geworkbench-core/components/masterregulator/src/org/geworkbench/components/masterregulator/TableViewer.java
geworkbench-core/components/masterregulator/src/org/geworkbench/components/masterregulator/help/.svn/entries
geworkbench-core/components/masterregulator/src/org/geworkbench/components/masterregulator/help/MasterRegulatorAnalysis_files/.svn/entries
geworkbench-core/components/matrixreduce/.svn/entries
geworkbench-core/components/matrixreduce/lib/.svn/entries
geworkbench-core/components/matrixreduce/src/.svn/entries
geworkbench-core/components/matrixreduce/src/org/.svn/entries
geworkbench-core/components/matrixreduce/src/org/geworkbench/.svn/entries
geworkbench-core/components/matrixreduce/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/matrixreduce/src/org/geworkbench/components/matrixreduce/.svn/entries
geworkbench-core/components/matrixreduce/src/org/geworkbench/components/matrixreduce/help/.svn/entries
geworkbench-core/components/matrixreduce/src/org/geworkbench/components/matrixreduce/help/MatrixReduce_files/.svn/entries
geworkbench-core/components/medusa/.svn/entries
geworkbench-core/components/medusa/data/.svn/entries
geworkbench-core/components/medusa/data/test/.svn/entries
geworkbench-core/components/medusa/data/test/dataset/.svn/entries
geworkbench-core/components/medusa/data/test/dataset/output/.svn/entries
geworkbench-core/components/medusa/data/test/dataset/pssm/.svn/entries
geworkbench-core/components/medusa/data/test/dataset/pssm/rules/.svn/entries
geworkbench-core/components/medusa/data/test/dataset/pssm/run1/.svn/entries
geworkbench-core/components/medusa/data/test/dataset/pssm/run1/state/.svn/entries
geworkbench-core/components/medusa/data/test/dataset/pssm/run1/state/data/.svn/entries
geworkbench-core/components/medusa/data/test/dataset/small_yeast/.svn/entries
geworkbench-core/components/medusa/lib/.svn/entries
geworkbench-core/components/medusa/src/.svn/entries
geworkbench-core/components/medusa/src/edu/.svn/entries
geworkbench-core/components/medusa/src/edu/columbia/.svn/entries
geworkbench-core/components/medusa/src/edu/columbia/ccls/.svn/entries
geworkbench-core/components/medusa/src/edu/columbia/ccls/medusa/.svn/entries
geworkbench-core/components/medusa/src/org/.svn/entries
geworkbench-core/components/medusa/src/org/geworkbench/.svn/entries
geworkbench-core/components/medusa/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/medusa/src/org/geworkbench/components/medusa/.svn/entries
geworkbench-core/components/medusa/src/org/geworkbench/components/medusa/gui/.svn/entries
geworkbench-core/components/microarrays/.svn/all-wcprops
geworkbench-core/components/microarrays/.svn/entries
geworkbench-core/components/microarrays/classes/org/geworkbench/components/microarrays/MicroarrayPanel.cwb.xml
geworkbench-core/components/microarrays/src/.svn/all-wcprops
geworkbench-core/components/microarrays/src/.svn/entries
geworkbench-core/components/microarrays/src/org/.svn/all-wcprops
geworkbench-core/components/microarrays/src/org/.svn/entries
geworkbench-core/components/microarrays/src/org/geworkbench/.svn/all-wcprops
geworkbench-core/components/microarrays/src/org/geworkbench/.svn/entries
geworkbench-core/components/microarrays/src/org/geworkbench/components/.svn/all-wcprops
geworkbench-core/components/microarrays/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/microarrays/src/org/geworkbench/components/microarrays/.svn/all-wcprops
geworkbench-core/components/microarrays/src/org/geworkbench/components/microarrays/.svn/entries
geworkbench-core/components/microarrays/src/org/geworkbench/components/microarrays/.svn/text-base/EVDPanel.java.svn-base
geworkbench-core/components/microarrays/src/org/geworkbench/components/microarrays/.svn/text-base/MicroarrayPanel.cwb.xml.svn-base
geworkbench-core/components/microarrays/src/org/geworkbench/components/microarrays/EVDPanel.java
geworkbench-core/components/microarrays/src/org/geworkbench/components/microarrays/MicroarrayPanel.cwb.xml
geworkbench-core/components/microarrays/src/org/geworkbench/components/microarrays/help/.svn/entries
geworkbench-core/components/microarrays/src/org/geworkbench/components/microarrays/help/expressionprofile/.svn/entries
geworkbench-core/components/microarrays/src/org/geworkbench/components/microarrays/help/expressionprofile/ExpProfile Viewed_files/.svn/entries
geworkbench-core/components/microarrays/src/org/geworkbench/components/microarrays/help/expressionprofile/images/.svn/entries
geworkbench-core/components/microarrays/src/org/geworkbench/components/microarrays/help/expressionvaluedist/.svn/entries
geworkbench-core/components/microarrays/src/org/geworkbench/components/microarrays/help/expressionvaluedist/EVD_help_files/.svn/entries
geworkbench-core/components/microarrays/src/org/geworkbench/components/microarrays/help/microarraypanel/.svn/entries
geworkbench-core/components/microarrays/src/org/geworkbench/components/microarrays/help/microarraypanel/Microarray_files/.svn/entries
geworkbench-core/components/microarrays/src/org/geworkbench/components/microarrays/help/microarraypanel/images/.svn/entries
geworkbench-core/components/microarrays/src/org/geworkbench/components/microarrays/help/tablepanel/.svn/entries
geworkbench-core/components/microarrays/src/org/geworkbench/components/microarrays/help/tablepanel/tabular_files/.svn/entries
geworkbench-core/components/mindy/.svn/all-wcprops
geworkbench-core/components/mindy/.svn/entries
geworkbench-core/components/mindy/lib/.svn/entries
geworkbench-core/components/mindy/src/.svn/all-wcprops
geworkbench-core/components/mindy/src/.svn/entries
geworkbench-core/components/mindy/src/org/.svn/all-wcprops
geworkbench-core/components/mindy/src/org/.svn/entries
geworkbench-core/components/mindy/src/org/geworkbench/.svn/all-wcprops
geworkbench-core/components/mindy/src/org/geworkbench/.svn/entries
geworkbench-core/components/mindy/src/org/geworkbench/components/.svn/all-wcprops
geworkbench-core/components/mindy/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/mindy/src/org/geworkbench/components/mindy/.svn/all-wcprops
geworkbench-core/components/mindy/src/org/geworkbench/components/mindy/.svn/entries
geworkbench-core/components/mindy/src/org/geworkbench/components/mindy/.svn/text-base/MindyAnalysis.java.svn-base
geworkbench-core/components/mindy/src/org/geworkbench/components/mindy/.svn/text-base/MindyParamPanel.java.svn-base
geworkbench-core/components/mindy/src/org/geworkbench/components/mindy/MindyAnalysis.java
geworkbench-core/components/mindy/src/org/geworkbench/components/mindy/MindyParamPanel.java
geworkbench-core/components/mindy/src/org/geworkbench/components/mindy/help/.svn/entries
geworkbench-core/components/mindy/src/org/geworkbench/components/mindy/help/mindy_files/.svn/entries
geworkbench-core/components/netboost/.svn/entries
geworkbench-core/components/netboost/conf/.svn/entries
geworkbench-core/components/netboost/src/.svn/entries
geworkbench-core/components/netboost/src/org/.svn/entries
geworkbench-core/components/netboost/src/org/geworkbench/.svn/entries
geworkbench-core/components/netboost/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/netboost/src/org/geworkbench/components/netboost/.svn/entries
geworkbench-core/components/netboost/src/org/geworkbench/components/netboost/help/.svn/entries
geworkbench-core/components/netboost/src/org/geworkbench/components/netboost/help/netboost_files/.svn/entries
geworkbench-core/components/normalization/.svn/entries
geworkbench-core/components/normalization/src/.svn/entries
geworkbench-core/components/normalization/src/org/.svn/entries
geworkbench-core/components/normalization/src/org/geworkbench/.svn/entries
geworkbench-core/components/normalization/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/normalization/src/org/geworkbench/components/normalization/.svn/entries
geworkbench-core/components/normalization/src/org/geworkbench/components/normalization/help/.svn/entries
geworkbench-core/components/normalization/src/org/geworkbench/components/normalization/help/Normalization_files/.svn/entries
geworkbench-core/components/plots/.svn/entries
geworkbench-core/components/plots/src/.svn/entries
geworkbench-core/components/plots/src/org/.svn/entries
geworkbench-core/components/plots/src/org/geworkbench/.svn/entries
geworkbench-core/components/plots/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/plots/src/org/geworkbench/components/plots/.svn/entries
geworkbench-core/components/plots/src/org/geworkbench/components/plots/help/.svn/entries
geworkbench-core/components/plots/src/org/geworkbench/components/plots/help/Volcano/.svn/entries
geworkbench-core/components/plots/src/org/geworkbench/components/plots/help/Volcano/images/.svn/entries
geworkbench-core/components/plots/src/org/geworkbench/components/plots/help/images/.svn/entries
geworkbench-core/components/poshistogram/.svn/all-wcprops
geworkbench-core/components/poshistogram/.svn/entries
geworkbench-core/components/poshistogram/classes/org/geworkbench/components/poshistogram/PositionHistogramAppComponent.cwb.xml
geworkbench-core/components/poshistogram/src/.svn/all-wcprops
geworkbench-core/components/poshistogram/src/.svn/entries
geworkbench-core/components/poshistogram/src/org/.svn/all-wcprops
geworkbench-core/components/poshistogram/src/org/.svn/entries
geworkbench-core/components/poshistogram/src/org/geworkbench/.svn/all-wcprops
geworkbench-core/components/poshistogram/src/org/geworkbench/.svn/entries
geworkbench-core/components/poshistogram/src/org/geworkbench/components/.svn/all-wcprops
geworkbench-core/components/poshistogram/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/poshistogram/src/org/geworkbench/components/poshistogram/.svn/all-wcprops
geworkbench-core/components/poshistogram/src/org/geworkbench/components/poshistogram/.svn/entries
geworkbench-core/components/poshistogram/src/org/geworkbench/components/poshistogram/.svn/text-base/PositionHistogramAppComponent.cwb.xml.svn-base
geworkbench-core/components/poshistogram/src/org/geworkbench/components/poshistogram/.svn/text-base/PositionHistogramAppComponent.java.svn-base
geworkbench-core/components/poshistogram/src/org/geworkbench/components/poshistogram/PositionHistogramAppComponent.cwb.xml
geworkbench-core/components/poshistogram/src/org/geworkbench/components/poshistogram/PositionHistogramAppComponent.java
geworkbench-core/components/poshistogram/src/org/geworkbench/components/poshistogram/help/.svn/entries
geworkbench-core/components/poshistogram/src/org/geworkbench/components/poshistogram/help/Position Histogram_files/.svn/entries
geworkbench-core/components/promoter/.svn/entries
geworkbench-core/components/promoter/lib/.svn/entries
geworkbench-core/components/promoter/src/.svn/entries
geworkbench-core/components/promoter/src/org/.svn/entries
geworkbench-core/components/promoter/src/org/geworkbench/.svn/entries
geworkbench-core/components/promoter/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/promoter/src/org/geworkbench/components/promoter/.svn/entries
geworkbench-core/components/promoter/src/org/geworkbench/components/promoter/help/.svn/entries
geworkbench-core/components/promoter/src/org/geworkbench/components/promoter/help/promoter panel_files/.svn/entries
geworkbench-core/components/promoter/src/org/geworkbench/components/promoter/help/promoter_files/.svn/entries
geworkbench-core/components/promoter/src/org/geworkbench/components/promoter/help/promoterpanel_files/.svn/entries
geworkbench-core/components/promoter/src/org/geworkbench/components/promoter/modulediscovery/.svn/entries
geworkbench-core/components/pudge/.svn/entries
geworkbench-core/components/pudge/lib/.svn/entries
geworkbench-core/components/pudge/src/.svn/entries
geworkbench-core/components/pudge/src/org/.svn/entries
geworkbench-core/components/pudge/src/org/geworkbench/.svn/entries
geworkbench-core/components/pudge/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/pudge/src/org/geworkbench/components/pudge/.svn/entries
geworkbench-core/components/pudge/src/org/geworkbench/components/pudge/help/.svn/entries
geworkbench-core/components/pudge/src/org/geworkbench/components/pudge/help/pudge_files/.svn/entries
geworkbench-core/components/selectors/.svn/all-wcprops
geworkbench-core/components/selectors/.svn/entries
geworkbench-core/components/selectors/src/.svn/all-wcprops
geworkbench-core/components/selectors/src/.svn/entries
geworkbench-core/components/selectors/src/org/.svn/all-wcprops
geworkbench-core/components/selectors/src/org/.svn/entries
geworkbench-core/components/selectors/src/org/geworkbench/.svn/all-wcprops
geworkbench-core/components/selectors/src/org/geworkbench/.svn/entries
geworkbench-core/components/selectors/src/org/geworkbench/components/.svn/all-wcprops
geworkbench-core/components/selectors/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/selectors/src/org/geworkbench/components/selectors/.svn/all-wcprops
geworkbench-core/components/selectors/src/org/geworkbench/components/selectors/.svn/entries
geworkbench-core/components/selectors/src/org/geworkbench/components/selectors/.svn/text-base/GenePanel.java.svn-base
geworkbench-core/components/selectors/src/org/geworkbench/components/selectors/.svn/text-base/PhenotypePanel.java.svn-base
geworkbench-core/components/selectors/src/org/geworkbench/components/selectors/.svn/text-base/SelectorPanel.java.svn-base
geworkbench-core/components/selectors/src/org/geworkbench/components/selectors/GenePanel.java
geworkbench-core/components/selectors/src/org/geworkbench/components/selectors/PhenotypePanel.java
geworkbench-core/components/selectors/src/org/geworkbench/components/selectors/SelectorPanel.java
geworkbench-core/components/selectors/src/org/geworkbench/components/selectors/help/.svn/entries
geworkbench-core/components/selectors/src/org/geworkbench/components/selectors/help/Classification_files/.svn/entries
geworkbench-core/components/selectors/src/org/geworkbench/components/selectors/help/Create panel_files/.svn/entries
geworkbench-core/components/selectors/src/org/geworkbench/components/selectors/help/Deactivate_files/.svn/entries
geworkbench-core/components/selectors/src/org/geworkbench/components/selectors/help/Load_files/.svn/entries
geworkbench-core/components/selectors/src/org/geworkbench/components/selectors/help/Save_files/.svn/entries
geworkbench-core/components/selectors/src/org/geworkbench/components/selectors/help/activate_files/.svn/entries
geworkbench-core/components/selectors/src/org/geworkbench/components/selectors/help/create_marker_panel_set_files/.svn/entries
geworkbench-core/components/selectors/src/org/geworkbench/components/selectors/help/images/.svn/entries
geworkbench-core/components/selectors/src/org/geworkbench/components/selectors/help/panel_files/.svn/entries
geworkbench-core/components/selectors/src/org/geworkbench/components/selectors/help/rename_files/.svn/entries
geworkbench-core/components/sequenceretriever/.svn/all-wcprops
geworkbench-core/components/sequenceretriever/.svn/entries
geworkbench-core/components/sequenceretriever/lib/.svn/entries
geworkbench-core/components/sequenceretriever/src/.svn/all-wcprops
geworkbench-core/components/sequenceretriever/src/.svn/entries
geworkbench-core/components/sequenceretriever/src/org/.svn/all-wcprops
geworkbench-core/components/sequenceretriever/src/org/.svn/entries
geworkbench-core/components/sequenceretriever/src/org/geworkbench/.svn/all-wcprops
geworkbench-core/components/sequenceretriever/src/org/geworkbench/.svn/entries
geworkbench-core/components/sequenceretriever/src/org/geworkbench/components/.svn/all-wcprops
geworkbench-core/components/sequenceretriever/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/sequenceretriever/src/org/geworkbench/components/sequenceretriever/.svn/all-wcprops
geworkbench-core/components/sequenceretriever/src/org/geworkbench/components/sequenceretriever/.svn/entries
geworkbench-core/components/sequenceretriever/src/org/geworkbench/components/sequenceretriever/.svn/text-base/RetrievedSequenceDisplayPanel.java.svn-base
geworkbench-core/components/sequenceretriever/src/org/geworkbench/components/sequenceretriever/.svn/text-base/RetrievedSequencesPanel.java.svn-base
geworkbench-core/components/sequenceretriever/src/org/geworkbench/components/sequenceretriever/.svn/text-base/SequenceRetriever.java.svn-base
geworkbench-core/components/sequenceretriever/src/org/geworkbench/components/sequenceretriever/RetrievedSequenceDisplayPanel.java
geworkbench-core/components/sequenceretriever/src/org/geworkbench/components/sequenceretriever/RetrievedSequencesPanel.java
geworkbench-core/components/sequenceretriever/src/org/geworkbench/components/sequenceretriever/SequenceRetriever.java
geworkbench-core/components/sequenceretriever/src/org/geworkbench/components/sequenceretriever/help/.svn/entries
geworkbench-core/components/sequenceretriever/src/org/geworkbench/components/sequenceretriever/help/SequenceRetriever_files/.svn/entries
geworkbench-core/components/sequences/.svn/entries
geworkbench-core/components/sequences/lib/.svn/entries
geworkbench-core/components/sequences/src/.svn/entries
geworkbench-core/components/sequences/src/org/.svn/entries
geworkbench-core/components/sequences/src/org/geworkbench/.svn/entries
geworkbench-core/components/sequences/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/sequences/src/org/geworkbench/components/sequences/.svn/entries
geworkbench-core/components/sequences/src/org/geworkbench/components/sequences/help/.svn/entries
geworkbench-core/components/sequences/src/org/geworkbench/components/sequences/help/SequenceRetriever_files/.svn/entries
geworkbench-core/components/sequences/src/org/geworkbench/components/sequences/help/Sequence_files/.svn/entries
geworkbench-core/components/skybase/.svn/entries
geworkbench-core/components/skybase/lib/.svn/entries
geworkbench-core/components/skybase/src/.svn/entries
geworkbench-core/components/skybase/src/org/.svn/entries
geworkbench-core/components/skybase/src/org/geworkbench/.svn/entries
geworkbench-core/components/skybase/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/skybase/src/org/geworkbench/components/skybase/.svn/entries
geworkbench-core/components/skybaseview/.svn/entries
geworkbench-core/components/skybaseview/lib/.svn/entries
geworkbench-core/components/skybaseview/src/.svn/entries
geworkbench-core/components/skybaseview/src/org/.svn/entries
geworkbench-core/components/skybaseview/src/org/geworkbench/.svn/entries
geworkbench-core/components/skybaseview/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/skybaseview/src/org/geworkbench/components/skybaseview/.svn/entries
geworkbench-core/components/skyline/.svn/entries
geworkbench-core/components/skyline/lib/.svn/entries
geworkbench-core/components/skyline/src/.svn/entries
geworkbench-core/components/skyline/src/org/.svn/entries
geworkbench-core/components/skyline/src/org/geworkbench/.svn/entries
geworkbench-core/components/skyline/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/skyline/src/org/geworkbench/components/skyline/.svn/entries
geworkbench-core/components/skylinecontour/.svn/entries
geworkbench-core/components/skylinecontour/lib/.svn/entries
geworkbench-core/components/skylinecontour/src/.svn/entries
geworkbench-core/components/skylinecontour/src/org/.svn/entries
geworkbench-core/components/skylinecontour/src/org/geworkbench/.svn/entries
geworkbench-core/components/skylinecontour/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/skylinecontour/src/org/geworkbench/components/skylinecontour/.svn/entries
geworkbench-core/components/skylinecontour/src/org/geworkbench/components/skylinecontour/db/.svn/entries
geworkbench-core/components/skylinecontour/src/org/geworkbench/components/skylinecontour/proto/.svn/entries
geworkbench-core/components/skylinecontour/src/org/geworkbench/components/skylinecontour/query/.svn/entries
geworkbench-core/components/skylinecontour/src/org/geworkbench/components/skylinecontour/swing/.svn/entries
geworkbench-core/components/skylinecontour/src/org/geworkbench/components/skylinecontour/util/.svn/entries
geworkbench-core/components/skylineview/.svn/entries
geworkbench-core/components/skylineview/lib/.svn/entries
geworkbench-core/components/skylineview/src/.svn/entries
geworkbench-core/components/skylineview/src/org/.svn/entries
geworkbench-core/components/skylineview/src/org/geworkbench/.svn/entries
geworkbench-core/components/skylineview/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/skylineview/src/org/geworkbench/components/skylineview/.svn/entries
geworkbench-core/components/somclustering/.settings/.svn/entries
geworkbench-core/components/somclustering/.svn/all-wcprops
geworkbench-core/components/somclustering/.svn/entries
geworkbench-core/components/somclustering/classes/org/geworkbench/components/somclustering/SOMDisplay.cwb.xml
geworkbench-core/components/somclustering/src/.svn/all-wcprops
geworkbench-core/components/somclustering/src/.svn/entries
geworkbench-core/components/somclustering/src/org/.svn/all-wcprops
geworkbench-core/components/somclustering/src/org/.svn/entries
geworkbench-core/components/somclustering/src/org/geworkbench/.svn/all-wcprops
geworkbench-core/components/somclustering/src/org/geworkbench/.svn/entries
geworkbench-core/components/somclustering/src/org/geworkbench/components/.svn/all-wcprops
geworkbench-core/components/somclustering/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/somclustering/src/org/geworkbench/components/somclustering/.svn/all-wcprops
geworkbench-core/components/somclustering/src/org/geworkbench/components/somclustering/.svn/entries
geworkbench-core/components/somclustering/src/org/geworkbench/components/somclustering/.svn/text-base/SOMDisplay.cwb.xml.svn-base
geworkbench-core/components/somclustering/src/org/geworkbench/components/somclustering/SOMDisplay.cwb.xml
geworkbench-core/components/synteny/.svn/entries
geworkbench-core/components/synteny/src/.svn/entries
geworkbench-core/components/synteny/src/org/.svn/entries
geworkbench-core/components/synteny/src/org/geworkbench/.svn/entries
geworkbench-core/components/synteny/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/synteny/src/org/geworkbench/components/alignment/.svn/entries
geworkbench-core/components/synteny/src/org/geworkbench/components/alignment/synteny/.svn/entries
geworkbench-core/components/synteny/src/org/geworkbench/components/alignment/synteny/help/.svn/entries
geworkbench-core/components/synteny/src/org/geworkbench/components/alignment/synteny/help/DotMatrixPanel_files/.svn/entries
geworkbench-core/components/synteny/src/org/geworkbench/components/alignment/synteny/help/syteny_files/.svn/entries
geworkbench-core/components/ttest/.svn/entries
geworkbench-core/components/ttest/classes/org/geworkbench/components/ttest/TtestAnalysis.cwb.xml
geworkbench-core/components/ttest/lib/.svn/entries
geworkbench-core/components/ttest/src/.svn/entries
geworkbench-core/components/ttest/src/org/.svn/entries
geworkbench-core/components/ttest/src/org/geworkbench/.svn/entries
geworkbench-core/components/ttest/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/ttest/src/org/geworkbench/components/analysis/.svn/entries
geworkbench-core/components/ttest/src/org/geworkbench/components/analysis/help/.svn/entries
geworkbench-core/components/ttest/src/org/geworkbench/components/analysis/help/clustering/.svn/entries
geworkbench-core/components/ttest/src/org/geworkbench/components/analysis/help/clustering/Ttest_files/.svn/entries
geworkbench-core/components/ttest/src/org/geworkbench/components/analysis/help/ttest/.svn/entries
geworkbench-core/components/ttest/src/org/geworkbench/components/analysis/help/ttest/MTest/.svn/entries
geworkbench-core/components/ttest/src/org/geworkbench/components/analysis/help/ttest/Ttest_files/.svn/entries
geworkbench-core/components/ttest/src/org/geworkbench/components/ttest/.svn/entries
geworkbench-core/components/versioninfo/.svn/entries
geworkbench-core/components/versioninfo/src/.svn/entries
geworkbench-core/components/versioninfo/src/org/.svn/entries
geworkbench-core/components/versioninfo/src/org/geworkbench/.svn/entries
geworkbench-core/components/versioninfo/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/versioninfo/src/org/geworkbench/components/versioninfo/.svn/entries
geworkbench-core/components/viewers/.svn/entries
geworkbench-core/components/viewers/src/.svn/entries
geworkbench-core/components/viewers/src/org/.svn/entries
geworkbench-core/components/viewers/src/org/geworkbench/.svn/entries
geworkbench-core/components/viewers/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/viewers/src/org/geworkbench/components/viewers/.svn/entries
geworkbench-core/conf/.svn/entries
geworkbench-core/conf/cruisecontrol/.svn/entries
geworkbench-core/data/.svn/entries
geworkbench-core/data/cardiogenomics.med.harvard.edu/.svn/entries
geworkbench-core/data/jaspar_CORE/.svn/entries
geworkbench-core/data/matrixreduce/.svn/entries
geworkbench-core/data/matrixreduce/microarray/.svn/entries
geworkbench-core/data/matrixreduce/sequence/.svn/entries
geworkbench-core/data/matrixreduce/topo/.svn/entries
geworkbench-core/data/medusa/.svn/entries
geworkbench-core/data/medusa/dataset/.svn/entries
geworkbench-core/data/medusa/dataset/small_yeast/.svn/entries
geworkbench-core/data/mindy/.svn/entries
geworkbench-core/data/public_data/.svn/entries
geworkbench-core/data/scripts/.svn/entries
geworkbench-core/data/testing/.svn/entries
geworkbench-core/dev/.svn/entries
geworkbench-core/gene_ontology.1_2.obo
geworkbench-core/geworkbench.log
geworkbench-core/lib/.svn/all-wcprops
geworkbench-core/lib/.svn/entries
geworkbench-core/lib/.svn/text-base/ginkgo-0.1-SNAPSHOT.jar.svn-base
geworkbench-core/lib/ginkgo-0.1-SNAPSHOT.jar
geworkbench-core/lib/medusa/.svn/entries
geworkbench-core/lib/mk/.svn/entries
geworkbench-core/lib64/.svn/entries
geworkbench-core/nbproject/.svn/entries
geworkbench-core/src/.svn/all-wcprops
geworkbench-core/src/.svn/entries
geworkbench-core/src/images/.svn/entries
geworkbench-core/src/org/.svn/all-wcprops
geworkbench-core/src/org/.svn/entries
geworkbench-core/src/org/geworkbench/.svn/all-wcprops
geworkbench-core/src/org/geworkbench/.svn/entries
geworkbench-core/src/org/geworkbench/analysis/.svn/all-wcprops
geworkbench-core/src/org/geworkbench/analysis/.svn/entries
geworkbench-core/src/org/geworkbench/analysis/.svn/text-base/AbstractAnalysis.java.svn-base
geworkbench-core/src/org/geworkbench/analysis/AbstractAnalysis.java
geworkbench-core/src/org/geworkbench/bison/.svn/all-wcprops
geworkbench-core/src/org/geworkbench/bison/.svn/entries
geworkbench-core/src/org/geworkbench/bison/algorithm/.svn/entries
geworkbench-core/src/org/geworkbench/bison/algorithm/classification/.svn/entries
geworkbench-core/src/org/geworkbench/bison/annotation/.svn/entries
geworkbench-core/src/org/geworkbench/bison/datastructure/.svn/all-wcprops
geworkbench-core/src/org/geworkbench/bison/datastructure/.svn/entries
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/.svn/all-wcprops
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/.svn/entries
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/gsea/.svn/entries
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/medusa/.svn/entries
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/microarrays/.svn/all-wcprops
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/microarrays/.svn/entries
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/microarrays/.svn/text-base/CSMicroarraySet.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/microarrays/CSMicroarraySet.java
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/pca/.svn/entries
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/sequences/.svn/entries
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/views/.svn/entries
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/.svn/all-wcprops
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/.svn/entries
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/markers/.svn/all-wcprops
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/markers/.svn/entries
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/markers/annotationparser/.svn/entries
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/markers/goterms/.svn/all-wcprops
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/markers/goterms/.svn/entries
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/markers/goterms/.svn/text-base/GeneOntologyTree.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/markers/goterms/GeneOntologyTree.java
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/microarray/.svn/entries
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/sequence/.svn/entries
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/structure/.svn/entries
geworkbench-core/src/org/geworkbench/bison/datastructure/complex/.svn/entries
geworkbench-core/src/org/geworkbench/bison/datastructure/complex/panels/.svn/entries
geworkbench-core/src/org/geworkbench/bison/datastructure/complex/pattern/.svn/entries
geworkbench-core/src/org/geworkbench/bison/datastructure/complex/pattern/matrix/.svn/entries
geworkbench-core/src/org/geworkbench/bison/datastructure/complex/pattern/sequence/.svn/entries
geworkbench-core/src/org/geworkbench/bison/datastructure/properties/.svn/entries
geworkbench-core/src/org/geworkbench/bison/model/.svn/entries
geworkbench-core/src/org/geworkbench/bison/model/analysis/.svn/entries
geworkbench-core/src/org/geworkbench/bison/model/clusters/.svn/entries
geworkbench-core/src/org/geworkbench/bison/parsers/.svn/entries
geworkbench-core/src/org/geworkbench/bison/parsers/resources/.svn/entries
geworkbench-core/src/org/geworkbench/bison/util/.svn/all-wcprops
geworkbench-core/src/org/geworkbench/bison/util/.svn/entries
geworkbench-core/src/org/geworkbench/bison/util/colorcontext/.svn/all-wcprops
geworkbench-core/src/org/geworkbench/bison/util/colorcontext/.svn/entries
geworkbench-core/src/org/geworkbench/bison/util/colorcontext/.svn/text-base/ExpressionPValueColorContext.java.svn-base
geworkbench-core/src/org/geworkbench/bison/util/colorcontext/ExpressionPValueColorContext.java
geworkbench-core/src/org/geworkbench/builtin/.svn/all-wcprops
geworkbench-core/src/org/geworkbench/builtin/.svn/entries
geworkbench-core/src/org/geworkbench/builtin/projects/.svn/all-wcprops
geworkbench-core/src/org/geworkbench/builtin/projects/.svn/entries
geworkbench-core/src/org/geworkbench/builtin/projects/.svn/text-base/FileOpenHandler.java.svn-base
geworkbench-core/src/org/geworkbench/builtin/projects/FileOpenHandler.java
geworkbench-core/src/org/geworkbench/builtin/projects/comments/.svn/entries
geworkbench-core/src/org/geworkbench/builtin/projects/comments/help/.svn/entries
geworkbench-core/src/org/geworkbench/builtin/projects/comments/help/Dataset annotation_files/.svn/entries
geworkbench-core/src/org/geworkbench/builtin/projects/experimentinformation/.svn/entries
geworkbench-core/src/org/geworkbench/builtin/projects/experimentinformation/help/.svn/entries
geworkbench-core/src/org/geworkbench/builtin/projects/experimentinformation/help/infoPanel_files/.svn/entries
geworkbench-core/src/org/geworkbench/builtin/projects/help/.svn/entries
geworkbench-core/src/org/geworkbench/builtin/projects/help/Manage_workspace_files/.svn/entries
geworkbench-core/src/org/geworkbench/builtin/projects/help/delete_dataset_files/.svn/entries
geworkbench-core/src/org/geworkbench/builtin/projects/help/manage_projected_files/.svn/entries
geworkbench-core/src/org/geworkbench/builtin/projects/help/merge_dataset_files/.svn/entries
geworkbench-core/src/org/geworkbench/builtin/projects/help/open_dataset_files/.svn/entries
geworkbench-core/src/org/geworkbench/builtin/projects/help/projects area_overviewed_files/.svn/entries
geworkbench-core/src/org/geworkbench/builtin/projects/help/remote_files/.svn/entries
geworkbench-core/src/org/geworkbench/builtin/projects/help/rename_dataset_files/.svn/entries
geworkbench-core/src/org/geworkbench/builtin/projects/help/user preference_files/.svn/entries
geworkbench-core/src/org/geworkbench/builtin/projects/history/.svn/entries
geworkbench-core/src/org/geworkbench/builtin/projects/history/help/.svn/entries
geworkbench-core/src/org/geworkbench/builtin/projects/history/help/historyPanel_files/.svn/entries
geworkbench-core/src/org/geworkbench/builtin/projects/history/help/images/.svn/entries
geworkbench-core/src/org/geworkbench/builtin/projects/remoteresources/.svn/entries
geworkbench-core/src/org/geworkbench/builtin/projects/remoteresources/carraydata/.svn/entries
geworkbench-core/src/org/geworkbench/builtin/projects/util/.svn/all-wcprops
geworkbench-core/src/org/geworkbench/builtin/projects/util/.svn/entries
geworkbench-core/src/org/geworkbench/builtin/projects/util/.svn/text-base/CaARRAYPanel.java.svn-base
geworkbench-core/src/org/geworkbench/builtin/projects/util/CaARRAYPanel.java
geworkbench-core/src/org/geworkbench/engine/.svn/all-wcprops
geworkbench-core/src/org/geworkbench/engine/.svn/entries
geworkbench-core/src/org/geworkbench/engine/ccm/.svn/entries
geworkbench-core/src/org/geworkbench/engine/config/.svn/entries
geworkbench-core/src/org/geworkbench/engine/config/events/.svn/entries
geworkbench-core/src/org/geworkbench/engine/config/rules/.svn/entries
geworkbench-core/src/org/geworkbench/engine/help/.svn/entries
geworkbench-core/src/org/geworkbench/engine/help/caWorkbench introduction_files/.svn/entries
geworkbench-core/src/org/geworkbench/engine/help/ccm_files/.svn/entries
geworkbench-core/src/org/geworkbench/engine/help/images/.svn/entries
geworkbench-core/src/org/geworkbench/engine/management/.svn/entries
geworkbench-core/src/org/geworkbench/engine/preferences/.svn/entries
geworkbench-core/src/org/geworkbench/engine/properties/.svn/entries
geworkbench-core/src/org/geworkbench/engine/skin/.svn/all-wcprops
geworkbench-core/src/org/geworkbench/engine/skin/.svn/entries
geworkbench-core/src/org/geworkbench/engine/skin/.svn/text-base/Skin.java.svn-base
geworkbench-core/src/org/geworkbench/engine/skin/Skin.java
geworkbench-core/src/org/geworkbench/events/.svn/entries
geworkbench-core/src/org/geworkbench/events/listeners/.svn/entries
geworkbench-core/src/org/geworkbench/parsers/.svn/all-wcprops
geworkbench-core/src/org/geworkbench/parsers/.svn/entries
geworkbench-core/src/org/geworkbench/parsers/.svn/text-base/MageTabFileFormat.java.svn-base
geworkbench-core/src/org/geworkbench/parsers/.svn/text-base/MicroarraySetParser.java.svn-base
geworkbench-core/src/org/geworkbench/parsers/.svn/text-base/SOFTFileFormat.java.svn-base
geworkbench-core/src/org/geworkbench/parsers/.svn/text-base/SampleFileParser.java.svn-base
geworkbench-core/src/org/geworkbench/parsers/.svn/text-base/TabDelimitedDataMatrixFileFormat.java.svn-base
geworkbench-core/src/org/geworkbench/parsers/MageTabFileFormat.java
geworkbench-core/src/org/geworkbench/parsers/MicroarraySetParser.java
geworkbench-core/src/org/geworkbench/parsers/SOFTFileFormat.java
geworkbench-core/src/org/geworkbench/parsers/SampleFileParser.java
geworkbench-core/src/org/geworkbench/parsers/TabDelimitedDataMatrixFileFormat.java
geworkbench-core/src/org/geworkbench/parsers/sequences/.svn/all-wcprops
geworkbench-core/src/org/geworkbench/parsers/sequences/.svn/entries
geworkbench-core/src/org/geworkbench/parsers/sequences/.svn/text-base/SequenceFileFormat.java.svn-base
geworkbench-core/src/org/geworkbench/parsers/sequences/SequenceFileFormat.java
geworkbench-core/src/org/geworkbench/util/.svn/all-wcprops
geworkbench-core/src/org/geworkbench/util/.svn/entries
geworkbench-core/src/org/geworkbench/util/.svn/text-base/splashscreen.png.svn-base
geworkbench-core/src/org/geworkbench/util/annotation/.svn/entries
geworkbench-core/src/org/geworkbench/util/associationdiscovery/.svn/entries
geworkbench-core/src/org/geworkbench/util/associationdiscovery/cluster/.svn/entries
geworkbench-core/src/org/geworkbench/util/associationdiscovery/statistics/.svn/entries
geworkbench-core/src/org/geworkbench/util/microarrayutils/.svn/entries
geworkbench-core/src/org/geworkbench/util/network/.svn/entries
geworkbench-core/src/org/geworkbench/util/pathwaydecoder/.svn/entries
geworkbench-core/src/org/geworkbench/util/pathwaydecoder/mutualinformation/.svn/entries
geworkbench-core/src/org/geworkbench/util/patterns/.svn/entries
geworkbench-core/src/org/geworkbench/util/sequences/.svn/entries
geworkbench-core/src/org/geworkbench/util/splashscreen.png
geworkbench-core/src/org/geworkbench/util/visualproperties/.svn/entries
geworkbench-core/test/.svn/entries
geworkbench-core/test/org/.svn/entries
geworkbench-core/test/org/geworkbench/.svn/entries
geworkbench-core/test/org/geworkbench/analysis/.svn/entries
geworkbench-core/test/org/geworkbench/bison/.svn/entries
geworkbench-core/test/org/geworkbench/bison/datastructure/.svn/entries
geworkbench-core/test/org/geworkbench/bison/datastructure/bioobjects/.svn/entries
geworkbench-core/test/org/geworkbench/bison/datastructure/bioobjects/microarray/.svn/entries
geworkbench-core/test/org/geworkbench/builtin/.svn/entries
geworkbench-core/test/org/geworkbench/builtin/projects/.svn/entries
geworkbench-core/test/org/geworkbench/builtin/projects/target/.svn/entries
geworkbench-core/test/org/geworkbench/components/.svn/entries
geworkbench-core/test/org/geworkbench/parsers/.svn/entries
diff --git a/create.sql b/create.sql
index f9eca5f..14a79f6 100644
--- a/create.sql
+++ b/create.sql
@@ -4,7 +4,7 @@ CREATE TABLE Friend (ID INTEGER AUTO_INCREMENT NOT NULL, MUTUAL TINYINT(1) defau
 CREATE TABLE INCOMINGWORKFLOW (ID INTEGER AUTO_INCREMENT NOT NULL, CREATEDAT DATETIME, NAME VARCHAR(255), RECEIVER_ID INTEGER, SENDER_ID INTEGER, WORKFLOW_ID INTEGER, PRIMARY KEY (ID))
 CREATE TABLE NETWORK (ID INTEGER AUTO_INCREMENT NOT NULL, NAME VARCHAR(255), owner INTEGER, PRIMARY KEY (ID))
 CREATE TABLE SETTING (ID INTEGER AUTO_INCREMENT NOT NULL, data_key VARCHAR(255), data_value VARCHAR(255), PRIMARY KEY (ID))
-CREATE TABLE TOOL (ID INTEGER AUTO_INCREMENT NOT NULL, DESCRIPTION VARCHAR(255), MOSTCOMMONPARAMETERS VARCHAR(255), MOSTCOMMONPARAMETERSCOUNT INTEGER, NAME VARCHAR(255), NUMRATING INTEGER, SUMRATING INTEGER, USAGECOUNT INTEGER, WFCOUNTHEAD INTEGER, PRIMARY KEY (ID))
+CREATE TABLE TOOL (ID INTEGER AUTO_INCREMENT NOT NULL, DESCRIPTION VARCHAR(255), MOSTCOMMONPARAMETERS VARCHAR(255), MOSTCOMMONPARAMETERSCOUNT INTEGER, NAME VARCHAR(255), NUMRATING INTEGER, SUMRATING INTEGER, USAGECOUNT INTEGER, WFCOUNTHEAD INTEGER, REPLACEDBY_ID INTEGER, PRIMARY KEY (ID))
 CREATE TABLE TOOLSTATCACHE (TOOLID INTEGER NOT NULL, UPDATED DATETIME, MOSTPOPULARBEFORE_ID INTEGER, MOSTPOPULARNEXT_ID INTEGER, PRIMARY KEY (TOOLID))
 CREATE TABLE TOOLRATING (ID INTEGER AUTO_INCREMENT NOT NULL, CREATEDAT DATETIME, RATING INTEGER, TOOL_ID INTEGER, CREATOR_ID INTEGER, PRIMARY KEY (ID))
 CREATE TABLE TOOLCOMMENT (ID INTEGER AUTO_INCREMENT NOT NULL, COMMENT VARCHAR(255), CREATEDAT DATETIME, CREATOR_ID INTEGER, TOOL_ID INTEGER, PRIMARY KEY (ID))
@@ -23,6 +23,7 @@ CREATE TABLE USAGEEVENT (ID INTEGER AUTO_INCREMENT NOT NULL, CREATEDAT DATETIME,
 CREATE TABLE ALIGNMENT (ID INTEGER AUTO_INCREMENT NOT NULL, COMMENTS VARCHAR(4000), DEFINITION VARCHAR(255), EMBLID VARCHAR(255) NOT NULL UNIQUE, KEYWORDS VARCHAR(2000), PRIMARY KEY (ID))
 CREATE TABLE REFERENCE (ID INTEGER AUTO_INCREMENT NOT NULL, AUTHORS VARCHAR(255), LOCATOR VARCHAR(255), TITLE VARCHAR(255), ALIGNMENT_ID INTEGER, PRIMARY KEY (ID))
 CREATE TABLE PROTEINSEQUENCE (ID INTEGER AUTO_INCREMENT NOT NULL, ABBREVATION VARCHAR(255), ACCESSIONNO VARCHAR(255) NOT NULL UNIQUE, DESCRIPTION VARCHAR(255), SEQUENCE VARCHAR(4000), PRIMARY KEY (ID))
+CREATE TABLE IGNOREDHOST (IP INTEGER NOT NULL, COMMENT VARCHAR(255), PRIMARY KEY (IP))
 CREATE TABLE PROTEINSEQUENCE_ALIGNMENT (alignments_ID INTEGER NOT NULL, sequences_ID INTEGER NOT NULL, PRIMARY KEY (alignments_ID, sequences_ID))
 ALTER TABLE ANALYSISEVENT ADD CONSTRAINT FK_ANALYSISEVENT_TOOL_ID FOREIGN KEY (TOOL_ID) REFERENCES TOOL (ID)
 ALTER TABLE ANALYSISEVENT ADD CONSTRAINT FK_ANALYSISEVENT_TRANSACTION_ID FOREIGN KEY (TRANSACTION_ID) REFERENCES TRANSACTION (ID)
@@ -33,6 +34,7 @@ ALTER TABLE INCOMINGWORKFLOW ADD CONSTRAINT FK_INCOMINGWORKFLOW_RECEIVER_ID FORE
 ALTER TABLE INCOMINGWORKFLOW ADD CONSTRAINT FK_INCOMINGWORKFLOW_SENDER_ID FOREIGN KEY (SENDER_ID) REFERENCES registration (ID)
 ALTER TABLE INCOMINGWORKFLOW ADD CONSTRAINT FK_INCOMINGWORKFLOW_WORKFLOW_ID FOREIGN KEY (WORKFLOW_ID) REFERENCES WORKFLOW (ID)
 ALTER TABLE NETWORK ADD CONSTRAINT FK_NETWORK_owner FOREIGN KEY (owner) REFERENCES registration (ID)
+ALTER TABLE TOOL ADD CONSTRAINT FK_TOOL_REPLACEDBY_ID FOREIGN KEY (REPLACEDBY_ID) REFERENCES TOOL (ID)
 ALTER TABLE TOOLSTATCACHE ADD CONSTRAINT FK_TOOLSTATCACHE_MOSTPOPULARNEXT_ID FOREIGN KEY (MOSTPOPULARNEXT_ID) REFERENCES TOOL (ID)
 ALTER TABLE TOOLSTATCACHE ADD CONSTRAINT FK_TOOLSTATCACHE_MOSTPOPULARBEFORE_ID FOREIGN KEY (MOSTPOPULARBEFORE_ID) REFERENCES TOOL (ID)
 ALTER TABLE TOOLRATING ADD CONSTRAINT FK_TOOLRATING_CREATOR_ID FOREIGN KEY (CREATOR_ID) REFERENCES registration (ID)
diff --git a/genspace-common/src/org/geworkbench/components/genspace/entity/Tool.java b/genspace-common/src/org/geworkbench/components/genspace/entity/Tool.java
index 28c4d62..00f71d0 100644
--- a/genspace-common/src/org/geworkbench/components/genspace/entity/Tool.java
+++ b/genspace-common/src/org/geworkbench/components/genspace/entity/Tool.java
@@ -15,6 +15,7 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlID;
 import javax.xml.bind.annotation.XmlIDREF;
+import javax.xml.bind.annotation.XmlTransient;


 @Entity
@@ -33,7 +34,8 @@ public class Tool extends LazyCycleBreaker implements Serializable {
 	private int wfCountHead;
 	private int sumRating =0;
 	private int numRating =0;
-
+	private Tool replacedBy;
+
 	@Id
 	@GeneratedValue(strategy=GenerationType.IDENTITY)
 	@XmlElement
@@ -110,6 +112,13 @@ public class Tool extends LazyCycleBreaker implements Serializable {
 	public int getNumRating() {
 		return numRating;
 	}
+	@XmlTransient
+	public Tool getReplacedBy() {
+		return replacedBy;
+	}
+	public void setReplacedBy(Tool replacedBy) {
+		this.replacedBy = replacedBy;
+	}
 	@Override
 	public boolean equals(Object o) {
 		if (o instanceof Tool) {
diff --git a/genspace-common/src/org/geworkbench/components/genspace/server/stubs/UserFacade.java b/genspace-common/src/org/geworkbench/components/genspace/server/stubs/UserFacade.java
index 07bee90..8297f39 100644
--- a/genspace-common/src/org/geworkbench/components/genspace/server/stubs/UserFacade.java
+++ b/genspace-common/src/org/geworkbench/components/genspace/server/stubs/UserFacade.java
@@ -38,17 +38,6 @@ public interface UserFacade {
     /**
      *
      * @param arg0
-     */
-    @WebMethod
-    @RequestWrapper(localName = "updateUser", targetNamespace = "http://server.genspace.components.geworkbench.org/", className = "org.geworkbench.components.genspace.server.stubs.UpdateUser")
-    @ResponseWrapper(localName = "updateUserResponse", targetNamespace = "http://server.genspace.components.geworkbench.org/", className = "org.geworkbench.components.genspace.server.stubs.UpdateUserResponse")
-    public void updateUser(
-        @WebParam(name = "arg0", targetNamespace = "")
-        User arg0);
-
-    /**
-     *
-     * @param arg0
      * @return
      *     returns boolean
      */
@@ -85,6 +74,17 @@ public interface UserFacade {
     /**
      *
      * @param arg0
+     */
+    @WebMethod
+    @RequestWrapper(localName = "updateUser", targetNamespace = "http://server.genspace.components.geworkbench.org/", className = "org.geworkbench.components.genspace.server.stubs.UpdateUser")
+    @ResponseWrapper(localName = "updateUserResponse", targetNamespace = "http://server.genspace.components.geworkbench.org/", className = "org.geworkbench.components.genspace.server.stubs.UpdateUserResponse")
+    public void updateUser(
+        @WebParam(name = "arg0", targetNamespace = "")
+        User arg0);
+
+    /**
+     *
+     * @param arg0
      * @return
      *     returns org.geworkbench.components.genspace.server.stubs.User
      */
diff --git a/genspace-common/src/org/geworkbench/components/genspace/server/stubs/WorkflowRepository.java b/genspace-common/src/org/geworkbench/components/genspace/server/stubs/WorkflowRepository.java
index 4f65807..82937f6 100644
--- a/genspace-common/src/org/geworkbench/components/genspace/server/stubs/WorkflowRepository.java
+++ b/genspace-common/src/org/geworkbench/components/genspace/server/stubs/WorkflowRepository.java
@@ -181,4 +181,21 @@ public interface WorkflowRepository {
     @ResponseWrapper(localName = "getIncomingWorkflowsResponse", targetNamespace = "http://server.genspace.components.geworkbench.org/", className = "org.geworkbench.components.genspace.server.stubs.GetIncomingWorkflowsResponse")
     public List<IncomingWorkflow> getIncomingWorkflows();

+    /**
+     *
+     * @param arg1
+     * @param arg0
+     * @return
+     *     returns org.geworkbench.components.genspace.server.stubs.WorkflowComment
+     */
+    @WebMethod
+    @WebResult(targetNamespace = "")
+    @RequestWrapper(localName = "addCommentToWf", targetNamespace = "http://server.genspace.components.geworkbench.org/", className = "org.geworkbench.components.genspace.server.stubs.AddCommentToWf")
+    @ResponseWrapper(localName = "addCommentToWfResponse", targetNamespace = "http://server.genspace.components.geworkbench.org/", className = "org.geworkbench.components.genspace.server.stubs.AddCommentToWfResponse")
+    public WorkflowComment addCommentToWf(
+        @WebParam(name = "arg0", targetNamespace = "")
+        WorkflowComment arg0,
+        @WebParam(name = "arg1", targetNamespace = "")
+        Workflow arg1);
+
 }
diff --git a/genspace-ejb/build/classes/META-INF/persistence.xml b/genspace-ejb/build/classes/META-INF/persistence.xml
index 88cb9a9..abb1ea1 100644
--- a/genspace-ejb/build/classes/META-INF/persistence.xml
+++ b/genspace-ejb/build/classes/META-INF/persistence.xml
@@ -29,6 +29,7 @@
          <class>org.geworkbench.components.genspace.entity.msa.Alignment</class>
          <class>org.geworkbench.components.genspace.entity.msa.Reference</class>
          <class>org.geworkbench.components.genspace.entity.msa.ProteinSequence</class>
+         <class>org.geworkbench.components.genspace.entity.IgnoredHost</class>

          <properties>
            <!--Use the java2db feature -->
diff --git a/genspace-ejb/ejbModule/META-INF/persistence.xml b/genspace-ejb/ejbModule/META-INF/persistence.xml
index 88cb9a9..abb1ea1 100644
--- a/genspace-ejb/ejbModule/META-INF/persistence.xml
+++ b/genspace-ejb/ejbModule/META-INF/persistence.xml
@@ -29,6 +29,7 @@
          <class>org.geworkbench.components.genspace.entity.msa.Alignment</class>
          <class>org.geworkbench.components.genspace.entity.msa.Reference</class>
          <class>org.geworkbench.components.genspace.entity.msa.ProteinSequence</class>
+         <class>org.geworkbench.components.genspace.entity.IgnoredHost</class>

          <properties>
            <!--Use the java2db feature -->
diff --git a/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/GenericUsageInformation.java b/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/GenericUsageInformation.java
index a867b7d..a398d60 100644
--- a/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/GenericUsageInformation.java
+++ b/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/GenericUsageInformation.java
@@ -2,7 +2,9 @@ package org.geworkbench.components.genspace.server;


 import java.util.ArrayList;
+import java.util.Calendar;
 import java.util.Date;
+import java.util.GregorianCalendar;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Vector;
@@ -84,7 +86,7 @@ public abstract class GenericUsageInformation extends AbstractFacade<Tool>
 	@SuppressWarnings("unchecked")
 	public List<Tool> getToolsByPopularity() {
 		Query q = getEntityManager().createQuery(
-				"select object(c) from Tool as c order by c.usageCount desc");
+				"select object(c) from Tool as c where c.replacedBy is null order by c.usageCount desc");
 		List<Tool> r = q.getResultList();
 		return r;

@@ -119,7 +121,7 @@ public abstract class GenericUsageInformation extends AbstractFacade<Tool>
     	logUsage();

 		Query q = getEntityManager().createQuery(
-				"select object(c) from Tool as c order by c.wfCountHead desc");
+				"select object(c) from Tool as c where c.replacedBy is null order by c.wfCountHead desc");
 		List<Tool> r = q.getResultList();
 		return r;
 	}
@@ -138,8 +140,12 @@ public abstract class GenericUsageInformation extends AbstractFacade<Tool>
 		{
 			c = statsMaintainer.calculateToolStats(tool);
 		}
-		if(c == null)
+		GregorianCalendar tenDaysAgo = new GregorianCalendar();
+		tenDaysAgo.add(Calendar.DATE, -10);
+		if(c == null || c.getUpdated().before(tenDaysAgo.getTime()))
+		{
 			c = statsMaintainer.calculateToolStats(tool);
+		}
 		return c;
 	}
 	public Tool getMostPopularPreviousTool(int tool) {
@@ -154,7 +160,7 @@ public abstract class GenericUsageInformation extends AbstractFacade<Tool>
     	logUsage();

 		Query q = getEntityManager().createQuery(
-				"select object(c) from Tool as c order by c.name asc");
+				"select object(c) from Tool as c where c.replacedBy is null order by c.name asc");
 		@SuppressWarnings("unchecked")
 		List<Tool> r = q.getResultList();
 		return r;
@@ -347,11 +353,13 @@ public abstract class GenericUsageInformation extends AbstractFacade<Tool>
 	@Override
 	public Transaction sendUsageEvent(AnalysisEvent e) {
 		e.setCreatedAt(new Date());
+//		System.out.println(">>>Incoming tool: " + e.getTool() + " -> " + e.getToolname());
 		e.setTransaction(createOrFindTransaction(e.getTransaction()));
 		return handleSingleUsageEvent(e);
 	}

 	private Transaction handleSingleUsageEvent(AnalysisEvent e) {
+//		System.out.println(e.getTool() + " -> " + e.getToolname());
 		if (e.getTool() == null || !getEntityManager().contains(e.getTool())) {
 			e.setTool(getToolByName(e.getToolname()));
 			if (e.getTool() == null) {
@@ -365,6 +373,8 @@ public abstract class GenericUsageInformation extends AbstractFacade<Tool>
 				getEntityManager().flush();
 			}
 		}
+		if(e.getTool().getReplacedBy() != null)
+			e.setTool(e.getTool().getReplacedBy());
 		if(e.getParameters() != null)
 			for(AnalysisEventParameter p : e.getParameters())
 			{
@@ -430,6 +440,8 @@ public abstract class GenericUsageInformation extends AbstractFacade<Tool>
 		Tool r = null;
 		try {
 			r = (Tool) q.getSingleResult();
+			if(r.getReplacedBy() != null)
+				return r.getReplacedBy();
 		} catch (NoResultException e) {

 		}
@@ -525,7 +537,7 @@ public abstract class GenericUsageInformation extends AbstractFacade<Tool>

 	private Transaction findTransactionByName(String name, User user) {
 		Query q;
-		System.out.println("Checking user " + user + " clientid <" +name+">");
+//		System.out.println("Checking user " + user + " clientid <" +name+">");
 		if (user == null)
 		{
 			q = getEntityManager()
diff --git a/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/WorkflowRepository.java b/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/WorkflowRepository.java
index a43bb19..7e899f9 100644
--- a/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/WorkflowRepository.java
+++ b/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/WorkflowRepository.java
@@ -130,7 +130,7 @@ public class WorkflowRepository extends AbstractFacade<Workflow> implements Work
 	@WebMethod
 	public WorkflowComment addComment(WorkflowComment wc) {
     	logUsage();
-
+    	System.out.println(wc.getWorkflow());
 		wc.setCreatedAt(new Date());
 		wc.setCreator(getUser());
 		getEntityManager().persist(wc);
@@ -140,6 +140,19 @@ public class WorkflowRepository extends AbstractFacade<Workflow> implements Work
 		return wc;
 	}

+	@WebMethod
+	public WorkflowComment addCommentToWf(WorkflowComment wc, Workflow w) {
+    	logUsage();
+		wc.setCreatedAt(new Date());
+		wc.setCreator(getUser());
+		wc.setWorkflow(w);
+		getEntityManager().persist(wc);
+		wc = getEntityManager().merge(wc);
+//		getEntityManager().refresh(wc.getWorkflow());
+		invalidateCache();
+		return wc;
+	}
+
 	@Override
 	@WebMethod
 	public UserWorkflow importWorkflow(UserWorkflow w) {
diff --git a/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/task/WorkflowStatisticsMaintainer.java b/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/task/WorkflowStatisticsMaintainer.java
index b465e8e..4a62d36 100644
--- a/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/task/WorkflowStatisticsMaintainer.java
+++ b/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/task/WorkflowStatisticsMaintainer.java
@@ -175,7 +175,7 @@ public class WorkflowStatisticsMaintainer {
 						"inner join WORKFLOWTOOL wt on wt.tool_id=t.id " +
 						"inner join WORKFLOWTOOL wt2 on wt2.workflow_id=wt.workflow_id and wt2.cardinality = wt.cardinality-1 " +
 						"inner join WORKFLOW w on w.id=wt.workflow_id " +
-						"where wt2.tool_id=? group by t.id order by SUM(w.usagecount) limit 1",
+						"where wt2.tool_id=? and t.replacedby_id is null group by t.id order by SUM(w.usagecount) limit 1",
 						Tool.class);
 		q.setParameter(1, t);
 		Tool r = null;
@@ -191,7 +191,7 @@ public class WorkflowStatisticsMaintainer {
 						"inner join WORKFLOWTOOL wt on wt.tool_id=t.id " +
 						"inner join WORKFLOWTOOL wt2 on wt2.workflow_id=wt.workflow_id and wt2.cardinality = wt.cardinality+1 " +
 						"inner join WORKFLOW w on w.id=wt.workflow_id " +
-						"where wt2.tool_id=? group by t.id order by SUM(w.usagecount) limit 1",
+						"where wt2.tool_id=? and t.replacedby_id is null group by t.id order by SUM(w.usagecount) limit 1",
 						Tool.class);
 		q.setParameter(1, t);
 		r = null;
diff --git a/geworkbench-core/.settings/.svn/entries b/geworkbench-core/.settings/.svn/entries
index 38d86ae..b7c7341 100644
--- a/geworkbench-core/.settings/.svn/entries
+++ b/geworkbench-core/.settings/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/.settings
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/.svn/all-wcprops b/geworkbench-core/.svn/all-wcprops
index 6ef486e..92a155c 100644
--- a/geworkbench-core/.svn/all-wcprops
+++ b/geworkbench-core/.svn/all-wcprops
@@ -1,7 +1,7 @@
 K 25
 svn:wc:ra_dav:version-url
 V 48
-/svn/geworkbench/!svn/ver/8676/trunk/geworkbench
+/svn/geworkbench/!svn/ver/8812/trunk/geworkbench
 END
 java.policy
 K 25
@@ -87,23 +87,17 @@ svn:wc:ra_dav:version-url
 V 70
 /svn/geworkbench/!svn/ver/2616/trunk/geworkbench/ReleaseNotes1.0.5.txt
 END
-ReleaseNotes1.6.0.txt
-K 25
-svn:wc:ra_dav:version-url
-V 70
-/svn/geworkbench/!svn/ver/4412/trunk/geworkbench/ReleaseNotes1.6.0.txt
-END
 ReleaseNotes1.5.1.txt
 K 25
 svn:wc:ra_dav:version-url
 V 70
 /svn/geworkbench/!svn/ver/4247/trunk/geworkbench/ReleaseNotes1.5.1.txt
 END
-ReleaseNotes1.6.1.txt
+ReleaseNotes1.6.0.txt
 K 25
 svn:wc:ra_dav:version-url
 V 70
-/svn/geworkbench/!svn/ver/4453/trunk/geworkbench/ReleaseNotes1.6.1.txt
+/svn/geworkbench/!svn/ver/4412/trunk/geworkbench/ReleaseNotes1.6.0.txt
 END
 ReleaseNotes1.7.0.txt
 K 25
@@ -111,11 +105,11 @@ svn:wc:ra_dav:version-url
 V 70
 /svn/geworkbench/!svn/ver/5445/trunk/geworkbench/ReleaseNotes1.7.0.txt
 END
-ReleaseNotes1.6.2.txt
+ReleaseNotes1.6.1.txt
 K 25
 svn:wc:ra_dav:version-url
 V 70
-/svn/geworkbench/!svn/ver/4470/trunk/geworkbench/ReleaseNotes1.6.2.txt
+/svn/geworkbench/!svn/ver/4453/trunk/geworkbench/ReleaseNotes1.6.1.txt
 END
 ReleaseNotes1.8.0.txt
 K 25
@@ -123,11 +117,11 @@ svn:wc:ra_dav:version-url
 V 70
 /svn/geworkbench/!svn/ver/5737/trunk/geworkbench/ReleaseNotes1.8.0.txt
 END
-ReleaseNotes1.6.3.txt
+ReleaseNotes1.6.2.txt
 K 25
 svn:wc:ra_dav:version-url
 V 70
-/svn/geworkbench/!svn/ver/4599/trunk/geworkbench/ReleaseNotes1.6.3.txt
+/svn/geworkbench/!svn/ver/4470/trunk/geworkbench/ReleaseNotes1.6.2.txt
 END
 YG_cDNA_annot.csv
 K 25
@@ -135,11 +129,11 @@ svn:wc:ra_dav:version-url
 V 65
 /svn/geworkbench/!svn/ver/147/trunk/geworkbench/YG_cDNA_annot.csv
 END
-build-component.xml
+ReleaseNotes1.6.3.txt
 K 25
 svn:wc:ra_dav:version-url
-V 68
-/svn/geworkbench/!svn/ver/7318/trunk/geworkbench/build-component.xml
+V 70
+/svn/geworkbench/!svn/ver/4599/trunk/geworkbench/ReleaseNotes1.6.3.txt
 END
 build.xml
 K 25
@@ -147,6 +141,12 @@ svn:wc:ra_dav:version-url
 V 58
 /svn/geworkbench/!svn/ver/8640/trunk/geworkbench/build.xml
 END
+build-component.xml
+K 25
+svn:wc:ra_dav:version-url
+V 68
+/svn/geworkbench/!svn/ver/7318/trunk/geworkbench/build-component.xml
+END
 .classpath
 K 25
 svn:wc:ra_dav:version-url
diff --git a/geworkbench-core/.svn/entries b/geworkbench-core/.svn/entries
index 2ca2263..6ac2951 100644
--- a/geworkbench-core/.svn/entries
+++ b/geworkbench-core/.svn/entries
@@ -1,15 +1,15 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2012-01-09T22:15:49.759555Z
-8676
-youmi
+2012-01-30T21:31:47.792401Z
+8812
+zji
 has-props


@@ -413,17 +413,17 @@ has-props

 17571

-usage.txt
+geworkbench-lite.ipr
 file




-2011-08-17T00:10:51.000000Z
-853f159edbdd0694ce5995fb9dea00aa
-2006-07-19T01:50:13.000000Z
-1679
-mkustagi
+2011-08-17T00:10:49.000000Z
+0961f5b52af0c5237c479a684a981bbf
+2007-05-16T20:46:26.000000Z
+2859
+mhall
 has-props


@@ -445,19 +445,19 @@ has-props



-3098
+14878

-geworkbench-lite.ipr
+usage.txt
 file




-2011-08-17T00:10:49.000000Z
-0961f5b52af0c5237c479a684a981bbf
-2007-05-16T20:46:26.000000Z
-2859
-mhall
+2011-08-17T00:10:51.000000Z
+853f159edbdd0694ce5995fb9dea00aa
+2006-07-19T01:50:13.000000Z
+1679
+mkustagi
 has-props


@@ -479,7 +479,7 @@ has-props



-14878
+3098

 nbproject
 dir
@@ -935,6 +935,12 @@ has-props

 25858

+components
+dir
+
+conf
+dir
+
 ReleaseNotes_2.0.1.txt
 file

@@ -969,23 +975,17 @@ has-props

 26231

-conf
-dir
-
-components
-dir
-
-ReleaseNotes_2.0.2.txt
+ReleaseNotes_2.2.0.txt
 file




-2011-08-17T00:10:35.000000Z
-6e4673bbc650b9e46d9dabbf58735804
-2010-08-09T23:17:05.434469Z
-6970
-smithken
+2011-08-17T00:18:52.000000Z
+441fb4f98b14f80b650554fef3cb80e5
+2011-05-25T14:25:11.688972Z
+7925
+zji
 has-props


@@ -1007,19 +1007,19 @@ has-props



-26638
+35965

-ReleaseNotes_2.2.0.txt
+ReleaseNotes_2.0.2.txt
 file




-2011-08-17T00:18:52.000000Z
-441fb4f98b14f80b650554fef3cb80e5
-2011-05-25T14:25:11.688972Z
-7925
-zji
+2011-08-17T00:10:35.000000Z
+6e4673bbc650b9e46d9dabbf58735804
+2010-08-09T23:17:05.434469Z
+6970
+smithken
 has-props


@@ -1041,19 +1041,22 @@ has-props



-35965
+26638

-caWorkbench_Readme_v3.0.txt
+src
+dir
+
+ReleaseNotes_2.2.1.txt
 file




-2011-08-17T00:10:35.000000Z
-50723c1aae0c25e1727d8f64fcd900bd
-2005-11-11T16:25:46.000000Z
-798
-xiaoqing
+2012-01-10T18:25:30.000000Z
+5d8ec97e006df208c36ba76bd1737afb
+2011-07-30T04:31:30.667242Z
+8187
+zji
 has-props


@@ -1075,19 +1078,19 @@ has-props



-2574
+44234

-ReleaseNotes_2.2.1.txt
+caWorkbench_Readme_v3.0.txt
 file




-2012-01-10T18:25:30.000000Z
-5d8ec97e006df208c36ba76bd1737afb
-2011-07-30T04:31:30.667242Z
-8187
-zji
+2011-08-17T00:10:35.000000Z
+50723c1aae0c25e1727d8f64fcd900bd
+2005-11-11T16:25:46.000000Z
+798
+xiaoqing
 has-props


@@ -1109,10 +1112,7 @@ has-props



-44234
-
-src
-dir
+2574

 ReleaseNotes_2.2.2.txt
 file
@@ -1250,17 +1250,17 @@ keshav

 19453

-ReleaseNotes1.6.2.txt
+ReleaseNotes1.8.0.txt
 file




 2011-08-17T00:10:35.000000Z
-15a71a541a6791503d59a5139564546e
-2008-11-18T21:03:08.000000Z
-4470
-keshav
+89fa8b9f9d6e97ed64267abc8ad487d7
+2009-11-09T17:14:11.000000Z
+5737
+jiz



@@ -1282,19 +1282,19 @@ keshav



-18940
+21345

-ReleaseNotes1.8.0.txt
+ReleaseNotes1.6.2.txt
 file




 2011-08-17T00:10:35.000000Z
-89fa8b9f9d6e97ed64267abc8ad487d7
-2009-11-09T17:14:11.000000Z
-5737
-jiz
+15a71a541a6791503d59a5139564546e
+2008-11-18T21:03:08.000000Z
+4470
+keshav



@@ -1316,20 +1316,20 @@ jiz



-21345
+18940

-ReleaseNotes1.6.3.txt
+YG_cDNA_annot.csv
 file




-2011-08-17T00:10:35.000000Z
-b68f3daf1435f2329e1d82b8a61c3f88
-2009-01-07T20:23:03.000000Z
-4599
-ksmith
-
+2012-01-10T19:15:22.000000Z
+2b4de95ab609266736ff57a56f7b2f6a
+2005-08-22T20:38:15.000000Z
+147
+manju
+has-props



@@ -1350,20 +1350,19 @@ ksmith



-19053
+1529229

-YG_cDNA_annot.csv
+ReleaseNotes1.6.3.txt
 file




-2012-01-10T19:15:22.000000Z
-2b4de95ab609266736ff57a56f7b2f6a
-2005-08-22T20:38:15.000000Z
-147
-manju
-has-props
+2011-08-17T00:10:35.000000Z
+b68f3daf1435f2329e1d82b8a61c3f88
+2009-01-07T20:23:03.000000Z
+4599
+ksmith



@@ -1384,7 +1383,8 @@ has-props



-1529229
+
+19053

 build-component.xml
 file
diff --git a/geworkbench-core/_all/.svn/entries b/geworkbench-core/_all/.svn/entries
index ac88466..688f289 100644
--- a/geworkbench-core/_all/.svn/entries
+++ b/geworkbench-core/_all/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/_all
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/annotation/.svn/entries b/geworkbench-core/annotation/.svn/entries
index db9709e..584ba38 100644
--- a/geworkbench-core/annotation/.svn/entries
+++ b/geworkbench-core/annotation/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/annotation
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/bin/.svn/entries b/geworkbench-core/bin/.svn/entries
index 75e0471..18bec58 100644
--- a/geworkbench-core/bin/.svn/entries
+++ b/geworkbench-core/bin/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/bin
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/bin/matrixreduce/.svn/entries b/geworkbench-core/bin/matrixreduce/.svn/entries
index 9e1ff98..c0b5525 100644
--- a/geworkbench-core/bin/matrixreduce/.svn/entries
+++ b/geworkbench-core/bin/matrixreduce/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/bin/matrixreduce
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/cascripts/.svn/entries b/geworkbench-core/cascripts/.svn/entries
index 5e7e7f8..c55c552 100644
--- a/geworkbench-core/cascripts/.svn/entries
+++ b/geworkbench-core/cascripts/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/cascripts
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/.svn/entries b/geworkbench-core/classes/.svn/entries
index 2579743..f8e294b 100644
--- a/geworkbench-core/classes/.svn/entries
+++ b/geworkbench-core/classes/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/conf
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/cruisecontrol/.svn/entries b/geworkbench-core/classes/cruisecontrol/.svn/entries
index 69aa552..962b7a4 100644
--- a/geworkbench-core/classes/cruisecontrol/.svn/entries
+++ b/geworkbench-core/classes/cruisecontrol/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/conf/cruisecontrol
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/images/.svn/entries b/geworkbench-core/classes/images/.svn/entries
index 1c4e287..d2043d7 100644
--- a/geworkbench-core/classes/images/.svn/entries
+++ b/geworkbench-core/classes/images/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/images
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/.svn/all-wcprops b/geworkbench-core/classes/org/.svn/all-wcprops
index 2e7e656..6e9993d 100644
--- a/geworkbench-core/classes/org/.svn/all-wcprops
+++ b/geworkbench-core/classes/org/.svn/all-wcprops
@@ -1,5 +1,5 @@
 K 25
 svn:wc:ra_dav:version-url
 V 56
-/svn/geworkbench/!svn/ver/8675/trunk/geworkbench/src/org
+/svn/geworkbench/!svn/ver/8807/trunk/geworkbench/src/org
 END
diff --git a/geworkbench-core/classes/org/.svn/entries b/geworkbench-core/classes/org/.svn/entries
index 0fd3cd3..2651f96 100644
--- a/geworkbench-core/classes/org/.svn/entries
+++ b/geworkbench-core/classes/org/.svn/entries
@@ -1,14 +1,14 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2012-01-09T20:51:15.137498Z
-8675
+2012-01-27T22:43:49.471007Z
+8807
 zji


diff --git a/geworkbench-core/classes/org/geworkbench/.svn/all-wcprops b/geworkbench-core/classes/org/geworkbench/.svn/all-wcprops
index 62de404..ad6972e 100644
--- a/geworkbench-core/classes/org/geworkbench/.svn/all-wcprops
+++ b/geworkbench-core/classes/org/geworkbench/.svn/all-wcprops
@@ -1,5 +1,5 @@
 K 25
 svn:wc:ra_dav:version-url
 V 68
-/svn/geworkbench/!svn/ver/8675/trunk/geworkbench/src/org/geworkbench
+/svn/geworkbench/!svn/ver/8807/trunk/geworkbench/src/org/geworkbench
 END
diff --git a/geworkbench-core/classes/org/geworkbench/.svn/entries b/geworkbench-core/classes/org/geworkbench/.svn/entries
index d83ef22..d863cbe 100644
--- a/geworkbench-core/classes/org/geworkbench/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/.svn/entries
@@ -1,14 +1,14 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2012-01-09T20:51:15.137498Z
-8675
+2012-01-27T22:43:49.471007Z
+8807
 zji


diff --git a/geworkbench-core/classes/org/geworkbench/analysis/.svn/all-wcprops b/geworkbench-core/classes/org/geworkbench/analysis/.svn/all-wcprops
index f445a68..e8997ac 100644
--- a/geworkbench-core/classes/org/geworkbench/analysis/.svn/all-wcprops
+++ b/geworkbench-core/classes/org/geworkbench/analysis/.svn/all-wcprops
@@ -1,7 +1,7 @@
 K 25
 svn:wc:ra_dav:version-url
 V 77
-/svn/geworkbench/!svn/ver/8478/trunk/geworkbench/src/org/geworkbench/analysis
+/svn/geworkbench/!svn/ver/8743/trunk/geworkbench/src/org/geworkbench/analysis
 END
 AbstractAnalysisLabelComparator.java
 K 25
@@ -25,7 +25,7 @@ AbstractAnalysis.java
 K 25
 svn:wc:ra_dav:version-url
 V 99
-/svn/geworkbench/!svn/ver/8478/trunk/geworkbench/src/org/geworkbench/analysis/AbstractAnalysis.java
+/svn/geworkbench/!svn/ver/8743/trunk/geworkbench/src/org/geworkbench/analysis/AbstractAnalysis.java
 END
 AbstractSaveableParameterPanel.java
 K 25
diff --git a/geworkbench-core/classes/org/geworkbench/analysis/.svn/entries b/geworkbench-core/classes/org/geworkbench/analysis/.svn/entries
index 299e652..3a67fbe 100644
--- a/geworkbench-core/classes/org/geworkbench/analysis/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/analysis/.svn/entries
@@ -1,15 +1,15 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/analysis
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2011-11-02T13:48:00.049131Z
-8478
-zji
+2012-01-20T16:26:44.505648Z
+8743
+youmi



@@ -134,11 +134,11 @@ file



-2012-01-10T19:15:27.000000Z
-d5d2872d1ed8cbdfacba1661f10ad848
-2011-11-02T13:48:00.049131Z
-8478
-zji
+2012-01-31T19:12:35.000000Z
+35abdf721fe296ac75336aba0ac9b5ae
+2012-01-20T16:26:44.505648Z
+8743
+youmi
 has-props


@@ -160,7 +160,7 @@ has-props



-19717
+24671

 AbstractSaveableParameterPanel.java
 file
diff --git a/geworkbench-core/classes/org/geworkbench/analysis/.svn/text-base/AbstractAnalysis.java.svn-base b/geworkbench-core/classes/org/geworkbench/analysis/.svn/text-base/AbstractAnalysis.java.svn-base
index e040cee..288ea21 100644
--- a/geworkbench-core/classes/org/geworkbench/analysis/.svn/text-base/AbstractAnalysis.java.svn-base
+++ b/geworkbench-core/classes/org/geworkbench/analysis/.svn/text-base/AbstractAnalysis.java.svn-base
@@ -11,6 +11,7 @@ import java.io.Serializable;
 import java.util.Collections;
 import java.util.Comparator;
 import java.util.HashMap;
+import java.util.Iterator;
 import java.util.LinkedHashMap;
 import java.util.Map;
 import java.util.Vector;
@@ -18,12 +19,22 @@ import java.util.Vector;
 import org.apache.commons.lang.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
+import org.geworkbench.bison.datastructure.biocollections.DSDataSet;
+import org.geworkbench.bison.datastructure.biocollections.microarrays.CSMicroarraySet;
+import org.geworkbench.bison.datastructure.biocollections.views.DSMicroarraySetView;
+import org.geworkbench.bison.datastructure.bioobjects.markers.CSExpressionMarker;
+import org.geworkbench.bison.datastructure.bioobjects.markers.DSGeneMarker;
+import org.geworkbench.bison.datastructure.bioobjects.microarray.DSMicroarray;
+import org.geworkbench.bison.datastructure.complex.panels.CSPanel;
+import org.geworkbench.bison.datastructure.complex.panels.DSItemList;
+import org.geworkbench.bison.datastructure.complex.panels.DSPanel;
 import org.geworkbench.bison.model.analysis.Analysis;
 import org.geworkbench.bison.model.analysis.ParamValidationResults;
 import org.geworkbench.bison.model.analysis.ParameterPanel;
 import org.geworkbench.engine.config.PluginRegistry;
 import org.geworkbench.engine.management.ComponentClassLoader;
 import org.geworkbench.util.FilePathnameUtils;
+import org.ginkgo.labs.util.FileTools;

 /**
  * <p>
@@ -32,12 +43,13 @@ import org.geworkbench.util.FilePathnameUtils;
  * <p>
  * Company: First Genetic Trust Inc.
  * </p>
- * <p/> Implementation of <code>Analysis</code> customized for use within the
+ * <p/>
+ * Implementation of <code>Analysis</code> customized for use within the
  * applications. It handles the saving of all named parameters sets (from within
  * the saveParametersUnderName method). It also provides a default
  * implementation for the validateParameters method by calling the corresponding
  * method in the <code>AbstractSaveableParameterPanel</code>.
- *
+ *
  * @author First Genetic Trust Inc.
  * @author keshav
  * @author yc2480
@@ -48,11 +60,12 @@ import org.geworkbench.util.FilePathnameUtils;
 public abstract class AbstractAnalysis implements Analysis, Serializable,
 		java.util.Observer {
 	private static final long serialVersionUID = 7028809841554763107L;
-
+
 	private static final String XML = "xml";
 	private static final String FILE_EXTENSION_SEPARATOR = ".";

-	private static final String ERR_TXT = FilePathnameUtils.getUserSettingDirectoryPath() + "err.txt";
+	private static final String ERR_TXT = FilePathnameUtils
+			.getUserSettingDirectoryPath() + "err.txt";

 	private Log log = LogFactory.getLog(this.getClass());

@@ -118,14 +131,14 @@ public abstract class AbstractAnalysis implements Analysis, Serializable,

 	public static final int SKYBASE_TYPE = 29;

-    public static final int PUDGE_TYPE = 30;
-
-    public static final int MEDUSA_TYPE = 31;
-
-    public static final int FOLD_CHANGE_TYPE=32;
-
-    public static final int  BLAST_TYPE= 33;
-
+	public static final int PUDGE_TYPE = 30;
+
+	public static final int MEDUSA_TYPE = 31;
+
+	public static final int FOLD_CHANGE_TYPE = 32;
+
+	public static final int BLAST_TYPE = 33;
+
 	/**
 	 * Parameters will be saved as XML files in "savedParams" directory under
 	 * each component directory.
@@ -137,6 +150,9 @@ public abstract class AbstractAnalysis implements Analysis, Serializable,
 	 * collect the analysis parameters from the user.
 	 */
 	protected AbstractSaveableParameterPanel aspp = null;
+
+	private boolean useMarkersFromSelector = true;
+

 	/**
 	 * Contains indices that are used in order to recover the set of named
@@ -173,7 +189,8 @@ public abstract class AbstractAnalysis implements Analysis, Serializable,
 	 *
 	 */
 	public AbstractAnalysis() {
-		parameterHash = Collections.synchronizedMap(new LinkedHashMap<ParameterKey, Map<Serializable, Serializable>>());
+		parameterHash = Collections
+				.synchronizedMap(new LinkedHashMap<ParameterKey, Map<Serializable, Serializable>>());
 		className = this.getClass().getSuperclass().getName();
 		String pluginName = PluginRegistry.getNameMap(className);
 		setLabel(pluginName);
@@ -205,7 +222,7 @@ public abstract class AbstractAnalysis implements Analysis, Serializable,
 		if (listOfFiles.length > 0) {
 			java.util.Arrays.sort(listOfFiles, new Comparator<File>() {
 				public int compare(File a, File b) {
-					return (int) ( a.lastModified() - b.lastModified());
+					return (int) (a.lastModified() - b.lastModified());
 				}
 			});
 			lastParameterSetName = unscrubFilename(listOfFiles[listOfFiles.length - 1]
@@ -217,16 +234,19 @@ public abstract class AbstractAnalysis implements Analysis, Serializable,
 						String setName = unscrubFilename(files);
 						Map<Serializable, Serializable> parameters = deserializeNamedParameterSet(setName);
 						ParameterKey key = new ParameterKey(getIndex(), setName);
-						log.debug("Try loading saved parameter file "+files);
-						log.debug("We are looking for "+key.toString());
-						log.debug("This one looks like it's for "+parameters.get(ParameterKey.class.getSimpleName()));
+						log.debug("Try loading saved parameter file " + files);
+						log.debug("We are looking for " + key.toString());
+						log.debug("This one looks like it's for "
+								+ parameters.get(ParameterKey.class
+										.getSimpleName()));
 						/*
 						 * Since one package can contain multiple components
 						 * which have different panels, we need to make sure we
 						 * got the right one.
 						 */
 						if (parameters != null)
-							if (parameters.get(ParameterKey.class.getSimpleName()).equals(
+							if (parameters.get(
+									ParameterKey.class.getSimpleName()).equals(
 									key.toString())) {
 								log.debug("put it in to parameterHash");
 								parameterHash.put(key, parameters);
@@ -239,7 +259,7 @@ public abstract class AbstractAnalysis implements Analysis, Serializable,
 	}

 	/**
-	 *
+	 *
 	 * @return Return the name of last saved parameter set.
 	 */
 	public String getLastSavedParameterSetName() {
@@ -248,16 +268,27 @@ public abstract class AbstractAnalysis implements Analysis, Serializable,
 		// parameter set from this launch.
 		return lastParameterSetName;
 	}
+
+
+
+	public void useMarkersFromSelector(boolean status) {
+		useMarkersFromSelector = status;
+	}
+
+
+	public boolean useMarkersFromSelector() {
+		return useMarkersFromSelector;
+	}
+

 	/*
 	 * Translate filename back to set name
 	 */
 	private String unscrubFilename(String filename) {
 		if (StringUtils.contains(filename, File.separatorChar))
-			filename = StringUtils.substringAfterLast(filename, System
-					.getProperty("file.separator"));
-		if (StringUtils.contains(filename, FILE_EXTENSION_SEPARATOR
-				+ XML))
+			filename = StringUtils.substringAfterLast(filename,
+					System.getProperty("file.separator"));
+		if (StringUtils.contains(filename, FILE_EXTENSION_SEPARATOR + XML))
 			filename = StringUtils.substringBeforeLast(filename,
 					FILE_EXTENSION_SEPARATOR + XML);
 		return filename;
@@ -265,9 +296,9 @@ public abstract class AbstractAnalysis implements Analysis, Serializable,

 	/**
 	 * Deletes a saved setting based on the saved parameter name.
-	 *
-	 * @param name -
-	 *            name of the saved parameter
+	 *
+	 * @param name
+	 *            - name of the saved parameter
 	 */
 	public void removeNamedParameter(String name) {
 		// remove from memory
@@ -280,7 +311,7 @@ public abstract class AbstractAnalysis implements Analysis, Serializable,
 	 * Returns the names of the parameter sets that were saved through a call to
 	 * saveParameters(String filename). Names can be removed using
 	 * <code>removeNamedParameter()</code>
-	 *
+	 *
 	 * @return Names of parameterSets as an array of Strings.
 	 */
 	public String[] getNamesOfStoredParameterSets() {
@@ -299,7 +330,7 @@ public abstract class AbstractAnalysis implements Analysis, Serializable,
 	/**
 	 * Similar to getNamedParameterSetPanel, but instead of return the panel, it
 	 * directly set (reuse) the current panel.
-	 *
+	 *
 	 * @param name
 	 */
 	public void setNamedParameterSetPanel(String name) {
@@ -312,7 +343,7 @@ public abstract class AbstractAnalysis implements Analysis, Serializable,
 	/**
 	 * Returns the parameter values that were stored (in parameterHash in
 	 * memory) under the designated name.
-	 *
+	 *
 	 * @param name
 	 * @return Return a Map<Serializable, Serializable>, which use parameter
 	 *         name as the key and parameter value as the value.
@@ -326,7 +357,7 @@ public abstract class AbstractAnalysis implements Analysis, Serializable,
 	/**
 	 * Returns the parameters panel populated with the parameter values that
 	 * where stored under the designated 'name'.
-	 *
+	 *
 	 * @param name
 	 * @return
 	 */
@@ -339,7 +370,8 @@ public abstract class AbstractAnalysis implements Analysis, Serializable,
 					this.getClass().getClassLoader()); // to avoid java bug
 			// #6329581
 			// newaspp = (AbstractSaveableParameterPanel) ois.readObject();
-			HashMap<Serializable, Serializable> parameters = (HashMap<Serializable, Serializable>) ois.readObject();
+			HashMap<Serializable, Serializable> parameters = (HashMap<Serializable, Serializable>) ois
+					.readObject();
 			this.setParameters(parameters);
 		} catch (Exception e) {
 			log.error(e, e);
@@ -351,7 +383,7 @@ public abstract class AbstractAnalysis implements Analysis, Serializable,
 	/**
 	 * Returns the parameters panel populated with the parameter values that
 	 * where stored under the designated 'name'.
-	 *
+	 *
 	 * @param name
 	 * @return
 	 */
@@ -375,7 +407,7 @@ public abstract class AbstractAnalysis implements Analysis, Serializable,

 	/**
 	 * Check if the inputed parameterSet already exist in memory or not.
-	 *
+	 *
 	 * @param parameterSet
 	 * @return
 	 */
@@ -385,8 +417,9 @@ public abstract class AbstractAnalysis implements Analysis, Serializable,
 		if (parameterSet.get(ParameterKey.class.getSimpleName()) != null)
 			result = parameterHash.values().contains(parameterSet);
 		else {// I'll need to loop through all the records. disregard the
-			// ParameterKey and compare others.
-			for (Map<Serializable, Serializable> property : parameterHash.values()) {
+				// ParameterKey and compare others.
+			for (Map<Serializable, Serializable> property : parameterHash
+					.values()) {
 				Map<Serializable, Serializable> pureParameter = new HashMap<Serializable, Serializable>();
 				pureParameter.putAll(property);
 				pureParameter.remove(ParameterKey.class.getSimpleName());
@@ -399,9 +432,9 @@ public abstract class AbstractAnalysis implements Analysis, Serializable,

 	/**
 	 * Convenience method - returns a string which should be unique for each
-	 * subclass of <code>AbstractAnalysis</code>. This string is used as part
-	 * of the hash that is used to store/recover named parameter sets.
-	 *
+	 * subclass of <code>AbstractAnalysis</code>. This string is used as part of
+	 * the hash that is used to store/recover named parameter sets.
+	 *
 	 * @return String Unique "tagging" string for an Analysis type.
 	 */
 	private String getIndex() {
@@ -415,7 +448,7 @@ public abstract class AbstractAnalysis implements Analysis, Serializable,
 	 * Set the panel for this analysis to the specific component's 'panel'. This
 	 * method also set the tmpDir to the tmpDir under that parameter panel's
 	 * directory, and load all saved parameter files under that directory.
-	 *
+	 *
 	 * @param panel
 	 */
 	public void setDefaultPanel(AbstractSaveableParameterPanel panel) {
@@ -429,7 +462,7 @@ public abstract class AbstractAnalysis implements Analysis, Serializable,
 	/**
 	 * Set the path to the parameter's temporary directory for the component. If
 	 * the directory does not exist, create it.
-	 *
+	 *
 	 * @param aspp
 	 */
 	private void setParameterFilesPath(AbstractSaveableParameterPanel aspp) {
@@ -452,7 +485,7 @@ public abstract class AbstractAnalysis implements Analysis, Serializable,

 	/*
 	 * (non-Javadoc)
-	 *
+	 *
 	 * @see org.geworkbench.bison.model.analysis.Analysis#getParameterPanel()
 	 */
 	public ParameterPanel getParameterPanel() {
@@ -461,7 +494,7 @@ public abstract class AbstractAnalysis implements Analysis, Serializable,

 	/*
 	 * (non-Javadoc)
-	 *
+	 *
 	 * @see org.geworkbench.bison.model.analysis.Analysis#validateParameters()
 	 */
 	public ParamValidationResults validateParameters() {
@@ -474,8 +507,10 @@ public abstract class AbstractAnalysis implements Analysis, Serializable,

 	/*
 	 * (non-Javadoc)
-	 *
-	 * @see org.geworkbench.bison.datastructure.properties.DSDescribable#addDescription(java.lang.String)
+	 *
+	 * @see
+	 * org.geworkbench.bison.datastructure.properties.DSDescribable#addDescription
+	 * (java.lang.String)
 	 */
 	public void setDescription(String desc) {
 		description = desc;
@@ -483,16 +518,19 @@ public abstract class AbstractAnalysis implements Analysis, Serializable,

 	/*
 	 * (non-Javadoc)
-	 *
-	 * @see org.geworkbench.bison.datastructure.properties.DSDescribable#getDescriptions()
+	 *
+	 * @see
+	 * org.geworkbench.bison.datastructure.properties.DSDescribable#getDescriptions
+	 * ()
 	 */
 	public String getDescription() {
 		return description;
 	}

 	private String label = null;
+
 	/**
-	 *
+	 *
 	 * @return
 	 */
 	public String getLabel() {
@@ -500,7 +538,7 @@ public abstract class AbstractAnalysis implements Analysis, Serializable,
 	}

 	/**
-	 *
+	 *
 	 * @param name
 	 */
 	public void setLabel(String label) {
@@ -509,7 +547,7 @@ public abstract class AbstractAnalysis implements Analysis, Serializable,

 	/*
 	 * (non-Javadoc)
-	 *
+	 *
 	 * @see java.util.Observer#update(java.util.Observable, java.lang.Object)
 	 */
 	public void update(java.util.Observable ob, Object o) {
@@ -521,13 +559,13 @@ public abstract class AbstractAnalysis implements Analysis, Serializable,

 	/**
 	 * Return a code identifying the type of the analysis.
-	 *
+	 *
 	 * @return
 	 */
 	public abstract int getAnalysisType();

 	/**
-	 *
+	 *
 	 * @return
 	 */
 	public String createHistory() {
@@ -536,7 +574,7 @@ public abstract class AbstractAnalysis implements Analysis, Serializable,

 	/*
 	 * (non-Javadoc)
-	 *
+	 *
 	 * @see org.geworkbench.bison.model.analysis.Analysis#getParameters()
 	 */
 	public Map<Serializable, Serializable> getParameters() {
@@ -545,8 +583,10 @@ public abstract class AbstractAnalysis implements Analysis, Serializable,

 	/*
 	 * (non-Javadoc)
-	 *
-	 * @see org.geworkbench.bison.model.analysis.Analysis#setParameters(java.util.Map)
+	 *
+	 * @see
+	 * org.geworkbench.bison.model.analysis.Analysis#setParameters(java.util
+	 * .Map)
 	 */
 	public void setParameters(Map<Serializable, Serializable> parameters) {
 		this.aspp.fillDefaultValues(parameters);
@@ -555,9 +595,11 @@ public abstract class AbstractAnalysis implements Analysis, Serializable,

 	/*
 	 * (non-Javadoc)
-	 *
-	 * @see org.geworkbench.bison.model.analysis.Analysis#saveParameters(java.lang.String)
-	 *
+	 *
+	 * @see
+	 * org.geworkbench.bison.model.analysis.Analysis#saveParameters(java.lang
+	 * .String)
+	 *
 	 * Current parameters will be saved in both memory and files under given
 	 * name.
 	 */
@@ -569,15 +611,13 @@ public abstract class AbstractAnalysis implements Analysis, Serializable,
 		 */
 		ParameterKey key = new ParameterKey(getIndex(), setName);

-	    parameterHash.put(key, aspp.getParameters());
-
+		parameterHash.put(key, aspp.getParameters());

 		writeParametersAsXml(setName);
 	}

 	/**
-	 * Saves current parameters this analysis using the
-	 * {@link XMLEncoder}.
+	 * Saves current parameters this analysis using the {@link XMLEncoder}.
 	 */
 	private void writeParametersAsXml(String name) {
 		FileOutputStream fos = null;
@@ -592,7 +632,7 @@ public abstract class AbstractAnalysis implements Analysis, Serializable,
 			 * Swap the loader to the loader that loads the actual panel, and
 			 * redirect the System.err printed by XMLEncoder when writing the
 			 * xml object.
-			 *
+			 *
 			 * See http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=6329581.
 			 */
 			currentClassLoader = Thread.currentThread().getContextClassLoader();
@@ -622,9 +662,11 @@ public abstract class AbstractAnalysis implements Analysis, Serializable,

 	/*
 	 * (non-Javadoc)
-	 *
-	 * @see org.geworkbench.bison.model.analysis.Analysis#deleteParameters(java.lang.String)
-	 *
+	 *
+	 * @see
+	 * org.geworkbench.bison.model.analysis.Analysis#deleteParameters(java.lang
+	 * .String)
+	 *
 	 * We generate the filename from the set's name, and delete the file
 	 */
 	public void deleteParameters(String name) {
@@ -640,12 +682,111 @@ public abstract class AbstractAnalysis implements Analysis, Serializable,
 		if (!StringUtils.startsWith(filename, tmpDir)) {
 			filename = tmpDir + filename;
 		}
-		if (!StringUtils.endsWith(filename, FILE_EXTENSION_SEPARATOR
-				+ XML)) {
-			filename = filename + FILE_EXTENSION_SEPARATOR
-					+ XML;
+		if (!StringUtils.endsWith(filename, FILE_EXTENSION_SEPARATOR + XML)) {
+			filename = filename + FILE_EXTENSION_SEPARATOR + XML;
 		}
 		return filename;
 	}

+	/**
+	 *
+	 * @param maSetView
+	 * @return
+	 */
+	public String generateHistoryForMaSetView(
+			DSMicroarraySetView<DSGeneMarker, DSMicroarray> maSetView, boolean useMarkersFromSelector) {
+		StringBuilder ans = new StringBuilder(
+				"=The MicroarraySetView used for analysis: ");
+		/* Generate text for microarrays/groups */
+		ans.append(FileTools.NEWLINE);
+		try {
+			log.debug("We got a " + maSetView.items().getClass().toString());
+			if (maSetView.items().getClass() == CSPanel.class) {
+				log.debug("situation 1: microarraySets selected");
+				DSItemList<DSPanel<DSMicroarray>> paneltest = ((DSPanel<DSMicroarray>) maSetView
+						.items()).panels();
+
+				ans.append("==Used Microarray Sets [")
+						.append(paneltest.size() + "]==")
+						.append(FileTools.NEWLINE);
+				for (DSPanel<DSMicroarray> temp : paneltest) {
+					ans.append(FileTools.TAB + temp.toString()).append(
+							FileTools.NEWLINE);
+					for (DSMicroarray temp2 : temp) {
+						ans.append(FileTools.TAB).append(FileTools.TAB)
+								.append(temp2.toString())
+								.append(FileTools.NEWLINE);
+					}
+				}
+			} else if (maSetView.items().getClass() == CSMicroarraySet.class) {
+				log.debug("situation 2: microarraySets not selected");
+				CSMicroarraySet exprSet = (CSMicroarraySet) maSetView.items();
+				ans.append("==Used Microarrays [").append(exprSet.size())
+						.append("]==").append(FileTools.NEWLINE);
+				for (Iterator<DSMicroarray> iterator = exprSet.iterator(); iterator
+						.hasNext();) {
+					DSMicroarray array = iterator.next();
+					ans.append(FileTools.TAB).append(array.getLabel())
+							.append(FileTools.NEWLINE);
+				}
+			}
+			ans.append("==End of Microarray Sets==").append(FileTools.NEWLINE);
+			/* Generate text for markers */
+
+			if (useMarkersFromSelector) {
+				DSPanel<DSGeneMarker> paneltest = maSetView.getMarkerPanel();
+				if (maSetView.useMarkerPanel()) {
+					if ((paneltest!=null) && (paneltest.size()>0)){
+						log.debug("situation 3: markers selected");
+
+						ans .append( "==Used Markers [" ).append( paneltest.size() ).append( "]==\n" );
+						for (Object obj : paneltest) {
+							CSExpressionMarker temp = (CSExpressionMarker) obj;
+							ans .append( "\t" ).append( temp.getLabel() ).append( "\n" );
+						}
+					}else{
+						log.debug("situation 4: no markers selected.");
+						DSItemList<DSGeneMarker> markers = maSetView.markers();
+						ans .append( "==Used Markers [" ).append( markers.size() ).append( "]==\n" );
+						for (DSGeneMarker marker : markers) {
+							ans .append( "\t" ).append( marker.getLabel() ).append( "\n" );
+						}
+					}
+				} else {
+					log.debug("situation 5: All Markers selected.");
+					DSItemList<DSGeneMarker> markers = maSetView.allMarkers();
+					ans .append( "==Used Markers [" ).append( markers.size() ).append( "]==" )
+							.append( FileTools.NEWLINE );
+					for (DSGeneMarker marker : markers) {
+						ans .append( FileTools.TAB ).append( marker.getLabel()
+						).append( FileTools.NEWLINE );
+					}
+				}
+
+
+				ans.append("==End of Used Markers==").append(FileTools.NEWLINE);
+			}
+		} catch (ClassCastException cce) {
+			/* it's not a DSPanel, we generate nothing for panel part */
+			log.error(cce);
+		}
+		ans.append("=End of MicroarraySetView data=");
+		return ans.toString();
+	}
+
+	@SuppressWarnings("rawtypes")
+	public String generateHistoryStringForGeneralDataSet(DSDataSet dataset) {
+		if (dataset == null) {
+			return "No information on the data set." + FileTools.NEWLINE;
+		} else {
+			StringBuilder sb = new StringBuilder();
+			sb.append("The data set used for analysis is [ ");
+			sb.append(dataset.getDataSetName());
+			sb.append(" ] from file [ ");
+			sb.append(dataset.getFile());
+			sb.append(" ]." + FileTools.NEWLINE);
+			return sb.toString();
+		}
+	}
+
 }
diff --git a/geworkbench-core/classes/org/geworkbench/bison/.svn/all-wcprops b/geworkbench-core/classes/org/geworkbench/bison/.svn/all-wcprops
index ec3b9d9..f4d38e0 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/.svn/all-wcprops
+++ b/geworkbench-core/classes/org/geworkbench/bison/.svn/all-wcprops
@@ -1,5 +1,5 @@
 K 25
 svn:wc:ra_dav:version-url
 V 74
-/svn/geworkbench/!svn/ver/8665/trunk/geworkbench/src/org/geworkbench/bison
+/svn/geworkbench/!svn/ver/8762/trunk/geworkbench/src/org/geworkbench/bison
 END
diff --git a/geworkbench-core/classes/org/geworkbench/bison/.svn/entries b/geworkbench-core/classes/org/geworkbench/bison/.svn/entries
index 37c5316..ede99e6 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/bison/.svn/entries
@@ -1,15 +1,15 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/bison
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2012-01-06T17:16:16.839429Z
-8665
-youmi
+2012-01-25T17:48:27.081994Z
+8762
+zji



diff --git a/geworkbench-core/classes/org/geworkbench/bison/algorithm/.svn/entries b/geworkbench-core/classes/org/geworkbench/bison/algorithm/.svn/entries
index 2c6859e..3df2f50 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/algorithm/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/bison/algorithm/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/bison/algorithm
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/bison/algorithm/classification/.svn/entries b/geworkbench-core/classes/org/geworkbench/bison/algorithm/classification/.svn/entries
index 657b1d5..62ae262 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/algorithm/classification/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/bison/algorithm/classification/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/bison/algorithm/classification
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/bison/annotation/.svn/entries b/geworkbench-core/classes/org/geworkbench/bison/annotation/.svn/entries
index 892f694..f141c2d 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/annotation/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/bison/annotation/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/bison/annotation
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/bison/datastructure/.svn/all-wcprops b/geworkbench-core/classes/org/geworkbench/bison/datastructure/.svn/all-wcprops
index 6d48ffa..d72bbb7 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/datastructure/.svn/all-wcprops
+++ b/geworkbench-core/classes/org/geworkbench/bison/datastructure/.svn/all-wcprops
@@ -1,5 +1,5 @@
 K 25
 svn:wc:ra_dav:version-url
 V 88
-/svn/geworkbench/!svn/ver/8665/trunk/geworkbench/src/org/geworkbench/bison/datastructure
+/svn/geworkbench/!svn/ver/8762/trunk/geworkbench/src/org/geworkbench/bison/datastructure
 END
diff --git a/geworkbench-core/classes/org/geworkbench/bison/datastructure/.svn/entries b/geworkbench-core/classes/org/geworkbench/bison/datastructure/.svn/entries
index ef73291..66da76b 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/datastructure/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/bison/datastructure/.svn/entries
@@ -1,15 +1,15 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/bison/datastructure
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2012-01-06T17:16:16.839429Z
-8665
-youmi
+2012-01-25T17:48:27.081994Z
+8762
+zji



diff --git a/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/.svn/all-wcprops b/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/.svn/all-wcprops
index 61de731..4fd10de 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/.svn/all-wcprops
+++ b/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/.svn/all-wcprops
@@ -1,7 +1,7 @@
 K 25
 svn:wc:ra_dav:version-url
 V 103
-/svn/geworkbench/!svn/ver/8665/trunk/geworkbench/src/org/geworkbench/bison/datastructure/biocollections
+/svn/geworkbench/!svn/ver/8761/trunk/geworkbench/src/org/geworkbench/bison/datastructure/biocollections
 END
 AdjacencyMatrix.java
 K 25
diff --git a/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/.svn/entries b/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/.svn/entries
index 671879d..e4bc44a 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/.svn/entries
@@ -1,15 +1,15 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/bison/datastructure/biocollections
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2012-01-06T17:16:16.839429Z
-8665
-youmi
+2012-01-25T17:34:14.733766Z
+8761
+zji



diff --git a/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/gsea/.svn/entries b/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/gsea/.svn/entries
index cc96cc9..e7a0418 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/gsea/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/gsea/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/bison/datastructure/biocollections/gsea
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/medusa/.svn/entries b/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/medusa/.svn/entries
index 22f3074..6df8a3b 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/medusa/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/medusa/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/bison/datastructure/biocollections/medusa
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/microarrays/.svn/all-wcprops b/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/microarrays/.svn/all-wcprops
index c56217a..9fa3013 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/microarrays/.svn/all-wcprops
+++ b/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/microarrays/.svn/all-wcprops
@@ -1,13 +1,13 @@
 K 25
 svn:wc:ra_dav:version-url
 V 115
-/svn/geworkbench/!svn/ver/8527/trunk/geworkbench/src/org/geworkbench/bison/datastructure/biocollections/microarrays
+/svn/geworkbench/!svn/ver/8761/trunk/geworkbench/src/org/geworkbench/bison/datastructure/biocollections/microarrays
 END
 CSMicroarraySet.java
 K 25
 svn:wc:ra_dav:version-url
 V 136
-/svn/geworkbench/!svn/ver/8527/trunk/geworkbench/src/org/geworkbench/bison/datastructure/biocollections/microarrays/CSMicroarraySet.java
+/svn/geworkbench/!svn/ver/8761/trunk/geworkbench/src/org/geworkbench/bison/datastructure/biocollections/microarrays/CSMicroarraySet.java
 END
 DSMicroarraySet.java
 K 25
diff --git a/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/microarrays/.svn/entries b/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/microarrays/.svn/entries
index 9f73f74..07ca36b 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/microarrays/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/microarrays/.svn/entries
@@ -1,14 +1,14 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/bison/datastructure/biocollections/microarrays
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2011-11-16T16:03:46.079217Z
-8527
+2012-01-25T17:34:14.733766Z
+8761
 zji


@@ -32,10 +32,10 @@ file



-2012-01-10T19:15:27.000000Z
-2cfb4482fd86ed7f4e5d61203bf0ed96
-2011-11-16T16:03:46.079217Z
-8527
+2012-01-31T19:12:36.000000Z
+ea46f8aad6cb2b9bb8732e8f21e7b872
+2012-01-25T17:34:14.733766Z
+8761
 zji
 has-props

@@ -58,7 +58,7 @@ has-props



-15706
+15463

 DSMicroarraySet.java
 file
diff --git a/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/microarrays/.svn/text-base/CSMicroarraySet.java.svn-base b/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/microarrays/.svn/text-base/CSMicroarraySet.java.svn-base
index 4ad2d43..1dbd1fd 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/microarrays/.svn/text-base/CSMicroarraySet.java.svn-base
+++ b/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/microarrays/.svn/text-base/CSMicroarraySet.java.svn-base
@@ -1,16 +1,14 @@
 package org.geworkbench.bison.datastructure.biocollections.microarrays;

 import java.io.BufferedWriter;
-import java.io.File;
+import java.io.File;
 import java.io.FileWriter;
 import java.io.IOException;
 import java.io.ObjectInputStream;
-import java.io.ObjectOutputStream;
-import java.util.ArrayList;
+import java.io.ObjectOutputStream;
 import java.util.Collections;
 import java.util.Comparator;
 import java.util.Iterator;
-import java.util.List;
 import java.util.TreeMap;
 import java.util.Vector;

@@ -23,7 +21,7 @@ import org.geworkbench.bison.annotation.CSAnnotationContextManager;
 import org.geworkbench.bison.annotation.DSAnnotationContext;
 import org.geworkbench.bison.annotation.DSAnnotationContextManager;
 import org.geworkbench.bison.datastructure.biocollections.CSDataSet;
-import org.geworkbench.bison.datastructure.biocollections.CSMarkerVector;
+import org.geworkbench.bison.datastructure.biocollections.CSMarkerVector;
 import org.geworkbench.bison.datastructure.bioobjects.markers.CSExpressionMarker;
 import org.geworkbench.bison.datastructure.bioobjects.markers.DSGeneMarker;
 import org.geworkbench.bison.datastructure.bioobjects.microarray.CSAffyMarkerValue;
@@ -259,33 +257,26 @@ final public class CSMicroarraySet extends CSDataSet<DSMicroarray> implements DS
 			DSAnnotationContextManager manager = CSAnnotationContextManager
 					.getInstance();
 			int n = manager.getNumberOfContexts(this);
-			List<String> arrayContext = new ArrayList<String>();
 			for (int i = 0; i < n; i++) {
 				DSAnnotationContext<DSMicroarray> context = manager.getContext(
 						this, i);
 				StringBuilder line = new StringBuilder("Description" + '\t'
 						+ context.getName());
-				int setCount = 0;
 				for (Iterator<DSMicroarray> iterator = this.iterator(); iterator
 						.hasNext();) {
 					DSMicroarray microarray = iterator.next();
+					String label = "";
 					String[] labels = context.getLabelsForItem(microarray);
 					if (labels.length > 0) {
-						String label = labels[0];
+						label = labels[0];
 						if (labels.length > 1) { // multiple labels
 							for (int j = 1; j < labels.length; j++)
 								label += "|" + labels[j];
 						}
-						line.append('\t' + label);
-						setCount++;
 					}
+					line.append('\t' + label);
 				}
-				if(setCount==this.size()) {
-					arrayContext.add(line.toString());
-				}
-			}
-			for(String line : arrayContext) {
-				writer.write(line);
+				writer.write(line.toString());
 				writer.newLine();
 			}

diff --git a/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/pca/.svn/entries b/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/pca/.svn/entries
index dc8e6ad..3faeec1 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/pca/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/pca/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/bison/datastructure/biocollections/pca
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/sequences/.svn/entries b/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/sequences/.svn/entries
index 625d08e..872d640 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/sequences/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/sequences/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/bison/datastructure/biocollections/sequences
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/views/.svn/entries b/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/views/.svn/entries
index 41baec0..9441252 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/views/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/views/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/bison/datastructure/biocollections/views
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/.svn/all-wcprops b/geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/.svn/all-wcprops
index 4f53828..f708f8e 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/.svn/all-wcprops
+++ b/geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/.svn/all-wcprops
@@ -1,7 +1,7 @@
 K 25
 svn:wc:ra_dav:version-url
 V 99
-/svn/geworkbench/!svn/ver/8648/trunk/geworkbench/src/org/geworkbench/bison/datastructure/bioobjects
+/svn/geworkbench/!svn/ver/8762/trunk/geworkbench/src/org/geworkbench/bison/datastructure/bioobjects
 END
 DSClassification.java
 K 25
diff --git a/geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/.svn/entries b/geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/.svn/entries
index d595126..de69fe1 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/.svn/entries
@@ -1,14 +1,14 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/bison/datastructure/bioobjects
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2012-01-04T22:17:55.887786Z
-8648
+2012-01-25T17:48:27.081994Z
+8762
 zji


@@ -60,17 +60,17 @@ has-props

 2398

-IdeaResultDataSet.java
+IdeaGLoc.java
 file




 2012-01-10T19:15:27.000000Z
-995a6ccbb9a5f44c403072b2de6ea6a1
-2011-11-02T15:43:58.696033Z
-8481
-zji
+dda175d92cb80ed50818890750f26209
+2011-09-06T22:30:11.516277Z
+8254
+maz



@@ -92,19 +92,19 @@ zji



-1438
+1869

-IdeaGLoc.java
+IdeaResultDataSet.java
 file




 2012-01-10T19:15:27.000000Z
-dda175d92cb80ed50818890750f26209
-2011-09-06T22:30:11.516277Z
-8254
-maz
+995a6ccbb9a5f44c403072b2de6ea6a1
+2011-11-02T15:43:58.696033Z
+8481
+zji



@@ -126,16 +126,16 @@ maz



-1869
+1438

-IdeaModule.java
+IdeaNode.java
 file




 2012-01-10T19:15:27.000000Z
-647a632f1a47fe916c04f9c50392422d
+f584cb4d22b0f0c7dd7e953a4c6802b0
 2011-09-06T22:30:11.516277Z
 8254
 maz
@@ -160,16 +160,16 @@ maz



-801
+2025

-IdeaNode.java
+IdeaModule.java
 file




 2012-01-10T19:15:27.000000Z
-f584cb4d22b0f0c7dd7e953a4c6802b0
+647a632f1a47fe916c04f9c50392422d
 2011-09-06T22:30:11.516277Z
 8254
 maz
@@ -194,7 +194,7 @@ maz



-2025
+801

 KMeansResult.java
 file
@@ -270,17 +270,17 @@ has-props
 markers
 dir

-IdeaEdge.java
+DSBioObject.java
 file




 2011-08-17T00:10:50.000000Z
-ea57aa0c85ebc8839222acf2d25f3b38
-2010-12-06T22:31:56.790698Z
-7296
-zji
+b4881ef5121d9cf4578d4ee789299b4a
+2006-03-03T18:05:24.000000Z
+1317
+mhall
 has-props


@@ -302,7 +302,7 @@ has-props



-3867
+377

 DSPValued.java
 file
@@ -338,17 +338,17 @@ has-props

 395

-DSBioObject.java
+IdeaEdge.java
 file




 2011-08-17T00:10:50.000000Z
-b4881ef5121d9cf4578d4ee789299b4a
-2006-03-03T18:05:24.000000Z
-1317
-mhall
+ea57aa0c85ebc8839222acf2d25f3b38
+2010-12-06T22:31:56.790698Z
+7296
+zji
 has-props


@@ -370,12 +370,12 @@ has-props



-377
+3867

-sequence
+microarray
 dir

-microarray
+sequence
 dir

 IdeaProbeGene.java
diff --git a/geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/markers/.svn/all-wcprops b/geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/markers/.svn/all-wcprops
index b8f15e0..98bf36b 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/markers/.svn/all-wcprops
+++ b/geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/markers/.svn/all-wcprops
@@ -1,7 +1,7 @@
 K 25
 svn:wc:ra_dav:version-url
 V 107
-/svn/geworkbench/!svn/ver/8648/trunk/geworkbench/src/org/geworkbench/bison/datastructure/bioobjects/markers
+/svn/geworkbench/!svn/ver/8762/trunk/geworkbench/src/org/geworkbench/bison/datastructure/bioobjects/markers
 END
 DSRangeMarker.java
 K 25
diff --git a/geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/markers/.svn/entries b/geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/markers/.svn/entries
index bc95a8b..15fbd4f 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/markers/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/markers/.svn/entries
@@ -1,14 +1,14 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/bison/datastructure/bioobjects/markers
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2012-01-04T22:17:55.887786Z
-8648
+2012-01-25T17:48:27.081994Z
+8762
 zji


diff --git a/geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/markers/annotationparser/.svn/entries b/geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/markers/annotationparser/.svn/entries
index 0b97fe1..d78d020 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/markers/annotationparser/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/markers/annotationparser/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/bison/datastructure/bioobjects/markers/annotationparser
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/markers/goterms/.svn/all-wcprops b/geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/markers/goterms/.svn/all-wcprops
index 9813345..9cc9dce 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/markers/goterms/.svn/all-wcprops
+++ b/geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/markers/goterms/.svn/all-wcprops
@@ -1,13 +1,13 @@
 K 25
 svn:wc:ra_dav:version-url
 V 115
-/svn/geworkbench/!svn/ver/7802/trunk/geworkbench/src/org/geworkbench/bison/datastructure/bioobjects/markers/goterms
+/svn/geworkbench/!svn/ver/8762/trunk/geworkbench/src/org/geworkbench/bison/datastructure/bioobjects/markers/goterms
 END
 GeneOntologyTree.java
 K 25
 svn:wc:ra_dav:version-url
 V 137
-/svn/geworkbench/!svn/ver/7802/trunk/geworkbench/src/org/geworkbench/bison/datastructure/bioobjects/markers/goterms/GeneOntologyTree.java
+/svn/geworkbench/!svn/ver/8762/trunk/geworkbench/src/org/geworkbench/bison/datastructure/bioobjects/markers/goterms/GeneOntologyTree.java
 END
 GOTerm.java
 K 25
diff --git a/geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/markers/goterms/.svn/entries b/geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/markers/goterms/.svn/entries
index 64176e4..df42203 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/markers/goterms/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/markers/goterms/.svn/entries
@@ -1,14 +1,14 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/bison/datastructure/bioobjects/markers/goterms
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2011-04-22T14:50:48.962423Z
-7802
+2012-01-25T17:48:27.081994Z
+8762
 zji


@@ -32,10 +32,10 @@ file



-2011-08-17T00:10:50.000000Z
-eb1f15ea25eb1bdcba2f5f6282baf8b4
-2011-04-22T14:50:48.962423Z
-7802
+2012-01-31T19:12:36.000000Z
+10d6bc2baf3b1ad63b5c4d870482336d
+2012-01-25T17:48:27.081994Z
+8762
 zji
 has-props

@@ -58,7 +58,7 @@ has-props



-13403
+14516

 GOTerm.java
 file
diff --git a/geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/markers/goterms/.svn/text-base/GeneOntologyTree.java.svn-base b/geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/markers/goterms/.svn/text-base/GeneOntologyTree.java.svn-base
index f6f55c3..76ff3db 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/markers/goterms/.svn/text-base/GeneOntologyTree.java.svn-base
+++ b/geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/markers/goterms/.svn/text-base/GeneOntologyTree.java.svn-base
@@ -59,7 +59,7 @@ public class GeneOntologyTree {
 			}.start();
 			System.out.println(new java.util.Date());
 		} else {
-			instance = new GeneOntologyTree(OboSourcePreference.DEFAULT_OBO_FILE);
+			instance = new GeneOntologyTree(OboSourcePreference.getInstance().getSourceLocation()); //OboSourcePreference.DEFAULT_OBO_FILE);
 		}
 	}

@@ -200,8 +200,14 @@ public class GeneOntologyTree {
 		try {
 			BufferedReader in = new BufferedReader(new FileReader(oboFileName));
 			parseOBOFile(in);
+		} catch (FileNotFoundException e) {
+			JOptionPane
+					.showMessageDialog(
+							null,
+							oboFileName
+									+ ", which is part of geworkbench istallation, is missing. Gene Ontology related funactionality will not work correctly unless you choose to use remote obo source.",
+							".obo fil missing", JOptionPane.ERROR_MESSAGE);
 		} catch (Exception e) {
-			// TODO Auto-generated catch block
 			e.printStackTrace();
 		}
 	}
@@ -443,6 +449,7 @@ public class GeneOntologyTree {
 				pw.close();
 				BufferedReader in2 = new BufferedReader(new FileReader(OBO_FILENAME));
 				parseOBOFile(in2);
+				actualUsedOboSource = null;
 			} else {
 				log.warn("error in reading remote obo from "+url);
 			}
@@ -472,7 +479,8 @@ public class GeneOntologyTree {
 				}

 			});
-			BufferedReader in = new BufferedReader(new FileReader(OboSourcePreference.DEFAULT_OBO_FILE));
+			actualUsedOboSource = OboSourcePreference.DEFAULT_OBO_FILE;
+			BufferedReader in = new BufferedReader(new FileReader(actualUsedOboSource));
 			parseOBOFile(in);
 		} catch (InterruptedException e1) {
 			e1.printStackTrace();
@@ -492,4 +500,29 @@ public class GeneOntologyTree {
 	public String getDate() {
 		return date;
 	}
+
+
+	private String actualUsedOboSource = null;
+	public String getActualSource() {
+		OboSourcePreference pref = OboSourcePreference.getInstance();
+		if (pref.getSourceType() == OboSourcePreference.Source.REMOTE
+				&& actualUsedOboSource!=null) {
+			return actualUsedOboSource;
+		} else {
+			return pref.getSourceLocation();
+		}
+	}
+
+	public String getActualFile() {
+		OboSourcePreference pref = OboSourcePreference.getInstance();
+		if (pref.getSourceType() == OboSourcePreference.Source.REMOTE) {
+			if(actualUsedOboSource==null) {
+				return GeneOntologyTree.OBO_FILENAME;
+			} else {
+				return actualUsedOboSource;
+			}
+		} else {
+			return pref.getSourceLocation();
+		}
+	}
 }
diff --git a/geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/microarray/.svn/entries b/geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/microarray/.svn/entries
index c737071..6471b61 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/microarray/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/microarray/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/bison/datastructure/bioobjects/microarray
 https://ncisvn.nci.nih.gov/svn/geworkbench

@@ -94,16 +94,16 @@ has-props

 3274

-CSTTestResultSet.java
+DSProbeIntensityArray.java
 file




-2012-01-10T19:15:28.000000Z
-0f2563abd6d0d41b320247c29230945d
-2011-10-19T16:34:53.735246Z
-8424
+2011-08-17T00:10:50.000000Z
+de0ffd60b4fb484ac0cefbfb17a1f9fd
+2011-03-12T15:27:59.845248Z
+7572
 zji
 has-props

@@ -126,7 +126,7 @@ has-props



-1840
+440

 CSMarkerValue.java
 file
@@ -162,16 +162,16 @@ has-props

 4881

-DSProbeIntensityArray.java
+CSTTestResultSet.java
 file




-2011-08-17T00:10:50.000000Z
-de0ffd60b4fb484ac0cefbfb17a1f9fd
-2011-03-12T15:27:59.845248Z
-7572
+2012-01-10T19:15:28.000000Z
+0f2563abd6d0d41b320247c29230945d
+2011-10-19T16:34:53.735246Z
+8424
 zji
 has-props

@@ -194,19 +194,19 @@ has-props



-440
+1840

-DSMarkerValue.java
+DSTTestResultSet.java
 file




 2011-08-17T00:10:50.000000Z
-85a30f90de860859094d1115f490ddbf
-2011-03-12T15:27:59.845248Z
-7572
-zji
+df4a443dd9703996cd2ac6ef8cbd3b9f
+2008-02-11T22:13:23.000000Z
+3498
+chiangy
 has-props


@@ -228,7 +228,7 @@ has-props



-2146
+245

 CSAnovaResultSet.java
 file
@@ -264,17 +264,17 @@ has-props

 11912

-DSTTestResultSet.java
+DSMarkerValue.java
 file




 2011-08-17T00:10:50.000000Z
-df4a443dd9703996cd2ac6ef8cbd3b9f
-2008-02-11T22:13:23.000000Z
-3498
-chiangy
+85a30f90de860859094d1115f490ddbf
+2011-03-12T15:27:59.845248Z
+7572
+zji
 has-props


@@ -296,7 +296,7 @@ has-props



-245
+2146

 DSAnovaResultSet.java
 file
diff --git a/geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/sequence/.svn/entries b/geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/sequence/.svn/entries
index 007dd84..704c926 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/sequence/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/sequence/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/bison/datastructure/bioobjects/sequence
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/structure/.svn/entries b/geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/structure/.svn/entries
index ad4749a..686867a 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/structure/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/structure/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/bison/datastructure/bioobjects/structure
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/bison/datastructure/complex/.svn/entries b/geworkbench-core/classes/org/geworkbench/bison/datastructure/complex/.svn/entries
index 06f5f64..09a6235 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/datastructure/complex/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/bison/datastructure/complex/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/bison/datastructure/complex
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/bison/datastructure/complex/panels/.svn/entries b/geworkbench-core/classes/org/geworkbench/bison/datastructure/complex/panels/.svn/entries
index 9d5a2b4..dcea1f0 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/datastructure/complex/panels/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/bison/datastructure/complex/panels/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/bison/datastructure/complex/panels
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/bison/datastructure/complex/pattern/.svn/entries b/geworkbench-core/classes/org/geworkbench/bison/datastructure/complex/pattern/.svn/entries
index 98ae792..38ca212 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/datastructure/complex/pattern/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/bison/datastructure/complex/pattern/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/bison/datastructure/complex/pattern
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/bison/datastructure/complex/pattern/matrix/.svn/entries b/geworkbench-core/classes/org/geworkbench/bison/datastructure/complex/pattern/matrix/.svn/entries
index a70fa37..92f2254 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/datastructure/complex/pattern/matrix/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/bison/datastructure/complex/pattern/matrix/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/bison/datastructure/complex/pattern/matrix
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/bison/datastructure/complex/pattern/sequence/.svn/entries b/geworkbench-core/classes/org/geworkbench/bison/datastructure/complex/pattern/sequence/.svn/entries
index 0735f7e..7bc0401 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/datastructure/complex/pattern/sequence/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/bison/datastructure/complex/pattern/sequence/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/bison/datastructure/complex/pattern/sequence
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/bison/datastructure/properties/.svn/entries b/geworkbench-core/classes/org/geworkbench/bison/datastructure/properties/.svn/entries
index fc18cba..7f8c8cf 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/datastructure/properties/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/bison/datastructure/properties/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/bison/datastructure/properties
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/bison/model/.svn/entries b/geworkbench-core/classes/org/geworkbench/bison/model/.svn/entries
index f2b2918..8beb264 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/model/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/bison/model/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/bison/model
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/bison/model/analysis/.svn/entries b/geworkbench-core/classes/org/geworkbench/bison/model/analysis/.svn/entries
index 6aa1e54..b54fa01 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/model/analysis/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/bison/model/analysis/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/bison/model/analysis
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/bison/model/clusters/.svn/entries b/geworkbench-core/classes/org/geworkbench/bison/model/clusters/.svn/entries
index 172d65b..66e37a8 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/model/clusters/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/bison/model/clusters/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/bison/model/clusters
 https://ncisvn.nci.nih.gov/svn/geworkbench

@@ -26,16 +26,16 @@ zji

 8b29bb6e-589a-435a-9a12-3ab907be3462

-SOMCluster.java
+NonRecursiveClusterSet.java
 file




-2011-08-17T00:19:07.000000Z
-19c5f4d23d6ca552d990a4b1b95c05ad
-2011-05-27T15:53:22.537336Z
-7941
+2011-08-17T00:10:50.000000Z
+11490a0abf46a60fe291e265a9e44cdb
+2010-08-03T18:14:21.529709Z
+6940
 zji
 has-props

@@ -58,18 +58,18 @@ has-props



-1632
+6006

-NonRecursiveClusterSet.java
+SOMCluster.java
 file




-2011-08-17T00:10:50.000000Z
-11490a0abf46a60fe291e265a9e44cdb
-2010-08-03T18:14:21.529709Z
-6940
+2011-08-17T00:19:07.000000Z
+19c5f4d23d6ca552d990a4b1b95c05ad
+2011-05-27T15:53:22.537336Z
+7941
 zji
 has-props

@@ -92,18 +92,18 @@ has-props



-6006
+1632

-DefaultSOMCluster.java
+AbstractCluster.java
 file




-2011-08-17T00:19:07.000000Z
-e610d483270f5456b39771998b551e04
-2011-05-27T15:53:22.537336Z
-7941
+2011-08-17T00:10:50.000000Z
+44b1a8e3b741ebbc0f5a6e6f00cfa7b7
+2011-02-08T22:28:38.286773Z
+7427
 zji
 has-props

@@ -126,18 +126,18 @@ has-props



-1628
+5979

-AbstractCluster.java
+DefaultSOMCluster.java
 file




-2011-08-17T00:10:50.000000Z
-44b1a8e3b741ebbc0f5a6e6f00cfa7b7
-2011-02-08T22:28:38.286773Z
-7427
+2011-08-17T00:19:07.000000Z
+e610d483270f5456b39771998b551e04
+2011-05-27T15:53:22.537336Z
+7941
 zji
 has-props

@@ -160,7 +160,7 @@ has-props



-5979
+1628

 DSClusterDataSet.java
 file
diff --git a/geworkbench-core/classes/org/geworkbench/bison/parsers/.svn/entries b/geworkbench-core/classes/org/geworkbench/bison/parsers/.svn/entries
index d5e9cfd..14051c4 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/parsers/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/bison/parsers/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/bison/parsers
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/bison/parsers/resources/.svn/entries b/geworkbench-core/classes/org/geworkbench/bison/parsers/resources/.svn/entries
index add407a..ab47336 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/parsers/resources/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/bison/parsers/resources/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/bison/parsers/resources
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/bison/util/.svn/all-wcprops b/geworkbench-core/classes/org/geworkbench/bison/util/.svn/all-wcprops
index 2ab9dde..eb6f0f6 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/util/.svn/all-wcprops
+++ b/geworkbench-core/classes/org/geworkbench/bison/util/.svn/all-wcprops
@@ -1,7 +1,7 @@
 K 25
 svn:wc:ra_dav:version-url
 V 79
-/svn/geworkbench/!svn/ver/8652/trunk/geworkbench/src/org/geworkbench/bison/util
+/svn/geworkbench/!svn/ver/8740/trunk/geworkbench/src/org/geworkbench/bison/util
 END
 RandomNumberGenerator.java
 K 25
diff --git a/geworkbench-core/classes/org/geworkbench/bison/util/.svn/entries b/geworkbench-core/classes/org/geworkbench/bison/util/.svn/entries
index 4fe3650..4727051 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/util/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/bison/util/.svn/entries
@@ -1,15 +1,15 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/bison/util
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2012-01-05T21:52:03.739505Z
-8652
-zji
+2012-01-19T19:57:03.107864Z
+8740
+wangmen



diff --git a/geworkbench-core/classes/org/geworkbench/bison/util/colorcontext/.svn/all-wcprops b/geworkbench-core/classes/org/geworkbench/bison/util/colorcontext/.svn/all-wcprops
index ebec618..605d5c2 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/util/colorcontext/.svn/all-wcprops
+++ b/geworkbench-core/classes/org/geworkbench/bison/util/colorcontext/.svn/all-wcprops
@@ -1,13 +1,13 @@
 K 25
 svn:wc:ra_dav:version-url
 V 92
-/svn/geworkbench/!svn/ver/8652/trunk/geworkbench/src/org/geworkbench/bison/util/colorcontext
+/svn/geworkbench/!svn/ver/8740/trunk/geworkbench/src/org/geworkbench/bison/util/colorcontext
 END
 ExpressionPValueColorContext.java
 K 25
 svn:wc:ra_dav:version-url
 V 126
-/svn/geworkbench/!svn/ver/8652/trunk/geworkbench/src/org/geworkbench/bison/util/colorcontext/ExpressionPValueColorContext.java
+/svn/geworkbench/!svn/ver/8740/trunk/geworkbench/src/org/geworkbench/bison/util/colorcontext/ExpressionPValueColorContext.java
 END
 ColorContext.java
 K 25
diff --git a/geworkbench-core/classes/org/geworkbench/bison/util/colorcontext/.svn/entries b/geworkbench-core/classes/org/geworkbench/bison/util/colorcontext/.svn/entries
index f1ec1ca..b211482 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/util/colorcontext/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/bison/util/colorcontext/.svn/entries
@@ -1,15 +1,15 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/bison/util/colorcontext
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2012-01-05T21:52:03.739505Z
-8652
-zji
+2012-01-19T19:57:03.107864Z
+8740
+wangmen



@@ -32,11 +32,11 @@ file



-2012-01-10T21:28:37.000000Z
-73852e9e689b14396f0a2d285fb7672c
-2012-01-05T21:52:03.739505Z
-8652
-zji
+2012-01-31T19:12:36.000000Z
+eb3dabaa48cdcbcbedf2944c2579285c
+2012-01-19T19:57:03.107864Z
+8740
+wangmen
 has-props


@@ -58,7 +58,7 @@ has-props



-4102
+4158

 ColorContext.java
 file
diff --git a/geworkbench-core/classes/org/geworkbench/bison/util/colorcontext/.svn/text-base/ExpressionPValueColorContext.java.svn-base b/geworkbench-core/classes/org/geworkbench/bison/util/colorcontext/.svn/text-base/ExpressionPValueColorContext.java.svn-base
index b36a6fc..36f1e90 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/util/colorcontext/.svn/text-base/ExpressionPValueColorContext.java.svn-base
+++ b/geworkbench-core/classes/org/geworkbench/bison/util/colorcontext/.svn/text-base/ExpressionPValueColorContext.java.svn-base
@@ -31,6 +31,8 @@ public class ExpressionPValueColorContext implements ColorContext, Serializable
 //        intensity *= 2;
         intensity = 2 / intensity;
         double value = mv.getValue();
+        if (lock == null)
+        	lock = new Object();
         synchronized (lock) {
         	org.geworkbench.bison.util.Range range = ((DSRangeMarker) mInfo).getRange();
 	        double mean = range.norm.getMean(); //(range.max + range.min) / 2.0;
diff --git a/geworkbench-core/classes/org/geworkbench/builtin/.svn/all-wcprops b/geworkbench-core/classes/org/geworkbench/builtin/.svn/all-wcprops
index 59861f5..7ac421f 100644
--- a/geworkbench-core/classes/org/geworkbench/builtin/.svn/all-wcprops
+++ b/geworkbench-core/classes/org/geworkbench/builtin/.svn/all-wcprops
@@ -1,5 +1,5 @@
 K 25
 svn:wc:ra_dav:version-url
 V 76
-/svn/geworkbench/!svn/ver/8650/trunk/geworkbench/src/org/geworkbench/builtin
+/svn/geworkbench/!svn/ver/8794/trunk/geworkbench/src/org/geworkbench/builtin
 END
diff --git a/geworkbench-core/classes/org/geworkbench/builtin/.svn/entries b/geworkbench-core/classes/org/geworkbench/builtin/.svn/entries
index e75c026..3a852c7 100644
--- a/geworkbench-core/classes/org/geworkbench/builtin/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/builtin/.svn/entries
@@ -1,14 +1,14 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/builtin
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2012-01-05T18:11:48.744157Z
-8650
+2012-01-27T16:59:16.159585Z
+8794
 zji


diff --git a/geworkbench-core/classes/org/geworkbench/builtin/projects/.svn/all-wcprops b/geworkbench-core/classes/org/geworkbench/builtin/projects/.svn/all-wcprops
index 2099929..0c5515e 100644
--- a/geworkbench-core/classes/org/geworkbench/builtin/projects/.svn/all-wcprops
+++ b/geworkbench-core/classes/org/geworkbench/builtin/projects/.svn/all-wcprops
@@ -1,7 +1,7 @@
 K 25
 svn:wc:ra_dav:version-url
 V 85
-/svn/geworkbench/!svn/ver/8650/trunk/geworkbench/src/org/geworkbench/builtin/projects
+/svn/geworkbench/!svn/ver/8794/trunk/geworkbench/src/org/geworkbench/builtin/projects
 END
 OboSourcePreference.java
 K 25
@@ -93,29 +93,29 @@ svn:wc:ra_dav:version-url
 V 100
 /svn/geworkbench/!svn/ver/8478/trunk/geworkbench/src/org/geworkbench/builtin/projects/ImageNode.java
 END
-structure16x16.gif
-K 25
-svn:wc:ra_dav:version-url
-V 104
-/svn/geworkbench/!svn/ver/1391/trunk/geworkbench/src/org/geworkbench/builtin/projects/structure16x16.gif
-END
 psam16x16.gif
 K 25
 svn:wc:ra_dav:version-url
 V 99
 /svn/geworkbench/!svn/ver/1589/trunk/geworkbench/src/org/geworkbench/builtin/projects/psam16x16.gif
 END
+structure16x16.gif
+K 25
+svn:wc:ra_dav:version-url
+V 104
+/svn/geworkbench/!svn/ver/1391/trunk/geworkbench/src/org/geworkbench/builtin/projects/structure16x16.gif
+END
 DataSetNode.java
 K 25
 svn:wc:ra_dav:version-url
 V 102
 /svn/geworkbench/!svn/ver/8424/trunk/geworkbench/src/org/geworkbench/builtin/projects/DataSetNode.java
 END
-ProjectTreeNode.java
+WorkspaceHandler.java
 K 25
 svn:wc:ra_dav:version-url
-V 106
-/svn/geworkbench/!svn/ver/3398/trunk/geworkbench/src/org/geworkbench/builtin/projects/ProjectTreeNode.java
+V 107
+/svn/geworkbench/!svn/ver/8323/trunk/geworkbench/src/org/geworkbench/builtin/projects/WorkspaceHandler.java
 END
 TreeNodeRenderer.java
 K 25
@@ -123,17 +123,17 @@ svn:wc:ra_dav:version-url
 V 107
 /svn/geworkbench/!svn/ver/8590/trunk/geworkbench/src/org/geworkbench/builtin/projects/TreeNodeRenderer.java
 END
-WorkspaceHandler.java
+ProjectTreeNode.java
 K 25
 svn:wc:ra_dav:version-url
-V 107
-/svn/geworkbench/!svn/ver/8323/trunk/geworkbench/src/org/geworkbench/builtin/projects/WorkspaceHandler.java
+V 106
+/svn/geworkbench/!svn/ver/3398/trunk/geworkbench/src/org/geworkbench/builtin/projects/ProjectTreeNode.java
 END
 FileOpenHandler.java
 K 25
 svn:wc:ra_dav:version-url
 V 106
-/svn/geworkbench/!svn/ver/8524/trunk/geworkbench/src/org/geworkbench/builtin/projects/FileOpenHandler.java
+/svn/geworkbench/!svn/ver/8794/trunk/geworkbench/src/org/geworkbench/builtin/projects/FileOpenHandler.java
 END
 project16x16.gif
 K 25
@@ -141,11 +141,11 @@ svn:wc:ra_dav:version-url
 V 102
 /svn/geworkbench/!svn/ver/6517/trunk/geworkbench/src/org/geworkbench/builtin/projects/project16x16.gif
 END
-InformationPanel.java
+DataSetSubNode.java
 K 25
 svn:wc:ra_dav:version-url
-V 107
-/svn/geworkbench/!svn/ver/8369/trunk/geworkbench/src/org/geworkbench/builtin/projects/InformationPanel.java
+V 105
+/svn/geworkbench/!svn/ver/7947/trunk/geworkbench/src/org/geworkbench/builtin/projects/DataSetSubNode.java
 END
 Phenotype16x16.gif
 K 25
@@ -153,11 +153,11 @@ svn:wc:ra_dav:version-url
 V 104
 /svn/geworkbench/!svn/ver/1120/trunk/geworkbench/src/org/geworkbench/builtin/projects/Phenotype16x16.gif
 END
-DataSetSubNode.java
+InformationPanel.java
 K 25
 svn:wc:ra_dav:version-url
-V 105
-/svn/geworkbench/!svn/ver/7947/trunk/geworkbench/src/org/geworkbench/builtin/projects/DataSetSubNode.java
+V 107
+/svn/geworkbench/!svn/ver/8369/trunk/geworkbench/src/org/geworkbench/builtin/projects/InformationPanel.java
 END
 busy.gif
 K 25
@@ -165,18 +165,18 @@ svn:wc:ra_dav:version-url
 V 94
 /svn/geworkbench/!svn/ver/1120/trunk/geworkbench/src/org/geworkbench/builtin/projects/busy.gif
 END
-RegisterBean.java
-K 25
-svn:wc:ra_dav:version-url
-V 103
-/svn/geworkbench/!svn/ver/7754/trunk/geworkbench/src/org/geworkbench/builtin/projects/RegisterBean.java
-END
 DataSetSaveNode.java
 K 25
 svn:wc:ra_dav:version-url
 V 106
 /svn/geworkbench/!svn/ver/8474/trunk/geworkbench/src/org/geworkbench/builtin/projects/DataSetSaveNode.java
 END
+RegisterBean.java
+K 25
+svn:wc:ra_dav:version-url
+V 103
+/svn/geworkbench/!svn/ver/7754/trunk/geworkbench/src/org/geworkbench/builtin/projects/RegisterBean.java
+END
 Icons.java
 K 25
 svn:wc:ra_dav:version-url
diff --git a/geworkbench-core/classes/org/geworkbench/builtin/projects/.svn/entries b/geworkbench-core/classes/org/geworkbench/builtin/projects/.svn/entries
index 35328a6..e10c203 100644
--- a/geworkbench-core/classes/org/geworkbench/builtin/projects/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/builtin/projects/.svn/entries
@@ -1,14 +1,14 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/builtin/projects
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2012-01-05T18:11:48.744157Z
-8650
+2012-01-27T16:59:16.159585Z
+8794
 zji


@@ -539,16 +539,16 @@ has-props

 1027

-psam16x16.gif
+structure16x16.gif
 file




 2011-08-17T00:10:50.000000Z
-462e83b2c31fdbe2e540c943503c8f99
-2006-06-28T14:35:15.000000Z
-1589
+bdec66f8aca2f7511e6bd96041656ca7
+2006-03-30T22:55:08.000000Z
+1391
 watkinson
 has-props

@@ -571,18 +571,18 @@ has-props



-168
+107

-structure16x16.gif
+psam16x16.gif
 file




 2011-08-17T00:10:50.000000Z
-bdec66f8aca2f7511e6bd96041656ca7
-2006-03-30T22:55:08.000000Z
-1391
+462e83b2c31fdbe2e540c943503c8f99
+2006-06-28T14:35:15.000000Z
+1589
 watkinson
 has-props

@@ -605,7 +605,7 @@ has-props



-107
+168

 DataSetNode.java
 file
@@ -641,17 +641,17 @@ has-props

 2343

-WorkspaceHandler.java
+ProjectTreeNode.java
 file




-2012-01-10T19:15:28.000000Z
-f5a148fd67eb62400a9221ff93a8c73a
-2011-09-22T18:34:51.160472Z
-8323
-maz
+2011-08-17T00:10:50.000000Z
+c47e07a526147ab351c79f788d5dfef7
+2008-01-03T19:28:20.000000Z
+3398
+keshav
 has-props


@@ -673,7 +673,7 @@ has-props



-11565
+995

 TreeNodeRenderer.java
 file
@@ -709,17 +709,17 @@ has-props

 3869

-ProjectTreeNode.java
+WorkspaceHandler.java
 file




-2011-08-17T00:10:50.000000Z
-c47e07a526147ab351c79f788d5dfef7
-2008-01-03T19:28:20.000000Z
-3398
-keshav
+2012-01-10T19:15:28.000000Z
+f5a148fd67eb62400a9221ff93a8c73a
+2011-09-22T18:34:51.160472Z
+8323
+maz
 has-props


@@ -741,7 +741,7 @@ has-props



-995
+11565

 FileOpenHandler.java
 file
@@ -749,10 +749,10 @@ file



-2012-01-10T19:15:28.000000Z
-d4b4787dbab07f6d2031a7e18487aab7
-2011-11-14T22:19:17.648563Z
-8524
+2012-01-31T19:12:36.000000Z
+3abe6cca8b963a32f7c5e6a50590e8cd
+2012-01-27T16:59:16.159585Z
+8794
 zji
 has-props

@@ -775,7 +775,7 @@ has-props



-17465
+17640

 project16x16.gif
 file
@@ -811,17 +811,17 @@ has-props

 151

-Phenotype16x16.gif
+InformationPanel.java
 file




-2011-08-17T00:10:50.000000Z
-8a9ed81c0ae807ca19535a038891e916
-2006-01-13T22:48:38.000000Z
-1120
-watkin
+2012-01-10T19:15:28.000000Z
+057ce4beac3b721488e4af641452d4f8
+2011-10-06T15:38:33.365082Z
+8369
+zji
 has-props


@@ -843,7 +843,7 @@ has-props



-910
+3100

 DataSetSubNode.java
 file
@@ -879,17 +879,17 @@ has-props

 776

-InformationPanel.java
+Phenotype16x16.gif
 file




-2012-01-10T19:15:28.000000Z
-057ce4beac3b721488e4af641452d4f8
-2011-10-06T15:38:33.365082Z
-8369
-zji
+2011-08-17T00:10:50.000000Z
+8a9ed81c0ae807ca19535a038891e916
+2006-01-13T22:48:38.000000Z
+1120
+watkin
 has-props


@@ -911,13 +911,7 @@ has-props



-3100
-
-remoteresources
-dir
-
-experimentinformation
-dir
+910

 busy.gif
 file
@@ -953,6 +947,12 @@ has-props

 7823

+experimentinformation
+dir
+
+remoteresources
+dir
+
 help
 dir

diff --git a/geworkbench-core/classes/org/geworkbench/builtin/projects/.svn/text-base/FileOpenHandler.java.svn-base b/geworkbench-core/classes/org/geworkbench/builtin/projects/.svn/text-base/FileOpenHandler.java.svn-base
index 59d1d90..7cf8260 100644
--- a/geworkbench-core/classes/org/geworkbench/builtin/projects/.svn/text-base/FileOpenHandler.java.svn-base
+++ b/geworkbench-core/classes/org/geworkbench/builtin/projects/.svn/text-base/FileOpenHandler.java.svn-base
@@ -38,7 +38,6 @@ import org.geworkbench.bison.util.colorcontext.ColorContext;
 import org.geworkbench.engine.config.rules.GeawConfigObject;
 import org.geworkbench.parsers.AdjacencyMatrixFileFormat;
 import org.geworkbench.parsers.DataSetFileFormat;
-import org.geworkbench.parsers.ExpressionFileFormat;
 import org.geworkbench.parsers.FileFormat;
 import org.geworkbench.parsers.InputFileFormatException;
 import org.geworkbench.parsers.PatternFileFormat;
@@ -263,36 +262,38 @@ public class FileOpenHandler {
 					projectPanel.addDataSetNode(mergedSet);
 				}
 			} else {
-				DSDataSet set = dataSets[0];
-
-				if (set == null) {
-					clearProjectPanelProgressBar();
-					log.info("null dataset encountered");
-					progressBarDialog.dispose();
-					projectPanelProgressBar.setString("");
-					projectPanelProgressBar.setIndeterminate(false);
-					projectPanel.getComponent().setCursor(Cursor
-							.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
-					return;
-				}
-
-				// Do initial color context update if it is a microarray
-				if (set instanceof DSMicroarraySet) {
-					ProjectPanel
-							.addColorContext((DSMicroarraySet) set);
-				}
-
-				if (set instanceof AdjacencyMatrixDataSet) {
-					// adjacency matrix as added as a sub node
-					AdjacencyMatrixDataSet adjMatrixDS = (AdjacencyMatrixDataSet) set;
-					projectPanel.addDataSetSubNode(adjMatrixDS);
-				} else {
-					if(set instanceof PatternResult) {
-						// Pattern Result added as a sub node
-						PatternResult patternResult = (PatternResult) set;
-						projectPanel.addDataSetSubNode(patternResult);
-					}else {
-						projectPanel.addDataSetNode(set);
+				for (int i = 0; i < dataSets.length; i++) {
+					DSDataSet set = dataSets[i];
+
+					if (set == null) {
+						clearProjectPanelProgressBar();
+						log.info("null dataset encountered");
+						progressBarDialog.dispose();
+						projectPanelProgressBar.setString("");
+						projectPanelProgressBar.setIndeterminate(false);
+						projectPanel.getComponent().setCursor(Cursor
+								.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
+						return;
+					}
+
+					// Do initial color context update if it is a microarray
+					if (set instanceof DSMicroarraySet) {
+						ProjectPanel
+								.addColorContext((DSMicroarraySet) set);
+					}
+
+					if (set instanceof AdjacencyMatrixDataSet) {
+						// adjacency matrix as added as a sub node
+						AdjacencyMatrixDataSet adjMatrixDS = (AdjacencyMatrixDataSet) set;
+						projectPanel.addDataSetSubNode(adjMatrixDS);
+					} else {
+						if(set instanceof PatternResult) {
+							// Pattern Result added as a sub node
+							PatternResult patternResult = (PatternResult) set;
+							projectPanel.addDataSetSubNode(patternResult);
+						}else {
+							projectPanel.addDataSetNode(set);
+						}
 					}
 				}
 			}
@@ -366,7 +367,7 @@ public class FileOpenHandler {
 				// different from the previous algorithm.
 				// also notice that this will block
 				String chipType = null; // ignored by other format
-				if(dataSetFileFormat instanceof ExpressionFileFormat)
+				if(dataSetFileFormat.isMergeSupported())
 					chipType = AffyAnnotationUtil.matchAffyAnnotationFile(null);
 				progressBarDialog.setVisible(true);

@@ -377,13 +378,18 @@ public class FileOpenHandler {
 					File dataSetFile = dataSetFiles[i];

 					try {
-						dataSets[i] = dataSetFileFormat.getDataFile(
-								dataSetFile, chipType);
-						AnnotationParser.setChipType(dataSets[i], chipType);
-						if (dataSets[i] instanceof CSMicroarraySet) {
-							((CSMicroarraySet) dataSets[i])
-									.setAnnotationFileName(AnnotationParser
-											.getLastAnnotationFileName());
+						if(chipType==null) {
+							dataSets[i] = dataSetFileFormat.getDataFile(
+									dataSetFile);
+						} else {
+							dataSets[i] = dataSetFileFormat.getDataFile(
+									dataSetFile, chipType);
+							AnnotationParser.setChipType(dataSets[i], chipType);
+							if (dataSets[i] instanceof CSMicroarraySet) {
+								((CSMicroarraySet) dataSets[i])
+										.setAnnotationFileName(AnnotationParser
+												.getLastAnnotationFileName());
+							}
 						}
 					} catch (OutOfMemoryError er) {
 						log.warn("Loading multiple files memory error: " + er);
@@ -486,7 +492,7 @@ public class FileOpenHandler {
 		if (mergedSet != null) {
 			mergedSet.setLabel("Merged array set");
 			mergedSet.setLabel(desc);
-			mergedSet.setDescription(desc);
+			mergedSet.setDescription(mergedSet.getDescription());
 			((CSMicroarraySet) mergedSet)
 					.setAnnotationFileName(((CSMicroarraySet) sets[0])
 							.getAnnotationFileName());
diff --git a/geworkbench-core/classes/org/geworkbench/builtin/projects/comments/.svn/entries b/geworkbench-core/classes/org/geworkbench/builtin/projects/comments/.svn/entries
index 84f14da..0788484 100644
--- a/geworkbench-core/classes/org/geworkbench/builtin/projects/comments/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/builtin/projects/comments/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/builtin/projects/comments
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/builtin/projects/comments/help/.svn/entries b/geworkbench-core/classes/org/geworkbench/builtin/projects/comments/help/.svn/entries
index 1aee899..70aac77 100644
--- a/geworkbench-core/classes/org/geworkbench/builtin/projects/comments/help/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/builtin/projects/comments/help/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/builtin/projects/comments/help
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/builtin/projects/comments/help/Dataset annotation_files/.svn/entries b/geworkbench-core/classes/org/geworkbench/builtin/projects/comments/help/Dataset annotation_files/.svn/entries
index 2a19051..756f1bb 100644
--- a/geworkbench-core/classes/org/geworkbench/builtin/projects/comments/help/Dataset annotation_files/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/builtin/projects/comments/help/Dataset annotation_files/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/builtin/projects/comments/help/Dataset%20annotation_files
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/builtin/projects/experimentinformation/.svn/entries b/geworkbench-core/classes/org/geworkbench/builtin/projects/experimentinformation/.svn/entries
index 957d5c9..1c1ddf3 100644
--- a/geworkbench-core/classes/org/geworkbench/builtin/projects/experimentinformation/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/builtin/projects/experimentinformation/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/builtin/projects/experimentinformation
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/builtin/projects/experimentinformation/help/.svn/entries b/geworkbench-core/classes/org/geworkbench/builtin/projects/experimentinformation/help/.svn/entries
index 82f0e48..af85d5d 100644
--- a/geworkbench-core/classes/org/geworkbench/builtin/projects/experimentinformation/help/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/builtin/projects/experimentinformation/help/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/builtin/projects/experimentinformation/help
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/builtin/projects/experimentinformation/help/infoPanel_files/.svn/entries b/geworkbench-core/classes/org/geworkbench/builtin/projects/experimentinformation/help/infoPanel_files/.svn/entries
index 751f5d5..7ebd76d 100644
--- a/geworkbench-core/classes/org/geworkbench/builtin/projects/experimentinformation/help/infoPanel_files/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/builtin/projects/experimentinformation/help/infoPanel_files/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/builtin/projects/experimentinformation/help/infoPanel_files
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/builtin/projects/help/.svn/entries b/geworkbench-core/classes/org/geworkbench/builtin/projects/help/.svn/entries
index 082e866..35a54e2 100644
--- a/geworkbench-core/classes/org/geworkbench/builtin/projects/help/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/builtin/projects/help/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/builtin/projects/help
 https://ncisvn.nci.nih.gov/svn/geworkbench

@@ -94,17 +94,17 @@ has-props

 1404

-cell.HTML
+Manage Project.HTML
 file




 2011-08-17T00:10:50.000000Z
-71653e83f27ce290465dd3a852a9049a
-2007-03-23T19:30:59.000000Z
-2616
-xiaoqing
+b3e54e2b65d9d92fd82de0b2de77e227
+2006-03-03T18:05:24.000000Z
+1317
+mhall
 has-props


@@ -126,19 +126,19 @@ has-props



-1068
+2791

-Manage Project.HTML
+cell.HTML
 file




 2011-08-17T00:10:50.000000Z
-b3e54e2b65d9d92fd82de0b2de77e227
-2006-03-03T18:05:24.000000Z
-1317
-mhall
+71653e83f27ce290465dd3a852a9049a
+2007-03-23T19:30:59.000000Z
+2616
+xiaoqing
 has-props


@@ -160,7 +160,7 @@ has-props



-2791
+1068

 projectPanelHelpSet.hs
 file
@@ -196,6 +196,9 @@ has-props

 601

+merge_dataset_files
+dir
+
 Affy File Matrix Format.HTML
 file

@@ -230,15 +233,6 @@ has-props

 4585

-merge_dataset_files
-dir
-
-Manage_workspace_files
-dir
-
-open_dataset_files
-dir
-
 Affy File.HTML
 file

@@ -273,20 +267,26 @@ has-props

 1589

+open_dataset_files
+dir
+
+Manage_workspace_files
+dir
+
 delete_dataset_files
 dir

-projectPaneltoc.xml
+RMA Format.HTML
 file




 2011-08-17T00:10:50.000000Z
-5b785db1e254c29b85478bf5cce0c308
-2007-01-12T16:52:18.000000Z
-2223
-edaly
+375d269318c3343af8f1618575be9640
+2008-09-08T11:48:43.000000Z
+4176
+hungc
 has-props


@@ -308,19 +308,19 @@ has-props



-715
+2070

-RMA Format.HTML
+projectPaneltoc.xml
 file




 2011-08-17T00:10:50.000000Z
-375d269318c3343af8f1618575be9640
-2008-09-08T11:48:43.000000Z
-4176
-hungc
+5b785db1e254c29b85478bf5cce0c308
+2007-01-12T16:52:18.000000Z
+2223
+edaly
 has-props


@@ -342,10 +342,7 @@ has-props



-2070
-
-rename_dataset_files
-dir
+715

 remote.HTML
 file
@@ -381,6 +378,9 @@ has-props

 3207

+rename_dataset_files
+dir
+
 user preference_files
 dir

diff --git a/geworkbench-core/classes/org/geworkbench/builtin/projects/help/Manage_workspace_files/.svn/entries b/geworkbench-core/classes/org/geworkbench/builtin/projects/help/Manage_workspace_files/.svn/entries
index f27d100..1f9593f 100644
--- a/geworkbench-core/classes/org/geworkbench/builtin/projects/help/Manage_workspace_files/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/builtin/projects/help/Manage_workspace_files/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/builtin/projects/help/Manage_workspace_files
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/builtin/projects/help/delete_dataset_files/.svn/entries b/geworkbench-core/classes/org/geworkbench/builtin/projects/help/delete_dataset_files/.svn/entries
index db75981..ff67e8b 100644
--- a/geworkbench-core/classes/org/geworkbench/builtin/projects/help/delete_dataset_files/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/builtin/projects/help/delete_dataset_files/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/builtin/projects/help/delete_dataset_files
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/builtin/projects/help/manage_projected_files/.svn/entries b/geworkbench-core/classes/org/geworkbench/builtin/projects/help/manage_projected_files/.svn/entries
index b7ae39a..230a134 100644
--- a/geworkbench-core/classes/org/geworkbench/builtin/projects/help/manage_projected_files/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/builtin/projects/help/manage_projected_files/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/builtin/projects/help/manage_projected_files
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/builtin/projects/help/merge_dataset_files/.svn/entries b/geworkbench-core/classes/org/geworkbench/builtin/projects/help/merge_dataset_files/.svn/entries
index 422c8b6..635b86d 100644
--- a/geworkbench-core/classes/org/geworkbench/builtin/projects/help/merge_dataset_files/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/builtin/projects/help/merge_dataset_files/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/builtin/projects/help/merge_dataset_files
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/builtin/projects/help/open_dataset_files/.svn/entries b/geworkbench-core/classes/org/geworkbench/builtin/projects/help/open_dataset_files/.svn/entries
index bac5b69..dc762fe 100644
--- a/geworkbench-core/classes/org/geworkbench/builtin/projects/help/open_dataset_files/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/builtin/projects/help/open_dataset_files/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/builtin/projects/help/open_dataset_files
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/builtin/projects/help/projects area_overviewed_files/.svn/entries b/geworkbench-core/classes/org/geworkbench/builtin/projects/help/projects area_overviewed_files/.svn/entries
index 316bc24..f710892 100644
--- a/geworkbench-core/classes/org/geworkbench/builtin/projects/help/projects area_overviewed_files/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/builtin/projects/help/projects area_overviewed_files/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/builtin/projects/help/projects%20area_overviewed_files
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/builtin/projects/help/remote_files/.svn/entries b/geworkbench-core/classes/org/geworkbench/builtin/projects/help/remote_files/.svn/entries
index 405e52e..75cfd99 100644
--- a/geworkbench-core/classes/org/geworkbench/builtin/projects/help/remote_files/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/builtin/projects/help/remote_files/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/builtin/projects/help/remote_files
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/builtin/projects/help/rename_dataset_files/.svn/entries b/geworkbench-core/classes/org/geworkbench/builtin/projects/help/rename_dataset_files/.svn/entries
index a3c92e6..7ae21e9 100644
--- a/geworkbench-core/classes/org/geworkbench/builtin/projects/help/rename_dataset_files/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/builtin/projects/help/rename_dataset_files/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/builtin/projects/help/rename_dataset_files
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/builtin/projects/help/user preference_files/.svn/entries b/geworkbench-core/classes/org/geworkbench/builtin/projects/help/user preference_files/.svn/entries
index 209b869..80e3139 100644
--- a/geworkbench-core/classes/org/geworkbench/builtin/projects/help/user preference_files/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/builtin/projects/help/user preference_files/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/builtin/projects/help/user%20preference_files
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/builtin/projects/history/.svn/entries b/geworkbench-core/classes/org/geworkbench/builtin/projects/history/.svn/entries
index 429b58f..a075705 100644
--- a/geworkbench-core/classes/org/geworkbench/builtin/projects/history/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/builtin/projects/history/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/builtin/projects/history
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/builtin/projects/history/help/.svn/entries b/geworkbench-core/classes/org/geworkbench/builtin/projects/history/help/.svn/entries
index 3f7542f..9f24442 100644
--- a/geworkbench-core/classes/org/geworkbench/builtin/projects/history/help/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/builtin/projects/history/help/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/builtin/projects/history/help
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/builtin/projects/history/help/historyPanel_files/.svn/entries b/geworkbench-core/classes/org/geworkbench/builtin/projects/history/help/historyPanel_files/.svn/entries
index 50f6692..6b3b348 100644
--- a/geworkbench-core/classes/org/geworkbench/builtin/projects/history/help/historyPanel_files/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/builtin/projects/history/help/historyPanel_files/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/builtin/projects/history/help/historyPanel_files
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/builtin/projects/history/help/images/.svn/entries b/geworkbench-core/classes/org/geworkbench/builtin/projects/history/help/images/.svn/entries
index e26a8d3..185617d 100644
--- a/geworkbench-core/classes/org/geworkbench/builtin/projects/history/help/images/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/builtin/projects/history/help/images/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/builtin/projects/history/help/images
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/builtin/projects/remoteresources/.svn/entries b/geworkbench-core/classes/org/geworkbench/builtin/projects/remoteresources/.svn/entries
index 17fb58a..380a57c 100644
--- a/geworkbench-core/classes/org/geworkbench/builtin/projects/remoteresources/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/builtin/projects/remoteresources/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/builtin/projects/remoteresources
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/builtin/projects/remoteresources/carraydata/.svn/entries b/geworkbench-core/classes/org/geworkbench/builtin/projects/remoteresources/carraydata/.svn/entries
index edd6707..0be6e07 100644
--- a/geworkbench-core/classes/org/geworkbench/builtin/projects/remoteresources/carraydata/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/builtin/projects/remoteresources/carraydata/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/builtin/projects/remoteresources/carraydata
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/builtin/projects/target/.svn/entries b/geworkbench-core/classes/org/geworkbench/builtin/projects/target/.svn/entries
index 635284a..057f510 100644
--- a/geworkbench-core/classes/org/geworkbench/builtin/projects/target/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/builtin/projects/target/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/test/org/geworkbench/builtin/projects/target
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/builtin/projects/util/.svn/all-wcprops b/geworkbench-core/classes/org/geworkbench/builtin/projects/util/.svn/all-wcprops
index c147789..79f2971 100644
--- a/geworkbench-core/classes/org/geworkbench/builtin/projects/util/.svn/all-wcprops
+++ b/geworkbench-core/classes/org/geworkbench/builtin/projects/util/.svn/all-wcprops
@@ -1,11 +1,11 @@
 K 25
 svn:wc:ra_dav:version-url
 V 90
-/svn/geworkbench/!svn/ver/8390/trunk/geworkbench/src/org/geworkbench/builtin/projects/util
+/svn/geworkbench/!svn/ver/8791/trunk/geworkbench/src/org/geworkbench/builtin/projects/util
 END
 CaARRAYPanel.java
 K 25
 svn:wc:ra_dav:version-url
 V 108
-/svn/geworkbench/!svn/ver/8390/trunk/geworkbench/src/org/geworkbench/builtin/projects/util/CaARRAYPanel.java
+/svn/geworkbench/!svn/ver/8791/trunk/geworkbench/src/org/geworkbench/builtin/projects/util/CaARRAYPanel.java
 END
diff --git a/geworkbench-core/classes/org/geworkbench/builtin/projects/util/.svn/entries b/geworkbench-core/classes/org/geworkbench/builtin/projects/util/.svn/entries
index dda849d..fbd5e7a 100644
--- a/geworkbench-core/classes/org/geworkbench/builtin/projects/util/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/builtin/projects/util/.svn/entries
@@ -1,14 +1,14 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/builtin/projects/util
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2011-10-11T20:53:07.889664Z
-8390
+2012-01-27T15:58:35.934783Z
+8791
 zji


@@ -32,10 +32,10 @@ file



-2012-01-10T19:15:28.000000Z
-6834a78995f1e2817304b52a4409d538
-2011-10-11T20:53:07.889664Z
-8390
+2012-01-31T19:12:36.000000Z
+7f603219d18a087e51461b07f24a3021
+2012-01-27T15:58:35.934783Z
+8791
 zji
 has-props

@@ -58,5 +58,5 @@ has-props



-27180
+27143

diff --git a/geworkbench-core/classes/org/geworkbench/builtin/projects/util/.svn/text-base/CaARRAYPanel.java.svn-base b/geworkbench-core/classes/org/geworkbench/builtin/projects/util/.svn/text-base/CaARRAYPanel.java.svn-base
index 27c3a91..08304e2 100644
--- a/geworkbench-core/classes/org/geworkbench/builtin/projects/util/.svn/text-base/CaARRAYPanel.java.svn-base
+++ b/geworkbench-core/classes/org/geworkbench/builtin/projects/util/.svn/text-base/CaARRAYPanel.java.svn-base
@@ -118,7 +118,7 @@ public class CaARRAYPanel extends JPanel implements Observer, VisualPlugin {
 	private TreeMap<String, CaArray2Experiment> treeMap;
 	private String currentSelectedExperimentName;
 	private Map<String, String> currentSelectedBioAssay;
-	private CaArray2Experiment[] currentLoadedExps;
+
 	private String currentQuantitationType;
 	private static final int INTERNALTIMEOUTLIMIT = 600;
 	private static final int INCREASE_EACHTIME = 300;
@@ -168,7 +168,7 @@ public class CaARRAYPanel extends JPanel implements Observer, VisualPlugin {
 		}

 		if (ce.getInfoType().equalsIgnoreCase(CaArrayEvent.EXPERIMENT)) {
-			currentLoadedExps = ce.getExperiments();
+			CaArray2Experiment[] currentLoadedExps = ce.getExperiments();
 			treeMap = new TreeMap<String, CaArray2Experiment>();
 			root = new DefaultMutableTreeNode("caARRAY experiments");
 			remoteTreeModel.setRoot(root);
@@ -177,9 +177,10 @@ public class CaARRAYPanel extends JPanel implements Observer, VisualPlugin {
 			}

 			for (int i = 0; i < currentLoadedExps.length; ++i) {
+				String experimentName = currentLoadedExps[i].getName();
 				DefaultMutableTreeNode node = new DefaultMutableTreeNode(
-						currentLoadedExps[i].getName());
-				treeMap.put(currentLoadedExps[i].getName(),
+						experimentName);
+				treeMap.put(experimentName,
 						currentLoadedExps[i]);
 				remoteTreeModel
 						.insertNodeInto(node, root, root.getChildCount());
@@ -188,11 +189,11 @@ public class CaARRAYPanel extends JPanel implements Observer, VisualPlugin {
 			experimentsLoaded = true;
 			previousResourceName = currentResourceName;
 			connectionSuccess = true;
-			if (currentLoadedExps != null) {
-				displayLabel.setText("Total Experiments: "
-						+ currentLoadedExps.length);
-				caArrayTreePanel.add(displayLabel, BorderLayout.SOUTH);
-			}
+
+			displayLabel.setText("Total Experiments: "
+					+ currentLoadedExps.length);
+			caArrayTreePanel.add(displayLabel, BorderLayout.SOUTH);
+
 			revalidate();
 		} else {
 			dispose();// make itself disappear.
diff --git a/geworkbench-core/classes/org/geworkbench/components/.svn/entries b/geworkbench-core/classes/org/geworkbench/components/.svn/entries
index 6165d40..619f9e2 100644
--- a/geworkbench-core/classes/org/geworkbench/components/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/components/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/test/org/geworkbench/components
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/components/caarray/.svn/all-wcprops b/geworkbench-core/classes/org/geworkbench/components/caarray/.svn/all-wcprops
index 241db0f..0f81ea2 100644
--- a/geworkbench-core/classes/org/geworkbench/components/caarray/.svn/all-wcprops
+++ b/geworkbench-core/classes/org/geworkbench/components/caarray/.svn/all-wcprops
@@ -1,5 +1,5 @@
 K 25
 svn:wc:ra_dav:version-url
 V 106
-/svn/geworkbench/!svn/ver/8463/trunk/geworkbench/components/caarray/src/org/geworkbench/components/caarray
+/svn/geworkbench/!svn/ver/8785/trunk/geworkbench/components/caarray/src/org/geworkbench/components/caarray
 END
diff --git a/geworkbench-core/classes/org/geworkbench/components/caarray/.svn/entries b/geworkbench-core/classes/org/geworkbench/components/caarray/.svn/entries
index a979e12..3944bc0 100644
--- a/geworkbench-core/classes/org/geworkbench/components/caarray/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/components/caarray/.svn/entries
@@ -1,15 +1,15 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/caarray/src/org/geworkbench/components/caarray
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2011-10-25T21:47:59.095740Z
-8463
-zji
+2012-01-26T21:17:35.990494Z
+8785
+maz



diff --git a/geworkbench-core/classes/org/geworkbench/components/caarray/arraydata/.svn/all-wcprops b/geworkbench-core/classes/org/geworkbench/components/caarray/arraydata/.svn/all-wcprops
index 0d10235..32e82d6 100644
--- a/geworkbench-core/classes/org/geworkbench/components/caarray/arraydata/.svn/all-wcprops
+++ b/geworkbench-core/classes/org/geworkbench/components/caarray/arraydata/.svn/all-wcprops
@@ -1,7 +1,7 @@
 K 25
 svn:wc:ra_dav:version-url
 V 116
-/svn/geworkbench/!svn/ver/8463/trunk/geworkbench/components/caarray/src/org/geworkbench/components/caarray/arraydata
+/svn/geworkbench/!svn/ver/8785/trunk/geworkbench/components/caarray/src/org/geworkbench/components/caarray/arraydata
 END
 CaArray2Component.cwb.xml
 K 25
@@ -19,5 +19,5 @@ CaArray2Component.java
 K 25
 svn:wc:ra_dav:version-url
 V 139
-/svn/geworkbench/!svn/ver/8463/trunk/geworkbench/components/caarray/src/org/geworkbench/components/caarray/arraydata/CaArray2Component.java
+/svn/geworkbench/!svn/ver/8785/trunk/geworkbench/components/caarray/src/org/geworkbench/components/caarray/arraydata/CaArray2Component.java
 END
diff --git a/geworkbench-core/classes/org/geworkbench/components/caarray/arraydata/.svn/entries b/geworkbench-core/classes/org/geworkbench/components/caarray/arraydata/.svn/entries
index 4fbd918..23b5639 100644
--- a/geworkbench-core/classes/org/geworkbench/components/caarray/arraydata/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/components/caarray/arraydata/.svn/entries
@@ -1,15 +1,15 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/caarray/src/org/geworkbench/components/caarray/arraydata
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2011-10-25T21:47:59.095740Z
-8463
-zji
+2012-01-26T21:17:35.990494Z
+8785
+maz



@@ -100,11 +100,11 @@ file



-2012-01-10T19:15:23.000000Z
-d3229869c319d4075bcd23e1dcfd8511
-2011-10-25T21:47:59.095740Z
-8463
-zji
+2012-01-31T19:12:32.000000Z
+b3b95a2a0bad374e68908f337cdc2ed2
+2012-01-26T21:17:35.990494Z
+8785
+maz
 has-props


@@ -126,5 +126,5 @@ has-props



-17394
+17308

diff --git a/geworkbench-core/classes/org/geworkbench/components/caarray/arraydata/.svn/text-base/CaArray2Component.java.svn-base b/geworkbench-core/classes/org/geworkbench/components/caarray/arraydata/.svn/text-base/CaArray2Component.java.svn-base
index 981d263..58b4ddf 100644
--- a/geworkbench-core/classes/org/geworkbench/components/caarray/arraydata/.svn/text-base/CaArray2Component.java.svn-base
+++ b/geworkbench-core/classes/org/geworkbench/components/caarray/arraydata/.svn/text-base/CaArray2Component.java.svn-base
@@ -336,8 +336,7 @@ public class CaArray2Component implements VisualPlugin {
 			throws Exception {
 		CSMicroarraySet microarraySet = null;

-		String desc = "";
-		if(hybridzations.size()>1)desc = "Merged DataSet: ";
+		String desc = "";

 		int number = 0;
 		CaArraySuccessEvent caArraySuccessEvent = new CaArraySuccessEvent(hybridzations.size());
@@ -361,7 +360,7 @@ public class CaArray2Component implements VisualPlugin {
 			}

 			microarraySet.add(microarray);
-			desc += experimentName + "_" + hybridizationName + " ";
+			desc = experimentName;

 			publishCaArraySuccessEvent(caArraySuccessEvent);
 			number++;
diff --git a/geworkbench-core/classes/org/geworkbench/components/genspace/.svn/all-wcprops b/geworkbench-core/classes/org/geworkbench/components/genspace/.svn/all-wcprops
index 2f0b5d4..924659c 100644
--- a/geworkbench-core/classes/org/geworkbench/components/genspace/.svn/all-wcprops
+++ b/geworkbench-core/classes/org/geworkbench/components/genspace/.svn/all-wcprops
@@ -1,19 +1,19 @@
 K 25
 svn:wc:ra_dav:version-url
 V 108
-/svn/geworkbench/!svn/ver/8667/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace
+/svn/geworkbench/!svn/ver/8793/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace
 END
-TransactionElement.java
+ObjectLogger.java
 K 25
 svn:wc:ra_dav:version-url
-V 132
-/svn/geworkbench/!svn/ver/7751/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/TransactionElement.java
+V 126
+/svn/geworkbench/!svn/ver/8662/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/ObjectLogger.java
 END
-GenSpaceMenu.cwb.xml
+RealTimeWorkFlowSuggestion.java
 K 25
 svn:wc:ra_dav:version-url
-V 129
-/svn/geworkbench/!svn/ver/8187/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/GenSpaceMenu.cwb.xml
+V 140
+/svn/geworkbench/!svn/ver/8187/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/RealTimeWorkFlowSuggestion.java
 END
 ObjectHandler.java
 K 25
@@ -21,17 +21,17 @@ svn:wc:ra_dav:version-url
 V 127
 /svn/geworkbench/!svn/ver/8511/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/ObjectHandler.java
 END
-GenSpaceServerFactory.java
+GenSpaceLogPreferences.java
 K 25
 svn:wc:ra_dav:version-url
-V 135
-/svn/geworkbench/!svn/ver/8666/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/GenSpaceServerFactory.java
+V 136
+/svn/geworkbench/!svn/ver/7751/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/GenSpaceLogPreferences.java
 END
-RealTimeWorkFlowSuggestion.java
+XMLLoader.java
 K 25
 svn:wc:ra_dav:version-url
-V 140
-/svn/geworkbench/!svn/ver/8187/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/RealTimeWorkFlowSuggestion.java
+V 123
+/svn/geworkbench/!svn/ver/8187/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/XMLLoader.java
 END
 BrowserLauncher.java
 K 25
@@ -39,29 +39,23 @@ svn:wc:ra_dav:version-url
 V 129
 /svn/geworkbench/!svn/ver/7751/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/BrowserLauncher.java
 END
-ObjectLogger.java
+login.conf
 K 25
 svn:wc:ra_dav:version-url
-V 126
-/svn/geworkbench/!svn/ver/8662/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/ObjectLogger.java
+V 119
+/svn/geworkbench/!svn/ver/7751/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/login.conf
 END
-GenSpaceLogPreferences.java
+GenspaceLogger.java
 K 25
 svn:wc:ra_dav:version-url
-V 136
-/svn/geworkbench/!svn/ver/7751/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/GenSpaceLogPreferences.java
+V 128
+/svn/geworkbench/!svn/ver/7751/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/GenspaceLogger.java
 END
-GenSpaceMenu.java
+ServerConfig.java
 K 25
 svn:wc:ra_dav:version-url
 V 126
-/svn/geworkbench/!svn/ver/8187/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/GenSpaceMenu.java
-END
-login.conf
-K 25
-svn:wc:ra_dav:version-url
-V 119
-/svn/geworkbench/!svn/ver/7751/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/login.conf
+/svn/geworkbench/!svn/ver/4670/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/ServerConfig.java
 END
 FindJar.java
 K 25
@@ -75,33 +69,33 @@ svn:wc:ra_dav:version-url
 V 131
 /svn/geworkbench/!svn/ver/8187/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/GenspaceLogger.cwb.xml
 END
-GenSpace.java
+TransactionElement.java
 K 25
 svn:wc:ra_dav:version-url
-V 122
-/svn/geworkbench/!svn/ver/8187/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/GenSpace.java
+V 132
+/svn/geworkbench/!svn/ver/7751/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/TransactionElement.java
 END
-GenspaceLogger.java
+RuntimeEnvironmentSettings.java
 K 25
 svn:wc:ra_dav:version-url
-V 128
-/svn/geworkbench/!svn/ver/7751/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/GenspaceLogger.java
+V 140
+/svn/geworkbench/!svn/ver/8187/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/RuntimeEnvironmentSettings.java
 END
-XMLLoader.java
+GenSpace.java
 K 25
 svn:wc:ra_dav:version-url
-V 123
-/svn/geworkbench/!svn/ver/8187/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/XMLLoader.java
+V 122
+/svn/geworkbench/!svn/ver/8187/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/GenSpace.java
 END
-RuntimeEnvironmentSettings.java
+GenSpaceMenu.java
 K 25
 svn:wc:ra_dav:version-url
-V 140
-/svn/geworkbench/!svn/ver/8187/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/RuntimeEnvironmentSettings.java
+V 126
+/svn/geworkbench/!svn/ver/8187/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/GenSpaceMenu.java
 END
-ServerConfig.java
+GenSpaceMenu.cwb.xml
 K 25
 svn:wc:ra_dav:version-url
-V 126
-/svn/geworkbench/!svn/ver/4670/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/ServerConfig.java
+V 129
+/svn/geworkbench/!svn/ver/8187/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/GenSpaceMenu.cwb.xml
 END
diff --git a/geworkbench-core/classes/org/geworkbench/components/genspace/.svn/entries b/geworkbench-core/classes/org/geworkbench/components/genspace/.svn/entries
index 5e37816..2c1bc2b 100644
--- a/geworkbench-core/classes/org/geworkbench/components/genspace/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/components/genspace/.svn/entries
@@ -1,15 +1,15 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2012-01-06T21:01:06.170581Z
-8667
-bellj
+2012-01-27T16:21:32.396819Z
+8793
+zji



@@ -26,14 +26,14 @@ bellj

 8b29bb6e-589a-435a-9a12-3ab907be3462

-TransactionElement.java
+BrowserLauncher.java
 file




 2011-08-17T00:19:03.000000Z
-8994a2940a8979d76e4b710b7b031e9c
+7f3bf87f78d2931944993c3502fcf11f
 2011-04-19T16:07:16.228867Z
 7751
 bellj
@@ -58,19 +58,16 @@ bellj



-665
-
-chat
-dir
+2068

-GenSpaceMenu.cwb.xml
+FindJar.java
 file




 2012-01-10T18:25:35.000000Z
-135fabcf1b017235b2a4fdc67a82db2e
+3bea4f252e736ed23f50663001e84a93
 2011-07-30T04:31:30.667242Z
 8187
 zji
@@ -95,44 +92,16 @@ zji



-1338
-
-ObjectHandler.java
-file
-
-
-
-
-
-ddc16e0c4f7e3c73ca8f7ce263adc665
-2011-11-07T21:42:53.414007Z
-8511
-zji
-has-props
-
-GenSpaceServerFactory.java
-file
-
-
-
-
-
-6a4cfcdba79de623fd80c9706e9d8f5c
-2012-01-06T20:06:43.164210Z
-8666
-bellj
-
-rating
-dir
+7178

-RealTimeWorkFlowSuggestion.java
+GenSpace.java
 file




 2011-08-02T04:26:22.000000Z
-e4736796bc9cfdbb408effbe68a0cbd1
+7a84d398d49dfb5106dfd5832e6ce573
 2011-07-30T04:31:30.667242Z
 8187
 zji
@@ -157,19 +126,20 @@ zji



-10022
+4750

-BrowserLauncher.java
+GenSpaceLogPreferences.java
 file




 2011-08-17T00:19:03.000000Z
-7f3bf87f78d2931944993c3502fcf11f
+386a02e7db45a8ad1c2db5fbebc464ec
 2011-04-19T16:07:16.228867Z
 7751
 bellj
+has-props



@@ -190,37 +160,20 @@ bellj



-
-2068
+4949

-ObjectLogger.java
+GenSpaceMenu.cwb.xml
 file




+2012-01-10T18:25:35.000000Z
+135fabcf1b017235b2a4fdc67a82db2e
+2011-07-30T04:31:30.667242Z
+8187
+zji

-09f819a80bdd93010df7e18f6f67fda0
-2012-01-06T04:04:23.177318Z
-8662
-bellj
-has-props
-
-help
-dir
-
-GenSpaceLogPreferences.java
-file
-
-
-
-
-2011-08-17T00:19:03.000000Z
-386a02e7db45a8ad1c2db5fbebc464ec
-2011-04-19T16:07:16.228867Z
-7751
-bellj
-has-props



@@ -241,7 +194,7 @@ has-props



-4949
+1338

 GenSpaceMenu.java
 file
@@ -277,16 +230,16 @@ zji

 1159

-login.conf
+GenSpaceServerFactory.java
 file
+8837



-
-2011-08-17T00:19:03.000000Z
-a1660ab13dcf97357c0c0a6ec5d0cdf2
-2011-04-19T16:07:16.228867Z
-7751
+2012-02-06T16:58:54.000000Z
+f4adcf2234e9e72892a727dccec769c8
+2012-02-06T16:59:30.615424Z
+8837
 bellj


@@ -309,16 +262,16 @@ bellj



-103
+10510

-FindJar.java
+GenspaceLogger.cwb.xml
 file




 2012-01-10T18:25:35.000000Z
-3bea4f252e736ed23f50663001e84a93
+beedfeb4603236beddc40cffd7e6aef2
 2011-07-30T04:31:30.667242Z
 8187
 zji
@@ -343,20 +296,20 @@ zji



-7178
+1342

-GenspaceLogger.cwb.xml
+GenspaceLogger.java
 file




-2012-01-10T18:25:35.000000Z
-beedfeb4603236beddc40cffd7e6aef2
-2011-07-30T04:31:30.667242Z
-8187
-zji
-
+2011-08-17T00:19:03.000000Z
+18e9462e8e9a50bff3be32c94cefca92
+2011-04-19T16:07:16.228867Z
+7751
+bellj
+has-props



@@ -377,27 +330,45 @@ zji



-1342
+1669

-bean
-dir
+ObjectHandler.java
+file
+
+
+
+
+
+ddc16e0c4f7e3c73ca8f7ce263adc665
+2011-11-07T21:42:53.414007Z
+8511
+zji
+has-props

-GenspaceLogger.java
+ObjectLogger.java
 file




-2011-08-17T00:19:03.000000Z
-18e9462e8e9a50bff3be32c94cefca92
-2011-04-19T16:07:16.228867Z
-7751
+
+09f819a80bdd93010df7e18f6f67fda0
+2012-01-06T04:04:23.177318Z
+8662
 bellj
 has-props
+
+RealTimeWorkFlowSuggestion.java
+file




+2011-08-02T04:26:22.000000Z
+e4736796bc9cfdbb408effbe68a0cbd1
+2011-07-30T04:31:30.667242Z
+8187
+zji



@@ -414,16 +385,21 @@ has-props



-1669
+
+
+
+
+
+10022

-GenSpace.java
+RuntimeEnvironmentSettings.java
 file




-2011-08-02T04:26:22.000000Z
-7a84d398d49dfb5106dfd5832e6ce573
+2011-08-17T00:19:03.000000Z
+a48b53341f7eb955278c752cc2978b9f
 2011-07-30T04:31:30.667242Z
 8187
 zji
@@ -448,23 +424,19 @@ zji



-4750
-
-server
-dir
+1620

-XMLLoader.java
+ServerConfig.java
 file




-2012-01-10T18:25:35.000000Z
-b75feb18b8d53e5533eb2f4ae5a70117
-2011-07-30T04:31:30.667242Z
-8187
-zji
-has-props
+2011-08-17T00:19:03.000000Z
+bb0abbbf476d58e9919f5c7f22d8bdd5
+2009-01-21T01:15:04.000000Z
+4670
+sheths



@@ -485,19 +457,55 @@ has-props



-9684
+
+273

-RuntimeEnvironmentSettings.java
+TransactionElement.java
 file




 2011-08-17T00:19:03.000000Z
-a48b53341f7eb955278c752cc2978b9f
+8994a2940a8979d76e4b710b7b031e9c
+2011-04-19T16:07:16.228867Z
+7751
+bellj
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+665
+
+XMLLoader.java
+file
+
+
+
+
+2012-01-10T18:25:35.000000Z
+b75feb18b8d53e5533eb2f4ae5a70117
 2011-07-30T04:31:30.667242Z
 8187
 zji
+has-props



@@ -518,23 +526,28 @@ zji



-
-1620
+9684

-workflowRepository
+bean
 dir

-ServerConfig.java
+chat
+dir
+
+help
+dir
+
+login.conf
 file




 2011-08-17T00:19:03.000000Z
-bb0abbbf476d58e9919f5c7f22d8bdd5
-2009-01-21T01:15:04.000000Z
-4670
-sheths
+a1660ab13dcf97357c0c0a6ec5d0cdf2
+2011-04-19T16:07:16.228867Z
+7751
+bellj



@@ -556,8 +569,17 @@ sheths



-273
+103
+
+rating
+dir
+
+server
+dir

 ui
 dir

+workflowRepository
+dir
+
diff --git a/geworkbench-core/classes/org/geworkbench/components/genspace/.svn/text-base/GenSpaceServerFactory.java.svn-base b/geworkbench-core/classes/org/geworkbench/components/genspace/.svn/text-base/GenSpaceServerFactory.java.svn-base
index 94653ce..7ad196f 100644
--- a/geworkbench-core/classes/org/geworkbench/components/genspace/.svn/text-base/GenSpaceServerFactory.java.svn-base
+++ b/geworkbench-core/classes/org/geworkbench/components/genspace/.svn/text-base/GenSpaceServerFactory.java.svn-base
@@ -2,14 +2,19 @@
 package org.geworkbench.components.genspace;


+import java.io.ByteArrayInputStream;
 import java.io.ByteArrayOutputStream;
 import java.io.IOException;
+import java.io.ObjectInputStream;
 import java.io.ObjectOutputStream;
 import java.io.Serializable;
+import java.net.MalformedURLException;
+import java.net.URL;
 import java.util.HashMap;
 import java.util.List;

 import javax.swing.JOptionPane;
+import javax.xml.namespace.QName;
 import javax.xml.ws.BindingProvider;

 import org.apache.log4j.Logger;
@@ -40,6 +45,7 @@ public class GenSpaceServerFactory {
 	private static User user;
 	private static String username = null;
 	private static String password = null;
+	private static String SERVER_ADDR = "http://genspace.cs.columbia.edu:8080";

 	public static Logger logger = Logger.getLogger(GenSpaceServerFactory.class);
 //	private static UserFacade userFacade;
@@ -57,6 +63,32 @@ public class GenSpaceServerFactory {
 		loadTools();
 	}

+	public static Object readObject(byte[] data)
+	{
+		ObjectInputStream is;
+		try {
+			is = new ObjectInputStream(new ByteArrayInputStream(data));
+			return is.readObject();
+		} catch (ClassNotFoundException e) {
+			e.printStackTrace();
+		} catch (IOException e) {
+			e.printStackTrace();
+		}
+		return null;
+	}
+	public static byte[] writeObject(Object o)
+	{
+		ByteArrayOutputStream bos = new ByteArrayOutputStream();
+		ObjectOutputStream oos;
+		try {
+			oos = new ObjectOutputStream(bos);
+			oos.writeObject(o);
+		} catch (IOException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}
+		return bos.toByteArray();
+	}
 	private static void loadTools()
 	{
 		if(RuntimeEnvironmentSettings.tools == null)
@@ -105,58 +137,92 @@ public class GenSpaceServerFactory {
 	}
 	public synchronized static WorkflowRepository getWorkflowOps()
 	{
-//		if(workflowFacade == null)
-//		{
 		WorkflowRepository workflowFacade;
 			loadTools();
-			workflowFacade = (new WorkflowRepositoryService()).getWorkflowRepositoryPort();
-			addCredentials((BindingProvider) workflowFacade);
-//		}
-		return workflowFacade;
+			try {
+				workflowFacade = (new WorkflowRepositoryService(new URL(SERVER_ADDR+"/WorkflowRepositoryService/WorkflowRepository?wsdl"),  new QName("http://server.genspace.components.geworkbench.org/", "WorkflowRepositoryService"))).getWorkflowRepositoryPort();
+				addCredentials((BindingProvider) workflowFacade);
+				return workflowFacade;
+
+			} catch (MalformedURLException e) {
+				return null;
+			}
 	}
 	public synchronized static ToolUsageInformation getUsageOps()
 	{
 		loadTools();
-		ToolUsageInformation toolUsageFacade = (new ToolUsageInformationService()).getToolUsageInformationPort();
-		return toolUsageFacade;
+		ToolUsageInformation toolUsageFacade;
+		try {
+			toolUsageFacade = (new ToolUsageInformationService(new URL(SERVER_ADDR+"/ToolUsageInformationService/ToolUsageInformation?wsdl"),  new QName("http://server.genspace.components.geworkbench.org/", "ToolUsageInformationService"))).getToolUsageInformationPort();
+			return toolUsageFacade;
+
+		} catch (MalformedURLException e) {
+			return null;
+		}
 	}
 	public synchronized static UserFacade getUserOps()
 	{

-		UserFacade userFacade = (new UserFacadeService()).getUserFacadePort();
-		addCredentials((BindingProvider) userFacade);
-		return userFacade;
+		UserFacade userFacade;
+		try {
+			userFacade = (new UserFacadeService(new URL(SERVER_ADDR+"/UserFacadeService/UserFacade?wsdl"),  new QName("http://server.genspace.components.geworkbench.org/", "UserFacadeService"))).getUserFacadePort();
+			addCredentials((BindingProvider) userFacade);
+			return userFacade;
+		} catch (MalformedURLException e) {
+			return null;
+		}
+
 	}

 	public synchronized static PublicFacade getPublicFacade()
 	{
 		loadTools();
-		PublicFacade publicFacade = (new PublicFacadeService()).getPublicFacadePort();
+		try{
+		PublicFacade publicFacade = (new PublicFacadeService(new URL(SERVER_ADDR+"/PublicFacadeService/PublicFacade?wsdl"),  new QName("http://server.genspace.components.geworkbench.org/", "PublicFacadeService"))).getPublicFacadePort();
 		addCredentials((BindingProvider) publicFacade);
 		return publicFacade;
+		} catch(MalformedURLException e)
+		{
+			return null;
+		}
 	}

 	public synchronized static UsageInformation getPrivUsageFacade()
 	{
 		if(user == null)
 			return null;
-			loadTools();
-		UsageInformation usageFacade = (new UsageInformationService()).getUsageInformationPort();
+		loadTools();
+		try
+		{
+		UsageInformation usageFacade = (new UsageInformationService(new URL(SERVER_ADDR+"/UsageInformationService/UsageInformation?wsdl"),  new QName("http://server.genspace.components.geworkbench.org/", "UsageInformationService"))).getUsageInformationPort();
 			addCredentials((BindingProvider) usageFacade);
 		return usageFacade;
+		} catch (MalformedURLException e)
+		{
+			return null;
+		}
 	}
 	public synchronized static FriendFacade getFriendOps()
 	{
-
-		FriendFacade friendFacade = (new FriendFacadeService()).getFriendFacadePort();
+try{
+		FriendFacade friendFacade = (new FriendFacadeService(new URL(SERVER_ADDR+"/FriendFacadeService/FriendFacade?wsdl"),  new QName("http://server.genspace.components.geworkbench.org/", "FriendFacadeService"))).getFriendFacadePort();
 			addCredentials((BindingProvider) friendFacade);
 		return friendFacade;
+} catch (MalformedURLException e)
+{
+	return null;
+}
 	}
 	public synchronized static NetworkFacade getNetworkOps()
 	{
-		NetworkFacade networkFacade = (new NetworkFacadeService()).getNetworkFacadePort();
+		try{
+		NetworkFacade networkFacade = (new NetworkFacadeService(new URL(SERVER_ADDR+"/NetworkFacadeService/NetworkFacade?wsdl"),  new QName("http://server.genspace.components.geworkbench.org/", "NetworkFacadeService"))).getNetworkFacadePort();
 		addCredentials((BindingProvider) networkFacade);
 		return networkFacade;
+		} catch (MalformedURLException e)
+		{
+			return null;
+		}
 	}


diff --git a/geworkbench-core/classes/org/geworkbench/components/genspace/bean/.svn/entries b/geworkbench-core/classes/org/geworkbench/components/genspace/bean/.svn/entries
index ebffc5a..bb3e636 100644
--- a/geworkbench-core/classes/org/geworkbench/components/genspace/bean/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/components/genspace/bean/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/bean
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/components/genspace/chat/.svn/all-wcprops b/geworkbench-core/classes/org/geworkbench/components/genspace/chat/.svn/all-wcprops
index 2792ea5..91844b4 100644
--- a/geworkbench-core/classes/org/geworkbench/components/genspace/chat/.svn/all-wcprops
+++ b/geworkbench-core/classes/org/geworkbench/components/genspace/chat/.svn/all-wcprops
@@ -1,7 +1,7 @@
 K 25
 svn:wc:ra_dav:version-url
 V 113
-/svn/geworkbench/!svn/ver/8666/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/chat
+/svn/geworkbench/!svn/ver/8793/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/chat
 END
 ChatTest.java
 K 25
@@ -19,7 +19,7 @@ ChatReceiver.java
 K 25
 svn:wc:ra_dav:version-url
 V 131
-/svn/geworkbench/!svn/ver/8666/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/chat/ChatReceiver.java
+/svn/geworkbench/!svn/ver/8793/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/chat/ChatReceiver.java
 END
 ScreenShareListener.java
 K 25
diff --git a/geworkbench-core/classes/org/geworkbench/components/genspace/chat/.svn/entries b/geworkbench-core/classes/org/geworkbench/components/genspace/chat/.svn/entries
index e08ef9b..023807f 100644
--- a/geworkbench-core/classes/org/geworkbench/components/genspace/chat/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/components/genspace/chat/.svn/entries
@@ -1,15 +1,15 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/chat
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2012-01-06T20:06:43.164210Z
-8666
-bellj
+2012-01-27T16:21:32.396819Z
+8793
+zji



@@ -100,11 +100,11 @@ file



-2012-01-10T21:28:12.000000Z
-b7ba99e2dc675e60da3137b1af72a990
-2012-01-06T20:06:43.164210Z
-8666
-bellj
+2012-01-31T19:12:30.000000Z
+ba313b6cf83f56fbdac997168f677b37
+2012-01-27T16:21:32.396819Z
+8793
+zji



@@ -126,7 +126,7 @@ bellj



-3947
+3894

 ScreenShareListener.java
 file
diff --git a/geworkbench-core/classes/org/geworkbench/components/genspace/chat/.svn/text-base/ChatReceiver.java.svn-base b/geworkbench-core/classes/org/geworkbench/components/genspace/chat/.svn/text-base/ChatReceiver.java.svn-base
index e8eb85f..8b89af3 100644
--- a/geworkbench-core/classes/org/geworkbench/components/genspace/chat/.svn/text-base/ChatReceiver.java.svn-base
+++ b/geworkbench-core/classes/org/geworkbench/components/genspace/chat/.svn/text-base/ChatReceiver.java.svn-base
@@ -5,7 +5,6 @@ import java.util.concurrent.ExecutionException;

 import javax.swing.SwingWorker;

-import org.geworkbench.components.genspace.GenSpace;
 import org.geworkbench.components.genspace.GenSpaceServerFactory;
 import org.geworkbench.components.genspace.RuntimeEnvironmentSettings;
 import org.geworkbench.components.genspace.ui.chat.ChatWindow;
diff --git a/geworkbench-core/classes/org/geworkbench/components/genspace/help/.svn/entries b/geworkbench-core/classes/org/geworkbench/components/genspace/help/.svn/entries
index 338c997..a589485 100644
--- a/geworkbench-core/classes/org/geworkbench/components/genspace/help/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/components/genspace/help/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/help
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/components/genspace/help/genspace_files/.svn/entries b/geworkbench-core/classes/org/geworkbench/components/genspace/help/genspace_files/.svn/entries
index 97cdd85..841ad2d 100644
--- a/geworkbench-core/classes/org/geworkbench/components/genspace/help/genspace_files/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/components/genspace/help/genspace_files/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/help/genspace_files
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/components/genspace/rating/.svn/entries b/geworkbench-core/classes/org/geworkbench/components/genspace/rating/.svn/entries
index 26c6a2a..622740b 100644
--- a/geworkbench-core/classes/org/geworkbench/components/genspace/rating/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/components/genspace/rating/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/rating
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/components/genspace/server/.svn/all-wcprops b/geworkbench-core/classes/org/geworkbench/components/genspace/server/.svn/all-wcprops
index 27e188a..1a64027 100644
--- a/geworkbench-core/classes/org/geworkbench/components/genspace/server/.svn/all-wcprops
+++ b/geworkbench-core/classes/org/geworkbench/components/genspace/server/.svn/all-wcprops
@@ -1,5 +1,5 @@
 K 25
 svn:wc:ra_dav:version-url
 V 115
-/svn/geworkbench/!svn/ver/8187/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/server
+/svn/geworkbench/!svn/ver/8699/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/server
 END
diff --git a/geworkbench-core/classes/org/geworkbench/components/genspace/server/.svn/entries b/geworkbench-core/classes/org/geworkbench/components/genspace/server/.svn/entries
index b71fa1d..0592862 100644
--- a/geworkbench-core/classes/org/geworkbench/components/genspace/server/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/components/genspace/server/.svn/entries
@@ -1,15 +1,15 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/server
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2011-07-30T04:31:30.667242Z
-8187
-zji
+2012-01-12T20:41:07.691376Z
+8699
+bellj



diff --git a/geworkbench-core/classes/org/geworkbench/components/genspace/server/wrapper/.svn/all-wcprops b/geworkbench-core/classes/org/geworkbench/components/genspace/server/wrapper/.svn/all-wcprops
index 9a48c19..b820f6e 100644
--- a/geworkbench-core/classes/org/geworkbench/components/genspace/server/wrapper/.svn/all-wcprops
+++ b/geworkbench-core/classes/org/geworkbench/components/genspace/server/wrapper/.svn/all-wcprops
@@ -1,7 +1,7 @@
 K 25
 svn:wc:ra_dav:version-url
 V 123
-/svn/geworkbench/!svn/ver/8187/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/server/wrapper
+/svn/geworkbench/!svn/ver/8699/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/server/wrapper
 END
 UserWrapper.java
 K 25
@@ -9,12 +9,6 @@ svn:wc:ra_dav:version-url
 V 140
 /svn/geworkbench/!svn/ver/8187/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/server/wrapper/UserWrapper.java
 END
-WorkflowWrapper.java
-K 25
-svn:wc:ra_dav:version-url
-V 144
-/svn/geworkbench/!svn/ver/8187/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/server/wrapper/WorkflowWrapper.java
-END
 ToolWrapper.java
 K 25
 svn:wc:ra_dav:version-url
diff --git a/geworkbench-core/classes/org/geworkbench/components/genspace/server/wrapper/.svn/entries b/geworkbench-core/classes/org/geworkbench/components/genspace/server/wrapper/.svn/entries
index be3a481..ab7ce1a 100644
--- a/geworkbench-core/classes/org/geworkbench/components/genspace/server/wrapper/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/components/genspace/server/wrapper/.svn/entries
@@ -1,15 +1,15 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/server/wrapper
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2011-07-30T04:31:30.667242Z
-8187
-zji
+2012-01-12T20:41:07.691376Z
+8699
+bellj



@@ -66,11 +66,11 @@ file



-2012-01-10T18:25:35.000000Z
-876d6f83aa4e2d189ac3fe913efaba95
-2011-07-30T04:31:30.667242Z
-8187
-zji
+2012-01-12T20:32:36.000000Z
+89d0c4c994ee2e9b1f919f2467214d06
+2012-01-12T20:41:07.691376Z
+8699
+bellj



@@ -92,7 +92,7 @@ zji



-4233
+4303

 ToolWrapper.java
 file
diff --git a/geworkbench-core/classes/org/geworkbench/components/genspace/server/wrapper/.svn/text-base/WorkflowWrapper.java.svn-base b/geworkbench-core/classes/org/geworkbench/components/genspace/server/wrapper/.svn/text-base/WorkflowWrapper.java.svn-base
index 2179d65..70b38fd 100644
--- a/geworkbench-core/classes/org/geworkbench/components/genspace/server/wrapper/.svn/text-base/WorkflowWrapper.java.svn-base
+++ b/geworkbench-core/classes/org/geworkbench/components/genspace/server/wrapper/.svn/text-base/WorkflowWrapper.java.svn-base
@@ -31,7 +31,11 @@ public class WorkflowWrapper {
 	}

 	public boolean equals(Object obj) {
-		return delegate.equals(obj);
+		if(obj instanceof Workflow)
+		{
+			return ((Workflow) obj).getId() == getId();
+		}
+		return false;
 	}
 	public List<Workflow> getChildren() {
 		return delegate.getChildren();
diff --git a/geworkbench-core/classes/org/geworkbench/components/genspace/ui/.svn/all-wcprops b/geworkbench-core/classes/org/geworkbench/components/genspace/ui/.svn/all-wcprops
index 3d82903..8ba35ec 100644
--- a/geworkbench-core/classes/org/geworkbench/components/genspace/ui/.svn/all-wcprops
+++ b/geworkbench-core/classes/org/geworkbench/components/genspace/ui/.svn/all-wcprops
@@ -1,7 +1,7 @@
 K 25
 svn:wc:ra_dav:version-url
 V 111
-/svn/geworkbench/!svn/ver/8667/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/ui
+/svn/geworkbench/!svn/ver/8699/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/ui
 END
 SocialTab.java
 K 25
@@ -45,35 +45,23 @@ svn:wc:ra_dav:version-url
 V 126
 /svn/geworkbench/!svn/ver/8187/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/ui/StatusBar.java
 END
-WorkflowVisualizationPanel.java
-K 25
-svn:wc:ra_dav:version-url
-V 143
-/svn/geworkbench/!svn/ver/8187/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/ui/WorkflowVisualizationPanel.java
-END
 GenSpaceLogin.java
 K 25
 svn:wc:ra_dav:version-url
 V 130
 /svn/geworkbench/!svn/ver/8187/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/ui/GenSpaceLogin.java
 END
-SocialNetworksHome.java
-K 25
-svn:wc:ra_dav:version-url
-V 135
-/svn/geworkbench/!svn/ver/8187/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/ui/SocialNetworksHome.java
-END
 GenSpaceRegistration.java
 K 25
 svn:wc:ra_dav:version-url
 V 137
 /svn/geworkbench/!svn/ver/8667/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/ui/GenSpaceRegistration.java
 END
-friendsTab.java
+SocialNetworksHome.java
 K 25
 svn:wc:ra_dav:version-url
-V 127
-/svn/geworkbench/!svn/ver/8187/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/ui/friendsTab.java
+V 135
+/svn/geworkbench/!svn/ver/8187/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/ui/SocialNetworksHome.java
 END
 DataVisibility.java
 K 25
@@ -81,6 +69,12 @@ svn:wc:ra_dav:version-url
 V 131
 /svn/geworkbench/!svn/ver/7751/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/ui/DataVisibility.java
 END
+friendsTab.java
+K 25
+svn:wc:ra_dav:version-url
+V 127
+/svn/geworkbench/!svn/ver/8187/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/ui/friendsTab.java
+END
 AutoCompleteCombo.java
 K 25
 svn:wc:ra_dav:version-url
diff --git a/geworkbench-core/classes/org/geworkbench/components/genspace/ui/.svn/entries b/geworkbench-core/classes/org/geworkbench/components/genspace/ui/.svn/entries
index bfe6740..c2e7207 100644
--- a/geworkbench-core/classes/org/geworkbench/components/genspace/ui/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/components/genspace/ui/.svn/entries
@@ -1,14 +1,14 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/ui
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2012-01-06T21:01:06.170581Z
-8667
+2012-01-12T20:41:07.691376Z
+8699
 bellj


@@ -273,11 +273,11 @@ file



-2012-01-10T18:25:35.000000Z
-21fef75103fd98ce0cb02d257e4d6e10
-2011-07-30T04:31:30.667242Z
-8187
-zji
+2012-01-12T20:35:32.000000Z
+d2925633063599c01c556c1372dbe93b
+2012-01-12T20:41:07.691376Z
+8699
+bellj



@@ -299,7 +299,7 @@ zji



-12878
+13288

 GenSpaceLogin.java
 file
@@ -471,9 +471,6 @@ zji

 10105

-graph
-dir
-
 friendsTab.java
 file

@@ -508,6 +505,9 @@ zji

 7441

+graph
+dir
+
 viewProfileTab.java
 file

diff --git a/geworkbench-core/classes/org/geworkbench/components/genspace/ui/.svn/text-base/WorkflowVisualizationPanel.java.svn-base b/geworkbench-core/classes/org/geworkbench/components/genspace/ui/.svn/text-base/WorkflowVisualizationPanel.java.svn-base
index 3cd4a9c..85a8354 100644
--- a/geworkbench-core/classes/org/geworkbench/components/genspace/ui/.svn/text-base/WorkflowVisualizationPanel.java.svn-base
+++ b/geworkbench-core/classes/org/geworkbench/components/genspace/ui/.svn/text-base/WorkflowVisualizationPanel.java.svn-base
@@ -13,6 +13,7 @@ import java.util.ArrayList;
 import java.util.Collections;
 import java.util.Comparator;
 import java.util.HashMap;
+import java.util.HashSet;
 import java.util.Hashtable;
 import java.util.List;
 import java.util.Timer;
@@ -49,7 +50,7 @@ public class WorkflowVisualizationPanel extends JPanel implements VisualPlugin {
 	 */
 	private static final long serialVersionUID = -3300246926475166675L;
 	private WorkflowVisualizationPopup popup = new WorkflowVisualizationPopup();
-
+
 	private myGraph graph;
 	private mxGraphComponent graphComponent;
 	private JScrollPane scroller = new JScrollPane();;
@@ -60,39 +61,39 @@ public class WorkflowVisualizationPanel extends JPanel implements VisualPlugin {
 		new Timer();
 		add(scroller, BorderLayout.CENTER);
 		this.addComponentListener(new ComponentListener() {
-
+
 			@Override
 			public void componentShown(ComponentEvent e) {
 			}
-
+
 			@Override
 			public void componentResized(ComponentEvent e) {
-				if(graphComponent != null)
-					graphComponent.setPreferredSize(getSize());
 				if(!redrawing)
 				{
 					redrawing = true;
+					if(graphComponent != null)
+						graphComponent.setPreferredSize(getSize());
 					SwingWorker<Void,Void> wrkr = new SwingWorker<Void, Void>()
-					{
+							{
 						int evt;
 						protected void done() {
 							GenSpace.getStatusBar().stop(evt);
+							redrawing = false;
 						};
-						protected Void doInBackground() throws Exception {
+						protected Void doInBackground(){
 							evt = GenSpace.getStatusBar().start("Resizing graph");
 							refreshLayout();
-							redrawing = false;
 							return null;
 						};
-					};
-					wrkr.execute();
-				}
+							};
+							wrkr.execute();
+				}
 			}
-
+
 			@Override
 			public void componentMoved(ComponentEvent e) {
 			}
-
+
 			@Override
 			public void componentHidden(ComponentEvent e) {
 			}
@@ -122,41 +123,45 @@ public class WorkflowVisualizationPanel extends JPanel implements VisualPlugin {
 			myStackLayout layout = new myStackLayout(graph,false,20,10,10);
 			layout.setResizeParent(true);
 			layout.execute(pool);
-
+
 			layout = new myStackLayout(graph,swimlanes.size() == 0,40,10,0);
 			if(swimlanes.size() == 0)
 			{
-				layout.setWrap((int) this.getSize().getWidth());
+				layout.setWrap((int) this.getSize().getWidth() - 60);
 			}
 			layout.setResizeParent(true);
 			layout.execute(parent);
-
+
 			if(swimlanesBack.size() > 0)
-			for(mxICell i : swimlanes.values())
-			{
-				WorkflowWrapper parentW = wkflwCache.get(swimlanesBack.get(i).getCachedParentId());
-				int drawOffset = 0;
-				if(parentW != null)
+				for(mxICell i : swimlanes.values())
 				{
-					if(wkflTails.get(parentW) != null)
-					{
-					drawOffset = (int) (wkflTails.get(parentW).getGeometry().getX()+wkflTails.get(parentW).getGeometry().getWidth());
-					Object[] es = graph.getEdgesBetween(wkflTails.get(parentW),i.getChildAt(0));
-					if(es.length == 1)
+					WorkflowWrapper parentW = wkflwCache.get(swimlanesBack.get(i).getCachedParentId());
+					int drawOffset = 0;
+					if(parentW != null)
 					{
-					mxICell edge = (mxICell) es[0];
-					ArrayList<mxPoint> pts = new ArrayList<mxPoint>();
-					pts.add(new mxPoint(wkflTails.get(parentW).getGeometry().getCenterX() +((mxICell) parent).getGeometry().getX(), (i.getChildAt(0)).getGeometry().getCenterY() + i.getGeometry().getY()));
-					edge.getGeometry().setPoints(pts);
-					}
+						if(wkflTails.get(parentW) != null)
+						{
+							drawOffset = (int) (wkflTails.get(parentW).getGeometry().getX()+wkflTails.get(parentW).getGeometry().getWidth());
+							Object[] es = graph.getEdgesBetween(wkflTails.get(parentW),i.getChildAt(0));
+							if(es.length == 1)
+							{
+								mxICell edge = (mxICell) es[0];
+								ArrayList<mxPoint> pts = new ArrayList<mxPoint>();
+								pts.add(new mxPoint(wkflTails.get(parentW).getGeometry().getCenterX() +((mxICell) parent).getGeometry().getX(), (i.getChildAt(0)).getGeometry().getCenterY() + i.getGeometry().getY()));
+								edge.getGeometry().setPoints(pts);
+							}
+						}
 					}
+					layout = new myStackLayout(graph,true,10,drawOffset,0);
+					layout.setWrap((int) this.getSize().getWidth() + drawOffset - 60);
+					layout.setResizeParent(true);
+					layout.execute(i);
+					layout.setWrap((int) i.getGeometry().getWidth());
+					layout.setResizeParent(true);
+					layout.execute(i);
+
 				}
-				layout = new myStackLayout(graph,true,10,drawOffset,0);
-				layout.setWrap((int) this.getSize().getWidth() + drawOffset);
-				layout.setResizeParent(true);
-				layout.execute(i);
-			}
-
+
 			this.removeAll();
 			add(graphComponent, BorderLayout.CENTER);
 			graphComponent.setVisible(true);
@@ -166,34 +171,34 @@ public class WorkflowVisualizationPanel extends JPanel implements VisualPlugin {
 		}
 	}
 	private void layoutAndShowGraph() {
-
-			graph.getModel().endUpdate();
-
-			graphComponent = new mxGraphComponent(graph);
-			graphComponent.getGraphControl().addMouseListener(new MouseAdapter()
+
+		graph.getModel().endUpdate();
+
+		graphComponent = new mxGraphComponent(graph);
+		graphComponent.getGraphControl().addMouseListener(new MouseAdapter()
+		{
+
+			public void mouseReleased(MouseEvent e)
 			{
-
-				public void mouseReleased(MouseEvent e)
+				Object cell = graphComponent.getCellAt(e.getX(), e.getY());
+
+				if (cell != null)
 				{
-					Object cell = graphComponent.getCellAt(e.getX(), e.getY());
-
-					if (cell != null)
+					if(cell instanceof mxCell)
 					{
-						if(cell instanceof mxCell)
-						{
-							mxCell mx = (mxCell) cell;
-							cell = mx.getValue();
-						}
-						if(cell.getClass().equals(WorkflowToolHolder.class))
-						{
-							WorkflowToolHolder selected = (WorkflowToolHolder) cell;
-							popup.initialize(selected.getTool(), (Workflow) selected.getWorkflow());
-							popup.show(WorkflowVisualizationPanel.this, (int) e.getX(),
-									(int) e.getY());
-						}
+						mxCell mx = (mxCell) cell;
+						cell = mx.getValue();
+					}
+					if(cell.getClass().equals(WorkflowToolHolder.class))
+					{
+						WorkflowToolHolder selected = (WorkflowToolHolder) cell;
+						popup.initialize(selected.getTool(), (Workflow) selected.getWorkflow());
+						popup.show(WorkflowVisualizationPanel.this, (int) e.getX(),
+								(int) e.getY());
 					}
 				}
-			});
+			}
+		});
 		refreshLayout();
 	}
 	@Override
@@ -213,19 +218,21 @@ public class WorkflowVisualizationPanel extends JPanel implements VisualPlugin {
 			@Override
 			public int compare(WorkflowWrapper o1, WorkflowWrapper o2) {
 				if(o1.getCachedChildrenCount() < o2.getCachedChildrenCount())
-					return -1;
-				else if(o1.getCachedChildrenCount() > o2.getCachedChildrenCount())
 					return 1;
+				else if(o1.getCachedChildrenCount() > o2.getCachedChildrenCount())
+					return -1;
 				else
 					return 0;
 			}
 		});
 		initGraph();
 		pool = graph.insertVertex(graph.getDefaultParent(), null, "", 0, 0, 10, 10,"POOL");
+		renderedWfs = new HashSet<Integer>();
 		renderAsSubs(ret,selected,false,null);
 		layoutAndShowGraph();
-
+
 	}
+	private HashSet<Integer> renderedWfs;
 	private HashMap<Integer,WorkflowWrapper> wkflwCache;
 	private HashMap<WorkflowWrapper, mxICell> wkflTails;
 	private HashMap<WorkflowWrapper, mxICell> swimlanes;
@@ -235,6 +242,8 @@ public class WorkflowVisualizationPanel extends JPanel implements VisualPlugin {
 			return;
 		for(WorkflowWrapper w: ret)
 		{
+			if(renderedWfs.contains(w.getId()))
+				continue;
 			if(parent == null)
 			{
 				if(!ret.contains(wkflwCache.get(w.getCachedParentId())))
@@ -243,8 +252,8 @@ public class WorkflowVisualizationPanel extends JPanel implements VisualPlugin {
 					{
 						Object lane = graph.insertVertex(pool, null, "", 0, 0, this.getWidth(), 10,"SWIMLANE");
 						swimlanes.put(w, (mxICell) lane);
+						renderedWfs.add(w.getId());
 						renderSingleWorkflow(w,selected,lane);
-
 						renderAsSubs(ret, selected, true, w);
 					}
 				}
@@ -255,6 +264,7 @@ public class WorkflowVisualizationPanel extends JPanel implements VisualPlugin {
 				{
 					Object lane = graph.insertVertex(pool, null, "", 0, 0, this.getWidth(), 10,"SWIMLANE");
 					swimlanes.put(w, (mxICell) lane);
+					renderedWfs.add(w.getId());
 					renderSingleWorkflow(w,selected,lane,wkflwCache.get(w.getCachedParentId()).getTools().size(),wkflTails.get(wkflwCache.get(w.getCachedParentId())));
 					renderAsSubs(ret, selected, true, w);
 				}
@@ -271,7 +281,7 @@ public class WorkflowVisualizationPanel extends JPanel implements VisualPlugin {
 			drawOffset = 10;
 		else
 			drawOffset = (int) (drawFrom.getGeometry().getX() + drawFrom.getGeometry().getWidth());
-
+
 		if(parent == null)
 			parent = graph.getDefaultParent();

@@ -282,7 +292,6 @@ public class WorkflowVisualizationPanel extends JPanel implements VisualPlugin {
 		{
 			if(to == null || to.getTool() == null)
 			{
-				System.out.println("Null tool");
 				continue;
 			}
 			if(i < toolOffset)
@@ -295,10 +304,10 @@ public class WorkflowVisualizationPanel extends JPanel implements VisualPlugin {
 				styl = "WORKFLOW;fillColor=#e8f2dd";
 			else
 				styl = "WORKFLOW";
-
+
 			Rectangle2D r = f.getStringBounds(to.getTool().getName(), ((Graphics2D) this.getGraphics()).getFontRenderContext());
 			Object v1 = graph.insertVertex(parent, null, new WorkflowToolHolder(to), 10, 10, r.getWidth()+10, r.getHeight()+10,styl);
-
+
 			if(lastCell != null)
 				graph.insertEdge(parent, null, "", lastCell, v1,"editable=0");
 			else if(drawFrom != null)
@@ -306,13 +315,13 @@ public class WorkflowVisualizationPanel extends JPanel implements VisualPlugin {
 				myStackLayout layout = new myStackLayout(graph,false,20,10,10);
 				layout.setResizeParent(true);
 				layout.execute(pool);
-
+
 				layout = new myStackLayout(graph,true,20,0,0);
 				layout.setWrap((int) this.getSize().getWidth());
 				layout.setResizeParent(true);
 				layout.execute(parent);

-
+
 				mxICell e = (mxICell) graph.insertEdge(graph.getDefaultParent(), null, "", drawFrom, v1,"CROSSOVER;editable=0");
 				ArrayList<mxPoint> pts = new ArrayList<mxPoint>();
 				pts.add(new mxPoint(drawFrom.getGeometry().getCenterX() +((mxICell) parent).getGeometry().getX(), ((mxICell) v1).getGeometry().getCenterY() + ((mxICell) parent).getGeometry().getY()));
@@ -326,10 +335,16 @@ public class WorkflowVisualizationPanel extends JPanel implements VisualPlugin {
 		layout.setWrap((int) this.getSize().getWidth() + drawOffset);
 		layout.setResizeParent(true);
 		layout.execute(parent);
+		if(swimlanes.get(w) != null)
+		{
+		layout.setWrap((int) swimlanes.get(w).getGeometry().getWidth());
+		layout.setResizeParent(true);
+		layout.execute(parent);
+		}
 		wkflTails.put(w, ((mxICell) lastCell));


-
+
 	}
 	private void renderSingleWorkflow(WorkflowWrapper w, Tool selected,Object parent) {
 		renderSingleWorkflow(w, selected, parent,0,null);
@@ -340,7 +355,7 @@ public class WorkflowVisualizationPanel extends JPanel implements VisualPlugin {


 		graph.getModel().beginUpdate();
-
+

 		Hashtable<String, Object> style = new Hashtable<String, Object>();
 		style.put(mxConstants.STYLE_SHAPE, mxConstants.SHAPE_RECTANGLE);
@@ -357,21 +372,21 @@ public class WorkflowVisualizationPanel extends JPanel implements VisualPlugin {
 		style2.put(mxConstants.STYLE_BENDABLE, true);
 		style2.put(mxConstants.STYLE_ELBOW, mxConstants.ELBOW_HORIZONTAL);
 		graph.getStylesheet().putCellStyle("CROSSOVER", style2);
-
-
+
+
 		Hashtable<String, Object> style3 = new Hashtable<String, Object>();
 		style3.put(mxConstants.STYLE_FILLCOLOR, "#E1E2E6");
 		style3.put(mxConstants.STYLE_STROKECOLOR, "#000000");
 		style3.put(mxConstants.STYLE_STROKEWIDTH, .5);
 		style3.put(mxConstants.STYLE_VERTICAL_ALIGN, mxConstants.ALIGN_CENTER);
-//		style3.put(mxConstants.STYLE_OPACITY, "0");
+		//		style3.put(mxConstants.STYLE_OPACITY, "0");
 		graph.getStylesheet().putCellStyle("SWIMLANE", style3);
-
+
 		Hashtable<String, Object> style4 = new Hashtable<String, Object>();
 		style4.put(mxConstants.STYLE_OPACITY, 0);
 		graph.getStylesheet().putCellStyle("POOL", style4);
-
-
+
+
 		graph.setConnectableEdges(false);
 		graph.setAllowDanglingEdges(false);
 		graph.setCellsEditable(false);
@@ -380,12 +395,12 @@ public class WorkflowVisualizationPanel extends JPanel implements VisualPlugin {
 		graph.setCellsResizable(false);
 		graph.setConnectableEdges(false);
 		graph.setEnabled(false);
-
+
 		wkflTails = new HashMap<WorkflowWrapper, mxICell>();
 		swimlanes = new HashMap<WorkflowWrapper, mxICell>();
 		swimlanesBack = new HashMap<mxICell, WorkflowWrapper>();
 	}
-
+

 }

diff --git a/geworkbench-core/classes/org/geworkbench/components/genspace/ui/chat/.svn/entries b/geworkbench-core/classes/org/geworkbench/components/genspace/ui/chat/.svn/entries
index 23caf8f..9a25826 100644
--- a/geworkbench-core/classes/org/geworkbench/components/genspace/ui/chat/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/components/genspace/ui/chat/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/ui/chat
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/components/genspace/ui/graph/.svn/all-wcprops b/geworkbench-core/classes/org/geworkbench/components/genspace/ui/graph/.svn/all-wcprops
index 4a48d68..8efad21 100644
--- a/geworkbench-core/classes/org/geworkbench/components/genspace/ui/graph/.svn/all-wcprops
+++ b/geworkbench-core/classes/org/geworkbench/components/genspace/ui/graph/.svn/all-wcprops
@@ -1,7 +1,7 @@
 K 25
 svn:wc:ra_dav:version-url
 V 117
-/svn/geworkbench/!svn/ver/7751/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/ui/graph
+/svn/geworkbench/!svn/ver/8699/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/ui/graph
 END
 myGraph.java
 K 25
@@ -9,9 +9,3 @@ svn:wc:ra_dav:version-url
 V 130
 /svn/geworkbench/!svn/ver/7751/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/ui/graph/myGraph.java
 END
-myStackLayout.java
-K 25
-svn:wc:ra_dav:version-url
-V 136
-/svn/geworkbench/!svn/ver/7751/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/ui/graph/myStackLayout.java
-END
diff --git a/geworkbench-core/classes/org/geworkbench/components/genspace/ui/graph/.svn/entries b/geworkbench-core/classes/org/geworkbench/components/genspace/ui/graph/.svn/entries
index 8965d4c..d2a0a0e 100644
--- a/geworkbench-core/classes/org/geworkbench/components/genspace/ui/graph/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/components/genspace/ui/graph/.svn/entries
@@ -1,14 +1,14 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/ui/graph
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2011-04-19T16:07:16.228867Z
-7751
+2012-01-12T20:41:07.691376Z
+8699
 bellj


@@ -66,10 +66,10 @@ file



-2011-08-17T00:19:03.000000Z
-9985e17cdc50246ea56ef0f67a6ad3e2
-2011-04-19T16:07:16.228867Z
-7751
+2012-01-10T22:32:37.000000Z
+c933ec87e27e4d1ac59b20b8d8620109
+2012-01-12T20:41:07.691376Z
+8699
 bellj


@@ -92,5 +92,5 @@ bellj



-4709
+4708

diff --git a/geworkbench-core/classes/org/geworkbench/components/genspace/ui/graph/.svn/text-base/myStackLayout.java.svn-base b/geworkbench-core/classes/org/geworkbench/components/genspace/ui/graph/.svn/text-base/myStackLayout.java.svn-base
index 21a2371..5302da9 100644
--- a/geworkbench-core/classes/org/geworkbench/components/genspace/ui/graph/.svn/text-base/myStackLayout.java.svn-base
+++ b/geworkbench-core/classes/org/geworkbench/components/genspace/ui/graph/.svn/text-base/myStackLayout.java.svn-base
@@ -123,7 +123,6 @@ public class myStackLayout extends mxStackLayout {
 												+ geo.getHeight() + 2 * spacing > wrap))
 								{
 									last = null;
-
 									if (horizontal)
 									{
 										y0 += tmp + spacing;
diff --git a/geworkbench-core/classes/org/geworkbench/components/genspace/workflowRepository/.svn/all-wcprops b/geworkbench-core/classes/org/geworkbench/components/genspace/workflowRepository/.svn/all-wcprops
index 946eae0..b18320e 100644
--- a/geworkbench-core/classes/org/geworkbench/components/genspace/workflowRepository/.svn/all-wcprops
+++ b/geworkbench-core/classes/org/geworkbench/components/genspace/workflowRepository/.svn/all-wcprops
@@ -3,17 +3,29 @@ svn:wc:ra_dav:version-url
 V 127
 /svn/geworkbench/!svn/ver/8617/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/workflowRepository
 END
+DynamicTree.java
+K 25
+svn:wc:ra_dav:version-url
+V 144
+/svn/geworkbench/!svn/ver/8617/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/workflowRepository/DynamicTree.java
+END
+InboxTablePanel.java
+K 25
+svn:wc:ra_dav:version-url
+V 148
+/svn/geworkbench/!svn/ver/8187/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/workflowRepository/InboxTablePanel.java
+END
 RepositoryPanel.java
 K 25
 svn:wc:ra_dav:version-url
 V 148
 /svn/geworkbench/!svn/ver/7751/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/workflowRepository/RepositoryPanel.java
 END
-WorkflowCommentsPanel.java
+WorkflowRepository.java
 K 25
 svn:wc:ra_dav:version-url
-V 154
-/svn/geworkbench/!svn/ver/8187/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/workflowRepository/WorkflowCommentsPanel.java
+V 151
+/svn/geworkbench/!svn/ver/8187/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/workflowRepository/WorkflowRepository.java
 END
 WorkflowDetailsPanel.java
 K 25
@@ -27,21 +39,3 @@ svn:wc:ra_dav:version-url
 V 145
 /svn/geworkbench/!svn/ver/8187/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/workflowRepository/WorkflowNode.java
 END
-DynamicTree.java
-K 25
-svn:wc:ra_dav:version-url
-V 144
-/svn/geworkbench/!svn/ver/8617/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/workflowRepository/DynamicTree.java
-END
-InboxTablePanel.java
-K 25
-svn:wc:ra_dav:version-url
-V 148
-/svn/geworkbench/!svn/ver/8187/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/workflowRepository/InboxTablePanel.java
-END
-WorkflowRepository.java
-K 25
-svn:wc:ra_dav:version-url
-V 151
-/svn/geworkbench/!svn/ver/8187/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/workflowRepository/WorkflowRepository.java
-END
diff --git a/geworkbench-core/classes/org/geworkbench/components/genspace/workflowRepository/.svn/entries b/geworkbench-core/classes/org/geworkbench/components/genspace/workflowRepository/.svn/entries
index ae7df04..b5edcc3 100644
--- a/geworkbench-core/classes/org/geworkbench/components/genspace/workflowRepository/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/components/genspace/workflowRepository/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/genspace/src/org/geworkbench/components/genspace/workflowRepository
 https://ncisvn.nci.nih.gov/svn/geworkbench

@@ -26,17 +26,17 @@ zji

 8b29bb6e-589a-435a-9a12-3ab907be3462

-RepositoryPanel.java
+DynamicTree.java
 file




-2011-08-17T00:19:03.000000Z
-51673eb783f47bf87acec4bc2ba46932
-2011-04-19T16:07:16.228867Z
-7751
-bellj
+2012-01-10T19:15:26.000000Z
+2111447f8bef7a615bb0cf73bd66f7c1
+2011-12-16T20:56:37.933310Z
+8617
+zji



@@ -58,16 +58,16 @@ bellj



-866
+12693

-WorkflowCommentsPanel.java
+InboxTablePanel.java
 file




 2012-01-10T18:25:35.000000Z
-86c8e67e9eae5f29814eb5e2024a8a92
+77a3d1cb5b342a013003cb71365aac2e
 2011-07-30T04:31:30.667242Z
 8187
 zji
@@ -92,19 +92,19 @@ zji



-9959
+11549

-WorkflowDetailsPanel.java
+RepositoryPanel.java
 file




-2012-01-10T18:25:35.000000Z
-87d171d0d49ff7a8eb55f9aef8c268ff
-2011-07-30T04:31:30.667242Z
-8187
-zji
+2011-08-17T00:19:03.000000Z
+51673eb783f47bf87acec4bc2ba46932
+2011-04-19T16:07:16.228867Z
+7751
+bellj



@@ -126,19 +126,19 @@ zji



-8700
+866

-WorkflowNode.java
+WorkflowCommentsPanel.java
 file
+8830



-
-2011-08-17T00:19:03.000000Z
-58ade80ef45c0df2e3bcb43e09fc9948
-2011-07-30T04:31:30.667242Z
-8187
-zji
+2012-02-01T23:14:45.000000Z
+1fae7a8fed3b883b044bae1403a580e4
+2012-02-01T23:18:53.227572Z
+8830
+bellj



@@ -160,18 +160,18 @@ zji



-455
+10708

-DynamicTree.java
+WorkflowDetailsPanel.java
 file




-2012-01-10T19:15:26.000000Z
-2111447f8bef7a615bb0cf73bd66f7c1
-2011-12-16T20:56:37.933310Z
-8617
+2012-01-10T18:25:35.000000Z
+87d171d0d49ff7a8eb55f9aef8c268ff
+2011-07-30T04:31:30.667242Z
+8187
 zji


@@ -194,16 +194,16 @@ zji



-12693
+8700

-InboxTablePanel.java
+WorkflowNode.java
 file




-2012-01-10T18:25:35.000000Z
-77a3d1cb5b342a013003cb71365aac2e
+2011-08-17T00:19:03.000000Z
+58ade80ef45c0df2e3bcb43e09fc9948
 2011-07-30T04:31:30.667242Z
 8187
 zji
@@ -228,7 +228,7 @@ zji



-11549
+455

 WorkflowRepository.java
 file
diff --git a/geworkbench-core/classes/org/geworkbench/components/genspace/workflowRepository/.svn/text-base/WorkflowCommentsPanel.java.svn-base b/geworkbench-core/classes/org/geworkbench/components/genspace/workflowRepository/.svn/text-base/WorkflowCommentsPanel.java.svn-base
index 69785df..0a535d8 100644
--- a/geworkbench-core/classes/org/geworkbench/components/genspace/workflowRepository/.svn/text-base/WorkflowCommentsPanel.java.svn-base
+++ b/geworkbench-core/classes/org/geworkbench/components/genspace/workflowRepository/.svn/text-base/WorkflowCommentsPanel.java.svn-base
@@ -140,7 +140,7 @@ ActionListener {

 	private void removeComment(final WorkflowComment wc,
 			final MyTableModel model) {
-		if (!wc.getCreator().equals(GenSpaceServerFactory.getUser())) {
+		if (wc.getCreator().getId() != GenSpaceServerFactory.getUser().getId()) {
 			JOptionPane.showMessageDialog(null, "You can only delete your own comments.");
 		}

@@ -149,6 +149,12 @@ ActionListener {
 				Boolean ret = GenSpaceServerFactory.getWorkflowOps()
 						.removeComment(wc.getId());
 				GenSpaceServerFactory.updateCachedUser();
+				if(GenSpaceServerFactory.isLoggedIn())
+				{
+					GenSpace.getInstance().getWorkflowRepository().repositoryPanel.tree.root = (GenSpaceServerFactory.getUserOps().getRootFolder());
+					GenSpace.getInstance().getWorkflowRepository().repositoryPanel.tree.recalculateAndReload();
+				}
+//				GenSpace.getInstance().getWorkflowRepository().updateFormFieldsBG();
 				return ret;
 			};

@@ -156,7 +162,15 @@ ActionListener {
 				try {
 					if (get()) {
 						model.removeComment(wc);
-					}
+						for(UserWorkflow w : GenSpace.getInstance().getWorkflowRepository().repositoryPanel.tree.root.getWorkflows())
+						{
+							if(w.getWorkflow().getId() == workflow.getId())
+							{
+								GenSpace.getInstance().getWorkflowRepository().workflowCommentsPanel.setData(w.getWorkflow());
+								GenSpace.getInstance().getWorkflowRepository().workflowCommentsPanel.repaint();
+							}
+						}
+				}
 				} catch (InterruptedException e) {
 					GenSpace.logger.warn("Unable to talk to server", e);
 				} catch (ExecutionException e) {
@@ -181,9 +195,8 @@ ActionListener {
 					wc.setComment(comment);
 					wc.setCreatedAt(DatatypeFactory.newInstance().newXMLGregorianCalendar(new GregorianCalendar()));
 					wc.setCreator(GenSpaceServerFactory.getUser());
-					wc.setWorkflow(workflow);
 					WorkflowComment ret =GenSpaceServerFactory.getWorkflowOps()
-							.addComment(wc);
+							.addCommentToWf(wc, workflow);
 					GenSpaceServerFactory.updateCachedUser();
 					if(GenSpaceServerFactory.isLoggedIn())
 					{
diff --git a/geworkbench-core/classes/org/geworkbench/engine/.svn/all-wcprops b/geworkbench-core/classes/org/geworkbench/engine/.svn/all-wcprops
index be406df..e00d380 100644
--- a/geworkbench-core/classes/org/geworkbench/engine/.svn/all-wcprops
+++ b/geworkbench-core/classes/org/geworkbench/engine/.svn/all-wcprops
@@ -1,7 +1,7 @@
 K 25
 svn:wc:ra_dav:version-url
 V 75
-/svn/geworkbench/!svn/ver/8534/trunk/geworkbench/src/org/geworkbench/engine
+/svn/geworkbench/!svn/ver/8726/trunk/geworkbench/src/org/geworkbench/engine
 END
 visualArea.png
 K 25
diff --git a/geworkbench-core/classes/org/geworkbench/engine/.svn/entries b/geworkbench-core/classes/org/geworkbench/engine/.svn/entries
index 13e32ac..98cb1bb 100644
--- a/geworkbench-core/classes/org/geworkbench/engine/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/engine/.svn/entries
@@ -1,14 +1,14 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/engine
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2011-11-17T16:19:54.410185Z
-8534
+2012-01-18T19:35:30.187399Z
+8726
 zji


@@ -199,6 +199,9 @@ has-props

 225

+properties
+dir
+
 visualPluginGrey.png
 file

@@ -233,7 +236,7 @@ has-props

 163

-properties
+preferences
 dir

 selectionArea.png
@@ -270,15 +273,15 @@ has-props

 224

-preferences
-dir
-
 ccm
 dir

 skin
 dir

+config
+dir
+
 visualPlugin.png
 file

@@ -313,9 +316,6 @@ has-props

 234

-config
-dir
-
 WelcomeScreen.java
 file

diff --git a/geworkbench-core/classes/org/geworkbench/engine/ccm/.svn/entries b/geworkbench-core/classes/org/geworkbench/engine/ccm/.svn/entries
index b203b1f..f83643e 100644
--- a/geworkbench-core/classes/org/geworkbench/engine/ccm/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/engine/ccm/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/engine/ccm
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/engine/config/.svn/entries b/geworkbench-core/classes/org/geworkbench/engine/config/.svn/entries
index bae3470..a27bae7 100644
--- a/geworkbench-core/classes/org/geworkbench/engine/config/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/engine/config/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/engine/config
 https://ncisvn.nci.nih.gov/svn/geworkbench

@@ -26,17 +26,17 @@ zji

 8b29bb6e-589a-435a-9a12-3ab907be3462

-UILauncher.java
+java.policy
 file




-2012-01-10T19:15:28.000000Z
-d6db60ca94f17547b8efd62dc4f8f95f
-2011-09-22T18:27:08.782243Z
-8322
-maz
+2011-08-17T00:10:50.000000Z
+7ddb05e48d53e8bdb44ed3e29e720e3f
+2005-07-28T22:36:56.000000Z
+50
+watkin
 has-props


@@ -58,18 +58,18 @@ has-props



-10369
+1127

-MenuItemInfo.java
+Bean24.gif
 file




 2011-08-17T00:10:50.000000Z
-522b03f8e0bc30c2f06f0eb0227fa026
-2005-12-19T17:14:25.000000Z
-1003
+135b090bf51203122bca26fd429051c5
+2005-07-28T22:36:56.000000Z
+50
 watkin
 has-props

@@ -92,18 +92,18 @@ has-props



-856
+737

-Bean24.gif
+MenuItemInfo.java
 file




 2011-08-17T00:10:50.000000Z
-135b090bf51203122bca26fd429051c5
-2005-07-28T22:36:56.000000Z
-50
+522b03f8e0bc30c2f06f0eb0227fa026
+2005-12-19T17:14:25.000000Z
+1003
 watkin
 has-props

@@ -126,19 +126,19 @@ has-props



-737
+856

-java.policy
+UILauncher.java
 file




-2011-08-17T00:10:50.000000Z
-7ddb05e48d53e8bdb44ed3e29e720e3f
-2005-07-28T22:36:56.000000Z
-50
-watkin
+2012-01-10T19:15:28.000000Z
+d6db60ca94f17547b8efd62dc4f8f95f
+2011-09-22T18:27:08.782243Z
+8322
+maz
 has-props


@@ -160,7 +160,7 @@ has-props



-1127
+10369

 Visualeye_Nonactive.gif
 file
@@ -264,17 +264,17 @@ has-props

 2343

-ComponentMetadata.java
+default.xml
 file




-2011-08-17T00:19:07.000000Z
-b1d5dc9df7e5979044c49adb159d61fa
-2011-05-27T16:30:27.302729Z
-7943
-zji
+2011-08-17T00:10:50.000000Z
+00175b1e46cfe48f771be687ca040e10
+2006-12-20T22:22:15.000000Z
+2117
+mhall
 has-props


@@ -296,19 +296,19 @@ has-props



-1962
+10541

-default.xml
+ComponentMetadata.java
 file




-2011-08-17T00:10:50.000000Z
-00175b1e46cfe48f771be687ca040e10
-2006-12-20T22:22:15.000000Z
-2117
-mhall
+2011-08-17T00:19:07.000000Z
+b1d5dc9df7e5979044c49adb159d61fa
+2011-05-27T16:30:27.302729Z
+7943
+zji
 has-props


@@ -330,7 +330,10 @@ has-props



-10541
+1962
+
+rules
+dir

 MenuListener.java
 file
@@ -366,9 +369,6 @@ has-props

 1106

-rules
-dir
-
 PreferencesMenu.cwb.xml
 file

diff --git a/geworkbench-core/classes/org/geworkbench/engine/config/events/.svn/entries b/geworkbench-core/classes/org/geworkbench/engine/config/events/.svn/entries
index 297bf60..94d4a7f 100644
--- a/geworkbench-core/classes/org/geworkbench/engine/config/events/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/engine/config/events/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/engine/config/events
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/engine/config/rules/.svn/entries b/geworkbench-core/classes/org/geworkbench/engine/config/rules/.svn/entries
index 03a1769..c1874d0 100644
--- a/geworkbench-core/classes/org/geworkbench/engine/config/rules/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/engine/config/rules/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/engine/config/rules
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/engine/help/.svn/entries b/geworkbench-core/classes/org/geworkbench/engine/help/.svn/entries
index cc7a80d..d136d16 100644
--- a/geworkbench-core/classes/org/geworkbench/engine/help/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/engine/help/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/engine/help
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/engine/help/caWorkbench introduction_files/.svn/entries b/geworkbench-core/classes/org/geworkbench/engine/help/caWorkbench introduction_files/.svn/entries
index e5b60a1..587f1f4 100644
--- a/geworkbench-core/classes/org/geworkbench/engine/help/caWorkbench introduction_files/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/engine/help/caWorkbench introduction_files/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/engine/help/caWorkbench%20introduction_files
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/engine/help/ccm_files/.svn/entries b/geworkbench-core/classes/org/geworkbench/engine/help/ccm_files/.svn/entries
index e095df0..f4af5fb 100644
--- a/geworkbench-core/classes/org/geworkbench/engine/help/ccm_files/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/engine/help/ccm_files/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/engine/help/ccm_files
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/engine/help/images/.svn/entries b/geworkbench-core/classes/org/geworkbench/engine/help/images/.svn/entries
index e356651..3ed2798 100644
--- a/geworkbench-core/classes/org/geworkbench/engine/help/images/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/engine/help/images/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/engine/help/images
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/engine/management/.svn/entries b/geworkbench-core/classes/org/geworkbench/engine/management/.svn/entries
index 18ee816..3edcc4c 100644
--- a/geworkbench-core/classes/org/geworkbench/engine/management/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/engine/management/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/engine/management
 https://ncisvn.nci.nih.gov/svn/geworkbench

@@ -264,14 +264,14 @@ has-props

 5549

-ComponentClassLoader.java
+TypeMap.java
 file




 2011-08-17T00:10:50.000000Z
-fec3c4a3560c164b6ec51d9de746b819
+6650e5eb166990d8578ddeaabf36680c
 2011-03-29T15:20:48.629658Z
 7680
 zji
@@ -296,16 +296,16 @@ has-props



-2142
+1540

-TypeMap.java
+ComponentClassLoader.java
 file




 2011-08-17T00:10:50.000000Z
-6650e5eb166990d8578ddeaabf36680c
+fec3c4a3560c164b6ec51d9de746b819
 2011-03-29T15:20:48.629658Z
 7680
 zji
@@ -330,7 +330,7 @@ has-props



-1540
+2142

 Subscribe.java
 file
@@ -434,16 +434,16 @@ has-props

 510

-Module.java
+ComponentObjectInputStream.java
 file




 2011-08-17T00:10:50.000000Z
-af00a7f10bf299cc18203a76f11c2805
-2005-07-28T22:36:56.000000Z
-50
+0b25699f779b889a54bb5ce0dbc1cc27
+2006-01-13T22:48:38.000000Z
+1120
 watkin
 has-props

@@ -466,18 +466,18 @@ has-props



-408
+760

-ComponentObjectInputStream.java
+Module.java
 file




 2011-08-17T00:10:50.000000Z
-0b25699f779b889a54bb5ce0dbc1cc27
-2006-01-13T22:48:38.000000Z
-1120
+af00a7f10bf299cc18203a76f11c2805
+2005-07-28T22:36:56.000000Z
+50
 watkin
 has-props

@@ -500,7 +500,7 @@ has-props



-760
+408

 Synchronous.java
 file
diff --git a/geworkbench-core/classes/org/geworkbench/engine/preferences/.svn/entries b/geworkbench-core/classes/org/geworkbench/engine/preferences/.svn/entries
index ddc53f0..920c490 100644
--- a/geworkbench-core/classes/org/geworkbench/engine/preferences/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/engine/preferences/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/engine/preferences
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/engine/properties/.svn/entries b/geworkbench-core/classes/org/geworkbench/engine/properties/.svn/entries
index 8b1fa92..2c5ae9a 100644
--- a/geworkbench-core/classes/org/geworkbench/engine/properties/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/engine/properties/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/engine/properties
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/engine/skin/.svn/all-wcprops b/geworkbench-core/classes/org/geworkbench/engine/skin/.svn/all-wcprops
index b822392..7796e9b 100644
--- a/geworkbench-core/classes/org/geworkbench/engine/skin/.svn/all-wcprops
+++ b/geworkbench-core/classes/org/geworkbench/engine/skin/.svn/all-wcprops
@@ -1,13 +1,7 @@
 K 25
 svn:wc:ra_dav:version-url
 V 80
-/svn/geworkbench/!svn/ver/8524/trunk/geworkbench/src/org/geworkbench/engine/skin
-END
-dock_active.gif
-K 25
-svn:wc:ra_dav:version-url
-V 94
-/svn/geworkbench/!svn/ver/50/trunk/geworkbench/src/org/geworkbench/engine/skin/dock_active.gif
+/svn/geworkbench/!svn/ver/8726/trunk/geworkbench/src/org/geworkbench/engine/skin
 END
 max_grey.gif
 K 25
@@ -15,29 +9,35 @@ svn:wc:ra_dav:version-url
 V 91
 /svn/geworkbench/!svn/ver/50/trunk/geworkbench/src/org/geworkbench/engine/skin/max_grey.gif
 END
+dock_active.gif
+K 25
+svn:wc:ra_dav:version-url
+V 94
+/svn/geworkbench/!svn/ver/50/trunk/geworkbench/src/org/geworkbench/engine/skin/dock_active.gif
+END
 ShortCutMenu.java
 K 25
 svn:wc:ra_dav:version-url
 V 98
 /svn/geworkbench/!svn/ver/6192/trunk/geworkbench/src/org/geworkbench/engine/skin/ShortCutMenu.java
 END
+min_active.gif
+K 25
+svn:wc:ra_dav:version-url
+V 93
+/svn/geworkbench/!svn/ver/50/trunk/geworkbench/src/org/geworkbench/engine/skin/min_active.gif
+END
 undock_active.gif
 K 25
 svn:wc:ra_dav:version-url
 V 96
 /svn/geworkbench/!svn/ver/50/trunk/geworkbench/src/org/geworkbench/engine/skin/undock_active.gif
 END
-min_active.gif
+max_active.gif
 K 25
 svn:wc:ra_dav:version-url
 V 93
-/svn/geworkbench/!svn/ver/50/trunk/geworkbench/src/org/geworkbench/engine/skin/min_active.gif
-END
-Skin.java
-K 25
-svn:wc:ra_dav:version-url
-V 90
-/svn/geworkbench/!svn/ver/8524/trunk/geworkbench/src/org/geworkbench/engine/skin/Skin.java
+/svn/geworkbench/!svn/ver/50/trunk/geworkbench/src/org/geworkbench/engine/skin/max_active.gif
 END
 dock.gif
 K 25
@@ -45,11 +45,11 @@ svn:wc:ra_dav:version-url
 V 87
 /svn/geworkbench/!svn/ver/50/trunk/geworkbench/src/org/geworkbench/engine/skin/dock.gif
 END
-max_active.gif
+Skin.java
 K 25
 svn:wc:ra_dav:version-url
-V 93
-/svn/geworkbench/!svn/ver/50/trunk/geworkbench/src/org/geworkbench/engine/skin/max_active.gif
+V 90
+/svn/geworkbench/!svn/ver/8726/trunk/geworkbench/src/org/geworkbench/engine/skin/Skin.java
 END
 Thumbs.db
 K 25
@@ -57,18 +57,18 @@ svn:wc:ra_dav:version-url
 V 88
 /svn/geworkbench/!svn/ver/50/trunk/geworkbench/src/org/geworkbench/engine/skin/Thumbs.db
 END
-undock.gif
-K 25
-svn:wc:ra_dav:version-url
-V 89
-/svn/geworkbench/!svn/ver/50/trunk/geworkbench/src/org/geworkbench/engine/skin/undock.gif
-END
 min.gif
 K 25
 svn:wc:ra_dav:version-url
 V 86
 /svn/geworkbench/!svn/ver/50/trunk/geworkbench/src/org/geworkbench/engine/skin/min.gif
 END
+undock.gif
+K 25
+svn:wc:ra_dav:version-url
+V 89
+/svn/geworkbench/!svn/ver/50/trunk/geworkbench/src/org/geworkbench/engine/skin/undock.gif
+END
 max.gif
 K 25
 svn:wc:ra_dav:version-url
diff --git a/geworkbench-core/classes/org/geworkbench/engine/skin/.svn/entries b/geworkbench-core/classes/org/geworkbench/engine/skin/.svn/entries
index 459eb7e..2b14ceb 100644
--- a/geworkbench-core/classes/org/geworkbench/engine/skin/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/engine/skin/.svn/entries
@@ -1,14 +1,14 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/engine/skin
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2011-11-14T22:19:17.648563Z
-8524
+2012-01-18T19:35:30.187399Z
+8726
 zji


@@ -26,14 +26,14 @@ zji

 8b29bb6e-589a-435a-9a12-3ab907be3462

-max_grey.gif
+dock_active.gif
 file




 2011-08-17T00:10:50.000000Z
-37db8f14e83e6f266c29097434485f5f
+3be3aea31a355eabf1c7e893d6b3d22a
 2005-07-28T22:36:56.000000Z
 50
 watkin
@@ -58,16 +58,16 @@ has-props



-82
+111

-dock_active.gif
+max_grey.gif
 file




 2011-08-17T00:10:50.000000Z
-3be3aea31a355eabf1c7e893d6b3d22a
+37db8f14e83e6f266c29097434485f5f
 2005-07-28T22:36:56.000000Z
 50
 watkin
@@ -92,7 +92,7 @@ has-props



-111
+82

 ShortCutMenu.java
 file
@@ -128,14 +128,14 @@ garbent

 666

-min_active.gif
+undock_active.gif
 file




-2011-08-17T00:10:50.000000Z
-ed7f0af14c69de0d17a21bc26d93ea7a
+2011-08-17T00:10:51.000000Z
+3fd8527e8b4eb649da68cc294bd16369
 2005-07-28T22:36:56.000000Z
 50
 watkin
@@ -160,16 +160,16 @@ has-props



-64
+109

-undock_active.gif
+min_active.gif
 file




-2011-08-17T00:10:51.000000Z
-3fd8527e8b4eb649da68cc294bd16369
+2011-08-17T00:10:50.000000Z
+ed7f0af14c69de0d17a21bc26d93ea7a
 2005-07-28T22:36:56.000000Z
 50
 watkin
@@ -194,19 +194,19 @@ has-props



-109
+64

-max_active.gif
+Skin.java
 file




-2011-08-17T00:10:50.000000Z
-cf6b900c9f4c7bba210b5fe9d85d67cd
-2005-07-28T22:36:56.000000Z
-50
-watkin
+2012-01-31T19:12:36.000000Z
+1d4a87b0a43192cc18c603d1aac06ca2
+2012-01-18T19:35:30.187399Z
+8726
+zji
 has-props


@@ -228,7 +228,7 @@ has-props



-82
+30452

 dock.gif
 file
@@ -264,17 +264,17 @@ has-props

 110

-Skin.java
+max_active.gif
 file




-2012-01-10T19:15:28.000000Z
-e442eb4db9b7c13c8986539498efefe1
-2011-11-14T22:19:17.648563Z
-8524
-zji
+2011-08-17T00:10:50.000000Z
+cf6b900c9f4c7bba210b5fe9d85d67cd
+2005-07-28T22:36:56.000000Z
+50
+watkin
 has-props


@@ -296,7 +296,7 @@ has-props



-30254
+82

 Thumbs.db
 file
@@ -332,14 +332,14 @@ has-props

 6

-min.gif
+undock.gif
 file




 2011-08-17T00:10:50.000000Z
-be0cc739070bb9279091e2419fa14057
+e7356e5312d1a2d080473af4ad766fd9
 2005-07-28T22:36:56.000000Z
 50
 watkin
@@ -364,16 +364,16 @@ has-props



-64
+108

-undock.gif
+min.gif
 file




 2011-08-17T00:10:50.000000Z
-e7356e5312d1a2d080473af4ad766fd9
+be0cc739070bb9279091e2419fa14057
 2005-07-28T22:36:56.000000Z
 50
 watkin
@@ -398,7 +398,7 @@ has-props



-108
+64

 max.gif
 file
diff --git a/geworkbench-core/classes/org/geworkbench/engine/skin/.svn/text-base/Skin.java.svn-base b/geworkbench-core/classes/org/geworkbench/engine/skin/.svn/text-base/Skin.java.svn-base
index ad85480..0c54463 100644
--- a/geworkbench-core/classes/org/geworkbench/engine/skin/.svn/text-base/Skin.java.svn-base
+++ b/geworkbench-core/classes/org/geworkbench/engine/skin/.svn/text-base/Skin.java.svn-base
@@ -669,7 +669,11 @@ public class Skin extends GUIFramework {
                 if (acceptors.contains(mainclass)) {
                     log.trace("Found component in "+screenRegion+" to show: " + mainclass.toString());
                     PluginDescriptor desc = ComponentRegistry.getRegistry().getDescriptorForPluginClass(mainclass);
-                    tabsToAdd.put(desc.getPreferredOrder(), component);
+                    int order = desc.getPreferredOrder();
+                    if(desc.getID().equals("informationPanel")) {
+                    	order = 100; // force information panel to behind
+                    }
+                    tabsToAdd.put(order, component);
                 }
             }
         }
diff --git a/geworkbench-core/classes/org/geworkbench/events/.svn/entries b/geworkbench-core/classes/org/geworkbench/events/.svn/entries
index 228e3b0..84b94a5 100644
--- a/geworkbench-core/classes/org/geworkbench/events/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/events/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/events
 https://ncisvn.nci.nih.gov/svn/geworkbench

@@ -672,17 +672,17 @@ has-props

 726

-AdjacencyMatrixCancelEvent.java
+PhenotypeSelectorEvent.java
 file




 2011-08-17T00:10:51.000000Z
-85ea53ecafcbb2b1cd74783c1a5dfad2
-2011-04-20T14:24:06.365699Z
-7757
-zji
+309301dfd1e65389f91b64c061c1abe5
+2006-01-13T22:48:38.000000Z
+1120
+watkin
 has-props


@@ -704,19 +704,19 @@ has-props



-714
+1000

-PhenotypeSelectorEvent.java
+AdjacencyMatrixCancelEvent.java
 file




 2011-08-17T00:10:51.000000Z
-309301dfd1e65389f91b64c061c1abe5
-2006-01-13T22:48:38.000000Z
-1120
-watkin
+85ea53ecafcbb2b1cd74783c1a5dfad2
+2011-04-20T14:24:06.365699Z
+7757
+zji
 has-props


@@ -738,7 +738,7 @@ has-props



-1000
+714

 CaArrayReturnHybridizationListEvent.java
 file
diff --git a/geworkbench-core/classes/org/geworkbench/events/listeners/.svn/entries b/geworkbench-core/classes/org/geworkbench/events/listeners/.svn/entries
index 5bd9abd..eee6d53 100644
--- a/geworkbench-core/classes/org/geworkbench/events/listeners/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/events/listeners/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/events/listeners
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/parsers/.svn/all-wcprops b/geworkbench-core/classes/org/geworkbench/parsers/.svn/all-wcprops
index fbbb1fb..890577d 100644
--- a/geworkbench-core/classes/org/geworkbench/parsers/.svn/all-wcprops
+++ b/geworkbench-core/classes/org/geworkbench/parsers/.svn/all-wcprops
@@ -1,13 +1,13 @@
 K 25
 svn:wc:ra_dav:version-url
 V 76
-/svn/geworkbench/!svn/ver/8668/trunk/geworkbench/src/org/geworkbench/parsers
+/svn/geworkbench/!svn/ver/8807/trunk/geworkbench/src/org/geworkbench/parsers
 END
 MicroarraySetParser.java
 K 25
 svn:wc:ra_dav:version-url
 V 101
-/svn/geworkbench/!svn/ver/8527/trunk/geworkbench/src/org/geworkbench/parsers/MicroarraySetParser.java
+/svn/geworkbench/!svn/ver/8761/trunk/geworkbench/src/org/geworkbench/parsers/MicroarraySetParser.java
 END
 SOFTSeriesParser.java
 K 25
@@ -15,23 +15,17 @@ svn:wc:ra_dav:version-url
 V 98
 /svn/geworkbench/!svn/ver/8621/trunk/geworkbench/src/org/geworkbench/parsers/SOFTSeriesParser.java
 END
-PlatformChooser.java
-K 25
-svn:wc:ra_dav:version-url
-V 97
-/svn/geworkbench/!svn/ver/7592/trunk/geworkbench/src/org/geworkbench/parsers/PlatformChooser.java
-END
 ExpressionResource.java
 K 25
 svn:wc:ra_dav:version-url
 V 100
 /svn/geworkbench/!svn/ver/7105/trunk/geworkbench/src/org/geworkbench/parsers/ExpressionResource.java
 END
-GenePixFileFormat.java
+PlatformChooser.java
 K 25
 svn:wc:ra_dav:version-url
-V 99
-/svn/geworkbench/!svn/ver/8463/trunk/geworkbench/src/org/geworkbench/parsers/GenePixFileFormat.java
+V 97
+/svn/geworkbench/!svn/ver/7592/trunk/geworkbench/src/org/geworkbench/parsers/PlatformChooser.java
 END
 ExpressionFileFormat.java
 K 25
@@ -39,11 +33,11 @@ svn:wc:ra_dav:version-url
 V 102
 /svn/geworkbench/!svn/ver/8430/trunk/geworkbench/src/org/geworkbench/parsers/ExpressionFileFormat.java
 END
-MageTabFileFormat.java
+GenePixFileFormat.java
 K 25
 svn:wc:ra_dav:version-url
 V 99
-/svn/geworkbench/!svn/ver/8604/trunk/geworkbench/src/org/geworkbench/parsers/MageTabFileFormat.java
+/svn/geworkbench/!svn/ver/8463/trunk/geworkbench/src/org/geworkbench/parsers/GenePixFileFormat.java
 END
 EdgeListFileFormat.java
 K 25
@@ -51,6 +45,12 @@ svn:wc:ra_dav:version-url
 V 100
 /svn/geworkbench/!svn/ver/7664/trunk/geworkbench/src/org/geworkbench/parsers/EdgeListFileFormat.java
 END
+MageTabFileFormat.java
+K 25
+svn:wc:ra_dav:version-url
+V 99
+/svn/geworkbench/!svn/ver/8807/trunk/geworkbench/src/org/geworkbench/parsers/MageTabFileFormat.java
+END
 CELFileFormat.java
 K 25
 svn:wc:ra_dav:version-url
@@ -63,23 +63,23 @@ svn:wc:ra_dav:version-url
 V 95
 /svn/geworkbench/!svn/ver/8559/trunk/geworkbench/src/org/geworkbench/parsers/PDBFileFormat.java
 END
-AdjacencyMatrixFileFormat.java
+TabDelimitedDataMatrixFileFormat.java
 K 25
 svn:wc:ra_dav:version-url
-V 107
-/svn/geworkbench/!svn/ver/8348/trunk/geworkbench/src/org/geworkbench/parsers/AdjacencyMatrixFileFormat.java
+V 114
+/svn/geworkbench/!svn/ver/8795/trunk/geworkbench/src/org/geworkbench/parsers/TabDelimitedDataMatrixFileFormat.java
 END
-TabDelimitedDataMatrixFileFormat.java
+AdjacencyMatrixFileFormat.java
 K 25
 svn:wc:ra_dav:version-url
-V 114
-/svn/geworkbench/!svn/ver/8621/trunk/geworkbench/src/org/geworkbench/parsers/TabDelimitedDataMatrixFileFormat.java
+V 107
+/svn/geworkbench/!svn/ver/8348/trunk/geworkbench/src/org/geworkbench/parsers/AdjacencyMatrixFileFormat.java
 END
 SOFTFileFormat.java
 K 25
 svn:wc:ra_dav:version-url
 V 96
-/svn/geworkbench/!svn/ver/8621/trunk/geworkbench/src/org/geworkbench/parsers/SOFTFileFormat.java
+/svn/geworkbench/!svn/ver/8807/trunk/geworkbench/src/org/geworkbench/parsers/SOFTFileFormat.java
 END
 PatternFileFormat.java
 K 25
@@ -121,5 +121,5 @@ SampleFileParser.java
 K 25
 svn:wc:ra_dav:version-url
 V 98
-/svn/geworkbench/!svn/ver/8621/trunk/geworkbench/src/org/geworkbench/parsers/SampleFileParser.java
+/svn/geworkbench/!svn/ver/8749/trunk/geworkbench/src/org/geworkbench/parsers/SampleFileParser.java
 END
diff --git a/geworkbench-core/classes/org/geworkbench/parsers/.svn/entries b/geworkbench-core/classes/org/geworkbench/parsers/.svn/entries
index abacb6a..6591325 100644
--- a/geworkbench-core/classes/org/geworkbench/parsers/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/parsers/.svn/entries
@@ -1,15 +1,15 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/parsers
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2012-01-06T22:02:05.925589Z
-8668
-poddutun
+2012-01-27T22:43:49.471007Z
+8807
+zji



@@ -32,10 +32,10 @@ file



-2012-01-10T19:15:28.000000Z
-201494997012cc12386adf2733b63654
-2011-11-16T16:03:46.079217Z
-8527
+2012-01-31T19:12:35.000000Z
+b29c89a55e94b1c3c4aa114dbeba9655
+2012-01-25T17:34:14.733766Z
+8761
 zji
 has-props

@@ -58,7 +58,7 @@ has-props



-11084
+11027

 SOFTSeriesParser.java
 file
@@ -94,16 +94,16 @@ has-props

 11459

-PlatformChooser.java
+ExpressionResource.java
 file




 2011-08-17T00:10:51.000000Z
-363b1347d4055e894aea846bc442082d
-2011-03-16T21:34:19.127070Z
-7592
+b9456cfa7785ac5b95d138377ecc1b23
+2010-10-08T19:08:39.167748Z
+7105
 zji
 has-props

@@ -126,18 +126,18 @@ has-props



-691
+940

-ExpressionResource.java
+PlatformChooser.java
 file




 2011-08-17T00:10:51.000000Z
-b9456cfa7785ac5b95d138377ecc1b23
-2010-10-08T19:08:39.167748Z
-7105
+363b1347d4055e894aea846bc442082d
+2011-03-16T21:34:19.127070Z
+7592
 zji
 has-props

@@ -160,18 +160,18 @@ has-props



-940
+691

-GenePixFileFormat.java
+ExpressionFileFormat.java
 file




 2012-01-10T19:15:28.000000Z
-8f175a625e3b6c8651ce4a1c67c59a19
-2011-10-25T21:47:59.095740Z
-8463
+9f0dce1dae4ed4fe95c36315c1efb6a6
+2011-10-19T19:21:07.649034Z
+8430
 zji
 has-props

@@ -194,18 +194,18 @@ has-props



-7032
+2475

-ExpressionFileFormat.java
+GenePixFileFormat.java
 file




 2012-01-10T19:15:28.000000Z
-9f0dce1dae4ed4fe95c36315c1efb6a6
-2011-10-19T19:21:07.649034Z
-8430
+8f175a625e3b6c8651ce4a1c67c59a19
+2011-10-25T21:47:59.095740Z
+8463
 zji
 has-props

@@ -228,19 +228,19 @@ has-props



-2475
+7032

-MageTabFileFormat.java
+EdgeListFileFormat.java
 file




-2012-01-10T19:15:28.000000Z
-8006a4328a87b79dfae95335e07b79f0
-2011-12-15T16:27:43.198334Z
-8604
-poddutun
+2011-08-17T00:10:51.000000Z
+c689d99d455c63e1acc372fb40e0726b
+2011-03-28T15:46:41.850577Z
+7664
+zji
 has-props


@@ -262,18 +262,18 @@ has-props



-15770
+9393

-EdgeListFileFormat.java
+MageTabFileFormat.java
 file




-2011-08-17T00:10:51.000000Z
-c689d99d455c63e1acc372fb40e0726b
-2011-03-28T15:46:41.850577Z
-7664
+2012-01-31T19:12:35.000000Z
+592031d5c15dd7b7d679dcbaa9965d13
+2012-01-27T22:43:49.471007Z
+8807
 zji
 has-props

@@ -296,7 +296,7 @@ has-props



-9393
+15839

 sequences
 dir
@@ -369,16 +369,16 @@ has-props

 2816

-AdjacencyMatrixFileFormat.java
+TabDelimitedDataMatrixFileFormat.java
 file




-2012-01-10T19:15:28.000000Z
-c886d13602a76971a9c106c64cb9104e
-2011-09-27T20:18:47.190462Z
-8348
+2012-01-31T19:12:35.000000Z
+2dbd0528b77a6014a4e9d58db7145ae5
+2012-01-27T19:28:26.078686Z
+8795
 zji
 has-props

@@ -401,19 +401,19 @@ has-props



-13294
+15035

-TabDelimitedDataMatrixFileFormat.java
+AdjacencyMatrixFileFormat.java
 file




 2012-01-10T19:15:28.000000Z
-8cfcfd9df6af7eded70ff143b9c4e34c
-2011-12-19T19:24:01.356405Z
-8621
-youmi
+c886d13602a76971a9c106c64cb9104e
+2011-09-27T20:18:47.190462Z
+8348
+zji
 has-props


@@ -435,7 +435,7 @@ has-props



-14886
+13294

 SOFTFileFormat.java
 file
@@ -443,11 +443,11 @@ file



-2012-01-10T19:15:28.000000Z
-12c3378554d62f8c88af639b3d5da326
-2011-12-19T19:24:01.356405Z
-8621
-youmi
+2012-01-31T19:12:35.000000Z
+bd173e6923c129e15714824213b145c8
+2012-01-27T22:43:49.471007Z
+8807
+zji
 has-props


@@ -469,7 +469,7 @@ has-props



-16046
+16101

 PatternFileFormat.java
 file
@@ -681,11 +681,11 @@ file



-2012-01-10T19:15:28.000000Z
-70877ab24b702de65cad2f9a38c6bb76
-2011-12-19T19:24:01.356405Z
-8621
-youmi
+2012-01-31T19:12:35.000000Z
+80c648e916c0187e7240dbf6319ca7cd
+2012-01-23T16:51:28.101508Z
+8749
+wangmen
 has-props


@@ -707,5 +707,5 @@ has-props



-10493
+10475

diff --git a/geworkbench-core/classes/org/geworkbench/parsers/.svn/text-base/MageTabFileFormat.java.svn-base b/geworkbench-core/classes/org/geworkbench/parsers/.svn/text-base/MageTabFileFormat.java.svn-base
index 363da1e..7c377d9 100644
--- a/geworkbench-core/classes/org/geworkbench/parsers/.svn/text-base/MageTabFileFormat.java.svn-base
+++ b/geworkbench-core/classes/org/geworkbench/parsers/.svn/text-base/MageTabFileFormat.java.svn-base
@@ -458,4 +458,8 @@ public class MageTabFileFormat extends DataSetFileFormat {
 			return returnVal;
 		}
 	}
+
+	@Override
+	public boolean isMergeSupported() {return false;}
+
 }
diff --git a/geworkbench-core/classes/org/geworkbench/parsers/.svn/text-base/MicroarraySetParser.java.svn-base b/geworkbench-core/classes/org/geworkbench/parsers/.svn/text-base/MicroarraySetParser.java.svn-base
index e148aeb..de3e8fb 100644
--- a/geworkbench-core/classes/org/geworkbench/parsers/.svn/text-base/MicroarraySetParser.java.svn-base
+++ b/geworkbench-core/classes/org/geworkbench/parsers/.svn/text-base/MicroarraySetParser.java.svn-base
@@ -125,6 +125,10 @@ public class MicroarraySetParser {
 			CSAnnotationContext.initializePhenotypeContext(context);
 			String[] labels = arrayInfo.get(phLabel);
 			for (int arrayIndex = 0; arrayIndex < labels.length; arrayIndex++) {
+				if (labels[arrayIndex] == null
+						|| labels[arrayIndex].length() == 0)
+					continue;
+
 				if (labels[arrayIndex].indexOf("|") > -1) {
 					for (String tok : labels[arrayIndex].split("\\|")) {
 						context.labelItem(microarraySet.get(arrayIndex), tok);
@@ -225,17 +229,13 @@ public class MicroarraySetParser {
 			}
 		} else if (line.substring(0, 11).equalsIgnoreCase("Description")) {
 			// This handles all the phenotype definition lines
-			String phLabel = new String(secondField);
-			List<String> labels = new ArrayList<String>();
-			while (tokenizer.hasMoreTokens()) {
-				String valueLabel = new String(tokenizer.nextToken());
-				if ((valueLabel != null) && (!valueLabel.equalsIgnoreCase(""))) {
-					labels.add( valueLabel );
-				}
-			}
-			if(labels.size()==arrayNames.size()) {
-				arrayInfo.put(phLabel, labels.toArray(new String[0]));
+			String[] f = line.split("\t", -1);
+			String[] labels = new String[(arrayNames.size())];
+			for(int i=0; i<Math.min(labels.length, f.length-2); i++) {
+				labels[i] = f[i+2];
 			}
+			String phLabel = new String(f[1]);
+			arrayInfo.put(phLabel, labels);
 		} else if (line.charAt(0) != '\t') {

 			CSExpressionMarker marker = new CSExpressionMarker(markerNumber);
diff --git a/geworkbench-core/classes/org/geworkbench/parsers/.svn/text-base/SOFTFileFormat.java.svn-base b/geworkbench-core/classes/org/geworkbench/parsers/.svn/text-base/SOFTFileFormat.java.svn-base
index f46482d..5fb69f6 100644
--- a/geworkbench-core/classes/org/geworkbench/parsers/.svn/text-base/SOFTFileFormat.java.svn-base
+++ b/geworkbench-core/classes/org/geworkbench/parsers/.svn/text-base/SOFTFileFormat.java.svn-base
@@ -494,4 +494,7 @@ public class SOFTFileFormat extends DataSetFileFormat {
 			return returnVal;
 		}
 	}
+
+	public boolean isMergeSupported() {return false;}
+
 }
diff --git a/geworkbench-core/classes/org/geworkbench/parsers/.svn/text-base/SampleFileParser.java.svn-base b/geworkbench-core/classes/org/geworkbench/parsers/.svn/text-base/SampleFileParser.java.svn-base
index 81c0aa9..3c86f02 100644
--- a/geworkbench-core/classes/org/geworkbench/parsers/.svn/text-base/SampleFileParser.java.svn-base
+++ b/geworkbench-core/classes/org/geworkbench/parsers/.svn/text-base/SampleFileParser.java.svn-base
@@ -93,9 +93,8 @@ public class SampleFileParser {
 							String temP1 = temp[0].trim();
 							if(temP1.equals("!Sample_title")){
 								String temp1 = tempName
-												+ " ("
-												+temp[1].trim()
-												+")";
+												+ ": "
+												+temp[1].trim();
 								arrayName = temp1;
 							}
 						}
diff --git a/geworkbench-core/classes/org/geworkbench/parsers/.svn/text-base/TabDelimitedDataMatrixFileFormat.java.svn-base b/geworkbench-core/classes/org/geworkbench/parsers/.svn/text-base/TabDelimitedDataMatrixFileFormat.java.svn-base
index 2f09b67..b3b88d4 100644
--- a/geworkbench-core/classes/org/geworkbench/parsers/.svn/text-base/TabDelimitedDataMatrixFileFormat.java.svn-base
+++ b/geworkbench-core/classes/org/geworkbench/parsers/.svn/text-base/TabDelimitedDataMatrixFileFormat.java.svn-base
@@ -206,18 +206,26 @@ public class TabDelimitedDataMatrixFileFormat extends DataSetFileFormat {
 	 *
 	 * @see org.geworkbench.components.parsers.microarray.DataSetFileFormat#getDataFile(java.io.File)
 	 */
+	@Override
 	public DSDataSet<? extends DSBioObject> getDataFile(File file) throws InputFileFormatException, InterruptedIOException{

-		  return (DSDataSet<? extends DSBioObject>) getMArraySet(file);
+		  return (DSDataSet<? extends DSBioObject>) getMArraySet(file, null);

 	}
+
+	@Override
+	public DSDataSet<? extends DSBioObject> getDataFile(File file,
+			String compatibilityLabel) throws InputFileFormatException,
+			InterruptedIOException {
+		  return (DSDataSet<? extends DSBioObject>) getMArraySet(file, compatibilityLabel);
+	}

 	/*
 	 * (non-Javadoc)
 	 *
 	 * @see org.geworkbench.components.parsers.FileFormat#getMArraySet(java.io.File)
 	 */
-	private CSMicroarraySet getMArraySet(File file)
+	private CSMicroarraySet getMArraySet(File file, String compatibilityLabel)
 			throws InputFileFormatException, InterruptedIOException {

 		try
@@ -380,18 +388,12 @@ public class TabDelimitedDataMatrixFileFormat extends DataSetFileFormat {
 					line = StringUtils.replace(line, "\"", "");
 				}
 				// Set chip-type
-				String result = null;
-				for (int i = 0; i < m; i++) {
-					result = AffyAnnotationUtil.matchAffyAnnotationFile(maSet);
-					if (result != null) {
-						break;
-					}
-				}
-				if (result == null) {
+				if (compatibilityLabel == null) {
 					AffyAnnotationUtil.matchAffyAnnotationFile(maSet);
 				} else {
-					maSet.setCompatibilityLabel(result);
+					maSet.setCompatibilityLabel(compatibilityLabel);
 				}
+
 				for (DSGeneMarker marker : maSet.getMarkers()) {
 					String token = marker.getLabel();
 					String[] locusResult = AnnotationParser.getInfo(token,
diff --git a/geworkbench-core/classes/org/geworkbench/parsers/sequences/.svn/all-wcprops b/geworkbench-core/classes/org/geworkbench/parsers/sequences/.svn/all-wcprops
index c265d98..10a6afb 100644
--- a/geworkbench-core/classes/org/geworkbench/parsers/sequences/.svn/all-wcprops
+++ b/geworkbench-core/classes/org/geworkbench/parsers/sequences/.svn/all-wcprops
@@ -1,7 +1,7 @@
 K 25
 svn:wc:ra_dav:version-url
 V 86
-/svn/geworkbench/!svn/ver/7661/trunk/geworkbench/src/org/geworkbench/parsers/sequences
+/svn/geworkbench/!svn/ver/8688/trunk/geworkbench/src/org/geworkbench/parsers/sequences
 END
 SequenceResource.java
 K 25
@@ -13,5 +13,5 @@ SequenceFileFormat.java
 K 25
 svn:wc:ra_dav:version-url
 V 110
-/svn/geworkbench/!svn/ver/7661/trunk/geworkbench/src/org/geworkbench/parsers/sequences/SequenceFileFormat.java
+/svn/geworkbench/!svn/ver/8688/trunk/geworkbench/src/org/geworkbench/parsers/sequences/SequenceFileFormat.java
 END
diff --git a/geworkbench-core/classes/org/geworkbench/parsers/sequences/.svn/entries b/geworkbench-core/classes/org/geworkbench/parsers/sequences/.svn/entries
index a2fbf8a..76748dd 100644
--- a/geworkbench-core/classes/org/geworkbench/parsers/sequences/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/parsers/sequences/.svn/entries
@@ -1,15 +1,15 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/parsers/sequences
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2011-03-28T14:19:10.040004Z
-7661
-zji
+2012-01-11T16:49:19.397839Z
+8688
+youmi



@@ -66,11 +66,11 @@ file



-2011-08-17T00:10:51.000000Z
-5749f880fd40e1cfc0d38c38c2f0dea1
-2011-03-28T14:19:10.040004Z
-7661
-zji
+2012-01-31T19:12:35.000000Z
+6d89237514e029c03081e3130f08dfec
+2012-01-11T16:49:19.397839Z
+8688
+youmi
 has-props


@@ -92,5 +92,5 @@ has-props



-4637
+5146

diff --git a/geworkbench-core/classes/org/geworkbench/parsers/sequences/.svn/text-base/SequenceFileFormat.java.svn-base b/geworkbench-core/classes/org/geworkbench/parsers/sequences/.svn/text-base/SequenceFileFormat.java.svn-base
index 0b622e2..2da66ef 100644
--- a/geworkbench-core/classes/org/geworkbench/parsers/sequences/.svn/text-base/SequenceFileFormat.java.svn-base
+++ b/geworkbench-core/classes/org/geworkbench/parsers/sequences/.svn/text-base/SequenceFileFormat.java.svn-base
@@ -72,7 +72,21 @@ public class SequenceFileFormat extends DataSetFileFormat {
             BufferedReader rd = new BufferedReader(new FileReader(file));
             try {
                 String str = null;
-
+
+                //check If the description line is missing
+                while ((str = rd.readLine()) != null){
+                    String trim = str.trim();
+                    if (trim.length() == 0){
+                        continue;
+                    }
+                    if (trim.charAt(0) != '>')
+                    	return false;
+                    else
+                    	break;
+
+                }
+
+                // check FASTA format
                 while ((str = rd.readLine()) != null){
                     String trim = str.trim();

diff --git a/geworkbench-core/classes/org/geworkbench/util/.svn/all-wcprops b/geworkbench-core/classes/org/geworkbench/util/.svn/all-wcprops
index ae932f3..51c98d4 100644
--- a/geworkbench-core/classes/org/geworkbench/util/.svn/all-wcprops
+++ b/geworkbench-core/classes/org/geworkbench/util/.svn/all-wcprops
@@ -1,7 +1,7 @@
 K 25
 svn:wc:ra_dav:version-url
 V 73
-/svn/geworkbench/!svn/ver/8675/trunk/geworkbench/src/org/geworkbench/util
+/svn/geworkbench/!svn/ver/8803/trunk/geworkbench/src/org/geworkbench/util
 END
 SaveImage.java
 K 25
@@ -99,11 +99,11 @@ svn:wc:ra_dav:version-url
 V 89
 /svn/geworkbench/!svn/ver/50/trunk/geworkbench/src/org/geworkbench/util/Combinations.java
 END
-Debug.java
+ProgressGraph.java
 K 25
 svn:wc:ra_dav:version-url
-V 82
-/svn/geworkbench/!svn/ver/50/trunk/geworkbench/src/org/geworkbench/util/Debug.java
+V 92
+/svn/geworkbench/!svn/ver/7667/trunk/geworkbench/src/org/geworkbench/util/ProgressGraph.java
 END
 ColorScale.java
 K 25
@@ -111,11 +111,11 @@ svn:wc:ra_dav:version-url
 V 89
 /svn/geworkbench/!svn/ver/4717/trunk/geworkbench/src/org/geworkbench/util/ColorScale.java
 END
-ProgressGraph.java
+Debug.java
 K 25
 svn:wc:ra_dav:version-url
-V 92
-/svn/geworkbench/!svn/ver/7667/trunk/geworkbench/src/org/geworkbench/util/ProgressGraph.java
+V 82
+/svn/geworkbench/!svn/ver/50/trunk/geworkbench/src/org/geworkbench/util/Debug.java
 END
 ProgressTask.java
 K 25
@@ -141,11 +141,11 @@ svn:wc:ra_dav:version-url
 V 98
 /svn/geworkbench/!svn/ver/7667/trunk/geworkbench/src/org/geworkbench/util/ClassifierException.java
 END
-UnAuthenticatedException.java
+ResultSetlUtil.java
 K 25
 svn:wc:ra_dav:version-url
-V 103
-/svn/geworkbench/!svn/ver/7959/trunk/geworkbench/src/org/geworkbench/util/UnAuthenticatedException.java
+V 93
+/svn/geworkbench/!svn/ver/8325/trunk/geworkbench/src/org/geworkbench/util/ResultSetlUtil.java
 END
 PropertiesMonitor.java
 K 25
@@ -153,11 +153,11 @@ svn:wc:ra_dav:version-url
 V 96
 /svn/geworkbench/!svn/ver/7667/trunk/geworkbench/src/org/geworkbench/util/PropertiesMonitor.java
 END
-ResultSetlUtil.java
+UnAuthenticatedException.java
 K 25
 svn:wc:ra_dav:version-url
-V 93
-/svn/geworkbench/!svn/ver/8325/trunk/geworkbench/src/org/geworkbench/util/ResultSetlUtil.java
+V 103
+/svn/geworkbench/!svn/ver/7959/trunk/geworkbench/src/org/geworkbench/util/UnAuthenticatedException.java
 END
 IndexSortComparator.java
 K 25
@@ -253,7 +253,7 @@ splashscreen.png
 K 25
 svn:wc:ra_dav:version-url
 V 90
-/svn/geworkbench/!svn/ver/7925/trunk/geworkbench/src/org/geworkbench/util/splashscreen.png
+/svn/geworkbench/!svn/ver/8803/trunk/geworkbench/src/org/geworkbench/util/splashscreen.png
 END
 TrainingTask.java
 K 25
diff --git a/geworkbench-core/classes/org/geworkbench/util/.svn/entries b/geworkbench-core/classes/org/geworkbench/util/.svn/entries
index 4209a2a..e7defb8 100644
--- a/geworkbench-core/classes/org/geworkbench/util/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/util/.svn/entries
@@ -1,15 +1,15 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/util
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2012-01-09T20:51:15.137498Z
-8675
-zji
+2012-01-27T20:57:15.487943Z
+8803
+maz



@@ -409,18 +409,17 @@ has-props

 2066

-AffyAnnotationUtil.java
+FilePathnameUtils.java
 file




-2012-01-10T19:15:28.000000Z
-4a26ede883b796a67c00e11fe31811f5
-2011-10-20T19:33:36.413507Z
-8445
-zji
-has-props
+2012-01-10T18:25:40.000000Z
+616c35def77148fd9a9582a61580a1cd
+2011-08-12T20:13:33.179054Z
+8212
+poddutun



@@ -441,20 +440,21 @@ has-props



-6408
+
+10119

-FilePathnameUtils.java
+AffyAnnotationUtil.java
 file




-2012-01-10T18:25:40.000000Z
-616c35def77148fd9a9582a61580a1cd
-2011-08-12T20:13:33.179054Z
-8212
-poddutun
-
+2012-01-10T19:15:28.000000Z
+4a26ede883b796a67c00e11fe31811f5
+2011-10-20T19:33:36.413507Z
+8445
+zji
+has-props



@@ -475,10 +475,7 @@ poddutun



-10119
-
-patterns
-dir
+6408

 RandomSequenceGenerator.java
 file
@@ -514,7 +511,7 @@ has-props

 4074

-associationdiscovery
+patterns
 dir

 ProgressDialog.java
@@ -551,6 +548,9 @@ has-props

 4093

+associationdiscovery
+dir
+
 Combinations.java
 file

@@ -585,17 +585,17 @@ has-props

 2303

-Debug.java
+ProgressGraph.java
 file




 2011-08-17T00:10:51.000000Z
-9c2289786f490f37c8408abe39c79e92
-2005-07-28T22:36:56.000000Z
-50
-watkin
+9f081bc3883005d028377d023e3b5259
+2011-03-28T19:04:31.299317Z
+7667
+zji
 has-props


@@ -617,7 +617,7 @@ has-props



-715
+6034

 ColorScale.java
 file
@@ -653,17 +653,17 @@ jiz

 2229

-ProgressGraph.java
+Debug.java
 file




 2011-08-17T00:10:51.000000Z
-9f081bc3883005d028377d023e3b5259
-2011-03-28T19:04:31.299317Z
-7667
-zji
+9c2289786f490f37c8408abe39c79e92
+2005-07-28T22:36:56.000000Z
+50
+watkin
 has-props


@@ -685,7 +685,7 @@ has-props



-6034
+715

 ProgressTask.java
 file
@@ -823,17 +823,18 @@ has-props

 345

-ResultSetlUtil.java
+PropertiesMonitor.java
 file




-2012-01-10T18:25:40.000000Z
-3718dff712bb3d84afd960f251a51d4a
-2011-09-22T19:47:09.833255Z
-8325
+2011-08-17T00:10:51.000000Z
+1ac06043b6b8d01c5442de40d0dba3b3
+2011-03-28T19:04:31.299317Z
+7667
 zji
+has-props



@@ -854,8 +855,7 @@ zji



-
-6444
+5929

 UnAuthenticatedException.java
 file
@@ -891,18 +891,17 @@ youmi

 655

-PropertiesMonitor.java
+ResultSetlUtil.java
 file




-2011-08-17T00:10:51.000000Z
-1ac06043b6b8d01c5442de40d0dba3b3
-2011-03-28T19:04:31.299317Z
-7667
+2012-01-10T18:25:40.000000Z
+3718dff712bb3d84afd960f251a51d4a
+2011-09-22T19:47:09.833255Z
+8325
 zji
-has-props



@@ -923,7 +922,8 @@ has-props



-5929
+
+6444

 IndexSortComparator.java
 file
@@ -1450,11 +1450,11 @@ file



-2011-08-17T00:19:07.000000Z
-78bebc8179b97b383dcc2f3d1b9b7a8f
-2011-05-25T14:25:11.688972Z
-7925
-zji
+2012-01-31T19:12:36.000000Z
+0f3ba32dbd1ae07158c65474d2e04522
+2012-01-27T20:57:15.487943Z
+8803
+maz
 has-props


@@ -1476,7 +1476,7 @@ has-props



-270164
+271290

 TrainingTask.java
 file
diff --git a/geworkbench-core/classes/org/geworkbench/util/.svn/text-base/splashscreen.png.svn-base b/geworkbench-core/classes/org/geworkbench/util/.svn/text-base/splashscreen.png.svn-base
index c56d46a..bce7b97 100644
Binary files a/geworkbench-core/classes/org/geworkbench/util/.svn/text-base/splashscreen.png.svn-base and b/geworkbench-core/classes/org/geworkbench/util/.svn/text-base/splashscreen.png.svn-base differ
diff --git a/geworkbench-core/classes/org/geworkbench/util/annotation/.svn/entries b/geworkbench-core/classes/org/geworkbench/util/annotation/.svn/entries
index 7841dc8..1024511 100644
--- a/geworkbench-core/classes/org/geworkbench/util/annotation/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/util/annotation/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/util/annotation
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/util/associationdiscovery/.svn/entries b/geworkbench-core/classes/org/geworkbench/util/associationdiscovery/.svn/entries
index dfbb3c1..54692a7 100644
--- a/geworkbench-core/classes/org/geworkbench/util/associationdiscovery/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/util/associationdiscovery/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/util/associationdiscovery
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/util/associationdiscovery/cluster/.svn/entries b/geworkbench-core/classes/org/geworkbench/util/associationdiscovery/cluster/.svn/entries
index 121f53b..109ce5d 100644
--- a/geworkbench-core/classes/org/geworkbench/util/associationdiscovery/cluster/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/util/associationdiscovery/cluster/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/util/associationdiscovery/cluster
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/util/associationdiscovery/statistics/.svn/entries b/geworkbench-core/classes/org/geworkbench/util/associationdiscovery/statistics/.svn/entries
index 8a6a20c..ea01802 100644
--- a/geworkbench-core/classes/org/geworkbench/util/associationdiscovery/statistics/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/util/associationdiscovery/statistics/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/util/associationdiscovery/statistics
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/util/microarrayutils/.svn/entries b/geworkbench-core/classes/org/geworkbench/util/microarrayutils/.svn/entries
index 40e8d67..69aae30 100644
--- a/geworkbench-core/classes/org/geworkbench/util/microarrayutils/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/util/microarrayutils/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/util/microarrayutils
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/util/network/.svn/entries b/geworkbench-core/classes/org/geworkbench/util/network/.svn/entries
index e16f9f3..a3f1d64 100644
--- a/geworkbench-core/classes/org/geworkbench/util/network/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/util/network/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/util/network
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/util/pathwaydecoder/.svn/entries b/geworkbench-core/classes/org/geworkbench/util/pathwaydecoder/.svn/entries
index de2679b..3be8361 100644
--- a/geworkbench-core/classes/org/geworkbench/util/pathwaydecoder/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/util/pathwaydecoder/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/util/pathwaydecoder
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/util/pathwaydecoder/mutualinformation/.svn/entries b/geworkbench-core/classes/org/geworkbench/util/pathwaydecoder/mutualinformation/.svn/entries
index 729db19..5e0e302 100644
--- a/geworkbench-core/classes/org/geworkbench/util/pathwaydecoder/mutualinformation/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/util/pathwaydecoder/mutualinformation/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/util/pathwaydecoder/mutualinformation
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/util/patterns/.svn/entries b/geworkbench-core/classes/org/geworkbench/util/patterns/.svn/entries
index 3049637..acf523c 100644
--- a/geworkbench-core/classes/org/geworkbench/util/patterns/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/util/patterns/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/util/patterns
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/util/sequences/.svn/entries b/geworkbench-core/classes/org/geworkbench/util/sequences/.svn/entries
index 28a6748..6b2831b 100644
--- a/geworkbench-core/classes/org/geworkbench/util/sequences/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/util/sequences/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/util/sequences
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/util/splashscreen.png b/geworkbench-core/classes/org/geworkbench/util/splashscreen.png
index c56d46a..bce7b97 100755
Binary files a/geworkbench-core/classes/org/geworkbench/util/splashscreen.png and b/geworkbench-core/classes/org/geworkbench/util/splashscreen.png differ
diff --git a/geworkbench-core/classes/org/geworkbench/util/visualproperties/.svn/entries b/geworkbench-core/classes/org/geworkbench/util/visualproperties/.svn/entries
index a48be40..31113ef 100644
--- a/geworkbench-core/classes/org/geworkbench/util/visualproperties/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/util/visualproperties/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/util/visualproperties
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/.svn/all-wcprops b/geworkbench-core/components/.svn/all-wcprops
index 68c81f3..7333cf9 100644
--- a/geworkbench-core/components/.svn/all-wcprops
+++ b/geworkbench-core/components/.svn/all-wcprops
@@ -1,5 +1,5 @@
 K 25
 svn:wc:ra_dav:version-url
 V 59
-/svn/geworkbench/!svn/ver/8676/trunk/geworkbench/components
+/svn/geworkbench/!svn/ver/8812/trunk/geworkbench/components
 END
diff --git a/geworkbench-core/components/.svn/entries b/geworkbench-core/components/.svn/entries
index b8021d9..ab296a9 100644
--- a/geworkbench-core/components/.svn/entries
+++ b/geworkbench-core/components/.svn/entries
@@ -1,15 +1,15 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2012-01-09T22:15:49.759555Z
-8676
-youmi
+2012-01-30T21:31:47.792401Z
+8812
+zji



@@ -68,28 +68,28 @@ dir
 idea
 dir

-ttest
+selectors
 dir

-selectors
+ttest
 dir

-cupid
+anova
 dir

 pudge
 dir

-anova
+cupid
 dir

-promoter
+cutenet
 dir

 discovery
 dir

-cutenet
+promoter
 dir

 skyline
@@ -101,19 +101,19 @@ dir
 caarray
 dir

-analysis
+filtering
 dir

-filtering
+analysis
 dir

 normalization
 dir

-cytoscape
+foldchange
 dir

-foldchange
+cytoscape
 dir

 geneontology2
diff --git a/geworkbench-core/components/alignment/.svn/all-wcprops b/geworkbench-core/components/alignment/.svn/all-wcprops
index f7dc131..8af26bc 100644
--- a/geworkbench-core/components/alignment/.svn/all-wcprops
+++ b/geworkbench-core/components/alignment/.svn/all-wcprops
@@ -1,7 +1,7 @@
 K 25
 svn:wc:ra_dav:version-url
 V 69
-/svn/geworkbench/!svn/ver/8676/trunk/geworkbench/components/alignment
+/svn/geworkbench/!svn/ver/8741/trunk/geworkbench/components/alignment
 END
 .classpath
 K 25
diff --git a/geworkbench-core/components/alignment/.svn/entries b/geworkbench-core/components/alignment/.svn/entries
index af155b1..b0bb188 100644
--- a/geworkbench-core/components/alignment/.svn/entries
+++ b/geworkbench-core/components/alignment/.svn/entries
@@ -1,15 +1,15 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/alignment
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2012-01-09T22:15:49.759555Z
-8676
-youmi
+2012-01-19T20:53:18.234124Z
+8741
+maz
 has-props


diff --git a/geworkbench-core/components/alignment/lib/.svn/entries b/geworkbench-core/components/alignment/lib/.svn/entries
index 430c935..c4f9ecc 100644
--- a/geworkbench-core/components/alignment/lib/.svn/entries
+++ b/geworkbench-core/components/alignment/lib/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/alignment/lib
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/alignment/src/.svn/all-wcprops b/geworkbench-core/components/alignment/src/.svn/all-wcprops
index 9f7c5ec..0622b32 100644
--- a/geworkbench-core/components/alignment/src/.svn/all-wcprops
+++ b/geworkbench-core/components/alignment/src/.svn/all-wcprops
@@ -1,7 +1,7 @@
 K 25
 svn:wc:ra_dav:version-url
 V 73
-/svn/geworkbench/!svn/ver/8676/trunk/geworkbench/components/alignment/src
+/svn/geworkbench/!svn/ver/8741/trunk/geworkbench/components/alignment/src
 END
 databaseInfo.xml
 K 25
diff --git a/geworkbench-core/components/alignment/src/.svn/entries b/geworkbench-core/components/alignment/src/.svn/entries
index 0bfbce9..c53b628 100644
--- a/geworkbench-core/components/alignment/src/.svn/entries
+++ b/geworkbench-core/components/alignment/src/.svn/entries
@@ -1,15 +1,15 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/alignment/src
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2012-01-09T22:15:49.759555Z
-8676
-youmi
+2012-01-19T20:53:18.234124Z
+8741
+maz



diff --git a/geworkbench-core/components/alignment/src/org/.svn/all-wcprops b/geworkbench-core/components/alignment/src/org/.svn/all-wcprops
index a4492b0..dbe8597 100644
--- a/geworkbench-core/components/alignment/src/org/.svn/all-wcprops
+++ b/geworkbench-core/components/alignment/src/org/.svn/all-wcprops
@@ -1,5 +1,5 @@
 K 25
 svn:wc:ra_dav:version-url
 V 77
-/svn/geworkbench/!svn/ver/8676/trunk/geworkbench/components/alignment/src/org
+/svn/geworkbench/!svn/ver/8741/trunk/geworkbench/components/alignment/src/org
 END
diff --git a/geworkbench-core/components/alignment/src/org/.svn/entries b/geworkbench-core/components/alignment/src/org/.svn/entries
index ffbc3d9..de0cbc1 100644
--- a/geworkbench-core/components/alignment/src/org/.svn/entries
+++ b/geworkbench-core/components/alignment/src/org/.svn/entries
@@ -1,15 +1,15 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/alignment/src/org
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2012-01-09T22:15:49.759555Z
-8676
-youmi
+2012-01-19T20:53:18.234124Z
+8741
+maz



diff --git a/geworkbench-core/components/alignment/src/org/geworkbench/.svn/all-wcprops b/geworkbench-core/components/alignment/src/org/geworkbench/.svn/all-wcprops
index c028f84..f680256 100644
--- a/geworkbench-core/components/alignment/src/org/geworkbench/.svn/all-wcprops
+++ b/geworkbench-core/components/alignment/src/org/geworkbench/.svn/all-wcprops
@@ -1,5 +1,5 @@
 K 25
 svn:wc:ra_dav:version-url
 V 89
-/svn/geworkbench/!svn/ver/8676/trunk/geworkbench/components/alignment/src/org/geworkbench
+/svn/geworkbench/!svn/ver/8741/trunk/geworkbench/components/alignment/src/org/geworkbench
 END
diff --git a/geworkbench-core/components/alignment/src/org/geworkbench/.svn/entries b/geworkbench-core/components/alignment/src/org/geworkbench/.svn/entries
index 1e48dbc..1b22818 100644
--- a/geworkbench-core/components/alignment/src/org/geworkbench/.svn/entries
+++ b/geworkbench-core/components/alignment/src/org/geworkbench/.svn/entries
@@ -1,15 +1,15 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/alignment/src/org/geworkbench
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2012-01-09T22:15:49.759555Z
-8676
-youmi
+2012-01-19T20:53:18.234124Z
+8741
+maz



diff --git a/geworkbench-core/components/alignment/src/org/geworkbench/components/.svn/all-wcprops b/geworkbench-core/components/alignment/src/org/geworkbench/components/.svn/all-wcprops
index 7094881..42b48e7 100644
--- a/geworkbench-core/components/alignment/src/org/geworkbench/components/.svn/all-wcprops
+++ b/geworkbench-core/components/alignment/src/org/geworkbench/components/.svn/all-wcprops
@@ -1,5 +1,5 @@
 K 25
 svn:wc:ra_dav:version-url
 V 100
-/svn/geworkbench/!svn/ver/8676/trunk/geworkbench/components/alignment/src/org/geworkbench/components
+/svn/geworkbench/!svn/ver/8741/trunk/geworkbench/components/alignment/src/org/geworkbench/components
 END
diff --git a/geworkbench-core/components/alignment/src/org/geworkbench/components/.svn/entries b/geworkbench-core/components/alignment/src/org/geworkbench/components/.svn/entries
index 75a9132..91b2920 100644
--- a/geworkbench-core/components/alignment/src/org/geworkbench/components/.svn/entries
+++ b/geworkbench-core/components/alignment/src/org/geworkbench/components/.svn/entries
@@ -1,15 +1,15 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/alignment/src/org/geworkbench/components
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2012-01-09T22:15:49.759555Z
-8676
-youmi
+2012-01-19T20:53:18.234124Z
+8741
+maz



diff --git a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/.svn/all-wcprops b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/.svn/all-wcprops
index ed95214..7fbbcb7 100644
--- a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/.svn/all-wcprops
+++ b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/.svn/all-wcprops
@@ -1,5 +1,5 @@
 K 25
 svn:wc:ra_dav:version-url
 V 110
-/svn/geworkbench/!svn/ver/8676/trunk/geworkbench/components/alignment/src/org/geworkbench/components/alignment
+/svn/geworkbench/!svn/ver/8741/trunk/geworkbench/components/alignment/src/org/geworkbench/components/alignment
 END
diff --git a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/.svn/entries b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/.svn/entries
index 97c454c..fde7098 100644
--- a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/.svn/entries
+++ b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/.svn/entries
@@ -1,15 +1,15 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/alignment/src/org/geworkbench/components/alignment
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2012-01-09T22:15:49.759555Z
-8676
-youmi
+2012-01-19T20:53:18.234124Z
+8741
+maz



diff --git a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/.svn/all-wcprops b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/.svn/all-wcprops
index 4f8e00c..6639b1c 100644
--- a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/.svn/all-wcprops
+++ b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/.svn/all-wcprops
@@ -1,7 +1,7 @@
 K 25
 svn:wc:ra_dav:version-url
 V 116
-/svn/geworkbench/!svn/ver/8676/trunk/geworkbench/components/alignment/src/org/geworkbench/components/alignment/blast
+/svn/geworkbench/!svn/ver/8741/trunk/geworkbench/components/alignment/src/org/geworkbench/components/alignment/blast
 END
 RemoteBlast.java
 K 25
@@ -19,25 +19,25 @@ BlastAnalysis.java
 K 25
 svn:wc:ra_dav:version-url
 V 135
-/svn/geworkbench/!svn/ver/8676/trunk/geworkbench/components/alignment/src/org/geworkbench/components/alignment/blast/BlastAnalysis.java
+/svn/geworkbench/!svn/ver/8741/trunk/geworkbench/components/alignment/src/org/geworkbench/components/alignment/blast/BlastAnalysis.java
 END
 BlastAnalysisPanel.java
 K 25
 svn:wc:ra_dav:version-url
 V 140
-/svn/geworkbench/!svn/ver/8366/trunk/geworkbench/components/alignment/src/org/geworkbench/components/alignment/blast/BlastAnalysisPanel.java
+/svn/geworkbench/!svn/ver/8741/trunk/geworkbench/components/alignment/src/org/geworkbench/components/alignment/blast/BlastAnalysisPanel.java
 END
 AlgorithmMatcher.java
 K 25
 svn:wc:ra_dav:version-url
 V 138
-/svn/geworkbench/!svn/ver/8362/trunk/geworkbench/components/alignment/src/org/geworkbench/components/alignment/blast/AlgorithmMatcher.java
+/svn/geworkbench/!svn/ver/8741/trunk/geworkbench/components/alignment/src/org/geworkbench/components/alignment/blast/AlgorithmMatcher.java
 END
 NCBIBlastParser.java
 K 25
 svn:wc:ra_dav:version-url
 V 137
-/svn/geworkbench/!svn/ver/8455/trunk/geworkbench/components/alignment/src/org/geworkbench/components/alignment/blast/NCBIBlastParser.java
+/svn/geworkbench/!svn/ver/8739/trunk/geworkbench/components/alignment/src/org/geworkbench/components/alignment/blast/NCBIBlastParser.java
 END
 ParameterSetting.java
 K 25
diff --git a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/.svn/entries b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/.svn/entries
index 49b127a..e07704c 100644
--- a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/.svn/entries
+++ b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/.svn/entries
@@ -1,15 +1,15 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/alignment/src/org/geworkbench/components/alignment/blast
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2012-01-09T22:15:49.759555Z
-8676
-youmi
+2012-01-19T20:53:18.234124Z
+8741
+maz



@@ -100,11 +100,11 @@ file



-2012-01-10T21:28:37.000000Z
-44409f177565706c780b079a1ecc9f43
-2012-01-09T22:15:49.759555Z
-8676
-youmi
+2012-01-31T19:12:35.000000Z
+db74f1aed03f8c3a65e49ce36acdf318
+2012-01-19T20:53:18.234124Z
+8741
+maz
 has-props


@@ -126,7 +126,7 @@ has-props



-14706
+14757

 BlastAnalysisPanel.java
 file
@@ -134,11 +134,11 @@ file



-2012-01-10T19:15:23.000000Z
-39f1be5e7d6614131b87036e37e1e122
-2011-10-05T20:25:11.006171Z
-8366
-zji
+2012-01-31T19:12:35.000000Z
+c6e183225dc576c024d335c137726b82
+2012-01-19T20:53:18.234124Z
+8741
+maz



@@ -160,7 +160,7 @@ zji



-52298
+52443

 AlgorithmMatcher.java
 file
@@ -168,11 +168,11 @@ file



-2012-01-10T19:15:23.000000Z
-6638b891f433914fe3b1f7d0a791fa59
-2011-10-04T16:02:03.460589Z
-8362
-youmi
+2012-01-31T19:12:35.000000Z
+2fe05fdae743f42ab7e91cdf85c756c3
+2012-01-19T20:53:18.234124Z
+8741
+maz
 has-props


@@ -194,7 +194,7 @@ has-props



-29704
+29765

 NCBIBlastParser.java
 file
@@ -202,11 +202,11 @@ file



-2012-01-10T19:15:23.000000Z
-ccb51674e9d247685c606d68abe661c1
-2011-10-24T22:06:10.214128Z
-8455
-youmi
+2012-01-31T19:12:35.000000Z
+f6c7a22ec0f7b238f1202f177f49ea13
+2012-01-19T19:49:36.115286Z
+8739
+zji
 has-props


@@ -228,7 +228,7 @@ has-props



-9229
+9238

 ParameterSetting.java
 file
diff --git a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/.svn/text-base/AlgorithmMatcher.java.svn-base b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/.svn/text-base/AlgorithmMatcher.java.svn-base
index 4923fbf..be952b1 100644
--- a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/.svn/text-base/AlgorithmMatcher.java.svn-base
+++ b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/.svn/text-base/AlgorithmMatcher.java.svn-base
@@ -506,24 +506,7 @@ public class AlgorithmMatcher {
             } else {
                 String dbName = ps.getDbName();
                 cmd="";
-                /*
-                String[] list = dbName.split("/");
-                if (list.length > 1) {
-                    String[] dbNameWithSuffix = list[list.length - 1].split(" ");
-                    dbName = dbNameWithSuffix[0];
-                }
-                */ //why split with "/"? , for bug 2019, it is commented out
-                ///cmd +="&db=nucleotide&stype=protein&GENETIC_CODE=1&DBTYPE=nr&NUM_ORG=1&HSP_RANGE_MAX=0";//debug
-                ///cmd +="&UNGAPPED_ALIGNMENT=no&BLAST_PROGRAMS=blastx&SELECTED_PROG_TYPE=blastx";
-                //cmd +="&SHOW_OVERVIEW=true&SHOW_LINKOUT=true&GET_SEQUENCE=true&FORMAT_OBJECT=Alignment";
-                //cmd +="&FORMAT_TYPE=HTML&ALIGNMENT_VIEW=Pairwise&MASK_CHAR=2&MASK_COLOR=1&DESCRIPTIONS=100&ALIGNMENTS=100&NEW_VIEW=true&OLD_BLAST=false&NCBI_GI=false&SHOW_CDS_FEATURE=false&NUM_OVERVIEW=100";
-                ///cmd +="&CLIENT=web&SERVICE=plain&CMD=request&SAVED_SEARCH=true";
-                //cmd +="&NUM_DIFFS=0&NUM_OPTS_DIFFS=0&UNIQ_DEFAULTS_NAME=A_SearchDefaults_1OjY85_zDC_DRGnXTKy2N7_23ttSh_c9WM6&PAGE_TYPE=BlastSearch&USER_DEFAULT_PROG_TYPE=megaBlast&USER_DEFAULT_MATCH_SCORES=0";
-                //cmd +="&DB_ABBR=Human20%G+T";
-                //cmd +="&SELECTED_PROG_TYPE=megaBlast";
-                ///cmd +="USER_DEFAULT_PROG_TYPE=blastx";
-                //above are some arguments may need in the future
-
+
                 cmd += "&DATABASE=" + dbName + "&PROGRAM=" +ps.getProgramName();
                 if (ps.isLowComplexityFilterOn()) {
                     cmd += "&FILTER=L";
@@ -591,7 +574,12 @@ public class AlgorithmMatcher {
                 if (ps.getProgramName().equalsIgnoreCase("blastp")||ps.getProgramName().equalsIgnoreCase("tblastn")){
                 	cmd +="&COMPOSITION_BASED_STATISTICS="+ compositional2number.get(ps.getCompositionalAdjustment());
                 }
-
+
+                if(ps.getMaxTargetNumber()!=null){
+                	cmd+="&MAX_NUM_SEQ=" + ps.getMaxTargetNumber();
+                	//cmd+="&NUM_DIFFS=3&NUM_OPTS_DIFFS=2&NUM_ORG=1&NUM_OVERVIEW=100&OLD_BLAST=false";
+                }
+
                 if (ps.getProgramName().equalsIgnoreCase("blastp")||ps.getProgramName().equalsIgnoreCase("blastn")){
 	                if (ps.isShortQueriesOn()){
 	                	cmd += "&SHORT_QUERY_ADJUST=yes";
@@ -614,7 +602,7 @@ public class AlgorithmMatcher {
                 }
                 cmd+="&HSP_RANGE_MAX=" + ps.getHspRange().trim();
                 String gapCost = ps.getGapCost();
-                if (gapCost != null) {
+                if ((gapCost != null)&&!(ps.getProgramName().equalsIgnoreCase("tblastx"))) {
                 	if(gapCost.equalsIgnoreCase("Linear")) gapCost="Existence: 0 Extension: 0";
                     String[] s = gapCost.split(" ");
                     if (s.length > 3) {
@@ -648,11 +636,7 @@ public class AlgorithmMatcher {
                 if((ps.getSpeciesRepeat()!=null)&&(ps.isHumanRepeatFilterOn())){
                 		cmd+="&REPEATS=" + specie_repeat.get(ps.getSpeciesRepeat());
                 }
-
-                if(ps.getMaxTargetNumber()!=null){
-                	cmd+="&MAX_NUM_SEQ=" + ps.getMaxTargetNumber();
-                }
-
+
                 if (ps.getProgramName().equals("blastp")||ps.getProgramName().equals("tblastn"))	//COMPOSITION only applies to blastp and tblastn
                 	cmd += "&EXPECT=" + ps.getExpect() + "&AUTO_FORMAT=Semiauto&CDD_SEARCH=on&SHOW_OVERVIEW=on&SERVICE=plain\r\n\r\n";
                 else
@@ -660,7 +644,8 @@ public class AlgorithmMatcher {
             }

         }
-
+        //cmd="&ALIGNMENT_VIEW=Pairwise&ALIGNMENTS=250&BLAST_PROGRAMS=blastp&BLAST_SPEC=&CDD_SEARCH=on&CLIENT=web&CMD=request&COMPOSITION_BASED_STATISTICS=2&DATABASE=swissprot&db=protein&DB_DIR_PREFIX=&DESCRIPTIONS=500&EQ_MENU=&EQ_TEXT=&EXPECT=10&EXPECT_HIGH=&EXPECT_LOW=&FILTER=m&FORMAT_EQ_TEXT=&FORMAT_NUM_ORG=1&FORMAT_OBJECT=Alignment&FORMAT_ORGANISM=&FORMAT_TYPE=HTML&GAPCOSTS=11%201&GENETIC_CODE=1&GET_SEQUENCE=on&HSP_RANGE_MAX=0&I_THRESH=&ID_FOR_PSSM=&JOB_TITLE=&MASK_CHAR=2&MASK_COLOR=1&MATCH_SCORES=&MATRIX_NAME=BLOSUM62&MAX_NUM_SEQ=500&MEGABLAST=&MIXED_DATABASE=&NCBI_GI=&NEW_VIEW=on&NO_COMMON=&NUM_DIFFS=3&NUM_OPTS_DIFFS=2&NUM_ORG=1&NUM_OVERVIEW=100&OLD_BLAST=FALSE&PAGE=Proteins&PAGE_TYPE=BlastSearch&PERC_IDENT_HIGH=&PERC_IDENT_LOW=&PHI_PATTERN=&PROGRAM=blastp&PSI_PSEUDOCOUNT=&PSSM=&QUERY=&QUERY_BELIEVE_DEFLINE=&QUERY_FROM=&QUERY_INDEX=0&QUERY_TO=&REPEATS=repeat_7165&RUN_PSIBLAST=&SAVED_PSSM=&SAVED_SEARCH=&SELECTED_PROG_TYPE=blastp&SERVICE=plain&SHORT_QUERY_ADJUST=on&SHOW_CDS_FEATURE=&SHOW_LINKOUT=on&SHOW_OVERVIEW=on&stype=protein&SUBJECTFILE=&SUBJECTS=&SUBJECTS_FROM=&SUBJECTS_TO=&TEMPLATE_LENGTH=0&TEMPLATE_TYPE=0&TWO_HITS=&UNIQ_DEFAULTS_NAME=&USER_DATABASE=&USER_DEFAULT_MATRIX=3&USER_DEFAULT_PROG_TYPE=blastp&USER_FORMAT_DEFAULTS=&USER_MATCH_SCORES=&USER_WORD_SIZE=&WORD_SIZE=3&WWW_BLAST_TYPE=";
+        //System.out.println(cmd);
         return cmd;
     }
 }
diff --git a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/.svn/text-base/BlastAnalysis.java.svn-base b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/.svn/text-base/BlastAnalysis.java.svn-base
index 20ce19e..910a530 100644
--- a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/.svn/text-base/BlastAnalysis.java.svn-base
+++ b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/.svn/text-base/BlastAnalysis.java.svn-base
@@ -170,7 +170,7 @@ public class BlastAnalysis extends AbstractAnalysis implements
 					pbTtest.setMessage("The Request ID is : " + BLAST_rid);

 					String resultURLString = "http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&FORMAT_TYPE=HTML&RID="
-							+ BLAST_rid;
+							+ BLAST_rid+"&ALIGNMENTS="+parameterSetting.getMaxTargetNumber();
 					Status status = blast.retrieveResult(resultURLString);
 					while (status == Status.WAITING && !this.stopAlgorithm) {

diff --git a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/.svn/text-base/BlastAnalysisPanel.java.svn-base b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/.svn/text-base/BlastAnalysisPanel.java.svn-base
index a324561..2f793ce 100644
--- a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/.svn/text-base/BlastAnalysisPanel.java.svn-base
+++ b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/.svn/text-base/BlastAnalysisPanel.java.svn-base
@@ -912,6 +912,11 @@ public class BlastAnalysisPanel extends AbstractSaveableParameterPanel {
 			} else {
 				lowComplexFilterBox.setSelected(true);
 			}
+			if (selectedProgramName.equalsIgnoreCase("tblastx")){
+				jGapcostsBox.setVisible(false);
+				jGapcostsLabel.setVisible(false);
+			}
+
 		}
 	}

diff --git a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/.svn/text-base/NCBIBlastParser.java.svn-base b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/.svn/text-base/NCBIBlastParser.java.svn-base
index 6a90d20..1f010f7 100644
--- a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/.svn/text-base/NCBIBlastParser.java.svn-base
+++ b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/.svn/text-base/NCBIBlastParser.java.svn-base
@@ -138,6 +138,8 @@ public class NCBIBlastParser {
 						description = tagSeparated[2].trim();
 						score = tagSeparated[3].trim();
 						evalue = tagSeparated[4].trim();
+						String[] tokens=evalue.split("\\s");
+						evalue=tokens[0];
 					} else if(tagSeparated.length==3) { // for database alu (without HTML links)
 						String[] fields = tagSeparated[0].split("\\|");
 						id = fields[0];
@@ -223,22 +225,21 @@ public class NCBIBlastParser {
 							each.setLength(new Integer(lengthVal[1].trim())
 									.intValue());
 						}
-						if (line.startsWith("Identities = ")) {
-							/*
-							 * TODO use Match pattern later.
-							 */
-							String alignmentLengthString = line.substring("Identities = ".length(), line.indexOf("/"));
-							int alignmentLength = Integer.parseInt(alignmentLengthString);
-							if(0==each.getAlignmentLength())
+						final Pattern p = Pattern
+								.compile("Identities\\s*=\\s*\\d+/(\\d+)\\s*.\\((\\d+)%\\).+");
+						Matcher m = p.matcher(line);
+						if (m.matches()) {
+							if (0 == each.getAlignmentLength()) {
+								String alignmentLengthString = m.group(1);
+								int alignmentLength = Integer
+										.parseInt(alignmentLengthString);
 								each.setAlignmentLength(alignmentLength);
-							StringTokenizer st1 = new StringTokenizer(line, "(");
-							st1.nextToken();
-							String identity = st1.nextToken();
-							String[] s = identity.split("%");
-							if(0==each.getPercentAligned())
-								each
-									.setPercentAligned(new Integer(s[0])
-											.intValue());
+							}
+							if (0 == each.getPercentAligned()) {
+								String percentString = m.group(2);
+								each.setPercentAligned(new Integer(
+										percentString).intValue());
+							}

 						}
 						// get the start point, end point and length
@@ -282,7 +283,7 @@ public class NCBIBlastParser {
 					each.setDetailedAlignment(detaillines.toString());

 					index++;
-					if (endofResult) {
+					if (endofResult || index>=hits.size()) {
 						endofResult = false;
 						break;
 					}
diff --git a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/AlgorithmMatcher.java b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/AlgorithmMatcher.java
index a1b33cb..c9fe6fb 100755
--- a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/AlgorithmMatcher.java
+++ b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/AlgorithmMatcher.java
@@ -22,7 +22,7 @@ import org.xml.sax.SAXException;
  * <p>Company: Columbia University</p>
  *
  * @author zji
- * @version $Id: AlgorithmMatcher.java 8362 2011-10-04 16:02:03Z youmi $
+ * @version $Id: AlgorithmMatcher.java 8741 2012-01-19 20:53:18Z maz $
  */
 public class AlgorithmMatcher {
 	Log log = LogFactory.getLog(AlgorithmMatcher.class);
@@ -506,24 +506,7 @@ public class AlgorithmMatcher {
             } else {
                 String dbName = ps.getDbName();
                 cmd="";
-                /*
-                String[] list = dbName.split("/");
-                if (list.length > 1) {
-                    String[] dbNameWithSuffix = list[list.length - 1].split(" ");
-                    dbName = dbNameWithSuffix[0];
-                }
-                */ //why split with "/"? , for bug 2019, it is commented out
-                ///cmd +="&db=nucleotide&stype=protein&GENETIC_CODE=1&DBTYPE=nr&NUM_ORG=1&HSP_RANGE_MAX=0";//debug
-                ///cmd +="&UNGAPPED_ALIGNMENT=no&BLAST_PROGRAMS=blastx&SELECTED_PROG_TYPE=blastx";
-                //cmd +="&SHOW_OVERVIEW=true&SHOW_LINKOUT=true&GET_SEQUENCE=true&FORMAT_OBJECT=Alignment";
-                //cmd +="&FORMAT_TYPE=HTML&ALIGNMENT_VIEW=Pairwise&MASK_CHAR=2&MASK_COLOR=1&DESCRIPTIONS=100&ALIGNMENTS=100&NEW_VIEW=true&OLD_BLAST=false&NCBI_GI=false&SHOW_CDS_FEATURE=false&NUM_OVERVIEW=100";
-                ///cmd +="&CLIENT=web&SERVICE=plain&CMD=request&SAVED_SEARCH=true";
-                //cmd +="&NUM_DIFFS=0&NUM_OPTS_DIFFS=0&UNIQ_DEFAULTS_NAME=A_SearchDefaults_1OjY85_zDC_DRGnXTKy2N7_23ttSh_c9WM6&PAGE_TYPE=BlastSearch&USER_DEFAULT_PROG_TYPE=megaBlast&USER_DEFAULT_MATCH_SCORES=0";
-                //cmd +="&DB_ABBR=Human20%G+T";
-                //cmd +="&SELECTED_PROG_TYPE=megaBlast";
-                ///cmd +="USER_DEFAULT_PROG_TYPE=blastx";
-                //above are some arguments may need in the future
-
+
                 cmd += "&DATABASE=" + dbName + "&PROGRAM=" +ps.getProgramName();
                 if (ps.isLowComplexityFilterOn()) {
                     cmd += "&FILTER=L";
@@ -591,7 +574,12 @@ public class AlgorithmMatcher {
                 if (ps.getProgramName().equalsIgnoreCase("blastp")||ps.getProgramName().equalsIgnoreCase("tblastn")){
                 	cmd +="&COMPOSITION_BASED_STATISTICS="+ compositional2number.get(ps.getCompositionalAdjustment());
                 }
-
+
+                if(ps.getMaxTargetNumber()!=null){
+                	cmd+="&MAX_NUM_SEQ=" + ps.getMaxTargetNumber();
+                	//cmd+="&NUM_DIFFS=3&NUM_OPTS_DIFFS=2&NUM_ORG=1&NUM_OVERVIEW=100&OLD_BLAST=false";
+                }
+
                 if (ps.getProgramName().equalsIgnoreCase("blastp")||ps.getProgramName().equalsIgnoreCase("blastn")){
 	                if (ps.isShortQueriesOn()){
 	                	cmd += "&SHORT_QUERY_ADJUST=yes";
@@ -614,7 +602,7 @@ public class AlgorithmMatcher {
                 }
                 cmd+="&HSP_RANGE_MAX=" + ps.getHspRange().trim();
                 String gapCost = ps.getGapCost();
-                if (gapCost != null) {
+                if ((gapCost != null)&&!(ps.getProgramName().equalsIgnoreCase("tblastx"))) {
                 	if(gapCost.equalsIgnoreCase("Linear")) gapCost="Existence: 0 Extension: 0";
                     String[] s = gapCost.split(" ");
                     if (s.length > 3) {
@@ -648,11 +636,7 @@ public class AlgorithmMatcher {
                 if((ps.getSpeciesRepeat()!=null)&&(ps.isHumanRepeatFilterOn())){
                 		cmd+="&REPEATS=" + specie_repeat.get(ps.getSpeciesRepeat());
                 }
-
-                if(ps.getMaxTargetNumber()!=null){
-                	cmd+="&MAX_NUM_SEQ=" + ps.getMaxTargetNumber();
-                }
-
+
                 if (ps.getProgramName().equals("blastp")||ps.getProgramName().equals("tblastn"))	//COMPOSITION only applies to blastp and tblastn
                 	cmd += "&EXPECT=" + ps.getExpect() + "&AUTO_FORMAT=Semiauto&CDD_SEARCH=on&SHOW_OVERVIEW=on&SERVICE=plain\r\n\r\n";
                 else
@@ -660,7 +644,8 @@ public class AlgorithmMatcher {
             }

         }
-
+        //cmd="&ALIGNMENT_VIEW=Pairwise&ALIGNMENTS=250&BLAST_PROGRAMS=blastp&BLAST_SPEC=&CDD_SEARCH=on&CLIENT=web&CMD=request&COMPOSITION_BASED_STATISTICS=2&DATABASE=swissprot&db=protein&DB_DIR_PREFIX=&DESCRIPTIONS=500&EQ_MENU=&EQ_TEXT=&EXPECT=10&EXPECT_HIGH=&EXPECT_LOW=&FILTER=m&FORMAT_EQ_TEXT=&FORMAT_NUM_ORG=1&FORMAT_OBJECT=Alignment&FORMAT_ORGANISM=&FORMAT_TYPE=HTML&GAPCOSTS=11%201&GENETIC_CODE=1&GET_SEQUENCE=on&HSP_RANGE_MAX=0&I_THRESH=&ID_FOR_PSSM=&JOB_TITLE=&MASK_CHAR=2&MASK_COLOR=1&MATCH_SCORES=&MATRIX_NAME=BLOSUM62&MAX_NUM_SEQ=500&MEGABLAST=&MIXED_DATABASE=&NCBI_GI=&NEW_VIEW=on&NO_COMMON=&NUM_DIFFS=3&NUM_OPTS_DIFFS=2&NUM_ORG=1&NUM_OVERVIEW=100&OLD_BLAST=FALSE&PAGE=Proteins&PAGE_TYPE=BlastSearch&PERC_IDENT_HIGH=&PERC_IDENT_LOW=&PHI_PATTERN=&PROGRAM=blastp&PSI_PSEUDOCOUNT=&PSSM=&QUERY=&QUERY_BELIEVE_DEFLINE=&QUERY_FROM=&QUERY_INDEX=0&QUERY_TO=&REPEATS=repeat_7165&RUN_PSIBLAST=&SAVED_PSSM=&SAVED_SEARCH=&SELECTED_PROG_TYPE=blastp&SERVICE=plain&SHORT_QUERY_ADJUST=on&SHOW_CDS_FEATURE=&SHOW_LINKOUT=on&SHOW_OVERVIEW=on&stype=protein&SUBJECTFILE=&SUBJECTS=&SUBJECTS_FROM=&SUBJECTS_TO=&TEMPLATE_LENGTH=0&TEMPLATE_TYPE=0&TWO_HITS=&UNIQ_DEFAULTS_NAME=&USER_DATABASE=&USER_DEFAULT_MATRIX=3&USER_DEFAULT_PROG_TYPE=blastp&USER_FORMAT_DEFAULTS=&USER_MATCH_SCORES=&USER_WORD_SIZE=&WORD_SIZE=3&WWW_BLAST_TYPE=";
+        //System.out.println(cmd);
         return cmd;
     }
 }
diff --git a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/BlastAnalysis.java b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/BlastAnalysis.java
index 5f62f97..c982106 100755
--- a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/BlastAnalysis.java
+++ b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/BlastAnalysis.java
@@ -38,7 +38,7 @@ import org.geworkbench.util.ProgressBar;
  *
  * @author XZ
  * @author zji
- * @version $Id: BlastAnalysis.java 8676 2012-01-09 22:15:49Z youmi $
+ * @version $Id: BlastAnalysis.java 8741 2012-01-19 20:53:18Z maz $
  */
 public class BlastAnalysis extends AbstractAnalysis implements
 		ProteinSequenceAnalysis {
@@ -170,7 +170,7 @@ public class BlastAnalysis extends AbstractAnalysis implements
 					pbTtest.setMessage("The Request ID is : " + BLAST_rid);

 					String resultURLString = "http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&FORMAT_TYPE=HTML&RID="
-							+ BLAST_rid;
+							+ BLAST_rid+"&ALIGNMENTS="+parameterSetting.getMaxTargetNumber();
 					Status status = blast.retrieveResult(resultURLString);
 					while (status == Status.WAITING && !this.stopAlgorithm) {

diff --git a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/BlastAnalysisPanel.java b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/BlastAnalysisPanel.java
index a324561..2f793ce 100644
--- a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/BlastAnalysisPanel.java
+++ b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/BlastAnalysisPanel.java
@@ -912,6 +912,11 @@ public class BlastAnalysisPanel extends AbstractSaveableParameterPanel {
 			} else {
 				lowComplexFilterBox.setSelected(true);
 			}
+			if (selectedProgramName.equalsIgnoreCase("tblastx")){
+				jGapcostsBox.setVisible(false);
+				jGapcostsLabel.setVisible(false);
+			}
+
 		}
 	}

diff --git a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/NCBIBlastParser.java b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/NCBIBlastParser.java
index cd47273..1f5e57e 100755
--- a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/NCBIBlastParser.java
+++ b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/NCBIBlastParser.java
@@ -2,7 +2,7 @@ package org.geworkbench.components.alignment.blast;

 /**
  *
- * @version $Id: NCBIBlastParser.java 8455 2011-10-24 22:06:10Z youmi $
+ * @version $Id: NCBIBlastParser.java 8739 2012-01-19 19:49:36Z zji $
  */

 import java.io.BufferedReader;
@@ -138,6 +138,8 @@ public class NCBIBlastParser {
 						description = tagSeparated[2].trim();
 						score = tagSeparated[3].trim();
 						evalue = tagSeparated[4].trim();
+						String[] tokens=evalue.split("\\s");
+						evalue=tokens[0];
 					} else if(tagSeparated.length==3) { // for database alu (without HTML links)
 						String[] fields = tagSeparated[0].split("\\|");
 						id = fields[0];
@@ -223,22 +225,21 @@ public class NCBIBlastParser {
 							each.setLength(new Integer(lengthVal[1].trim())
 									.intValue());
 						}
-						if (line.startsWith("Identities = ")) {
-							/*
-							 * TODO use Match pattern later.
-							 */
-							String alignmentLengthString = line.substring("Identities = ".length(), line.indexOf("/"));
-							int alignmentLength = Integer.parseInt(alignmentLengthString);
-							if(0==each.getAlignmentLength())
+						final Pattern p = Pattern
+								.compile("Identities\\s*=\\s*\\d+/(\\d+)\\s*.\\((\\d+)%\\).+");
+						Matcher m = p.matcher(line);
+						if (m.matches()) {
+							if (0 == each.getAlignmentLength()) {
+								String alignmentLengthString = m.group(1);
+								int alignmentLength = Integer
+										.parseInt(alignmentLengthString);
 								each.setAlignmentLength(alignmentLength);
-							StringTokenizer st1 = new StringTokenizer(line, "(");
-							st1.nextToken();
-							String identity = st1.nextToken();
-							String[] s = identity.split("%");
-							if(0==each.getPercentAligned())
-								each
-									.setPercentAligned(new Integer(s[0])
-											.intValue());
+							}
+							if (0 == each.getPercentAligned()) {
+								String percentString = m.group(2);
+								each.setPercentAligned(new Integer(
+										percentString).intValue());
+							}

 						}
 						// get the start point, end point and length
@@ -282,7 +283,7 @@ public class NCBIBlastParser {
 					each.setDetailedAlignment(detaillines.toString());

 					index++;
-					if (endofResult) {
+					if (endofResult || index>=hits.size()) {
 						endofResult = false;
 						break;
 					}
diff --git a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/help/.svn/entries b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/help/.svn/entries
index 3766e12..3d39322 100644
--- a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/help/.svn/entries
+++ b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/help/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/alignment/src/org/geworkbench/components/alignment/help
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/help/blast_files/.svn/entries b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/help/blast_files/.svn/entries
index 1db759f..36a89b5 100644
--- a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/help/blast_files/.svn/entries
+++ b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/help/blast_files/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/alignment/src/org/geworkbench/components/alignment/help/blast_files
 https://ncisvn.nci.nih.gov/svn/geworkbench

@@ -94,14 +94,14 @@ has-props

 50

-Blast_Wilms_NM_include_5prime.png
+index_004.css
 file




-2011-08-17T00:10:37.000000Z
-9228e002a5fa526e9224df5950d2f56d
+2012-01-10T18:25:30.000000Z
+59a83e6f432f762a5525136d8c017853
 2011-07-30T04:31:30.667242Z
 8187
 zji
@@ -126,16 +126,16 @@ has-props



-59575
+75

-index_004.css
+Blast_Wilms_NM_include_5prime.png
 file




-2012-01-10T18:25:30.000000Z
-59a83e6f432f762a5525136d8c017853
+2011-08-17T00:10:37.000000Z
+9228e002a5fa526e9224df5950d2f56d
 2011-07-30T04:31:30.667242Z
 8187
 zji
@@ -160,16 +160,16 @@ has-props



-75
+59575

-T_SequenceAlignment_BLAST_general_controls.png
+Blast_blastp_advanced.png
 file




-2011-08-17T00:10:37.000000Z
-15cc38ad9c72a9d5fed588801c27a59a
+2012-01-10T18:25:30.000000Z
+fbc86da3fb79dbd324e920c035901dc3
 2011-07-30T04:31:30.667242Z
 8187
 zji
@@ -194,7 +194,7 @@ has-props



-1721
+37716

 Blast_sequence_uploading.png
 file
@@ -230,14 +230,14 @@ has-props

 14869

-Blast_blastp_advanced.png
+T_SequenceAlignment_BLAST_general_controls.png
 file




-2012-01-10T18:25:30.000000Z
-fbc86da3fb79dbd324e920c035901dc3
+2011-08-17T00:10:37.000000Z
+15cc38ad9c72a9d5fed588801c27a59a
 2011-07-30T04:31:30.667242Z
 8187
 zji
@@ -262,7 +262,7 @@ has-props



-37716
+1721

 Blast_blastn_blastn_advanced.png
 file
@@ -298,14 +298,14 @@ has-props

 36566

-T_SequenceAlignment_BLAST_start_stop.png
+Blast_blastx_main_options.png
 file




 2011-08-17T00:10:37.000000Z
-3cdd2570f807aa40afa953545419bc1e
+c23d0d6732765e32a140860b5b7c173c
 2011-07-30T04:31:30.667242Z
 8187
 zji
@@ -330,16 +330,16 @@ has-props



-1057
+23520

-Blast_blastx_main_options.png
+T_SequenceAlignment_BLAST_start_stop.png
 file




 2011-08-17T00:10:37.000000Z
-c23d0d6732765e32a140860b5b7c173c
+3cdd2570f807aa40afa953545419bc1e
 2011-07-30T04:31:30.667242Z
 8187
 zji
@@ -364,16 +364,16 @@ has-props



-23520
+1057

-Blast_result_projects_folder.png
+Blast_blastx_advanced.png
 file




-2011-08-17T00:10:37.000000Z
-0c95fdcc4f9f7d0db3a4587eeaec7ef7
+2012-01-10T18:25:30.000000Z
+a690a598b9a6cbd9e89d58bf8b90b4a0
 2011-07-30T04:31:30.667242Z
 8187
 zji
@@ -398,16 +398,16 @@ has-props



-13162
+32121

-Blast_blastx_advanced.png
+Blast_result_projects_folder.png
 file




-2012-01-10T18:25:30.000000Z
-a690a598b9a6cbd9e89d58bf8b90b4a0
+2011-08-17T00:10:37.000000Z
+0c95fdcc4f9f7d0db3a4587eeaec7ef7
 2011-07-30T04:31:30.667242Z
 8187
 zji
@@ -432,7 +432,7 @@ has-props



-32121
+13162

 Blast_Wilms_NM_result.png
 file
diff --git a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/.svn/entries b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/.svn/entries
index 355d3cb..274514a 100644
--- a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/.svn/entries
+++ b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/alignment/src/org/geworkbench/components/alignment/panels
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/analysis/.classpath b/geworkbench-core/components/analysis/.classpath
index a62a27d..a76605f 100755
--- a/geworkbench-core/components/analysis/.classpath
+++ b/geworkbench-core/components/analysis/.classpath
@@ -1,48 +1,51 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
-	<classpathentry kind="src" path="src"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
-	<classpathentry kind="lib" path="lib/JSciCore.jar"/>
-	<classpathentry kind="lib" path="lib/commons-cli-2.0.jar"/>
-	<classpathentry kind="lib" path="lib/jaxrpc.jar"/>
-	<classpathentry kind="lib" path="lib/jce-jdk13-125.jar"/>
-	<classpathentry kind="lib" path="lib/jgss.jar"/>
-	<classpathentry kind="lib" path="lib/junit.jar"/>
-	<classpathentry kind="lib" path="lib/log4j-1.2.8.jar"/>
-	<classpathentry kind="lib" path="lib/mageUtility.jar"/>
-	<classpathentry kind="lib" path="lib/microarrayUtility.jar"/>
-	<classpathentry kind="lib" path="lib/saaj.jar"/>
-	<classpathentry kind="lib" path="lib/statmlutil.jar"/>
-	<classpathentry kind="lib" path="lib/wsdl4j.jar"/>
-	<classpathentry kind="lib" path="lib/wsrf_common.jar"/>
-	<classpathentry kind="lib" path="lib/wsrf_core_registry_stubs.jar"/>
-	<classpathentry kind="lib" path="lib/wsrf_core_registry.jar"/>
-	<classpathentry kind="lib" path="lib/wsrf_core_stubs.jar"/>
-	<classpathentry kind="lib" path="lib/wsrf_core.jar"/>
-	<classpathentry kind="lib" path="lib/wsrf_provider_jce.jar"/>
-	<classpathentry kind="lib" path="lib/wsrf_tools.jar"/>
-	<classpathentry kind="lib" path="lib/wss4j.jar"/>
-	<classpathentry kind="lib" path="lib/xmlsec.jar"/>
-	<classpathentry kind="lib" path="lib/Dispatcher-client.jar" sourcepath="C:/java/apps/eclipse_cagrid_workspace/Dispatcher/src"/>
-	<classpathentry kind="lib" path="lib/axis.jar" sourcepath="C:/java/jar_source/axis-1_2RC2/src"/>
-	<classpathentry kind="lib" path="lib/addressing-1.0.jar"/>
-	<classpathentry kind="lib" path="lib/cog-axis.jar"/>
-	<classpathentry kind="lib" path="lib/cog-jglobus.jar"/>
-	<classpathentry kind="lib" path="lib/cog-tomcat.jar"/>
-	<classpathentry kind="lib" path="lib/cog-url.jar"/>
-	<classpathentry kind="lib" path="lib/binding-2.0.4.jar"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/geworkbench-core"/>
-	<classpathentry kind="lib" path="lib/caGrid-core-1.4.jar"/>
-	<classpathentry kind="lib" path="lib/caGrid-discovery-1.4.jar"/>
-	<classpathentry kind="lib" path="lib/caGrid-metadata-common-1.4.jar"/>
-	<classpathentry kind="lib" path="lib/caGrid-metadata-data-1.4.jar"/>
-	<classpathentry kind="lib" path="lib/caGrid-metadata-security-1.4.jar"/>
-	<classpathentry kind="lib" path="lib/caGrid-metadatautils-1.4.jar"/>
-	<classpathentry kind="lib" path="lib/caGrid-ServiceSecurityProvider-client-1.4.jar"/>
-	<classpathentry kind="lib" path="lib/caGrid-ServiceSecurityProvider-common-1.4.jar"/>
-	<classpathentry kind="lib" path="lib/caGrid-ServiceSecurityProvider-service-1.4.jar"/>
-	<classpathentry kind="lib" path="lib/caGrid-ServiceSecurityProvider-stubs-1.4.jar"/>
-	<classpathentry kind="lib" path="lib/Dispatcher-common.jar"/>
-	<classpathentry kind="lib" path="lib/Dispatcher-stubs.jar"/>
-	<classpathentry kind="output" path="classes"/>
-</classpath>
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="src" path="src"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
+	<classpathentry kind="lib" path="lib/JSciCore.jar"/>
+	<classpathentry kind="lib" path="lib/commons-cli-2.0.jar"/>
+	<classpathentry kind="lib" path="lib/jaxrpc.jar"/>
+	<classpathentry kind="lib" path="lib/jce-jdk13-125.jar"/>
+	<classpathentry kind="lib" path="lib/jgss.jar"/>
+	<classpathentry kind="lib" path="lib/junit.jar"/>
+	<classpathentry kind="lib" path="lib/log4j-1.2.8.jar"/>
+	<classpathentry kind="lib" path="lib/mageUtility.jar"/>
+	<classpathentry kind="lib" path="lib/microarrayUtility.jar"/>
+	<classpathentry kind="lib" path="lib/saaj.jar"/>
+	<classpathentry kind="lib" path="lib/statmlutil.jar"/>
+	<classpathentry kind="lib" path="lib/wsdl4j.jar"/>
+	<classpathentry kind="lib" path="lib/wsrf_common.jar"/>
+	<classpathentry kind="lib" path="lib/wsrf_core_registry_stubs.jar"/>
+	<classpathentry kind="lib" path="lib/wsrf_core_registry.jar"/>
+	<classpathentry kind="lib" path="lib/wsrf_core_stubs.jar"/>
+	<classpathentry kind="lib" path="lib/wsrf_core.jar"/>
+	<classpathentry kind="lib" path="lib/wsrf_provider_jce.jar"/>
+	<classpathentry kind="lib" path="lib/wsrf_tools.jar"/>
+	<classpathentry kind="lib" path="lib/wss4j.jar"/>
+	<classpathentry kind="lib" path="lib/xmlsec.jar"/>
+	<classpathentry kind="lib" path="lib/Dispatcher-client.jar" sourcepath="C:/java/apps/eclipse_cagrid_workspace/Dispatcher/src"/>
+	<classpathentry kind="lib" path="lib/axis.jar" sourcepath="C:/java/jar_source/axis-1_2RC2/src"/>
+	<classpathentry kind="lib" path="lib/addressing-1.0.jar"/>
+	<classpathentry kind="lib" path="lib/cog-axis.jar"/>
+	<classpathentry kind="lib" path="lib/cog-jglobus.jar"/>
+	<classpathentry kind="lib" path="lib/cog-tomcat.jar"/>
+	<classpathentry kind="lib" path="lib/cog-url.jar"/>
+	<classpathentry kind="lib" path="lib/binding-2.0.4.jar"/>
+	<classpathentry combineaccessrules="false" kind="src" path="/geworkbench-core"/>
+	<classpathentry kind="lib" path="lib/caGrid-core-1.4.jar"/>
+	<classpathentry kind="lib" path="lib/caGrid-discovery-1.4.jar"/>
+	<classpathentry kind="lib" path="lib/caGrid-metadata-common-1.4.jar"/>
+	<classpathentry kind="lib" path="lib/caGrid-metadata-data-1.4.jar"/>
+	<classpathentry kind="lib" path="lib/caGrid-metadata-security-1.4.jar"/>
+	<classpathentry kind="lib" path="lib/caGrid-metadatautils-1.4.jar"/>
+	<classpathentry kind="lib" path="lib/caGrid-ServiceSecurityProvider-client-1.4.jar"/>
+	<classpathentry kind="lib" path="lib/caGrid-ServiceSecurityProvider-common-1.4.jar"/>
+	<classpathentry kind="lib" path="lib/caGrid-ServiceSecurityProvider-service-1.4.jar"/>
+	<classpathentry kind="lib" path="lib/caGrid-ServiceSecurityProvider-stubs-1.4.jar"/>
+	<classpathentry kind="lib" path="lib/Dispatcher-common.jar"/>
+	<classpathentry kind="lib" path="lib/Dispatcher-stubs.jar"/>
+	<classpathentry kind="lib" path="lib/caGrid-Transfer-client-1.4.jar"/>
+	<classpathentry kind="lib" path="lib/caGrid-Transfer-common-1.4.jar"/>
+	<classpathentry kind="lib" path="lib/caGrid-Transfer-stubs-1.4.jar"/>
+	<classpathentry kind="output" path="classes"/>
+</classpath>
diff --git a/geworkbench-core/components/analysis/.svn/all-wcprops b/geworkbench-core/components/analysis/.svn/all-wcprops
index f45aae9..e7aa5ca 100644
--- a/geworkbench-core/components/analysis/.svn/all-wcprops
+++ b/geworkbench-core/components/analysis/.svn/all-wcprops
@@ -1,13 +1,13 @@
 K 25
 svn:wc:ra_dav:version-url
 V 68
-/svn/geworkbench/!svn/ver/8650/trunk/geworkbench/components/analysis
+/svn/geworkbench/!svn/ver/8773/trunk/geworkbench/components/analysis
 END
 .classpath
 K 25
 svn:wc:ra_dav:version-url
 V 79
-/svn/geworkbench/!svn/ver/8612/trunk/geworkbench/components/analysis/.classpath
+/svn/geworkbench/!svn/ver/8737/trunk/geworkbench/components/analysis/.classpath
 END
 .project
 K 25
diff --git a/geworkbench-core/components/analysis/.svn/entries b/geworkbench-core/components/analysis/.svn/entries
index d1818af..4168146 100644
--- a/geworkbench-core/components/analysis/.svn/entries
+++ b/geworkbench-core/components/analysis/.svn/entries
@@ -1,15 +1,15 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/analysis
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2012-01-05T18:11:48.744157Z
-8650
-zji
+2012-01-25T22:33:51.735887Z
+8773
+wangmen
 has-props


@@ -32,10 +32,10 @@ file



-2012-01-10T19:15:23.000000Z
-6377f0382e7da63e932ebcc37063ba49
-2011-12-15T22:06:14.698630Z
-8612
+2012-01-31T19:12:32.000000Z
+4b5ee227beba5fa8148a37453e32e501
+2012-01-19T16:03:43.681238Z
+8737
 wangmen
 has-props

@@ -58,7 +58,7 @@ has-props



-2955
+3221

 .project
 file
diff --git a/geworkbench-core/components/analysis/.svn/text-base/.classpath.svn-base b/geworkbench-core/components/analysis/.svn/text-base/.classpath.svn-base
index a62a27d..a76605f 100644
--- a/geworkbench-core/components/analysis/.svn/text-base/.classpath.svn-base
+++ b/geworkbench-core/components/analysis/.svn/text-base/.classpath.svn-base
@@ -1,48 +1,51 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
-	<classpathentry kind="src" path="src"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
-	<classpathentry kind="lib" path="lib/JSciCore.jar"/>
-	<classpathentry kind="lib" path="lib/commons-cli-2.0.jar"/>
-	<classpathentry kind="lib" path="lib/jaxrpc.jar"/>
-	<classpathentry kind="lib" path="lib/jce-jdk13-125.jar"/>
-	<classpathentry kind="lib" path="lib/jgss.jar"/>
-	<classpathentry kind="lib" path="lib/junit.jar"/>
-	<classpathentry kind="lib" path="lib/log4j-1.2.8.jar"/>
-	<classpathentry kind="lib" path="lib/mageUtility.jar"/>
-	<classpathentry kind="lib" path="lib/microarrayUtility.jar"/>
-	<classpathentry kind="lib" path="lib/saaj.jar"/>
-	<classpathentry kind="lib" path="lib/statmlutil.jar"/>
-	<classpathentry kind="lib" path="lib/wsdl4j.jar"/>
-	<classpathentry kind="lib" path="lib/wsrf_common.jar"/>
-	<classpathentry kind="lib" path="lib/wsrf_core_registry_stubs.jar"/>
-	<classpathentry kind="lib" path="lib/wsrf_core_registry.jar"/>
-	<classpathentry kind="lib" path="lib/wsrf_core_stubs.jar"/>
-	<classpathentry kind="lib" path="lib/wsrf_core.jar"/>
-	<classpathentry kind="lib" path="lib/wsrf_provider_jce.jar"/>
-	<classpathentry kind="lib" path="lib/wsrf_tools.jar"/>
-	<classpathentry kind="lib" path="lib/wss4j.jar"/>
-	<classpathentry kind="lib" path="lib/xmlsec.jar"/>
-	<classpathentry kind="lib" path="lib/Dispatcher-client.jar" sourcepath="C:/java/apps/eclipse_cagrid_workspace/Dispatcher/src"/>
-	<classpathentry kind="lib" path="lib/axis.jar" sourcepath="C:/java/jar_source/axis-1_2RC2/src"/>
-	<classpathentry kind="lib" path="lib/addressing-1.0.jar"/>
-	<classpathentry kind="lib" path="lib/cog-axis.jar"/>
-	<classpathentry kind="lib" path="lib/cog-jglobus.jar"/>
-	<classpathentry kind="lib" path="lib/cog-tomcat.jar"/>
-	<classpathentry kind="lib" path="lib/cog-url.jar"/>
-	<classpathentry kind="lib" path="lib/binding-2.0.4.jar"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/geworkbench-core"/>
-	<classpathentry kind="lib" path="lib/caGrid-core-1.4.jar"/>
-	<classpathentry kind="lib" path="lib/caGrid-discovery-1.4.jar"/>
-	<classpathentry kind="lib" path="lib/caGrid-metadata-common-1.4.jar"/>
-	<classpathentry kind="lib" path="lib/caGrid-metadata-data-1.4.jar"/>
-	<classpathentry kind="lib" path="lib/caGrid-metadata-security-1.4.jar"/>
-	<classpathentry kind="lib" path="lib/caGrid-metadatautils-1.4.jar"/>
-	<classpathentry kind="lib" path="lib/caGrid-ServiceSecurityProvider-client-1.4.jar"/>
-	<classpathentry kind="lib" path="lib/caGrid-ServiceSecurityProvider-common-1.4.jar"/>
-	<classpathentry kind="lib" path="lib/caGrid-ServiceSecurityProvider-service-1.4.jar"/>
-	<classpathentry kind="lib" path="lib/caGrid-ServiceSecurityProvider-stubs-1.4.jar"/>
-	<classpathentry kind="lib" path="lib/Dispatcher-common.jar"/>
-	<classpathentry kind="lib" path="lib/Dispatcher-stubs.jar"/>
-	<classpathentry kind="output" path="classes"/>
-</classpath>
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="src" path="src"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
+	<classpathentry kind="lib" path="lib/JSciCore.jar"/>
+	<classpathentry kind="lib" path="lib/commons-cli-2.0.jar"/>
+	<classpathentry kind="lib" path="lib/jaxrpc.jar"/>
+	<classpathentry kind="lib" path="lib/jce-jdk13-125.jar"/>
+	<classpathentry kind="lib" path="lib/jgss.jar"/>
+	<classpathentry kind="lib" path="lib/junit.jar"/>
+	<classpathentry kind="lib" path="lib/log4j-1.2.8.jar"/>
+	<classpathentry kind="lib" path="lib/mageUtility.jar"/>
+	<classpathentry kind="lib" path="lib/microarrayUtility.jar"/>
+	<classpathentry kind="lib" path="lib/saaj.jar"/>
+	<classpathentry kind="lib" path="lib/statmlutil.jar"/>
+	<classpathentry kind="lib" path="lib/wsdl4j.jar"/>
+	<classpathentry kind="lib" path="lib/wsrf_common.jar"/>
+	<classpathentry kind="lib" path="lib/wsrf_core_registry_stubs.jar"/>
+	<classpathentry kind="lib" path="lib/wsrf_core_registry.jar"/>
+	<classpathentry kind="lib" path="lib/wsrf_core_stubs.jar"/>
+	<classpathentry kind="lib" path="lib/wsrf_core.jar"/>
+	<classpathentry kind="lib" path="lib/wsrf_provider_jce.jar"/>
+	<classpathentry kind="lib" path="lib/wsrf_tools.jar"/>
+	<classpathentry kind="lib" path="lib/wss4j.jar"/>
+	<classpathentry kind="lib" path="lib/xmlsec.jar"/>
+	<classpathentry kind="lib" path="lib/Dispatcher-client.jar" sourcepath="C:/java/apps/eclipse_cagrid_workspace/Dispatcher/src"/>
+	<classpathentry kind="lib" path="lib/axis.jar" sourcepath="C:/java/jar_source/axis-1_2RC2/src"/>
+	<classpathentry kind="lib" path="lib/addressing-1.0.jar"/>
+	<classpathentry kind="lib" path="lib/cog-axis.jar"/>
+	<classpathentry kind="lib" path="lib/cog-jglobus.jar"/>
+	<classpathentry kind="lib" path="lib/cog-tomcat.jar"/>
+	<classpathentry kind="lib" path="lib/cog-url.jar"/>
+	<classpathentry kind="lib" path="lib/binding-2.0.4.jar"/>
+	<classpathentry combineaccessrules="false" kind="src" path="/geworkbench-core"/>
+	<classpathentry kind="lib" path="lib/caGrid-core-1.4.jar"/>
+	<classpathentry kind="lib" path="lib/caGrid-discovery-1.4.jar"/>
+	<classpathentry kind="lib" path="lib/caGrid-metadata-common-1.4.jar"/>
+	<classpathentry kind="lib" path="lib/caGrid-metadata-data-1.4.jar"/>
+	<classpathentry kind="lib" path="lib/caGrid-metadata-security-1.4.jar"/>
+	<classpathentry kind="lib" path="lib/caGrid-metadatautils-1.4.jar"/>
+	<classpathentry kind="lib" path="lib/caGrid-ServiceSecurityProvider-client-1.4.jar"/>
+	<classpathentry kind="lib" path="lib/caGrid-ServiceSecurityProvider-common-1.4.jar"/>
+	<classpathentry kind="lib" path="lib/caGrid-ServiceSecurityProvider-service-1.4.jar"/>
+	<classpathentry kind="lib" path="lib/caGrid-ServiceSecurityProvider-stubs-1.4.jar"/>
+	<classpathentry kind="lib" path="lib/Dispatcher-common.jar"/>
+	<classpathentry kind="lib" path="lib/Dispatcher-stubs.jar"/>
+	<classpathentry kind="lib" path="lib/caGrid-Transfer-client-1.4.jar"/>
+	<classpathentry kind="lib" path="lib/caGrid-Transfer-common-1.4.jar"/>
+	<classpathentry kind="lib" path="lib/caGrid-Transfer-stubs-1.4.jar"/>
+	<classpathentry kind="output" path="classes"/>
+</classpath>
diff --git a/geworkbench-core/components/analysis/lib/.svn/all-wcprops b/geworkbench-core/components/analysis/lib/.svn/all-wcprops
index 26d3808..f6be00c 100644
--- a/geworkbench-core/components/analysis/lib/.svn/all-wcprops
+++ b/geworkbench-core/components/analysis/lib/.svn/all-wcprops
@@ -1,7 +1,7 @@
 K 25
 svn:wc:ra_dav:version-url
 V 72
-/svn/geworkbench/!svn/ver/8612/trunk/geworkbench/components/analysis/lib
+/svn/geworkbench/!svn/ver/8737/trunk/geworkbench/components/analysis/lib
 END
 axis.jar
 K 25
@@ -49,7 +49,7 @@ Dispatcher-common.jar
 K 25
 svn:wc:ra_dav:version-url
 V 94
-/svn/geworkbench/!svn/ver/5218/trunk/geworkbench/components/analysis/lib/Dispatcher-common.jar
+/svn/geworkbench/!svn/ver/8737/trunk/geworkbench/components/analysis/lib/Dispatcher-common.jar
 END
 caGrid-metadata-security-1.4.jar
 K 25
@@ -79,7 +79,7 @@ Dispatcher-stubs.jar
 K 25
 svn:wc:ra_dav:version-url
 V 93
-/svn/geworkbench/!svn/ver/5218/trunk/geworkbench/components/analysis/lib/Dispatcher-stubs.jar
+/svn/geworkbench/!svn/ver/8737/trunk/geworkbench/components/analysis/lib/Dispatcher-stubs.jar
 END
 jaxrpc.jar
 K 25
@@ -87,6 +87,12 @@ svn:wc:ra_dav:version-url
 V 83
 /svn/geworkbench/!svn/ver/2527/trunk/geworkbench/components/analysis/lib/jaxrpc.jar
 END
+caGrid-Transfer-client-1.4.jar
+K 25
+svn:wc:ra_dav:version-url
+V 103
+/svn/geworkbench/!svn/ver/8737/trunk/geworkbench/components/analysis/lib/caGrid-Transfer-client-1.4.jar
+END
 caGrid-metadatautils-1.4.jar
 K 25
 svn:wc:ra_dav:version-url
@@ -121,7 +127,7 @@ Dispatcher-client.jar
 K 25
 svn:wc:ra_dav:version-url
 V 94
-/svn/geworkbench/!svn/ver/5218/trunk/geworkbench/components/analysis/lib/Dispatcher-client.jar
+/svn/geworkbench/!svn/ver/8737/trunk/geworkbench/components/analysis/lib/Dispatcher-client.jar
 END
 jgss.jar
 K 25
@@ -129,11 +135,11 @@ svn:wc:ra_dav:version-url
 V 81
 /svn/geworkbench/!svn/ver/2527/trunk/geworkbench/components/analysis/lib/jgss.jar
 END
-wss4j.jar
+caGrid-Transfer-stubs-1.4.jar
 K 25
 svn:wc:ra_dav:version-url
-V 82
-/svn/geworkbench/!svn/ver/2527/trunk/geworkbench/components/analysis/lib/wss4j.jar
+V 102
+/svn/geworkbench/!svn/ver/8737/trunk/geworkbench/components/analysis/lib/caGrid-Transfer-stubs-1.4.jar
 END
 cog-axis.jar
 K 25
@@ -141,6 +147,12 @@ svn:wc:ra_dav:version-url
 V 85
 /svn/geworkbench/!svn/ver/2527/trunk/geworkbench/components/analysis/lib/cog-axis.jar
 END
+wss4j.jar
+K 25
+svn:wc:ra_dav:version-url
+V 82
+/svn/geworkbench/!svn/ver/2527/trunk/geworkbench/components/analysis/lib/wss4j.jar
+END
 wsrf_provider_jce.jar
 K 25
 svn:wc:ra_dav:version-url
@@ -153,18 +165,18 @@ svn:wc:ra_dav:version-url
 V 92
 /svn/geworkbench/!svn/ver/2527/trunk/geworkbench/components/analysis/lib/commons-cli-2.0.jar
 END
-saaj.jar
-K 25
-svn:wc:ra_dav:version-url
-V 81
-/svn/geworkbench/!svn/ver/2527/trunk/geworkbench/components/analysis/lib/saaj.jar
-END
 caGrid-metadata-data-1.4.jar
 K 25
 svn:wc:ra_dav:version-url
 V 101
 /svn/geworkbench/!svn/ver/8612/trunk/geworkbench/components/analysis/lib/caGrid-metadata-data-1.4.jar
 END
+saaj.jar
+K 25
+svn:wc:ra_dav:version-url
+V 81
+/svn/geworkbench/!svn/ver/2527/trunk/geworkbench/components/analysis/lib/saaj.jar
+END
 addressing-1.0.jar
 K 25
 svn:wc:ra_dav:version-url
@@ -243,6 +255,12 @@ svn:wc:ra_dav:version-url
 V 87
 /svn/geworkbench/!svn/ver/2527/trunk/geworkbench/components/analysis/lib/wsrf_tools.jar
 END
+caGrid-Transfer-common-1.4.jar
+K 25
+svn:wc:ra_dav:version-url
+V 103
+/svn/geworkbench/!svn/ver/8737/trunk/geworkbench/components/analysis/lib/caGrid-Transfer-common-1.4.jar
+END
 statmlutil.jar
 K 25
 svn:wc:ra_dav:version-url
diff --git a/geworkbench-core/components/analysis/lib/.svn/entries b/geworkbench-core/components/analysis/lib/.svn/entries
index 8e2e5ec..80f0ec9 100644
--- a/geworkbench-core/components/analysis/lib/.svn/entries
+++ b/geworkbench-core/components/analysis/lib/.svn/entries
@@ -1,14 +1,14 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/analysis/lib
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2011-12-15T22:06:14.698630Z
-8612
+2012-01-19T16:03:43.681238Z
+8737
 wangmen


@@ -270,11 +270,11 @@ file



-2011-08-17T00:10:37.000000Z
-9ff5494c5f2459cb08d661d35813c42c
-2009-06-12T01:31:06.000000Z
-5218
-jiz
+2012-01-31T19:12:32.000000Z
+3c640d633ee8fca3a5539448054e8211
+2012-01-19T16:03:43.681238Z
+8737
+wangmen
 has-props


@@ -296,7 +296,7 @@ has-props



-4534
+3008

 caGrid-metadata-security-1.4.jar
 file
@@ -440,11 +440,11 @@ file



-2011-08-17T00:10:37.000000Z
-9d225a470ff1a415029b210b80d147f3
-2009-06-12T01:31:06.000000Z
-5218
-jiz
+2012-01-31T19:12:32.000000Z
+e6b12825fc9c2becd24643d4d8b72de6
+2012-01-19T16:03:43.681238Z
+8737
+wangmen
 has-props


@@ -466,7 +466,7 @@ has-props



-35994
+38087

 jaxrpc.jar
 file
@@ -502,6 +502,40 @@ has-props

 35081

+caGrid-Transfer-client-1.4.jar
+file
+
+
+
+
+2012-01-31T19:12:32.000000Z
+40206274d993486833a36fd638b4f34e
+2012-01-19T16:03:43.681238Z
+8737
+wangmen
+has-props
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+22805
+
 caGrid-metadatautils-1.4.jar
 file

@@ -678,11 +712,11 @@ file



-2011-08-17T00:10:37.000000Z
-673cbfd2ffece8bc7096c4a1993888cb
-2009-06-12T01:31:06.000000Z
-5218
-jiz
+2012-01-31T19:12:32.000000Z
+cfbb4d44454f0c2c1bf53f8bf61706de
+2012-01-19T16:03:43.681238Z
+8737
+wangmen
 has-props


@@ -704,7 +738,7 @@ has-props



-13924
+9624

 jgss.jar
 file
@@ -740,17 +774,17 @@ has-props

 6567

-cog-axis.jar
+caGrid-Transfer-stubs-1.4.jar
 file




-2011-08-17T00:10:37.000000Z
-38fb9f4d4d9b2b0d7b038686803db11b
-2007-03-14T20:34:44.000000Z
-2527
-keshav
+2012-01-31T19:12:32.000000Z
+54d99581120c49013f01d5ae7911f863
+2012-01-19T16:03:43.681238Z
+8737
+wangmen
 has-props


@@ -772,7 +806,7 @@ has-props



-30127
+64209

 wss4j.jar
 file
@@ -808,14 +842,14 @@ has-props

 514673

-wsrf_provider_jce.jar
+cog-axis.jar
 file




 2011-08-17T00:10:37.000000Z
-26b6c4a3ff9dbb20da06c6edf08d81dd
+38fb9f4d4d9b2b0d7b038686803db11b
 2007-03-14T20:34:44.000000Z
 2527
 keshav
@@ -840,16 +874,16 @@ has-props



-10019
+30127

-commons-cli-2.0.jar
+wsrf_provider_jce.jar
 file




 2011-08-17T00:10:37.000000Z
-c025dd25b35dd0ef7f4faa189adf346e
+26b6c4a3ff9dbb20da06c6edf08d81dd
 2007-03-14T20:34:44.000000Z
 2527
 keshav
@@ -874,16 +908,16 @@ has-props



-131140
+10019

-saaj.jar
+commons-cli-2.0.jar
 file




 2011-08-17T00:10:37.000000Z
-fa0706bd9bcb29f522c1a08db1cbcd94
+c025dd25b35dd0ef7f4faa189adf346e
 2007-03-14T20:34:44.000000Z
 2527
 keshav
@@ -908,7 +942,7 @@ has-props



-19712
+131140

 caGrid-metadata-data-1.4.jar
 file
@@ -944,6 +978,40 @@ has-props

 37519

+saaj.jar
+file
+
+
+
+
+2011-08-17T00:10:37.000000Z
+fa0706bd9bcb29f522c1a08db1cbcd94
+2007-03-14T20:34:44.000000Z
+2527
+keshav
+has-props
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+19712
+
 addressing-1.0.jar
 file

@@ -1386,6 +1454,40 @@ has-props

 49998

+caGrid-Transfer-common-1.4.jar
+file
+
+
+
+
+2012-01-31T19:12:32.000000Z
+222526359dd2f8841e38921d94f510ef
+2012-01-19T16:03:43.681238Z
+8737
+wangmen
+has-props
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+7196
+
 statmlutil.jar
 file

diff --git a/geworkbench-core/components/analysis/lib/.svn/text-base/Dispatcher-client.jar.svn-base b/geworkbench-core/components/analysis/lib/.svn/text-base/Dispatcher-client.jar.svn-base
index 51c1b34..b2d5a78 100644
Binary files a/geworkbench-core/components/analysis/lib/.svn/text-base/Dispatcher-client.jar.svn-base and b/geworkbench-core/components/analysis/lib/.svn/text-base/Dispatcher-client.jar.svn-base differ
diff --git a/geworkbench-core/components/analysis/lib/.svn/text-base/Dispatcher-common.jar.svn-base b/geworkbench-core/components/analysis/lib/.svn/text-base/Dispatcher-common.jar.svn-base
index c04779d..885f66f 100644
Binary files a/geworkbench-core/components/analysis/lib/.svn/text-base/Dispatcher-common.jar.svn-base and b/geworkbench-core/components/analysis/lib/.svn/text-base/Dispatcher-common.jar.svn-base differ
diff --git a/geworkbench-core/components/analysis/lib/.svn/text-base/Dispatcher-stubs.jar.svn-base b/geworkbench-core/components/analysis/lib/.svn/text-base/Dispatcher-stubs.jar.svn-base
index 06f4c94..159248c 100644
Binary files a/geworkbench-core/components/analysis/lib/.svn/text-base/Dispatcher-stubs.jar.svn-base and b/geworkbench-core/components/analysis/lib/.svn/text-base/Dispatcher-stubs.jar.svn-base differ
diff --git a/geworkbench-core/components/analysis/lib/Dispatcher-client.jar b/geworkbench-core/components/analysis/lib/Dispatcher-client.jar
index 51c1b34..b2d5a78 100755
Binary files a/geworkbench-core/components/analysis/lib/Dispatcher-client.jar and b/geworkbench-core/components/analysis/lib/Dispatcher-client.jar differ
diff --git a/geworkbench-core/components/analysis/lib/Dispatcher-common.jar b/geworkbench-core/components/analysis/lib/Dispatcher-common.jar
index c04779d..885f66f 100755
Binary files a/geworkbench-core/components/analysis/lib/Dispatcher-common.jar and b/geworkbench-core/components/analysis/lib/Dispatcher-common.jar differ
diff --git a/geworkbench-core/components/analysis/lib/Dispatcher-stubs.jar b/geworkbench-core/components/analysis/lib/Dispatcher-stubs.jar
index 06f4c94..159248c 100755
Binary files a/geworkbench-core/components/analysis/lib/Dispatcher-stubs.jar and b/geworkbench-core/components/analysis/lib/Dispatcher-stubs.jar differ
diff --git a/geworkbench-core/components/analysis/src/.svn/all-wcprops b/geworkbench-core/components/analysis/src/.svn/all-wcprops
index c873ba3..77dc34d 100644
--- a/geworkbench-core/components/analysis/src/.svn/all-wcprops
+++ b/geworkbench-core/components/analysis/src/.svn/all-wcprops
@@ -1,5 +1,5 @@
 K 25
 svn:wc:ra_dav:version-url
 V 72
-/svn/geworkbench/!svn/ver/8650/trunk/geworkbench/components/analysis/src
+/svn/geworkbench/!svn/ver/8773/trunk/geworkbench/components/analysis/src
 END
diff --git a/geworkbench-core/components/analysis/src/.svn/entries b/geworkbench-core/components/analysis/src/.svn/entries
index 5cdc0ac..6105723 100644
--- a/geworkbench-core/components/analysis/src/.svn/entries
+++ b/geworkbench-core/components/analysis/src/.svn/entries
@@ -1,15 +1,15 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/analysis/src
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2012-01-05T18:11:48.744157Z
-8650
-zji
+2012-01-25T22:33:51.735887Z
+8773
+wangmen



diff --git a/geworkbench-core/components/analysis/src/edu/.svn/entries b/geworkbench-core/components/analysis/src/edu/.svn/entries
index 7d16caf..3653593 100644
--- a/geworkbench-core/components/analysis/src/edu/.svn/entries
+++ b/geworkbench-core/components/analysis/src/edu/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/analysis/src/edu
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/analysis/src/edu/columbia/.svn/entries b/geworkbench-core/components/analysis/src/edu/columbia/.svn/entries
index d9b63b7..367f743 100644
--- a/geworkbench-core/components/analysis/src/edu/columbia/.svn/entries
+++ b/geworkbench-core/components/analysis/src/edu/columbia/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/analysis/src/edu/columbia
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/analysis/src/edu/columbia/geworkbench/.svn/entries b/geworkbench-core/components/analysis/src/edu/columbia/geworkbench/.svn/entries
index b3bae2e..9a4f30b 100644
--- a/geworkbench-core/components/analysis/src/edu/columbia/geworkbench/.svn/entries
+++ b/geworkbench-core/components/analysis/src/edu/columbia/geworkbench/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/analysis/src/edu/columbia/geworkbench
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/analysis/src/edu/columbia/geworkbench/cagrid/.svn/entries b/geworkbench-core/components/analysis/src/edu/columbia/geworkbench/cagrid/.svn/entries
index 142766a..2eb4457 100644
--- a/geworkbench-core/components/analysis/src/edu/columbia/geworkbench/cagrid/.svn/entries
+++ b/geworkbench-core/components/analysis/src/edu/columbia/geworkbench/cagrid/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/analysis/src/edu/columbia/geworkbench/cagrid
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/analysis/src/edu/columbia/geworkbench/cagrid/discovery/.svn/entries b/geworkbench-core/components/analysis/src/edu/columbia/geworkbench/cagrid/discovery/.svn/entries
index 078b7cb..3bc5bc5 100644
--- a/geworkbench-core/components/analysis/src/edu/columbia/geworkbench/cagrid/discovery/.svn/entries
+++ b/geworkbench-core/components/analysis/src/edu/columbia/geworkbench/cagrid/discovery/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/analysis/src/edu/columbia/geworkbench/cagrid/discovery
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/analysis/src/edu/columbia/geworkbench/cagrid/discovery/client/.svn/entries b/geworkbench-core/components/analysis/src/edu/columbia/geworkbench/cagrid/discovery/client/.svn/entries
index 6636e00..26c96fe 100644
--- a/geworkbench-core/components/analysis/src/edu/columbia/geworkbench/cagrid/discovery/client/.svn/entries
+++ b/geworkbench-core/components/analysis/src/edu/columbia/geworkbench/cagrid/discovery/client/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/analysis/src/edu/columbia/geworkbench/cagrid/discovery/client
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/analysis/src/org/.svn/all-wcprops b/geworkbench-core/components/analysis/src/org/.svn/all-wcprops
index 7200c00..b4ca1ee 100644
--- a/geworkbench-core/components/analysis/src/org/.svn/all-wcprops
+++ b/geworkbench-core/components/analysis/src/org/.svn/all-wcprops
@@ -1,5 +1,5 @@
 K 25
 svn:wc:ra_dav:version-url
 V 76
-/svn/geworkbench/!svn/ver/8650/trunk/geworkbench/components/analysis/src/org
+/svn/geworkbench/!svn/ver/8773/trunk/geworkbench/components/analysis/src/org
 END
diff --git a/geworkbench-core/components/analysis/src/org/.svn/entries b/geworkbench-core/components/analysis/src/org/.svn/entries
index 8dbece0..7cdb44b 100644
--- a/geworkbench-core/components/analysis/src/org/.svn/entries
+++ b/geworkbench-core/components/analysis/src/org/.svn/entries
@@ -1,15 +1,15 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/analysis/src/org
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2012-01-05T18:11:48.744157Z
-8650
-zji
+2012-01-25T22:33:51.735887Z
+8773
+wangmen



diff --git a/geworkbench-core/components/analysis/src/org/geworkbench/.svn/all-wcprops b/geworkbench-core/components/analysis/src/org/geworkbench/.svn/all-wcprops
index c1090f7..8568a68 100644
--- a/geworkbench-core/components/analysis/src/org/geworkbench/.svn/all-wcprops
+++ b/geworkbench-core/components/analysis/src/org/geworkbench/.svn/all-wcprops
@@ -1,5 +1,5 @@
 K 25
 svn:wc:ra_dav:version-url
 V 88
-/svn/geworkbench/!svn/ver/8650/trunk/geworkbench/components/analysis/src/org/geworkbench
+/svn/geworkbench/!svn/ver/8773/trunk/geworkbench/components/analysis/src/org/geworkbench
 END
diff --git a/geworkbench-core/components/analysis/src/org/geworkbench/.svn/entries b/geworkbench-core/components/analysis/src/org/geworkbench/.svn/entries
index 4c8b1a0..1ce3aa1 100644
--- a/geworkbench-core/components/analysis/src/org/geworkbench/.svn/entries
+++ b/geworkbench-core/components/analysis/src/org/geworkbench/.svn/entries
@@ -1,15 +1,15 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/analysis/src/org/geworkbench
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2012-01-05T18:11:48.744157Z
-8650
-zji
+2012-01-25T22:33:51.735887Z
+8773
+wangmen



diff --git a/geworkbench-core/components/analysis/src/org/geworkbench/components/.svn/all-wcprops b/geworkbench-core/components/analysis/src/org/geworkbench/components/.svn/all-wcprops
index 1d389a5..c71b8b5 100644
--- a/geworkbench-core/components/analysis/src/org/geworkbench/components/.svn/all-wcprops
+++ b/geworkbench-core/components/analysis/src/org/geworkbench/components/.svn/all-wcprops
@@ -1,5 +1,5 @@
 K 25
 svn:wc:ra_dav:version-url
 V 99
-/svn/geworkbench/!svn/ver/8650/trunk/geworkbench/components/analysis/src/org/geworkbench/components
+/svn/geworkbench/!svn/ver/8773/trunk/geworkbench/components/analysis/src/org/geworkbench/components
 END
diff --git a/geworkbench-core/components/analysis/src/org/geworkbench/components/.svn/entries b/geworkbench-core/components/analysis/src/org/geworkbench/components/.svn/entries
index 5db3484..cf587d5 100644
--- a/geworkbench-core/components/analysis/src/org/geworkbench/components/.svn/entries
+++ b/geworkbench-core/components/analysis/src/org/geworkbench/components/.svn/entries
@@ -1,15 +1,15 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/analysis/src/org/geworkbench/components
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2012-01-05T18:11:48.744157Z
-8650
-zji
+2012-01-25T22:33:51.735887Z
+8773
+wangmen



diff --git a/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/.svn/all-wcprops b/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/.svn/all-wcprops
index efa814f..13b1e7c 100644
--- a/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/.svn/all-wcprops
+++ b/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/.svn/all-wcprops
@@ -1,13 +1,13 @@
 K 25
 svn:wc:ra_dav:version-url
 V 108
-/svn/geworkbench/!svn/ver/8650/trunk/geworkbench/components/analysis/src/org/geworkbench/components/analysis
+/svn/geworkbench/!svn/ver/8773/trunk/geworkbench/components/analysis/src/org/geworkbench/components/analysis
 END
 AnalysisPanel.java
 K 25
 svn:wc:ra_dav:version-url
 V 127
-/svn/geworkbench/!svn/ver/8650/trunk/geworkbench/components/analysis/src/org/geworkbench/components/analysis/AnalysisPanel.java
+/svn/geworkbench/!svn/ver/8744/trunk/geworkbench/components/analysis/src/org/geworkbench/components/analysis/AnalysisPanel.java
 END
 AnalysisPanel.cwb.xml
 K 25
@@ -19,5 +19,5 @@ PollingThread.java
 K 25
 svn:wc:ra_dav:version-url
 V 127
-/svn/geworkbench/!svn/ver/7362/trunk/geworkbench/components/analysis/src/org/geworkbench/components/analysis/PollingThread.java
+/svn/geworkbench/!svn/ver/8773/trunk/geworkbench/components/analysis/src/org/geworkbench/components/analysis/PollingThread.java
 END
diff --git a/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/.svn/entries b/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/.svn/entries
index cca7c5f..9c88755 100644
--- a/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/.svn/entries
+++ b/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/.svn/entries
@@ -1,15 +1,15 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/analysis/src/org/geworkbench/components/analysis
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2012-01-05T18:11:48.744157Z
-8650
-zji
+2012-01-25T22:33:51.735887Z
+8773
+wangmen



@@ -32,11 +32,11 @@ file



-2012-01-10T21:28:12.000000Z
-18402ea73e448eaac0ae73325bfc3e4c
-2012-01-05T18:11:48.744157Z
-8650
-zji
+2012-01-31T19:12:32.000000Z
+58259330c6a4e1dc39404e784b1c1be2
+2012-01-20T16:27:33.262292Z
+8744
+youmi
 has-props


@@ -58,7 +58,7 @@ has-props



-43532
+40244

 help
 dir
@@ -103,11 +103,11 @@ file



-2011-08-17T00:10:37.000000Z
-07aa1d152a23e5a857b9a5c49ae32228
-2010-12-21T22:09:19.155263Z
-7362
-zji
+2012-01-31T19:12:32.000000Z
+e36bd80ed2a9f829e00ce6bea64c3df8
+2012-01-25T22:33:51.735887Z
+8773
+wangmen
 has-props


@@ -129,5 +129,5 @@ has-props



-2473
+2604

diff --git a/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/.svn/text-base/AnalysisPanel.java.svn-base b/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/.svn/text-base/AnalysisPanel.java.svn-base
index 430bbc6..0bd9755 100644
--- a/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/.svn/text-base/AnalysisPanel.java.svn-base
+++ b/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/.svn/text-base/AnalysisPanel.java.svn-base
@@ -47,20 +47,17 @@ import org.geworkbench.analysis.HighlightCurrentParameterThread;
 import org.geworkbench.analysis.ParameterKey;
 import org.geworkbench.analysis.ReHighlightable;
 import org.geworkbench.bison.datastructure.biocollections.DSAncillaryDataSet;
-import org.geworkbench.bison.datastructure.biocollections.DSDataSet;
-import org.geworkbench.bison.datastructure.biocollections.microarrays.CSMicroarraySet;
+import org.geworkbench.bison.datastructure.biocollections.DSDataSet;
 import org.geworkbench.bison.datastructure.biocollections.microarrays.DSMicroarraySet;
 import org.geworkbench.bison.datastructure.biocollections.sequences.CSSequenceSet;
 import org.geworkbench.bison.datastructure.biocollections.views.CSMicroarraySetView;
 import org.geworkbench.bison.datastructure.biocollections.views.DSMicroarraySetView;
-import org.geworkbench.bison.datastructure.bioobjects.DSBioObject;
-import org.geworkbench.bison.datastructure.bioobjects.markers.CSExpressionMarker;
+import org.geworkbench.bison.datastructure.bioobjects.DSBioObject;
 import org.geworkbench.bison.datastructure.bioobjects.markers.DSGeneMarker;
 import org.geworkbench.bison.datastructure.bioobjects.microarray.DSMarkerValue;
 import org.geworkbench.bison.datastructure.bioobjects.microarray.DSMicroarray;
 import org.geworkbench.bison.datastructure.bioobjects.structure.CSProteinStructure;
-import org.geworkbench.bison.datastructure.complex.panels.CSPanel;
-import org.geworkbench.bison.datastructure.complex.panels.DSItemList;
+import org.geworkbench.bison.datastructure.complex.panels.CSPanel;
 import org.geworkbench.bison.datastructure.complex.panels.DSPanel;
 import org.geworkbench.bison.model.analysis.AlgorithmExecutionResults;
 import org.geworkbench.bison.model.analysis.Analysis;
@@ -248,8 +245,9 @@ public class AnalysisPanel extends CommandBase implements

 		analyze.addActionListener(new ActionListener() {
 			public void actionPerformed(ActionEvent e) {
-				analyze_actionPerformed(e);
-				hideDialog();
+				if(startAnalysis()) {
+					hideDialog();
+				}
 			}

 		});
@@ -377,87 +375,7 @@ public class AnalysisPanel extends CommandBase implements

 	}

-	/**
-	 *
-	 * @param maSetView
-	 * @return
-	 */
-	private String generateHistoryString(DSMicroarraySetView<DSGeneMarker, DSMicroarray> maSetView) {
-		StringBuilder ans = new StringBuilder("=The MicroarraySetView used for analysis contains the following data: ");
-		/* Generate text for microarrays/groups */
-		ans .append( FileTools.NEWLINE );
-		try {
-			log.debug("We got a " + maSetView.items().getClass().toString());
-			if (maSetView.items().getClass() == CSPanel.class) {
-				log.debug("situation 1: microarraySets selected");
-				DSItemList<DSPanel<DSMicroarray>> paneltest = ((DSPanel<DSMicroarray>) maSetView.items()).panels();
-
-				ans .append( "==Microarray Sets [" ).append( paneltest.size() + "]==" ).append(
-						 FileTools.NEWLINE );
-				for(DSPanel<DSMicroarray> temp: paneltest) {
-					ans .append( FileTools.TAB + temp.toString() ).append( FileTools.NEWLINE );
-					for (DSMicroarray temp2: temp) {
-						ans .append( FileTools.TAB ).append( FileTools.TAB ).append( temp2.toString() )
-								.append( FileTools.NEWLINE );
-					}
-				}
-			} else if (maSetView.items().getClass() == CSMicroarraySet.class) {
-				log.debug("situation 2: microarraySets not selected");
-				CSMicroarraySet exprSet = (CSMicroarraySet) maSetView
-						.items();
-				ans .append( "==Used Microarrays [" ).append( exprSet.size() ).append( "]==" )
-						.append( FileTools.NEWLINE );
-				for (Iterator<DSMicroarray> iterator = exprSet.iterator(); iterator
-						.hasNext();) {
-					DSMicroarray array = iterator.next();
-					ans .append( FileTools.TAB ).append( array.getLabel() ).append( FileTools.NEWLINE );
-				}
-			}
-			ans .append( "==End of Microarray Sets==" ).append( FileTools.NEWLINE );
-			/* Generate text for markers */
-			DSPanel<DSGeneMarker> paneltest = maSetView.getMarkerPanel();
-			if ((paneltest != null) && (paneltest.size() > 0)) {
-				log.debug("situation 3: markers selected");
-
-				ans .append( "==Used Markers [" ).append( paneltest.size() + "]==" )
-						.append( FileTools.NEWLINE );
-				for (DSGeneMarker obj: paneltest) {
-					CSExpressionMarker temp = (CSExpressionMarker) obj;
-					ans .append( FileTools.TAB ).append( temp.getLabel() ).append( FileTools.NEWLINE );
-				}
-			} else {
-				log.debug("situation 4: no markers selected.");
-				DSItemList<DSGeneMarker> markers = maSetView.markers();
-				ans .append( "==Used Markers [" ).append( markers.size() ).append( "]==" )
-						.append( FileTools.NEWLINE );
-				for (DSGeneMarker marker : markers) {
-					ans .append( FileTools.TAB ).append( marker.getLabel() )
-							.append( FileTools.NEWLINE );
-				}
-			}
-			ans .append( "==End of Used Markers==" ).append( FileTools.NEWLINE );
-		} catch (ClassCastException cce) {
-			/* it's not a DSPanel, we generate nothing for panel part */
-			log.error(cce);
-		}
-		ans .append( "=End of MicroarraySetView data=");
-		return ans.toString();
-	}
-
-	@SuppressWarnings("rawtypes")
-	private String generateHistoryStringForGeneralDataSet(DSDataSet dataset) {
-		if (dataset == null) {
-			return "No information on the data set." + FileTools.NEWLINE;
-		} else {
-			StringBuilder sb = new StringBuilder();
-			sb.append("The data set used for analysis is [ ");
-			sb.append(dataset.getDataSetName());
-			sb.append(" ] from file [ ");
-			sb.append(dataset.getFile());
-			sb.append(" ]." + FileTools.NEWLINE);
-			return sb.toString();
-		}
-	}
+

 	@Subscribe
 	public void receive(org.geworkbench.events.PendingNodeCancelledEvent e,
@@ -871,9 +789,10 @@ public class AnalysisPanel extends CommandBase implements
 	 * Listener invoked when the "Analyze" button is pressed.
 	 *
 	 * @param e
+	 * @return true if the analysis is actual started instead abort, e.g. for invalid input
 	 */
 	@SuppressWarnings("unchecked")
-	private void analyze_actionPerformed(ActionEvent e) {
+	private boolean startAnalysis() {
 		maSetView = getDataSetView();

 		boolean onlyActivatedArrays = false;
@@ -892,7 +811,7 @@ public class AnalysisPanel extends CommandBase implements
 				int result = JOptionPane.showConfirmDialog((Component) null,
 						theMessage, "alert", JOptionPane.YES_NO_OPTION);
 				if (result == JOptionPane.NO_OPTION)
-					return;
+					return false;
 			}
 		} else {
 			onlyActivatedArrays = !chkAllArrays.isSelected();
@@ -900,7 +819,7 @@ public class AnalysisPanel extends CommandBase implements

 		if (selectedAnalysis == null
 				|| ((refMASet == null) && (refOtherSet == null))) {
-			return;
+			return false;
 		}

 		if (refOtherSet != null) { /*
@@ -921,6 +840,7 @@ public class AnalysisPanel extends CommandBase implements
 		if (!pvr.isValid()) {
 			JOptionPane.showMessageDialog(null, pvr.getMessage(),
 					"Parameter Validation Error", JOptionPane.ERROR_MESSAGE);
+			return false;
 		} else {
 			analyze.setEnabled(false);
 			maSetView.useMarkerPanel(!chkAllMarkers.isSelected());
@@ -939,12 +859,14 @@ public class AnalysisPanel extends CommandBase implements
 			});
 			t.setPriority(Thread.MIN_PRIORITY);
 			t.start();
+			return true;
 		}
 	}

 	private void submitAsCaGridService() {

 		Date startDate = new Date();
+		Long startTime =startDate.getTime();

 		AbstractGridAnalysis selectedGridAnalysis = (AbstractGridAnalysis) selectedAnalysis;

@@ -1016,7 +938,7 @@ public class AnalysisPanel extends CommandBase implements
 		}

 		/* generate history for grid analysis */
-		String history = "Grid service started at: " + Util.formatDateStandard(startDate) + FileTools.NEWLINE;
+		String history = "Grid service started at: " + Util.formatDateStandard(startDate) + ", milliseconds=" + startTime + FileTools.NEWLINE;
 		history += "Grid service information:" + FileTools.NEWLINE;
 		history += FileTools.TAB + "Index server url: "
 				+ jGridServicePanel.getIndexServerUrl() + FileTools.NEWLINE;
@@ -1024,13 +946,13 @@ public class AnalysisPanel extends CommandBase implements
 				+ FileTools.NEWLINE;
 		history += FileTools.TAB + "Service url: " + url + FileTools.NEWLINE
 				+ FileTools.NEWLINE;
-		history += selectedAnalysis.createHistory()
+		history += selectedGridAnalysis.createHistory()
 	            + FileTools.NEWLINE;

 		if (refOtherSet != null) {
-			history += generateHistoryStringForGeneralDataSet(refOtherSet);
+			history += selectedGridAnalysis.generateHistoryStringForGeneralDataSet(refOtherSet);
 		} else if (maSetView != null && refMASet != null) {
-			history += generateHistoryString(maSetView);
+			history += selectedGridAnalysis.generateHistoryForMaSetView(maSetView, selectedGridAnalysis.useMarkersFromSelector());
 		}

 		ProjectPanel.getInstance().addPendingNode(gridEpr,
@@ -1096,6 +1018,7 @@ public class AnalysisPanel extends CommandBase implements
 			//add start/end time to history
 			String history = "Analysis started at: " + Util.formatDateStandard(startDate) +  FileTools.NEWLINE;
 			HistoryPanel.addBeforeToHistory(dataSet, history);
+
 			Date endDate = new Date();
 			long endTime = endDate.getTime();
 			history = "\nAnalysis finished at: "
diff --git a/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/.svn/text-base/PollingThread.java.svn-base b/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/.svn/text-base/PollingThread.java.svn-base
index d07a46a..3b1504a 100644
--- a/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/.svn/text-base/PollingThread.java.svn-base
+++ b/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/.svn/text-base/PollingThread.java.svn-base
@@ -47,23 +47,27 @@ public class PollingThread extends Thread {
 					return;
 				try {
 					result = dispatcherClient.getResults(gridEPR);
-				} catch (Exception e) {
+				} catch (Throwable e) {
 					result = e;
 				}
 			}
 			DSAncillaryDataSet<? extends DSBioObject> ancillaryDataSet = null;
-			if (result instanceof Exception) {
+			if (result instanceof Throwable) {
 				/*
 				 * Generate user understandable messages. Detailed information
 				 * is located on dispatcher server's log.debug
 				 */
 				String errorMessage = "";
-				errorMessage += ((Exception) result).getMessage();
+				errorMessage += ((Throwable) result).getMessage();

 				/* This filters out some messages */
 				errorMessage = org.geworkbench.util.Util.filter(
 						errorMessage, "java.rmi.RemoteException: ");

+				if (result instanceof OutOfMemoryError){
+					errorMessage += "\nPlease increase max heap size then try it again.";
+				}
+
 				JOptionPane.showMessageDialog(null, errorMessage,
 						"Your analysis has been canceled.",
 						JOptionPane.ERROR_MESSAGE);
diff --git a/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/AnalysisPanel.java b/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/AnalysisPanel.java
index 59a62c4..4ff706b 100755
--- a/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/AnalysisPanel.java
+++ b/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/AnalysisPanel.java
@@ -47,20 +47,17 @@ import org.geworkbench.analysis.HighlightCurrentParameterThread;
 import org.geworkbench.analysis.ParameterKey;
 import org.geworkbench.analysis.ReHighlightable;
 import org.geworkbench.bison.datastructure.biocollections.DSAncillaryDataSet;
-import org.geworkbench.bison.datastructure.biocollections.DSDataSet;
-import org.geworkbench.bison.datastructure.biocollections.microarrays.CSMicroarraySet;
+import org.geworkbench.bison.datastructure.biocollections.DSDataSet;
 import org.geworkbench.bison.datastructure.biocollections.microarrays.DSMicroarraySet;
 import org.geworkbench.bison.datastructure.biocollections.sequences.CSSequenceSet;
 import org.geworkbench.bison.datastructure.biocollections.views.CSMicroarraySetView;
 import org.geworkbench.bison.datastructure.biocollections.views.DSMicroarraySetView;
-import org.geworkbench.bison.datastructure.bioobjects.DSBioObject;
-import org.geworkbench.bison.datastructure.bioobjects.markers.CSExpressionMarker;
+import org.geworkbench.bison.datastructure.bioobjects.DSBioObject;
 import org.geworkbench.bison.datastructure.bioobjects.markers.DSGeneMarker;
 import org.geworkbench.bison.datastructure.bioobjects.microarray.DSMarkerValue;
 import org.geworkbench.bison.datastructure.bioobjects.microarray.DSMicroarray;
 import org.geworkbench.bison.datastructure.bioobjects.structure.CSProteinStructure;
-import org.geworkbench.bison.datastructure.complex.panels.CSPanel;
-import org.geworkbench.bison.datastructure.complex.panels.DSItemList;
+import org.geworkbench.bison.datastructure.complex.panels.CSPanel;
 import org.geworkbench.bison.datastructure.complex.panels.DSPanel;
 import org.geworkbench.bison.model.analysis.AlgorithmExecutionResults;
 import org.geworkbench.bison.model.analysis.Analysis;
@@ -101,7 +98,7 @@ import edu.columbia.geworkbench.cagrid.dispatcher.client.DispatcherClient;
  * @author First Genetic Trust Inc.
  * @author keshav
  * @author yc2480
- * @version $Id: AnalysisPanel.java 8650 2012-01-05 18:11:48Z zji $
+ * @version $Id: AnalysisPanel.java 8744 2012-01-20 16:27:33Z youmi $
  *
  */
 @AcceptTypes( { DSMicroarraySet.class, EdgeListDataSet.class,
@@ -248,8 +245,9 @@ public class AnalysisPanel extends CommandBase implements

 		analyze.addActionListener(new ActionListener() {
 			public void actionPerformed(ActionEvent e) {
-				analyze_actionPerformed(e);
-				hideDialog();
+				if(startAnalysis()) {
+					hideDialog();
+				}
 			}

 		});
@@ -377,87 +375,7 @@ public class AnalysisPanel extends CommandBase implements

 	}

-	/**
-	 *
-	 * @param maSetView
-	 * @return
-	 */
-	private String generateHistoryString(DSMicroarraySetView<DSGeneMarker, DSMicroarray> maSetView) {
-		StringBuilder ans = new StringBuilder("=The MicroarraySetView used for analysis contains the following data: ");
-		/* Generate text for microarrays/groups */
-		ans .append( FileTools.NEWLINE );
-		try {
-			log.debug("We got a " + maSetView.items().getClass().toString());
-			if (maSetView.items().getClass() == CSPanel.class) {
-				log.debug("situation 1: microarraySets selected");
-				DSItemList<DSPanel<DSMicroarray>> paneltest = ((DSPanel<DSMicroarray>) maSetView.items()).panels();
-
-				ans .append( "==Microarray Sets [" ).append( paneltest.size() + "]==" ).append(
-						 FileTools.NEWLINE );
-				for(DSPanel<DSMicroarray> temp: paneltest) {
-					ans .append( FileTools.TAB + temp.toString() ).append( FileTools.NEWLINE );
-					for (DSMicroarray temp2: temp) {
-						ans .append( FileTools.TAB ).append( FileTools.TAB ).append( temp2.toString() )
-								.append( FileTools.NEWLINE );
-					}
-				}
-			} else if (maSetView.items().getClass() == CSMicroarraySet.class) {
-				log.debug("situation 2: microarraySets not selected");
-				CSMicroarraySet exprSet = (CSMicroarraySet) maSetView
-						.items();
-				ans .append( "==Used Microarrays [" ).append( exprSet.size() ).append( "]==" )
-						.append( FileTools.NEWLINE );
-				for (Iterator<DSMicroarray> iterator = exprSet.iterator(); iterator
-						.hasNext();) {
-					DSMicroarray array = iterator.next();
-					ans .append( FileTools.TAB ).append( array.getLabel() ).append( FileTools.NEWLINE );
-				}
-			}
-			ans .append( "==End of Microarray Sets==" ).append( FileTools.NEWLINE );
-			/* Generate text for markers */
-			DSPanel<DSGeneMarker> paneltest = maSetView.getMarkerPanel();
-			if ((paneltest != null) && (paneltest.size() > 0)) {
-				log.debug("situation 3: markers selected");
-
-				ans .append( "==Used Markers [" ).append( paneltest.size() + "]==" )
-						.append( FileTools.NEWLINE );
-				for (DSGeneMarker obj: paneltest) {
-					CSExpressionMarker temp = (CSExpressionMarker) obj;
-					ans .append( FileTools.TAB ).append( temp.getLabel() ).append( FileTools.NEWLINE );
-				}
-			} else {
-				log.debug("situation 4: no markers selected.");
-				DSItemList<DSGeneMarker> markers = maSetView.markers();
-				ans .append( "==Used Markers [" ).append( markers.size() ).append( "]==" )
-						.append( FileTools.NEWLINE );
-				for (DSGeneMarker marker : markers) {
-					ans .append( FileTools.TAB ).append( marker.getLabel() )
-							.append( FileTools.NEWLINE );
-				}
-			}
-			ans .append( "==End of Used Markers==" ).append( FileTools.NEWLINE );
-		} catch (ClassCastException cce) {
-			/* it's not a DSPanel, we generate nothing for panel part */
-			log.error(cce);
-		}
-		ans .append( "=End of MicroarraySetView data=");
-		return ans.toString();
-	}
-
-	@SuppressWarnings("rawtypes")
-	private String generateHistoryStringForGeneralDataSet(DSDataSet dataset) {
-		if (dataset == null) {
-			return "No information on the data set." + FileTools.NEWLINE;
-		} else {
-			StringBuilder sb = new StringBuilder();
-			sb.append("The data set used for analysis is [ ");
-			sb.append(dataset.getDataSetName());
-			sb.append(" ] from file [ ");
-			sb.append(dataset.getFile());
-			sb.append(" ]." + FileTools.NEWLINE);
-			return sb.toString();
-		}
-	}
+

 	@Subscribe
 	public void receive(org.geworkbench.events.PendingNodeCancelledEvent e,
@@ -871,9 +789,10 @@ public class AnalysisPanel extends CommandBase implements
 	 * Listener invoked when the "Analyze" button is pressed.
 	 *
 	 * @param e
+	 * @return true if the analysis is actual started instead abort, e.g. for invalid input
 	 */
 	@SuppressWarnings("unchecked")
-	private void analyze_actionPerformed(ActionEvent e) {
+	private boolean startAnalysis() {
 		maSetView = getDataSetView();

 		boolean onlyActivatedArrays = false;
@@ -892,7 +811,7 @@ public class AnalysisPanel extends CommandBase implements
 				int result = JOptionPane.showConfirmDialog((Component) null,
 						theMessage, "alert", JOptionPane.YES_NO_OPTION);
 				if (result == JOptionPane.NO_OPTION)
-					return;
+					return false;
 			}
 		} else {
 			onlyActivatedArrays = !chkAllArrays.isSelected();
@@ -900,7 +819,7 @@ public class AnalysisPanel extends CommandBase implements

 		if (selectedAnalysis == null
 				|| ((refMASet == null) && (refOtherSet == null))) {
-			return;
+			return false;
 		}

 		if (refOtherSet != null) { /*
@@ -921,6 +840,7 @@ public class AnalysisPanel extends CommandBase implements
 		if (!pvr.isValid()) {
 			JOptionPane.showMessageDialog(null, pvr.getMessage(),
 					"Parameter Validation Error", JOptionPane.ERROR_MESSAGE);
+			return false;
 		} else {
 			analyze.setEnabled(false);
 			maSetView.useMarkerPanel(!chkAllMarkers.isSelected());
@@ -939,12 +859,14 @@ public class AnalysisPanel extends CommandBase implements
 			});
 			t.setPriority(Thread.MIN_PRIORITY);
 			t.start();
+			return true;
 		}
 	}

 	private void submitAsCaGridService() {

 		Date startDate = new Date();
+		Long startTime =startDate.getTime();

 		AbstractGridAnalysis selectedGridAnalysis = (AbstractGridAnalysis) selectedAnalysis;

@@ -1016,7 +938,7 @@ public class AnalysisPanel extends CommandBase implements
 		}

 		/* generate history for grid analysis */
-		String history = "Grid service started at: " + Util.formatDateStandard(startDate) + FileTools.NEWLINE;
+		String history = "Grid service started at: " + Util.formatDateStandard(startDate) + ", milliseconds=" + startTime + FileTools.NEWLINE;
 		history += "Grid service information:" + FileTools.NEWLINE;
 		history += FileTools.TAB + "Index server url: "
 				+ jGridServicePanel.getIndexServerUrl() + FileTools.NEWLINE;
@@ -1024,13 +946,13 @@ public class AnalysisPanel extends CommandBase implements
 				+ FileTools.NEWLINE;
 		history += FileTools.TAB + "Service url: " + url + FileTools.NEWLINE
 				+ FileTools.NEWLINE;
-		history += selectedAnalysis.createHistory()
+		history += selectedGridAnalysis.createHistory()
 	            + FileTools.NEWLINE;

 		if (refOtherSet != null) {
-			history += generateHistoryStringForGeneralDataSet(refOtherSet);
+			history += selectedGridAnalysis.generateHistoryStringForGeneralDataSet(refOtherSet);
 		} else if (maSetView != null && refMASet != null) {
-			history += generateHistoryString(maSetView);
+			history += selectedGridAnalysis.generateHistoryForMaSetView(maSetView, selectedGridAnalysis.useMarkersFromSelector());
 		}

 		ProjectPanel.getInstance().addPendingNode(gridEpr,
@@ -1096,6 +1018,7 @@ public class AnalysisPanel extends CommandBase implements
 			//add start/end time to history
 			String history = "Analysis started at: " + Util.formatDateStandard(startDate) +  FileTools.NEWLINE;
 			HistoryPanel.addBeforeToHistory(dataSet, history);
+
 			Date endDate = new Date();
 			long endTime = endDate.getTime();
 			history = "\nAnalysis finished at: "
diff --git a/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/PollingThread.java b/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/PollingThread.java
index 37cebcd..549b4c1 100755
--- a/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/PollingThread.java
+++ b/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/PollingThread.java
@@ -15,7 +15,7 @@ import edu.columbia.geworkbench.cagrid.dispatcher.client.DispatcherClient;
  * A thread that handles remote service polling.
  *
  * @author keshav
- * @version $Id: PollingThread.java 7362 2010-12-21 22:09:19Z zji $
+ * @version $Id: PollingThread.java 8773 2012-01-25 22:33:51Z wangmen $
  */
 public class PollingThread extends Thread {

@@ -47,23 +47,27 @@ public class PollingThread extends Thread {
 					return;
 				try {
 					result = dispatcherClient.getResults(gridEPR);
-				} catch (Exception e) {
+				} catch (Throwable e) {
 					result = e;
 				}
 			}
 			DSAncillaryDataSet<? extends DSBioObject> ancillaryDataSet = null;
-			if (result instanceof Exception) {
+			if (result instanceof Throwable) {
 				/*
 				 * Generate user understandable messages. Detailed information
 				 * is located on dispatcher server's log.debug
 				 */
 				String errorMessage = "";
-				errorMessage += ((Exception) result).getMessage();
+				errorMessage += ((Throwable) result).getMessage();

 				/* This filters out some messages */
 				errorMessage = org.geworkbench.util.Util.filter(
 						errorMessage, "java.rmi.RemoteException: ");

+				if (result instanceof OutOfMemoryError){
+					errorMessage += "\nPlease increase max heap size then try it again.";
+				}
+
 				JOptionPane.showMessageDialog(null, errorMessage,
 						"Your analysis has been canceled.",
 						JOptionPane.ERROR_MESSAGE);
diff --git a/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/.svn/entries b/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/.svn/entries
index bae32aa..b69f502 100644
--- a/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/.svn/entries
+++ b/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/analysis/src/org/geworkbench/components/analysis/help
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/Pattern Discovery/.svn/entries b/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/Pattern Discovery/.svn/entries
index 977729c..82fddf8 100644
--- a/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/Pattern Discovery/.svn/entries
+++ b/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/Pattern Discovery/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/analysis/src/org/geworkbench/components/analysis/help/Pattern%20Discovery
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/Pattern Discovery/DiscoveryOverviewed_files/.svn/entries b/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/Pattern Discovery/DiscoveryOverviewed_files/.svn/entries
index 5d29e04..090fdab 100644
--- a/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/Pattern Discovery/DiscoveryOverviewed_files/.svn/entries
+++ b/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/Pattern Discovery/DiscoveryOverviewed_files/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/analysis/src/org/geworkbench/components/analysis/help/Pattern%20Discovery/DiscoveryOverviewed_files
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/Pattern Discovery/Pattern Discovery Parameter Settings_files/.svn/entries b/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/Pattern Discovery/Pattern Discovery Parameter Settings_files/.svn/entries
index 2f4d050..0cdb010 100644
--- a/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/Pattern Discovery/Pattern Discovery Parameter Settings_files/.svn/entries
+++ b/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/Pattern Discovery/Pattern Discovery Parameter Settings_files/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/analysis/src/org/geworkbench/components/analysis/help/Pattern%20Discovery/Pattern%20Discovery%20Parameter%20Settings_files
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/clustering/.svn/entries b/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/clustering/.svn/entries
index c287a72..097af80 100644
--- a/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/clustering/.svn/entries
+++ b/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/clustering/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/analysis/src/org/geworkbench/components/analysis/help/clustering
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/clustering/Hierarchical Clusteringed_files/.svn/entries b/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/clustering/Hierarchical Clusteringed_files/.svn/entries
index 687ed26..7d33044 100644
--- a/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/clustering/Hierarchical Clusteringed_files/.svn/entries
+++ b/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/clustering/Hierarchical Clusteringed_files/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/analysis/src/org/geworkbench/components/analysis/help/clustering/Hierarchical%20Clusteringed_files
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/clustering/SOMCluster_files/.svn/entries b/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/clustering/SOMCluster_files/.svn/entries
index 2c87d8f..78324db 100644
--- a/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/clustering/SOMCluster_files/.svn/entries
+++ b/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/clustering/SOMCluster_files/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/analysis/src/org/geworkbench/components/analysis/help/clustering/SOMCluster_files
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/clustering/images/.svn/entries b/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/clustering/images/.svn/entries
index fa609ce..26a4cdf 100644
--- a/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/clustering/images/.svn/entries
+++ b/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/clustering/images/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/analysis/src/org/geworkbench/components/analysis/help/clustering/images
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/normalizers/.svn/entries b/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/normalizers/.svn/entries
index 46bdb8e..c1b660b 100644
--- a/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/normalizers/.svn/entries
+++ b/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/normalizers/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/analysis/src/org/geworkbench/components/analysis/help/normalizers
 https://ncisvn.nci.nih.gov/svn/geworkbench

@@ -378,7 +378,7 @@ has-props

 1853

-MarkerMean Normalizer.htm
+MarkerMeanNormalizer.htm
 file


@@ -386,8 +386,8 @@ file

 2011-08-17T00:10:37.000000Z
 589b4cf47ba2e9d0af7e344c3a60076a
-2005-11-14T21:51:55.000000Z
-831
+2007-01-16T17:33:02.000000Z
+2240
 edaly
 has-props

@@ -412,7 +412,7 @@ has-props

 1982

-MarkerMeanNormalizer.htm
+MarkerMean Normalizer.htm
 file


@@ -420,8 +420,8 @@ file

 2011-08-17T00:10:37.000000Z
 589b4cf47ba2e9d0af7e344c3a60076a
-2007-01-16T17:33:02.000000Z
-2240
+2005-11-14T21:51:55.000000Z
+831
 edaly
 has-props

@@ -588,16 +588,16 @@ has-props

 8077

-FilterNorm Overview.htm.bak
+Housekeeping Gene Normalization.HTML.bak
 file




 2011-08-17T00:10:37.000000Z
-1ad30021a38a0cdb6f3e4ca42219acc9
-2005-10-31T20:08:45.000000Z
-601
+a24bbea5a04a584a16723cb85db2a12d
+2005-11-21T21:47:37.000000Z
+924
 edaly
 has-props

@@ -620,18 +620,18 @@ has-props



-4840
+8277

-Housekeeping Gene Normalization.HTML.bak
+FilterNorm Overview.htm.bak
 file




 2011-08-17T00:10:37.000000Z
-a24bbea5a04a584a16723cb85db2a12d
-2005-11-21T21:47:37.000000Z
-924
+1ad30021a38a0cdb6f3e4ca42219acc9
+2005-10-31T20:08:45.000000Z
+601
 edaly
 has-props

@@ -654,16 +654,16 @@ has-props



-8277
+4840

-Threshold.HTML
+Housekeeping Gene Normalization.HTML
 file




 2011-08-17T00:10:37.000000Z
-112043435a6b856abbfc36ecfaae94f9
+a24bbea5a04a584a16723cb85db2a12d
 2005-11-21T21:47:37.000000Z
 924
 edaly
@@ -688,7 +688,7 @@ has-props



-2011
+8277

 FilterNorm Overview.htm
 file
@@ -724,14 +724,14 @@ has-props

 3558

-Housekeeping Gene Normalization.HTML
+Threshold.HTML
 file




 2011-08-17T00:10:37.000000Z
-a24bbea5a04a584a16723cb85db2a12d
+112043435a6b856abbfc36ecfaae94f9
 2005-11-21T21:47:37.000000Z
 924
 edaly
@@ -756,19 +756,19 @@ has-props



-8277
+2011

-MisValCal Normalizer.htm.bak
+foo.txt
 file




-2011-08-17T00:10:37.000000Z
-92ec183b88367d30f92449e71b6f76be
-2005-10-31T20:08:45.000000Z
-601
-edaly
+2011-09-08T15:05:43.000000Z
+d41d8cd98f00b204e9800998ecf8427e
+2005-07-28T22:36:56.000000Z
+50
+watkin
 has-props


@@ -790,19 +790,19 @@ has-props



-1853
+0

-foo.txt
+MisValCal Normalizer.htm.bak
 file




-2011-09-08T15:05:43.000000Z
-d41d8cd98f00b204e9800998ecf8427e
-2005-07-28T22:36:56.000000Z
-50
-watkin
+2011-08-17T00:10:37.000000Z
+92ec183b88367d30f92449e71b6f76be
+2005-10-31T20:08:45.000000Z
+601
+edaly
 has-props


@@ -824,7 +824,7 @@ has-props



-0
+1853

 MisValCal Normalizer.htm
 file
diff --git a/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/normalizers/Housekeeping%20Gene%20Normalization[2]_files/.svn/entries b/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/normalizers/Housekeeping%20Gene%20Normalization[2]_files/.svn/entries
index d4ffefc..b64686f 100644
--- a/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/normalizers/Housekeeping%20Gene%20Normalization[2]_files/.svn/entries
+++ b/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/normalizers/Housekeeping%20Gene%20Normalization[2]_files/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/analysis/src/org/geworkbench/components/analysis/help/normalizers/Housekeeping%2520Gene%2520Normalization%5B2%5D_files
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/normalizers/Housekeeping_files/.svn/entries b/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/normalizers/Housekeeping_files/.svn/entries
index 6e56dc0..1ac36c1 100644
--- a/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/normalizers/Housekeeping_files/.svn/entries
+++ b/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/normalizers/Housekeeping_files/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/analysis/src/org/geworkbench/components/analysis/help/normalizers/Housekeeping_files
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/normalizers/MarkerMean Normalizered_files/.svn/entries b/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/normalizers/MarkerMean Normalizered_files/.svn/entries
index 60d73e4..23e12e8 100644
--- a/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/normalizers/MarkerMean Normalizered_files/.svn/entries
+++ b/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/normalizers/MarkerMean Normalizered_files/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/analysis/src/org/geworkbench/components/analysis/help/normalizers/MarkerMean%20Normalizered_files
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/normalizers/Normalizers Overviewed_files/.svn/entries b/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/normalizers/Normalizers Overviewed_files/.svn/entries
index 313dc92..6eeadbd 100644
--- a/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/normalizers/Normalizers Overviewed_files/.svn/entries
+++ b/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/normalizers/Normalizers Overviewed_files/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/analysis/src/org/geworkbench/components/analysis/help/normalizers/Normalizers%20Overviewed_files
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/normalizers/Quantile_files/.svn/entries b/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/normalizers/Quantile_files/.svn/entries
index 4b1dba7..4023e90 100644
--- a/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/normalizers/Quantile_files/.svn/entries
+++ b/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/normalizers/Quantile_files/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/analysis/src/org/geworkbench/components/analysis/help/normalizers/Quantile_files
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/normalizers/images/.svn/entries b/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/normalizers/images/.svn/entries
index 81fdcbe..e6f775d 100644
--- a/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/normalizers/images/.svn/entries
+++ b/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/normalizers/images/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/analysis/src/org/geworkbench/components/analysis/help/normalizers/images
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/ttest/.svn/entries b/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/ttest/.svn/entries
index 2c06a54..817ff44 100644
--- a/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/ttest/.svn/entries
+++ b/geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/help/ttest/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/analysis/src/org/geworkbench/components/analysis/help/ttest
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/analysis/src/org/geworkbench/components/cagrid/.svn/entries b/geworkbench-core/components/analysis/src/org/geworkbench/components/cagrid/.svn/entries
index 006542f..58b1e60 100644
--- a/geworkbench-core/components/analysis/src/org/geworkbench/components/cagrid/.svn/entries
+++ b/geworkbench-core/components/analysis/src/org/geworkbench/components/cagrid/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/analysis/src/org/geworkbench/components/cagrid
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/analysis/src/org/geworkbench/components/cagrid/gui/.svn/entries b/geworkbench-core/components/analysis/src/org/geworkbench/components/cagrid/gui/.svn/entries
index abaee35..4f1b446 100644
--- a/geworkbench-core/components/analysis/src/org/geworkbench/components/cagrid/gui/.svn/entries
+++ b/geworkbench-core/components/analysis/src/org/geworkbench/components/cagrid/gui/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/analysis/src/org/geworkbench/components/cagrid/gui
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/annotations/.classpath b/geworkbench-core/components/annotations/.classpath
index 039b39a..5d103e5 100755
--- a/geworkbench-core/components/annotations/.classpath
+++ b/geworkbench-core/components/annotations/.classpath
@@ -1,8 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
 	<classpathentry kind="src" path="src"/>
-	<classpathentry kind="src" path="lib"/>
-	<classpathentry kind="src" path="conf"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
 	<classpathentry kind="lib" path="lib/TableViewer.jar"/>
 	<classpathentry combineaccessrules="false" kind="src" path="/geworkbench-core"/>
diff --git a/geworkbench-core/components/annotations/.svn/all-wcprops b/geworkbench-core/components/annotations/.svn/all-wcprops
index fced834..b23e90e 100644
--- a/geworkbench-core/components/annotations/.svn/all-wcprops
+++ b/geworkbench-core/components/annotations/.svn/all-wcprops
@@ -1,13 +1,13 @@
 K 25
 svn:wc:ra_dav:version-url
 V 71
-/svn/geworkbench/!svn/ver/8424/trunk/geworkbench/components/annotations
+/svn/geworkbench/!svn/ver/8723/trunk/geworkbench/components/annotations
 END
 .classpath
 K 25
 svn:wc:ra_dav:version-url
 V 82
-/svn/geworkbench/!svn/ver/6062/trunk/geworkbench/components/annotations/.classpath
+/svn/geworkbench/!svn/ver/8723/trunk/geworkbench/components/annotations/.classpath
 END
 .project
 K 25
diff --git a/geworkbench-core/components/annotations/.svn/entries b/geworkbench-core/components/annotations/.svn/entries
index 8765ac4..6d57ff4 100644
--- a/geworkbench-core/components/annotations/.svn/entries
+++ b/geworkbench-core/components/annotations/.svn/entries
@@ -1,14 +1,14 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/annotations
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2011-10-19T16:34:53.735246Z
-8424
+2012-01-18T15:33:17.747022Z
+8723
 zji
 has-props

@@ -32,11 +32,11 @@ file



-2011-08-17T00:10:37.000000Z
-6e0a167e16a34688273a26a2fd22c401
-2010-02-24T20:59:09.998872Z
-6062
-wangmen
+2012-01-31T19:12:31.000000Z
+e868d28c26c5b202acd844637f264452
+2012-01-18T15:33:17.747022Z
+8723
+zji
 has-props


@@ -58,7 +58,7 @@ has-props



-2177
+2092

 .project
 file
diff --git a/geworkbench-core/components/annotations/.svn/text-base/.classpath.svn-base b/geworkbench-core/components/annotations/.svn/text-base/.classpath.svn-base
index 039b39a..5d103e5 100644
--- a/geworkbench-core/components/annotations/.svn/text-base/.classpath.svn-base
+++ b/geworkbench-core/components/annotations/.svn/text-base/.classpath.svn-base
@@ -1,8 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
 	<classpathentry kind="src" path="src"/>
-	<classpathentry kind="src" path="lib"/>
-	<classpathentry kind="src" path="conf"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
 	<classpathentry kind="lib" path="lib/TableViewer.jar"/>
 	<classpathentry combineaccessrules="false" kind="src" path="/geworkbench-core"/>
diff --git a/geworkbench-core/components/annotations/conf/.svn/entries b/geworkbench-core/components/annotations/conf/.svn/entries
index 417a4af..6d3f8dc 100644
--- a/geworkbench-core/components/annotations/conf/.svn/entries
+++ b/geworkbench-core/components/annotations/conf/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/annotations/conf
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/annotations/lib/.svn/entries b/geworkbench-core/components/annotations/lib/.svn/entries
index c8d4b00..8818bb4 100644
--- a/geworkbench-core/components/annotations/lib/.svn/entries
+++ b/geworkbench-core/components/annotations/lib/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/annotations/lib
 https://ncisvn.nci.nih.gov/svn/geworkbench

@@ -502,17 +502,17 @@ has-props

 135636

-sdk-client-framework.jar
+batik-xml.jar
 file




 2011-08-17T00:10:37.000000Z
-2e0ae0a30c2d0bef36e5a5fd72a15aac
-2010-02-24T20:59:09.998872Z
-6062
-wangmen
+90023095a58978482976b987f366d493
+2005-07-28T22:36:56.000000Z
+50
+watkin
 has-props


@@ -534,19 +534,19 @@ has-props



-79841
+19876

-batik-xml.jar
+sdk-client-framework.jar
 file




 2011-08-17T00:10:37.000000Z
-90023095a58978482976b987f366d493
-2005-07-28T22:36:56.000000Z
-50
-watkin
+2e0ae0a30c2d0bef36e5a5fd72a15aac
+2010-02-24T20:59:09.998872Z
+6062
+wangmen
 has-props


@@ -568,7 +568,7 @@ has-props



-19876
+79841

 batik.jar
 file
@@ -638,17 +638,17 @@ has-props

 139652

-batik-transcoder.jar
+hibernate-annotations.jar
 file




 2011-08-17T00:10:37.000000Z
-ab2f8d83b35adb2637b362656bdc8766
-2005-07-28T22:36:56.000000Z
-50
-watkin
+de740335083745b06fefdd10093f6a21
+2009-06-11T21:07:21.000000Z
+5216
+chiangy
 has-props


@@ -670,19 +670,19 @@ has-props



-61780
+265130

-batik-script.jar
+commons-logging-1.1.jar
 file




 2011-08-17T00:10:37.000000Z
-009d3ba879acd500d66dbfc9271d3b89
-2005-07-28T22:36:56.000000Z
-50
-watkin
+6b62417e77b000a87de66ee3935edbf5
+2009-06-11T21:07:21.000000Z
+5216
+chiangy
 has-props


@@ -704,19 +704,19 @@ has-props



-30885
+52915

-commons-logging-1.1.jar
+batik-script.jar
 file




 2011-08-17T00:10:37.000000Z
-6b62417e77b000a87de66ee3935edbf5
-2009-06-11T21:07:21.000000Z
-5216
-chiangy
+009d3ba879acd500d66dbfc9271d3b89
+2005-07-28T22:36:56.000000Z
+50
+watkin
 has-props


@@ -738,19 +738,19 @@ has-props



-52915
+30885

-hibernate-annotations.jar
+batik-transcoder.jar
 file




 2011-08-17T00:10:37.000000Z
-de740335083745b06fefdd10093f6a21
-2009-06-11T21:07:21.000000Z
-5216
-chiangy
+ab2f8d83b35adb2637b362656bdc8766
+2005-07-28T22:36:56.000000Z
+50
+watkin
 has-props


@@ -772,7 +772,7 @@ has-props



-265130
+61780

 log4j-1.2.14.jar
 file
@@ -808,14 +808,14 @@ has-props

 367444

-batik-svg-dom.jar
+batik-extension.jar
 file




 2011-08-17T00:10:37.000000Z
-5d916332345a679f839122fce7672218
+42cab37430eee526f13bd553a8f65ba9
 2005-07-28T22:36:56.000000Z
 50
 watkin
@@ -840,16 +840,16 @@ has-props



-376951
+44832

-batik-extension.jar
+batik-svg-dom.jar
 file




 2011-08-17T00:10:37.000000Z
-42cab37430eee526f13bd553a8f65ba9
+5d916332345a679f839122fce7672218
 2005-07-28T22:36:56.000000Z
 50
 watkin
@@ -874,19 +874,19 @@ has-props



-44832
+376951

-batik-util.jar
+hibernate-commons-annotations.jar
 file




 2011-08-17T00:10:37.000000Z
-c5417e00da6d4c5247032ddc9ba8d7c5
-2005-07-28T22:36:56.000000Z
-50
-watkin
+1ccefbe43fedffc16835ceb1a777d199
+2009-06-11T21:07:21.000000Z
+5216
+chiangy
 has-props


@@ -908,19 +908,19 @@ has-props



-76261
+66426

-hibernate-commons-annotations.jar
+batik-util.jar
 file




 2011-08-17T00:10:37.000000Z
-1ccefbe43fedffc16835ceb1a777d199
-2009-06-11T21:07:21.000000Z
-5216
-chiangy
+c5417e00da6d4c5247032ddc9ba8d7c5
+2005-07-28T22:36:56.000000Z
+50
+watkin
 has-props


@@ -942,7 +942,7 @@ has-props



-66426
+76261

 batik-squiggle.jar
 file
diff --git a/geworkbench-core/components/annotations/src/.svn/entries b/geworkbench-core/components/annotations/src/.svn/entries
index adedbf4..c7be0a0 100644
--- a/geworkbench-core/components/annotations/src/.svn/entries
+++ b/geworkbench-core/components/annotations/src/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/annotations/src
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/annotations/src/org/.svn/entries b/geworkbench-core/components/annotations/src/org/.svn/entries
index 90ed24b..1c052ed 100644
--- a/geworkbench-core/components/annotations/src/org/.svn/entries
+++ b/geworkbench-core/components/annotations/src/org/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/annotations/src/org
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/annotations/src/org/geworkbench/.svn/entries b/geworkbench-core/components/annotations/src/org/geworkbench/.svn/entries
index 7657c8b..f29c473 100644
--- a/geworkbench-core/components/annotations/src/org/geworkbench/.svn/entries
+++ b/geworkbench-core/components/annotations/src/org/geworkbench/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/annotations/src/org/geworkbench
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/annotations/src/org/geworkbench/components/.svn/entries b/geworkbench-core/components/annotations/src/org/geworkbench/components/.svn/entries
index 746111c..8a403f0 100644
--- a/geworkbench-core/components/annotations/src/org/geworkbench/components/.svn/entries
+++ b/geworkbench-core/components/annotations/src/org/geworkbench/components/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/annotations/src/org/geworkbench/components
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/annotations/src/org/geworkbench/components/annotations/.svn/entries b/geworkbench-core/components/annotations/src/org/geworkbench/components/annotations/.svn/entries
index f21eeee..1b3aaaf 100644
--- a/geworkbench-core/components/annotations/src/org/geworkbench/components/annotations/.svn/entries
+++ b/geworkbench-core/components/annotations/src/org/geworkbench/components/annotations/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/annotations/src/org/geworkbench/components/annotations
 https://ncisvn.nci.nih.gov/svn/geworkbench

@@ -26,17 +26,17 @@ zji

 8b29bb6e-589a-435a-9a12-3ab907be3462

-AnnotationsPanel2.java
+PathwayImpl.java
 file




-2012-01-10T19:15:23.000000Z
-6071d6a45fe0c9adf0d9ead5ea8383c1
-2011-10-19T16:34:53.735246Z
-8424
-zji
+2011-08-17T00:10:38.000000Z
+8ab9f15cde5bd68121d3f41192c9b1e4
+2007-01-09T21:42:21.000000Z
+2184
+mhall
 has-props


@@ -58,19 +58,19 @@ has-props



-72789
+2159

-PathwayImpl.java
+AnnotationsPanel2.java
 file




-2011-08-17T00:10:38.000000Z
-8ab9f15cde5bd68121d3f41192c9b1e4
-2007-01-09T21:42:21.000000Z
-2184
-mhall
+2012-01-10T19:15:23.000000Z
+6071d6a45fe0c9adf0d9ead5ea8383c1
+2011-10-19T16:34:53.735246Z
+8424
+zji
 has-props


@@ -92,7 +92,7 @@ has-props



-2159
+72789

 RetrieveAllTask.java
 file
@@ -196,18 +196,17 @@ has-props

 15572

-ExportTask.java
+EvsIdData.java
 file




 2011-08-17T00:10:38.000000Z
-65bd90313c28facdf9ad6395f13a75d3
-2010-11-10T21:09:20.990598Z
-7184
-wangmen
-has-props
+ef3cfe63a4a70e653142519464ff27b4
+2010-07-19T20:53:10.920475Z
+6891
+zji



@@ -228,20 +227,21 @@ has-props



-2180
+
+315

-EvsIdData.java
+ExportTask.java
 file




 2011-08-17T00:10:38.000000Z
-ef3cfe63a4a70e653142519464ff27b4
-2010-07-19T20:53:10.920475Z
-6891
-zji
-
+65bd90313c28facdf9ad6395f13a75d3
+2010-11-10T21:09:20.990598Z
+7184
+wangmen
+has-props



@@ -262,7 +262,7 @@ zji



-315
+2180

 PubmedData.java
 file
@@ -298,14 +298,14 @@ zji

 309

-DiseaseData.java
+PathwayData.java
 file




 2011-08-17T00:10:38.000000Z
-931ccd68a366dfb998909ac6de4a8d53
+5e081793bd7b1caf218eab21e50a5208
 2010-07-19T21:49:35.420613Z
 6894
 zji
@@ -330,16 +330,16 @@ zji



-568
+453

-PathwayData.java
+DiseaseData.java
 file




 2011-08-17T00:10:38.000000Z
-5e081793bd7b1caf218eab21e50a5208
+931ccd68a366dfb998909ac6de4a8d53
 2010-07-19T21:49:35.420613Z
 6894
 zji
@@ -364,7 +364,10 @@ zji



-453
+568
+
+help
+dir

 GeneData.java
 file
@@ -400,20 +403,17 @@ zji

 1070

-help
-dir
-
-GeneAnnotation.java
+GeneSearchCriteriaImpl.java
 file




-2011-08-17T00:10:38.000000Z
-5338234f3c2bfd1c2fcfb585481fc315
-2010-11-10T20:40:33.247546Z
-7182
-wangmen
+2012-01-10T18:25:31.000000Z
+8a7fe59120527c9555520434ad19de0c
+2011-07-30T04:31:30.667242Z
+8187
+zji
 has-props


@@ -435,7 +435,7 @@ has-props



-1727
+4516

 AnnotData.java
 file
@@ -471,17 +471,17 @@ has-props

 729

-GeneSearchCriteriaImpl.java
+GeneAnnotation.java
 file




-2012-01-10T18:25:31.000000Z
-8a7fe59120527c9555520434ad19de0c
-2011-07-30T04:31:30.667242Z
-8187
-zji
+2011-08-17T00:10:38.000000Z
+5338234f3c2bfd1c2fcfb585481fc315
+2010-11-10T20:40:33.247546Z
+7182
+wangmen
 has-props


@@ -503,7 +503,7 @@ has-props



-4516
+1727

 DupTask.java
 file
diff --git a/geworkbench-core/components/annotations/src/org/geworkbench/components/annotations/help/.svn/entries b/geworkbench-core/components/annotations/src/org/geworkbench/components/annotations/help/.svn/entries
index a6f882e..a37273f 100644
--- a/geworkbench-core/components/annotations/src/org/geworkbench/components/annotations/help/.svn/entries
+++ b/geworkbench-core/components/annotations/src/org/geworkbench/components/annotations/help/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/annotations/src/org/geworkbench/components/annotations/help
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/annotations/src/org/geworkbench/components/annotations/help/annotationspanel/.svn/entries b/geworkbench-core/components/annotations/src/org/geworkbench/components/annotations/help/annotationspanel/.svn/entries
index a9d70f5..3039e9f 100644
--- a/geworkbench-core/components/annotations/src/org/geworkbench/components/annotations/help/annotationspanel/.svn/entries
+++ b/geworkbench-core/components/annotations/src/org/geworkbench/components/annotations/help/annotationspanel/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/annotations/src/org/geworkbench/components/annotations/help/annotationspanel
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/annotations/src/org/geworkbench/components/annotations/help/annotationspanel/images/.svn/entries b/geworkbench-core/components/annotations/src/org/geworkbench/components/annotations/help/annotationspanel/images/.svn/entries
index 223d1f5..3acc35d 100644
--- a/geworkbench-core/components/annotations/src/org/geworkbench/components/annotations/help/annotationspanel/images/.svn/entries
+++ b/geworkbench-core/components/annotations/src/org/geworkbench/components/annotations/help/annotationspanel/images/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/annotations/src/org/geworkbench/components/annotations/help/annotationspanel/images
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/annotations/src/org/geworkbench/components/annotations/help/annotationspanel/markerannotationsed_final_files/.svn/entries b/geworkbench-core/components/annotations/src/org/geworkbench/components/annotations/help/annotationspanel/markerannotationsed_final_files/.svn/entries
index 14d5eb3..28fd3f1 100644
--- a/geworkbench-core/components/annotations/src/org/geworkbench/components/annotations/help/annotationspanel/markerannotationsed_final_files/.svn/entries
+++ b/geworkbench-core/components/annotations/src/org/geworkbench/components/annotations/help/annotationspanel/markerannotationsed_final_files/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/annotations/src/org/geworkbench/components/annotations/help/annotationspanel/markerannotationsed_final_files
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/annotations/src/org/geworkbench/components/annotations/help/pathwaypanel/.svn/entries b/geworkbench-core/components/annotations/src/org/geworkbench/components/annotations/help/pathwaypanel/.svn/entries
index 700d49a..f491fb6 100644
--- a/geworkbench-core/components/annotations/src/org/geworkbench/components/annotations/help/pathwaypanel/.svn/entries
+++ b/geworkbench-core/components/annotations/src/org/geworkbench/components/annotations/help/pathwaypanel/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/annotations/src/org/geworkbench/components/annotations/help/pathwaypanel
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/annotations/src/org/geworkbench/components/annotations/help/pathwaypanel/pathwaysed_files/.svn/entries b/geworkbench-core/components/annotations/src/org/geworkbench/components/annotations/help/pathwaypanel/pathwaysed_files/.svn/entries
index 8f80f79..aaa5b59 100644
--- a/geworkbench-core/components/annotations/src/org/geworkbench/components/annotations/help/pathwaypanel/pathwaysed_files/.svn/entries
+++ b/geworkbench-core/components/annotations/src/org/geworkbench/components/annotations/help/pathwaypanel/pathwaysed_files/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/annotations/src/org/geworkbench/components/annotations/help/pathwaypanel/pathwaysed_files
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/anova/.settings/.svn/entries b/geworkbench-core/components/anova/.settings/.svn/entries
index 6d5383c..682612d 100644
--- a/geworkbench-core/components/anova/.settings/.svn/entries
+++ b/geworkbench-core/components/anova/.settings/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/anova/.settings
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/anova/.svn/entries b/geworkbench-core/components/anova/.svn/entries
index eb2f930..d5e30b0 100644
--- a/geworkbench-core/components/anova/.svn/entries
+++ b/geworkbench-core/components/anova/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/anova
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/anova/conf/.svn/entries b/geworkbench-core/components/anova/conf/.svn/entries
index 0d501f0..4a8b8ea 100644
--- a/geworkbench-core/components/anova/conf/.svn/entries
+++ b/geworkbench-core/components/anova/conf/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/anova/conf
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/anova/lib/.svn/entries b/geworkbench-core/components/anova/lib/.svn/entries
index a5bbb28..5648e30 100644
--- a/geworkbench-core/components/anova/lib/.svn/entries
+++ b/geworkbench-core/components/anova/lib/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/anova/lib
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/anova/src/.svn/entries b/geworkbench-core/components/anova/src/.svn/entries
index 5be9cfe..6605e78 100644
--- a/geworkbench-core/components/anova/src/.svn/entries
+++ b/geworkbench-core/components/anova/src/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/anova/src
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/anova/src/org/.svn/entries b/geworkbench-core/components/anova/src/org/.svn/entries
index 6391d3d..d869e49 100644
--- a/geworkbench-core/components/anova/src/org/.svn/entries
+++ b/geworkbench-core/components/anova/src/org/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/anova/src/org
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/anova/src/org/geworkbench/.svn/entries b/geworkbench-core/components/anova/src/org/geworkbench/.svn/entries
index 7c1427e..aa58d15 100644
--- a/geworkbench-core/components/anova/src/org/geworkbench/.svn/entries
+++ b/geworkbench-core/components/anova/src/org/geworkbench/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/anova/src/org/geworkbench
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/anova/src/org/geworkbench/components/.svn/entries b/geworkbench-core/components/anova/src/org/geworkbench/components/.svn/entries
index 8bfb26a..1bef08d 100644
--- a/geworkbench-core/components/anova/src/org/geworkbench/components/.svn/entries
+++ b/geworkbench-core/components/anova/src/org/geworkbench/components/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/anova/src/org/geworkbench/components
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/anova/src/org/geworkbench/components/anova/.svn/entries b/geworkbench-core/components/anova/src/org/geworkbench/components/anova/.svn/entries
index 6cf12b2..a5a69a1 100644
--- a/geworkbench-core/components/anova/src/org/geworkbench/components/anova/.svn/entries
+++ b/geworkbench-core/components/anova/src/org/geworkbench/components/anova/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/anova/src/org/geworkbench/components/anova
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/anova/src/org/geworkbench/components/anova/gui/.svn/entries b/geworkbench-core/components/anova/src/org/geworkbench/components/anova/gui/.svn/entries
index a6796ad..77feac2 100644
--- a/geworkbench-core/components/anova/src/org/geworkbench/components/anova/gui/.svn/entries
+++ b/geworkbench-core/components/anova/src/org/geworkbench/components/anova/gui/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/anova/src/org/geworkbench/components/anova/gui
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/anova/src/org/geworkbench/components/anova/help/.svn/entries b/geworkbench-core/components/anova/src/org/geworkbench/components/anova/help/.svn/entries
index 97e6f2c..c6e7f73 100644
--- a/geworkbench-core/components/anova/src/org/geworkbench/components/anova/help/.svn/entries
+++ b/geworkbench-core/components/anova/src/org/geworkbench/components/anova/help/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/anova/src/org/geworkbench/components/anova/help
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/anova/src/org/geworkbench/components/anova/help/anova_files/.svn/entries b/geworkbench-core/components/anova/src/org/geworkbench/components/anova/help/anova_files/.svn/entries
index d5d6a4a..553d6d7 100644
--- a/geworkbench-core/components/anova/src/org/geworkbench/components/anova/help/anova_files/.svn/entries
+++ b/geworkbench-core/components/anova/src/org/geworkbench/components/anova/help/anova_files/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/anova/src/org/geworkbench/components/anova/help/anova_files
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/aracne-java/.svn/all-wcprops b/geworkbench-core/components/aracne-java/.svn/all-wcprops
index b09ee2e..4eb01d8 100644
--- a/geworkbench-core/components/aracne-java/.svn/all-wcprops
+++ b/geworkbench-core/components/aracne-java/.svn/all-wcprops
@@ -1,7 +1,7 @@
 K 25
 svn:wc:ra_dav:version-url
 V 71
-/svn/geworkbench/!svn/ver/8585/trunk/geworkbench/components/aracne-java
+/svn/geworkbench/!svn/ver/8811/trunk/geworkbench/components/aracne-java
 END
 .classpath
 K 25
diff --git a/geworkbench-core/components/aracne-java/.svn/entries b/geworkbench-core/components/aracne-java/.svn/entries
index 03a2fc7..d6953f6 100644
--- a/geworkbench-core/components/aracne-java/.svn/entries
+++ b/geworkbench-core/components/aracne-java/.svn/entries
@@ -1,15 +1,15 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/aracne-java
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2011-12-07T20:29:45.151430Z
-8585
-poddutun
+2012-01-30T21:29:41.579403Z
+8811
+zji
 has-props


diff --git a/geworkbench-core/components/aracne-java/lib/.svn/entries b/geworkbench-core/components/aracne-java/lib/.svn/entries
index 70b6cdd..ca2f84b 100644
--- a/geworkbench-core/components/aracne-java/lib/.svn/entries
+++ b/geworkbench-core/components/aracne-java/lib/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/aracne-java/lib
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/aracne-java/src/.svn/all-wcprops b/geworkbench-core/components/aracne-java/src/.svn/all-wcprops
index d50a100..6cf7775 100644
--- a/geworkbench-core/components/aracne-java/src/.svn/all-wcprops
+++ b/geworkbench-core/components/aracne-java/src/.svn/all-wcprops
@@ -1,5 +1,5 @@
 K 25
 svn:wc:ra_dav:version-url
 V 75
-/svn/geworkbench/!svn/ver/8585/trunk/geworkbench/components/aracne-java/src
+/svn/geworkbench/!svn/ver/8811/trunk/geworkbench/components/aracne-java/src
 END
diff --git a/geworkbench-core/components/aracne-java/src/.svn/entries b/geworkbench-core/components/aracne-java/src/.svn/entries
index 23de00d..f76d74d 100644
--- a/geworkbench-core/components/aracne-java/src/.svn/entries
+++ b/geworkbench-core/components/aracne-java/src/.svn/entries
@@ -1,15 +1,15 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/aracne-java/src
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2011-12-07T20:29:45.151430Z
-8585
-poddutun
+2012-01-30T21:29:41.579403Z
+8811
+zji



diff --git a/geworkbench-core/components/aracne-java/src/org/.svn/all-wcprops b/geworkbench-core/components/aracne-java/src/org/.svn/all-wcprops
index 660039f..fa27c44 100644
--- a/geworkbench-core/components/aracne-java/src/org/.svn/all-wcprops
+++ b/geworkbench-core/components/aracne-java/src/org/.svn/all-wcprops
@@ -1,5 +1,5 @@
 K 25
 svn:wc:ra_dav:version-url
 V 79
-/svn/geworkbench/!svn/ver/8585/trunk/geworkbench/components/aracne-java/src/org
+/svn/geworkbench/!svn/ver/8811/trunk/geworkbench/components/aracne-java/src/org
 END
diff --git a/geworkbench-core/components/aracne-java/src/org/.svn/entries b/geworkbench-core/components/aracne-java/src/org/.svn/entries
index a0659cd..2ceb7b9 100644
--- a/geworkbench-core/components/aracne-java/src/org/.svn/entries
+++ b/geworkbench-core/components/aracne-java/src/org/.svn/entries
@@ -1,15 +1,15 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/aracne-java/src/org
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2011-12-07T20:29:45.151430Z
-8585
-poddutun
+2012-01-30T21:29:41.579403Z
+8811
+zji



diff --git a/geworkbench-core/components/aracne-java/src/org/geworkbench/.svn/all-wcprops b/geworkbench-core/components/aracne-java/src/org/geworkbench/.svn/all-wcprops
index ee28355..b879917 100644
--- a/geworkbench-core/components/aracne-java/src/org/geworkbench/.svn/all-wcprops
+++ b/geworkbench-core/components/aracne-java/src/org/geworkbench/.svn/all-wcprops
@@ -1,5 +1,5 @@
 K 25
 svn:wc:ra_dav:version-url
 V 91
-/svn/geworkbench/!svn/ver/8585/trunk/geworkbench/components/aracne-java/src/org/geworkbench
+/svn/geworkbench/!svn/ver/8811/trunk/geworkbench/components/aracne-java/src/org/geworkbench
 END
diff --git a/geworkbench-core/components/aracne-java/src/org/geworkbench/.svn/entries b/geworkbench-core/components/aracne-java/src/org/geworkbench/.svn/entries
index 858c496..8d89264 100644
--- a/geworkbench-core/components/aracne-java/src/org/geworkbench/.svn/entries
+++ b/geworkbench-core/components/aracne-java/src/org/geworkbench/.svn/entries
@@ -1,15 +1,15 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/aracne-java/src/org/geworkbench
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2011-12-07T20:29:45.151430Z
-8585
-poddutun
+2012-01-30T21:29:41.579403Z
+8811
+zji



diff --git a/geworkbench-core/components/aracne-java/src/org/geworkbench/components/.svn/all-wcprops b/geworkbench-core/components/aracne-java/src/org/geworkbench/components/.svn/all-wcprops
index 9a2b396..f0a5a63 100644
--- a/geworkbench-core/components/aracne-java/src/org/geworkbench/components/.svn/all-wcprops
+++ b/geworkbench-core/components/aracne-java/src/org/geworkbench/components/.svn/all-wcprops
@@ -1,5 +1,5 @@
 K 25
 svn:wc:ra_dav:version-url
 V 102
-/svn/geworkbench/!svn/ver/8585/trunk/geworkbench/components/aracne-java/src/org/geworkbench/components
+/svn/geworkbench/!svn/ver/8811/trunk/geworkbench/components/aracne-java/src/org/geworkbench/components
 END
diff --git a/geworkbench-core/components/aracne-java/src/org/geworkbench/components/.svn/entries b/geworkbench-core/components/aracne-java/src/org/geworkbench/components/.svn/entries
index 464e7f5..2cb782e 100644
--- a/geworkbench-core/components/aracne-java/src/org/geworkbench/components/.svn/entries
+++ b/geworkbench-core/components/aracne-java/src/org/geworkbench/components/.svn/entries
@@ -1,15 +1,15 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/aracne-java/src/org/geworkbench/components
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2011-12-07T20:29:45.151430Z
-8585
-poddutun
+2012-01-30T21:29:41.579403Z
+8811
+zji



diff --git a/geworkbench-core/components/aracne-java/src/org/geworkbench/components/aracne/.svn/all-wcprops b/geworkbench-core/components/aracne-java/src/org/geworkbench/components/aracne/.svn/all-wcprops
index c84c6e8..13b9c68 100644
--- a/geworkbench-core/components/aracne-java/src/org/geworkbench/components/aracne/.svn/all-wcprops
+++ b/geworkbench-core/components/aracne-java/src/org/geworkbench/components/aracne/.svn/all-wcprops
@@ -1,7 +1,7 @@
 K 25
 svn:wc:ra_dav:version-url
 V 109
-/svn/geworkbench/!svn/ver/8585/trunk/geworkbench/components/aracne-java/src/org/geworkbench/components/aracne
+/svn/geworkbench/!svn/ver/8811/trunk/geworkbench/components/aracne-java/src/org/geworkbench/components/aracne
 END
 HardenedAracne.java
 K 25
@@ -25,7 +25,7 @@ AracneAnalysis.java
 K 25
 svn:wc:ra_dav:version-url
 V 129
-/svn/geworkbench/!svn/ver/8424/trunk/geworkbench/components/aracne-java/src/org/geworkbench/components/aracne/AracneAnalysis.java
+/svn/geworkbench/!svn/ver/8811/trunk/geworkbench/components/aracne-java/src/org/geworkbench/components/aracne/AracneAnalysis.java
 END
 AracneProgress.java
 K 25
diff --git a/geworkbench-core/components/aracne-java/src/org/geworkbench/components/aracne/.svn/entries b/geworkbench-core/components/aracne-java/src/org/geworkbench/components/aracne/.svn/entries
index 15d3e3a..7cfcca8 100644
--- a/geworkbench-core/components/aracne-java/src/org/geworkbench/components/aracne/.svn/entries
+++ b/geworkbench-core/components/aracne-java/src/org/geworkbench/components/aracne/.svn/entries
@@ -1,15 +1,15 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/aracne-java/src/org/geworkbench/components/aracne
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2011-12-07T20:29:45.151430Z
-8585
-poddutun
+2012-01-30T21:29:41.579403Z
+8811
+zji



@@ -137,10 +137,10 @@ file



-2012-01-10T19:15:23.000000Z
-a7faf358c7a1101ad2f1eb310164fa46
-2011-10-19T16:34:53.735246Z
-8424
+2012-01-31T19:12:35.000000Z
+a40952058520e27240050041e044a189
+2012-01-30T21:29:41.579403Z
+8811
 zji
 has-props

@@ -163,7 +163,7 @@ has-props



-26701
+23862

 AracneProgress.java
 file
diff --git a/geworkbench-core/components/aracne-java/src/org/geworkbench/components/aracne/.svn/text-base/AracneAnalysis.java.svn-base b/geworkbench-core/components/aracne-java/src/org/geworkbench/components/aracne/.svn/text-base/AracneAnalysis.java.svn-base
index 2d0b0c1..f7e2f78 100644
--- a/geworkbench-core/components/aracne-java/src/org/geworkbench/components/aracne/.svn/text-base/AracneAnalysis.java.svn-base
+++ b/geworkbench-core/components/aracne-java/src/org/geworkbench/components/aracne/.svn/text-base/AracneAnalysis.java.svn-base
@@ -4,13 +4,12 @@ import java.io.Serializable;
 import java.lang.reflect.InvocationTargetException;
 import java.util.ArrayList;
 import java.util.HashMap;
-import java.util.Iterator;
+
 import java.util.Map;
 import java.util.Vector;

 import javax.swing.JOptionPane;
 import javax.swing.SwingUtilities;
-
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.geworkbench.analysis.AbstractAnalysis;
@@ -18,14 +17,11 @@ import org.geworkbench.analysis.AbstractGridAnalysis;
 import org.geworkbench.bison.datastructure.biocollections.AdjacencyMatrix;
 import org.geworkbench.bison.datastructure.biocollections.AdjacencyMatrix.NodeType;
 import org.geworkbench.bison.datastructure.biocollections.AdjacencyMatrixDataSet;
-import org.geworkbench.bison.datastructure.biocollections.DSDataSet;
-import org.geworkbench.bison.datastructure.biocollections.microarrays.CSMicroarraySet;
+import org.geworkbench.bison.datastructure.biocollections.DSDataSet;
 import org.geworkbench.bison.datastructure.biocollections.microarrays.DSMicroarraySet;
 import org.geworkbench.bison.datastructure.biocollections.views.DSMicroarraySetView;
-import org.geworkbench.bison.datastructure.bioobjects.markers.CSExpressionMarker;
 import org.geworkbench.bison.datastructure.bioobjects.markers.DSGeneMarker;
 import org.geworkbench.bison.datastructure.bioobjects.microarray.DSMicroarray;
-import org.geworkbench.bison.datastructure.complex.panels.CSPanel;
 import org.geworkbench.bison.datastructure.complex.panels.DSItemList;
 import org.geworkbench.bison.datastructure.complex.panels.DSPanel;
 import org.geworkbench.bison.model.analysis.AlgorithmExecutionResults;
@@ -36,8 +32,7 @@ import org.geworkbench.engine.management.Publish;
 import org.geworkbench.engine.management.Subscribe;
 import org.geworkbench.events.GeneSelectorEvent;
 import org.geworkbench.events.ProjectNodeAddedEvent;
-import org.ginkgo.labs.util.FileTools;
-
+
 import wb.data.Marker;
 import wb.data.MarkerSet;
 import wb.data.Microarray;
@@ -349,7 +344,7 @@ public class AracneAnalysis extends AbstractGridAnalysis implements
 								.getMicroarraySet());
 				StringBuilder paramDescB = new StringBuilder(
 						"Generated with ARACNE run with data:\n");
-				paramDescB.append(generateHistoryString(this.mSetView));
+				paramDescB.append(generateHistoryForMaSetView(this.mSetView, useMarkersFromSelector()));
 				String s=prune?"yes":"no";
 				HistoryPanel.addToHistory(dataSet,
 						"Generated with ARACNE run with paramters:\n"
@@ -713,8 +708,26 @@ public class AracneAnalysis extends AbstractGridAnalysis implements
 	@Subscribe
 	public void receive(GeneSelectorEvent e, Object source) {
 		if (e.getPanel() != null) {
-			DSPanel<DSGeneMarker> selectorPanel = e.getPanel();
-			((AracneParamPanel) aspp).setSelectorPanel(selectorPanel);
+			final DSPanel<DSGeneMarker> selectorPanel = e.getPanel();
+			if (SwingUtilities.isEventDispatchThread()) {
+				((AracneParamPanel) aspp).setSelectorPanel(selectorPanel);
+			} else {
+				try {
+					SwingUtilities.invokeAndWait(new Runnable() {
+
+						@Override
+						public void run() {
+							((AracneParamPanel) aspp)
+									.setSelectorPanel(selectorPanel);
+						}
+
+					});
+				} catch (InterruptedException e1) {
+					e1.printStackTrace();
+				} catch (InvocationTargetException e1) {
+					e1.printStackTrace();
+				}
+			}
 		} else
 			log.debug("Aracne Received Gene Selector Event: Selection panel sent was null");
 	}
@@ -746,74 +759,6 @@ public class AracneAnalysis extends AbstractGridAnalysis implements
 						+ "consider relaxing your thresholds.");
 	}

-	@SuppressWarnings({ "unchecked" })
-	private String generateHistoryString(DSMicroarraySetView<DSGeneMarker, DSMicroarray> maSetView) {
-		StringBuilder ans = new StringBuilder(
-				"=The MicroarraySetView used for analysis contains following data=\n");
-		try {
-			log.debug("We got a "+maSetView.items().getClass().toString());
-			if (maSetView.items().getClass() == CSPanel.class){
-				log.debug("situation 1: microarraySets selected");
-				DSItemList<DSPanel<DSMicroarray>> paneltest = ((DSPanel<DSMicroarray>) maSetView.items()).panels();
-
-				ans .append( "==Microarray Sets [" ).append( paneltest.size() ).append( "]==\n" );
-				for (Object obj : paneltest) {
-					DSPanel<DSMicroarray> temp = (DSPanel<DSMicroarray>) obj;
-					ans .append( "\t" ).append( temp.toString() ).append( "\n" );
-					// microarrays in the group
-					for (Object temp2 : temp) {
-						ans .append( "\t\t" ).append( temp2.toString() ).append( "\n" );
-					}
-				}
-			}else if (maSetView.items().getClass() == CSMicroarraySet.class){
-				log.debug("situation 2: microarraySets not selected");
-				CSMicroarraySet exprSet = (CSMicroarraySet)maSetView.items();
-				ans .append( "==Used Microarrays [" ).append( exprSet.size() ).append( "]==\n" );
-				for (Iterator<DSMicroarray> iterator = exprSet.iterator(); iterator.hasNext();) {
-					DSMicroarray array = iterator.next();
-					ans .append( "\t"+ array.getLabel()).append("\n");
-				}
-			}
-			ans .append( "==End of Microarray Sets==\n" );
-			// generate text for markers; iterations over markers could be refactored into one
-			DSPanel<DSGeneMarker> paneltest = maSetView.getMarkerPanel();
-
-			if (maSetView.useMarkerPanel()) {
-				if ((paneltest!=null) && (paneltest.size()>0)){
-					log.debug("situation 3: markers selected");
-
-					ans .append( "==Used Markers [" ).append( paneltest.size() ).append( "]==\n" );
-					for (Object obj : paneltest) {
-						CSExpressionMarker temp = (CSExpressionMarker) obj;
-						ans .append( "\t" ).append( temp.getLabel() ).append( "\n" );
-					}
-				}else{
-					log.debug("situation 4: no markers selected.");
-					DSItemList<DSGeneMarker> markers = maSetView.markers();
-					ans .append( "==Used Markers [" ).append( markers.size() ).append( "]==\n" );
-					for (DSGeneMarker marker : markers) {
-						ans .append( "\t" ).append( marker.getLabel() ).append( "\n" );
-					}
-				}
-			} else {
-				log.debug("situation 5: All Markers selected.");
-				DSItemList<DSGeneMarker> markers = maSetView.allMarkers();
-				ans .append( "==Used Markers [" ).append( markers.size() ).append( "]==" )
-						.append( FileTools.NEWLINE );
-				for (DSGeneMarker marker : markers) {
-					ans .append( FileTools.TAB ).append( marker.getLabel()
-					).append( FileTools.NEWLINE );
-				}
-			}
-
-
-			ans .append( "==End of Used Markers==\n" );
-		} catch (ClassCastException cce) {
-			// it's not a DSPanel, we generate nothing for panel part
-			log.error(cce);
-		}
-		ans .append( "=End of MicroarraySetView data=" );
-		return ans.toString();
-	}
+

 }
diff --git a/geworkbench-core/components/aracne-java/src/org/geworkbench/components/aracne/AracneAnalysis.java b/geworkbench-core/components/aracne-java/src/org/geworkbench/components/aracne/AracneAnalysis.java
index 5e0ea40..f14697d 100755
--- a/geworkbench-core/components/aracne-java/src/org/geworkbench/components/aracne/AracneAnalysis.java
+++ b/geworkbench-core/components/aracne-java/src/org/geworkbench/components/aracne/AracneAnalysis.java
@@ -4,13 +4,12 @@ import java.io.Serializable;
 import java.lang.reflect.InvocationTargetException;
 import java.util.ArrayList;
 import java.util.HashMap;
-import java.util.Iterator;
+
 import java.util.Map;
 import java.util.Vector;

 import javax.swing.JOptionPane;
 import javax.swing.SwingUtilities;
-
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.geworkbench.analysis.AbstractAnalysis;
@@ -18,14 +17,11 @@ import org.geworkbench.analysis.AbstractGridAnalysis;
 import org.geworkbench.bison.datastructure.biocollections.AdjacencyMatrix;
 import org.geworkbench.bison.datastructure.biocollections.AdjacencyMatrix.NodeType;
 import org.geworkbench.bison.datastructure.biocollections.AdjacencyMatrixDataSet;
-import org.geworkbench.bison.datastructure.biocollections.DSDataSet;
-import org.geworkbench.bison.datastructure.biocollections.microarrays.CSMicroarraySet;
+import org.geworkbench.bison.datastructure.biocollections.DSDataSet;
 import org.geworkbench.bison.datastructure.biocollections.microarrays.DSMicroarraySet;
 import org.geworkbench.bison.datastructure.biocollections.views.DSMicroarraySetView;
-import org.geworkbench.bison.datastructure.bioobjects.markers.CSExpressionMarker;
 import org.geworkbench.bison.datastructure.bioobjects.markers.DSGeneMarker;
 import org.geworkbench.bison.datastructure.bioobjects.microarray.DSMicroarray;
-import org.geworkbench.bison.datastructure.complex.panels.CSPanel;
 import org.geworkbench.bison.datastructure.complex.panels.DSItemList;
 import org.geworkbench.bison.datastructure.complex.panels.DSPanel;
 import org.geworkbench.bison.model.analysis.AlgorithmExecutionResults;
@@ -36,8 +32,7 @@ import org.geworkbench.engine.management.Publish;
 import org.geworkbench.engine.management.Subscribe;
 import org.geworkbench.events.GeneSelectorEvent;
 import org.geworkbench.events.ProjectNodeAddedEvent;
-import org.ginkgo.labs.util.FileTools;
-
+
 import wb.data.Marker;
 import wb.data.MarkerSet;
 import wb.data.Microarray;
@@ -48,7 +43,7 @@ import edu.columbia.c2b2.aracne.Parameter;

 /**
  * @author Matt Hall
- * @version $Id: AracneAnalysis.java 8424 2011-10-19 16:34:53Z zji $
+ * @version $Id: AracneAnalysis.java 8811 2012-01-30 21:29:41Z zji $
  */
 public class AracneAnalysis extends AbstractGridAnalysis implements
 		ClusteringAnalysis {
@@ -349,7 +344,7 @@ public class AracneAnalysis extends AbstractGridAnalysis implements
 								.getMicroarraySet());
 				StringBuilder paramDescB = new StringBuilder(
 						"Generated with ARACNE run with data:\n");
-				paramDescB.append(generateHistoryString(this.mSetView));
+				paramDescB.append(generateHistoryForMaSetView(this.mSetView, useMarkersFromSelector()));
 				String s=prune?"yes":"no";
 				HistoryPanel.addToHistory(dataSet,
 						"Generated with ARACNE run with paramters:\n"
@@ -713,8 +708,26 @@ public class AracneAnalysis extends AbstractGridAnalysis implements
 	@Subscribe
 	public void receive(GeneSelectorEvent e, Object source) {
 		if (e.getPanel() != null) {
-			DSPanel<DSGeneMarker> selectorPanel = e.getPanel();
-			((AracneParamPanel) aspp).setSelectorPanel(selectorPanel);
+			final DSPanel<DSGeneMarker> selectorPanel = e.getPanel();
+			if (SwingUtilities.isEventDispatchThread()) {
+				((AracneParamPanel) aspp).setSelectorPanel(selectorPanel);
+			} else {
+				try {
+					SwingUtilities.invokeAndWait(new Runnable() {
+
+						@Override
+						public void run() {
+							((AracneParamPanel) aspp)
+									.setSelectorPanel(selectorPanel);
+						}
+
+					});
+				} catch (InterruptedException e1) {
+					e1.printStackTrace();
+				} catch (InvocationTargetException e1) {
+					e1.printStackTrace();
+				}
+			}
 		} else
 			log.debug("Aracne Received Gene Selector Event: Selection panel sent was null");
 	}
@@ -746,74 +759,6 @@ public class AracneAnalysis extends AbstractGridAnalysis implements
 						+ "consider relaxing your thresholds.");
 	}

-	@SuppressWarnings({ "unchecked" })
-	private String generateHistoryString(DSMicroarraySetView<DSGeneMarker, DSMicroarray> maSetView) {
-		StringBuilder ans = new StringBuilder(
-				"=The MicroarraySetView used for analysis contains following data=\n");
-		try {
-			log.debug("We got a "+maSetView.items().getClass().toString());
-			if (maSetView.items().getClass() == CSPanel.class){
-				log.debug("situation 1: microarraySets selected");
-				DSItemList<DSPanel<DSMicroarray>> paneltest = ((DSPanel<DSMicroarray>) maSetView.items()).panels();
-
-				ans .append( "==Microarray Sets [" ).append( paneltest.size() ).append( "]==\n" );
-				for (Object obj : paneltest) {
-					DSPanel<DSMicroarray> temp = (DSPanel<DSMicroarray>) obj;
-					ans .append( "\t" ).append( temp.toString() ).append( "\n" );
-					// microarrays in the group
-					for (Object temp2 : temp) {
-						ans .append( "\t\t" ).append( temp2.toString() ).append( "\n" );
-					}
-				}
-			}else if (maSetView.items().getClass() == CSMicroarraySet.class){
-				log.debug("situation 2: microarraySets not selected");
-				CSMicroarraySet exprSet = (CSMicroarraySet)maSetView.items();
-				ans .append( "==Used Microarrays [" ).append( exprSet.size() ).append( "]==\n" );
-				for (Iterator<DSMicroarray> iterator = exprSet.iterator(); iterator.hasNext();) {
-					DSMicroarray array = iterator.next();
-					ans .append( "\t"+ array.getLabel()).append("\n");
-				}
-			}
-			ans .append( "==End of Microarray Sets==\n" );
-			// generate text for markers; iterations over markers could be refactored into one
-			DSPanel<DSGeneMarker> paneltest = maSetView.getMarkerPanel();
-
-			if (maSetView.useMarkerPanel()) {
-				if ((paneltest!=null) && (paneltest.size()>0)){
-					log.debug("situation 3: markers selected");
-
-					ans .append( "==Used Markers [" ).append( paneltest.size() ).append( "]==\n" );
-					for (Object obj : paneltest) {
-						CSExpressionMarker temp = (CSExpressionMarker) obj;
-						ans .append( "\t" ).append( temp.getLabel() ).append( "\n" );
-					}
-				}else{
-					log.debug("situation 4: no markers selected.");
-					DSItemList<DSGeneMarker> markers = maSetView.markers();
-					ans .append( "==Used Markers [" ).append( markers.size() ).append( "]==\n" );
-					for (DSGeneMarker marker : markers) {
-						ans .append( "\t" ).append( marker.getLabel() ).append( "\n" );
-					}
-				}
-			} else {
-				log.debug("situation 5: All Markers selected.");
-				DSItemList<DSGeneMarker> markers = maSetView.allMarkers();
-				ans .append( "==Used Markers [" ).append( markers.size() ).append( "]==" )
-						.append( FileTools.NEWLINE );
-				for (DSGeneMarker marker : markers) {
-					ans .append( FileTools.TAB ).append( marker.getLabel()
-					).append( FileTools.NEWLINE );
-				}
-			}
-
-
-			ans .append( "==End of Used Markers==\n" );
-		} catch (ClassCastException cce) {
-			// it's not a DSPanel, we generate nothing for panel part
-			log.error(cce);
-		}
-		ans .append( "=End of MicroarraySetView data=" );
-		return ans.toString();
-	}
+

 }
diff --git a/geworkbench-core/components/aracne-java/src/org/geworkbench/components/aracne/help/.svn/entries b/geworkbench-core/components/aracne-java/src/org/geworkbench/components/aracne/help/.svn/entries
index f60b585..3710648 100644
--- a/geworkbench-core/components/aracne-java/src/org/geworkbench/components/aracne/help/.svn/entries
+++ b/geworkbench-core/components/aracne-java/src/org/geworkbench/components/aracne/help/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/aracne-java/src/org/geworkbench/components/aracne/help
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/aracne-java/src/org/geworkbench/components/aracne/help/aracne_files/.svn/entries b/geworkbench-core/components/aracne-java/src/org/geworkbench/components/aracne/help/aracne_files/.svn/entries
index e3d970b..8273430 100644
--- a/geworkbench-core/components/aracne-java/src/org/geworkbench/components/aracne/help/aracne_files/.svn/entries
+++ b/geworkbench-core/components/aracne-java/src/org/geworkbench/components/aracne/help/aracne_files/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/aracne-java/src/org/geworkbench/components/aracne/help/aracne_files
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/caarray/.svn/all-wcprops b/geworkbench-core/components/caarray/.svn/all-wcprops
index 491a8eb..55287a1 100644
--- a/geworkbench-core/components/caarray/.svn/all-wcprops
+++ b/geworkbench-core/components/caarray/.svn/all-wcprops
@@ -1,7 +1,7 @@
 K 25
 svn:wc:ra_dav:version-url
 V 67
-/svn/geworkbench/!svn/ver/8463/trunk/geworkbench/components/caarray
+/svn/geworkbench/!svn/ver/8785/trunk/geworkbench/components/caarray
 END
 .classpath
 K 25
diff --git a/geworkbench-core/components/caarray/.svn/entries b/geworkbench-core/components/caarray/.svn/entries
index a1cb155..0286b9b 100644
--- a/geworkbench-core/components/caarray/.svn/entries
+++ b/geworkbench-core/components/caarray/.svn/entries
@@ -1,15 +1,15 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/caarray
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2011-10-25T21:47:59.095740Z
-8463
-zji
+2012-01-26T21:17:35.990494Z
+8785
+maz
 has-props


diff --git a/geworkbench-core/components/caarray/lib/.svn/entries b/geworkbench-core/components/caarray/lib/.svn/entries
index eef2c9e..6099c4b 100644
--- a/geworkbench-core/components/caarray/lib/.svn/entries
+++ b/geworkbench-core/components/caarray/lib/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/caarray/lib
 https://ncisvn.nci.nih.gov/svn/geworkbench

@@ -298,16 +298,16 @@ has-props

 109043

-jboss-ejb3x-4.0.5.GA.jar
+caarray-client-external-v1_0.jar
 file




 2011-08-17T00:10:38.000000Z
-6ea1388744f664ba96110946f8f099b8
-2009-08-24T14:49:17.000000Z
-5492
+24700f2ad0d430bf5a06a1dcf75842ef
+2009-10-02T19:45:53.000000Z
+5638
 jiz
 has-props

@@ -330,7 +330,7 @@ has-props



-19858
+144231

 jboss-cache-1.4.0.SP1.jar
 file
@@ -366,16 +366,16 @@ has-props

 692813

-caarray-client-external-v1_0.jar
+jboss-ejb3x-4.0.5.GA.jar
 file




 2011-08-17T00:10:38.000000Z
-24700f2ad0d430bf5a06a1dcf75842ef
-2009-10-02T19:45:53.000000Z
-5638
+6ea1388744f664ba96110946f8f099b8
+2009-08-24T14:49:17.000000Z
+5492
 jiz
 has-props

@@ -398,7 +398,7 @@ has-props



-144231
+19858

 dozer-4.4.1.jar
 file
diff --git a/geworkbench-core/components/caarray/src/.svn/all-wcprops b/geworkbench-core/components/caarray/src/.svn/all-wcprops
index cfcb7cb..12132e3 100644
--- a/geworkbench-core/components/caarray/src/.svn/all-wcprops
+++ b/geworkbench-core/components/caarray/src/.svn/all-wcprops
@@ -1,5 +1,5 @@
 K 25
 svn:wc:ra_dav:version-url
 V 71
-/svn/geworkbench/!svn/ver/8463/trunk/geworkbench/components/caarray/src
+/svn/geworkbench/!svn/ver/8785/trunk/geworkbench/components/caarray/src
 END
diff --git a/geworkbench-core/components/caarray/src/.svn/entries b/geworkbench-core/components/caarray/src/.svn/entries
index aabedd0..9a2b802 100644
--- a/geworkbench-core/components/caarray/src/.svn/entries
+++ b/geworkbench-core/components/caarray/src/.svn/entries
@@ -1,15 +1,15 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/caarray/src
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2011-10-25T21:47:59.095740Z
-8463
-zji
+2012-01-26T21:17:35.990494Z
+8785
+maz



diff --git a/geworkbench-core/components/caarray/src/org/.svn/all-wcprops b/geworkbench-core/components/caarray/src/org/.svn/all-wcprops
index eda5347..5ee2515 100644
--- a/geworkbench-core/components/caarray/src/org/.svn/all-wcprops
+++ b/geworkbench-core/components/caarray/src/org/.svn/all-wcprops
@@ -1,5 +1,5 @@
 K 25
 svn:wc:ra_dav:version-url
 V 75
-/svn/geworkbench/!svn/ver/8463/trunk/geworkbench/components/caarray/src/org
+/svn/geworkbench/!svn/ver/8785/trunk/geworkbench/components/caarray/src/org
 END
diff --git a/geworkbench-core/components/caarray/src/org/.svn/entries b/geworkbench-core/components/caarray/src/org/.svn/entries
index 3722c78..13caede 100644
--- a/geworkbench-core/components/caarray/src/org/.svn/entries
+++ b/geworkbench-core/components/caarray/src/org/.svn/entries
@@ -1,15 +1,15 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/caarray/src/org
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2011-10-25T21:47:59.095740Z
-8463
-zji
+2012-01-26T21:17:35.990494Z
+8785
+maz



diff --git a/geworkbench-core/components/caarray/src/org/geworkbench/.svn/all-wcprops b/geworkbench-core/components/caarray/src/org/geworkbench/.svn/all-wcprops
index cdfb727..ddb8691 100644
--- a/geworkbench-core/components/caarray/src/org/geworkbench/.svn/all-wcprops
+++ b/geworkbench-core/components/caarray/src/org/geworkbench/.svn/all-wcprops
@@ -1,5 +1,5 @@
 K 25
 svn:wc:ra_dav:version-url
 V 87
-/svn/geworkbench/!svn/ver/8463/trunk/geworkbench/components/caarray/src/org/geworkbench
+/svn/geworkbench/!svn/ver/8785/trunk/geworkbench/components/caarray/src/org/geworkbench
 END
diff --git a/geworkbench-core/components/caarray/src/org/geworkbench/.svn/entries b/geworkbench-core/components/caarray/src/org/geworkbench/.svn/entries
index f8cbca8..1952799 100644
--- a/geworkbench-core/components/caarray/src/org/geworkbench/.svn/entries
+++ b/geworkbench-core/components/caarray/src/org/geworkbench/.svn/entries
@@ -1,15 +1,15 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/caarray/src/org/geworkbench
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2011-10-25T21:47:59.095740Z
-8463
-zji
+2012-01-26T21:17:35.990494Z
+8785
+maz



diff --git a/geworkbench-core/components/caarray/src/org/geworkbench/components/.svn/all-wcprops b/geworkbench-core/components/caarray/src/org/geworkbench/components/.svn/all-wcprops
index f673a16..b079e3c 100644
--- a/geworkbench-core/components/caarray/src/org/geworkbench/components/.svn/all-wcprops
+++ b/geworkbench-core/components/caarray/src/org/geworkbench/components/.svn/all-wcprops
@@ -1,5 +1,5 @@
 K 25
 svn:wc:ra_dav:version-url
 V 98
-/svn/geworkbench/!svn/ver/8463/trunk/geworkbench/components/caarray/src/org/geworkbench/components
+/svn/geworkbench/!svn/ver/8785/trunk/geworkbench/components/caarray/src/org/geworkbench/components
 END
diff --git a/geworkbench-core/components/caarray/src/org/geworkbench/components/.svn/entries b/geworkbench-core/components/caarray/src/org/geworkbench/components/.svn/entries
index 9d0b7e9..6a81a51 100644
--- a/geworkbench-core/components/caarray/src/org/geworkbench/components/.svn/entries
+++ b/geworkbench-core/components/caarray/src/org/geworkbench/components/.svn/entries
@@ -1,15 +1,15 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/caarray/src/org/geworkbench/components
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2011-10-25T21:47:59.095740Z
-8463
-zji
+2012-01-26T21:17:35.990494Z
+8785
+maz



diff --git a/geworkbench-core/components/caarray/src/org/geworkbench/components/caarray/.svn/all-wcprops b/geworkbench-core/components/caarray/src/org/geworkbench/components/caarray/.svn/all-wcprops
index 241db0f..0f81ea2 100644
--- a/geworkbench-core/components/caarray/src/org/geworkbench/components/caarray/.svn/all-wcprops
+++ b/geworkbench-core/components/caarray/src/org/geworkbench/components/caarray/.svn/all-wcprops
@@ -1,5 +1,5 @@
 K 25
 svn:wc:ra_dav:version-url
 V 106
-/svn/geworkbench/!svn/ver/8463/trunk/geworkbench/components/caarray/src/org/geworkbench/components/caarray
+/svn/geworkbench/!svn/ver/8785/trunk/geworkbench/components/caarray/src/org/geworkbench/components/caarray
 END
diff --git a/geworkbench-core/components/caarray/src/org/geworkbench/components/caarray/.svn/entries b/geworkbench-core/components/caarray/src/org/geworkbench/components/caarray/.svn/entries
index a979e12..3944bc0 100644
--- a/geworkbench-core/components/caarray/src/org/geworkbench/components/caarray/.svn/entries
+++ b/geworkbench-core/components/caarray/src/org/geworkbench/components/caarray/.svn/entries
@@ -1,15 +1,15 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/caarray/src/org/geworkbench/components/caarray
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2011-10-25T21:47:59.095740Z
-8463
-zji
+2012-01-26T21:17:35.990494Z
+8785
+maz



diff --git a/geworkbench-core/components/caarray/src/org/geworkbench/components/caarray/arraydata/.svn/all-wcprops b/geworkbench-core/components/caarray/src/org/geworkbench/components/caarray/arraydata/.svn/all-wcprops
index 0d10235..32e82d6 100644
--- a/geworkbench-core/components/caarray/src/org/geworkbench/components/caarray/arraydata/.svn/all-wcprops
+++ b/geworkbench-core/components/caarray/src/org/geworkbench/components/caarray/arraydata/.svn/all-wcprops
@@ -1,7 +1,7 @@
 K 25
 svn:wc:ra_dav:version-url
 V 116
-/svn/geworkbench/!svn/ver/8463/trunk/geworkbench/components/caarray/src/org/geworkbench/components/caarray/arraydata
+/svn/geworkbench/!svn/ver/8785/trunk/geworkbench/components/caarray/src/org/geworkbench/components/caarray/arraydata
 END
 CaArray2Component.cwb.xml
 K 25
@@ -19,5 +19,5 @@ CaArray2Component.java
 K 25
 svn:wc:ra_dav:version-url
 V 139
-/svn/geworkbench/!svn/ver/8463/trunk/geworkbench/components/caarray/src/org/geworkbench/components/caarray/arraydata/CaArray2Component.java
+/svn/geworkbench/!svn/ver/8785/trunk/geworkbench/components/caarray/src/org/geworkbench/components/caarray/arraydata/CaArray2Component.java
 END
diff --git a/geworkbench-core/components/caarray/src/org/geworkbench/components/caarray/arraydata/.svn/entries b/geworkbench-core/components/caarray/src/org/geworkbench/components/caarray/arraydata/.svn/entries
index 4fbd918..23b5639 100644
--- a/geworkbench-core/components/caarray/src/org/geworkbench/components/caarray/arraydata/.svn/entries
+++ b/geworkbench-core/components/caarray/src/org/geworkbench/components/caarray/arraydata/.svn/entries
@@ -1,15 +1,15 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/caarray/src/org/geworkbench/components/caarray/arraydata
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2011-10-25T21:47:59.095740Z
-8463
-zji
+2012-01-26T21:17:35.990494Z
+8785
+maz



@@ -100,11 +100,11 @@ file



-2012-01-10T19:15:23.000000Z
-d3229869c319d4075bcd23e1dcfd8511
-2011-10-25T21:47:59.095740Z
-8463
-zji
+2012-01-31T19:12:32.000000Z
+b3b95a2a0bad374e68908f337cdc2ed2
+2012-01-26T21:17:35.990494Z
+8785
+maz
 has-props


@@ -126,5 +126,5 @@ has-props



-17394
+17308

diff --git a/geworkbench-core/components/caarray/src/org/geworkbench/components/caarray/arraydata/.svn/text-base/CaArray2Component.java.svn-base b/geworkbench-core/components/caarray/src/org/geworkbench/components/caarray/arraydata/.svn/text-base/CaArray2Component.java.svn-base
index 981d263..58b4ddf 100644
--- a/geworkbench-core/components/caarray/src/org/geworkbench/components/caarray/arraydata/.svn/text-base/CaArray2Component.java.svn-base
+++ b/geworkbench-core/components/caarray/src/org/geworkbench/components/caarray/arraydata/.svn/text-base/CaArray2Component.java.svn-base
@@ -336,8 +336,7 @@ public class CaArray2Component implements VisualPlugin {
 			throws Exception {
 		CSMicroarraySet microarraySet = null;

-		String desc = "";
-		if(hybridzations.size()>1)desc = "Merged DataSet: ";
+		String desc = "";

 		int number = 0;
 		CaArraySuccessEvent caArraySuccessEvent = new CaArraySuccessEvent(hybridzations.size());
@@ -361,7 +360,7 @@ public class CaArray2Component implements VisualPlugin {
 			}

 			microarraySet.add(microarray);
-			desc += experimentName + "_" + hybridizationName + " ";
+			desc = experimentName;

 			publishCaArraySuccessEvent(caArraySuccessEvent);
 			number++;
diff --git a/geworkbench-core/components/caarray/src/org/geworkbench/components/caarray/arraydata/CaArray2Component.java b/geworkbench-core/components/caarray/src/org/geworkbench/components/caarray/arraydata/CaArray2Component.java
index fcd6e2b..86abcd2 100755
--- a/geworkbench-core/components/caarray/src/org/geworkbench/components/caarray/arraydata/CaArray2Component.java
+++ b/geworkbench-core/components/caarray/src/org/geworkbench/components/caarray/arraydata/CaArray2Component.java
@@ -56,7 +56,7 @@ import org.geworkbench.util.AffyAnnotationUtil;
  * The wrapper class for CaArray Component.
  *
  * @author xiaoqing
- * @version $Id: CaArray2Component.java 8463 2011-10-25 21:47:59Z zji $
+ * @version $Id: CaArray2Component.java 8785 2012-01-26 21:17:35Z maz $
  *
  */
 @AcceptTypes( { DSMicroarraySet.class, CSSequenceSet.class })
@@ -336,8 +336,7 @@ public class CaArray2Component implements VisualPlugin {
 			throws Exception {
 		CSMicroarraySet microarraySet = null;

-		String desc = "";
-		if(hybridzations.size()>1)desc = "Merged DataSet: ";
+		String desc = "";

 		int number = 0;
 		CaArraySuccessEvent caArraySuccessEvent = new CaArraySuccessEvent(hybridzations.size());
@@ -361,7 +360,7 @@ public class CaArray2Component implements VisualPlugin {
 			}

 			microarraySet.add(microarray);
-			desc += experimentName + "_" + hybridizationName + " ";
+			desc = experimentName;

 			publishCaArraySuccessEvent(caArraySuccessEvent);
 			number++;
diff --git a/geworkbench-core/components/celprocessing/.svn/entries b/geworkbench-core/components/celprocessing/.svn/entries
index a39f2d3..af43550 100644
--- a/geworkbench-core/components/celprocessing/.svn/entries
+++ b/geworkbench-core/components/celprocessing/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/celprocessing
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/celprocessing/src/.svn/entries b/geworkbench-core/components/celprocessing/src/.svn/entries
index f830a43..a942691 100644
--- a/geworkbench-core/components/celprocessing/src/.svn/entries
+++ b/geworkbench-core/components/celprocessing/src/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/celprocessing/src
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/celprocessing/src/org/.svn/entries b/geworkbench-core/components/celprocessing/src/org/.svn/entries
index f3e8079..279de18 100644
--- a/geworkbench-core/components/celprocessing/src/org/.svn/entries
+++ b/geworkbench-core/components/celprocessing/src/org/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/celprocessing/src/org
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/celprocessing/src/org/geworkbench/.svn/entries b/geworkbench-core/components/celprocessing/src/org/geworkbench/.svn/entries
index 890168b..9c8cef9 100644
--- a/geworkbench-core/components/celprocessing/src/org/geworkbench/.svn/entries
+++ b/geworkbench-core/components/celprocessing/src/org/geworkbench/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/celprocessing/src/org/geworkbench
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/celprocessing/src/org/geworkbench/components/.svn/entries b/geworkbench-core/components/celprocessing/src/org/geworkbench/components/.svn/entries
index 68111a9..79aa6b8 100644
--- a/geworkbench-core/components/celprocessing/src/org/geworkbench/components/.svn/entries
+++ b/geworkbench-core/components/celprocessing/src/org/geworkbench/components/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/celprocessing/src/org/geworkbench/components
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/celprocessing/src/org/geworkbench/components/celprocessing/.svn/entries b/geworkbench-core/components/celprocessing/src/org/geworkbench/components/celprocessing/.svn/entries
index 0fcccb1..7cdbfb8 100644
--- a/geworkbench-core/components/celprocessing/src/org/geworkbench/components/celprocessing/.svn/entries
+++ b/geworkbench-core/components/celprocessing/src/org/geworkbench/components/celprocessing/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/celprocessing/src/org/geworkbench/components/celprocessing
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/celprocessing/src/org/geworkbench/components/celprocessing/help/.svn/entries b/geworkbench-core/components/celprocessing/src/org/geworkbench/components/celprocessing/help/.svn/entries
index 70079cb..30940de 100644
--- a/geworkbench-core/components/celprocessing/src/org/geworkbench/components/celprocessing/help/.svn/entries
+++ b/geworkbench-core/components/celprocessing/src/org/geworkbench/components/celprocessing/help/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/celprocessing/src/org/geworkbench/components/celprocessing/help
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/celprocessing/src/org/geworkbench/components/celprocessing/help/open_dataset_files/.svn/entries b/geworkbench-core/components/celprocessing/src/org/geworkbench/components/celprocessing/help/open_dataset_files/.svn/entries
index e9f91c5..62a4ca6 100644
--- a/geworkbench-core/components/celprocessing/src/org/geworkbench/components/celprocessing/help/open_dataset_files/.svn/entries
+++ b/geworkbench-core/components/celprocessing/src/org/geworkbench/components/celprocessing/help/open_dataset_files/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/celprocessing/src/org/geworkbench/components/celprocessing/help/open_dataset_files
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/cgems/.svn/entries b/geworkbench-core/components/cgems/.svn/entries
index e462b40..c6fe295 100644
--- a/geworkbench-core/components/cgems/.svn/entries
+++ b/geworkbench-core/components/cgems/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/cgems
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/cgems/conf/.svn/entries b/geworkbench-core/components/cgems/conf/.svn/entries
index 6741a3b..11cb994 100644
--- a/geworkbench-core/components/cgems/conf/.svn/entries
+++ b/geworkbench-core/components/cgems/conf/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/cgems/conf
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/cgems/lib/.svn/entries b/geworkbench-core/components/cgems/lib/.svn/entries
index cac9b6e..e12e8e7 100644
--- a/geworkbench-core/components/cgems/lib/.svn/entries
+++ b/geworkbench-core/components/cgems/lib/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/cgems/lib
 https://ncisvn.nci.nih.gov/svn/geworkbench

@@ -536,14 +536,14 @@ has-props

 30489

-batik-svg-dom.jar
+batik-extension.jar
 file




 2011-08-17T00:10:39.000000Z
-5d916332345a679f839122fce7672218
+42cab37430eee526f13bd553a8f65ba9
 2007-01-17T18:05:24.000000Z
 2244
 keshav
@@ -568,16 +568,16 @@ has-props



-376951
+44832

-batik-extension.jar
+batik-svg-dom.jar
 file




 2011-08-17T00:10:39.000000Z
-42cab37430eee526f13bd553a8f65ba9
+5d916332345a679f839122fce7672218
 2007-01-17T18:05:24.000000Z
 2244
 keshav
@@ -602,7 +602,7 @@ has-props



-44832
+376951

 batik-util.jar
 file
@@ -842,14 +842,14 @@ has-props

 1421

-batik-ext.jar
+batik-gvt.jar
 file




 2011-08-17T00:10:39.000000Z
-05911a0b89a9df70ac1323eb57831b88
+0bb0c4fac6ea5ece14c07495f5f13d42
 2007-01-17T18:05:24.000000Z
 2244
 keshav
@@ -874,16 +874,16 @@ has-props



-76733
+143597

-batik-gvt.jar
+batik-ext.jar
 file




 2011-08-17T00:10:39.000000Z
-0bb0c4fac6ea5ece14c07495f5f13d42
+05911a0b89a9df70ac1323eb57831b88
 2007-01-17T18:05:24.000000Z
 2244
 keshav
@@ -908,18 +908,18 @@ has-props



-143597
+76733

-commons-lang-2.2.jar
+batik-slideshow.jar
 file




 2011-08-17T00:10:39.000000Z
-547741aaaa60474d7f1b383319db9b85
-2007-01-23T21:24:47.000000Z
-2312
+58387ff2857faa8903db9151efbc7fad
+2007-01-17T18:05:24.000000Z
+2244
 keshav
 has-props

@@ -942,18 +942,18 @@ has-props



-243016
+8420

-batik-slideshow.jar
+commons-lang-2.2.jar
 file




 2011-08-17T00:10:39.000000Z
-58387ff2857faa8903db9151efbc7fad
-2007-01-17T18:05:24.000000Z
-2244
+547741aaaa60474d7f1b383319db9b85
+2007-01-23T21:24:47.000000Z
+2312
 keshav
 has-props

@@ -976,7 +976,7 @@ has-props



-8420
+243016

 cgom-cgems-client.jar
 file
diff --git a/geworkbench-core/components/cgems/src/.svn/entries b/geworkbench-core/components/cgems/src/.svn/entries
index 98e2038..464addc 100644
--- a/geworkbench-core/components/cgems/src/.svn/entries
+++ b/geworkbench-core/components/cgems/src/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/cgems/src
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/cgems/src/gov/.svn/entries b/geworkbench-core/components/cgems/src/gov/.svn/entries
index ccc3e3c..9581919 100644
--- a/geworkbench-core/components/cgems/src/gov/.svn/entries
+++ b/geworkbench-core/components/cgems/src/gov/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/cgems/src/gov
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/cgems/src/gov/nih/.svn/entries b/geworkbench-core/components/cgems/src/gov/nih/.svn/entries
index 348508c..88dc165 100644
--- a/geworkbench-core/components/cgems/src/gov/nih/.svn/entries
+++ b/geworkbench-core/components/cgems/src/gov/nih/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/cgems/src/gov/nih
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/cgems/src/gov/nih/nci/.svn/entries b/geworkbench-core/components/cgems/src/gov/nih/nci/.svn/entries
index d745445..af1e500 100644
--- a/geworkbench-core/components/cgems/src/gov/nih/nci/.svn/entries
+++ b/geworkbench-core/components/cgems/src/gov/nih/nci/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/cgems/src/gov/nih/nci
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/cgems/src/gov/nih/nci/system/.svn/entries b/geworkbench-core/components/cgems/src/gov/nih/nci/system/.svn/entries
index 0f57556..5f33d6b 100644
--- a/geworkbench-core/components/cgems/src/gov/nih/nci/system/.svn/entries
+++ b/geworkbench-core/components/cgems/src/gov/nih/nci/system/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/cgems/src/gov/nih/nci/system
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/cgems/src/gov/nih/nci/system/comm/.svn/entries b/geworkbench-core/components/cgems/src/gov/nih/nci/system/comm/.svn/entries
index 47245eb..56322a3 100644
--- a/geworkbench-core/components/cgems/src/gov/nih/nci/system/comm/.svn/entries
+++ b/geworkbench-core/components/cgems/src/gov/nih/nci/system/comm/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/cgems/src/gov/nih/nci/system/comm
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/cgems/src/gov/nih/nci/system/comm/client/.svn/entries b/geworkbench-core/components/cgems/src/gov/nih/nci/system/comm/client/.svn/entries
index 7aef128..6053679 100644
--- a/geworkbench-core/components/cgems/src/gov/nih/nci/system/comm/client/.svn/entries
+++ b/geworkbench-core/components/cgems/src/gov/nih/nci/system/comm/client/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/cgems/src/gov/nih/nci/system/comm/client
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/cgems/src/org/.svn/entries b/geworkbench-core/components/cgems/src/org/.svn/entries
index f557c4c..03cd67f 100644
--- a/geworkbench-core/components/cgems/src/org/.svn/entries
+++ b/geworkbench-core/components/cgems/src/org/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/cgems/src/org
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/cgems/src/org/geworkbench/.svn/entries b/geworkbench-core/components/cgems/src/org/geworkbench/.svn/entries
index ca4857b..d2fd534 100644
--- a/geworkbench-core/components/cgems/src/org/geworkbench/.svn/entries
+++ b/geworkbench-core/components/cgems/src/org/geworkbench/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/cgems/src/org/geworkbench
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/cgems/src/org/geworkbench/components/.svn/entries b/geworkbench-core/components/cgems/src/org/geworkbench/components/.svn/entries
index 2ab48a9..728d5ad 100644
--- a/geworkbench-core/components/cgems/src/org/geworkbench/components/.svn/entries
+++ b/geworkbench-core/components/cgems/src/org/geworkbench/components/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/cgems/src/org/geworkbench/components
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/cgems/src/org/geworkbench/components/cgems/.svn/entries b/geworkbench-core/components/cgems/src/org/geworkbench/components/cgems/.svn/entries
index 0c7434c..44321fb 100644
--- a/geworkbench-core/components/cgems/src/org/geworkbench/components/cgems/.svn/entries
+++ b/geworkbench-core/components/cgems/src/org/geworkbench/components/cgems/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/cgems/src/org/geworkbench/components/cgems
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/components/colormosaic/.svn/all-wcprops b/geworkbench-core/components/colormosaic/.svn/all-wcprops
index d1af490..7a87953 100644
--- a/geworkbench-core/components/colormosaic/.svn/all-wcprops
+++ b/geworkbench-core/components/colormosaic/.svn/all-wcprops
@@ -1,7 +1,7 @@
 K 25
 svn:wc:ra_dav:version-url
 V 71
-/svn/geworkbench/!svn/ver/8424/trunk/geworkbench/components/colormosaic
+/svn/geworkbench/!svn/ver/8812/trunk/geworkbench/components/colormosaic
 END
 .classpath
 K 25
diff --git a/geworkbench-core/components/colormosaic/.svn/entries b/geworkbench-core/components/colormosaic/.svn/entries
index d4ec7c8..71782e9 100644
--- a/geworkbench-core/components/colormosaic/.svn/entries
+++ b/geworkbench-core/components/colormosaic/.svn/entries
@@ -1,14 +1,14 @@
 10

 dir
-8680
+8812
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/colormosaic
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2011-10-19T16:34:53.735246Z
-8424
+2012-01-30T21:31:47.792401Z<