readded svn folders...

Jonathan Bell [2012-01-04 20:35:21]
 readded svn folders...
Filename
geworkbench-core/.settings/.svn/entries
geworkbench-core/.settings/org.eclipse.wst.common.component
geworkbench-core/.svn/all-wcprops
geworkbench-core/.svn/entries
geworkbench-core/.svn/text-base/build.xml.svn-base
geworkbench-core/.svn/tmp/.classpath.2.tmp
geworkbench-core/.svn/tmp/.classpath.tmp
geworkbench-core/.svn/tmp/tempfile.2.tmp
geworkbench-core/.svn/tmp/tempfile.tmp
geworkbench-core/_all/.svn/entries
geworkbench-core/annotation/.svn/entries
geworkbench-core/bin/.svn/entries
geworkbench-core/bin/matrixreduce/.svn/entries
geworkbench-core/build.xml
geworkbench-core/cascripts/.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/prop-base/BlastAlgorithm.java.svn-base
geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/.svn/prop-base/BlastObj.java.svn-base
geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/.svn/text-base/BlastAlgorithm.java.svn-base
geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/.svn/text-base/BlastObj.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/BlastAlgorithm.java
geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/BlastObj.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/all-wcprops
geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/.svn/entries
geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/.svn/prop-base/AlgorithmMatcher.java.svn-base
geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/.svn/prop-base/BlastAppComponent.java.svn-base
geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/.svn/prop-base/ParameterSetting.java.svn-base
geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/.svn/text-base/AlgorithmMatcher.java.svn-base
geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/.svn/text-base/BlastAppComponent.cwb.xml.svn-base
geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/.svn/text-base/BlastAppComponent.java.svn-base
geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/.svn/text-base/BlastViewComponent.cwb.xml.svn-base
geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/.svn/text-base/BlastViewComponent.java.svn-base
geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/.svn/text-base/BlastViewPanel.java.svn-base
geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/.svn/text-base/ParameterSetting.java.svn-base
geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/AlgorithmMatcher.java
geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/BlastAppComponent.cwb.xml
geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/BlastAppComponent.java
geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/BlastViewComponent.cwb.xml
geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/BlastViewComponent.java
geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/BlastViewPanel.java
geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/ParameterSetting.java
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/prop-base/caGrid-ServiceSecurityProvider-client-1.3.jar.svn-base
geworkbench-core/components/analysis/lib/.svn/prop-base/caGrid-ServiceSecurityProvider-common-1.3.jar.svn-base
geworkbench-core/components/analysis/lib/.svn/prop-base/caGrid-ServiceSecurityProvider-service-1.3.jar.svn-base
geworkbench-core/components/analysis/lib/.svn/prop-base/caGrid-ServiceSecurityProvider-stubs-1.3.jar.svn-base
geworkbench-core/components/analysis/lib/.svn/prop-base/caGrid-core-1.3.jar.svn-base
geworkbench-core/components/analysis/lib/.svn/prop-base/caGrid-discovery-1.3.jar.svn-base
geworkbench-core/components/analysis/lib/.svn/prop-base/caGrid-metadata-common-1.3.jar.svn-base
geworkbench-core/components/analysis/lib/.svn/prop-base/caGrid-metadata-data-1.3.jar.svn-base
geworkbench-core/components/analysis/lib/.svn/prop-base/caGrid-metadata-security-1.3.jar.svn-base
geworkbench-core/components/analysis/lib/.svn/prop-base/caGrid-metadatautils-1.3.jar.svn-base
geworkbench-core/components/analysis/lib/.svn/text-base/caGrid-ServiceSecurityProvider-client-1.3.jar.svn-base
geworkbench-core/components/analysis/lib/.svn/text-base/caGrid-ServiceSecurityProvider-common-1.3.jar.svn-base
geworkbench-core/components/analysis/lib/.svn/text-base/caGrid-ServiceSecurityProvider-service-1.3.jar.svn-base
geworkbench-core/components/analysis/lib/.svn/text-base/caGrid-ServiceSecurityProvider-stubs-1.3.jar.svn-base
geworkbench-core/components/analysis/lib/.svn/text-base/caGrid-core-1.3.jar.svn-base
geworkbench-core/components/analysis/lib/.svn/text-base/caGrid-discovery-1.3.jar.svn-base
geworkbench-core/components/analysis/lib/.svn/text-base/caGrid-metadata-common-1.3.jar.svn-base
geworkbench-core/components/analysis/lib/.svn/text-base/caGrid-metadata-data-1.3.jar.svn-base
geworkbench-core/components/analysis/lib/.svn/text-base/caGrid-metadata-security-1.3.jar.svn-base
geworkbench-core/components/analysis/lib/.svn/text-base/caGrid-metadatautils-1.3.jar.svn-base
geworkbench-core/components/analysis/lib/caGrid-ServiceSecurityProvider-client-1.3.jar
geworkbench-core/components/analysis/lib/caGrid-ServiceSecurityProvider-common-1.3.jar
geworkbench-core/components/analysis/lib/caGrid-ServiceSecurityProvider-service-1.3.jar
geworkbench-core/components/analysis/lib/caGrid-ServiceSecurityProvider-stubs-1.3.jar
geworkbench-core/components/analysis/lib/caGrid-core-1.3.jar
geworkbench-core/components/analysis/lib/caGrid-discovery-1.3.jar
geworkbench-core/components/analysis/lib/caGrid-metadata-common-1.3.jar
geworkbench-core/components/analysis/lib/caGrid-metadata-data-1.3.jar
geworkbench-core/components/analysis/lib/caGrid-metadata-security-1.3.jar
geworkbench-core/components/analysis/lib/caGrid-metadatautils-1.3.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.cwb.xml.svn-base
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/AnalysisPanel.cwb.xml
geworkbench-core/components/analysis/src/org/geworkbench/components/analysis/AnalysisPanel.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/all-wcprops
geworkbench-core/components/analysis/src/org/geworkbench/components/cagrid/.svn/entries
geworkbench-core/components/analysis/src/org/geworkbench/components/cagrid/gui/.svn/all-wcprops
geworkbench-core/components/analysis/src/org/geworkbench/components/cagrid/gui/.svn/entries
geworkbench-core/components/analysis/src/org/geworkbench/components/cagrid/gui/.svn/text-base/GridServicePanel.java.svn-base
geworkbench-core/components/analysis/src/org/geworkbench/components/cagrid/gui/GridServicePanel.java
geworkbench-core/components/annotations/.svn/all-wcprops
geworkbench-core/components/annotations/.svn/entries
geworkbench-core/components/annotations/conf/.svn/entries
geworkbench-core/components/annotations/lib/.svn/entries
geworkbench-core/components/annotations/src/.svn/all-wcprops
geworkbench-core/components/annotations/src/.svn/entries
geworkbench-core/components/annotations/src/org/.svn/all-wcprops
geworkbench-core/components/annotations/src/org/.svn/entries
geworkbench-core/components/annotations/src/org/geworkbench/.svn/all-wcprops
geworkbench-core/components/annotations/src/org/geworkbench/.svn/entries
geworkbench-core/components/annotations/src/org/geworkbench/components/.svn/all-wcprops
geworkbench-core/components/annotations/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/annotations/src/org/geworkbench/components/annotations/.svn/all-wcprops
geworkbench-core/components/annotations/src/org/geworkbench/components/annotations/.svn/entries
geworkbench-core/components/annotations/src/org/geworkbench/components/annotations/.svn/text-base/AnnotationsPanel2.java.svn-base
geworkbench-core/components/annotations/src/org/geworkbench/components/annotations/AnnotationsPanel2.java
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/all-wcprops
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/all-wcprops
geworkbench-core/components/anova/src/.svn/entries
geworkbench-core/components/anova/src/org/.svn/all-wcprops
geworkbench-core/components/anova/src/org/.svn/entries
geworkbench-core/components/anova/src/org/geworkbench/.svn/all-wcprops
geworkbench-core/components/anova/src/org/geworkbench/.svn/entries
geworkbench-core/components/anova/src/org/geworkbench/components/.svn/all-wcprops
geworkbench-core/components/anova/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/anova/src/org/geworkbench/components/anova/.svn/all-wcprops
geworkbench-core/components/anova/src/org/geworkbench/components/anova/.svn/entries
geworkbench-core/components/anova/src/org/geworkbench/components/anova/.svn/text-base/AnovaAnalysis.java.svn-base
geworkbench-core/components/anova/src/org/geworkbench/components/anova/AnovaAnalysis.java
geworkbench-core/components/anova/src/org/geworkbench/components/anova/gui/.svn/all-wcprops
geworkbench-core/components/anova/src/org/geworkbench/components/anova/gui/.svn/entries
geworkbench-core/components/anova/src/org/geworkbench/components/anova/gui/.svn/text-base/AnovaAnalysisPanel.java.svn-base
geworkbench-core/components/anova/src/org/geworkbench/components/anova/gui/AnovaAnalysisPanel.java
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/.svn/text-base/AracneParamPanel.java.svn-base
geworkbench-core/components/aracne-java/src/org/geworkbench/components/aracne/.svn/text-base/AracneProgress.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/AracneParamPanel.java
geworkbench-core/components/aracne-java/src/org/geworkbench/components/aracne/AracneProgress.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/prop-base/CaArray2Component.java.svn-base
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/.svn/text-base/CaArrayClient.java.svn-base
geworkbench-core/components/caarray/src/org/geworkbench/components/caarray/arraydata/CaArray2Component.java
geworkbench-core/components/caarray/src/org/geworkbench/components/caarray/arraydata/CaArrayClient.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/all-wcprops
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/all-wcprops
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/all-wcprops
geworkbench-core/components/cgems/src/org/.svn/entries
geworkbench-core/components/cgems/src/org/geworkbench/.svn/all-wcprops
geworkbench-core/components/cgems/src/org/geworkbench/.svn/entries
geworkbench-core/components/cgems/src/org/geworkbench/components/.svn/all-wcprops
geworkbench-core/components/cgems/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/cgems/src/org/geworkbench/components/cgems/.svn/all-wcprops
geworkbench-core/components/cgems/src/org/geworkbench/components/cgems/.svn/entries
geworkbench-core/components/cgems/src/org/geworkbench/components/cgems/.svn/text-base/CGemsPanel.java.svn-base
geworkbench-core/components/cgems/src/org/geworkbench/components/cgems/CGemsPanel.java
geworkbench-core/components/colormosaic/.svn/all-wcprops
geworkbench-core/components/colormosaic/.svn/entries
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/ColorMosaicImage.java.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/.svn/text-base/EisenBlock.java.svn-base
geworkbench-core/components/colormosaic/src/org/geworkbench/components/colormosaic/ColorMosaicImage.java
geworkbench-core/components/colormosaic/src/org/geworkbench/components/colormosaic/ColorMosaicPanel.java
geworkbench-core/components/colormosaic/src/org/geworkbench/components/colormosaic/EisenBlock.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/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/.classpath
geworkbench-core/components/cytoscape/.svn/all-wcprops
geworkbench-core/components/cytoscape/.svn/entries
geworkbench-core/components/cytoscape/.svn/text-base/.classpath.svn-base
geworkbench-core/components/cytoscape/lib/.svn/all-wcprops
geworkbench-core/components/cytoscape/lib/.svn/entries
geworkbench-core/components/cytoscape/lib/.svn/prop-base/AdvancedNetworkMerge.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/AutomaticLayout.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/CytoscapeEditor.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/ManualLayout.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/SBMLReader.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/TableImport.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/biojava-1.4.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/biomartClient.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/browser.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/cPath.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/colt.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/coltginy.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/com-nerius-math-xform.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/commons-cli-1.x-cytoscape-custom.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/concurrent.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/cpath2.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/cytoscape-cruft-obo.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/cytoscape-geom-rtree.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/cytoscape-geom-spacial.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/cytoscape-graph-dynamic.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/cytoscape-graph-fixed.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/cytoscape-render-export.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/cytoscape-render-immed.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/cytoscape-render-stateful.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/cytoscape-task.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/cytoscape-util-intr.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/ding.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/filter.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/filters.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/fing.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/freehep-export-2.1.1.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/freehep-graphics2d-2.1.1.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/freehep-graphicsio-2.1.1.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/freehep-graphicsio-java-2.1.1.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/freehep-graphicsio-ps-2.1.1.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/freehep-graphicsio-svg-2.1.1.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/freehep-io-2.0.2.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/freehep-jas-plotter-2.2.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/freehep-swing-2.0.3.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/freehep-util-2.0.2.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/freehep-xml-2.1.1.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/giny.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/glf.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/i4jruntime.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/itext-2.0.4.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/jdom-1.0.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/jnlp.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/junit.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/l2fprod-common-all.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/linkout.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/looks-2.1.4.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/ncbiClient.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/phoebe.dnd.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/piccolo.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/psi_mi.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/quick_find.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/sjsxp.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/stax-ex.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/swing-layout-1.0.3.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/swingx-1.0.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/swingx-beaninfo-1.0.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/tclib.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/undo.support.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/violinstrings-1.0.2.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/prop-base/yLayouts.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/AdvancedNetworkMerge.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/AutomaticLayout.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/CytoscapeEditor.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/ManualLayout.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/SBMLReader.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/TableImport.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/biojava-1.4.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/biomartClient.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/browser.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/cPath.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/colt.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/coltginy.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/com-nerius-math-xform.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/commons-cli-1.x-cytoscape-custom.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/concurrent.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/cpath2.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/cytoscape-cruft-obo.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/cytoscape-geom-rtree.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/cytoscape-geom-spacial.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/cytoscape-graph-dynamic.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/cytoscape-graph-fixed.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/cytoscape-render-export.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/cytoscape-render-immed.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/cytoscape-render-stateful.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/cytoscape-task.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/cytoscape-util-intr.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/cytoscape.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/ding.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/filter.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/filters.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/fing.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/freehep-export-2.1.1.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/freehep-graphics2d-2.1.1.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/freehep-graphicsio-2.1.1.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/freehep-graphicsio-java-2.1.1.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/freehep-graphicsio-ps-2.1.1.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/freehep-graphicsio-svg-2.1.1.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/freehep-io-2.0.2.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/freehep-jas-plotter-2.2.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/freehep-swing-2.0.3.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/freehep-util-2.0.2.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/freehep-xml-2.1.1.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/giny.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/glf.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/i4jruntime.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/itext-2.0.4.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/jdom-1.0.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/jnlp.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/junit.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/l2fprod-common-all.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/linkout.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/looks-2.1.4.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/ncbiClient.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/phoebe.dnd.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/piccolo.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/psi_mi.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/quick_find.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/sjsxp.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/stax-ex.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/swing-layout-1.0.3.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/swingx-1.0.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/swingx-beaninfo-1.0.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/tclib.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/undo.support.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/violinstrings-1.0.2.jar.svn-base
geworkbench-core/components/cytoscape/lib/.svn/text-base/yLayouts.jar.svn-base
geworkbench-core/components/cytoscape/lib/AdvancedNetworkMerge.jar
geworkbench-core/components/cytoscape/lib/AutomaticLayout.jar
geworkbench-core/components/cytoscape/lib/CytoscapeEditor.jar
geworkbench-core/components/cytoscape/lib/ManualLayout.jar
geworkbench-core/components/cytoscape/lib/SBMLReader.jar
geworkbench-core/components/cytoscape/lib/TableImport.jar
geworkbench-core/components/cytoscape/lib/biojava-1.4.jar
geworkbench-core/components/cytoscape/lib/biomartClient.jar
geworkbench-core/components/cytoscape/lib/browser.jar
geworkbench-core/components/cytoscape/lib/cPath.jar
geworkbench-core/components/cytoscape/lib/colt.jar
geworkbench-core/components/cytoscape/lib/coltginy.jar
geworkbench-core/components/cytoscape/lib/com-nerius-math-xform.jar
geworkbench-core/components/cytoscape/lib/commons-cli-1.x-cytoscape-custom.jar
geworkbench-core/components/cytoscape/lib/concurrent.jar
geworkbench-core/components/cytoscape/lib/cpath2.jar
geworkbench-core/components/cytoscape/lib/cytoscape-cruft-obo.jar
geworkbench-core/components/cytoscape/lib/cytoscape-geom-rtree.jar
geworkbench-core/components/cytoscape/lib/cytoscape-geom-spacial.jar
geworkbench-core/components/cytoscape/lib/cytoscape-graph-dynamic.jar
geworkbench-core/components/cytoscape/lib/cytoscape-graph-fixed.jar
geworkbench-core/components/cytoscape/lib/cytoscape-render-export.jar
geworkbench-core/components/cytoscape/lib/cytoscape-render-immed.jar
geworkbench-core/components/cytoscape/lib/cytoscape-render-stateful.jar
geworkbench-core/components/cytoscape/lib/cytoscape-task.jar
geworkbench-core/components/cytoscape/lib/cytoscape-util-intr.jar
geworkbench-core/components/cytoscape/lib/cytoscape.jar
geworkbench-core/components/cytoscape/lib/ding.jar
geworkbench-core/components/cytoscape/lib/filter.jar
geworkbench-core/components/cytoscape/lib/filters.jar
geworkbench-core/components/cytoscape/lib/fing.jar
geworkbench-core/components/cytoscape/lib/freehep-export-2.1.1.jar
geworkbench-core/components/cytoscape/lib/freehep-graphics2d-2.1.1.jar
geworkbench-core/components/cytoscape/lib/freehep-graphicsio-2.1.1.jar
geworkbench-core/components/cytoscape/lib/freehep-graphicsio-java-2.1.1.jar
geworkbench-core/components/cytoscape/lib/freehep-graphicsio-ps-2.1.1.jar
geworkbench-core/components/cytoscape/lib/freehep-graphicsio-svg-2.1.1.jar
geworkbench-core/components/cytoscape/lib/freehep-io-2.0.2.jar
geworkbench-core/components/cytoscape/lib/freehep-jas-plotter-2.2.jar
geworkbench-core/components/cytoscape/lib/freehep-swing-2.0.3.jar
geworkbench-core/components/cytoscape/lib/freehep-util-2.0.2.jar
geworkbench-core/components/cytoscape/lib/freehep-xml-2.1.1.jar
geworkbench-core/components/cytoscape/lib/giny.jar
geworkbench-core/components/cytoscape/lib/glf.jar
geworkbench-core/components/cytoscape/lib/i4jruntime.jar
geworkbench-core/components/cytoscape/lib/itext-2.0.4.jar
geworkbench-core/components/cytoscape/lib/jdom-1.0.jar
geworkbench-core/components/cytoscape/lib/jnlp.jar
geworkbench-core/components/cytoscape/lib/junit.jar
geworkbench-core/components/cytoscape/lib/l2fprod-common-all.jar
geworkbench-core/components/cytoscape/lib/linkout.jar
geworkbench-core/components/cytoscape/lib/looks-2.1.4.jar
geworkbench-core/components/cytoscape/lib/ncbiClient.jar
geworkbench-core/components/cytoscape/lib/phoebe.dnd.jar
geworkbench-core/components/cytoscape/lib/piccolo.jar
geworkbench-core/components/cytoscape/lib/psi_mi.jar
geworkbench-core/components/cytoscape/lib/quick_find.jar
geworkbench-core/components/cytoscape/lib/sjsxp.jar
geworkbench-core/components/cytoscape/lib/stax-ex.jar
geworkbench-core/components/cytoscape/lib/swing-layout-1.0.3.jar
geworkbench-core/components/cytoscape/lib/swingx-1.0.jar
geworkbench-core/components/cytoscape/lib/swingx-beaninfo-1.0.jar
geworkbench-core/components/cytoscape/lib/tclib.jar
geworkbench-core/components/cytoscape/lib/undo.support.jar
geworkbench-core/components/cytoscape/lib/violinstrings-1.0.2.jar
geworkbench-core/components/cytoscape/lib/yLayouts.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/ArraysSelectionPanel.java.svn-base
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/.svn/text-base/ExpandMenuListener.java.svn-base
geworkbench-core/components/cytoscape/src/org/geworkbench/components/cytoscape/.svn/text-base/InitParam.java.svn-base
geworkbench-core/components/cytoscape/src/org/geworkbench/components/cytoscape/.svn/text-base/MarkerSelectionPanel.java.svn-base
geworkbench-core/components/cytoscape/src/org/geworkbench/components/cytoscape/.svn/text-base/NetworkRedrawWindow.java.svn-base
geworkbench-core/components/cytoscape/src/org/geworkbench/components/cytoscape/.svn/text-base/TTestResultSelectionPanel.java.svn-base
geworkbench-core/components/cytoscape/src/org/geworkbench/components/cytoscape/ArraysSelectionPanel.java
geworkbench-core/components/cytoscape/src/org/geworkbench/components/cytoscape/CytoscapeWidget.java
geworkbench-core/components/cytoscape/src/org/geworkbench/components/cytoscape/ExpandMenuListener.java
geworkbench-core/components/cytoscape/src/org/geworkbench/components/cytoscape/InitParam.java
geworkbench-core/components/cytoscape/src/org/geworkbench/components/cytoscape/MarkerSelectionPanel.java
geworkbench-core/components/cytoscape/src/org/geworkbench/components/cytoscape/NetworkRedrawWindow.java
geworkbench-core/components/cytoscape/src/org/geworkbench/components/cytoscape/TTestResultSelectionPanel.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/prop-base/ParameterPanel.java.svn-base
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/.svn/prop-base/ParameterTranslation.java.svn-base
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/.svn/prop-base/PatFilter.java.svn-base
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/.svn/prop-base/PatternDataSource.java.svn-base
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/.svn/prop-base/PatternTableModel.java.svn-base
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/.svn/prop-base/PatternTableModelWrapper.java.svn-base
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/.svn/prop-base/PatternTableView.java.svn-base
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/.svn/prop-base/SequenceDiscoveryViewAppComponent.java.svn-base
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/.svn/prop-base/SequenceDiscoveryViewWidget.java.svn-base
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/.svn/prop-base/load.gif.svn-base
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/.svn/prop-base/parameters.gif.svn-base
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/.svn/prop-base/start.gif.svn-base
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/.svn/prop-base/stop.gif.svn-base
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/.svn/text-base/ParameterPanel.java.svn-base
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/.svn/text-base/ParameterTranslation.java.svn-base
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/.svn/text-base/PatFilter.java.svn-base
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/.svn/text-base/PatternDataSource.java.svn-base
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/.svn/text-base/PatternTableModel.java.svn-base
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/.svn/text-base/PatternTableModelWrapper.java.svn-base
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/.svn/text-base/PatternTableView.java.svn-base
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/.svn/text-base/SequenceDiscoveryViewAppComponent.cwb.xml.svn-base
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/.svn/text-base/SequenceDiscoveryViewAppComponent.java.svn-base
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/.svn/text-base/SequenceDiscoveryViewWidget.java.svn-base
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/.svn/text-base/load.gif.svn-base
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/.svn/text-base/parameters.gif.svn-base
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/.svn/text-base/start.gif.svn-base
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/.svn/text-base/stop.gif.svn-base
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/ParameterPanel.java
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/ParameterTranslation.java
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/PatFilter.java
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/PatternDataSource.java
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/PatternTableModel.java
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/PatternTableModelWrapper.java
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/PatternTableView.java
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/SequenceDiscoveryViewAppComponent.cwb.xml
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/SequenceDiscoveryViewAppComponent.java
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/SequenceDiscoveryViewWidget.java
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/algorithm/.svn/all-wcprops
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/algorithm/.svn/entries
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/algorithm/.svn/prop-base/AlgorithmStub.java.svn-base
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/algorithm/.svn/prop-base/RegularDiscoveryFileLoader.java.svn-base
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/algorithm/.svn/prop-base/ServerBaseDiscovery.java.svn-base
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/algorithm/.svn/text-base/AlgorithmStub.java.svn-base
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/algorithm/.svn/text-base/RegularDiscoveryFileLoader.java.svn-base
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/algorithm/.svn/text-base/ServerBaseDiscovery.java.svn-base
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/algorithm/AlgorithmStub.java
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/algorithm/RegularDiscoveryFileLoader.java
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/algorithm/ServerBaseDiscovery.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/load.gif
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/parameters.gif
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/session/.svn/all-wcprops
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/session/.svn/entries
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/session/.svn/text-base/DiscoverySession.java.svn-base
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/session/DiscoverySession.java
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/start.gif
geworkbench-core/components/discovery/src/org/geworkbench/components/discovery/stop.gif
geworkbench-core/components/evidenceintegration/.svn/all-wcprops
geworkbench-core/components/evidenceintegration/.svn/entries
geworkbench-core/components/evidenceintegration/lib/.svn/entries
geworkbench-core/components/evidenceintegration/src/.svn/all-wcprops
geworkbench-core/components/evidenceintegration/src/.svn/entries
geworkbench-core/components/evidenceintegration/src/org/.svn/all-wcprops
geworkbench-core/components/evidenceintegration/src/org/.svn/entries
geworkbench-core/components/evidenceintegration/src/org/geworkbench/.svn/all-wcprops
geworkbench-core/components/evidenceintegration/src/org/geworkbench/.svn/entries
geworkbench-core/components/evidenceintegration/src/org/geworkbench/components/.svn/all-wcprops
geworkbench-core/components/evidenceintegration/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/evidenceintegration/src/org/geworkbench/components/ei/.svn/all-wcprops
geworkbench-core/components/evidenceintegration/src/org/geworkbench/components/ei/.svn/entries
geworkbench-core/components/evidenceintegration/src/org/geworkbench/components/ei/.svn/prop-base/EvidenceIntegrationParamPanel.java.svn-base
geworkbench-core/components/evidenceintegration/src/org/geworkbench/components/ei/.svn/text-base/EvidenceIntegrationAnalysis.java.svn-base
geworkbench-core/components/evidenceintegration/src/org/geworkbench/components/ei/.svn/text-base/EvidenceIntegrationDataSet.java.svn-base
geworkbench-core/components/evidenceintegration/src/org/geworkbench/components/ei/.svn/text-base/EvidenceIntegrationParamPanel.java.svn-base
geworkbench-core/components/evidenceintegration/src/org/geworkbench/components/ei/.svn/text-base/GenericDisplayPanel.java.svn-base
geworkbench-core/components/evidenceintegration/src/org/geworkbench/components/ei/EvidenceIntegrationAnalysis.java
geworkbench-core/components/evidenceintegration/src/org/geworkbench/components/ei/EvidenceIntegrationDataSet.java
geworkbench-core/components/evidenceintegration/src/org/geworkbench/components/ei/EvidenceIntegrationParamPanel.java
geworkbench-core/components/evidenceintegration/src/org/geworkbench/components/ei/GenericDisplayPanel.java
geworkbench-core/components/example/.svn/all-wcprops
geworkbench-core/components/example/.svn/entries
geworkbench-core/components/example/.svn/prop-base/example.iml.svn-base
geworkbench-core/components/example/.svn/text-base/example.iml.svn-base
geworkbench-core/components/example/example.iml
geworkbench-core/components/example/src/.svn/all-wcprops
geworkbench-core/components/example/src/.svn/entries
geworkbench-core/components/example/src/org/.svn/all-wcprops
geworkbench-core/components/example/src/org/.svn/entries
geworkbench-core/components/example/src/org/geworkbench/.svn/all-wcprops
geworkbench-core/components/example/src/org/geworkbench/.svn/entries
geworkbench-core/components/example/src/org/geworkbench/components/.svn/all-wcprops
geworkbench-core/components/example/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/example/src/org/geworkbench/components/example/.svn/all-wcprops
geworkbench-core/components/example/src/org/geworkbench/components/example/.svn/entries
geworkbench-core/components/example/src/org/geworkbench/components/example/.svn/prop-base/JProfileTable.java.svn-base
geworkbench-core/components/example/src/org/geworkbench/components/example/.svn/prop-base/ProfileGroup.java.svn-base
geworkbench-core/components/example/src/org/geworkbench/components/example/.svn/prop-base/TProfilerResults.java.svn-base
geworkbench-core/components/example/src/org/geworkbench/components/example/.svn/text-base/ExampleComponent.java.svn-base
geworkbench-core/components/example/src/org/geworkbench/components/example/.svn/text-base/JProfileTable.java.svn-base
geworkbench-core/components/example/src/org/geworkbench/components/example/.svn/text-base/ProfileGroup.java.svn-base
geworkbench-core/components/example/src/org/geworkbench/components/example/.svn/text-base/TProfilerResults.java.svn-base
geworkbench-core/components/example/src/org/geworkbench/components/example/ExampleComponent.java
geworkbench-core/components/example/src/org/geworkbench/components/example/JProfileTable.java
geworkbench-core/components/example/src/org/geworkbench/components/example/ProfileGroup.java
geworkbench-core/components/example/src/org/geworkbench/components/example/TProfilerResults.java
geworkbench-core/components/filtering/.svn/all-wcprops
geworkbench-core/components/filtering/.svn/entries
geworkbench-core/components/filtering/src/.svn/all-wcprops
geworkbench-core/components/filtering/src/.svn/entries
geworkbench-core/components/filtering/src/org/.svn/all-wcprops
geworkbench-core/components/filtering/src/org/.svn/entries
geworkbench-core/components/filtering/src/org/geworkbench/.svn/all-wcprops
geworkbench-core/components/filtering/src/org/geworkbench/.svn/entries
geworkbench-core/components/filtering/src/org/geworkbench/components/.svn/all-wcprops
geworkbench-core/components/filtering/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/filtering/src/org/geworkbench/components/filtering/.svn/all-wcprops
geworkbench-core/components/filtering/src/org/geworkbench/components/filtering/.svn/entries
geworkbench-core/components/filtering/src/org/geworkbench/components/filtering/.svn/prop-base/DeviationBasedFilterPanel.java.svn-base
geworkbench-core/components/filtering/src/org/geworkbench/components/filtering/.svn/text-base/CoefficientOfVariationFilter.java.svn-base
geworkbench-core/components/filtering/src/org/geworkbench/components/filtering/.svn/text-base/DeviationBasedFilter.cwb.xml.svn-base
geworkbench-core/components/filtering/src/org/geworkbench/components/filtering/.svn/text-base/DeviationBasedFilter.java.svn-base
geworkbench-core/components/filtering/src/org/geworkbench/components/filtering/.svn/text-base/DeviationBasedFilterPanel.java.svn-base
geworkbench-core/components/filtering/src/org/geworkbench/components/filtering/.svn/text-base/FilteringPanel.cwb.xml.svn-base
geworkbench-core/components/filtering/src/org/geworkbench/components/filtering/.svn/text-base/FilteringPanel.java.svn-base
geworkbench-core/components/filtering/src/org/geworkbench/components/filtering/.svn/text-base/GenepixFlagsFilter.java.svn-base
geworkbench-core/components/filtering/src/org/geworkbench/components/filtering/.svn/text-base/MultipleEntrezGeneIDFilter.cwb.xml.svn-base
geworkbench-core/components/filtering/src/org/geworkbench/components/filtering/.svn/text-base/MultipleEntrezGeneIDFilter.java.svn-base
geworkbench-core/components/filtering/src/org/geworkbench/components/filtering/.svn/text-base/MultipleProbesetFilter.java.svn-base
geworkbench-core/components/filtering/src/org/geworkbench/components/filtering/.svn/text-base/PreviewDialog.java.svn-base
geworkbench-core/components/filtering/src/org/geworkbench/components/filtering/CoefficientOfVariationFilter.java
geworkbench-core/components/filtering/src/org/geworkbench/components/filtering/DeviationBasedFilter.cwb.xml
geworkbench-core/components/filtering/src/org/geworkbench/components/filtering/DeviationBasedFilter.java
geworkbench-core/components/filtering/src/org/geworkbench/components/filtering/DeviationBasedFilterPanel.java
geworkbench-core/components/filtering/src/org/geworkbench/components/filtering/FilteringPanel.cwb.xml
geworkbench-core/components/filtering/src/org/geworkbench/components/filtering/FilteringPanel.java
geworkbench-core/components/filtering/src/org/geworkbench/components/filtering/GenepixFlagsFilter.java
geworkbench-core/components/filtering/src/org/geworkbench/components/filtering/MultipleEntrezGeneIDFilter.cwb.xml
geworkbench-core/components/filtering/src/org/geworkbench/components/filtering/MultipleEntrezGeneIDFilter.java
geworkbench-core/components/filtering/src/org/geworkbench/components/filtering/MultipleProbesetFilter.java
geworkbench-core/components/filtering/src/org/geworkbench/components/filtering/PreviewDialog.java
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/all-wcprops
geworkbench-core/components/foldchange/.svn/entries
geworkbench-core/components/foldchange/src/.svn/all-wcprops
geworkbench-core/components/foldchange/src/.svn/entries
geworkbench-core/components/foldchange/src/org/.svn/all-wcprops
geworkbench-core/components/foldchange/src/org/.svn/entries
geworkbench-core/components/foldchange/src/org/geworkbench/.svn/all-wcprops
geworkbench-core/components/foldchange/src/org/geworkbench/.svn/entries
geworkbench-core/components/foldchange/src/org/geworkbench/components/.svn/all-wcprops
geworkbench-core/components/foldchange/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/foldchange/src/org/geworkbench/components/foldchange/.svn/all-wcprops
geworkbench-core/components/foldchange/src/org/geworkbench/components/foldchange/.svn/entries
geworkbench-core/components/foldchange/src/org/geworkbench/components/foldchange/.svn/text-base/FoldChangeAnalysis.java.svn-base
geworkbench-core/components/foldchange/src/org/geworkbench/components/foldchange/FoldChangeAnalysis.java
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/GoAnalysis.java.svn-base
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/.svn/text-base/GoTableModel.java.svn-base
geworkbench-core/components/geneontology2/src/org/geworkbench/components/geneontology2/GoAnalysis.java
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/geneontology2/src/org/geworkbench/components/geneontology2/GoTableModel.java
geworkbench-core/components/genspace/.svn/all-wcprops
geworkbench-core/components/genspace/.svn/entries
geworkbench-core/components/genspace/lib/.svn/entries
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/prop-base/ObjectHandler.java.svn-base
geworkbench-core/components/genspace/src/org/geworkbench/components/genspace/.svn/text-base/ObjectHandler.java.svn-base
geworkbench-core/components/genspace/src/org/geworkbench/components/genspace/ObjectHandler.java
geworkbench-core/components/genspace/src/org/geworkbench/components/genspace/ObjectLogger.java
geworkbench-core/components/genspace/src/org/geworkbench/components/genspace/bean/.svn/entries
geworkbench-core/components/genspace/src/org/geworkbench/components/genspace/chat/.svn/entries
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/entries
geworkbench-core/components/genspace/src/org/geworkbench/components/genspace/server/.svn/entries
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/.svn/text-base/WorkflowStatistics.java.svn-base
geworkbench-core/components/genspace/src/org/geworkbench/components/genspace/ui/WorkflowStatistics.java
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/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/DynamicTree.java.svn-base
geworkbench-core/components/genspace/src/org/geworkbench/components/genspace/workflowRepository/DynamicTree.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/.svn/text-base/GPHelpPanel.java.svn-base
geworkbench-core/components/gpmodule_v3_0/src/org/geworkbench/components/gpmodule/GPHelpPanel.java
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/AbstractTraining.java.svn-base
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/AbstractTraining.java
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/cart/.svn/all-wcprops
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/cart/.svn/text-base/CARTTraining.java.svn-base
geworkbench-core/components/gpmodule_v3_0/src/org/geworkbench/components/gpmodule/classification/cart/CARTTraining.java
geworkbench-core/components/gpmodule_v3_0/src/org/geworkbench/components/gpmodule/classification/gui/.svn/all-wcprops
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/.svn/text-base/GPClassificationVisualComponent.java.svn-base
geworkbench-core/components/gpmodule_v3_0/src/org/geworkbench/components/gpmodule/classification/gui/.svn/text-base/GPClassificationVisualizationPanel.java.svn-base
geworkbench-core/components/gpmodule_v3_0/src/org/geworkbench/components/gpmodule/classification/gui/GPClassificationVisualComponent.java
geworkbench-core/components/gpmodule_v3_0/src/org/geworkbench/components/gpmodule/classification/gui/GPClassificationVisualizationPanel.java
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/all-wcprops
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/all-wcprops
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/.svn/text-base/SVMTraining.java.svn-base
geworkbench-core/components/gpmodule_v3_0/src/org/geworkbench/components/gpmodule/classification/svm/SVMTraining.java
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/all-wcprops
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/classification/wv/.svn/text-base/WVTraining.java.svn-base
geworkbench-core/components/gpmodule_v3_0/src/org/geworkbench/components/gpmodule/classification/wv/WVTraining.java
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/all-wcprops
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/.svn/text-base/GSEAAnalysis.java.svn-base
geworkbench-core/components/gpmodule_v3_0/src/org/geworkbench/components/gpmodule/gsea/GSEAAnalysis.java
geworkbench-core/components/gpmodule_v3_0/src/org/geworkbench/components/gpmodule/gsea/browser/.svn/all-wcprops
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/gsea/browser/.svn/text-base/GSEABrowser.java.svn-base
geworkbench-core/components/gpmodule_v3_0/src/org/geworkbench/components/gpmodule/gsea/browser/GSEABrowser.java
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/all-wcprops
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/kmeans/.svn/text-base/KMAnalysis.java.svn-base
geworkbench-core/components/gpmodule_v3_0/src/org/geworkbench/components/gpmodule/kmeans/.svn/text-base/KMeansViewer.java.svn-base
geworkbench-core/components/gpmodule_v3_0/src/org/geworkbench/components/gpmodule/kmeans/KMAnalysis.java
geworkbench-core/components/gpmodule_v3_0/src/org/geworkbench/components/gpmodule/kmeans/KMeansViewer.java
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/all-wcprops
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/.svn/text-base/PCA.java.svn-base
geworkbench-core/components/gpmodule_v3_0/src/org/geworkbench/components/gpmodule/pca/.svn/text-base/PCAAnalysis.java.svn-base
geworkbench-core/components/gpmodule_v3_0/src/org/geworkbench/components/gpmodule/pca/PCA.java
geworkbench-core/components/gpmodule_v3_0/src/org/geworkbench/components/gpmodule/pca/PCAAnalysis.java
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/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/prop-base/HierClusterViewAppComponent.java.svn-base
geworkbench-core/components/hierarchicalclustering/src/org/geworkbench/components/hierarchicalclustering/.svn/text-base/FastHierClustAnalysis.java.svn-base
geworkbench-core/components/hierarchicalclustering/src/org/geworkbench/components/hierarchicalclustering/.svn/text-base/HierClusterDisplay.java.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/FastHierClustAnalysis.java
geworkbench-core/components/hierarchicalclustering/src/org/geworkbench/components/hierarchicalclustering/HierClusterDisplay.java
geworkbench-core/components/hierarchicalclustering/src/org/geworkbench/components/hierarchicalclustering/HierClusterViewAppComponent.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/prop-base/AnnotationParser.java.svn-base
geworkbench-core/components/idea/src/org/geworkbench/components/idea/.svn/prop-base/IdeaLauncher.java.svn-base
geworkbench-core/components/idea/src/org/geworkbench/components/idea/.svn/text-base/AnnotationParser.java.svn-base
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/IdeaLauncher.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/MutualInfo.java.svn-base
geworkbench-core/components/idea/src/org/geworkbench/components/idea/.svn/text-base/NullDistribution.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/AnnotationParser.java
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/IdeaLauncher.java
geworkbench-core/components/idea/src/org/geworkbench/components/idea/IdeaNetworkEdge.java
geworkbench-core/components/idea/src/org/geworkbench/components/idea/MutualInfo.java
geworkbench-core/components/idea/src/org/geworkbench/components/idea/NullDistribution.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/CellSelectionlTableTest.java.svn-base
geworkbench-core/components/interactions/src/org/geworkbench/components/interactions/cellularnetwork/.svn/text-base/CellularNetworkKnowledgeWidget.java.svn-base
geworkbench-core/components/interactions/src/org/geworkbench/components/interactions/cellularnetwork/.svn/text-base/CellularNetworkPreferencePanel.java.svn-base
geworkbench-core/components/interactions/src/org/geworkbench/components/interactions/cellularnetwork/.svn/text-base/Constants.java.svn-base
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/.svn/text-base/InteractionParticipant.java.svn-base
geworkbench-core/components/interactions/src/org/geworkbench/components/interactions/cellularnetwork/CellSelectionlTableTest.java
geworkbench-core/components/interactions/src/org/geworkbench/components/interactions/cellularnetwork/CellularNetworkKnowledgeWidget.java
geworkbench-core/components/interactions/src/org/geworkbench/components/interactions/cellularnetwork/CellularNetworkPreferencePanel.java
geworkbench-core/components/interactions/src/org/geworkbench/components/interactions/cellularnetwork/Constants.java
geworkbench-core/components/interactions/src/org/geworkbench/components/interactions/cellularnetwork/ExportSelectionPanel.java
geworkbench-core/components/interactions/src/org/geworkbench/components/interactions/cellularnetwork/InteractionParticipant.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/all-wcprops
geworkbench-core/components/markus/.svn/entries
geworkbench-core/components/markus/lib/.svn/entries
geworkbench-core/components/markus/src/.svn/all-wcprops
geworkbench-core/components/markus/src/.svn/entries
geworkbench-core/components/markus/src/org/.svn/all-wcprops
geworkbench-core/components/markus/src/org/.svn/entries
geworkbench-core/components/markus/src/org/geworkbench/.svn/all-wcprops
geworkbench-core/components/markus/src/org/geworkbench/.svn/entries
geworkbench-core/components/markus/src/org/geworkbench/components/.svn/all-wcprops
geworkbench-core/components/markus/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/markus/src/org/geworkbench/components/markus/.svn/all-wcprops
geworkbench-core/components/markus/src/org/geworkbench/components/markus/.svn/entries
geworkbench-core/components/markus/src/org/geworkbench/components/markus/.svn/text-base/MarkUsBrowser.java.svn-base
geworkbench-core/components/markus/src/org/geworkbench/components/markus/MarkUsBrowser.java
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/DetailedTFGraphViewer.java.svn-base
geworkbench-core/components/masterregulator/src/org/geworkbench/components/masterregulator/.svn/text-base/MasterRegulatorAnalysis.cwb.xml.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/TAnalysis.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/DetailedTFGraphViewer.java
geworkbench-core/components/masterregulator/src/org/geworkbench/components/masterregulator/MasterRegulatorAnalysis.cwb.xml
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/TAnalysis.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/all-wcprops
geworkbench-core/components/matrixreduce/.svn/entries
geworkbench-core/components/matrixreduce/lib/.svn/all-wcprops
geworkbench-core/components/matrixreduce/lib/.svn/entries
geworkbench-core/components/matrixreduce/lib/.svn/text-base/MatrixREDUCE.jar.svn-base
geworkbench-core/components/matrixreduce/lib/MatrixREDUCE.jar
geworkbench-core/components/matrixreduce/src/.svn/all-wcprops
geworkbench-core/components/matrixreduce/src/.svn/entries
geworkbench-core/components/matrixreduce/src/org/.svn/all-wcprops
geworkbench-core/components/matrixreduce/src/org/.svn/entries
geworkbench-core/components/matrixreduce/src/org/geworkbench/.svn/all-wcprops
geworkbench-core/components/matrixreduce/src/org/geworkbench/.svn/entries
geworkbench-core/components/matrixreduce/src/org/geworkbench/components/.svn/all-wcprops
geworkbench-core/components/matrixreduce/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/matrixreduce/src/org/geworkbench/components/matrixreduce/.svn/all-wcprops
geworkbench-core/components/matrixreduce/src/org/geworkbench/components/matrixreduce/.svn/entries
geworkbench-core/components/matrixreduce/src/org/geworkbench/components/matrixreduce/.svn/text-base/MatrixReduceAnalysis.java.svn-base
geworkbench-core/components/matrixreduce/src/org/geworkbench/components/matrixreduce/.svn/text-base/MatrixReduceViewer.java.svn-base
geworkbench-core/components/matrixreduce/src/org/geworkbench/components/matrixreduce/.svn/text-base/SequenceGraph.java.svn-base
geworkbench-core/components/matrixreduce/src/org/geworkbench/components/matrixreduce/MatrixReduceAnalysis.java
geworkbench-core/components/matrixreduce/src/org/geworkbench/components/matrixreduce/MatrixReduceViewer.java
geworkbench-core/components/matrixreduce/src/org/geworkbench/components/matrixreduce/SequenceGraph.java
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/all-wcprops
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/all-wcprops
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/all-wcprops
geworkbench-core/components/medusa/src/org/.svn/entries
geworkbench-core/components/medusa/src/org/geworkbench/.svn/all-wcprops
geworkbench-core/components/medusa/src/org/geworkbench/.svn/entries
geworkbench-core/components/medusa/src/org/geworkbench/components/.svn/all-wcprops
geworkbench-core/components/medusa/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/medusa/src/org/geworkbench/components/medusa/.svn/all-wcprops
geworkbench-core/components/medusa/src/org/geworkbench/components/medusa/.svn/entries
geworkbench-core/components/medusa/src/org/geworkbench/components/medusa/.svn/text-base/MedusaAnalysis.java.svn-base
geworkbench-core/components/medusa/src/org/geworkbench/components/medusa/.svn/text-base/MedusaUtil.java.svn-base
geworkbench-core/components/medusa/src/org/geworkbench/components/medusa/MedusaAnalysis.java
geworkbench-core/components/medusa/src/org/geworkbench/components/medusa/MedusaUtil.java
geworkbench-core/components/medusa/src/org/geworkbench/components/medusa/gui/.svn/all-wcprops
geworkbench-core/components/medusa/src/org/geworkbench/components/medusa/gui/.svn/entries
geworkbench-core/components/medusa/src/org/geworkbench/components/medusa/gui/.svn/text-base/MedusaVisualComponent.java.svn-base
geworkbench-core/components/medusa/src/org/geworkbench/components/medusa/gui/MedusaVisualComponent.java
geworkbench-core/components/microarrays/.svn/all-wcprops
geworkbench-core/components/microarrays/.svn/entries
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/MicroarrayDisplay.java.svn-base
geworkbench-core/components/microarrays/src/org/geworkbench/components/microarrays/.svn/text-base/MicroarrayPanel.java.svn-base
geworkbench-core/components/microarrays/src/org/geworkbench/components/microarrays/.svn/text-base/SimpleTTest.java.svn-base
geworkbench-core/components/microarrays/src/org/geworkbench/components/microarrays/.svn/text-base/TabularMicroarrayPanel.java.svn-base
geworkbench-core/components/microarrays/src/org/geworkbench/components/microarrays/EVDPanel.java
geworkbench-core/components/microarrays/src/org/geworkbench/components/microarrays/MicroarrayDisplay.java
geworkbench-core/components/microarrays/src/org/geworkbench/components/microarrays/MicroarrayPanel.java
geworkbench-core/components/microarrays/src/org/geworkbench/components/microarrays/SimpleTTest.java
geworkbench-core/components/microarrays/src/org/geworkbench/components/microarrays/TabularMicroarrayPanel.java
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/ColumnHeaderListener.java.svn-base
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/MindyPlugin.java.svn-base
geworkbench-core/components/mindy/src/org/geworkbench/components/mindy/.svn/text-base/MindyTableTab.java.svn-base
geworkbench-core/components/mindy/src/org/geworkbench/components/mindy/.svn/text-base/ModulatorHeatMap.java.svn-base
geworkbench-core/components/mindy/src/org/geworkbench/components/mindy/ColumnHeaderListener.java
geworkbench-core/components/mindy/src/org/geworkbench/components/mindy/MindyAnalysis.java
geworkbench-core/components/mindy/src/org/geworkbench/components/mindy/MindyPlugin.java
geworkbench-core/components/mindy/src/org/geworkbench/components/mindy/MindyTableTab.java
geworkbench-core/components/mindy/src/org/geworkbench/components/mindy/ModulatorHeatMap.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/all-wcprops
geworkbench-core/components/normalization/.svn/entries
geworkbench-core/components/normalization/src/.svn/all-wcprops
geworkbench-core/components/normalization/src/.svn/entries
geworkbench-core/components/normalization/src/org/.svn/all-wcprops
geworkbench-core/components/normalization/src/org/.svn/entries
geworkbench-core/components/normalization/src/org/geworkbench/.svn/all-wcprops
geworkbench-core/components/normalization/src/org/geworkbench/.svn/entries
geworkbench-core/components/normalization/src/org/geworkbench/components/.svn/all-wcprops
geworkbench-core/components/normalization/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/normalization/src/org/geworkbench/components/normalization/.svn/all-wcprops
geworkbench-core/components/normalization/src/org/geworkbench/components/normalization/.svn/entries
geworkbench-core/components/normalization/src/org/geworkbench/components/normalization/.svn/text-base/HouseKeepingGeneNormalizer.java.svn-base
geworkbench-core/components/normalization/src/org/geworkbench/components/normalization/.svn/text-base/LogTransformationNormalizer.java.svn-base
geworkbench-core/components/normalization/src/org/geworkbench/components/normalization/.svn/text-base/MarkerCenteringNormalizer.java.svn-base
geworkbench-core/components/normalization/src/org/geworkbench/components/normalization/.svn/text-base/MarkerMeanVarianceNormalizer.java.svn-base
geworkbench-core/components/normalization/src/org/geworkbench/components/normalization/.svn/text-base/MicroarrayCenteringNormalizer.java.svn-base
geworkbench-core/components/normalization/src/org/geworkbench/components/normalization/.svn/text-base/MissingValueNormalizer.java.svn-base
geworkbench-core/components/normalization/src/org/geworkbench/components/normalization/.svn/text-base/NormalizationPanel.cwb.xml.svn-base
geworkbench-core/components/normalization/src/org/geworkbench/components/normalization/.svn/text-base/NormalizationPanel.java.svn-base
geworkbench-core/components/normalization/src/org/geworkbench/components/normalization/.svn/text-base/QuantileNormalizer.java.svn-base
geworkbench-core/components/normalization/src/org/geworkbench/components/normalization/.svn/text-base/ThresholdNormalizer.java.svn-base
geworkbench-core/components/normalization/src/org/geworkbench/components/normalization/HouseKeepingGeneNormalizer.java
geworkbench-core/components/normalization/src/org/geworkbench/components/normalization/LogTransformationNormalizer.java
geworkbench-core/components/normalization/src/org/geworkbench/components/normalization/MarkerCenteringNormalizer.java
geworkbench-core/components/normalization/src/org/geworkbench/components/normalization/MarkerMeanVarianceNormalizer.java
geworkbench-core/components/normalization/src/org/geworkbench/components/normalization/MicroarrayCenteringNormalizer.java
geworkbench-core/components/normalization/src/org/geworkbench/components/normalization/MissingValueNormalizer.java
geworkbench-core/components/normalization/src/org/geworkbench/components/normalization/NormalizationPanel.cwb.xml
geworkbench-core/components/normalization/src/org/geworkbench/components/normalization/NormalizationPanel.java
geworkbench-core/components/normalization/src/org/geworkbench/components/normalization/QuantileNormalizer.java
geworkbench-core/components/normalization/src/org/geworkbench/components/normalization/ThresholdNormalizer.java
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/all-wcprops
geworkbench-core/components/plots/.svn/entries
geworkbench-core/components/plots/src/.svn/all-wcprops
geworkbench-core/components/plots/src/.svn/entries
geworkbench-core/components/plots/src/org/.svn/all-wcprops
geworkbench-core/components/plots/src/org/.svn/entries
geworkbench-core/components/plots/src/org/geworkbench/.svn/all-wcprops
geworkbench-core/components/plots/src/org/geworkbench/.svn/entries
geworkbench-core/components/plots/src/org/geworkbench/components/.svn/all-wcprops
geworkbench-core/components/plots/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/plots/src/org/geworkbench/components/plots/.svn/all-wcprops
geworkbench-core/components/plots/src/org/geworkbench/components/plots/.svn/entries
geworkbench-core/components/plots/src/org/geworkbench/components/plots/.svn/text-base/ScatterPlot.java.svn-base
geworkbench-core/components/plots/src/org/geworkbench/components/plots/.svn/text-base/VolcanoPlot.java.svn-base
geworkbench-core/components/plots/src/org/geworkbench/components/plots/ScatterPlot.java
geworkbench-core/components/plots/src/org/geworkbench/components/plots/VolcanoPlot.java
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/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/all-wcprops
geworkbench-core/components/promoter/.svn/entries
geworkbench-core/components/promoter/lib/.svn/entries
geworkbench-core/components/promoter/src/.svn/all-wcprops
geworkbench-core/components/promoter/src/.svn/entries
geworkbench-core/components/promoter/src/org/.svn/all-wcprops
geworkbench-core/components/promoter/src/org/.svn/entries
geworkbench-core/components/promoter/src/org/geworkbench/.svn/all-wcprops
geworkbench-core/components/promoter/src/org/geworkbench/.svn/entries
geworkbench-core/components/promoter/src/org/geworkbench/components/.svn/all-wcprops
geworkbench-core/components/promoter/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/promoter/src/org/geworkbench/components/promoter/.svn/all-wcprops
geworkbench-core/components/promoter/src/org/geworkbench/components/promoter/.svn/entries
geworkbench-core/components/promoter/src/org/geworkbench/components/promoter/.svn/text-base/Matrix.java.svn-base
geworkbench-core/components/promoter/src/org/geworkbench/components/promoter/.svn/text-base/PromoterView.java.svn-base
geworkbench-core/components/promoter/src/org/geworkbench/components/promoter/.svn/text-base/PromoterViewPanel.java.svn-base
geworkbench-core/components/promoter/src/org/geworkbench/components/promoter/Matrix.java
geworkbench-core/components/promoter/src/org/geworkbench/components/promoter/PromoterView.java
geworkbench-core/components/promoter/src/org/geworkbench/components/promoter/PromoterViewPanel.java
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/all-wcprops
geworkbench-core/components/pudge/.svn/entries
geworkbench-core/components/pudge/lib/.svn/entries
geworkbench-core/components/pudge/src/.svn/all-wcprops
geworkbench-core/components/pudge/src/.svn/entries
geworkbench-core/components/pudge/src/org/.svn/all-wcprops
geworkbench-core/components/pudge/src/org/.svn/entries
geworkbench-core/components/pudge/src/org/geworkbench/.svn/all-wcprops
geworkbench-core/components/pudge/src/org/geworkbench/.svn/entries
geworkbench-core/components/pudge/src/org/geworkbench/components/.svn/all-wcprops
geworkbench-core/components/pudge/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/pudge/src/org/geworkbench/components/pudge/.svn/all-wcprops
geworkbench-core/components/pudge/src/org/geworkbench/components/pudge/.svn/entries
geworkbench-core/components/pudge/src/org/geworkbench/components/pudge/.svn/text-base/PudgeBrowser.java.svn-base
geworkbench-core/components/pudge/src/org/geworkbench/components/pudge/PudgeBrowser.java
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/SequenceFetcher.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/SequenceFetcher.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/all-wcprops
geworkbench-core/components/sequences/.svn/entries
geworkbench-core/components/sequences/lib/.svn/entries
geworkbench-core/components/sequences/src/.svn/all-wcprops
geworkbench-core/components/sequences/src/.svn/entries
geworkbench-core/components/sequences/src/org/.svn/all-wcprops
geworkbench-core/components/sequences/src/org/.svn/entries
geworkbench-core/components/sequences/src/org/geworkbench/.svn/all-wcprops
geworkbench-core/components/sequences/src/org/geworkbench/.svn/entries
geworkbench-core/components/sequences/src/org/geworkbench/components/.svn/all-wcprops
geworkbench-core/components/sequences/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/sequences/src/org/geworkbench/components/sequences/.svn/all-wcprops
geworkbench-core/components/sequences/src/org/geworkbench/components/sequences/.svn/entries
geworkbench-core/components/sequences/src/org/geworkbench/components/sequences/.svn/text-base/SequenceViewAppComponent.java.svn-base
geworkbench-core/components/sequences/src/org/geworkbench/components/sequences/SequenceViewAppComponent.java
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/all-wcprops
geworkbench-core/components/skybaseview/.svn/entries
geworkbench-core/components/skybaseview/lib/.svn/entries
geworkbench-core/components/skybaseview/src/.svn/all-wcprops
geworkbench-core/components/skybaseview/src/.svn/entries
geworkbench-core/components/skybaseview/src/org/.svn/all-wcprops
geworkbench-core/components/skybaseview/src/org/.svn/entries
geworkbench-core/components/skybaseview/src/org/geworkbench/.svn/all-wcprops
geworkbench-core/components/skybaseview/src/org/geworkbench/.svn/entries
geworkbench-core/components/skybaseview/src/org/geworkbench/components/.svn/all-wcprops
geworkbench-core/components/skybaseview/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/skybaseview/src/org/geworkbench/components/skybaseview/.svn/all-wcprops
geworkbench-core/components/skybaseview/src/org/geworkbench/components/skybaseview/.svn/entries
geworkbench-core/components/skybaseview/src/org/geworkbench/components/skybaseview/.svn/text-base/SkyBaseViewer.java.svn-base
geworkbench-core/components/skybaseview/src/org/geworkbench/components/skybaseview/SkyBaseViewer.java
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/all-wcprops
geworkbench-core/components/skylineview/.svn/entries
geworkbench-core/components/skylineview/lib/.svn/entries
geworkbench-core/components/skylineview/src/.svn/all-wcprops
geworkbench-core/components/skylineview/src/.svn/entries
geworkbench-core/components/skylineview/src/org/.svn/all-wcprops
geworkbench-core/components/skylineview/src/org/.svn/entries
geworkbench-core/components/skylineview/src/org/geworkbench/.svn/all-wcprops
geworkbench-core/components/skylineview/src/org/geworkbench/.svn/entries
geworkbench-core/components/skylineview/src/org/geworkbench/components/.svn/all-wcprops
geworkbench-core/components/skylineview/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/skylineview/src/org/geworkbench/components/skylineview/.svn/all-wcprops
geworkbench-core/components/skylineview/src/org/geworkbench/components/skylineview/.svn/entries
geworkbench-core/components/skylineview/src/org/geworkbench/components/skylineview/.svn/text-base/SkyLineViewAllPanel.java.svn-base
geworkbench-core/components/skylineview/src/org/geworkbench/components/skylineview/.svn/text-base/SkyLineViewEachPanel.java.svn-base
geworkbench-core/components/skylineview/src/org/geworkbench/components/skylineview/SkyLineViewAllPanel.java
geworkbench-core/components/skylineview/src/org/geworkbench/components/skylineview/SkyLineViewEachPanel.java
geworkbench-core/components/somclustering/.settings/.svn/entries
geworkbench-core/components/somclustering/.svn/all-wcprops
geworkbench-core/components/somclustering/.svn/entries
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/SOMAnalysis.java.svn-base
geworkbench-core/components/somclustering/src/org/geworkbench/components/somclustering/SOMAnalysis.java
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/all-wcprops
geworkbench-core/components/ttest/.svn/entries
geworkbench-core/components/ttest/lib/.svn/entries
geworkbench-core/components/ttest/src/.svn/all-wcprops
geworkbench-core/components/ttest/src/.svn/entries
geworkbench-core/components/ttest/src/org/.svn/all-wcprops
geworkbench-core/components/ttest/src/org/.svn/entries
geworkbench-core/components/ttest/src/org/geworkbench/.svn/all-wcprops
geworkbench-core/components/ttest/src/org/geworkbench/.svn/entries
geworkbench-core/components/ttest/src/org/geworkbench/components/.svn/all-wcprops
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/all-wcprops
geworkbench-core/components/ttest/src/org/geworkbench/components/ttest/.svn/entries
geworkbench-core/components/ttest/src/org/geworkbench/components/ttest/.svn/text-base/MultiTTestAnalysis.java.svn-base
geworkbench-core/components/ttest/src/org/geworkbench/components/ttest/.svn/text-base/MultiTTestAnalysisPanel.java.svn-base
geworkbench-core/components/ttest/src/org/geworkbench/components/ttest/.svn/text-base/TTestUtil.java.svn-base
geworkbench-core/components/ttest/src/org/geworkbench/components/ttest/.svn/text-base/TtestAnalysis.java.svn-base
geworkbench-core/components/ttest/src/org/geworkbench/components/ttest/MultiTTestAnalysis.java
geworkbench-core/components/ttest/src/org/geworkbench/components/ttest/MultiTTestAnalysisPanel.java
geworkbench-core/components/ttest/src/org/geworkbench/components/ttest/TTestUtil.java
geworkbench-core/components/ttest/src/org/geworkbench/components/ttest/TtestAnalysis.java
geworkbench-core/components/versioninfo/.svn/all-wcprops
geworkbench-core/components/versioninfo/.svn/entries
geworkbench-core/components/versioninfo/src/.svn/all-wcprops
geworkbench-core/components/versioninfo/src/.svn/entries
geworkbench-core/components/versioninfo/src/org/.svn/all-wcprops
geworkbench-core/components/versioninfo/src/org/.svn/entries
geworkbench-core/components/versioninfo/src/org/geworkbench/.svn/all-wcprops
geworkbench-core/components/versioninfo/src/org/geworkbench/.svn/entries
geworkbench-core/components/versioninfo/src/org/geworkbench/components/.svn/all-wcprops
geworkbench-core/components/versioninfo/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/versioninfo/src/org/geworkbench/components/versioninfo/.svn/all-wcprops
geworkbench-core/components/versioninfo/src/org/geworkbench/components/versioninfo/.svn/entries
geworkbench-core/components/versioninfo/src/org/geworkbench/components/versioninfo/.svn/text-base/VersionInfoDialog.java.svn-base
geworkbench-core/components/versioninfo/src/org/geworkbench/components/versioninfo/VersionInfoDialog.java
geworkbench-core/components/viewers/.svn/all-wcprops
geworkbench-core/components/viewers/.svn/entries
geworkbench-core/components/viewers/src/.svn/all-wcprops
geworkbench-core/components/viewers/src/.svn/entries
geworkbench-core/components/viewers/src/org/.svn/all-wcprops
geworkbench-core/components/viewers/src/org/.svn/entries
geworkbench-core/components/viewers/src/org/geworkbench/.svn/all-wcprops
geworkbench-core/components/viewers/src/org/geworkbench/.svn/entries
geworkbench-core/components/viewers/src/org/geworkbench/components/.svn/all-wcprops
geworkbench-core/components/viewers/src/org/geworkbench/components/.svn/entries
geworkbench-core/components/viewers/src/org/geworkbench/components/viewers/.svn/all-wcprops
geworkbench-core/components/viewers/src/org/geworkbench/components/viewers/.svn/entries
geworkbench-core/components/viewers/src/org/geworkbench/components/viewers/.svn/prop-base/ImageViewer.java.svn-base
geworkbench-core/components/viewers/src/org/geworkbench/components/viewers/.svn/text-base/ImageViewer.java.svn-base
geworkbench-core/components/viewers/src/org/geworkbench/components/viewers/ImageViewer.java
geworkbench-core/conf/.svn/all-wcprops
geworkbench-core/conf/.svn/entries
geworkbench-core/conf/.svn/text-base/all.xml.svn-base
geworkbench-core/conf/all.xml
geworkbench-core/conf/cruisecontrol/.svn/all-wcprops
geworkbench-core/conf/cruisecontrol/.svn/entries
geworkbench-core/conf/cruisecontrol/.svn/prop-base/build-geworkbench.xml.svn-base
geworkbench-core/conf/cruisecontrol/.svn/prop-base/config.xml.svn-base
geworkbench-core/conf/cruisecontrol/.svn/text-base/build-geworkbench.xml.svn-base
geworkbench-core/conf/cruisecontrol/.svn/text-base/config.xml.svn-base
geworkbench-core/conf/cruisecontrol/build-geworkbench.xml
geworkbench-core/conf/cruisecontrol/config.xml
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/lib/.svn/entries
geworkbench-core/lib/medusa/.svn/entries
geworkbench-core/lib/mk/.svn/entries
geworkbench-core/lib64/.svn/entries
geworkbench-core/nbproject/.svn/all-wcprops
geworkbench-core/nbproject/.svn/entries
geworkbench-core/nbproject/.svn/prop-base/ide-file-targets.xml.svn-base
geworkbench-core/nbproject/.svn/prop-base/ide-targets.xml.svn-base
geworkbench-core/nbproject/.svn/prop-base/project.xml.svn-base
geworkbench-core/nbproject/.svn/text-base/ide-file-targets.xml.svn-base
geworkbench-core/nbproject/.svn/text-base/ide-targets.xml.svn-base
geworkbench-core/nbproject/.svn/text-base/project.xml.svn-base
geworkbench-core/nbproject/ide-file-targets.xml
geworkbench-core/nbproject/ide-targets.xml
geworkbench-core/nbproject/project.xml
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/all-wcprops
geworkbench-core/src/org/geworkbench/bison/algorithm/.svn/entries
geworkbench-core/src/org/geworkbench/bison/algorithm/classification/.svn/all-wcprops
geworkbench-core/src/org/geworkbench/bison/algorithm/classification/.svn/entries
geworkbench-core/src/org/geworkbench/bison/algorithm/classification/.svn/text-base/CSClassifier.java.svn-base
geworkbench-core/src/org/geworkbench/bison/algorithm/classification/CSClassifier.java
geworkbench-core/src/org/geworkbench/bison/annotation/.svn/all-wcprops
geworkbench-core/src/org/geworkbench/bison/annotation/.svn/entries
geworkbench-core/src/org/geworkbench/bison/annotation/.svn/text-base/CSAnnotationContextManager.java.svn-base
geworkbench-core/src/org/geworkbench/bison/annotation/.svn/text-base/DSAnnotationContextManager.java.svn-base
geworkbench-core/src/org/geworkbench/bison/annotation/CSAnnotationContextManager.java
geworkbench-core/src/org/geworkbench/bison/annotation/DSAnnotationContextManager.java
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/.svn/prop-base/CSDataSet.jbx.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/.svn/prop-base/DSMatrixDataSet.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/.svn/text-base/AdjacencyMatrix.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/.svn/text-base/AdjacencyMatrixDataSet.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/.svn/text-base/CSDataSet.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/.svn/text-base/CSDataSet.jbx.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/.svn/text-base/CSMarkerVector.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/.svn/text-base/DSAncillaryDataSet.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/.svn/text-base/DSDataSet.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/.svn/text-base/DSMatrixDataSet.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/.svn/text-base/GoAnalysisResult.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/AdjacencyMatrix.java
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/AdjacencyMatrixDataSet.java
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/CSDataSet.java
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/CSDataSet.jbx
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/CSMarkerVector.java
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/DSAncillaryDataSet.java
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/DSDataSet.java
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/DSMatrixDataSet.java
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/GoAnalysisResult.java
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/gsea/.svn/all-wcprops
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/gsea/.svn/entries
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/gsea/.svn/text-base/CSGSEAResultDataSet.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/gsea/CSGSEAResultDataSet.java
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/medusa/.svn/all-wcprops
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/medusa/.svn/entries
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/medusa/.svn/text-base/MedusaData.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/medusa/.svn/text-base/MedusaDataSet.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/medusa/MedusaData.java
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/medusa/MedusaDataSet.java
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/prop-base/CSExprMicroarraySet.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/microarrays/.svn/prop-base/CSMicroarraySet.jbx.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/microarrays/.svn/text-base/CSExprMicroarraySet.java.svn-base
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/.svn/text-base/CSMicroarraySet.jbx.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/microarrays/.svn/text-base/DSMicroarraySet.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/microarrays/CSExprMicroarraySet.java
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/microarrays/CSMicroarraySet.java
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/microarrays/CSMicroarraySet.jbx
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/microarrays/DSMicroarraySet.java
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/pca/.svn/all-wcprops
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/pca/.svn/entries
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/pca/.svn/text-base/CSPCADataSet.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/pca/CSPCADataSet.java
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/sequences/.svn/all-wcprops
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/sequences/.svn/entries
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/sequences/.svn/text-base/CSSequenceSet.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/sequences/CSSequenceSet.java
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/views/.svn/all-wcprops
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/views/.svn/entries
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/views/.svn/text-base/CSMicroarraySetView.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/views/.svn/text-base/DSMicroarraySetView.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/views/CSMicroarraySetView.java
geworkbench-core/src/org/geworkbench/bison/datastructure/biocollections/views/DSMicroarraySetView.java
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/.svn/text-base/FoldChangeResult.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/.svn/text-base/IdeaResult.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/.svn/text-base/KMeansResult.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/.svn/text-base/KMeansResultMarkers.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/FoldChangeResult.java
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/IdeaResult.java
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/KMeansResult.java
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/KMeansResultMarkers.java
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/.svn/prop-base/DSRangeMarker.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/markers/.svn/text-base/CSExpressionMarker.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/markers/.svn/text-base/CSGeneMarker.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/markers/.svn/text-base/DSGeneMarker.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/markers/.svn/text-base/DSRangeMarker.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/markers/CSExpressionMarker.java
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/markers/CSGeneMarker.java
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/markers/DSGeneMarker.java
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/markers/DSRangeMarker.java
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/markers/annotationparser/.svn/all-wcprops
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/markers/annotationparser/.svn/entries
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/markers/annotationparser/.svn/prop-base/chiptypeMap.txt.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/markers/annotationparser/.svn/text-base/APSerializable.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/markers/annotationparser/.svn/text-base/AnnotationManager.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/markers/annotationparser/.svn/text-base/AnnotationParser.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/markers/annotationparser/.svn/text-base/chiptypeMap.txt.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/markers/annotationparser/APSerializable.java
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/markers/annotationparser/AnnotationManager.java
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/markers/annotationparser/AnnotationParser.java
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/markers/annotationparser/chiptypeMap.txt
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/markers/goterms/.svn/entries
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/microarray/.svn/all-wcprops
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/microarray/.svn/entries
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/microarray/.svn/text-base/CSAnovaResultSet.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/microarray/.svn/text-base/CSGenepixMarkerValue.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/microarray/.svn/text-base/CSMasterRegulatorResultSet.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/microarray/.svn/text-base/CSMicroarray.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/microarray/.svn/text-base/CSSignificanceResultSet.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/microarray/.svn/text-base/CSTTestResultSet.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/microarray/.svn/text-base/DSMasterRagulatorResultSet.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/microarray/.svn/text-base/DSMicroarray.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/microarray/.svn/text-base/DSSignificanceResultSet.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/microarray/CSAnovaResultSet.java
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/microarray/CSGenepixMarkerValue.java
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/microarray/CSMasterRegulatorResultSet.java
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/microarray/CSMicroarray.java
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/microarray/CSSignificanceResultSet.java
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/microarray/CSTTestResultSet.java
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/microarray/DSMasterRagulatorResultSet.java
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/microarray/DSMicroarray.java
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/microarray/DSSignificanceResultSet.java
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/sequence/.svn/all-wcprops
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/sequence/.svn/entries
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/sequence/.svn/prop-base/CSSequence.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/sequence/.svn/text-base/CSAlignmentResultSet.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/sequence/.svn/text-base/CSSequence.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/sequence/.svn/text-base/DSAlignmentResultSet.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/sequence/CSAlignmentResultSet.java
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/sequence/CSSequence.java
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/sequence/DSAlignmentResultSet.java
geworkbench-core/src/org/geworkbench/bison/datastructure/bioobjects/structure/.svn/entries
geworkbench-core/src/org/geworkbench/bison/datastructure/complex/.svn/all-wcprops
geworkbench-core/src/org/geworkbench/bison/datastructure/complex/.svn/entries
geworkbench-core/src/org/geworkbench/bison/datastructure/complex/panels/.svn/all-wcprops
geworkbench-core/src/org/geworkbench/bison/datastructure/complex/panels/.svn/entries
geworkbench-core/src/org/geworkbench/bison/datastructure/complex/panels/.svn/prop-base/DSAnnotPanel.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/complex/panels/.svn/text-base/CSPanel.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/complex/panels/.svn/text-base/DSAnnotPanel.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/complex/panels/.svn/text-base/DSItemList.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/complex/panels/.svn/text-base/DSPanel.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/complex/panels/CSPanel.java
geworkbench-core/src/org/geworkbench/bison/datastructure/complex/panels/DSAnnotPanel.java
geworkbench-core/src/org/geworkbench/bison/datastructure/complex/panels/DSItemList.java
geworkbench-core/src/org/geworkbench/bison/datastructure/complex/panels/DSPanel.java
geworkbench-core/src/org/geworkbench/bison/datastructure/complex/pattern/.svn/all-wcprops
geworkbench-core/src/org/geworkbench/bison/datastructure/complex/pattern/.svn/entries
geworkbench-core/src/org/geworkbench/bison/datastructure/complex/pattern/.svn/text-base/PatternResult.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/complex/pattern/PatternResult.java
geworkbench-core/src/org/geworkbench/bison/datastructure/complex/pattern/matrix/.svn/all-wcprops
geworkbench-core/src/org/geworkbench/bison/datastructure/complex/pattern/matrix/.svn/entries
geworkbench-core/src/org/geworkbench/bison/datastructure/complex/pattern/matrix/.svn/text-base/CSMatrixReduceExperiment.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/complex/pattern/matrix/.svn/text-base/CSMatrixReduceSet.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/complex/pattern/matrix/.svn/text-base/CSPositionSpecificAffinityMatrix.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/complex/pattern/matrix/.svn/text-base/DSPositionSpecificAffintyMatrix.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/complex/pattern/matrix/CSMatrixReduceExperiment.java
geworkbench-core/src/org/geworkbench/bison/datastructure/complex/pattern/matrix/CSMatrixReduceSet.java
geworkbench-core/src/org/geworkbench/bison/datastructure/complex/pattern/matrix/CSPositionSpecificAffinityMatrix.java
geworkbench-core/src/org/geworkbench/bison/datastructure/complex/pattern/matrix/DSPositionSpecificAffintyMatrix.java
geworkbench-core/src/org/geworkbench/bison/datastructure/complex/pattern/sequence/.svn/entries
geworkbench-core/src/org/geworkbench/bison/datastructure/properties/.svn/all-wcprops
geworkbench-core/src/org/geworkbench/bison/datastructure/properties/.svn/entries
geworkbench-core/src/org/geworkbench/bison/datastructure/properties/.svn/prop-base/CSDescribable.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/properties/.svn/prop-base/DSDescribable.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/properties/.svn/text-base/CSDescribable.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/properties/.svn/text-base/DSDescribable.java.svn-base
geworkbench-core/src/org/geworkbench/bison/datastructure/properties/CSDescribable.java
geworkbench-core/src/org/geworkbench/bison/datastructure/properties/DSDescribable.java
geworkbench-core/src/org/geworkbench/bison/model/.svn/all-wcprops
geworkbench-core/src/org/geworkbench/bison/model/.svn/entries
geworkbench-core/src/org/geworkbench/bison/model/analysis/.svn/all-wcprops
geworkbench-core/src/org/geworkbench/bison/model/analysis/.svn/entries
geworkbench-core/src/org/geworkbench/bison/model/analysis/.svn/text-base/FilteringAnalysis.java.svn-base
geworkbench-core/src/org/geworkbench/bison/model/analysis/FilteringAnalysis.java
geworkbench-core/src/org/geworkbench/bison/model/clusters/.svn/all-wcprops
geworkbench-core/src/org/geworkbench/bison/model/clusters/.svn/entries
geworkbench-core/src/org/geworkbench/bison/model/clusters/.svn/text-base/CSHierClusterDataSet.java.svn-base
geworkbench-core/src/org/geworkbench/bison/model/clusters/.svn/text-base/CSSOMClusterDataSet.java.svn-base
geworkbench-core/src/org/geworkbench/bison/model/clusters/CSHierClusterDataSet.java
geworkbench-core/src/org/geworkbench/bison/model/clusters/CSSOMClusterDataSet.java
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/prop-base/ColorContextUtils.java.svn-base
geworkbench-core/src/org/geworkbench/bison/util/colorcontext/.svn/text-base/ColorContextUtils.java.svn-base
geworkbench-core/src/org/geworkbench/bison/util/colorcontext/.svn/text-base/DefaultColorContext.java.svn-base
geworkbench-core/src/org/geworkbench/bison/util/colorcontext/.svn/text-base/ExpressionPValueColorContext.java.svn-base
geworkbench-core/src/org/geworkbench/bison/util/colorcontext/ColorContextUtils.java
geworkbench-core/src/org/geworkbench/bison/util/colorcontext/DefaultColorContext.java
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/prop-base/ImageFileFilter.java.svn-base
geworkbench-core/src/org/geworkbench/builtin/projects/.svn/prop-base/LoadDataDialog.java.svn-base
geworkbench-core/src/org/geworkbench/builtin/projects/.svn/prop-base/PendingTreeNode.java.svn-base
geworkbench-core/src/org/geworkbench/builtin/projects/.svn/text-base/DataSetNode.java.svn-base
geworkbench-core/src/org/geworkbench/builtin/projects/.svn/text-base/DataSetSaveNode.java.svn-base
geworkbench-core/src/org/geworkbench/builtin/projects/.svn/text-base/DefaultIconAssignments.java.svn-base
geworkbench-core/src/org/geworkbench/builtin/projects/.svn/text-base/FileOpenHandler.java.svn-base
geworkbench-core/src/org/geworkbench/builtin/projects/.svn/text-base/ImageFileFilter.java.svn-base
geworkbench-core/src/org/geworkbench/builtin/projects/.svn/text-base/ImageNode.java.svn-base
geworkbench-core/src/org/geworkbench/builtin/projects/.svn/text-base/LoadDataDialog.java.svn-base
geworkbench-core/src/org/geworkbench/builtin/projects/.svn/text-base/PDBDialog.java.svn-base
geworkbench-core/src/org/geworkbench/builtin/projects/.svn/text-base/PendingTreeNode.java.svn-base
geworkbench-core/src/org/geworkbench/builtin/projects/.svn/text-base/ProjectPanel.cwb.xml.svn-base
geworkbench-core/src/org/geworkbench/builtin/projects/.svn/text-base/ProjectPanel.java.svn-base
geworkbench-core/src/org/geworkbench/builtin/projects/.svn/text-base/ProjectSelection.java.svn-base
geworkbench-core/src/org/geworkbench/builtin/projects/.svn/text-base/RWspHandler.java.svn-base
geworkbench-core/src/org/geworkbench/builtin/projects/.svn/text-base/SaveFileFilterFactory.java.svn-base
geworkbench-core/src/org/geworkbench/builtin/projects/.svn/text-base/SaveTree.java.svn-base
geworkbench-core/src/org/geworkbench/builtin/projects/.svn/text-base/TreeNodeRenderer.java.svn-base
geworkbench-core/src/org/geworkbench/builtin/projects/.svn/text-base/WorkspaceHandler.java.svn-base
geworkbench-core/src/org/geworkbench/builtin/projects/DataSetNode.java
geworkbench-core/src/org/geworkbench/builtin/projects/DataSetSaveNode.java
geworkbench-core/src/org/geworkbench/builtin/projects/DefaultIconAssignments.java
geworkbench-core/src/org/geworkbench/builtin/projects/FileOpenHandler.java
geworkbench-core/src/org/geworkbench/builtin/projects/ImageFileFilter.java
geworkbench-core/src/org/geworkbench/builtin/projects/ImageNode.java
geworkbench-core/src/org/geworkbench/builtin/projects/LoadDataDialog.java
geworkbench-core/src/org/geworkbench/builtin/projects/PDBDialog.java
geworkbench-core/src/org/geworkbench/builtin/projects/PendingTreeNode.java
geworkbench-core/src/org/geworkbench/builtin/projects/ProjectPanel.cwb.xml
geworkbench-core/src/org/geworkbench/builtin/projects/ProjectPanel.java
geworkbench-core/src/org/geworkbench/builtin/projects/ProjectSelection.java
geworkbench-core/src/org/geworkbench/builtin/projects/RWspHandler.java
geworkbench-core/src/org/geworkbench/builtin/projects/SaveFileFilterFactory.java
geworkbench-core/src/org/geworkbench/builtin/projects/SaveTree.java
geworkbench-core/src/org/geworkbench/builtin/projects/TreeNodeRenderer.java
geworkbench-core/src/org/geworkbench/builtin/projects/WorkspaceHandler.java
geworkbench-core/src/org/geworkbench/builtin/projects/comments/.svn/all-wcprops
geworkbench-core/src/org/geworkbench/builtin/projects/comments/.svn/entries
geworkbench-core/src/org/geworkbench/builtin/projects/comments/.svn/text-base/CommentsPanel.java.svn-base
geworkbench-core/src/org/geworkbench/builtin/projects/comments/CommentsPanel.java
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/all-wcprops
geworkbench-core/src/org/geworkbench/builtin/projects/experimentinformation/.svn/entries
geworkbench-core/src/org/geworkbench/builtin/projects/experimentinformation/.svn/text-base/ExperimentInformationPanel.java.svn-base
geworkbench-core/src/org/geworkbench/builtin/projects/experimentinformation/ExperimentInformationPanel.java
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/all-wcprops
geworkbench-core/src/org/geworkbench/builtin/projects/history/.svn/entries
geworkbench-core/src/org/geworkbench/builtin/projects/history/.svn/text-base/HistoryPanel.java.svn-base
geworkbench-core/src/org/geworkbench/builtin/projects/history/HistoryPanel.java
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/all-wcprops
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/remoteresources/query/.svn/all-wcprops
geworkbench-core/src/org/geworkbench/builtin/projects/remoteresources/query/.svn/entries
geworkbench-core/src/org/geworkbench/builtin/projects/remoteresources/query/.svn/prop-base/CaARRAYQueryPanel.java.svn-base
geworkbench-core/src/org/geworkbench/builtin/projects/remoteresources/query/.svn/text-base/CaARRAYQueryPanel.java.svn-base
geworkbench-core/src/org/geworkbench/builtin/projects/remoteresources/query/CaARRAYQueryPanel.java
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/all-wcprops
geworkbench-core/src/org/geworkbench/engine/ccm/.svn/entries
geworkbench-core/src/org/geworkbench/engine/ccm/.svn/text-base/ComponentConfigurationManager.java.svn-base
geworkbench-core/src/org/geworkbench/engine/ccm/ComponentConfigurationManager.java
geworkbench-core/src/org/geworkbench/engine/config/.svn/all-wcprops
geworkbench-core/src/org/geworkbench/engine/config/.svn/entries
geworkbench-core/src/org/geworkbench/engine/config/.svn/text-base/GUIFramework.java.svn-base
geworkbench-core/src/org/geworkbench/engine/config/.svn/text-base/UILauncher.java.svn-base
geworkbench-core/src/org/geworkbench/engine/config/GUIFramework.java
geworkbench-core/src/org/geworkbench/engine/config/UILauncher.java
geworkbench-core/src/org/geworkbench/engine/config/events/.svn/entries
geworkbench-core/src/org/geworkbench/engine/config/rules/.svn/all-wcprops
geworkbench-core/src/org/geworkbench/engine/config/rules/.svn/entries
geworkbench-core/src/org/geworkbench/engine/config/rules/.svn/text-base/GeawConfigObject.java.svn-base
geworkbench-core/src/org/geworkbench/engine/config/rules/.svn/text-base/PluginObject.java.svn-base
geworkbench-core/src/org/geworkbench/engine/config/rules/GeawConfigObject.java
geworkbench-core/src/org/geworkbench/engine/config/rules/PluginObject.java
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/all-wcprops
geworkbench-core/src/org/geworkbench/engine/management/.svn/entries
geworkbench-core/src/org/geworkbench/engine/management/.svn/prop-base/Script.java.svn-base
geworkbench-core/src/org/geworkbench/engine/management/.svn/text-base/Script.java.svn-base
geworkbench-core/src/org/geworkbench/engine/management/Script.java
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/all-wcprops
geworkbench-core/src/org/geworkbench/events/.svn/entries
geworkbench-core/src/org/geworkbench/events/.svn/prop-base/CaArrayQueryResultEvent.java.svn-base
geworkbench-core/src/org/geworkbench/events/.svn/prop-base/CommentsEvent.java.svn-base
geworkbench-core/src/org/geworkbench/events/.svn/prop-base/NormalizationEvent.java.svn-base
geworkbench-core/src/org/geworkbench/events/.svn/prop-base/StructureAnalysisEvent.java.svn-base
geworkbench-core/src/org/geworkbench/events/.svn/text-base/CaArrayQueryResultEvent.java.svn-base
geworkbench-core/src/org/geworkbench/events/.svn/text-base/CaArrayRequestEvent.java.svn-base
geworkbench-core/src/org/geworkbench/events/.svn/text-base/CaArraySuccessEvent.java.svn-base
geworkbench-core/src/org/geworkbench/events/.svn/text-base/CommentsEvent.java.svn-base
geworkbench-core/src/org/geworkbench/events/.svn/text-base/FilteringEvent.java.svn-base
geworkbench-core/src/org/geworkbench/events/.svn/text-base/NormalizationEvent.java.svn-base
geworkbench-core/src/org/geworkbench/events/.svn/text-base/ProjectEvent.java.svn-base
geworkbench-core/src/org/geworkbench/events/.svn/text-base/SequenceDiscoveryTableEvent.java.svn-base
geworkbench-core/src/org/geworkbench/events/.svn/text-base/StructureAnalysisEvent.java.svn-base
geworkbench-core/src/org/geworkbench/events/CaArrayQueryResultEvent.java
geworkbench-core/src/org/geworkbench/events/CaArrayRequestEvent.java
geworkbench-core/src/org/geworkbench/events/CaArraySuccessEvent.java
geworkbench-core/src/org/geworkbench/events/CommentsEvent.java
geworkbench-core/src/org/geworkbench/events/FilteringEvent.java
geworkbench-core/src/org/geworkbench/events/NormalizationEvent.java
geworkbench-core/src/org/geworkbench/events/ProjectEvent.java
geworkbench-core/src/org/geworkbench/events/SequenceDiscoveryTableEvent.java
geworkbench-core/src/org/geworkbench/events/StructureAnalysisEvent.java
geworkbench-core/src/org/geworkbench/events/listeners/.svn/all-wcprops
geworkbench-core/src/org/geworkbench/events/listeners/.svn/entries
geworkbench-core/src/org/geworkbench/events/listeners/.svn/text-base/ParameterActionListener.java.svn-base
geworkbench-core/src/org/geworkbench/events/listeners/ParameterActionListener.java
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/AdjacencyMatrixFileFormat.java.svn-base
geworkbench-core/src/org/geworkbench/parsers/.svn/text-base/AffyFileFormat.java.svn-base
geworkbench-core/src/org/geworkbench/parsers/.svn/text-base/CELFileFormat.java.svn-base
geworkbench-core/src/org/geworkbench/parsers/.svn/text-base/ExpressionFileFormat.java.svn-base
geworkbench-core/src/org/geworkbench/parsers/.svn/text-base/FileFormat.java.svn-base
geworkbench-core/src/org/geworkbench/parsers/.svn/text-base/GenePixFileFormat.java.svn-base
geworkbench-core/src/org/geworkbench/parsers/.svn/text-base/GeoSeriesMatrixParser.java.svn-base
geworkbench-core/src/org/geworkbench/parsers/.svn/text-base/MageTabFileFormat.java.svn-base
geworkbench-core/src/org/geworkbench/parsers/.svn/text-base/PDBFileFormat.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/SOFTSeriesParser.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/AdjacencyMatrixFileFormat.java
geworkbench-core/src/org/geworkbench/parsers/AffyFileFormat.java
geworkbench-core/src/org/geworkbench/parsers/CELFileFormat.java
geworkbench-core/src/org/geworkbench/parsers/ExpressionFileFormat.java
geworkbench-core/src/org/geworkbench/parsers/FileFormat.java
geworkbench-core/src/org/geworkbench/parsers/GenePixFileFormat.java
geworkbench-core/src/org/geworkbench/parsers/GeoSeriesMatrixParser.java
geworkbench-core/src/org/geworkbench/parsers/MageTabFileFormat.java
geworkbench-core/src/org/geworkbench/parsers/PDBFileFormat.java
geworkbench-core/src/org/geworkbench/parsers/SOFTFileFormat.java
geworkbench-core/src/org/geworkbench/parsers/SOFTSeriesParser.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/entries
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/ProgressDialog.java.svn-base
geworkbench-core/src/org/geworkbench/util/.svn/text-base/SaveImage.java.svn-base
geworkbench-core/src/org/geworkbench/util/.svn/text-base/Util.java.svn-base
geworkbench-core/src/org/geworkbench/util/.svn/text-base/ValidationUtils.java.svn-base
geworkbench-core/src/org/geworkbench/util/ProgressDialog.java
geworkbench-core/src/org/geworkbench/util/SaveImage.java
geworkbench-core/src/org/geworkbench/util/Util.java
geworkbench-core/src/org/geworkbench/util/ValidationUtils.java
geworkbench-core/src/org/geworkbench/util/annotation/.svn/all-wcprops
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/all-wcprops
geworkbench-core/src/org/geworkbench/util/microarrayutils/.svn/entries
geworkbench-core/src/org/geworkbench/util/microarrayutils/.svn/text-base/MicroarrayViewEventBase.java.svn-base
geworkbench-core/src/org/geworkbench/util/microarrayutils/.svn/text-base/MicroarrayVisualizer.java.svn-base
geworkbench-core/src/org/geworkbench/util/microarrayutils/MicroarrayViewEventBase.java
geworkbench-core/src/org/geworkbench/util/microarrayutils/MicroarrayVisualizer.java
geworkbench-core/src/org/geworkbench/util/network/.svn/entries
geworkbench-core/src/org/geworkbench/util/pathwaydecoder/.svn/all-wcprops
geworkbench-core/src/org/geworkbench/util/pathwaydecoder/.svn/entries
geworkbench-core/src/org/geworkbench/util/pathwaydecoder/mutualinformation/.svn/all-wcprops
geworkbench-core/src/org/geworkbench/util/pathwaydecoder/mutualinformation/.svn/entries
geworkbench-core/src/org/geworkbench/util/pathwaydecoder/mutualinformation/.svn/text-base/EdgeListDataSet.java.svn-base
geworkbench-core/src/org/geworkbench/util/pathwaydecoder/mutualinformation/.svn/text-base/MindyData.java.svn-base
geworkbench-core/src/org/geworkbench/util/pathwaydecoder/mutualinformation/.svn/text-base/MindyDataSet.java.svn-base
geworkbench-core/src/org/geworkbench/util/pathwaydecoder/mutualinformation/.svn/text-base/NetBoostDataSet.java.svn-base
geworkbench-core/src/org/geworkbench/util/pathwaydecoder/mutualinformation/EdgeListDataSet.java
geworkbench-core/src/org/geworkbench/util/pathwaydecoder/mutualinformation/MindyData.java
geworkbench-core/src/org/geworkbench/util/pathwaydecoder/mutualinformation/MindyDataSet.java
geworkbench-core/src/org/geworkbench/util/pathwaydecoder/mutualinformation/NetBoostDataSet.java
geworkbench-core/src/org/geworkbench/util/patterns/.svn/all-wcprops
geworkbench-core/src/org/geworkbench/util/patterns/.svn/entries
geworkbench-core/src/org/geworkbench/util/patterns/.svn/prop-base/DataSource.java.svn-base
geworkbench-core/src/org/geworkbench/util/patterns/.svn/prop-base/SequentialPatternSource.java.svn-base
geworkbench-core/src/org/geworkbench/util/patterns/.svn/text-base/CSMatchedSeqPattern.java.svn-base
geworkbench-core/src/org/geworkbench/util/patterns/.svn/text-base/DataSource.java.svn-base
geworkbench-core/src/org/geworkbench/util/patterns/.svn/text-base/SequentialPatternSource.java.svn-base
geworkbench-core/src/org/geworkbench/util/patterns/CSMatchedSeqPattern.java
geworkbench-core/src/org/geworkbench/util/patterns/DataSource.java
geworkbench-core/src/org/geworkbench/util/patterns/SequentialPatternSource.java
geworkbench-core/src/org/geworkbench/util/sequences/.svn/all-wcprops
geworkbench-core/src/org/geworkbench/util/sequences/.svn/entries
geworkbench-core/src/org/geworkbench/util/sequences/.svn/text-base/SequenceViewWidget.java.svn-base
geworkbench-core/src/org/geworkbench/util/sequences/.svn/text-base/SequenceViewWidgetPanel.java.svn-base
geworkbench-core/src/org/geworkbench/util/sequences/SequenceViewWidget.java
geworkbench-core/src/org/geworkbench/util/sequences/SequenceViewWidgetPanel.java
geworkbench-core/src/org/geworkbench/util/visualproperties/.svn/entries
geworkbench-core/test/.svn/all-wcprops
geworkbench-core/test/.svn/entries
geworkbench-core/test/org/.svn/all-wcprops
geworkbench-core/test/org/.svn/entries
geworkbench-core/test/org/geworkbench/.svn/all-wcprops
geworkbench-core/test/org/geworkbench/.svn/entries
geworkbench-core/test/org/geworkbench/analysis/.svn/entries
geworkbench-core/test/org/geworkbench/bison/.svn/all-wcprops
geworkbench-core/test/org/geworkbench/bison/.svn/entries
geworkbench-core/test/org/geworkbench/bison/datastructure/.svn/all-wcprops
geworkbench-core/test/org/geworkbench/bison/datastructure/.svn/entries
geworkbench-core/test/org/geworkbench/bison/datastructure/bioobjects/.svn/all-wcprops
geworkbench-core/test/org/geworkbench/bison/datastructure/bioobjects/.svn/entries
geworkbench-core/test/org/geworkbench/bison/datastructure/bioobjects/microarray/.svn/all-wcprops
geworkbench-core/test/org/geworkbench/bison/datastructure/bioobjects/microarray/.svn/entries
geworkbench-core/test/org/geworkbench/bison/datastructure/bioobjects/microarray/.svn/text-base/CSAnovaResultSetTest.java.svn-base
geworkbench-core/test/org/geworkbench/bison/datastructure/bioobjects/microarray/CSAnovaResultSetTest.java
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/all-wcprops
geworkbench-core/test/org/geworkbench/parsers/.svn/entries
geworkbench-core/test/org/geworkbench/parsers/.svn/text-base/DataSetFileFormatTest.java.svn-base
geworkbench-core/test/org/geworkbench/parsers/DataSetFileFormatTest.java
diff --git a/geworkbench-core/.settings/.svn/entries b/geworkbench-core/.settings/.svn/entries
index ccc08cf..b920c27 100644
--- a/geworkbench-core/.settings/.svn/entries
+++ b/geworkbench-core/.settings/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8215
+8644
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/.settings
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/.settings/org.eclipse.wst.common.component b/geworkbench-core/.settings/org.eclipse.wst.common.component
index 24f061d..40c22bb 100644
--- a/geworkbench-core/.settings/org.eclipse.wst.common.component
+++ b/geworkbench-core/.settings/org.eclipse.wst.common.component
@@ -6,6 +6,5 @@
         <wb-resource deploy-path="/" source-path="/annotation"/>
         <wb-resource deploy-path="/" source-path="/test"/>
         <wb-resource deploy-path="/" source-path="/components/genspace/src"/>
-        <wb-resource deploy-path="/" source-path="/components/genspace/test"/>
     </wb-module>
 </project-modules>
diff --git a/geworkbench-core/.svn/all-wcprops b/geworkbench-core/.svn/all-wcprops
index adea0d9..d1b6dae 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/8215/trunk/geworkbench
+/svn/geworkbench/!svn/ver/8644/trunk/geworkbench
 END
 java.policy
 K 25
@@ -75,6 +75,12 @@ svn:wc:ra_dav:version-url
 V 71
 /svn/geworkbench/!svn/ver/8187/trunk/geworkbench/ReleaseNotes_2.2.1.txt
 END
+ReleaseNotes_2.2.2.txt
+K 25
+svn:wc:ra_dav:version-url
+V 71
+/svn/geworkbench/!svn/ver/8232/trunk/geworkbench/ReleaseNotes_2.2.2.txt
+END
 ReleaseNotes1.0.5.txt
 K 25
 svn:wc:ra_dav:version-url
@@ -133,7 +139,7 @@ build.xml
 K 25
 svn:wc:ra_dav:version-url
 V 58
-/svn/geworkbench/!svn/ver/8187/trunk/geworkbench/build.xml
+/svn/geworkbench/!svn/ver/8640/trunk/geworkbench/build.xml
 END
 build-component.xml
 K 25
diff --git a/geworkbench-core/.svn/entries b/geworkbench-core/.svn/entries
index 16aaa37..9bf7417 100644
--- a/geworkbench-core/.svn/entries
+++ b/geworkbench-core/.svn/entries
@@ -1,15 +1,15 @@
 10

 dir
-8215
+8644
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2011-08-15T19:37:34.116726Z
-8215
-zji
+2011-12-23T16:28:44.773024Z
+8644
+poddutun
 has-props


@@ -32,7 +32,7 @@ file



-2011-08-02T04:32:49.000000Z
+2011-08-17T00:10:49.000000Z
 7ddb05e48d53e8bdb44ed3e29e720e3f
 2005-07-28T22:36:56.000000Z
 50
@@ -66,7 +66,7 @@ file



-2011-08-02T04:32:49.000000Z
+2011-08-17T00:10:49.000000Z
 fd7ba602ed4a20313bcecdb32876d8b7
 2006-03-03T18:05:24.000000Z
 1317
@@ -134,7 +134,7 @@ file



-2011-08-02T04:32:49.000000Z
+2011-08-17T00:10:35.000000Z
 a39155ba74eca7f95b7a8b55835ef01b
 2010-09-13T14:40:56.329012Z
 7051
@@ -168,7 +168,7 @@ file



-2011-08-02T04:32:49.000000Z
+2011-08-17T00:10:35.000000Z
 1996b5d7893eab9883a59aefbd8a57e8
 2008-09-23T17:27:37.000000Z
 4247
@@ -202,7 +202,7 @@ file



-2011-08-02T04:32:49.000000Z
+2011-08-17T00:10:35.000000Z
 82c53def33f31f896b8a40a5a6fffd28
 2009-07-22T15:34:34.000000Z
 5445
@@ -236,11 +236,11 @@ file



-2011-08-02T04:32:49.000000Z
-f3f41dbc5101a9724bec9fb448523427
-2011-07-30T04:31:30.667242Z
-8187
-zji
+2011-12-29T06:11:39.000000Z
+22f584cd0bb33ed09a2970937175dc34
+2011-12-22T22:00:33.835889Z
+8640
+maz
 has-props


@@ -262,7 +262,7 @@ has-props



-26647
+26988

 .classpath
 file
@@ -283,7 +283,7 @@ file



-2011-08-02T04:32:49.000000Z
+2011-08-17T00:10:35.000000Z
 88f74ac365067bca30b04287cd5830ee
 2005-12-07T23:44:35.000000Z
 971
@@ -317,7 +317,7 @@ file



-2011-08-02T04:32:49.000000Z
+2011-08-17T00:10:49.000000Z
 78e2980cea04dd63ddebaa36e5bde77a
 2007-05-01T18:45:35.000000Z
 2739
@@ -351,7 +351,7 @@ file



-2011-06-22T00:54:28.000000Z
+2011-08-17T00:10:33.000000Z
 a27bf73fe918461924238212fbbe5b13
 2009-06-09T20:27:29.000000Z
 5187
@@ -385,7 +385,7 @@ file



-2011-08-02T04:32:49.000000Z
+2011-08-17T00:10:49.000000Z
 7cf15ce814998288e8624388152d83eb
 2010-06-10T02:39:43.512944Z
 6786
@@ -419,7 +419,7 @@ file



-2011-08-02T04:32:49.000000Z
+2011-08-17T00:10:49.000000Z
 0961f5b52af0c5237c479a684a981bbf
 2007-05-16T20:46:26.000000Z
 2859
@@ -453,7 +453,7 @@ file



-2011-08-02T04:32:49.000000Z
+2011-08-17T00:10:51.000000Z
 853f159edbdd0694ce5995fb9dea00aa
 2006-07-19T01:50:13.000000Z
 1679
@@ -490,7 +490,7 @@ file



-2011-08-02T04:32:49.000000Z
+2011-08-17T00:10:49.000000Z
 a50513f514d4ae6ff475196c6df6d6b7
 2007-05-01T20:10:16.000000Z
 2747
@@ -524,7 +524,7 @@ file



-2011-08-02T04:32:50.000000Z
+2011-09-30T16:54:42.000000Z
 b4d2959294acf9789462517afc3918d0
 2006-02-01T16:15:10.000000Z
 1164
@@ -561,7 +561,7 @@ file



-2011-08-02T04:32:50.000000Z
+2011-08-17T00:10:34.000000Z
 927a40b378617b6420377213c2b7ef96
 2009-06-18T17:05:17.000000Z
 5271
@@ -595,7 +595,7 @@ file



-2011-08-02T04:32:50.000000Z
+2011-08-17T00:10:49.000000Z
 bba2ba563208b5b6ade639a2ca9a6cc7
 2009-11-09T17:14:11.000000Z
 5737
@@ -629,7 +629,7 @@ file



-2011-08-02T04:32:50.000000Z
+2011-08-17T00:10:49.000000Z
 e90d6080360ec3796eae11f321e09309
 2006-07-13T14:41:35.000000Z
 1658
@@ -663,7 +663,7 @@ file



-2011-08-02T04:32:50.000000Z
+2011-08-17T00:10:34.000000Z
 604c35743a55022310bd27f784751305
 2009-06-18T17:05:17.000000Z
 5271
@@ -697,7 +697,7 @@ file



-2011-08-02T04:32:50.000000Z
+2011-08-17T00:10:34.000000Z
 c1c9a464a0a8e6f90ae0f92caacf1e36
 2009-11-09T17:14:11.000000Z
 5737
@@ -731,7 +731,7 @@ file



-2011-08-02T04:32:50.000000Z
+2011-08-17T00:10:49.000000Z
 d50a512a511ff2b24aca03abf2f07ede
 2006-07-13T14:41:35.000000Z
 1658
@@ -765,7 +765,7 @@ file



-2011-08-02T04:32:50.000000Z
+2011-08-17T00:10:51.000000Z
 0b10003972c377763fb06fbfe06abf6e
 2006-09-22T17:04:38.000000Z
 1893
@@ -799,7 +799,7 @@ file



-2011-08-02T04:32:50.000000Z
+2011-08-17T00:18:54.000000Z
 17aaf2f82dc995231704d501b04a0bd4
 2011-07-30T04:31:30.667242Z
 8187
@@ -836,7 +836,7 @@ file



-2011-08-02T04:32:50.000000Z
+2011-08-17T00:10:35.000000Z
 615522f98d7411d0337dea0ae5f57144
 2010-04-28T13:17:26.274091Z
 6424
@@ -870,7 +870,7 @@ file



-2011-08-02T04:32:50.000000Z
+2011-08-17T00:10:49.000000Z
 6ca7399d6d58a9c12ca8dc16bd76803f
 2010-04-28T13:17:26.274091Z
 6424
@@ -907,7 +907,7 @@ file



-2011-08-02T04:32:50.000000Z
+2011-08-17T00:10:35.000000Z
 73451a37b511dfd0559a31a3d4661441
 2010-08-09T23:14:34.986255Z
 6969
@@ -947,7 +947,7 @@ file



-2011-08-02T04:32:50.000000Z
+2011-08-17T00:10:35.000000Z
 f2d46005bfe7fafc55b84f07690ff2d0
 2010-08-09T21:24:49.707603Z
 6966
@@ -981,7 +981,7 @@ file



-2011-08-02T04:32:50.000000Z
+2011-08-17T00:18:52.000000Z
 441fb4f98b14f80b650554fef3cb80e5
 2011-05-25T14:25:11.688972Z
 7925
@@ -1015,7 +1015,7 @@ file



-2011-08-02T04:32:50.000000Z
+2011-08-17T00:10:35.000000Z
 6e4673bbc650b9e46d9dabbf58735804
 2010-08-09T23:17:05.434469Z
 6970
@@ -1052,7 +1052,7 @@ file



-2011-08-02T04:32:50.000000Z
+2011-08-17T00:18:52.000000Z
 5d8ec97e006df208c36ba76bd1737afb
 2011-07-30T04:31:30.667242Z
 8187
@@ -1086,7 +1086,7 @@ file



-2011-08-02T04:32:50.000000Z
+2011-08-17T00:10:35.000000Z
 50723c1aae0c25e1727d8f64fcd900bd
 2005-11-11T16:25:46.000000Z
 798
@@ -1114,13 +1114,47 @@ has-props

 2574

+ReleaseNotes_2.2.2.txt
+file
+
+
+
+
+2011-12-29T06:13:05.000000Z
+d41d124953562d892065a0f3341491b6
+2011-08-19T22:37:49.729086Z
+8232
+smithken
+has-props
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+45796
+
 ReleaseNotes1.0.5.txt
 file




-2011-08-02T04:32:50.000000Z
+2011-08-17T00:10:35.000000Z
 33907373d13ba00dbbbb64a09e1bb3a0
 2007-03-23T19:30:59.000000Z
 2616
@@ -1154,7 +1188,7 @@ file



-2011-08-02T04:32:50.000000Z
+2011-08-17T00:10:35.000000Z
 c59b578b450c3014da8ccb2ba1b22880
 2008-10-29T16:14:26.000000Z
 4412
@@ -1188,7 +1222,7 @@ file



-2011-08-02T04:32:50.000000Z
+2011-08-17T00:10:35.000000Z
 d45aa202e1c3eda297edb6b43ed2349d
 2008-11-12T17:04:22.000000Z
 4453
@@ -1222,7 +1256,7 @@ file



-2011-08-02T04:32:50.000000Z
+2011-08-17T00:10:35.000000Z
 89fa8b9f9d6e97ed64267abc8ad487d7
 2009-11-09T17:14:11.000000Z
 5737
@@ -1256,7 +1290,7 @@ file



-2011-08-02T04:32:50.000000Z
+2011-08-17T00:10:35.000000Z
 15a71a541a6791503d59a5139564546e
 2008-11-18T21:03:08.000000Z
 4470
@@ -1290,7 +1324,7 @@ file



-2011-08-02T04:32:50.000000Z
+2011-09-30T16:54:42.000000Z
 2b4de95ab609266736ff57a56f7b2f6a
 2005-08-22T20:38:15.000000Z
 147
@@ -1324,7 +1358,7 @@ file



-2011-08-02T04:32:50.000000Z
+2011-08-17T00:10:35.000000Z
 b68f3daf1435f2329e1d82b8a61c3f88
 2009-01-07T20:23:03.000000Z
 4599
@@ -1358,7 +1392,7 @@ file



-2011-08-02T04:32:50.000000Z
+2011-08-17T00:10:35.000000Z
 5a3e5b1df4159642c44163a1c973e395
 2010-12-09T22:30:57.417842Z
 7318
@@ -1401,7 +1435,7 @@ file



-2011-08-02T04:32:50.000000Z
+2011-08-17T00:10:51.000000Z
 c129b33428b4f8761704c79edac402f6
 2006-09-29T16:55:19.000000Z
 1909
@@ -1441,7 +1475,7 @@ file



-2011-08-02T04:32:50.000000Z
+2011-08-17T00:10:49.000000Z
 0e0e16db6b5ccce28b0c632de1f07bbc
 2006-01-31T22:00:54.000000Z
 1160
@@ -1475,7 +1509,7 @@ file



-2011-08-02T04:32:50.000000Z
+2011-08-17T00:10:35.000000Z
 dbeec2e21f249f77c905bfb2add94c20
 2005-11-11T16:29:14.000000Z
 799
@@ -1509,7 +1543,7 @@ file



-2011-08-02T04:32:50.000000Z
+2011-08-17T00:10:35.000000Z
 d55b6faffa14f8510207a6fbbd40119e
 2008-09-09T17:35:24.000000Z
 4181
@@ -1543,7 +1577,7 @@ file



-2011-08-02T04:32:50.000000Z
+2011-08-17T00:10:49.000000Z
 77b680987a1b6bd2f21c1277669d1199
 2005-07-29T20:57:18.000000Z
 59
@@ -1577,7 +1611,7 @@ file



-2011-08-02T04:32:50.000000Z
+2011-08-17T00:10:46.000000Z
 69f51ba4d3a6da774f757e90ffb7671b
 2009-09-25T21:14:28.000000Z
 5614
@@ -1611,7 +1645,7 @@ file



-2011-08-02T04:32:50.000000Z
+2011-08-17T00:10:51.000000Z
 f2d3de5a23a7b01892764a046f21224d
 2011-04-25T17:24:20.190278Z
 7819
@@ -1645,7 +1679,7 @@ file



-2011-08-02T04:32:50.000000Z
+2011-12-29T06:11:16.000000Z
 45e5130804b03d5ada07f23fb07f6e1d
 2005-08-22T20:38:15.000000Z
 147
@@ -1685,7 +1719,7 @@ file



-2011-08-02T04:32:50.000000Z
+2011-08-17T00:10:49.000000Z
 736d6bc486a42574b73317214206fa52
 2006-03-30T22:55:08.000000Z
 1391
@@ -1719,7 +1753,7 @@ file



-2011-08-02T04:32:50.000000Z
+2011-08-17T00:10:34.000000Z
 3334d87680327bafe7e9c4ea1ffb20af
 2009-06-18T17:05:17.000000Z
 5271
@@ -1753,7 +1787,7 @@ file



-2011-08-02T04:32:50.000000Z
+2011-08-17T00:10:35.000000Z
 111864d49a35c305265caf817f51af4a
 2006-07-10T12:10:09.000000Z
 1630
@@ -1787,7 +1821,7 @@ file



-2011-08-02T04:32:50.000000Z
+2011-08-17T00:10:49.000000Z
 d99fe7228c626c02b144dc33640c989c
 2006-03-03T18:05:24.000000Z
 1317
diff --git a/geworkbench-core/.svn/text-base/build.xml.svn-base b/geworkbench-core/.svn/text-base/build.xml.svn-base
index 7150bc3..0daf382 100644
--- a/geworkbench-core/.svn/text-base/build.xml.svn-base
+++ b/geworkbench-core/.svn/text-base/build.xml.svn-base
@@ -106,6 +106,7 @@
 				<include name="celprocessing" />
 				<include name="cgems" />
 				<include name="colormosaic" />
+				<include name="cupid" />
 				<include name="cytoscape" />
 				<include name="discovery" />
 				<include name="evidenceintegration" />
@@ -511,13 +512,23 @@
 		</jar>
 		<jar destfile="geworkbench-others.jar" basedir="${classes}" excludes="org/geworkbench/bison/**,org/geworkbench/engine/**,org/geworkbench/events/**,org/geworkbench/parsers/**,org/geworkbench/util/**,org/geworkbench/builtin/**">
 		</jar>
+
+		<!-- jar components -->
+		<subant target="jar" genericantfile="build-component.xml">
+			<dirset dir="components">
+				<include name="analysis" />
+				<include name="ttest" />
+				<include name="hierarchicalclustering" />
+				<!-- exclude the dead projets -->
+				<exclude name="skylinecontour" />
+			</dirset>
+		</subant>
 	</target>
 	<!-- ====================================================================== -->
 	<!-- CREATE   DISTRIBUTION-->
 	<!-- ====================================================================== -->
 	<target name="createDist" depends="compile, jar" description="Creating a new folder for depositing...">
 		<java classname="org.geworkbench.components.versioninfo.VersionInfoDialog" failonerror="true" >
-			<arg value="2.2.1"/>
 			<arg value="./components/versioninfo/classes/org/geworkbench/components/versioninfo/" />
 			<classpath>
 				<path refid="classpath" />
diff --git a/geworkbench-core/.svn/tmp/.classpath.2.tmp b/geworkbench-core/.svn/tmp/.classpath.2.tmp
deleted file mode 100644
index 4f795db..0000000
--- a/geworkbench-core/.svn/tmp/.classpath.2.tmp
+++ /dev/null
@@ -1,114 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
-	<classpathentry kind="src" path="conf"/>
-	<classpathentry kind="src" path="src"/>
-	<classpathentry kind="src" path="annotation"/>
-	<classpathentry kind="src" path="test"/>
-	<classpathentry kind="src" path="components/caarray/src"/>
-	<classpathentry kind="src" path="components/genspace/src"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER">
-		<attributes>
-			<attribute name="owner.project.facets" value="java"/>
-		</attributes>
-	</classpathentry>
-<<<<<<< .mine
-	<classpathentry kind="lib" path="components/genspace/lib/intellij.jar"/>
-	<classpathentry kind="lib" path="components/genspace/lib/jgraphx.jar"/>
-	<classpathentry kind="lib" path="components/genspace/lib/jimi.jar"/>
-	<classpathentry kind="lib" path="components/genspace/lib/mina-core-1.1.7.jar"/>
-	<classpathentry kind="lib" path="components/genspace/lib/smack.jar"/>
-	<classpathentry kind="lib" path="components/genspace/lib/smackx.jar"/>
-	<classpathentry kind="lib" path="components/genspace/lib/swing-layout-1.0.3.jar"/>
-	<classpathentry kind="lib" path="lib/AffxFusion.jar"/>
-	<classpathentry kind="lib" path="lib/ant-launcher.jar"/>
-	<classpathentry kind="lib" path="lib/ant.jar"/>
-=======
-	<classpathentry exported="true" kind="lib" path="lib/AffxFusion.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/ant.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/ant-launcher.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/bcel-5.1.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/cglib-nodep-2.1.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/collections-generic-4.0.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/commons-beanutils.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/commons-collections.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/commons-digester.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/commons-discovery.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/commons-logging.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/docking.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/forms-1.0.5.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/jai_codec.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/jai_core.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/jaxb-rt-1.0-ea.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/jaxrpc.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/jcommon-1.0.5.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/jdom.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/jfreechart-1.0.2.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/jhall.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/jsr173_api.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/log4j-1.2.8.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/mail.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/ostermillerutils_1_04_03_for_kaffe.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/stax-1.2.0_rc1-dev.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/xml-apis.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/commons-codec-1.3.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/j3dcore.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/j3dutils.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/vecmath.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/commons-lang-2.4.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/ginkgo-0.1-SNAPSHOT.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/commons-math-2.2.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/commons-httpclient-3.1.jar"/>
-	<classpathentry kind="lib" path="lib/xalan.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/junit.jar"/>
-	<classpathentry kind="lib" path="lib/jaxen.jar"/>
-	<classpathentry kind="lib" path="lib/axis2-kernel-1.5.3.jar"/>
->>>>>>> .r8215
-	<classpathentry kind="lib" path="lib/axiom-api-1.2.10.jar"/>
-	<classpathentry kind="lib" path="lib/axiom-impl-1.2.10.jar"/>
-	<classpathentry kind="lib" path="lib/axis2-adb-1.5.3.jar"/>
-	<classpathentry kind="lib" path="lib/axis2-kernel-1.5.3.jar"/>
-	<classpathentry kind="lib" path="lib/axis2-transport-http-1.5.3.jar"/>
-	<classpathentry kind="lib" path="lib/axis2-transport-local-1.5.3.jar"/>
-	<classpathentry kind="lib" path="lib/axis2-upload-client.jar"/>
-	<classpathentry kind="lib" path="lib/bcel-5.1.jar"/>
-	<classpathentry kind="lib" path="lib/cglib-nodep-2.1.jar"/>
-	<classpathentry kind="lib" path="lib/collections-generic-4.0.jar"/>
-	<classpathentry kind="lib" path="lib/commons-beanutils.jar"/>
-	<classpathentry kind="lib" path="lib/commons-codec-1.3.jar"/>
-	<classpathentry kind="lib" path="lib/commons-collections.jar"/>
-	<classpathentry kind="lib" path="lib/commons-digester.jar"/>
-	<classpathentry kind="lib" path="lib/commons-discovery.jar"/>
-	<classpathentry kind="lib" path="lib/commons-httpclient-3.1.jar"/>
-	<classpathentry kind="lib" path="lib/commons-lang-2.4.jar"/>
-	<classpathentry kind="lib" path="lib/commons-logging.jar"/>
-	<classpathentry kind="lib" path="lib/docking.jar"/>
-	<classpathentry kind="lib" path="lib/forms-1.0.5.jar"/>
-	<classpathentry kind="lib" path="lib/ginkgo-0.1-SNAPSHOT.jar"/>
-	<classpathentry kind="lib" path="lib/httpcore-4.0.jar"/>
-	<classpathentry kind="lib" path="lib/j3dcore.jar"/>
-	<classpathentry kind="lib" path="lib/j3dutils.jar"/>
-	<classpathentry kind="lib" path="lib/jai_codec.jar"/>
-	<classpathentry kind="lib" path="lib/jai_core.jar"/>
-	<classpathentry kind="lib" path="lib/jaxb-rt-1.0-ea.jar"/>
-	<classpathentry kind="lib" path="lib/jaxen.jar"/>
-	<classpathentry kind="lib" path="lib/jaxrpc.jar"/>
-	<classpathentry kind="lib" path="lib/jcommon-1.0.5.jar"/>
-	<classpathentry kind="lib" path="lib/jdom.jar"/>
-	<classpathentry kind="lib" path="lib/jfreechart-1.0.2.jar"/>
-	<classpathentry kind="lib" path="lib/jhall.jar"/>
-	<classpathentry kind="lib" path="lib/jsr173_api.jar"/>
-	<classpathentry kind="lib" path="lib/junit.jar"/>
-	<classpathentry kind="lib" path="lib/log4j-1.2.8.jar"/>
-	<classpathentry kind="lib" path="lib/mail.jar"/>
-	<classpathentry kind="lib" path="lib/neethi-2.0.4.jar"/>
-	<classpathentry kind="lib" path="lib/ostermillerutils_1_04_03_for_kaffe.jar"/>
-	<classpathentry kind="lib" path="lib/stax-1.2.0_rc1-dev.jar"/>
-	<classpathentry kind="lib" path="lib/vecmath.jar"/>
-	<classpathentry kind="lib" path="lib/wsdl4j-1.6.2.jar"/>
-	<classpathentry kind="lib" path="lib/xalan.jar"/>
-	<classpathentry kind="lib" path="lib/xml-apis.jar"/>
-	<classpathentry kind="lib" path="lib/XmlSchema-1.4.3.jar"/>
-	<classpathentry kind="lib" path="components/genspace/lib/ha-api.jar"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/genspace-common"/>
-	<classpathentry kind="output" path="classes"/>
-</classpath>
diff --git a/geworkbench-core/.svn/tmp/.classpath.tmp b/geworkbench-core/.svn/tmp/.classpath.tmp
deleted file mode 100644
index 4f795db..0000000
--- a/geworkbench-core/.svn/tmp/.classpath.tmp
+++ /dev/null
@@ -1,114 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
-	<classpathentry kind="src" path="conf"/>
-	<classpathentry kind="src" path="src"/>
-	<classpathentry kind="src" path="annotation"/>
-	<classpathentry kind="src" path="test"/>
-	<classpathentry kind="src" path="components/caarray/src"/>
-	<classpathentry kind="src" path="components/genspace/src"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER">
-		<attributes>
-			<attribute name="owner.project.facets" value="java"/>
-		</attributes>
-	</classpathentry>
-<<<<<<< .mine
-	<classpathentry kind="lib" path="components/genspace/lib/intellij.jar"/>
-	<classpathentry kind="lib" path="components/genspace/lib/jgraphx.jar"/>
-	<classpathentry kind="lib" path="components/genspace/lib/jimi.jar"/>
-	<classpathentry kind="lib" path="components/genspace/lib/mina-core-1.1.7.jar"/>
-	<classpathentry kind="lib" path="components/genspace/lib/smack.jar"/>
-	<classpathentry kind="lib" path="components/genspace/lib/smackx.jar"/>
-	<classpathentry kind="lib" path="components/genspace/lib/swing-layout-1.0.3.jar"/>
-	<classpathentry kind="lib" path="lib/AffxFusion.jar"/>
-	<classpathentry kind="lib" path="lib/ant-launcher.jar"/>
-	<classpathentry kind="lib" path="lib/ant.jar"/>
-=======
-	<classpathentry exported="true" kind="lib" path="lib/AffxFusion.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/ant.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/ant-launcher.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/bcel-5.1.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/cglib-nodep-2.1.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/collections-generic-4.0.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/commons-beanutils.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/commons-collections.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/commons-digester.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/commons-discovery.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/commons-logging.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/docking.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/forms-1.0.5.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/jai_codec.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/jai_core.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/jaxb-rt-1.0-ea.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/jaxrpc.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/jcommon-1.0.5.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/jdom.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/jfreechart-1.0.2.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/jhall.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/jsr173_api.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/log4j-1.2.8.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/mail.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/ostermillerutils_1_04_03_for_kaffe.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/stax-1.2.0_rc1-dev.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/xml-apis.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/commons-codec-1.3.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/j3dcore.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/j3dutils.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/vecmath.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/commons-lang-2.4.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/ginkgo-0.1-SNAPSHOT.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/commons-math-2.2.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/commons-httpclient-3.1.jar"/>
-	<classpathentry kind="lib" path="lib/xalan.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/junit.jar"/>
-	<classpathentry kind="lib" path="lib/jaxen.jar"/>
-	<classpathentry kind="lib" path="lib/axis2-kernel-1.5.3.jar"/>
->>>>>>> .r8215
-	<classpathentry kind="lib" path="lib/axiom-api-1.2.10.jar"/>
-	<classpathentry kind="lib" path="lib/axiom-impl-1.2.10.jar"/>
-	<classpathentry kind="lib" path="lib/axis2-adb-1.5.3.jar"/>
-	<classpathentry kind="lib" path="lib/axis2-kernel-1.5.3.jar"/>
-	<classpathentry kind="lib" path="lib/axis2-transport-http-1.5.3.jar"/>
-	<classpathentry kind="lib" path="lib/axis2-transport-local-1.5.3.jar"/>
-	<classpathentry kind="lib" path="lib/axis2-upload-client.jar"/>
-	<classpathentry kind="lib" path="lib/bcel-5.1.jar"/>
-	<classpathentry kind="lib" path="lib/cglib-nodep-2.1.jar"/>
-	<classpathentry kind="lib" path="lib/collections-generic-4.0.jar"/>
-	<classpathentry kind="lib" path="lib/commons-beanutils.jar"/>
-	<classpathentry kind="lib" path="lib/commons-codec-1.3.jar"/>
-	<classpathentry kind="lib" path="lib/commons-collections.jar"/>
-	<classpathentry kind="lib" path="lib/commons-digester.jar"/>
-	<classpathentry kind="lib" path="lib/commons-discovery.jar"/>
-	<classpathentry kind="lib" path="lib/commons-httpclient-3.1.jar"/>
-	<classpathentry kind="lib" path="lib/commons-lang-2.4.jar"/>
-	<classpathentry kind="lib" path="lib/commons-logging.jar"/>
-	<classpathentry kind="lib" path="lib/docking.jar"/>
-	<classpathentry kind="lib" path="lib/forms-1.0.5.jar"/>
-	<classpathentry kind="lib" path="lib/ginkgo-0.1-SNAPSHOT.jar"/>
-	<classpathentry kind="lib" path="lib/httpcore-4.0.jar"/>
-	<classpathentry kind="lib" path="lib/j3dcore.jar"/>
-	<classpathentry kind="lib" path="lib/j3dutils.jar"/>
-	<classpathentry kind="lib" path="lib/jai_codec.jar"/>
-	<classpathentry kind="lib" path="lib/jai_core.jar"/>
-	<classpathentry kind="lib" path="lib/jaxb-rt-1.0-ea.jar"/>
-	<classpathentry kind="lib" path="lib/jaxen.jar"/>
-	<classpathentry kind="lib" path="lib/jaxrpc.jar"/>
-	<classpathentry kind="lib" path="lib/jcommon-1.0.5.jar"/>
-	<classpathentry kind="lib" path="lib/jdom.jar"/>
-	<classpathentry kind="lib" path="lib/jfreechart-1.0.2.jar"/>
-	<classpathentry kind="lib" path="lib/jhall.jar"/>
-	<classpathentry kind="lib" path="lib/jsr173_api.jar"/>
-	<classpathentry kind="lib" path="lib/junit.jar"/>
-	<classpathentry kind="lib" path="lib/log4j-1.2.8.jar"/>
-	<classpathentry kind="lib" path="lib/mail.jar"/>
-	<classpathentry kind="lib" path="lib/neethi-2.0.4.jar"/>
-	<classpathentry kind="lib" path="lib/ostermillerutils_1_04_03_for_kaffe.jar"/>
-	<classpathentry kind="lib" path="lib/stax-1.2.0_rc1-dev.jar"/>
-	<classpathentry kind="lib" path="lib/vecmath.jar"/>
-	<classpathentry kind="lib" path="lib/wsdl4j-1.6.2.jar"/>
-	<classpathentry kind="lib" path="lib/xalan.jar"/>
-	<classpathentry kind="lib" path="lib/xml-apis.jar"/>
-	<classpathentry kind="lib" path="lib/XmlSchema-1.4.3.jar"/>
-	<classpathentry kind="lib" path="components/genspace/lib/ha-api.jar"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/genspace-common"/>
-	<classpathentry kind="output" path="classes"/>
-</classpath>
diff --git a/geworkbench-core/.svn/tmp/tempfile.2.tmp b/geworkbench-core/.svn/tmp/tempfile.2.tmp
deleted file mode 100644
index 10a48e5..0000000
--- a/geworkbench-core/.svn/tmp/tempfile.2.tmp
+++ /dev/null
@@ -1,72 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
-	<classpathentry kind="src" path="conf"/>
-	<classpathentry kind="src" path="src"/>
-	<classpathentry kind="src" path="annotation"/>
-	<classpathentry kind="src" path="test"/>
-	<classpathentry kind="src" path="components/caarray/src"/>
-	<classpathentry kind="src" path="components/genspace/src"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER">
-		<attributes>
-			<attribute name="owner.project.facets" value="java"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="lib" path="components/genspace/lib/intellij.jar"/>
-	<classpathentry kind="lib" path="components/genspace/lib/jgraphx.jar"/>
-	<classpathentry kind="lib" path="components/genspace/lib/jimi.jar"/>
-	<classpathentry kind="lib" path="components/genspace/lib/mina-core-1.1.7.jar"/>
-	<classpathentry kind="lib" path="components/genspace/lib/smack.jar"/>
-	<classpathentry kind="lib" path="components/genspace/lib/smackx.jar"/>
-	<classpathentry kind="lib" path="components/genspace/lib/swing-layout-1.0.3.jar"/>
-	<classpathentry kind="lib" path="lib/AffxFusion.jar"/>
-	<classpathentry kind="lib" path="lib/ant-launcher.jar"/>
-	<classpathentry kind="lib" path="lib/ant.jar"/>
-	<classpathentry kind="lib" path="lib/axiom-api-1.2.10.jar"/>
-	<classpathentry kind="lib" path="lib/axiom-impl-1.2.10.jar"/>
-	<classpathentry kind="lib" path="lib/axis2-adb-1.5.3.jar"/>
-	<classpathentry kind="lib" path="lib/axis2-kernel-1.5.3.jar"/>
-	<classpathentry kind="lib" path="lib/axis2-transport-http-1.5.3.jar"/>
-	<classpathentry kind="lib" path="lib/axis2-transport-local-1.5.3.jar"/>
-	<classpathentry kind="lib" path="lib/axis2-upload-client.jar"/>
-	<classpathentry kind="lib" path="lib/bcel-5.1.jar"/>
-	<classpathentry kind="lib" path="lib/cglib-nodep-2.1.jar"/>
-	<classpathentry kind="lib" path="lib/collections-generic-4.0.jar"/>
-	<classpathentry kind="lib" path="lib/commons-beanutils.jar"/>
-	<classpathentry kind="lib" path="lib/commons-codec-1.3.jar"/>
-	<classpathentry kind="lib" path="lib/commons-collections.jar"/>
-	<classpathentry kind="lib" path="lib/commons-digester.jar"/>
-	<classpathentry kind="lib" path="lib/commons-discovery.jar"/>
-	<classpathentry kind="lib" path="lib/commons-httpclient-3.1.jar"/>
-	<classpathentry kind="lib" path="lib/commons-lang-2.4.jar"/>
-	<classpathentry kind="lib" path="lib/commons-logging.jar"/>
-	<classpathentry kind="lib" path="lib/docking.jar"/>
-	<classpathentry kind="lib" path="lib/forms-1.0.5.jar"/>
-	<classpathentry kind="lib" path="lib/ginkgo-0.1-SNAPSHOT.jar"/>
-	<classpathentry kind="lib" path="lib/httpcore-4.0.jar"/>
-	<classpathentry kind="lib" path="lib/j3dcore.jar"/>
-	<classpathentry kind="lib" path="lib/j3dutils.jar"/>
-	<classpathentry kind="lib" path="lib/jai_codec.jar"/>
-	<classpathentry kind="lib" path="lib/jai_core.jar"/>
-	<classpathentry kind="lib" path="lib/jaxb-rt-1.0-ea.jar"/>
-	<classpathentry kind="lib" path="lib/jaxen.jar"/>
-	<classpathentry kind="lib" path="lib/jaxrpc.jar"/>
-	<classpathentry kind="lib" path="lib/jcommon-1.0.5.jar"/>
-	<classpathentry kind="lib" path="lib/jdom.jar"/>
-	<classpathentry kind="lib" path="lib/jfreechart-1.0.2.jar"/>
-	<classpathentry kind="lib" path="lib/jhall.jar"/>
-	<classpathentry kind="lib" path="lib/jsr173_api.jar"/>
-	<classpathentry kind="lib" path="lib/junit.jar"/>
-	<classpathentry kind="lib" path="lib/log4j-1.2.8.jar"/>
-	<classpathentry kind="lib" path="lib/mail.jar"/>
-	<classpathentry kind="lib" path="lib/neethi-2.0.4.jar"/>
-	<classpathentry kind="lib" path="lib/ostermillerutils_1_04_03_for_kaffe.jar"/>
-	<classpathentry kind="lib" path="lib/stax-1.2.0_rc1-dev.jar"/>
-	<classpathentry kind="lib" path="lib/vecmath.jar"/>
-	<classpathentry kind="lib" path="lib/wsdl4j-1.6.2.jar"/>
-	<classpathentry kind="lib" path="lib/xalan.jar"/>
-	<classpathentry kind="lib" path="lib/xml-apis.jar"/>
-	<classpathentry kind="lib" path="lib/XmlSchema-1.4.3.jar"/>
-	<classpathentry kind="lib" path="components/genspace/lib/ha-api.jar"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/genspace-common"/>
-	<classpathentry kind="output" path="classes"/>
-</classpath>
diff --git a/geworkbench-core/.svn/tmp/tempfile.tmp b/geworkbench-core/.svn/tmp/tempfile.tmp
deleted file mode 100644
index 10a48e5..0000000
--- a/geworkbench-core/.svn/tmp/tempfile.tmp
+++ /dev/null
@@ -1,72 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
-	<classpathentry kind="src" path="conf"/>
-	<classpathentry kind="src" path="src"/>
-	<classpathentry kind="src" path="annotation"/>
-	<classpathentry kind="src" path="test"/>
-	<classpathentry kind="src" path="components/caarray/src"/>
-	<classpathentry kind="src" path="components/genspace/src"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER">
-		<attributes>
-			<attribute name="owner.project.facets" value="java"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="lib" path="components/genspace/lib/intellij.jar"/>
-	<classpathentry kind="lib" path="components/genspace/lib/jgraphx.jar"/>
-	<classpathentry kind="lib" path="components/genspace/lib/jimi.jar"/>
-	<classpathentry kind="lib" path="components/genspace/lib/mina-core-1.1.7.jar"/>
-	<classpathentry kind="lib" path="components/genspace/lib/smack.jar"/>
-	<classpathentry kind="lib" path="components/genspace/lib/smackx.jar"/>
-	<classpathentry kind="lib" path="components/genspace/lib/swing-layout-1.0.3.jar"/>
-	<classpathentry kind="lib" path="lib/AffxFusion.jar"/>
-	<classpathentry kind="lib" path="lib/ant-launcher.jar"/>
-	<classpathentry kind="lib" path="lib/ant.jar"/>
-	<classpathentry kind="lib" path="lib/axiom-api-1.2.10.jar"/>
-	<classpathentry kind="lib" path="lib/axiom-impl-1.2.10.jar"/>
-	<classpathentry kind="lib" path="lib/axis2-adb-1.5.3.jar"/>
-	<classpathentry kind="lib" path="lib/axis2-kernel-1.5.3.jar"/>
-	<classpathentry kind="lib" path="lib/axis2-transport-http-1.5.3.jar"/>
-	<classpathentry kind="lib" path="lib/axis2-transport-local-1.5.3.jar"/>
-	<classpathentry kind="lib" path="lib/axis2-upload-client.jar"/>
-	<classpathentry kind="lib" path="lib/bcel-5.1.jar"/>
-	<classpathentry kind="lib" path="lib/cglib-nodep-2.1.jar"/>
-	<classpathentry kind="lib" path="lib/collections-generic-4.0.jar"/>
-	<classpathentry kind="lib" path="lib/commons-beanutils.jar"/>
-	<classpathentry kind="lib" path="lib/commons-codec-1.3.jar"/>
-	<classpathentry kind="lib" path="lib/commons-collections.jar"/>
-	<classpathentry kind="lib" path="lib/commons-digester.jar"/>
-	<classpathentry kind="lib" path="lib/commons-discovery.jar"/>
-	<classpathentry kind="lib" path="lib/commons-httpclient-3.1.jar"/>
-	<classpathentry kind="lib" path="lib/commons-lang-2.4.jar"/>
-	<classpathentry kind="lib" path="lib/commons-logging.jar"/>
-	<classpathentry kind="lib" path="lib/docking.jar"/>
-	<classpathentry kind="lib" path="lib/forms-1.0.5.jar"/>
-	<classpathentry kind="lib" path="lib/ginkgo-0.1-SNAPSHOT.jar"/>
-	<classpathentry kind="lib" path="lib/httpcore-4.0.jar"/>
-	<classpathentry kind="lib" path="lib/j3dcore.jar"/>
-	<classpathentry kind="lib" path="lib/j3dutils.jar"/>
-	<classpathentry kind="lib" path="lib/jai_codec.jar"/>
-	<classpathentry kind="lib" path="lib/jai_core.jar"/>
-	<classpathentry kind="lib" path="lib/jaxb-rt-1.0-ea.jar"/>
-	<classpathentry kind="lib" path="lib/jaxen.jar"/>
-	<classpathentry kind="lib" path="lib/jaxrpc.jar"/>
-	<classpathentry kind="lib" path="lib/jcommon-1.0.5.jar"/>
-	<classpathentry kind="lib" path="lib/jdom.jar"/>
-	<classpathentry kind="lib" path="lib/jfreechart-1.0.2.jar"/>
-	<classpathentry kind="lib" path="lib/jhall.jar"/>
-	<classpathentry kind="lib" path="lib/jsr173_api.jar"/>
-	<classpathentry kind="lib" path="lib/junit.jar"/>
-	<classpathentry kind="lib" path="lib/log4j-1.2.8.jar"/>
-	<classpathentry kind="lib" path="lib/mail.jar"/>
-	<classpathentry kind="lib" path="lib/neethi-2.0.4.jar"/>
-	<classpathentry kind="lib" path="lib/ostermillerutils_1_04_03_for_kaffe.jar"/>
-	<classpathentry kind="lib" path="lib/stax-1.2.0_rc1-dev.jar"/>
-	<classpathentry kind="lib" path="lib/vecmath.jar"/>
-	<classpathentry kind="lib" path="lib/wsdl4j-1.6.2.jar"/>
-	<classpathentry kind="lib" path="lib/xalan.jar"/>
-	<classpathentry kind="lib" path="lib/xml-apis.jar"/>
-	<classpathentry kind="lib" path="lib/XmlSchema-1.4.3.jar"/>
-	<classpathentry kind="lib" path="components/genspace/lib/ha-api.jar"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/genspace-common"/>
-	<classpathentry kind="output" path="classes"/>
-</classpath>
diff --git a/geworkbench-core/_all/.svn/entries b/geworkbench-core/_all/.svn/entries
index 2362468..483e714 100644
--- a/geworkbench-core/_all/.svn/entries
+++ b/geworkbench-core/_all/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8215
+8644
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/_all
 https://ncisvn.nci.nih.gov/svn/geworkbench

@@ -32,7 +32,7 @@ file



-2011-08-02T04:32:49.000000Z
+2011-08-17T00:10:35.000000Z
 e0bbdac04f36344bc47b9f7ad44a29fd
 2005-08-15T20:06:29.000000Z
 116
diff --git a/geworkbench-core/annotation/.svn/entries b/geworkbench-core/annotation/.svn/entries
index 936b074..8f8dd18 100644
--- a/geworkbench-core/annotation/.svn/entries
+++ b/geworkbench-core/annotation/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8215
+8644
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/annotation
 https://ncisvn.nci.nih.gov/svn/geworkbench

@@ -32,7 +32,7 @@ file



-2011-08-02T04:32:49.000000Z
+2011-08-17T00:10:35.000000Z
 103617ef7feed3b36e150b2d1e187927
 2005-07-28T22:36:56.000000Z
 50
@@ -66,7 +66,7 @@ file



-2011-08-02T04:32:49.000000Z
+2011-08-17T00:10:35.000000Z
 e92ac27624948d9845b772ec2ed929a7
 2005-07-28T22:36:56.000000Z
 50
@@ -100,7 +100,7 @@ file



-2011-08-02T04:32:49.000000Z
+2011-08-17T00:10:35.000000Z
 0eb70f5ad5896a9bd623fbc15281d885
 2005-07-28T22:36:56.000000Z
 50
@@ -134,7 +134,7 @@ file



-2011-08-02T04:32:49.000000Z
+2011-08-17T00:10:35.000000Z
 e80f2e17af587c577902100cdffe87db
 2005-07-28T22:36:56.000000Z
 50
@@ -168,7 +168,7 @@ file



-2011-08-02T04:32:49.000000Z
+2011-08-17T00:10:35.000000Z
 18344a9c5c28a1242444879670a63453
 2005-07-28T22:36:56.000000Z
 50
@@ -202,7 +202,7 @@ file



-2011-08-02T04:32:49.000000Z
+2011-08-17T00:10:35.000000Z
 866890614ddd858c8615b0de6050dedb
 2005-07-28T22:36:56.000000Z
 50
@@ -236,7 +236,7 @@ file



-2011-08-02T04:32:49.000000Z
+2011-08-17T00:10:35.000000Z
 080c8ad4ef273c74d51b39f02471a5bd
 2005-07-28T22:36:56.000000Z
 50
@@ -270,7 +270,7 @@ file



-2011-08-02T04:32:49.000000Z
+2011-08-17T00:10:35.000000Z
 4a6e98917af86a1c17674a3ef3068869
 2005-07-28T22:36:56.000000Z
 50
diff --git a/geworkbench-core/bin/.svn/entries b/geworkbench-core/bin/.svn/entries
index b2389b1..09f4395 100644
--- a/geworkbench-core/bin/.svn/entries
+++ b/geworkbench-core/bin/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8215
+8644
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/bin
 https://ncisvn.nci.nih.gov/svn/geworkbench

@@ -32,7 +32,7 @@ file



-2011-08-02T04:32:09.000000Z
+2011-12-29T06:11:16.000000Z
 eaf3f6e6969c579cf5a210c0501f993f
 2006-07-06T14:55:11.000000Z
 1613
diff --git a/geworkbench-core/bin/matrixreduce/.svn/entries b/geworkbench-core/bin/matrixreduce/.svn/entries
index 32b0f6e..7e975f6 100644
--- a/geworkbench-core/bin/matrixreduce/.svn/entries
+++ b/geworkbench-core/bin/matrixreduce/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8215
+8644
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/bin/matrixreduce
 https://ncisvn.nci.nih.gov/svn/geworkbench

@@ -32,7 +32,7 @@ file



-2011-08-02T04:32:09.000000Z
+2011-08-17T00:18:54.000000Z
 fdfc491740f0add6c2595f7203efa534
 2009-12-11T15:11:41.275428Z
 5821
@@ -66,7 +66,7 @@ file



-2011-08-02T04:32:09.000000Z
+2011-08-17T00:18:54.000000Z
 353d2f09522052122f68990a30f3456e
 2009-06-15T19:40:14.000000Z
 5242
@@ -100,7 +100,7 @@ file



-2011-08-02T04:32:09.000000Z
+2011-08-17T00:18:54.000000Z
 320d01e4d29c2b53fcac61c9596ea9f3
 2009-12-11T15:12:23.602469Z
 5822
diff --git a/geworkbench-core/build.xml b/geworkbench-core/build.xml
index 7150bc3..0daf382 100755
--- a/geworkbench-core/build.xml
+++ b/geworkbench-core/build.xml
@@ -106,6 +106,7 @@
 				<include name="celprocessing" />
 				<include name="cgems" />
 				<include name="colormosaic" />
+				<include name="cupid" />
 				<include name="cytoscape" />
 				<include name="discovery" />
 				<include name="evidenceintegration" />
@@ -511,13 +512,23 @@
 		</jar>
 		<jar destfile="geworkbench-others.jar" basedir="${classes}" excludes="org/geworkbench/bison/**,org/geworkbench/engine/**,org/geworkbench/events/**,org/geworkbench/parsers/**,org/geworkbench/util/**,org/geworkbench/builtin/**">
 		</jar>
+
+		<!-- jar components -->
+		<subant target="jar" genericantfile="build-component.xml">
+			<dirset dir="components">
+				<include name="analysis" />
+				<include name="ttest" />
+				<include name="hierarchicalclustering" />
+				<!-- exclude the dead projets -->
+				<exclude name="skylinecontour" />
+			</dirset>
+		</subant>
 	</target>
 	<!-- ====================================================================== -->
 	<!-- CREATE   DISTRIBUTION-->
 	<!-- ====================================================================== -->
 	<target name="createDist" depends="compile, jar" description="Creating a new folder for depositing...">
 		<java classname="org.geworkbench.components.versioninfo.VersionInfoDialog" failonerror="true" >
-			<arg value="2.2.1"/>
 			<arg value="./components/versioninfo/classes/org/geworkbench/components/versioninfo/" />
 			<classpath>
 				<path refid="classpath" />
diff --git a/geworkbench-core/cascripts/.svn/entries b/geworkbench-core/cascripts/.svn/entries
index d340d44..eb9d6f9 100644
--- a/geworkbench-core/cascripts/.svn/entries
+++ b/geworkbench-core/cascripts/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8215
+8644
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/cascripts
 https://ncisvn.nci.nih.gov/svn/geworkbench

@@ -32,7 +32,7 @@ file



-2011-08-02T04:26:14.000000Z
+2011-08-17T00:10:35.000000Z
 9831cd21fa385ec4ce97a3744d19fc72
 2007-06-21T18:52:02.000000Z
 3033
@@ -66,7 +66,7 @@ file



-2011-08-02T04:26:14.000000Z
+2011-08-17T00:10:35.000000Z
 23ee1fb373ca32a06711a8f080fe5310
 2007-05-10T17:37:53.000000Z
 2801
@@ -100,7 +100,7 @@ file



-2011-08-02T04:26:14.000000Z
+2011-08-17T00:10:35.000000Z
 7b81b0a496613cfb3165d7c9d02aa73f
 2007-06-21T17:19:43.000000Z
 3029
diff --git a/geworkbench-core/components/.svn/all-wcprops b/geworkbench-core/components/.svn/all-wcprops
index 73dec72..ded1c66 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/8215/trunk/geworkbench/components
+/svn/geworkbench/!svn/ver/8644/trunk/geworkbench/components
 END
diff --git a/geworkbench-core/components/.svn/entries b/geworkbench-core/components/.svn/entries
index 8a0098b..f50a387 100644
--- a/geworkbench-core/components/.svn/entries
+++ b/geworkbench-core/components/.svn/entries
@@ -1,15 +1,15 @@
 10

 dir
-8215
+8644
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2011-08-15T19:37:34.116726Z
-8215
-zji
+2011-12-23T16:28:44.773024Z
+8644
+poddutun



@@ -68,25 +68,28 @@ dir
 idea
 dir

+selectors
+dir
+
 ttest
 dir

-selectors
+anova
 dir

 pudge
 dir

-anova
+cupid
 dir

-promoter
+cutenet
 dir

 discovery
 dir

-cutenet
+promoter
 dir

 skyline
@@ -98,27 +101,27 @@ dir
 caarray
 dir

-analysis
-dir
-
 filtering
 dir

-normalization
+analysis
 dir

-cytoscape
+normalization
 dir

 foldchange
 dir

-sequences
+cytoscape
 dir

 geneontology2
 dir

+sequences
+dir
+
 matrixreduce
 dir

diff --git a/geworkbench-core/components/alignment/.svn/all-wcprops b/geworkbench-core/components/alignment/.svn/all-wcprops
index 798c87a..319e180 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/8213/trunk/geworkbench/components/alignment
+/svn/geworkbench/!svn/ver/8479/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 cee00a2..160dcfb 100644
--- a/geworkbench-core/components/alignment/.svn/entries
+++ b/geworkbench-core/components/alignment/.svn/entries
@@ -1,14 +1,14 @@
 10

 dir
-8215
+8644
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/alignment
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2011-08-15T19:17:06.034628Z
-8213
+2011-11-02T15:39:37.175113Z
+8479
 zji
 has-props

@@ -32,7 +32,7 @@ file



-2011-08-16T23:58:09.000000Z
+2011-09-19T15:08:49.000000Z
 bfd2fa0ba5a20c611e7f4db24315c284
 2011-08-15T19:17:06.034628Z
 8213
@@ -66,7 +66,7 @@ file



-2011-08-02T04:31:32.000000Z
+2011-08-17T00:10:36.000000Z
 9e2d827919a52896e7de632914215d60
 2010-08-13T17:26:58.088987Z
 6989
@@ -106,7 +106,7 @@ file



-2011-08-02T04:31:32.000000Z
+2011-08-17T00:10:36.000000Z
 d7948dcb85fc6b7eec16bd74108557cb
 2009-06-22T16:14:06.000000Z
 5296
diff --git a/geworkbench-core/components/alignment/lib/.svn/entries b/geworkbench-core/components/alignment/lib/.svn/entries
index 0966e53..8e38da3 100644
--- a/geworkbench-core/components/alignment/lib/.svn/entries
+++ b/geworkbench-core/components/alignment/lib/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8215
+8644
 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 5932b4f..a0108d8 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/8187/trunk/geworkbench/components/alignment/src
+/svn/geworkbench/!svn/ver/8479/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 c619152..ec5a962 100644
--- a/geworkbench-core/components/alignment/src/.svn/entries
+++ b/geworkbench-core/components/alignment/src/.svn/entries
@@ -1,14 +1,14 @@
 10

 dir
-8215
+8644
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/alignment/src
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2011-07-30T04:31:30.667242Z
-8187
+2011-11-02T15:39:37.175113Z
+8479
 zji


@@ -32,7 +32,7 @@ file



-2011-08-02T04:31:32.000000Z
+2011-08-17T00:10:36.000000Z
 37a464e03a158f1523c63278e9cd08c0
 2010-12-09T21:12:10.278328Z
 7317
diff --git a/geworkbench-core/components/alignment/src/org/.svn/all-wcprops b/geworkbench-core/components/alignment/src/org/.svn/all-wcprops
index 3e95e45..9b89740 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/8187/trunk/geworkbench/components/alignment/src/org
+/svn/geworkbench/!svn/ver/8479/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 89c303f..b112650 100644
--- a/geworkbench-core/components/alignment/src/org/.svn/entries
+++ b/geworkbench-core/components/alignment/src/org/.svn/entries
@@ -1,14 +1,14 @@
 10

 dir
-8215
+8644
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/alignment/src/org
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2011-07-30T04:31:30.667242Z
-8187
+2011-11-02T15:39:37.175113Z
+8479
 zji


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 c57b88a..eadbc3b 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/8187/trunk/geworkbench/components/alignment/src/org/geworkbench
+/svn/geworkbench/!svn/ver/8479/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 094ba73..1f8db2d 100644
--- a/geworkbench-core/components/alignment/src/org/geworkbench/.svn/entries
+++ b/geworkbench-core/components/alignment/src/org/geworkbench/.svn/entries
@@ -1,14 +1,14 @@
 10

 dir
-8215
+8644
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/alignment/src/org/geworkbench
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2011-07-30T04:31:30.667242Z
-8187
+2011-11-02T15:39:37.175113Z
+8479
 zji


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 4b9a4be..be785f4 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/8187/trunk/geworkbench/components/alignment/src/org/geworkbench/components
+/svn/geworkbench/!svn/ver/8479/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 8253d6d..0be46c5 100644
--- a/geworkbench-core/components/alignment/src/org/geworkbench/components/.svn/entries
+++ b/geworkbench-core/components/alignment/src/org/geworkbench/components/.svn/entries
@@ -1,14 +1,14 @@
 10

 dir
-8215
+8644
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/alignment/src/org/geworkbench/components
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2011-07-30T04:31:30.667242Z
-8187
+2011-11-02T15:39:37.175113Z
+8479
 zji


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 10903fb..c457a9c 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/8187/trunk/geworkbench/components/alignment/src/org/geworkbench/components/alignment
+/svn/geworkbench/!svn/ver/8479/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 7b83e18..06d2f99 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
@@ -1,14 +1,14 @@
 10

 dir
-8215
+8644
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/alignment/src/org/geworkbench/components/alignment
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2011-07-30T04:31:30.667242Z
-8187
+2011-11-02T15:39:37.175113Z
+8479
 zji


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 5359fdf..fa445c5 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
@@ -1,13 +1,7 @@
 K 25
 svn:wc:ra_dav:version-url
 V 116
-/svn/geworkbench/!svn/ver/8187/trunk/geworkbench/components/alignment/src/org/geworkbench/components/alignment/blast
-END
-BlastObj.java
-K 25
-svn:wc:ra_dav:version-url
-V 130
-/svn/geworkbench/!svn/ver/7378/trunk/geworkbench/components/alignment/src/org/geworkbench/components/alignment/blast/BlastObj.java
+/svn/geworkbench/!svn/ver/8455/trunk/geworkbench/components/alignment/src/org/geworkbench/components/alignment/blast
 END
 RemoteBlast.java
 K 25
@@ -15,15 +9,39 @@ svn:wc:ra_dav:version-url
 V 133
 /svn/geworkbench/!svn/ver/6930/trunk/geworkbench/components/alignment/src/org/geworkbench/components/alignment/blast/RemoteBlast.java
 END
-BlastAlgorithm.java
+BlastAnalysis.cwb.xml
+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/BlastAnalysis.cwb.xml
+END
+BlastAnalysis.java
 K 25
 svn:wc:ra_dav:version-url
-V 136
-/svn/geworkbench/!svn/ver/7316/trunk/geworkbench/components/alignment/src/org/geworkbench/components/alignment/blast/BlastAlgorithm.java
+V 135
+/svn/geworkbench/!svn/ver/8455/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
+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
 END
 NCBIBlastParser.java
 K 25
 svn:wc:ra_dav:version-url
 V 137
-/svn/geworkbench/!svn/ver/8187/trunk/geworkbench/components/alignment/src/org/geworkbench/components/alignment/blast/NCBIBlastParser.java
+/svn/geworkbench/!svn/ver/8455/trunk/geworkbench/components/alignment/src/org/geworkbench/components/alignment/blast/NCBIBlastParser.java
+END
+ParameterSetting.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/ParameterSetting.java
 END
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 8d3c1f0..752f9ed 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
-8215
+8644
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/alignment/src/org/geworkbench/components/alignment/blast
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2011-07-30T04:31:30.667242Z
-8187
-zji
+2011-10-24T22:06:10.214128Z
+8455
+youmi



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

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

-BlastObj.java
+RemoteBlast.java
 file




-2011-08-02T04:31:32.000000Z
-7ce9adbb878aebef7b6765dc789e1c9b
-2011-01-11T17:08:21.747681Z
-7378
-maz
+2011-08-17T00:10:37.000000Z
+ee212f0af17f3d94c3eb804aad3099b8
+2010-07-29T19:01:21.942013Z
+6930
+zji
 has-props


@@ -58,19 +58,53 @@ has-props



-12074
+9932

-RemoteBlast.java
+BlastAnalysis.cwb.xml
 file




-2011-08-02T04:31:32.000000Z
-ee212f0af17f3d94c3eb804aad3099b8
-2010-07-29T19:01:21.942013Z
-6930
-zji
+2011-12-29T06:11:37.000000Z
+e3cbfdb00760a9bd48bf8d09bb43298c
+2011-10-04T16:02:03.460589Z
+8362
+youmi
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+1556
+
+BlastAnalysis.java
+file
+
+
+
+
+2011-12-29T06:11:37.000000Z
+0447b7d1a9057d478f398aac00278185
+2011-10-24T22:06:10.214128Z
+8455
+youmi
 has-props


@@ -92,19 +126,53 @@ has-props



-9932
+14604
+
+BlastAnalysisPanel.java
+file
+
+
+
+
+2011-12-29T06:11:37.000000Z
+39f1be5e7d6614131b87036e37e1e122
+2011-10-05T20:25:11.006171Z
+8366
+zji
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+52298

-BlastAlgorithm.java
+AlgorithmMatcher.java
 file




-2011-08-02T04:31:32.000000Z
-dcf3ac92577d85e3c19e873083ee6e7a
-2010-12-09T19:57:45.788737Z
-7316
-maz
+2011-12-29T06:11:37.000000Z
+6638b891f433914fe3b1f7d0a791fa59
+2011-10-04T16:02:03.460589Z
+8362
+youmi
 has-props


@@ -126,7 +194,7 @@ has-props



-13440
+29704

 NCBIBlastParser.java
 file
@@ -134,11 +202,45 @@ file



-2011-08-02T04:31:32.000000Z
-90317133a88632636ec6eaf9bfd12888
-2011-07-30T04:31:30.667242Z
-8187
-zji
+2011-12-29T06:11:37.000000Z
+ccb51674e9d247685c606d68abe661c1
+2011-10-24T22:06:10.214128Z
+8455
+youmi
+has-props
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+9229
+
+ParameterSetting.java
+file
+
+
+
+
+2011-12-29T06:11:37.000000Z
+e4b3981b11f5e27a0b8e2f94e6fd27cd
+2011-10-04T16:02:03.460589Z
+8362
+youmi
 has-props


@@ -160,5 +262,5 @@ has-props



-9154
+7367

diff --git a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/.svn/prop-base/BlastAlgorithm.java.svn-base b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/.svn/prop-base/BlastAlgorithm.java.svn-base
deleted file mode 100644
index 8df8946..0000000
--- a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/.svn/prop-base/BlastAlgorithm.java.svn-base
+++ /dev/null
@@ -1,9 +0,0 @@
-K 14
-svn:executable
-V 1
-*
-K 12
-svn:keywords
-V 2
-Id
-END
diff --git a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/.svn/prop-base/BlastObj.java.svn-base b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/.svn/prop-base/BlastObj.java.svn-base
deleted file mode 100644
index 8df8946..0000000
--- a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/.svn/prop-base/BlastObj.java.svn-base
+++ /dev/null
@@ -1,9 +0,0 @@
-K 14
-svn:executable
-V 1
-*
-K 12
-svn:keywords
-V 2
-Id
-END
diff --git a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/.svn/text-base/BlastAlgorithm.java.svn-base b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/.svn/text-base/BlastAlgorithm.java.svn-base
deleted file mode 100644
index 7012f18..0000000
--- a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/.svn/text-base/BlastAlgorithm.java.svn-base
+++ /dev/null
@@ -1,386 +0,0 @@
-package org.geworkbench.components.alignment.blast;
-
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileReader;
-import java.io.IOException;
-import java.util.Date;
-import java.util.concurrent.ExecutionException;
-
-import javax.swing.JOptionPane;
-import javax.swing.SwingWorker;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-import org.geworkbench.bison.datastructure.biocollections.sequences.CSSequenceSet;
-import org.geworkbench.bison.datastructure.biocollections.sequences.DSSequenceSet;
-import org.geworkbench.bison.datastructure.bioobjects.sequence.CSAlignmentResultSet;
-import org.geworkbench.bison.datastructure.bioobjects.sequence.CSSequence;
-import org.geworkbench.bison.datastructure.bioobjects.sequence.DSSequence;
-import org.geworkbench.bison.util.RandomNumberGenerator;
-import org.geworkbench.builtin.projects.ProjectPanel;
-import org.geworkbench.components.alignment.blast.RemoteBlast.NcbiResponseException;
-import org.geworkbench.components.alignment.blast.RemoteBlast.Status;
-import org.geworkbench.components.alignment.panels.AlgorithmMatcher;
-import org.geworkbench.components.alignment.panels.BlastAppComponent;
-import org.geworkbench.components.alignment.panels.ParameterSetting;
-import org.geworkbench.events.ProjectNodeAddedEvent;
-import org.geworkbench.util.BrowserLauncher;
-import org.geworkbench.util.FilePathnameUtils;
-
-/**
- * BlastAlgorithm.
- *
- * @author XZ
- * @author zji
- * @version $Id$
- */
-public class BlastAlgorithm extends SwingWorker<CSAlignmentResultSet, Integer> {
-
-	static private Log log = LogFactory.getLog(RemoteBlast.class);
-
-	private BlastAppComponent blastAppComponent = null;
-
-	private boolean startBrowser;
-	private boolean jobFinished = false;
-
-	private ParameterSetting parameterSetting;
-
-	private CSSequenceSet<CSSequence> sequenceDB;
-	private DSSequenceSet<? extends DSSequence> parentSequenceDB;
-
-	private final static int TIMEGAP = 4000;
-	private final static String LINEBREAK = System.getProperty("line.separator");
-
-	public void setBlastAppComponent(BlastAppComponent _blastAppComponent) {
-		blastAppComponent = _blastAppComponent;
-	}
-
-	/**
-	 * Update Progress with finished percentage and related information.
-	 *
-	 * @param percent
-	 *            double
-	 * @param text
-	 *            String
-	 */
-	void updateProgressStatus(final double percent, final String text) {
-		if (blastAppComponent != null) {
-			blastAppComponent.updateProgressBar(percent, text);
-		}
-	}
-
-	/**
-	 * Update progress only with String information.
-	 *
-	 * @param text
-	 *            String
-	 */
-	void updateStatus(String text) {
-		if (blastAppComponent != null) {
-			blastAppComponent.updateProgressBar(text);
-		}
-	}
-
-	/**
-	 * Update the component's progressBar with information and reset the
-	 * ProgressBar.
-	 *
-	 * @param boo
-	 *            boolean
-	 * @param text
-	 *            String
-	 */
-
-	void updateStatus(boolean boo, String text) {
-		if (blastAppComponent != null) {
-			blastAppComponent.updateProgressBar(boo, text);
-		}
-	}
-
-	/**
-	 * Show error message and update status
-	 *
-	 * @param e
-	 */
-	private void processExceptionFromNcbi(Exception e, CSSequence sequence) {
-		if (blastAppComponent != null) {
-			String exceptionName = e.getClass().getName();
-			blastAppComponent.reportError("Sequence " + sequence
-					+ " cannot be blasted due to " + exceptionName + ":\n"
-					+ e.getMessage(), "Error: " + exceptionName);
-
-		}
-		updateStatus(false, "NCBI Blast is stopped at " + new Date());
-	}
-
-	/**
-	 * The workhorse to run Blast program.
-	 *
-	 * This method is invoked by from the working thread.
-	 */
-	@Override
-	protected CSAlignmentResultSet doInBackground() throws Exception {
-		if (sequenceDB == null || parentSequenceDB == null) {
-			throw new Exception("null sequenceDB or null parentSequenceDB");
-		}
-
-		String tempFolder = FilePathnameUtils.getTemporaryFilesDirectoryPath();
-
-		/* generate a new file name for the coming output file. */
-		String outputFile = tempFolder + "Blast"
-				+ RandomNumberGenerator.getID() + ".html";
-
-		RemoteBlast blast;
-		DSSequenceSet<? extends DSSequence> parentSequenceSet = parentSequenceDB;
-
-		for (CSSequence sequence : sequenceDB) {
-			updateStatus("Uploading sequence: " + sequence);
-			blast = new RemoteBlast(sequence.getSequence(), outputFile, AlgorithmMatcher
-					.translateToCommandline(parameterSetting));
-			String BLAST_rid = null;
-			try {
-				BLAST_rid = blast.submitBlast();
-			} catch (NcbiResponseException e1) {
-				processExceptionFromNcbi(e1, sequence);
-				return null;
-			}
-			if (isCancelled()) {
-				return null;
-			}
-			if (BLAST_rid == null) {
-				if (blastAppComponent != null) {
-					blastAppComponent
-							.reportError(
-									"Sequence "
-											+ sequence
-											+ " cannot be blasted, please check your parameters.",
-									"Parameter Error");
-
-				}
-				updateStatus(false, "NCBI Blast is stopped at "
-						+ new Date());
-				return null;
-
-			}
-			updateStatus("The Request ID is : " + BLAST_rid);
-
-			String resultURLString = "http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&FORMAT_TYPE=HTML&RID="
-					+ BLAST_rid;
-			Status status = blast.retrieveResult(resultURLString);
-			while(status==Status.WAITING && !isCancelled()) {
-				updateStatus("For sequence " + sequence
-						+ ",  the blast job is running. ");
-				try {
-					Thread.sleep(TIMEGAP);
-				} catch (InterruptedException e) {
-					// do nothing
-				}
-				status = blast.retrieveResult(resultURLString);
-			}
-			if(isCancelled()) return null;
-			else if(status!=Status.READY) {
-				String msg = parseError(outputFile);
-				processExceptionFromNcbi(new Exception(msg), sequence);
-				return null;
-			}
-		}
-		if(isCancelled()){
-			updateStatus(false, "NCBI Blast is canceled at " + new Date());
-			return null;
-		}
-		updateStatus(false, "NCBI Blast is finisheded at " + new Date());
-		String outputFilePath = "file://"
-				+ new File(outputFile).getAbsolutePath();
-		if (parameterSetting.isViewInBrowser()) {
-			if ((new File(outputFile)).canRead()) {
-				try {
-					String osName = System.getProperty("os.name");
-					if (osName.startsWith("Mac OS")) {
-						BrowserLauncher.openURL(outputFilePath);
-					} else {
-						BrowserLauncher.openURL("file:///"+new File(outputFile)
-								.getAbsolutePath().replace("\\", "/").replace(" ", "%20"));
-					}
-				} catch (Exception ex) {
-					ex.printStackTrace();
-					JOptionPane.showMessageDialog(null,
-							"No web browser can be launched, the result is saved at "
-									+ outputFile, "No Web Browser",
-							JOptionPane.ERROR_MESSAGE);
-
-				}
-			} else {
-
-				JOptionPane.showMessageDialog(null,
-						"The result cannot be read at " + outputFile,
-						"File cannot be read", JOptionPane.ERROR_MESSAGE);
-
-			}
-
-		}
-
-		CSAlignmentResultSet blastResult = new CSAlignmentResultSet(outputFile, sequenceDB
-				.getFASTAFileName(), sequenceDB, parentSequenceSet);
-		blastResult.setLabel(BlastAppComponent.NCBILABEL);
-		ProjectNodeAddedEvent event = new ProjectNodeAddedEvent(null, null,
-				blastResult);
-		if(isCancelled())return null;
-		blastAppComponent.publishProjectNodeAddedEvent(event);
-		log.debug("blast result node added");
-		return blastResult;
-	}
-
-	private static String parseError(String outputFile) {
-		BufferedReader br = null;
-		try {
-			br = new BufferedReader(new FileReader(outputFile));
-			String line = br.readLine();
-			while(line!=null) {
-				int index = line.indexOf("Error: ");
-				if(index>=0) {
-					int index2 = line.indexOf("</font>", index);
-					return line.substring(index, index2);
-				}
-				line = br.readLine();
-			}
-		} catch (FileNotFoundException e) {
-			// TODO Auto-generated catch block
-			e.printStackTrace();
-			return "FileNotFoundException in parsing error";
-		} catch (IOException e) {
-			// TODO Auto-generated catch block
-			e.printStackTrace();
-			return "IOException in parsing error";
-		} finally {
-			try {
-				br.close();
-			} catch (IOException e) {
-			}
-		}
-		return "Other error (not able to be parsed)";
-	}
-
-	@Override
-    protected void done() {
-		if(isCancelled())return;
-
-		CSAlignmentResultSet blastResult;
-		try {
-			blastResult = get();
-			if (blastResult==null)return;
-
-			String historyStr = generateHistoryStr(sequenceDB);
-			ProjectPanel.addToHistory(blastResult, historyStr);
-		} catch (InterruptedException e) {
-			// TODO Auto-generated catch block
-			e.printStackTrace();
-		} catch (ExecutionException e) {
-			// TODO Auto-generated catch block
-			e.printStackTrace();
-		}
-    }
-
-	private String generateHistoryStr(CSSequenceSet<CSSequence> activeSequenceDB) {
-		String histStr = "";
-		if(parameterSetting!=null){
-
-			// Header
-			histStr += "Blast run with the following parameters:\n";
-			histStr += "----------------------------------------\n";
-
-				String dbName=parameterSetting.getDbName();
-				histStr += "Database: " + dbName + LINEBREAK;
-				histStr += "BLAST Program: " + parameterSetting.getProgramName() + LINEBREAK;
-
-				histStr += "Exclude of Models(XM/XP): " + parameterSetting.isExcludeModelsOn() + LINEBREAK;
-				histStr += "Exclude of Uncultured/environmental sequences: " + parameterSetting.isExcludeUncultureOn() + LINEBREAK;
-				if (parameterSetting.getFromQuery()!=null)
-					histStr +="Query subrange from: "+parameterSetting.getFromQuery() +LINEBREAK;
-				if (parameterSetting.getToQuery()!=null)
-					histStr +="Query subrange to: "+parameterSetting.getToQuery() +LINEBREAK;
-				if(parameterSetting.getEntrezQuery()!=null)
-					histStr += "Entrez Query: "+parameterSetting.getEntrezQuery() + LINEBREAK;
-				if(parameterSetting.getProgramName().equalsIgnoreCase("blastn")){
-					String optimizeFor="";
-					if (parameterSetting.isMegaBlastOn()) optimizeFor="Highly similar sequences (megablast)";
-					else if(parameterSetting.isDiscontiguousOn()) optimizeFor="More dissimilar sequences (discontiguous megablast)";
-					else optimizeFor="Optimize for Somewhat similar sequences (blastn)";
-					histStr += "Optimize For: " + optimizeFor + LINEBREAK;
-				}
-				if (parameterSetting.getProgramName().equalsIgnoreCase("blastx")||parameterSetting.getProgramName().equalsIgnoreCase("tblastx")){
-					histStr += "Genetic Code: " + parameterSetting.getGeneticCode() + LINEBREAK;
-				}
-
-				histStr += "Short Queries: " + parameterSetting.isShortQueriesOn()+ LINEBREAK;
-
-				histStr += "Expect: " + parameterSetting.getExpect() + LINEBREAK;
-				histStr += "Word Size: " + parameterSetting.getWordsize() + LINEBREAK;
-				histStr += "Max match in a query range: "+parameterSetting.getHspRange()+ LINEBREAK;
-				if(!parameterSetting.getProgramName().equalsIgnoreCase("blastn"))
-					histStr += "Matrix: " + parameterSetting.getMatrix() + LINEBREAK;
-				histStr += "Match/mismatch Scores: " + parameterSetting.getMatchScores() + LINEBREAK;
-				histStr += "Gap Cost: " + parameterSetting.getGapCost() + LINEBREAK;
-				if (parameterSetting.getProgramName().equalsIgnoreCase("blastp")||parameterSetting.getProgramName().equalsIgnoreCase("tblastn")){
-					histStr += "Compositional Adjustment: " + parameterSetting.getCompositionalAdjustment()+ LINEBREAK;
-				}
-				histStr += "Low Complexity Filter On: " + parameterSetting.isLowComplexityFilterOn() + LINEBREAK;
-				if(parameterSetting.getProgramName().equalsIgnoreCase("blastn")){
-					histStr += "Species-specific repeats Filter On: " + parameterSetting.isHumanRepeatFilterOn() + LINEBREAK;
-					histStr += "Species-specific repeats Filter For: " + parameterSetting.getSpeciesRepeat() + LINEBREAK;
-				}
-				histStr += "Mask Low Case: " + parameterSetting.isMaskLowCase() + LINEBREAK;
-				histStr += "Mask Lookup Table: " + parameterSetting.isMaskLookupTable() + LINEBREAK;
-				if(parameterSetting.isDiscontiguousOn()&&parameterSetting.getProgramName().equalsIgnoreCase("blastn")){
-					histStr += "Template Length: " + parameterSetting.getTemplateLength() + LINEBREAK;
-					histStr += "Template Type: " + parameterSetting.getTemplateType() + LINEBREAK;
-				}
-
-				histStr += "Number of Sequences: " + activeSequenceDB.size() + LINEBREAK;
-				for (CSSequence marker : activeSequenceDB) {
-					histStr += "\t" + marker.getLabel() + "\n";
-				}
-		}
-		return histStr;
-	}
-
-	public boolean isStartBrowser() {
-		return startBrowser;
-	}
-
-	public BlastAppComponent getBlastAppComponent() {
-		return blastAppComponent;
-	}
-
-	public ParameterSetting getParameterSetting() {
-		return parameterSetting;
-	}
-
-	public boolean isJobFinished() {
-		return jobFinished;
-	}
-
-	public void setStartBrowser(boolean startBrowser) {
-		this.startBrowser = startBrowser;
-	}
-
-	public void setParameterSetting(ParameterSetting parameterSetting) {
-		this.parameterSetting = parameterSetting;
-	}
-
-	public void setJobFinished(boolean jobFinished) {
-		this.jobFinished = jobFinished;
-	}
-
-	public void setSequenceDB(CSSequenceSet<CSSequence> sequenceDB) {
-		this.sequenceDB = sequenceDB;
-
-	}
-
-	public void setParentSequenceDB(DSSequenceSet<? extends DSSequence> parentSequenceDB) {
-		this.parentSequenceDB = parentSequenceDB;
-
-	}
-
-}
diff --git a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/.svn/text-base/BlastObj.java.svn-base b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/.svn/text-base/BlastObj.java.svn-base
deleted file mode 100644
index f219faf..0000000
--- a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/.svn/text-base/BlastObj.java.svn-base
+++ /dev/null
@@ -1,538 +0,0 @@
-package org.geworkbench.components.alignment.blast;
-
-import java.io.BufferedReader;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.net.URL;
-
-import org.apache.commons.httpclient.DefaultHttpMethodRetryHandler;
-import org.apache.commons.httpclient.HttpClient;
-import org.apache.commons.httpclient.HttpException;
-import org.apache.commons.httpclient.HttpStatus;
-import org.apache.commons.httpclient.cookie.CookiePolicy;
-import org.apache.commons.httpclient.methods.GetMethod;
-import org.apache.commons.httpclient.params.HttpMethodParams;
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-import org.geworkbench.bison.datastructure.bioobjects.sequence.CSSequence;
-
-/**
- * BlastObj.java A class to hold information about each individual hit of a
- * Blast database search on a protein sequence. <br>
- *
- * @author zji
- * @version $Id$
- */
-public class BlastObj {
-	private static Log log = LogFactory.getLog(BlastObj.class);
-
-	/**
-	 * The Database ID of the protein sequence hit in this BlastObj.
-	 */
-	String databaseID;
-	/**
-	 * Set up the upper boundary of whole sequence size.
-	 */
-	static final int MAXSEQUENCESIZE = 100000;
-	int maxSize = MAXSEQUENCESIZE;
-
-	/**
-	 * The accession number of the protein sequence hit in this BlastObj.
-	 */
-	String name;
-	/**
-	 * The description of the protein sequence hit in this BlastObj.
-	 */
-	String description;
-	/**
-	 * The percentage of the query that's aligned with protein sequence hit in
-	 * this BlastObj.
-	 */
-	int percentAligned;
-
-	/**
-	 * The percentage of the alignment of query and hit in this BlastObj that's
-	 * gapped.
-	 */
-	int percentGapped = 0;
-
-	/**
-	 * The percentage of the alignment of query and hit in this BlastObj that's
-	 * "positive"/conserved.
-	 */
-	int percentPos;
-
-	/**
-	 * The score of the alignment of query and hit in this BlastObj; initialized
-	 * to -1.
-	 */
-	int score = -1;
-
-	/**
-	 * The score of the alignment of query and hit in this BlastObj.
-	 */
-	String evalue;
-	/**
-	 * The length of the alignment of query and hit in this BlastObj.
-	 */
-	int length;
-	String seqID;
-	int[] subject_align = new int[2];
-
-	/**
-	 * The 2 element array containing the position in query sequence where the
-	 * alignment start and stop. change to public for temp.
-	 *
-	 * @todo add getter method later.
-	 */
-	public int[] query_align = new int[2];
-	/**
-	 * The String of query sequence in alignment with hit in this BlastObj.
-	 */
-	String query;
-	/**
-	 * The String of hit sequence in this BlastObj in alignment with query
-	 * sequence.
-	 */
-	String subject;
-	/**
-	 * The String of alignment sequence between query sequence and hit in this
-	 * BlastObj.
-	 */
-	String align;
-	/**
-	 * whether this BlastObj is included in the MSA analysis
-	 */
-	boolean include = false;
-	/**
-	 * check whether the whole sequece can be retrived.
-	 */
-	boolean retriveWholeSeq = false;
-
-	/**
-	 * the URL of hit info
-	 */
-	URL infoURL;
-	/**
-	 * URL of seq.
-	 */
-	URL seqURL;
-	private String detailedAlignment = "";
-	private String identity;
-	private int startPoint;
-	private int alignmentLength;
-	private int endPoint;
-
-	public BlastObj(boolean retriveWholeSeq, String databaseID, String name, String description,
-			String score, String evalue) {
-		this.retriveWholeSeq = retriveWholeSeq;
-		this.databaseID = databaseID;
-		this.description = description;
-		this.name = name;
-
-		try {
-			this.score = Integer.parseInt(score);
-		} catch (NumberFormatException e) {
-			// ignored
-		}
-
-		this.evalue = evalue;
-	}
-
-	/* Get methods for class variables. */
-
-	/**
-	 * Returns the database name of the hit sequence stored in this BlastObj.
-	 *
-	 * @return the accession number as a String.
-	 */
-	public String getDatabaseID() {
-		return databaseID;
-	}
-
-	/**
-	 * Returns the accession number of the hit sequence stored in this BlastObj.
-	 *
-	 * @return the accession number as a String.
-	 */
-
-	/**
-	 * Returns the description of the hit protein sequence stored in this
-	 * BlastObj.
-	 *
-	 * @return the description as a String.
-	 */
-	public String getDescription() {
-		return description;
-	}
-
-	/**
-	 * Returns the length of the alignment of query and hit seq stored in this
-	 * BlastObj.
-	 *
-	 * @return the length as an int.
-	 */
-
-	/**
-	 * Returns the percentage of the query that's aligned with protein sequence
-	 * hit in this BlastObj.
-	 *
-	 * @return percentAligned as an int.
-	 */
-
-	public int getPercentAligned() {
-		return percentAligned;
-	}
-
-	/**
-	 * Returns the percentage of the alignment that's gapped with protein
-	 * sequence hit in this BlastObj.
-	 *
-	 * @return percentGapped as an int.
-	 */
-	public int getPercentGapped() {
-		return percentGapped;
-	}
-
-	/**
-	 * Returns the percentage of the query that's conserved with protein
-	 * sequence hit in this BlastObj.
-	 *
-	 * @return percentPos as an int.
-	 */
-	public int getPercentPos() {
-		return percentPos;
-	}
-
-	/**
-	 * Returns the score of the alignment of query and protein sequence hit in
-	 * this BlastObj.
-	 *
-	 * @return score as an int.
-	 */
-	public int getScore() {
-		return score;
-	}
-
-	/**
-	 * Returns the e-value of the alignment of query and protein sequence hit in
-	 * this BlastObj.
-	 *
-	 * @return evalue as a String.
-	 */
-	public String getEvalue() {
-		return evalue;
-	}
-
-	/**
-	 * Returns the query in alignment with protein sequence hit in this
-	 * BlastObj.
-	 *
-	 * @return query as a String.
-	 */
-	public String getQuery() {
-		return query;
-	}
-
-	/**
-	 * Returns the protein sequence hit in this BlastObj in alignment with the
-	 * query.
-	 *
-	 * @return subject as a String.
-	 */
-	public String getSubject() {
-		return subject;
-	}
-
-	/**
-	 * Returns the alignment of query and protein sequence hit in this BlastObj.
-	 *
-	 * @return align as an String.
-	 */
-	public String getAlign() {
-		return align;
-	}
-
-	/**
-	 * Returns whether this BlastObj is included in MSA analysis.
-	 *
-	 * @return include as a Boolean.
-	 */
-	public boolean getInclude() {
-		return include;
-	}
-
-	/* Set methods for class variables */
-
-	/**
-	 * Sets the percentage of the query that's aligned with protein sequence hit
-	 * in this BlastObj.
-	 *
-	 * @param i,
-	 *            the new alignment percentage of this BlastObj.
-	 */
-	public void setPercentAligned(int i) {
-		percentAligned = i;
-	}
-
-	/**
-	 * Sets the percentage of the alignment that's gapped of query and hit
-	 * protein sequence hit in this BlastObj.
-	 *
-	 * @param i,
-	 *            the new gapped percentage of this BlastObj.
-	 */
-	public void setPercentGapped(int i) {
-		percentGapped = i;
-	}
-
-	/**
-	 * Sets the percentage of the query that's conserved with protein sequence
-	 * hit in this BlastObj.
-	 *
-	 * @param i,
-	 *            the new conserved percentage of this BlastObj.
-	 */
-
-	public void setPercentPos(int i) {
-		percentPos = i;
-	}
-
-	/**
-	 * Sets the query sequence of the alignment with protein sequence hit in
-	 * this BlastObj.
-	 *
-	 * @param s,
-	 *            the new query seq of this BlastObj.
-	 */
-	public void setQuery(String s) {
-		query = s;
-	}
-
-	/**
-	 * Sets hit protein sequence hit in this BlastObj in alignment w/ the query.
-	 *
-	 * @param s,
-	 *            the new subject seq of this BlastObj.
-	 */
-	public void setSubject(String s) {
-		subject = s;
-	}
-
-	/**
-	 * Sets the alignment sequence of the query with protein sequence hit in
-	 * this BlastObj.
-	 *
-	 * @param s,
-	 *            the new align seq of this BlastObj.
-	 */
-	public void setAlign(String s) {
-		align = s;
-	}
-
-	/**
-	 * Sets whether this BlastObj is included in MSA analysis.
-	 *
-	 * @param b,
-	 *            the new include Boolean of this BlastObj.
-	 */
-	public void setInclude(boolean b) {
-		include = b;
-	}
-
-	public URL getInfoURL() {
-		return infoURL;
-	}
-
-	public void setInfoURL(URL infoURL) {
-		this.infoURL = infoURL;
-	}
-
-	public URL getSeqURL() {
-		return seqURL;
-	}
-
-	public void setSeqURL(URL seqURL) {
-		this.seqURL = seqURL;
-	}
-
-	public boolean isRetriveWholeSeq() {
-		return retriveWholeSeq;
-	}
-
-	public String getName() {
-		return name;
-	}
-
-	public int getLength() {
-		return length;
-	}
-
-	public void setLength(int length) {
-		this.length = length;
-	}
-
-	public String getDetailedAlignment() {
-		return detailedAlignment;
-	}
-
-	public void setDetailedAlignment(String detailedAlignment) {
-		this.detailedAlignment = detailedAlignment;
-	}
-
-	public String toString() {
-		return databaseID + detailedAlignment + score + evalue;
-	}
-
-	public CSSequence getAlignedSeq() {
-		CSSequence seq = new CSSequence(">" + databaseID + "|" + name
-				+ "---PARTIALLY INCLUDED", subject);
-
-		return seq;
-
-	}
-
-	/**
-	 * Create Entrez Programming Utilities query URL from web query URL.
-	 *
-	 * @param queryUrl
-	 * @return
-	 */
-	private static String EUtilsUrl(String queryUrl) {
-		// parse GI from the url
-		final String proteinUrl = "http://www.ncbi.nlm.nih.gov/protein/";
-		final String nucleotideUrl = "http://www.ncbi.nlm.nih.gov/nucleotide/";
-		int indexQ = queryUrl.indexOf("?");
-		String GI = null;
-		String databaseName = null;
-		if(indexQ==-1) {
-			log.error("unexpected query URL format :"+queryUrl);
-			return null;
-		} else if(queryUrl.startsWith(proteinUrl)) {
-			GI = queryUrl.substring(proteinUrl.length(), indexQ);
-			databaseName = "protein";
-		} else if(queryUrl.startsWith(nucleotideUrl)) {
-			GI = queryUrl.substring(nucleotideUrl.length(), indexQ);
-			databaseName = "nucleotide";
-		} else {
-			log.error("unexpected query URL format :"+queryUrl);
-			return null;
-		}
-
-		return "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db="+databaseName+"&id="
-				+ GI + "&rettype=fasta";
-	}
-
-	/**
-	 * getWholeSeq
-	 *
-	 * @return Object
-	 */
-	public CSSequence getWholeSeq() {
-
-		if (!retriveWholeSeq ) {
-			// this field is kept for now, but never set false
-			log.error("retriveWholeSeq is false");
-			return null;
-		}
-		if (seqURL == null)
-			return null;
-
-		log.debug("URL" + seqURL);
-		HttpClient client = new HttpClient();
-		DefaultHttpMethodRetryHandler retryhandler = new DefaultHttpMethodRetryHandler(
-				10, true);
-		client.getParams().setParameter(HttpMethodParams.RETRY_HANDLER,
-				retryhandler);
-		client.getParams().setCookiePolicy(CookiePolicy.IGNORE_COOKIES);
-
-		GetMethod getMethod = new GetMethod(EUtilsUrl(seqURL.toString()));
-		String sequenceLabel = null, sequence = null;
-		try {
-			int statusCode = client.executeMethod(getMethod);
-
-			if (statusCode == HttpStatus.SC_OK) {
-				InputStream stream = getMethod.getResponseBodyAsStream();
-				BufferedReader in = new BufferedReader(new InputStreamReader(
-						stream));
-				sequenceLabel = in.readLine();
-				StringBuilder sb = new StringBuilder();
-				String line = null;
-				while ((line = in.readLine()) != null) {
-					if (line.trim().length() > 0)
-						sb.append(line).append('\n');
-				}
-				stream.close();
-				sequence = sb.toString();
-			} else {
-				log.error("E Utilties failed for " + seqURL);
-				log.error("status code=" + statusCode);
-				return null;
-			}
-		} catch (HttpException e) {
-			e.printStackTrace();
-			return null;
-		} catch (IOException e) {
-			e.printStackTrace();
-			return null;
-		} finally {
-			getMethod.releaseConnection();
-		}
-
-		log.debug("label\n" + sequenceLabel);
-		log.debug("sequence\n" + sequence);
-		return new CSSequence(sequenceLabel, sequence);
-	}
-
-	public String getSeqID() {
-		return seqID;
-	}
-
-	public void setSeqID(String seqID) {
-		this.seqID = seqID;
-	}
-
-	public String getIdentity() {
-		return identity;
-	}
-
-	public int getStartPoint() {
-
-		return startPoint;
-	}
-
-	public int getAlignmentLength() {
-		return alignmentLength;
-	}
-
-	public int getEndPoint() {
-		return endPoint;
-	}
-
-	public int getMaxSize() {
-		return maxSize;
-	}
-
-	public void setIdentity(String identity) {
-		this.identity = identity;
-	}
-
-	public void setStartPoint(int startPoint) {
-
-		this.startPoint = startPoint;
-	}
-
-	public void setAlignmentLength(int alignmentLength) {
-		this.alignmentLength = alignmentLength;
-	}
-
-	public void setEndPoint(int endPoint) {
-		this.endPoint = endPoint;
-	}
-
-	public void setMaxSize(int maxSize) {
-		this.maxSize = maxSize;
-	}
-
-}
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 04241b5..6a90d20 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
@@ -20,6 +20,7 @@ import java.util.regex.Pattern;

 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
+import org.geworkbench.bison.datastructure.bioobjects.sequence.BlastObj;

 /**
  * BlastParser is a class that reads in from a text file generated by
diff --git a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/BlastAlgorithm.java b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/BlastAlgorithm.java
deleted file mode 100755
index ebfe1fb..0000000
--- a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/BlastAlgorithm.java
+++ /dev/null
@@ -1,386 +0,0 @@
-package org.geworkbench.components.alignment.blast;
-
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileReader;
-import java.io.IOException;
-import java.util.Date;
-import java.util.concurrent.ExecutionException;
-
-import javax.swing.JOptionPane;
-import javax.swing.SwingWorker;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-import org.geworkbench.bison.datastructure.biocollections.sequences.CSSequenceSet;
-import org.geworkbench.bison.datastructure.biocollections.sequences.DSSequenceSet;
-import org.geworkbench.bison.datastructure.bioobjects.sequence.CSAlignmentResultSet;
-import org.geworkbench.bison.datastructure.bioobjects.sequence.CSSequence;
-import org.geworkbench.bison.datastructure.bioobjects.sequence.DSSequence;
-import org.geworkbench.bison.util.RandomNumberGenerator;
-import org.geworkbench.builtin.projects.ProjectPanel;
-import org.geworkbench.components.alignment.blast.RemoteBlast.NcbiResponseException;
-import org.geworkbench.components.alignment.blast.RemoteBlast.Status;
-import org.geworkbench.components.alignment.panels.AlgorithmMatcher;
-import org.geworkbench.components.alignment.panels.BlastAppComponent;
-import org.geworkbench.components.alignment.panels.ParameterSetting;
-import org.geworkbench.events.ProjectNodeAddedEvent;
-import org.geworkbench.util.BrowserLauncher;
-import org.geworkbench.util.FilePathnameUtils;
-
-/**
- * BlastAlgorithm.
- *
- * @author XZ
- * @author zji
- * @version $Id: BlastAlgorithm.java 7316 2010-12-09 19:57:45Z maz $
- */
-public class BlastAlgorithm extends SwingWorker<CSAlignmentResultSet, Integer> {
-
-	static private Log log = LogFactory.getLog(RemoteBlast.class);
-
-	private BlastAppComponent blastAppComponent = null;
-
-	private boolean startBrowser;
-	private boolean jobFinished = false;
-
-	private ParameterSetting parameterSetting;
-
-	private CSSequenceSet<CSSequence> sequenceDB;
-	private DSSequenceSet<? extends DSSequence> parentSequenceDB;
-
-	private final static int TIMEGAP = 4000;
-	private final static String LINEBREAK = System.getProperty("line.separator");
-
-	public void setBlastAppComponent(BlastAppComponent _blastAppComponent) {
-		blastAppComponent = _blastAppComponent;
-	}
-
-	/**
-	 * Update Progress with finished percentage and related information.
-	 *
-	 * @param percent
-	 *            double
-	 * @param text
-	 *            String
-	 */
-	void updateProgressStatus(final double percent, final String text) {
-		if (blastAppComponent != null) {
-			blastAppComponent.updateProgressBar(percent, text);
-		}
-	}
-
-	/**
-	 * Update progress only with String information.
-	 *
-	 * @param text
-	 *            String
-	 */
-	void updateStatus(String text) {
-		if (blastAppComponent != null) {
-			blastAppComponent.updateProgressBar(text);
-		}
-	}
-
-	/**
-	 * Update the component's progressBar with information and reset the
-	 * ProgressBar.
-	 *
-	 * @param boo
-	 *            boolean
-	 * @param text
-	 *            String
-	 */
-
-	void updateStatus(boolean boo, String text) {
-		if (blastAppComponent != null) {
-			blastAppComponent.updateProgressBar(boo, text);
-		}
-	}
-
-	/**
-	 * Show error message and update status
-	 *
-	 * @param e
-	 */
-	private void processExceptionFromNcbi(Exception e, CSSequence sequence) {
-		if (blastAppComponent != null) {
-			String exceptionName = e.getClass().getName();
-			blastAppComponent.reportError("Sequence " + sequence
-					+ " cannot be blasted due to " + exceptionName + ":\n"
-					+ e.getMessage(), "Error: " + exceptionName);
-
-		}
-		updateStatus(false, "NCBI Blast is stopped at " + new Date());
-	}
-
-	/**
-	 * The workhorse to run Blast program.
-	 *
-	 * This method is invoked by from the working thread.
-	 */
-	@Override
-	protected CSAlignmentResultSet doInBackground() throws Exception {
-		if (sequenceDB == null || parentSequenceDB == null) {
-			throw new Exception("null sequenceDB or null parentSequenceDB");
-		}
-
-		String tempFolder = FilePathnameUtils.getTemporaryFilesDirectoryPath();
-
-		/* generate a new file name for the coming output file. */
-		String outputFile = tempFolder + "Blast"
-				+ RandomNumberGenerator.getID() + ".html";
-
-		RemoteBlast blast;
-		DSSequenceSet<? extends DSSequence> parentSequenceSet = parentSequenceDB;
-
-		for (CSSequence sequence : sequenceDB) {
-			updateStatus("Uploading sequence: " + sequence);
-			blast = new RemoteBlast(sequence.getSequence(), outputFile, AlgorithmMatcher
-					.translateToCommandline(parameterSetting));
-			String BLAST_rid = null;
-			try {
-				BLAST_rid = blast.submitBlast();
-			} catch (NcbiResponseException e1) {
-				processExceptionFromNcbi(e1, sequence);
-				return null;
-			}
-			if (isCancelled()) {
-				return null;
-			}
-			if (BLAST_rid == null) {
-				if (blastAppComponent != null) {
-					blastAppComponent
-							.reportError(
-									"Sequence "
-											+ sequence
-											+ " cannot be blasted, please check your parameters.",
-									"Parameter Error");
-
-				}
-				updateStatus(false, "NCBI Blast is stopped at "
-						+ new Date());
-				return null;
-
-			}
-			updateStatus("The Request ID is : " + BLAST_rid);
-
-			String resultURLString = "http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&FORMAT_TYPE=HTML&RID="
-					+ BLAST_rid;
-			Status status = blast.retrieveResult(resultURLString);
-			while(status==Status.WAITING && !isCancelled()) {
-				updateStatus("For sequence " + sequence
-						+ ",  the blast job is running. ");
-				try {
-					Thread.sleep(TIMEGAP);
-				} catch (InterruptedException e) {
-					// do nothing
-				}
-				status = blast.retrieveResult(resultURLString);
-			}
-			if(isCancelled()) return null;
-			else if(status!=Status.READY) {
-				String msg = parseError(outputFile);
-				processExceptionFromNcbi(new Exception(msg), sequence);
-				return null;
-			}
-		}
-		if(isCancelled()){
-			updateStatus(false, "NCBI Blast is canceled at " + new Date());
-			return null;
-		}
-		updateStatus(false, "NCBI Blast is finisheded at " + new Date());
-		String outputFilePath = "file://"
-				+ new File(outputFile).getAbsolutePath();
-		if (parameterSetting.isViewInBrowser()) {
-			if ((new File(outputFile)).canRead()) {
-				try {
-					String osName = System.getProperty("os.name");
-					if (osName.startsWith("Mac OS")) {
-						BrowserLauncher.openURL(outputFilePath);
-					} else {
-						BrowserLauncher.openURL("file:///"+new File(outputFile)
-								.getAbsolutePath().replace("\\", "/").replace(" ", "%20"));
-					}
-				} catch (Exception ex) {
-					ex.printStackTrace();
-					JOptionPane.showMessageDialog(null,
-							"No web browser can be launched, the result is saved at "
-									+ outputFile, "No Web Browser",
-							JOptionPane.ERROR_MESSAGE);
-
-				}
-			} else {
-
-				JOptionPane.showMessageDialog(null,
-						"The result cannot be read at " + outputFile,
-						"File cannot be read", JOptionPane.ERROR_MESSAGE);
-
-			}
-
-		}
-
-		CSAlignmentResultSet blastResult = new CSAlignmentResultSet(outputFile, sequenceDB
-				.getFASTAFileName(), sequenceDB, parentSequenceSet);
-		blastResult.setLabel(BlastAppComponent.NCBILABEL);
-		ProjectNodeAddedEvent event = new ProjectNodeAddedEvent(null, null,
-				blastResult);
-		if(isCancelled())return null;
-		blastAppComponent.publishProjectNodeAddedEvent(event);
-		log.debug("blast result node added");
-		return blastResult;
-	}
-
-	private static String parseError(String outputFile) {
-		BufferedReader br = null;
-		try {
-			br = new BufferedReader(new FileReader(outputFile));
-			String line = br.readLine();
-			while(line!=null) {
-				int index = line.indexOf("Error: ");
-				if(index>=0) {
-					int index2 = line.indexOf("</font>", index);
-					return line.substring(index, index2);
-				}
-				line = br.readLine();
-			}
-		} catch (FileNotFoundException e) {
-			// TODO Auto-generated catch block
-			e.printStackTrace();
-			return "FileNotFoundException in parsing error";
-		} catch (IOException e) {
-			// TODO Auto-generated catch block
-			e.printStackTrace();
-			return "IOException in parsing error";
-		} finally {
-			try {
-				br.close();
-			} catch (IOException e) {
-			}
-		}
-		return "Other error (not able to be parsed)";
-	}
-
-	@Override
-    protected void done() {
-		if(isCancelled())return;
-
-		CSAlignmentResultSet blastResult;
-		try {
-			blastResult = get();
-			if (blastResult==null)return;
-
-			String historyStr = generateHistoryStr(sequenceDB);
-			ProjectPanel.addToHistory(blastResult, historyStr);
-		} catch (InterruptedException e) {
-			// TODO Auto-generated catch block
-			e.printStackTrace();
-		} catch (ExecutionException e) {
-			// TODO Auto-generated catch block
-			e.printStackTrace();
-		}
-    }
-
-	private String generateHistoryStr(CSSequenceSet<CSSequence> activeSequenceDB) {
-		String histStr = "";
-		if(parameterSetting!=null){
-
-			// Header
-			histStr += "Blast run with the following parameters:\n";
-			histStr += "----------------------------------------\n";
-
-				String dbName=parameterSetting.getDbName();
-				histStr += "Database: " + dbName + LINEBREAK;
-				histStr += "BLAST Program: " + parameterSetting.getProgramName() + LINEBREAK;
-
-				histStr += "Exclude of Models(XM/XP): " + parameterSetting.isExcludeModelsOn() + LINEBREAK;
-				histStr += "Exclude of Uncultured/environmental sequences: " + parameterSetting.isExcludeUncultureOn() + LINEBREAK;
-				if (parameterSetting.getFromQuery()!=null)
-					histStr +="Query subrange from: "+parameterSetting.getFromQuery() +LINEBREAK;
-				if (parameterSetting.getToQuery()!=null)
-					histStr +="Query subrange to: "+parameterSetting.getToQuery() +LINEBREAK;
-				if(parameterSetting.getEntrezQuery()!=null)
-					histStr += "Entrez Query: "+parameterSetting.getEntrezQuery() + LINEBREAK;
-				if(parameterSetting.getProgramName().equalsIgnoreCase("blastn")){
-					String optimizeFor="";
-					if (parameterSetting.isMegaBlastOn()) optimizeFor="Highly similar sequences (megablast)";
-					else if(parameterSetting.isDiscontiguousOn()) optimizeFor="More dissimilar sequences (discontiguous megablast)";
-					else optimizeFor="Optimize for Somewhat similar sequences (blastn)";
-					histStr += "Optimize For: " + optimizeFor + LINEBREAK;
-				}
-				if (parameterSetting.getProgramName().equalsIgnoreCase("blastx")||parameterSetting.getProgramName().equalsIgnoreCase("tblastx")){
-					histStr += "Genetic Code: " + parameterSetting.getGeneticCode() + LINEBREAK;
-				}
-
-				histStr += "Short Queries: " + parameterSetting.isShortQueriesOn()+ LINEBREAK;
-
-				histStr += "Expect: " + parameterSetting.getExpect() + LINEBREAK;
-				histStr += "Word Size: " + parameterSetting.getWordsize() + LINEBREAK;
-				histStr += "Max match in a query range: "+parameterSetting.getHspRange()+ LINEBREAK;
-				if(!parameterSetting.getProgramName().equalsIgnoreCase("blastn"))
-					histStr += "Matrix: " + parameterSetting.getMatrix() + LINEBREAK;
-				histStr += "Match/mismatch Scores: " + parameterSetting.getMatchScores() + LINEBREAK;
-				histStr += "Gap Cost: " + parameterSetting.getGapCost() + LINEBREAK;
-				if (parameterSetting.getProgramName().equalsIgnoreCase("blastp")||parameterSetting.getProgramName().equalsIgnoreCase("tblastn")){
-					histStr += "Compositional Adjustment: " + parameterSetting.getCompositionalAdjustment()+ LINEBREAK;
-				}
-				histStr += "Low Complexity Filter On: " + parameterSetting.isLowComplexityFilterOn() + LINEBREAK;
-				if(parameterSetting.getProgramName().equalsIgnoreCase("blastn")){
-					histStr += "Species-specific repeats Filter On: " + parameterSetting.isHumanRepeatFilterOn() + LINEBREAK;
-					histStr += "Species-specific repeats Filter For: " + parameterSetting.getSpeciesRepeat() + LINEBREAK;
-				}
-				histStr += "Mask Low Case: " + parameterSetting.isMaskLowCase() + LINEBREAK;
-				histStr += "Mask Lookup Table: " + parameterSetting.isMaskLookupTable() + LINEBREAK;
-				if(parameterSetting.isDiscontiguousOn()&&parameterSetting.getProgramName().equalsIgnoreCase("blastn")){
-					histStr += "Template Length: " + parameterSetting.getTemplateLength() + LINEBREAK;
-					histStr += "Template Type: " + parameterSetting.getTemplateType() + LINEBREAK;
-				}
-
-				histStr += "Number of Sequences: " + activeSequenceDB.size() + LINEBREAK;
-				for (CSSequence marker : activeSequenceDB) {
-					histStr += "\t" + marker.getLabel() + "\n";
-				}
-		}
-		return histStr;
-	}
-
-	public boolean isStartBrowser() {
-		return startBrowser;
-	}
-
-	public BlastAppComponent getBlastAppComponent() {
-		return blastAppComponent;
-	}
-
-	public ParameterSetting getParameterSetting() {
-		return parameterSetting;
-	}
-
-	public boolean isJobFinished() {
-		return jobFinished;
-	}
-
-	public void setStartBrowser(boolean startBrowser) {
-		this.startBrowser = startBrowser;
-	}
-
-	public void setParameterSetting(ParameterSetting parameterSetting) {
-		this.parameterSetting = parameterSetting;
-	}
-
-	public void setJobFinished(boolean jobFinished) {
-		this.jobFinished = jobFinished;
-	}
-
-	public void setSequenceDB(CSSequenceSet<CSSequence> sequenceDB) {
-		this.sequenceDB = sequenceDB;
-
-	}
-
-	public void setParentSequenceDB(DSSequenceSet<? extends DSSequence> parentSequenceDB) {
-		this.parentSequenceDB = parentSequenceDB;
-
-	}
-
-}
diff --git a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/BlastObj.java b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/BlastObj.java
deleted file mode 100755
index 0146a21..0000000
--- a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/blast/BlastObj.java
+++ /dev/null
@@ -1,538 +0,0 @@
-package org.geworkbench.components.alignment.blast;
-
-import java.io.BufferedReader;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.net.URL;
-
-import org.apache.commons.httpclient.DefaultHttpMethodRetryHandler;
-import org.apache.commons.httpclient.HttpClient;
-import org.apache.commons.httpclient.HttpException;
-import org.apache.commons.httpclient.HttpStatus;
-import org.apache.commons.httpclient.cookie.CookiePolicy;
-import org.apache.commons.httpclient.methods.GetMethod;
-import org.apache.commons.httpclient.params.HttpMethodParams;
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-import org.geworkbench.bison.datastructure.bioobjects.sequence.CSSequence;
-
-/**
- * BlastObj.java A class to hold information about each individual hit of a
- * Blast database search on a protein sequence. <br>
- *
- * @author zji
- * @version $Id: BlastObj.java 7378 2011-01-11 17:08:21Z maz $
- */
-public class BlastObj {
-	private static Log log = LogFactory.getLog(BlastObj.class);
-
-	/**
-	 * The Database ID of the protein sequence hit in this BlastObj.
-	 */
-	String databaseID;
-	/**
-	 * Set up the upper boundary of whole sequence size.
-	 */
-	static final int MAXSEQUENCESIZE = 100000;
-	int maxSize = MAXSEQUENCESIZE;
-
-	/**
-	 * The accession number of the protein sequence hit in this BlastObj.
-	 */
-	String name;
-	/**
-	 * The description of the protein sequence hit in this BlastObj.
-	 */
-	String description;
-	/**
-	 * The percentage of the query that's aligned with protein sequence hit in
-	 * this BlastObj.
-	 */
-	int percentAligned;
-
-	/**
-	 * The percentage of the alignment of query and hit in this BlastObj that's
-	 * gapped.
-	 */
-	int percentGapped = 0;
-
-	/**
-	 * The percentage of the alignment of query and hit in this BlastObj that's
-	 * "positive"/conserved.
-	 */
-	int percentPos;
-
-	/**
-	 * The score of the alignment of query and hit in this BlastObj; initialized
-	 * to -1.
-	 */
-	int score = -1;
-
-	/**
-	 * The score of the alignment of query and hit in this BlastObj.
-	 */
-	String evalue;
-	/**
-	 * The length of the alignment of query and hit in this BlastObj.
-	 */
-	int length;
-	String seqID;
-	int[] subject_align = new int[2];
-
-	/**
-	 * The 2 element array containing the position in query sequence where the
-	 * alignment start and stop. change to public for temp.
-	 *
-	 * @todo add getter method later.
-	 */
-	public int[] query_align = new int[2];
-	/**
-	 * The String of query sequence in alignment with hit in this BlastObj.
-	 */
-	String query;
-	/**
-	 * The String of hit sequence in this BlastObj in alignment with query
-	 * sequence.
-	 */
-	String subject;
-	/**
-	 * The String of alignment sequence between query sequence and hit in this
-	 * BlastObj.
-	 */
-	String align;
-	/**
-	 * whether this BlastObj is included in the MSA analysis
-	 */
-	boolean include = false;
-	/**
-	 * check whether the whole sequece can be retrived.
-	 */
-	boolean retriveWholeSeq = false;
-
-	/**
-	 * the URL of hit info
-	 */
-	URL infoURL;
-	/**
-	 * URL of seq.
-	 */
-	URL seqURL;
-	private String detailedAlignment = "";
-	private String identity;
-	private int startPoint;
-	private int alignmentLength;
-	private int endPoint;
-
-	public BlastObj(boolean retriveWholeSeq, String databaseID, String name, String description,
-			String score, String evalue) {
-		this.retriveWholeSeq = retriveWholeSeq;
-		this.databaseID = databaseID;
-		this.description = description;
-		this.name = name;
-
-		try {
-			this.score = Integer.parseInt(score);
-		} catch (NumberFormatException e) {
-			// ignored
-		}
-
-		this.evalue = evalue;
-	}
-
-	/* Get methods for class variables. */
-
-	/**
-	 * Returns the database name of the hit sequence stored in this BlastObj.
-	 *
-	 * @return the accession number as a String.
-	 */
-	public String getDatabaseID() {
-		return databaseID;
-	}
-
-	/**
-	 * Returns the accession number of the hit sequence stored in this BlastObj.
-	 *
-	 * @return the accession number as a String.
-	 */
-
-	/**
-	 * Returns the description of the hit protein sequence stored in this
-	 * BlastObj.
-	 *
-	 * @return the description as a String.
-	 */
-	public String getDescription() {
-		return description;
-	}
-
-	/**
-	 * Returns the length of the alignment of query and hit seq stored in this
-	 * BlastObj.
-	 *
-	 * @return the length as an int.
-	 */
-
-	/**
-	 * Returns the percentage of the query that's aligned with protein sequence
-	 * hit in this BlastObj.
-	 *
-	 * @return percentAligned as an int.
-	 */
-
-	public int getPercentAligned() {
-		return percentAligned;
-	}
-
-	/**
-	 * Returns the percentage of the alignment that's gapped with protein
-	 * sequence hit in this BlastObj.
-	 *
-	 * @return percentGapped as an int.
-	 */
-	public int getPercentGapped() {
-		return percentGapped;
-	}
-
-	/**
-	 * Returns the percentage of the query that's conserved with protein
-	 * sequence hit in this BlastObj.
-	 *
-	 * @return percentPos as an int.
-	 */
-	public int getPercentPos() {
-		return percentPos;
-	}
-
-	/**
-	 * Returns the score of the alignment of query and protein sequence hit in
-	 * this BlastObj.
-	 *
-	 * @return score as an int.
-	 */
-	public int getScore() {
-		return score;
-	}
-
-	/**
-	 * Returns the e-value of the alignment of query and protein sequence hit in
-	 * this BlastObj.
-	 *
-	 * @return evalue as a String.
-	 */
-	public String getEvalue() {
-		return evalue;
-	}
-
-	/**
-	 * Returns the query in alignment with protein sequence hit in this
-	 * BlastObj.
-	 *
-	 * @return query as a String.
-	 */
-	public String getQuery() {
-		return query;
-	}
-
-	/**
-	 * Returns the protein sequence hit in this BlastObj in alignment with the
-	 * query.
-	 *
-	 * @return subject as a String.
-	 */
-	public String getSubject() {
-		return subject;
-	}
-
-	/**
-	 * Returns the alignment of query and protein sequence hit in this BlastObj.
-	 *
-	 * @return align as an String.
-	 */
-	public String getAlign() {
-		return align;
-	}
-
-	/**
-	 * Returns whether this BlastObj is included in MSA analysis.
-	 *
-	 * @return include as a Boolean.
-	 */
-	public boolean getInclude() {
-		return include;
-	}
-
-	/* Set methods for class variables */
-
-	/**
-	 * Sets the percentage of the query that's aligned with protein sequence hit
-	 * in this BlastObj.
-	 *
-	 * @param i,
-	 *            the new alignment percentage of this BlastObj.
-	 */
-	public void setPercentAligned(int i) {
-		percentAligned = i;
-	}
-
-	/**
-	 * Sets the percentage of the alignment that's gapped of query and hit
-	 * protein sequence hit in this BlastObj.
-	 *
-	 * @param i,
-	 *            the new gapped percentage of this BlastObj.
-	 */
-	public void setPercentGapped(int i) {
-		percentGapped = i;
-	}
-
-	/**
-	 * Sets the percentage of the query that's conserved with protein sequence
-	 * hit in this BlastObj.
-	 *
-	 * @param i,
-	 *            the new conserved percentage of this BlastObj.
-	 */
-
-	public void setPercentPos(int i) {
-		percentPos = i;
-	}
-
-	/**
-	 * Sets the query sequence of the alignment with protein sequence hit in
-	 * this BlastObj.
-	 *
-	 * @param s,
-	 *            the new query seq of this BlastObj.
-	 */
-	public void setQuery(String s) {
-		query = s;
-	}
-
-	/**
-	 * Sets hit protein sequence hit in this BlastObj in alignment w/ the query.
-	 *
-	 * @param s,
-	 *            the new subject seq of this BlastObj.
-	 */
-	public void setSubject(String s) {
-		subject = s;
-	}
-
-	/**
-	 * Sets the alignment sequence of the query with protein sequence hit in
-	 * this BlastObj.
-	 *
-	 * @param s,
-	 *            the new align seq of this BlastObj.
-	 */
-	public void setAlign(String s) {
-		align = s;
-	}
-
-	/**
-	 * Sets whether this BlastObj is included in MSA analysis.
-	 *
-	 * @param b,
-	 *            the new include Boolean of this BlastObj.
-	 */
-	public void setInclude(boolean b) {
-		include = b;
-	}
-
-	public URL getInfoURL() {
-		return infoURL;
-	}
-
-	public void setInfoURL(URL infoURL) {
-		this.infoURL = infoURL;
-	}
-
-	public URL getSeqURL() {
-		return seqURL;
-	}
-
-	public void setSeqURL(URL seqURL) {
-		this.seqURL = seqURL;
-	}
-
-	public boolean isRetriveWholeSeq() {
-		return retriveWholeSeq;
-	}
-
-	public String getName() {
-		return name;
-	}
-
-	public int getLength() {
-		return length;
-	}
-
-	public void setLength(int length) {
-		this.length = length;
-	}
-
-	public String getDetailedAlignment() {
-		return detailedAlignment;
-	}
-
-	public void setDetailedAlignment(String detailedAlignment) {
-		this.detailedAlignment = detailedAlignment;
-	}
-
-	public String toString() {
-		return databaseID + detailedAlignment + score + evalue;
-	}
-
-	public CSSequence getAlignedSeq() {
-		CSSequence seq = new CSSequence(">" + databaseID + "|" + name
-				+ "---PARTIALLY INCLUDED", subject);
-
-		return seq;
-
-	}
-
-	/**
-	 * Create Entrez Programming Utilities query URL from web query URL.
-	 *
-	 * @param queryUrl
-	 * @return
-	 */
-	private static String EUtilsUrl(String queryUrl) {
-		// parse GI from the url
-		final String proteinUrl = "http://www.ncbi.nlm.nih.gov/protein/";
-		final String nucleotideUrl = "http://www.ncbi.nlm.nih.gov/nucleotide/";
-		int indexQ = queryUrl.indexOf("?");
-		String GI = null;
-		String databaseName = null;
-		if(indexQ==-1) {
-			log.error("unexpected query URL format :"+queryUrl);
-			return null;
-		} else if(queryUrl.startsWith(proteinUrl)) {
-			GI = queryUrl.substring(proteinUrl.length(), indexQ);
-			databaseName = "protein";
-		} else if(queryUrl.startsWith(nucleotideUrl)) {
-			GI = queryUrl.substring(nucleotideUrl.length(), indexQ);
-			databaseName = "nucleotide";
-		} else {
-			log.error("unexpected query URL format :"+queryUrl);
-			return null;
-		}
-
-		return "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db="+databaseName+"&id="
-				+ GI + "&rettype=fasta";
-	}
-
-	/**
-	 * getWholeSeq
-	 *
-	 * @return Object
-	 */
-	public CSSequence getWholeSeq() {
-
-		if (!retriveWholeSeq ) {
-			// this field is kept for now, but never set false
-			log.error("retriveWholeSeq is false");
-			return null;
-		}
-		if (seqURL == null)
-			return null;
-
-		log.debug("URL" + seqURL);
-		HttpClient client = new HttpClient();
-		DefaultHttpMethodRetryHandler retryhandler = new DefaultHttpMethodRetryHandler(
-				10, true);
-		client.getParams().setParameter(HttpMethodParams.RETRY_HANDLER,
-				retryhandler);
-		client.getParams().setCookiePolicy(CookiePolicy.IGNORE_COOKIES);
-
-		GetMethod getMethod = new GetMethod(EUtilsUrl(seqURL.toString()));
-		String sequenceLabel = null, sequence = null;
-		try {
-			int statusCode = client.executeMethod(getMethod);
-
-			if (statusCode == HttpStatus.SC_OK) {
-				InputStream stream = getMethod.getResponseBodyAsStream();
-				BufferedReader in = new BufferedReader(new InputStreamReader(
-						stream));
-				sequenceLabel = in.readLine();
-				StringBuilder sb = new StringBuilder();
-				String line = null;
-				while ((line = in.readLine()) != null) {
-					if (line.trim().length() > 0)
-						sb.append(line).append('\n');
-				}
-				stream.close();
-				sequence = sb.toString();
-			} else {
-				log.error("E Utilties failed for " + seqURL);
-				log.error("status code=" + statusCode);
-				return null;
-			}
-		} catch (HttpException e) {
-			e.printStackTrace();
-			return null;
-		} catch (IOException e) {
-			e.printStackTrace();
-			return null;
-		} finally {
-			getMethod.releaseConnection();
-		}
-
-		log.debug("label\n" + sequenceLabel);
-		log.debug("sequence\n" + sequence);
-		return new CSSequence(sequenceLabel, sequence);
-	}
-
-	public String getSeqID() {
-		return seqID;
-	}
-
-	public void setSeqID(String seqID) {
-		this.seqID = seqID;
-	}
-
-	public String getIdentity() {
-		return identity;
-	}
-
-	public int getStartPoint() {
-
-		return startPoint;
-	}
-
-	public int getAlignmentLength() {
-		return alignmentLength;
-	}
-
-	public int getEndPoint() {
-		return endPoint;
-	}
-
-	public int getMaxSize() {
-		return maxSize;
-	}
-
-	public void setIdentity(String identity) {
-		this.identity = identity;
-	}
-
-	public void setStartPoint(int startPoint) {
-
-		this.startPoint = startPoint;
-	}
-
-	public void setAlignmentLength(int alignmentLength) {
-		this.alignmentLength = alignmentLength;
-	}
-
-	public void setEndPoint(int endPoint) {
-		this.endPoint = endPoint;
-	}
-
-	public void setMaxSize(int maxSize) {
-		this.maxSize = maxSize;
-	}
-
-}
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 cf43f74..cd47273 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 8187 2011-07-30 04:31:30Z zji $
+ * @version $Id: NCBIBlastParser.java 8455 2011-10-24 22:06:10Z youmi $
  */

 import java.io.BufferedReader;
@@ -20,6 +20,7 @@ import java.util.regex.Pattern;

 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
+import org.geworkbench.bison.datastructure.bioobjects.sequence.BlastObj;

 /**
  * BlastParser is a class that reads in from a text file generated by
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 233d5d5..75bd9fb 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
-8215
+8644
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/alignment/src/org/geworkbench/components/alignment/help
 https://ncisvn.nci.nih.gov/svn/geworkbench

@@ -32,7 +32,7 @@ file



-2011-08-02T04:31:32.000000Z
+2011-08-17T00:19:01.000000Z
 f3092f5b4e2bba0d0a8772531eaadf00
 2011-07-30T04:31:30.667242Z
 8187
@@ -66,7 +66,7 @@ file



-2011-08-02T04:31:32.000000Z
+2011-08-17T00:19:01.000000Z
 09b121a21764644539cf2d7ee1f28ae0
 2011-07-30T04:31:30.667242Z
 8187
@@ -100,7 +100,7 @@ file



-2011-08-02T04:31:32.000000Z
+2011-08-17T00:10:37.000000Z
 1f848289e789b9a0980ce8b7ba0b0efb
 2005-07-28T22:36:56.000000Z
 50
@@ -137,7 +137,7 @@ file



-2011-08-02T04:31:32.000000Z
+2011-08-17T00:19:01.000000Z
 c4455962610d6e8634f95d52c09d3d8c
 2011-07-30T04:31:30.667242Z
 8187
@@ -171,7 +171,7 @@ file



-2011-08-02T04:31:32.000000Z
+2011-08-17T00:19:01.000000Z
 ee8326bb0ea50a49d984471c0aed80cd
 2011-07-30T04:31:30.667242Z
 8187
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 f16b174..5bbede1 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
-8215
+8644
 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

@@ -32,7 +32,7 @@ file



-2011-08-02T04:31:32.000000Z
+2011-08-17T00:19:01.000000Z
 1af216a5213de867307298bda621b8ed
 2011-07-30T04:31:30.667242Z
 8187
@@ -66,7 +66,7 @@ file



-2011-08-02T04:31:32.000000Z
+2011-08-17T00:19:01.000000Z
 00bb617ac348ca1eba387234bcdc0ede
 2011-07-30T04:31:30.667242Z
 8187
@@ -100,7 +100,7 @@ file



-2011-08-02T04:31:32.000000Z
+2011-08-17T00:10:37.000000Z
 9228e002a5fa526e9224df5950d2f56d
 2011-07-30T04:31:30.667242Z
 8187
@@ -134,7 +134,7 @@ file



-2011-08-02T04:31:32.000000Z
+2011-08-17T00:19:01.000000Z
 59a83e6f432f762a5525136d8c017853
 2011-07-30T04:31:30.667242Z
 8187
@@ -168,7 +168,7 @@ file



-2011-08-02T04:31:32.000000Z
+2011-08-17T00:10:37.000000Z
 15cc38ad9c72a9d5fed588801c27a59a
 2011-07-30T04:31:30.667242Z
 8187
@@ -202,7 +202,7 @@ file



-2011-08-02T04:31:32.000000Z
+2011-08-17T00:19:01.000000Z
 e142cf63cb89b907dc181a351ea82d00
 2011-07-30T04:31:30.667242Z
 8187
@@ -236,7 +236,7 @@ file



-2011-08-02T04:31:32.000000Z
+2011-08-17T00:19:01.000000Z
 fbc86da3fb79dbd324e920c035901dc3
 2011-07-30T04:31:30.667242Z
 8187
@@ -270,7 +270,7 @@ file



-2011-08-02T04:31:32.000000Z
+2011-08-17T00:19:01.000000Z
 9c7cb03ec3cdafcd3eb4509847a475a4
 2011-07-30T04:31:30.667242Z
 8187
@@ -304,7 +304,7 @@ file



-2011-08-02T04:31:32.000000Z
+2011-08-17T00:10:37.000000Z
 3cdd2570f807aa40afa953545419bc1e
 2011-07-30T04:31:30.667242Z
 8187
@@ -338,7 +338,7 @@ file



-2011-08-02T04:31:32.000000Z
+2011-08-17T00:10:37.000000Z
 c23d0d6732765e32a140860b5b7c173c
 2011-07-30T04:31:30.667242Z
 8187
@@ -372,7 +372,7 @@ file



-2011-08-02T04:31:32.000000Z
+2011-08-17T00:10:37.000000Z
 0c95fdcc4f9f7d0db3a4587eeaec7ef7
 2011-07-30T04:31:30.667242Z
 8187
@@ -406,7 +406,7 @@ file



-2011-08-02T04:31:32.000000Z
+2011-08-17T00:19:01.000000Z
 a690a598b9a6cbd9e89d58bf8b90b4a0
 2011-07-30T04:31:30.667242Z
 8187
@@ -440,7 +440,7 @@ file



-2011-08-02T04:31:32.000000Z
+2011-08-17T00:10:37.000000Z
 20849be5e783fd5216b5963e91608df6
 2011-07-30T04:31:30.667242Z
 8187
@@ -474,7 +474,7 @@ file



-2011-08-02T04:31:32.000000Z
+2011-08-17T00:19:01.000000Z
 0257a641ab2ed3788aef2f01e69a3e34
 2011-07-30T04:31:30.667242Z
 8187
@@ -508,7 +508,7 @@ file



-2011-08-02T04:31:32.000000Z
+2011-08-17T00:19:01.000000Z
 bb883d0f9391e0e95a98467e3406893f
 2011-07-30T04:31:30.667242Z
 8187
@@ -542,7 +542,7 @@ file



-2011-08-02T04:31:32.000000Z
+2011-08-17T00:19:01.000000Z
 953d51a5cc7854ca7f559c209db719c1
 2011-07-30T04:31:30.667242Z
 8187
@@ -576,7 +576,7 @@ file



-2011-08-02T04:31:32.000000Z
+2011-08-17T00:10:37.000000Z
 4b938802dd89579b9cce3ca2075b3605
 2011-07-30T04:31:30.667242Z
 8187
@@ -610,7 +610,7 @@ file



-2011-08-02T04:31:32.000000Z
+2011-08-17T00:19:01.000000Z
 17875e776a5bb438cf8e422a08b09f6a
 2011-07-30T04:31:30.667242Z
 8187
@@ -644,7 +644,7 @@ file



-2011-08-02T04:31:32.000000Z
+2011-08-17T00:19:01.000000Z
 592938295f1066a04cf9179fe7622c2c
 2011-07-30T04:31:30.667242Z
 8187
@@ -678,7 +678,7 @@ file



-2011-08-02T04:31:32.000000Z
+2011-08-17T00:19:01.000000Z
 86be0e90bdbe166025a654d605daf015
 2011-07-30T04:31:30.667242Z
 8187
diff --git a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/.svn/all-wcprops b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/.svn/all-wcprops
index 0ae59e9..8ed7954 100644
--- a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/.svn/all-wcprops
+++ b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/.svn/all-wcprops
@@ -1,13 +1,13 @@
 K 25
 svn:wc:ra_dav:version-url
 V 117
-/svn/geworkbench/!svn/ver/8187/trunk/geworkbench/components/alignment/src/org/geworkbench/components/alignment/panels
+/svn/geworkbench/!svn/ver/8479/trunk/geworkbench/components/alignment/src/org/geworkbench/components/alignment/panels
 END
 BlastViewPanel.java
 K 25
 svn:wc:ra_dav:version-url
 V 137
-/svn/geworkbench/!svn/ver/8187/trunk/geworkbench/components/alignment/src/org/geworkbench/components/alignment/panels/BlastViewPanel.java
+/svn/geworkbench/!svn/ver/8455/trunk/geworkbench/components/alignment/src/org/geworkbench/components/alignment/panels/BlastViewPanel.java
 END
 start.gif
 K 25
@@ -15,23 +15,11 @@ svn:wc:ra_dav:version-url
 V 127
 /svn/geworkbench/!svn/ver/1332/trunk/geworkbench/components/alignment/src/org/geworkbench/components/alignment/panels/start.gif
 END
-BlastAppComponent.cwb.xml
-K 25
-svn:wc:ra_dav:version-url
-V 143
-/svn/geworkbench/!svn/ver/7668/trunk/geworkbench/components/alignment/src/org/geworkbench/components/alignment/panels/BlastAppComponent.cwb.xml
-END
 BlastViewComponent.java
 K 25
 svn:wc:ra_dav:version-url
 V 141
-/svn/geworkbench/!svn/ver/8187/trunk/geworkbench/components/alignment/src/org/geworkbench/components/alignment/panels/BlastViewComponent.java
-END
-BlastAppComponent.java
-K 25
-svn:wc:ra_dav:version-url
-V 140
-/svn/geworkbench/!svn/ver/7338/trunk/geworkbench/components/alignment/src/org/geworkbench/components/alignment/panels/BlastAppComponent.java
+/svn/geworkbench/!svn/ver/8479/trunk/geworkbench/components/alignment/src/org/geworkbench/components/alignment/panels/BlastViewComponent.java
 END
 stop.gif
 K 25
@@ -39,21 +27,9 @@ svn:wc:ra_dav:version-url
 V 126
 /svn/geworkbench/!svn/ver/1332/trunk/geworkbench/components/alignment/src/org/geworkbench/components/alignment/panels/stop.gif
 END
-AlgorithmMatcher.java
-K 25
-svn:wc:ra_dav:version-url
-V 139
-/svn/geworkbench/!svn/ver/7629/trunk/geworkbench/components/alignment/src/org/geworkbench/components/alignment/panels/AlgorithmMatcher.java
-END
 BlastViewComponent.cwb.xml
 K 25
 svn:wc:ra_dav:version-url
 V 144
-/svn/geworkbench/!svn/ver/7673/trunk/geworkbench/components/alignment/src/org/geworkbench/components/alignment/panels/BlastViewComponent.cwb.xml
-END
-ParameterSetting.java
-K 25
-svn:wc:ra_dav:version-url
-V 139
-/svn/geworkbench/!svn/ver/7316/trunk/geworkbench/components/alignment/src/org/geworkbench/components/alignment/panels/ParameterSetting.java
+/svn/geworkbench/!svn/ver/8362/trunk/geworkbench/components/alignment/src/org/geworkbench/components/alignment/panels/BlastViewComponent.cwb.xml
 END
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 6414165..c8e048b 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
@@ -1,14 +1,14 @@
 10

 dir
-8215
+8644
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/components/alignment/src/org/geworkbench/components/alignment/panels
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2011-07-30T04:31:30.667242Z
-8187
+2011-11-02T15:39:37.175113Z
+8479
 zji


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



-2011-08-02T04:31:31.000000Z
-4a65d42e00488424d2a5d7ce28de5587
-2011-07-30T04:31:30.667242Z
-8187
-zji
+2011-12-29T06:11:36.000000Z
+b3b94caa947d57bb59cac6c44e499c7a
+2011-10-24T22:06:10.214128Z
+8455
+youmi
 has-props


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



-20278
+19925

 start.gif
 file
@@ -66,7 +66,7 @@ file



-2011-08-02T04:31:31.000000Z
+2011-08-17T00:10:37.000000Z
 18140a4a2fbc0dfd3aa41a63e24634bc
 2006-03-07T21:06:44.000000Z
 1332
@@ -94,50 +94,16 @@ has-props

 239

-BlastAppComponent.cwb.xml
-file
-
-
-
-
-2011-08-02T04:31:31.000000Z
-7153b6b8ebe36525e68a6b48a04c4e08
-2011-03-28T20:05:18.132977Z
-7668
-smithken
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-1509
-
 BlastViewComponent.java
 file




-2011-08-02T04:31:31.000000Z
-e30352eea574dd00de0c5aa89022bb1f
-2011-07-30T04:31:30.667242Z
-8187
+2011-12-29T06:11:36.000000Z
+086855b153288a41a2ca712445b2030b
+2011-11-02T15:39:37.175113Z
+8479
 zji
 has-props

@@ -160,41 +126,7 @@ has-props



-4211
-
-BlastAppComponent.java
-file
-
-
-
-
-2011-08-02T04:31:31.000000Z
-3bfa17d087d301b3833fcfd58f2bd89d
-2010-12-16T16:46:53.281032Z
-7338
-maz
-has-props
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-59141
+3805

 stop.gif
 file
@@ -202,7 +134,7 @@ file



-2011-08-02T04:31:31.000000Z
+2011-08-17T00:10:37.000000Z
 d36021b22ed88b6b9a215c2f57c77824
 2006-03-07T21:06:44.000000Z
 1332
@@ -230,86 +162,18 @@ has-props

 313

-AlgorithmMatcher.java
-file
-
-
-
-
-2011-08-02T04:31:31.000000Z
-64048cf976a44283210c83490671f17b
-2011-03-24T18:57:49.748578Z
-7629
-youmi
-has-props
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-29705
-
 BlastViewComponent.cwb.xml
 file




-2011-08-02T04:31:31.000000Z
-9323b9ae2098586ef73d6426652fb576
-2011-03-28T20:49:09.224686Z
-7673
-smithken
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-1469
-
-ParameterSetting.java
-file
-
-
-
+2011-12-29T06:11:36.000000Z
+9e98a96557fef8128036f1aa6ebe224c
+2011-10-04T16:02:03.460589Z
+8362
+youmi

-2011-08-02T04:31:31.000000Z
-5f4c9ce9ce73035f9da298ee4201f4b8
-2010-12-09T19:57:45.788737Z
-7316
-maz
-has-props



@@ -330,5 +194,5 @@ has-props



-7750
+1464

diff --git a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/.svn/prop-base/AlgorithmMatcher.java.svn-base b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/.svn/prop-base/AlgorithmMatcher.java.svn-base
deleted file mode 100644
index 8df8946..0000000
--- a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/.svn/prop-base/AlgorithmMatcher.java.svn-base
+++ /dev/null
@@ -1,9 +0,0 @@
-K 14
-svn:executable
-V 1
-*
-K 12
-svn:keywords
-V 2
-Id
-END
diff --git a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/.svn/prop-base/BlastAppComponent.java.svn-base b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/.svn/prop-base/BlastAppComponent.java.svn-base
deleted file mode 100644
index 8df8946..0000000
--- a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/.svn/prop-base/BlastAppComponent.java.svn-base
+++ /dev/null
@@ -1,9 +0,0 @@
-K 14
-svn:executable
-V 1
-*
-K 12
-svn:keywords
-V 2
-Id
-END
diff --git a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/.svn/prop-base/ParameterSetting.java.svn-base b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/.svn/prop-base/ParameterSetting.java.svn-base
deleted file mode 100644
index 8df8946..0000000
--- a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/.svn/prop-base/ParameterSetting.java.svn-base
+++ /dev/null
@@ -1,9 +0,0 @@
-K 14
-svn:executable
-V 1
-*
-K 12
-svn:keywords
-V 2
-Id
-END
diff --git a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/.svn/text-base/AlgorithmMatcher.java.svn-base b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/.svn/text-base/AlgorithmMatcher.java.svn-base
deleted file mode 100644
index 1ca6472..0000000
--- a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/.svn/text-base/AlgorithmMatcher.java.svn-base
+++ /dev/null
@@ -1,666 +0,0 @@
-package org.geworkbench.components.alignment.panels;
-
-import java.io.File;
-import java.io.IOException;
-import java.io.UnsupportedEncodingException;
-import java.net.URLEncoder;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import org.apache.commons.digester.Digester;
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-import org.geworkbench.engine.management.ComponentClassLoader;
-import org.geworkbench.engine.management.ComponentResource;
-import org.xml.sax.SAXException;
-
-/**
- * Utility used by BlastAppComponent and BlastAlgorithm.
- *
- * <p>Company: Columbia University</p>
- *
- * @author zji
- * @version $Id$
- */
-public class AlgorithmMatcher {
-	Log log = LogFactory.getLog(AlgorithmMatcher.class);
-
-	private static AlgorithmMatcher instance;
-	private List<DatabaseInfo> databaseList = null;
-
-	@SuppressWarnings("unchecked")
-	private AlgorithmMatcher() {
-        String componentDirectory = null;
-		ClassLoader classLoader = AlgorithmMatcher.class.getClassLoader();
-        if (classLoader instanceof ComponentClassLoader) {
-            ComponentClassLoader ccl = (ComponentClassLoader) classLoader;
-            ComponentResource componentResource = ccl.getComponentResource();
-            componentDirectory = componentResource.getDir();
-        } else {
-        	log.error("not loaded by ComponentClassLoader");
-        }
-
-		Digester digester = new Digester();
-		digester.setValidating( false );
-
-		digester.setUseContextClassLoader(true);
-		digester.addObjectCreate("database_list", ArrayList.class);
-		digester.addObjectCreate("database_list/database", DatabaseInfo.class);
-		digester.addSetProperties( "database_list/database", "name", "abbreviation" );
-		digester.addSetProperties( "database_list/database", "type", "type" );
-		digester.addBeanPropertySetter( "database_list/database/description", "description" );
-        digester.addBeanPropertySetter( "database_list/database/detail", "detail" );
-        digester.addSetNext("database_list/database", "add" );
-
-        File input = new File( componentDirectory+"/classes/databaseInfo.xml" );
-
-		try {
-			databaseList = (List<DatabaseInfo>)digester.parse( input );
-		} catch (IOException e) {
-			// TODO Auto-generated catch block
-			e.printStackTrace();
-		} catch (SAXException e) {
-			// TODO Auto-generated catch block
-			e.printStackTrace();
-		}
-
-    	List<DatabaseInfo> proteinList = new ArrayList<DatabaseInfo>();
-    	List<DatabaseInfo> nucleotideList = new ArrayList<DatabaseInfo>();
-    	for(DatabaseInfo d: databaseList) {
-    		if(d.getType().equals("protein"))proteinList.add(d);
-    		else if(d.getType().equals("nucleotide"))nucleotideList.add(d);
-    		else {
-    			log.error("wrong type "+d.getType()+" "+d.abbreviation);
-    		}
-    	}
-    	proteinDBdescriptionArray  = new String[proteinList.size()][2];
-    	int i = 0;
-		for(DatabaseInfo d: proteinList) {
-			proteinDBdescriptionArray[i][1] = d.getAbbreviation();
-			proteinDBdescriptionArray[i][0] = d.getDescription();
-			i++;
-		}
-		nucleotideDBdescriptionArray = new String[nucleotideList.size()][2];
-    	i = 0;
-		for(DatabaseInfo d: nucleotideList) {
-			nucleotideDBdescriptionArray[i][1] = d.getAbbreviation();
-			nucleotideDBdescriptionArray[i][0] = d.getDescription();
-			i++;
-		}
-	} // end of constructor
-
-	private String[][] nucleotideDBdescriptionArray = null;
-	private String[][] proteinDBdescriptionArray = null;
-
-	static AlgorithmMatcher getInstance() {
-		if(instance==null) {
-			instance = new AlgorithmMatcher();
-		}
-		return instance;
-	}
-
-	static public class DatabaseInfo {
-		private String abbreviation;
-		private String description;
-		private String detail;
-		private String type;
-
-		public DatabaseInfo() {
-		}
-
-		public void setAbbreviation(String abbreviation) {
-			this.abbreviation = abbreviation;
-		}
-
-		public void setDescription(String description) {
-			this.description = description;
-		}
-
-		public void setDetail(String detail) {
-			this.detail = detail;
-		}
-
-		public void setType(String type) {
-			this.type = type;
-		}
-
-		String getAbbreviation() {
-			return abbreviation;
-		}
-
-		String getDescription() {
-			return description;
-		}
-
-		String getDetail() {
-			return detail;
-		}
-
-		String getType() {
-			return type;
-		}
-	}
-
-	static private Map<String, String> program2type = new HashMap<String, String>();
-	static {
-		program2type.put("blastn", "nucleotide");
-		program2type.put("blastp", "protein");
-		program2type.put("blastx", "protein");
-		program2type.put("tblastn", "nucleotide");
-		program2type.put("tblastx", "nucleotide");
-	}
-
-	static private Map<String, String> template2number= new HashMap<String, String>();
-	static{
-		template2number.put("None", "0");
-		template2number.put("16", "16");
-		template2number.put("18", "18");
-		template2number.put("21", "21");
-		template2number.put("Coding", "0");
-		template2number.put("Maximal", "1");
-		template2number.put("Two template", "2");
-	}
-
-	static private Map<String, String> compositional2number= new HashMap<String, String>();
-	static{
-		compositional2number.put("No adjustment", "0");
-		compositional2number.put("Composition-based statistics", "1");
-		compositional2number.put("Conditional compositional score matrix adjustment", "2");
-		compositional2number.put("Universal compositional score matrix adjustment", "3");
-	}
-
-	static private Map<String, String> geneticCode2number=new HashMap<String, String>();
-	static{
-		geneticCode2number.put("Standard (1)","1");
-		geneticCode2number.put("Vertebrate Mitochondrial (2)","2");
-		geneticCode2number.put("Yeast Mitochondrial (3)","3");
-		geneticCode2number.put("Mold Mitochondrial (4)","4");
-		geneticCode2number.put("Invertebrate Mitochondrial (5)","5");
-		geneticCode2number.put("Ciliate Nuclear (6)","6");
-		geneticCode2number.put("Echinoderm Mitochondrial (9)","9");
-		geneticCode2number.put("Euplotid Nuclear (10)","10");
-		geneticCode2number.put("Bacteria and Archaea (11)","11");
-		geneticCode2number.put("Alternative Yeast Nuclear (12)","12");
-		geneticCode2number.put("Ascidian Mitochondrial (13)","13");
-		geneticCode2number.put("Flatworm Mitochondrial (14)","14");
-		geneticCode2number.put("Blepharisma Macronuclear (15)","15");
-	}
-
-	private static final String GAPB0_1 = "Linear";
-    private static final String GAPB0_2 = "Existence: 5 Extension: 2";
-    private static final String GAPB0_3 = "Existence: 2 Extension: 2";
-    private static final String GAPB0_4 = "Existence: 1 Extension: 2";
-    private static final String GAPB0_5 = "Existence: 0 Extension: 2";
-    private static final String GAPB0_6 = "Existence: 3 Extension: 1";
-    private static final String GAPB0_7 = "Existence: 2 Extension: 1";
-    private static final String GAPB0_8 = "Existence: 1 Extension: 1";
-
-    private static final String GAPB1_1 = "Existence: 4 Extension: 4";
-    private static final String GAPB1_2 = "Existence: 2 Extension: 4";
-    private static final String GAPB1_3 = "Existence: 0 Extension: 4";
-    private static final String GAPB1_4 = "Existence: 3 Extension: 3";
-    private static final String GAPB1_5 = "Existence: 6 Extension: 2";
-    private static final String GAPB1_6 = "Existence: 5 Extension: 2";
-    private static final String GAPB1_7 = "Existence: 4 Extension: 2";
-    private static final String GAPB1_8 = "Existence: 2 Extension: 2";
-
-	private static final String GAP0 = "Existence: 11 Extension: 1";
-    private static final String GAP1 = "Existence: 9 Extension: 2";
-    private static final String GAP2 = "Existence: 8 Extension: 2";
-    private static final String GAP3 = "Existence: 7 Extension: 2";
-    private static final String GAP4 = "Existence: 12 Extension: 1";
-    private static final String GAP5 = "Existence: 10 Extension: 1";
-
-    private static final String GAPB45_1 = "Existence: 15 Extension: 2";
-    private static final String GAPB45_2 = "Existence: 13 Extension: 3";
-    private static final String GAPB45_3 = "Existence: 12 Extension: 3";
-    private static final String GAPB45_4 = "Existence: 11 Extension: 3";
-    private static final String GAPB45_5 = "Existence: 10 Extension: 3";
-    private static final String GAPB45_6 = "Existence: 14 Extension: 2";
-    private static final String GAPB45_7 = "Existence: 13 Extension: 2";
-    private static final String GAPB45_8 = "Existence: 12 Extension: 2";
-    private static final String GAPB45_9 = "Existence: 19 Extension: 1";
-    private static final String GAPB45_10 = "Existence: 18 Extension: 1";
-    private static final String GAPB45_11 = "Existence: 17 Extension: 1";
-    private static final String GAPB45_12 = "Existence: 16 Extension: 1";
-    private static final String GAPB80_1 = "Existence: 10 Extension: 1";
-    private static final String GAPB80_2 = "Existence: 8 Extension: 2";
-    private static final String GAPB80_3 = "Existence: 7 Extension: 2";
-    private static final String GAPB80_4 = "Existence: 6 Extension: 2";
-    private static final String GAPB80_5 = "Existence: 11 Extension: 1";
-    private static final String GAPB80_6 = "Existence: 9 Extension: 1";
-    private static final String GAPP30_1 = "Existence: 9 Extension: 1";
-    private static final String GAPP30_2 = "Existence: 7 Extension: 2";
-    private static final String GAPP30_3 = "Existence: 6 Extension: 2";
-    private static final String GAPP30_4 = "Existence: 5 Extension: 2";
-    private static final String GAPP30_5 = "Existence: 8 Extension: 1";
-    private static final String GAPP30_6 = "Existence: 10 Extension: 1";
-    private static final String GAPP70_1 = "Existence: 10 Extension: 1";
-    private static final String GAPP70_2 = "Existence: 7 Extension: 2";
-    private static final String GAPP70_3 = "Existence: 6 Extension: 2";
-    private static final String GAPP70_4 = "Existence: 8 Extension: 2";
-    private static final String GAPP70_5 = "Existence: 9 Extension: 1";
-    private static final String GAPP70_6 = "Existence: 11 Extension: 1";
-
-    private static final String MATRIX1 = "BLOSUM62";
-    private static final String MATRIX2 = "BLOSUM45";
-    private static final String MATRIX3 = "BLOSUM80";
-    private static final String MATRIX4 = "PAM30";
-    private static final String MATRIX5 = "PAM70";
-    private static final String MATRIX0 = "dna.mat";
-
-    /**
-     * Match to correct database.
-     *
-     */
-    String[][] translateToArray(String programName) {
-    	String type = program2type.get(programName);
-		if (type==null) {
-			log.error("no database type for program "+programName);
-			return null;
-		} else if (type.equalsIgnoreCase("protein")) {
-			return proteinDBdescriptionArray;
-		} else if (type.equalsIgnoreCase("nucleotide")) {
-			return nucleotideDBdescriptionArray;
-		} else {
-			log.error("wrong database type "+type+" for program "+programName);
-			return null;
-		}
-	}
-
-    /**
-     * Given program + the index of database, return the detail
-     * @param programName
-     * @param selection
-     * @return
-     */
-    String getDatabaseDetail(String programName, String databaseName) {
-    	String type = program2type.get(programName);
-    	for(DatabaseInfo d: databaseList) {
-    		if (d.getType().equals(type)
-					&& d.getAbbreviation().equals(databaseName))
-				return d.getDetail();
-    	}
-    	log.error("no matching database for program "+programName);
-    	return null;
-	}
-
-    /**
-     * Static utility used in BlastAppComponent: Match to correct matrix.
-     * @param programName String
-     * @return String[]
-     */
-    static String[] translateToMatrices(String programName) {
-        if (programName.equalsIgnoreCase("blastn")) {
-            return new String[] {MATRIX0};
-        } else {
-            return new String[] {MATRIX4,MATRIX5, MATRIX3, MATRIX1, MATRIX2
-            };
-        }
-    }
-
-    /**
-     * Static utility used in BlastAppComponent: Match matrix name with gap costs.
-     * @param programName String
-     * @return String[]
-     */
-    static String[] translateToGapcosts(String programName) {
-    	if (programName.equalsIgnoreCase(MATRIX0)) {
-            return new String[] {GAPB0_1, GAPB0_2, GAPB0_3, GAPB0_4, GAPB0_5, GAPB0_6,GAPB0_7,GAPB0_8};
-
-        } else if (programName.equalsIgnoreCase(MATRIX1)) {
-            return new String[] {GAP1, GAP2, GAP3, GAP4, GAP0, GAP5};
-
-        } else if (programName.equalsIgnoreCase(MATRIX2)) {
-            return new String[] { GAPB45_2, GAPB45_3, GAPB45_4,
-                    GAPB45_5, GAPB45_1, GAPB45_6, GAPB45_7, GAPB45_8, GAPB45_9, GAPB45_10,
-                    GAPB45_11, GAPB45_12
-            };
-        } else if (programName.equalsIgnoreCase(MATRIX3)) {
-            return new String[] {GAPB80_2, GAPB80_3, GAPB80_4,
-                    GAPB80_5, GAPB80_1, GAPB80_6};
-        } else if (programName.equalsIgnoreCase(MATRIX4)) {
-            return new String[] {GAPP30_2, GAPP30_3, GAPP30_4,
-            		GAPP30_6,GAPP30_1, GAPP30_5};
-        } else if (programName.equalsIgnoreCase(MATRIX5)) {
-            return new String[] {GAPP70_4, GAPP70_2, GAPP70_3,
-            		GAPP70_6, GAPP70_1, GAPP70_5, };
-        }
-
-        String[] defaultGAPCOSTS = new String[] {GAP1, GAP2, GAP3, GAP4, GAP0, GAP5};
-        return defaultGAPCOSTS;
-
-    }
-
-    static String[] translateToGapcosts(String selectedProgramName, String optimizeFor) {
-    	if (selectedProgramName.equalsIgnoreCase("blastn")) {
-    		if (optimizeFor.equalsIgnoreCase("megablast")){
-    			return new String[] {GAPB0_1, GAPB0_2, GAPB0_3, GAPB0_4, GAPB0_5, GAPB0_6,GAPB0_7,GAPB0_8};
-    		}
-    		else {
-    			return new String[] {GAPB1_1, GAPB1_2, GAPB1_3, GAPB1_4, GAPB1_5, GAPB1_6,GAPB1_7,GAPB1_8};
-    		}
-
-    	}
-    	String[] defaultGAPCOSTS = new String[] {GAP1, GAP2, GAP3, GAP4, GAP0, GAP5};
-        return defaultGAPCOSTS;
-    }
-
-
-    static Map<String, Integer> defaultGapcostIndex = new HashMap<String, Integer>();
-    static {
-    	defaultGapcostIndex.put(MATRIX1, 4);
-    	defaultGapcostIndex.put(MATRIX2, 4);
-    	defaultGapcostIndex.put(MATRIX3, 4);
-    	defaultGapcostIndex.put(MATRIX4, 4);
-    	defaultGapcostIndex.put(MATRIX5, 4);
-    	defaultGapcostIndex.put("megablast", 0);
-    	defaultGapcostIndex.put("discontiguous", 5);
-    }
-
-    /**
-     * Static utility ussed in BlastAppComponent: translate program name to word size.
-     *
-     * @param selectedProgramName String
-     * @return String[]
-     */
-
-    static String[] translateToWordSize(String selectedProgramName, String optimizeFor) {
-        if (selectedProgramName.trim().equalsIgnoreCase("blastn")) {
-            if(optimizeFor.trim().equalsIgnoreCase("megablast")){
-            	return new String[]{"16","20","24","28","32","48","64","128","256"};
-            }
-            else
-            	return new String[] {"11", "12"};
-        } else {
-            return new String[] {"2", "3"};
-        }
-
-    }
-
-
-    /**
-     * Utility to create command-line parameter, only used by BlastAlgorithm.execute();
-     *
-     * @param ps
-     * @return
-     */
-    public static String translateToCommandline(ParameterSetting ps) {
-        String cmd = null;
-        if (ps != null) {
-            if (!ps.isUseNCBI()) {
-                cmd = "pb blastall -p " + ps.getProgramName() + "   -d   " +
-                      ps.getDbName() + " -e " + ps.getExpect() + " -M " +
-                      ps.getMatrix();
-                if (ps.isLowComplexityFilterOn()) {
-                    cmd += " -F T ";
-                } else {
-                    cmd += " -F F ";
-                }
-                if (ps.isMaskLowCase()) {
-                    cmd += " -U T ";
-                } else {
-                    cmd += " -U F ";
-                }
-                if (ps.getWordsize() != null) {
-                    cmd += " -W " + ps.getWordsize() + " ";
-                }
-                if (!ps.getProgramName().equals("blastn")) {
-
-                    String gapCost = ps.getGapCost();
-                    if (gapCost.equals(GAP1)) {
-                        cmd += " -G 9 -E 2 ";
-                    } else if (gapCost.equals(GAP2)) {
-                        cmd += " -G 8 -E 2 ";
-                    } else if (gapCost.equals(GAP3)) {
-                        cmd += " -G 7 -E 2 ";
-                    } else if (gapCost.equals(GAP4)) {
-                        cmd += " -G 12 -E 1 ";
-                    } else if (gapCost.equals(GAP5)) {
-                        cmd += " -G 10 -E 1 ";
-                    } else if (gapCost.equals(GAPB45_1)) {
-                        cmd += " -G 15 -E 2 ";
-                    } else if (gapCost.equals(GAPB45_2)) {
-                        cmd += " -G 13 -E 3 ";
-                    } else if (gapCost.equals(GAPB45_3)) {
-                        cmd += " -G 12 -E 3 ";
-                    } else if (gapCost.equals(GAPB45_4)) {
-                        cmd += " -G 11 -E 3 ";
-                    } else if (gapCost.equals(GAPB45_5)) {
-                        cmd += " -G 10 -E 3 ";
-                    } else if (gapCost.equals(GAPB45_6)) {
-                        cmd += " -G 14 -E 2 ";
-                    } else if (gapCost.equals(GAPB45_7)) {
-                        cmd += " -G 13 -E 2 ";
-                    } else if (gapCost.equals(GAPB45_8)) {
-                        cmd += " -G 12 -E 2 ";
-                    } else if (gapCost.equals(GAPB45_9)) {
-                        cmd += " -G 19 -E 1 ";
-                    } else if (gapCost.equals(GAPB45_10)) {
-                        cmd += " -G 18 -E 1 ";
-                    } else if (gapCost.equals(GAPB45_11)) {
-                        cmd += " -G 17 -E 1 ";
-                    } else if (gapCost.equals(GAPB45_12)) {
-                        cmd += " -G 16 -E 1 ";
-                    } else if (gapCost.equals(GAPB45_6)) {
-                        cmd += " -G 11 -E 1 ";
-                    } else if (gapCost.equals(GAPP30_1)) {
-                        cmd += " -G 9 -E 1 ";
-                    } else if (gapCost.equals(GAPP30_4)) {
-                        cmd += " -G 5 -E 2 ";
-                    } else if (gapCost.equals(GAPP30_2)) {
-                        cmd += " -G 7 -E 2 ";
-                    } else if (gapCost.equals(GAPP30_3)) {
-                        cmd += " -G 6 -E 2 ";
-                    } else if (gapCost.equals(GAPP30_5)) {
-                        cmd += " -G 8 -E 1 ";
-                    } else if (gapCost.equals(GAPB80_1)) {
-                        cmd += " -G 10 -E 1 ";
-                    } else if (gapCost.equals(GAPB80_2)) {
-                        cmd += " -G 8 -E 2 ";
-                    } else if (gapCost.equals(GAPB80_3)) {
-                        cmd += " -G 7 -E 2 ";
-                    } else if (gapCost.equals(GAPB80_4)) {
-                        cmd += " -G 6 -E 2 ";
-                    } else if (gapCost.equals(GAPB80_5)) {
-                        cmd += " -G 11 -E 1 ";
-                    } else if (gapCost.equals(GAPB80_6)) {
-                        cmd += " -G 9 -E 1 ";
-                    }  else if (gapCost.equalsIgnoreCase("Linear")) {
-                        cmd += " -G 0 -E 0 ";
-                    } else if (gapCost.equals(GAPB0_2)) {
-                        cmd += " -G 5 -E 2 ";
-                    } else if (gapCost.equals(GAPB0_3)) {
-                        cmd += " -G 2 -E 2 ";
-                    } else if (gapCost.equals(GAPB0_4)) {
-                        cmd += " -G 1 -E 2 ";
-                    } else if (gapCost.equals(GAPB0_5)) {
-                        cmd += " -G 0 -E 2 ";
-                    } else if (gapCost.equals(GAPB0_6)) {
-                        cmd += " -G 3 -E 1 ";
-                    } else if (gapCost.equals(GAPB0_7)) {
-                        cmd += " -G 2 -E 1 ";
-                    } else if (gapCost.equals(GAPB0_8)) {
-                        cmd += " -G 1 -E 1 ";
-                    } else if (gapCost.equals(GAPB1_1)) {
-                        cmd += " -G 4 -E 4 ";
-                    } else if (gapCost.equals(GAPB1_2)) {
-                        cmd += " -G 2 -E 4 ";
-                    } else if (gapCost.equals(GAPB1_3)) {
-                        cmd += " -G 0 -E 4 ";
-                    } else if (gapCost.equals(GAPB1_4)) {
-                        cmd += " -G 3 -E 3 ";
-                    } else if (gapCost.equals(GAPB1_5)) {
-                        cmd += " -G 6 -E 2 ";
-                    } else if (gapCost.equals(GAPB1_6)) {
-                        cmd += " -G 5 -E 2 ";
-                    } else if (gapCost.equals(GAPB1_7)) {
-                        cmd += " -G 4 -E 2 ";
-                    } else if (gapCost.equals(GAPB1_8)) {
-                        cmd += " -G 2 -E 2 ";
-                    }
-                }
-
-            } 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";
-                }
-                if (ps.isHumanRepeatFilterOn()) {
-                    cmd += "&FILTER=R";
-                }
-
-                if (ps.isExcludeModelsOn()){
-                	cmd += "&EXCLUDE_MODELS=yes";
-                }
-                if (ps.isExcludeUncultureOn()){
-                	cmd += "&EXCLUDE_SEQ_UNCULT=yes";
-                }
-                if (!(ps.getEntrezQuery()==null)||(ps.getEntrezQuery().trim()!="")){
-                	String entrezQuery = ps.getEntrezQuery();
-                	try {
-                		entrezQuery = URLEncoder.encode(entrezQuery, "UTF-8");
-        		    } catch (UnsupportedEncodingException ex) {
-        			    throw new RuntimeException("UTF-8 not supported", ex);
-        		    }
-                	cmd += "&EQ_TEXT="+entrezQuery;
-                }
-                if (!(ps.getFromQuery()==null)||(ps.getFromQuery().trim()!="")){
-                	cmd += "&QUERY_FROM="+ps.getFromQuery();
-                }
-                if (!(ps.getToQuery()==null)||(ps.getToQuery().trim()!="")){
-                	cmd += "&QUERY_TO="+ps.getToQuery();
-                }
-
-                if(ps.getProgramName().equalsIgnoreCase("blastn")){
-                	cmd +="&PAGE=MegaBlast";
-	                if (ps.isMegaBlastOn()){
-	                	cmd += "&BLAST_PROGRAMS=megaBlast";
-	                	cmd+="&MEGABLAST=on";
-	            		cmd+="&SELECTED_PROG_TYPE=megaBlast";
-	                }
-	                else if (ps.isDiscontiguousOn()){
-	                	cmd += "&BLAST_PROGRAMS=discoMegablast";
-	                	cmd+="&SELECTED_PROG_TYPE=discoMegablast";
-	                	cmd+="&MEGABLAST=on";
-
-	                    if (ps.getTemplateLength() != null) {
-	                       cmd += "&TEMPLATE_LENGTH=" + template2number.get(ps.getTemplateLength());
-	                    }
-	                    if (ps.getTemplateType() != null) {
-	                        cmd += "&TEMPLATE_TYPE=" + template2number.get(ps.getTemplateType());
-	                    }
-
-	                }
-	                else if (ps.isBlastnBtnOn()){
-	                	cmd += "&BLAST_PROGRAMS=blastn";
-	                }
-                }
-                else cmd += "&BLAST_PROGRAMS="+ps.getProgramName();
-                if (ps.getProgramName().equalsIgnoreCase("blastp"))
-                	cmd +="&PAGE=Proteins";
-                if(ps.getProgramName().equalsIgnoreCase("blastx")||ps.getProgramName().equalsIgnoreCase("tblastn")||ps.getProgramName().equalsIgnoreCase("tblastx")){
-                	cmd +="&PAGE=Translations";
-                	cmd +="&PAGE_TYPE=BlastSearch";
-                }
-                if (ps.getProgramName().equalsIgnoreCase("blastx")||ps.getProgramName().equalsIgnoreCase("tblastx")){
-                	cmd +="&GENETIC_CODE="+ geneticCode2number.get(ps.getGeneticCode());
-                }
-                if (ps.getProgramName().equalsIgnoreCase("blastp")||ps.getProgramName().equalsIgnoreCase("tblastn")){
-                	cmd +="&COMPOSITION_BASED_STATISTICS="+ compositional2number.get(ps.getCompositionalAdjustment());
-                }
-
-                if (ps.getProgramName().equalsIgnoreCase("blastp")||ps.getProgramName().equalsIgnoreCase("blastn")){
-	                if (ps.isShortQueriesOn()){
-	                	cmd += "&SHORT_QUERY_ADJUST=yes";
-	                }
-	            	else cmd += "&SHORT_QUERY_ADJUST=";
-                }
-
-                if (ps.isMaskLowCase()) {
-                    cmd += "&LCASE_MASK=yes";
-                }
-
-                if (ps.isMaskLookupTable()) {
-                    cmd += "&FILTER=m";
-                }
-                if (!ps.getMatrix().startsWith("dna")) {
-                    cmd += "&MATRIX_NAME=" + ps.getMatrix().trim();
-                }
-                if (ps.getWordsize() != null) {
-                    cmd += "&WORD_SIZE=" + ps.getWordsize().trim();
-                }
-                cmd+="&HSP_RANGE_MAX=" + ps.getHspRange().trim();
-                String gapCost = ps.getGapCost();
-                if (gapCost != null) {
-                	if(gapCost.equalsIgnoreCase("Linear")) gapCost="Existence: 0 Extension: 0";
-                    String[] s = gapCost.split(" ");
-                    if (s.length > 3) {
-                        cmd += "&GAPCOSTS=" + s[1].trim() + "%20" +
-                                s[3].trim();
-                    }
-                }
-
-                if(ps.getProgramName().equalsIgnoreCase("blastn")){
-	                String matchScores=ps.getMatchScores();
-	                if(matchScores!=null){
-	                	String[] s=matchScores.split(",");
-	                	if(s.length>1){
-	                		cmd+="&MATCH_SCORES=" + s[0].trim() + "%2C" + s[1].trim();
-	                	}
-	                }
-                }
-        		cmd+="&PAGE_TYPE=BlastSearch";
-
-                Map<String, String> specie_repeat=new HashMap<String,String>();
-                specie_repeat.put("Human","repeat_9606");
-                specie_repeat.put("Rodents","repeat_9989");
-                specie_repeat.put("Arabidopsis","repeat_3702");
-                specie_repeat.put("Rice","repeat_4530");
-                specie_repeat.put("Mammals","repeat_40674");
-                specie_repeat.put("Fungi","repeat_4751");
-                specie_repeat.put("C.elegans","repeat_6239");
-                specie_repeat.put("A.gambiae","repeat_7165");
-                specie_repeat.put("Zebrafish","repeat_7955");
-                specie_repeat.put("Fruit fly","repeat_7227");
-                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
-                	cmd += "&EXPECT=" + ps.getExpect() + "&AUTO_FORMAT=Semiauto&SHOW_OVERVIEW=on&SERVICE=plain\r\n\r\n";
-            }
-
-        }
-
-        return cmd;
-    }
-}
diff --git a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/.svn/text-base/BlastAppComponent.cwb.xml.svn-base b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/.svn/text-base/BlastAppComponent.cwb.xml.svn-base
deleted file mode 100644
index a6f9c89..0000000
--- a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/.svn/text-base/BlastAppComponent.cwb.xml.svn-base
+++ /dev/null
@@ -1,34 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<component-descriptor xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-	xsi:noNamespaceSchemaLocation="Descriptor Schema.xsd">
-
-	<component name="BLAST Analysis"
-		class="org.geworkbench.components.alignment.panels.BlastAppComponent"
-		version="1.0"
-		author="geWorkbench Development Team"
-		authorURL="http://wiki.c2b2.columbia.edu/workbench/index.php/Home"
-		toolURL="http://wiki.c2b2.columbia.edu/workbench/index.php/Home"
-		tutorialURL="http://wiki.c2b2.columbia.edu/workbench/index.php/BLAST"
-		description="The Sequence Alignment component allows amino-acid (protein)
- or nucleotide (DNA) sequences to be submitted to the NCBI BLAST server
- for sequence similarity search against various databases."
-		category="analysis" loadByDefault="true">
-		<required-component
-			class="org.geworkbench.components.alignment.panels.BlastViewComponent" />
-		<required-component
-			class="org.geworkbench.components.sequences.SequenceViewAppComponent" />
-		<related-component class="org.geworkbench.components.promoter.PromoterView" />
-		<license><![CDATA[
-			<html><head><meta http-equiv=Content-Type content="text/html; charset=windows-1252"></head>
-				<body>----</body>
-			</html>
-		]]></license>
-
-	</component>
-
-	<plugin id="BlastAppComponent" name="Sequence Alignment"
-		class="org.geworkbench.components.alignment.panels.BlastAppComponent"
-		source="alignment">
-		<gui-area name="CommandArea" />
-	</plugin>
-</component-descriptor>
diff --git a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/.svn/text-base/BlastAppComponent.java.svn-base b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/.svn/text-base/BlastAppComponent.java.svn-base
deleted file mode 100644
index 72d23c3..0000000
--- a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/.svn/text-base/BlastAppComponent.java.svn-base
+++ /dev/null
@@ -1,1473 +0,0 @@
-package org.geworkbench.components.alignment.panels;
-
-import java.awt.BorderLayout;
-import java.awt.Color;
-import java.awt.Component;
-import java.awt.Container;
-import java.awt.Dimension;
-import java.awt.FlowLayout;
-import java.awt.Font;
-import java.awt.GridBagConstraints;
-import java.awt.GridBagLayout;
-import java.awt.Insets;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.util.Date;
-
-import javax.swing.BorderFactory;
-import javax.swing.Box;
-import javax.swing.BoxLayout;
-import javax.swing.ButtonGroup;
-import javax.swing.DefaultComboBoxModel;
-import javax.swing.ImageIcon;
-import javax.swing.JButton;
-import javax.swing.JCheckBox;
-import javax.swing.JComboBox;
-import javax.swing.JFileChooser;
-import javax.swing.JLabel;
-import javax.swing.JOptionPane;
-import javax.swing.JPanel;
-import javax.swing.JProgressBar;
-import javax.swing.JRadioButton;
-import javax.swing.JScrollPane;
-import javax.swing.JTabbedPane;
-import javax.swing.JTable;
-import javax.swing.JTextArea;
-import javax.swing.JTextField;
-import javax.swing.JToolBar;
-import javax.swing.JViewport;
-import javax.swing.ListSelectionModel;
-import javax.swing.SwingConstants;
-import javax.swing.SwingUtilities;
-import javax.swing.UIManager;
-import javax.swing.border.Border;
-import javax.swing.border.TitledBorder;
-import javax.swing.event.ListSelectionEvent;
-import javax.swing.event.ListSelectionListener;
-import javax.swing.table.AbstractTableModel;
-import javax.swing.table.TableColumn;
-import javax.swing.table.TableModel;
-
-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.sequences.CSSequenceSet;
-import org.geworkbench.bison.datastructure.biocollections.sequences.DSSequenceSet;
-import org.geworkbench.bison.datastructure.bioobjects.markers.DSGeneMarker;
-import org.geworkbench.bison.datastructure.bioobjects.sequence.CSSequence;
-import org.geworkbench.bison.datastructure.bioobjects.sequence.DSSequence;
-import org.geworkbench.bison.datastructure.complex.panels.DSPanel;
-import org.geworkbench.components.alignment.blast.BlastAlgorithm;
-import org.geworkbench.engine.config.VisualPlugin;
-import org.geworkbench.engine.management.AcceptTypes;
-import org.geworkbench.engine.management.Asynchronous;
-import org.geworkbench.engine.management.Publish;
-import org.geworkbench.engine.management.Subscribe;
-import org.geworkbench.events.GeneSelectorEvent;
-
-/**
- *
- * @author not attributable
- * @version $Id$
- */
-//test
-@SuppressWarnings("unchecked")
-@AcceptTypes( {CSSequenceSet.class})
-public class BlastAppComponent implements VisualPlugin {
-	private static final String SELECT_A_PROGRAM_PROMPT = "Select a program";
-
-	private static final int DATABASE_NAME_INDEX = 1;
-
-	Log log = LogFactory.getLog(BlastAppComponent.class);
-
-	private static AlgorithmMatcher algorithmMatcher = AlgorithmMatcher.getInstance();
-
-	// members from the base class in the previous version
-	private DSSequenceSet<DSSequence> sequenceDB = null;
-	private CSSequenceSet<? extends DSSequence> activeSequenceDB = null;
-	private boolean activateMarkers = true;
-	private DSPanel<? extends DSGeneMarker> activatedMarkers = null;
-
-	private JPanel mainPanel;
-	private JToolBar displayToolBar;
-	private JCheckBox chkAllMarkers = new JCheckBox("All Markers");
-	private JTextField sequenceNumberField;
-
-	// members from originally in this class
-	private JPanel jBasicPane = new JPanel();
-    private JTabbedPane jTabbedPane1 = new JTabbedPane();
-    private JTabbedPane jTabbedBlastPane = new JTabbedPane();
-
-    //boxes for bug2019
-    private JCheckBox excludeModels = null;
-    private JCheckBox excludeUnculture = null;
-    private JLabel jexcludeLabel = new JLabel("Exclude: ");
-    private JLabel jEntrezQueryLabel=new JLabel("Entrez Query: ");
-    private JTextField jEntrezQueryText=new JTextField(10);
-    private JTextField jQueryFromText=new JTextField(5);
-    private JTextField jQueryToText=new JTextField(5);
-
-    private JRadioButton megablastBtn=null;
-    private JLabel jmegablastLabel = new JLabel("Optimize for: ");
-    private JRadioButton discontiguousBtn=null;
-    private JRadioButton blastnBtn=null;
-    private ButtonGroup programBtnGroup=new ButtonGroup();
-
-    private JLabel jgeneticCodeLabel = new JLabel("Genetic Code: ");
-    private JComboBox jgeneticCodeBox=new JComboBox();
-
-    // five check boxes in filter panel+...
-    private JCheckBox shortQueriesBox =null;
-    private JCheckBox lowComplexFilterBox = null;
-    private JCheckBox speciesRepeatFilter = null;
-    private JLabel jMaskLabel =new JLabel("Mask:");
-    private JCheckBox maskLowCaseBox = null;
-    private JCheckBox maskLookupOnlyBox = null;
-    private JLabel jDisplayLabel =new JLabel("Browser:");
-    private JCheckBox jDisplayInWebBox = null;
-
-    JPanel jAdvancedPane = new JPanel();
-    JFileChooser jFileChooser1 = new JFileChooser();
-
-    static final int BLAST = 0;//keep unchanged
-
-    public static final String NCBILABEL = "NCBI BLAST Result";
-    public static final String ERROR1 = "Interrupted";
-    public static final String ERROR2 = "The connection to the Columbia Blast Server cannot be established, please try NCBI Blast Server.";
-
-    private JTable databaseTable = null;
-    private JButton blastButton = new JButton();
-    private JScrollPane jScrollPane1 = new JScrollPane();
-
-    private JComboBox jProgramBox = new JComboBox();
-
-    private JPanel speciesRepeatPanel = new JPanel();
-    private JButton defaultButton = new JButton();
-
-    // pairs of label and combo box on blastxSettingPanel
-    private JLabel jMatrixLabel= new JLabel("Matrix:");
-    private JComboBox jMatrixBox = new JComboBox();
-    private JLabel maxTargetLabel= new JLabel("Max target sequences:");
-    private JComboBox jMaxTargetBox=new JComboBox();
-
-    private JComboBox jExpectBox = new JComboBox();
-    private JComboBox jWordsizeBox = new JComboBox();
-    private JTextField jHspRangeBox=new JTextField(5);
-
-    private JLabel jScoresLabel= new JLabel("Match/mismatch Scores:");
-    private JComboBox jScoresBox=new JComboBox();
-    private JLabel jGapcostsLabel = new JLabel("Gap costs:");
-    private JComboBox jGapcostsBox = new JComboBox();
-    private JLabel jCompositionalLabel= new JLabel("Compositional Adjustments:");
-    private JComboBox jCompositionalBox=new JComboBox();
-    private JComboBox jSpeciesBox=new JComboBox();
-    private JLabel jTemplateLengthLabel = new JLabel("Template Length:");
-    private JComboBox jTemplateLengthBox=new JComboBox();
-    private JLabel jTemplateTypeLabel = new JLabel("Template Type:");
-    private JComboBox jTemplateTypeBox=new JComboBox();
-
-    private BlastAppComponent blastAppComponent = null;
-    private JPanel subSeqPanel;
-    private JPanel subSeqPanel2;
-
-    private JTextField jstartPointField = new JTextField();
-    private JTextField jendPointField = new JTextField();
-    private JProgressBar serviceProgressBar = new JProgressBar();
-
-    private JButton blastStopButton = new JButton();
-
-    private JToolBar jToolBar2 = new JToolBar();
-
-    private Border border1 = BorderFactory.createEtchedBorder(Color.white,
-            new Color(165, 163, 151));
-    private Border border2 = new TitledBorder(border1,
-                                      "Please specify Program and Database");
-    private Border border3 = new TitledBorder(border1, "Database Details");
-    private JTextArea textArea = new JTextArea();
-
-    private ImageIcon startButtonIcon = new ImageIcon(this.getClass().getResource(
-            "start.gif"));
-    private ImageIcon stopButtonIcon = new ImageIcon(this.getClass().getResource(
-            "stop.gif"));
-
-    private JPanel jPanel3 = new JPanel();
-    private BorderLayout borderLayout2 = new BorderLayout();
-
-    private BorderLayout borderLayout3 = new BorderLayout();
-    private JScrollPane jScrollPane4 = new JScrollPane();
-    private static final int MAIN = 0;
-    private static final int SERVER = 2;
-
-    private boolean stopButtonPushed;
-
-	private JPanel discontiguousWordOptionsPanel;
-
-	private JPanel geneticCodePanel;
-
-    private static JLabel DatabaseLabel = new JLabel("Database:");
-
-    private String programForDefaultButton="blastn";
-
-    private JPanel chooseSearchPanel=new JPanel();
-
-    public BlastAppComponent() {
-        try {
-        	init1();
-        	init2();
-        } catch (Exception e) {
-            e.printStackTrace();
-        }
-    }
-
-    private void init2() throws Exception {
-
-        jBasicPane = new JPanel();
-        jTabbedPane1 = new JTabbedPane();
-        jTabbedBlastPane = new JTabbedPane();
-
-        jScrollPane4 = new JScrollPane();
-
-        databaseTable = new JTable() // customized only to hide the header
-        {
-			private static final long serialVersionUID = -7546361375519248646L;
-
-			protected void configureEnclosingScrollPane() {
-                Container p = getParent();
-                if (p instanceof JViewport) {
-                    Container gp = p.getParent();
-                    if (gp instanceof JScrollPane) {
-                        JScrollPane scrollPane = (JScrollPane)gp;
-                        // Make certain we are the viewPort's view and not, for
-                        // example, the rowHeaderView of the scrollPane -
-                        // an implementor of fixed columns might do this.
-                        JViewport viewport = scrollPane.getViewport();
-                        if (viewport == null || viewport.getView() != this) {
-                            return;
-                        }
-//                        scrollPane.setColumnHeaderView(getTableHeader());
-                        scrollPane.getViewport().setScrollMode(JViewport.BACKINGSTORE_SCROLL_MODE );
-                        scrollPane.setBorder(UIManager.getBorder("Table.scrollPaneBorder"));
-                    }
-                }
-            }
-        };
-
-        blastButton = new JButton();
-        jScrollPane1 = new JScrollPane();
-        jProgramBox = new JComboBox();
-
-        jstartPointField = new JTextField();
-        jendPointField = new JTextField();
-        serviceProgressBar = new JProgressBar();
-
-        blastStopButton = new JButton();
-
-        jToolBar2 = new JToolBar();
-
-        border1 = BorderFactory.createEtchedBorder(Color.white,
-                new Color(165, 163, 151));
-        border2 = new TitledBorder(border1,
-                                   "Please specify Program and Database");
-
-        startButtonIcon = new ImageIcon(this.getClass().getResource(
-                "start.gif"));
-        stopButtonIcon = new ImageIcon(this.getClass().getResource(
-                "stop.gif"));
-
-        jPanel3 = new JPanel();
-        borderLayout2 = new BorderLayout();
-
-        borderLayout3 = new BorderLayout();
-
-        geneticCodePanel = new JPanel();
-
-        //above is part of code to get rid of npe.
-        //sgePanel.setPv(this);
-        subSeqPanel = new JPanel();
-        subSeqPanel.setBorder(border2);
-        subSeqPanel2 = new JPanel();
-        subSeqPanel2.setBorder(border3);
-
-        jBasicPane.setPreferredSize(new Dimension(364, 250));
-        jBasicPane.setLayout(borderLayout2);
-
-        jPanel3.setLayout(borderLayout3);
-
-        databaseTable.setToolTipText("Select a database");
-        databaseTable.setVerifyInputWhenFocusTarget(true);
-        databaseTable.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
-        jProgramBox.addItem(SELECT_A_PROGRAM_PROMPT);
-        jProgramBox.addItem("blastn");
-        jProgramBox.addItem("blastp");
-        jProgramBox.addItem("blastx");
-        jProgramBox.addItem("tblastn");
-        jProgramBox.addItem("tblastx");
-
-        defaultButton.setText("Restore Defaults");
-        defaultButton.addActionListener(new
-                BlastAppComponent_default_actionAdapter());
-
-        blastButton.setFont(new java.awt.Font("Arial Black", 0, 11));
-        blastButton.setHorizontalAlignment(SwingConstants.LEFT);
-        blastButton.setHorizontalTextPosition(SwingConstants.CENTER);
-        //blastButton.setText("BLAST");
-        blastButton.setIcon(startButtonIcon);
-
-        blastButton.setToolTipText("Start BLAST");
-
-        blastButton.addActionListener(new
-                                      BlastAppComponent_blastButton_actionAdapter());
-        jTabbedPane1.setDebugGraphicsOptions(0);
-        jTabbedPane1.setMinimumSize(new Dimension(5, 5));
-        jProgramBox.addActionListener(new
-                                      BlastAppComponent_jProgramBox_actionAdapter());
-        databaseTable.getSelectionModel().addListSelectionListener(new BlastAppComponent_jDBList_listSelectionListener() );
-
-        // details of four combo boxes on plastx panel
-        // (1)
-        jMatrixBox
-				.addActionListener(new BlastAppComponent_jMatrixBox_actionAdapter());
-        jMatrixBox.addItem("dna.mat");
-        jMatrixBox.setVerifyInputWhenFocusTarget(true);
-        jMatrixBox.setSelectedIndex(0);
-        // (2)
-
-        jExpectBox.setVerifyInputWhenFocusTarget(true);
-        jExpectBox.addItem("0.000000001");
-        jExpectBox.addItem("0.01");
-        jExpectBox.addItem("0.1");
-        jExpectBox.addItem("1");
-        jExpectBox.addItem("10");
-        jExpectBox.addItem("100");
-        jExpectBox.addItem("1000");
-        jExpectBox.setEditable(true);
-
-        // (3)
-        jGapcostsBox.setVerifyInputWhenFocusTarget(true);
-    	String defaulMatrixName = "BLOSUM62";
-        String[] model = AlgorithmMatcher.translateToGapcosts(defaulMatrixName);
-       	jGapcostsBox.setModel(new DefaultComboBoxModel(model));
-       	Integer index = AlgorithmMatcher.defaultGapcostIndex.get(defaulMatrixName);
-       	if(index==null) index = 0;
-       	jGapcostsBox.setSelectedIndex(index);
-
-        // (4)
-        jWordsizeBox.addItem("3");
-        jWordsizeBox.addItem("2");
-        jWordsizeBox.addItem("7");
-        jWordsizeBox.addItem("11");
-        jWordsizeBox.addItem("15");
-        jWordsizeBox.setMaximumRowCount(10);
-
-        //(5)
-        jScoresBox.addItem("1,-2");
-        jScoresBox.addItem("1,-3");
-        jScoresBox.addItem("1,-4");
-        jScoresBox.addItem("2,-3");
-        jScoresBox.addItem("4,-5");
-        jScoresBox.addItem("1,-1");
-
-        jCompositionalBox.addItem("No adjustment");
-        jCompositionalBox.addItem("Composition-based statistics");
-        jCompositionalBox.addItem("Conditional compositional score matrix adjustment");
-        jCompositionalBox.addItem("Universal compositional score matrix adjustment");
-
-        jSpeciesBox.addItem("Human");
-        jSpeciesBox.addItem("Rodents");
-        jSpeciesBox.addItem("Arabidopsis");
-        jSpeciesBox.addItem("Rice");
-        jSpeciesBox.addItem("Mammals");
-        jSpeciesBox.addItem("Fungi");
-        jSpeciesBox.addItem("C.elegans");
-        jSpeciesBox.addItem("A.gambiae");
-        jSpeciesBox.addItem("Zebrafish");
-        jSpeciesBox.addItem("Fruit fly");
-        jSpeciesBox.setMaximumRowCount(10);
-
-        jTemplateLengthBox.addItem("None");
-        jTemplateLengthBox.addItem("16");
-        jTemplateLengthBox.addItem("18");
-        jTemplateLengthBox.addItem("21");
-
-        jTemplateTypeBox.addItem("Coding");
-        jTemplateTypeBox.addItem("Maximal");
-        jTemplateTypeBox.addItem("Two template");
-
-        jgeneticCodeBox.addItem("Standard (1)");
-        jgeneticCodeBox.addItem("Vertebrate Mitochondrial (2)");
-        jgeneticCodeBox.addItem("Yeast Mitochondrial (3)");
-        jgeneticCodeBox.addItem("Mold Mitochondrial (4)");
-        jgeneticCodeBox.addItem("Invertebrate Mitochondrial (5)");
-        jgeneticCodeBox.addItem("Ciliate Nuclear(6)");
-        jgeneticCodeBox.addItem("Echinoderm Mitochondrial (9)");
-        jgeneticCodeBox.addItem("Euplotid Nuclear (10)");
-        jgeneticCodeBox.addItem("Bacteria and Archaea (11)");
-        jgeneticCodeBox.addItem("Alternative Yeast Nuclear (12)");
-        jgeneticCodeBox.addItem("Ascidian Mitochondrial (13)");
-        jgeneticCodeBox.addItem("Flatworm Mitochondrial (14)");
-        jgeneticCodeBox.addItem("Blepharisma Macronuclear (15)");
-        jgeneticCodeBox.setMaximumRowCount(13);
-
-        jMaxTargetBox.addItem("10");
-        jMaxTargetBox.addItem("50");
-        jMaxTargetBox.addItem("100");
-        jMaxTargetBox.addItem("250");
-        jMaxTargetBox.addItem("500");
-        jMaxTargetBox.addItem("1000");
-        jMaxTargetBox.addItem("5000");
-        jMaxTargetBox.addItem("10000");
-        jMaxTargetBox.addItem("20000");
-        jMaxTargetBox.setMaximumRowCount(10);
-
-        jAdvancedPane.setLayout(new GridBagLayout());
-
-        jProgramBox.setAutoscrolls(false);
-        subSeqPanel.setLayout(new BoxLayout(subSeqPanel, BoxLayout.Y_AXIS));
-        subSeqPanel2.setLayout(new BoxLayout(subSeqPanel2, BoxLayout.Y_AXIS));
-
-        jstartPointField.setText("1");
-        jendPointField.setText("");
-
-        blastStopButton.setFont(new java.awt.Font("Arial Black", 0, 11));
-        blastStopButton.setVerifyInputWhenFocusTarget(true);
-        //blastStopButton.setText("STOP");
-        blastStopButton.setIcon(stopButtonIcon);
-        blastStopButton.setToolTipText("Stop the Query");
-
-        blastStopButton.addActionListener(new
-                                          BlastAppComponent_blastStopButton_actionAdapter());
-
-        jToolBar2.setLayout(new BoxLayout(jToolBar2, BoxLayout.LINE_AXIS));
-        jToolBar2.add(serviceProgressBar);
-        serviceProgressBar.setOrientation(JProgressBar.HORIZONTAL);
-        serviceProgressBar.setBorder(BorderFactory.createEtchedBorder());
-        serviceProgressBar.setStringPainted(true);
-
-        jTabbedPane1.add(jTabbedBlastPane, "BLAST");
-
-        excludeModels = new JCheckBox();
-        excludeModels.setMinimumSize(new Dimension(10, 23));
-        excludeModels.setMnemonic(0);
-        excludeModels.setSelected(false);
-        excludeModels.setText("Models(XM/XP)");
-
-        excludeUnculture = new JCheckBox();
-        excludeUnculture.setMinimumSize(new Dimension(10, 23));
-        excludeUnculture.setMnemonic(0);
-        excludeUnculture.setSelected(false);
-        excludeUnculture.setText("Uncultured/environmental sequences");
-
-        megablastBtn=new JRadioButton();
-        megablastBtn.setMinimumSize(new Dimension(10,23));
-        megablastBtn.setMnemonic(0);
-        megablastBtn.setSelected(true);
-        megablastBtn.setText("Highly similar sequences (megablast)");
-        megablastBtn.addActionListener(new BlastAppComponent_megablastBtn_actionAdapter());
-
-        discontiguousBtn=new JRadioButton();
-        discontiguousBtn.setMinimumSize(new Dimension(10,23));
-        discontiguousBtn.setMnemonic(0);
-        discontiguousBtn.setText("More dissimilar sequences (discontiguous megablast)");
-        discontiguousBtn.addActionListener(new BlastAppComponent_discontiguousBtn_actionAdapter());
-
-        blastnBtn=new JRadioButton();
-        blastnBtn.setMinimumSize(new Dimension(10,23));
-        blastnBtn.setMnemonic(0);
-        blastnBtn.setText("Somewhat similar sequences (blastn)");
-        blastnBtn.addActionListener(new BlastAppComponent_discontiguousBtn_actionAdapter());
-
-        programBtnGroup.add(megablastBtn);
-        programBtnGroup.add(discontiguousBtn);
-        programBtnGroup.add(blastnBtn);
-
-        // 5 check boxes on filter panel+...
-        shortQueriesBox=new JCheckBox();
-        shortQueriesBox.setMnemonic('0');
-        shortQueriesBox.setSelected(true);
-        shortQueriesBox.setText("Automatically adjust parameters for short input sequences");
-
-        lowComplexFilterBox = new JCheckBox();
-        lowComplexFilterBox.setMnemonic('0');
-        lowComplexFilterBox.setSelected(false);
-        lowComplexFilterBox.setText("Low Complexity");
-
-        maskLowCaseBox = new JCheckBox();
-        maskLowCaseBox.setToolTipText("Filterl lower case sequences.");
-        maskLowCaseBox.setText("Mask lower case letter");
-
-        maskLookupOnlyBox = new JCheckBox();
-        maskLookupOnlyBox.setText("Mask for lookup table only");
-        maskLookupOnlyBox.setMnemonic('0');
-        maskLookupOnlyBox.setSelected(false);
-
-        speciesRepeatFilter = new JCheckBox();
-        speciesRepeatFilter.setToolTipText("Species_specific Repeat Filter");
-        speciesRepeatFilter.setSelected(false);
-        speciesRepeatFilter.setText("Species-specific repeats for");
-
-        jDisplayInWebBox = new JCheckBox();
-        jDisplayInWebBox.setSelected(true);
-        jDisplayInWebBox.setText("Display result in your web browser");
-
-        // speciesRepeatPanel: including 2 items
-        speciesRepeatPanel = new JPanel();
-        speciesRepeatPanel.setLayout(new FlowLayout(FlowLayout.LEADING));
-        speciesRepeatPanel.add(new JLabel("          "));
-        speciesRepeatPanel.add(speciesRepeatFilter);
-        speciesRepeatPanel.add(jSpeciesBox);
-
-        // update tooltip text
-        // based on information from http://blast.ncbi.nlm.nih.gov/Blast.cgi and http://www.ncbi.nlm.nih.gov/BLAST/matrix_info.html
-        jMaxTargetBox.setToolTipText("Select the maximum number of aligned sequences to display");
-        jExpectBox.setToolTipText("Random background noise");
-        jWordsizeBox.setToolTipText("The length of the words governing the sensitivity");
-        jHspRangeBox.setToolTipText("Limit the number of matches to a query range");
-        jMatrixBox.setToolTipText("Assigns a score for aligning any possible pair of residues");
-        jGapcostsBox.setToolTipText("Score subtracted due to the gaps");
-        excludeModels.setToolTipText("Models(XM/XP)");
-        excludeUnculture.setToolTipText("Uncultured/environmental sample sequences");
-        jEntrezQueryText.setToolTipText("Enter an Entrez query to limit search ");
-        jQueryFromText.setToolTipText("Sequence coordinates are from 1 to the sequence length");
-        jQueryToText.setToolTipText("Sequence coordinates are from 1 to the sequence length");
-        megablastBtn.setToolTipText("Highly similar sequences (megablast)");
-        discontiguousBtn.setToolTipText("More dissimilar sequences (discontiguous megablast)");
-        blastnBtn.setToolTipText("Somewhat similar sequences (blastn)");
-
-		// jTabbedBlastPane contains two panels
-		jTabbedBlastPane.add(jBasicPane, "Main");
-        jTabbedBlastPane.add(new JScrollPane(jAdvancedPane), "Algorithm Parameters");
-        jAdvancedPane.setEnabled(false);
-
-        // mainPanel contains one tabbed pane
-        mainPanel.add(jTabbedPane1, java.awt.BorderLayout.CENTER);
-
-        JPanel programPanel = new JPanel();
-        programPanel.setLayout(new FlowLayout(FlowLayout.LEADING) );
-        programPanel.add(new JLabel("Program: "));
-        programPanel.add(jProgramBox);
-        programPanel.setAlignmentX(Component.LEFT_ALIGNMENT);
-        subSeqPanel.add(programPanel);
-
-        JPanel discontinguousPanel = new JPanel();
-        discontinguousPanel.setLayout(new BoxLayout(discontinguousPanel, BoxLayout.X_AXIS) );
-        discontinguousPanel.setBorder(BorderFactory.createEmptyBorder(10,10,10,10));
-        jmegablastLabel.setAlignmentY(Component.TOP_ALIGNMENT);
-        discontinguousPanel.add(jmegablastLabel);
-        JPanel discontinguousOptionsPanel = new JPanel();
-        discontinguousOptionsPanel.setLayout(new BoxLayout(discontinguousOptionsPanel, BoxLayout.Y_AXIS));
-        discontinguousOptionsPanel.add(megablastBtn);
-        discontinguousOptionsPanel.add(discontiguousBtn);
-        discontinguousOptionsPanel.add(blastnBtn);
-        discontinguousOptionsPanel.setAlignmentY(Component.TOP_ALIGNMENT);
-        discontinguousPanel.add(discontinguousOptionsPanel);
-        discontinguousPanel.setAlignmentX(Component.LEFT_ALIGNMENT);
-        subSeqPanel.add(discontinguousPanel);
-        enableBlastnRelateOptions(false);
-
-        geneticCodePanel.setLayout(new FlowLayout(FlowLayout.LEADING));
-        geneticCodePanel.add(jgeneticCodeLabel);
-        geneticCodePanel.add(jgeneticCodeBox);
-        geneticCodePanel.setAlignmentX(Component.LEFT_ALIGNMENT);
-        subSeqPanel.add(geneticCodePanel);
-        geneticCodePanel.setVisible(false);
-
-        DatabaseLabel.setAlignmentX(Component.LEFT_ALIGNMENT);
-        subSeqPanel.add(DatabaseLabel);
-        jScrollPane1.setPreferredSize(new Dimension(300, 100));
-        jScrollPane1.setAlignmentX(Component.LEFT_ALIGNMENT);
-        subSeqPanel.add(jScrollPane1);
-
-        textArea.setBackground(subSeqPanel2.getBackground());
-        textArea.setEditable(false);
-        textArea.setLineWrap(true); //wrap text around
-        textArea.setFont(new Font("Monospaced", Font.PLAIN, 12));
-        textArea.setPreferredSize(new Dimension(350, 100));
-        subSeqPanel2.add(textArea);
-
-        chooseSearchPanel.setLayout(new GridBagLayout());
-
-        JPanel excludePanel = new JPanel();
-        excludePanel.setLayout(new BoxLayout(excludePanel, BoxLayout.Y_AXIS) );
-        excludePanel.setBorder(new TitledBorder(border1, "Search Choice (optional)"));
-
-        JPanel excludeOptions1Panel = new JPanel();
-        excludeOptions1Panel.setLayout(new FlowLayout(FlowLayout.LEADING) );
-        excludeOptions1Panel.add(jexcludeLabel);
-        excludeOptions1Panel.add(excludeModels);
-        excludePanel.add(excludeOptions1Panel);
-        JPanel excludeOptions2Panel = new JPanel();
-        excludeOptions2Panel.setLayout(new FlowLayout(FlowLayout.LEADING) );
-        excludeOptions2Panel.add(new JLabel("                "));
-        excludeOptions2Panel.add(excludeUnculture);
-        excludePanel.add(excludeOptions2Panel);
-
-        JPanel entrezQueryPanel = new JPanel();
-        entrezQueryPanel.setLayout(new FlowLayout(FlowLayout.LEADING) );
-        entrezQueryPanel.add(jEntrezQueryLabel);
-        entrezQueryPanel.add(jEntrezQueryText);
-
-        jEntrezQueryText.setText("");
-        jEntrezQueryLabel.setVisible(false);
-		jEntrezQueryText.setVisible(false);
-        excludePanel.add(entrezQueryPanel);
-
-        GridBagConstraints b = new GridBagConstraints(0, 0, 1, 1,
-				0.0, 0.0, GridBagConstraints.WEST,
-				GridBagConstraints.NONE, new Insets(2, 2, 2, 2), 0, 0);
-        b.gridx = 0;
-        b.gridy = 0;
-        chooseSearchPanel.add(excludePanel,b);
-
-		JPanel querySubrangePanel=new JPanel();
-		querySubrangePanel.setBorder(new TitledBorder(border1, "Query Subrange"));
-		querySubrangePanel.setLayout(new BoxLayout(querySubrangePanel, BoxLayout.Y_AXIS) );
-		//querySubrangePanel.setBorder(BorderFactory.createEmptyBorder(10,10,10,10));
-
-		JPanel queryFromPanel = new JPanel();
-		queryFromPanel.setLayout(new FlowLayout(FlowLayout.LEADING));
-		queryFromPanel.add(new JLabel("From:"));
-		queryFromPanel.add(jQueryFromText);
-		querySubrangePanel.add(queryFromPanel);
-
-		JPanel queryToPanel = new JPanel();
-		queryToPanel.setLayout(new FlowLayout(FlowLayout.LEADING));
-		queryToPanel.add(new JLabel("To:     "));
-		queryToPanel.add(jQueryToText);
-		querySubrangePanel.add(queryToPanel);
-        b.gridx = 1;
-        b.gridy = 0;
-        chooseSearchPanel.add(querySubrangePanel,b);
-        chooseSearchPanel.setAlignmentX(Component.LEFT_ALIGNMENT);
-		subSeqPanel.add(chooseSearchPanel);
-		chooseSearchPanel.setVisible(false);
-
-        displayToolBar.add(Box.createHorizontalStrut(10), null);
-        displayToolBar.add(blastButton);
-        displayToolBar.add(Box.createHorizontalStrut(5), null);
-        displayToolBar.add(blastStopButton);
-        jScrollPane4.getViewport().add(jPanel3);
-        jPanel3.add(subSeqPanel, BorderLayout.CENTER);
-        jPanel3.add(subSeqPanel2, BorderLayout.EAST);
-        jBasicPane.add(jScrollPane4, java.awt.BorderLayout.CENTER);
-        jBasicPane.add(jToolBar2, java.awt.BorderLayout.NORTH);
-
-        jTabbedPane1.setSelectedComponent(jTabbedBlastPane);
-        jTabbedBlastPane.setSelectedComponent(jBasicPane);
-    }
-
-    static private class UneditableTableModel extends AbstractTableModel {
-		private static final long serialVersionUID = 1231350431097267149L;
-
-		private String[][] data;
-
-    	UneditableTableModel(String[][] data) {
-    		this.data = data;
-    	}
-
-		@Override
-		public int getColumnCount() {
-			return 2;
-		}
-
-		@Override
-		public int getRowCount() {
-			return data.length;
-		}
-
-		@Override
-		public Object getValueAt(int rowIndex, int columnIndex) {
-			return data[rowIndex][columnIndex];
-		}
-
-		@Override
-		public boolean isCellEditable(int rowIndex,
-                int columnIndex) {
-			return false;
-		}
-    }
-
-    private void enableBlastnRelateOptions(Boolean b){
-    	geneticCodePanel.setVisible(false);
-    	if(((String) jProgramBox.getSelectedItem()).equalsIgnoreCase("blastn")&&b){
-    		megablastBtn.setVisible(b);
-    		discontiguousBtn.setVisible(b);
-    		blastnBtn.setVisible(b);
-    		jmegablastLabel.setVisible(b);
-    	}
-    	else{
-    		megablastBtn.setVisible(false);
-    		discontiguousBtn.setVisible(false);
-    		blastnBtn.setVisible(false);
-    		jmegablastLabel.setVisible(false);
-    	}
-    	jexcludeLabel.setVisible(b);
-		excludeModels.setVisible(b);
-		excludeUnculture.setVisible(b);
-    }
-
-    private void setAdvancedOptions(){
-    	String selectedProgramName = programForDefaultButton;
-		jAdvancedPane.removeAll();
-		jEntrezQueryLabel.setVisible(true);
-		jEntrezQueryText.setVisible(true);
-		enableBlastnRelateOptions(true);
-		if(selectedProgramName.equalsIgnoreCase("blastx")||selectedProgramName.equalsIgnoreCase("tblastx")){
-			geneticCodePanel.setVisible(true);
-		}
-
-        JPanel generalParametersPanel = new JPanel();
-        generalParametersPanel.setBorder( new TitledBorder(border1, "General Parameters"));
-        generalParametersPanel.setLayout(new BoxLayout(generalParametersPanel, BoxLayout.Y_AXIS));
-        JPanel maxTargetPanel = new JPanel();
-        maxTargetPanel.setLayout(new FlowLayout(FlowLayout.LEADING) );
-        maxTargetPanel.add(maxTargetLabel);
-        maxTargetPanel.add(jMaxTargetBox);
-        maxTargetPanel.setAlignmentX(Component.LEFT_ALIGNMENT);
-        generalParametersPanel.add(maxTargetPanel);
-        shortQueriesBox.setAlignmentX(Component.LEFT_ALIGNMENT);
-        generalParametersPanel.add(shortQueriesBox);
-        JPanel expectThresholdPanel = new JPanel();
-        expectThresholdPanel.setLayout(new FlowLayout(FlowLayout.LEADING) );
-		expectThresholdPanel.add(new JLabel("Expect threshold:"));
-        expectThresholdPanel.add(jExpectBox);
-        expectThresholdPanel.setAlignmentX(Component.LEFT_ALIGNMENT);
-        generalParametersPanel.add(expectThresholdPanel);
-        JPanel wordSizePanel = new JPanel();
-        wordSizePanel.setLayout(new FlowLayout(FlowLayout.LEADING) );
-        wordSizePanel.add(new JLabel("Word size:"));
-        wordSizePanel.add(jWordsizeBox);
-        wordSizePanel.setAlignmentX(Component.LEFT_ALIGNMENT);
-        generalParametersPanel.add(wordSizePanel);
-        JPanel hspRangePanel = new JPanel();
-        hspRangePanel.setLayout(new FlowLayout(FlowLayout.LEADING) );
-        hspRangePanel.add(new JLabel("Max matches in a query range:"));
-        hspRangePanel.add(jHspRangeBox);
-        hspRangePanel.setAlignmentX(Component.LEFT_ALIGNMENT);
-        generalParametersPanel.add(hspRangePanel);
-        jHspRangeBox.setText("0");
-
-        GridBagConstraints c = new GridBagConstraints(0, 0, 1, 1,
-				0.0, 0.0, GridBagConstraints.WEST,
-				GridBagConstraints.NONE, new Insets(2, 2, 2, 2), 0, 0);
-        jAdvancedPane.add(generalParametersPanel, c);
-
-        JPanel scoringParametersPanel = new JPanel();
-        scoringParametersPanel.setBorder(new TitledBorder(border1, "Scoring Paremeters"));
-        scoringParametersPanel.setLayout(new BoxLayout(scoringParametersPanel, BoxLayout.Y_AXIS));
-        JPanel maxtrixPanel = new JPanel();
-        maxtrixPanel.setLayout(new FlowLayout(FlowLayout.LEADING) );
-        maxtrixPanel.add(jMatrixLabel);
-        maxtrixPanel.add(jMatrixBox);
-        maxtrixPanel.setAlignmentX(Component.LEFT_ALIGNMENT);
-        scoringParametersPanel.add(maxtrixPanel);
-        JPanel scoresPanel = new JPanel();
-        scoresPanel.setLayout(new FlowLayout(FlowLayout.LEADING));
-        scoresPanel.add(jScoresLabel);
-        scoresPanel.add(jScoresBox);
-        scoresPanel.setAlignmentX(Component.LEFT_ALIGNMENT);
-        scoringParametersPanel.add(scoresPanel);
-        JPanel gapCostsPanel = new JPanel();
-        gapCostsPanel.setLayout(new FlowLayout(FlowLayout.LEADING));
-        gapCostsPanel.add(jGapcostsLabel);
-        gapCostsPanel.add(jGapcostsBox);
-        gapCostsPanel.setAlignmentX(Component.LEFT_ALIGNMENT);
-        scoringParametersPanel.add(gapCostsPanel);
-        JPanel compositionalPanel = new JPanel();
-        compositionalPanel.setLayout(new FlowLayout(FlowLayout.LEADING));
-        compositionalPanel.add(jCompositionalLabel);
-        compositionalPanel.add(jCompositionalBox);
-        compositionalPanel.setAlignmentX(Component.LEFT_ALIGNMENT);
-        scoringParametersPanel.add(compositionalPanel);
-        c.gridy = 1;
-        jAdvancedPane.add(scoringParametersPanel, c);
-
-        JPanel filterAndMaskPanel = new JPanel();
-        filterAndMaskPanel.setBorder(new TitledBorder(border1, "Filters and Masking"));
-        filterAndMaskPanel.setLayout(new BoxLayout(filterAndMaskPanel, BoxLayout.Y_AXIS));
-        JPanel filter1Panel = new JPanel();
-        filter1Panel.setLayout(new FlowLayout(FlowLayout.LEADING));
-        filter1Panel.add(new JLabel("Filter:"));
-        filter1Panel.add(lowComplexFilterBox);
-        filterAndMaskPanel.add(filter1Panel);
-        filterAndMaskPanel.add(speciesRepeatPanel);
-        JPanel mask1Panel = new JPanel();
-        mask1Panel.setLayout(new FlowLayout(FlowLayout.LEADING));
-        mask1Panel.add(jMaskLabel);
-        mask1Panel.add(maskLookupOnlyBox);
-        filterAndMaskPanel.add(mask1Panel);
-        JPanel mask2Panel = new JPanel();
-        mask2Panel.setLayout(new FlowLayout(FlowLayout.LEADING));
-        mask2Panel.add(new JLabel("          "));
-        mask2Panel.add(maskLowCaseBox);
-        filterAndMaskPanel.add(mask2Panel);
-        c.gridx = 1;
-        c.gridy = 0;
-        jAdvancedPane.add(filterAndMaskPanel, c);
-
-        JPanel browserPanel = new JPanel();
-        browserPanel.setLayout(new FlowLayout(FlowLayout.LEADING) );
-        browserPanel.add(jDisplayLabel);
-        browserPanel.add(jDisplayInWebBox);
-        browserPanel.setAlignmentX(Component.LEFT_ALIGNMENT);
-        c.gridx = 0;
-        c.gridy = 2;
-        jAdvancedPane.add(browserPanel, c);
-
-        JPanel defaultButtonPanel = new JPanel();
-        defaultButtonPanel.setLayout(new FlowLayout(FlowLayout.LEADING) );
-        defaultButtonPanel.add(defaultButton);
-        defaultButtonPanel.setAlignmentX(Component.LEFT_ALIGNMENT);
-        c.gridx = 1;
-        c.gridy = 2;
-        jAdvancedPane.add(defaultButtonPanel, c);
-
-        discontiguousWordOptionsPanel = new JPanel();
-        discontiguousWordOptionsPanel.setBorder(new TitledBorder(border1, "Discontiguous Word Options"));
-        discontiguousWordOptionsPanel.setLayout( new BoxLayout(discontiguousWordOptionsPanel, BoxLayout.Y_AXIS) );
-        JPanel templeateLengthPanel = new JPanel();
-        templeateLengthPanel.setLayout(new FlowLayout(FlowLayout.LEADING) );
-        templeateLengthPanel.add(jTemplateLengthLabel);
-        templeateLengthPanel.add(jTemplateLengthBox);
-        jTemplateLengthBox.setSelectedIndex(2);
-        discontiguousWordOptionsPanel.add(templeateLengthPanel);
-        JPanel templeateTypePanel = new JPanel();
-        templeateTypePanel.setLayout(new FlowLayout(FlowLayout.LEADING) );
-        templeateTypePanel.add(jTemplateTypeLabel);
-        templeateTypePanel.add(jTemplateTypeBox);
-        jTemplateTypeBox.setSelectedIndex(0);
-        discontiguousWordOptionsPanel.add(templeateTypePanel);
-        c.gridx = 1;
-        c.gridy = 1;
-        jAdvancedPane.add(discontiguousWordOptionsPanel, c);
-
-        discontiguousWordOptionsPanel.setVisible(false);
-
-		jCompositionalLabel.setVisible(false);
-		jCompositionalBox.setVisible(false);
-
-		shortQueriesBox.setVisible(false);
-
-		jAdvancedPane.setEnabled(true);
-
-		String[] model = AlgorithmMatcher
-				.translateToMatrices(selectedProgramName);
-		jMatrixBox.setModel(new DefaultComboBoxModel(model));
-
-		jWordsizeBox.setVerifyInputWhenFocusTarget(true);
-       	String defaultOptimizeFor="megablast";
-		String[] model2 = AlgorithmMatcher
-				.translateToWordSize(selectedProgramName,defaultOptimizeFor);
-		jWordsizeBox.setModel(new DefaultComboBoxModel(model2));
-		jMaxTargetBox.setSelectedIndex(2);
-		jExpectBox.setSelectedIndex(4);
-		jSpeciesBox.setSelectedIndex(0);
-		shortQueriesBox.setSelected(true);
-		jDisplayInWebBox.setSelected(true);
-
-		if (selectedProgramName.equalsIgnoreCase("blastn")) {
-			String[] capModel = AlgorithmMatcher.translateToGapcosts("blastn","megablast");
-	       	jGapcostsBox.setModel(new DefaultComboBoxModel(capModel));
-	       	Integer index = AlgorithmMatcher.defaultGapcostIndex.get("megablast");
-	       	if(index==null) index = 0;
-	       	jGapcostsBox.setSelectedIndex(index);
-			jWordsizeBox.setSelectedIndex(3);//default selection
-			jScoresLabel.setVisible(true);
-			jScoresBox.setVisible(true);
-			jScoresBox.setSelectedIndex(0);
-			speciesRepeatPanel.setVisible(true);
-			jGapcostsBox.setEditable(false);
-			jGapcostsBox.setVisible(true);
-			jGapcostsLabel.setVisible(true);
-			maskLookupOnlyBox.setSelected(true);
-			shortQueriesBox.setVisible(true);
-			jMatrixLabel.setVisible(false);
-			jMatrixBox.setVisible(false);
-			if (megablastBtn.isSelected())
-				megaBlastSet();
-			else
-				discontiguosSet();
-
-		} else {
-			jScoresLabel.setVisible(false);
-			jScoresBox.setVisible(false);
-			jMatrixBox.setSelectedIndex(3);
-			jWordsizeBox.setSelectedIndex(1);
-			speciesRepeatPanel.setVisible(false);
-			jGapcostsBox.setEditable(false);
-			jGapcostsBox.setVisible(true);
-			jGapcostsLabel.setVisible(true);
-			maskLookupOnlyBox.setSelected(false);
-			maskLowCaseBox.setSelected(false);
-			jMatrixLabel.setVisible(true);
-			jMatrixBox.setVisible(true);
-			if (selectedProgramName.equalsIgnoreCase("blastp")||selectedProgramName.equalsIgnoreCase("tblastn")){
-				jCompositionalLabel.setVisible(true);
-				jCompositionalBox.setVisible(true);
-				jCompositionalBox.setSelectedIndex(2);
-
-			}
-			if (selectedProgramName.equalsIgnoreCase("blastp")){
-				lowComplexFilterBox.setSelected(false);
-				shortQueriesBox.setVisible(true);
-			}
-			else{
-				lowComplexFilterBox.setSelected(true);
-			}
-		}
-    }
-
-    private void jDefaultButton_actionPerformed(ActionEvent e) {
-    	setAdvancedOptions();
-    }
-
-    private void jProgramBox_actionPerformed(ActionEvent e) {
-
-        JComboBox cb = (JComboBox) e.getSource();
-		// Get the new item
-		String selectedProgramName = (String) cb.getSelectedItem();
-		programForDefaultButton=selectedProgramName;
-		jAdvancedPane.removeAll();
-		if (selectedProgramName == null
-				|| selectedProgramName
-						.equalsIgnoreCase(SELECT_A_PROGRAM_PROMPT)) {
-			jScrollPane1.getViewport().removeAll();
-			textArea.setText( "" );
-			jAdvancedPane.setEnabled(false);
-			enableBlastnRelateOptions(false);
-			jEntrezQueryLabel.setVisible(false);
-			jEntrezQueryText.setVisible(false);
-			chooseSearchPanel.setVisible(false);
-			return;
-		}
-
-		String[][] arrayT = algorithmMatcher
-				.translateToArray((String) selectedProgramName);
-		String[][] array = null;
-		/*though blastn, tblastn, tblastx are all type "nucleotide", however, their database choices are different.
-		 * for tblastn, tblastx, there are no database choices:dbindex/9606/rna and dbindex/10090/rna
-		 */
-		if(arrayT!=null){
-			if(selectedProgramName.equalsIgnoreCase("tblastn")||selectedProgramName.equalsIgnoreCase("tblastx")){
-				int num=0;
-				for(int i=0;i<arrayT.length;i++){
-					if(arrayT[i][1].equalsIgnoreCase("dbindex/9606/allcontig_and_rna")||arrayT[i][1].equalsIgnoreCase("dbindex/10090/allcontig_and_rna")){
-						num++;
-					}
-				}
-				array=new String[arrayT.length-num][2];
-				int i=0;
-				for(int j=0;j<arrayT.length;j++){
-					if (!(arrayT[j][1].equalsIgnoreCase("dbindex/9606/allcontig_and_rna")||arrayT[j][1].equalsIgnoreCase("dbindex/10090/allcontig_and_rna"))){
-						array[i]=arrayT[j];
-						i++;
-					}
-				}
-			}
-			else {
-				array=arrayT;
-			}
-		}
-		else
-			return;
-
-		TableModel listModel = new UneditableTableModel(array);
-		databaseTable.setModel(listModel);
-		databaseTable.setAutoResizeMode(JTable.AUTO_RESIZE_LAST_COLUMN);
-		// make the first column large enough
-		int vColIndex = 0;
-		TableColumn col = databaseTable.getColumnModel().getColumn(vColIndex);
-		int width = 250;
-		col.setPreferredWidth(width);
-		(jScrollPane1.getViewport()).add(databaseTable, null);
-		excludeModels.setSelected(false);
-	    excludeUnculture.setSelected(false);
-	    jEntrezQueryText.setText("");
-	    jQueryFromText.setText("");
-		jQueryToText.setText("");
-	    megablastBtn.setSelected(true);
-	    chooseSearchPanel.setVisible(true);
-
-		setAdvancedOptions();
-    }
-
-    private void jMegaBlastBtn_actionPerformed(ActionEvent e) {
-    	megaBlastSet();
-    }
-    private void megaBlastSet(){
-    	String[] model2 = AlgorithmMatcher
-		.translateToWordSize("blastn","megablast");
-		jWordsizeBox.setModel(new DefaultComboBoxModel(model2));
-		jWordsizeBox.setSelectedIndex(3);
-		jScoresBox.setSelectedIndex(0);
-		String[] capModel = AlgorithmMatcher.translateToGapcosts("blastn","megablast");
-		jGapcostsBox.setModel(new DefaultComboBoxModel(capModel));
-		Integer index = AlgorithmMatcher.defaultGapcostIndex.get("megablast");
-		if(index==null) index = 0;
-		jGapcostsBox.setSelectedIndex(index);
-		lowComplexFilterBox.setSelected(true);
-		speciesRepeatFilter.setSelected(false);
-		maskLookupOnlyBox.setSelected(true);
-		maskLowCaseBox.setSelected(false);
-
-		discontiguousWordOptionsPanel.setVisible(false);
-    }
-
-    private void jDiscontiguousBtn_actionPerformed(ActionEvent e) {
-    	discontiguosSet();
-    }
-
-    private void discontiguosSet(){
-    	String[] model2 = AlgorithmMatcher
-		.translateToWordSize("blastn","discontiguous");
-    	jWordsizeBox.setModel(new DefaultComboBoxModel(model2));
-    	jWordsizeBox.setSelectedIndex(0);
-    	jScoresBox.setSelectedIndex(3);
-    	String[] capModel = AlgorithmMatcher.translateToGapcosts("blastn","discontiguous");
-		jGapcostsBox.setModel(new DefaultComboBoxModel(capModel));
-		Integer index = AlgorithmMatcher.defaultGapcostIndex.get("discontiguous");
-		if(index==null) index = 0;
-		jGapcostsBox.setSelectedIndex(index);
-		lowComplexFilterBox.setSelected(true);
-		speciesRepeatFilter.setSelected(false);
-		maskLookupOnlyBox.setSelected(true);
-		maskLowCaseBox.setSelected(false);
-
-		if (discontiguousBtn.isSelected()){
-			discontiguousWordOptionsPanel.setVisible(true);
-		}
-		else{
-			discontiguousWordOptionsPanel.setVisible(false);
-		}
-    }
-
-    private void jMatrixBox_actionPerformed(ActionEvent e) {
-    	String matrixName = jMatrixBox.getSelectedItem().toString();
-        String[] model = AlgorithmMatcher.translateToGapcosts(matrixName
-                );
-       	jGapcostsBox.setModel(new DefaultComboBoxModel(model));
-       	Integer index = AlgorithmMatcher.defaultGapcostIndex.get(matrixName);
-       	if(index==null) index = 0;
-       	jGapcostsBox.setSelectedIndex(index);
-    }
-
-    public void reportError(String message, String title) {
-        JOptionPane.showMessageDialog(null, message, title,
-                                      JOptionPane.ERROR_MESSAGE);
-    }
-
-    private BlastAlgorithm blastAlgo = null;
-    private void runBlastAlgorithm() {
-        ParameterSetting parameterSetting = collectParameters();
-        if (parameterSetting == null) {
-            return;
-        }
-        parameterSetting.setUseNCBI(true);
-        if (activeSequenceDB != null) {
-            if (sequenceDB == null) {
-                reportError("Please select a sequence file first!",
-                            "Parameter Error");
-                return;
-            } else { //to handle new sequenceDB.
-
-                try {
-
-                    serviceProgressBar.setForeground(Color.BLACK);
-                    serviceProgressBar.setBackground(Color.WHITE);
-
-                    updateProgressBar(10, "Wait...");
-
-                    blastAlgo = new BlastAlgorithm();
-                    blastAlgo.setParameterSetting(parameterSetting);
-
-                    blastAlgo.setBlastAppComponent(this);
-
-                    blastAlgo.setSequenceDB( (CSSequenceSet<CSSequence>) activeSequenceDB);
-                    blastAlgo.setParentSequenceDB(sequenceDB);
-
-                    blastAlgo.execute();
-                } catch (Exception e) {
-                    e.printStackTrace();
-                }
-
-            }
-        }
-    }
-
-    /**
-     * Collect all selected parameters and save it to a ParameterSetting object.
-     * @return ParameterSetting
-     */
-    @SuppressWarnings("rawtypes")
-	private ParameterSetting collectParameters() {
-        String programName = (String) jProgramBox.getSelectedItem();
-        if (programName == null ||
-            programName.equalsIgnoreCase(SELECT_A_PROGRAM_PROMPT)) {
-            reportError("Please select a PROGRAM to search!", "Parameter Error");
-            return null;
-        }
-        int selectedRow = databaseTable.getSelectedRow();
-        String dbName = null;
-        if(selectedRow!=-1) {
-        	dbName = (String)databaseTable.getModel().getValueAt(selectedRow, DATABASE_NAME_INDEX);
-        }
-        if (dbName == null) {
-            reportError("Please select a DATABASE to search!",
-                        "Parameter Error");
-            return null;
-        }
-
-        boolean lowComplexFilterOn = lowComplexFilterBox.isSelected();
-        boolean maskLowCaseOn = maskLowCaseBox.isSelected();
-        String expectString = (String) jExpectBox.getSelectedItem();
-        double expectValue = 10;
-        if (expectString != null) {
-            expectValue = Double.parseDouble(expectString.trim());
-        }
-        String endPoint = jendPointField.getSelectedText();
-        String startPoint = jstartPointField.getSelectedText();
-        DSSequenceSet fastaFile = null;
-		if (activeSequenceDB != null) {
-            fastaFile = activeSequenceDB;
-        } else if (fastaFile == null && sequenceDB != null) {
-            fastaFile = sequenceDB;
-        }
-
-        int endValue = -1;
-        int startValue = 1;
-        if (endPoint != null) {
-            try {
-                endValue = Integer.parseInt(endPoint.trim());
-                startValue = Integer.parseInt(startPoint.trim());
-            } catch (NumberFormatException e) {
-
-            }
-        }
-        String wordsize = (String) jWordsizeBox.getSelectedItem();
-
-        boolean humanRepeatFilterOn = speciesRepeatFilter.isSelected();
-
-        boolean excludeModelsOn = excludeModels.isSelected();
-        boolean excludeUncultureOn = excludeUnculture.isSelected();
-        boolean megaBlastOn=megablastBtn.isSelected();
-        boolean discontiguousOn=discontiguousBtn.isSelected();
-        boolean blastnBtnOn=blastnBtn.isSelected();
-        boolean shortQueriesOn=shortQueriesBox.isSelected();
-        String matchScores=(String) jScoresBox.getSelectedItem();
-        String compositionalAdjustment=(String) jCompositionalBox.getSelectedItem();
-        String speciesRepeat=(String) jSpeciesBox.getSelectedItem();
-        String templateLength=(String) jTemplateLengthBox.getSelectedItem();
-        String templateType=(String) jTemplateTypeBox.getSelectedItem();
-        String geneticCode=(String) jgeneticCodeBox.getSelectedItem();
-        String maxTargetNumber=(String) jMaxTargetBox.getSelectedItem();
-        String entrezQuery=jEntrezQueryText.getText().trim();
-        String fromQuery=jQueryFromText.getText().trim();
-        String toQuery=jQueryToText.getText().trim();
-        String hspRange=jHspRangeBox.getText().trim();
-
-        ParameterSetting ps = new ParameterSetting(dbName, programName,
-				jDisplayInWebBox.isSelected(), expectValue, lowComplexFilterOn,
-				humanRepeatFilterOn, maskLowCaseOn, (String) jMatrixBox
-						.getSelectedItem(), maskLookupOnlyBox.isSelected(),
-						excludeModelsOn,excludeUncultureOn, entrezQuery, fromQuery, toQuery, megaBlastOn,
-						discontiguousOn,blastnBtnOn,shortQueriesOn,matchScores,compositionalAdjustment,
-						speciesRepeat, templateLength, templateType, geneticCode, maxTargetNumber, hspRange);
-        if (startValue <= 1 && endValue >= fastaFile.getMaxLength()) {
-            //just use whole sequence. No end to reset.
-        } else {
-            ps.setStartPoint(startValue);
-            ps.setEndPoint(endValue);
-        }
-        if (wordsize != null) {
-            ps.setWordsize(wordsize);
-        }
-        String gapCost = (String) jGapcostsBox.getSelectedItem();
-        if (gapCost != null) {
-            ps.setGapCost(gapCost);
-        }
-
-        return ps;
-    }
-
-    private void blastButton_actionPerformed(ActionEvent e) {
-        stopButtonPushed = false;
-        if (jTabbedPane1.getSelectedIndex() == BlastAppComponent.BLAST) {
-            jTabbedBlastPane.setSelectedIndex(BlastAppComponent.MAIN);
-
-			// only support NCBI server now
-			runBlastAlgorithm();
-        } else {
-            log.warn("unexpected selectedIndex of jTabbedPane1 "+jTabbedPane1.getSelectedIndex());
-        }
-
-    }
-
-    public void setBlastDisplayPanel(int selectedPanel) {
-        if (selectedPanel == BlastAppComponent.SERVER) {
-            jTabbedBlastPane.setSelectedIndex(BlastAppComponent.SERVER);
-
-        } else {
-            jTabbedBlastPane.setSelectedIndex(BlastAppComponent.MAIN);
-        }
-
-    }
-
-    private void blastStopButton_actionPerformed(ActionEvent e) {
-        stopButtonPushed = true;
-        if (this.jTabbedPane1.getSelectedIndex() == BlastAppComponent.BLAST) {
-			serviceProgressBar.setForeground(Color.ORANGE);
-			serviceProgressBar.setBackground(Color.ORANGE);
-			updateProgressBar(false, "Stopped on " + new Date());
-		}
-
-        if(blastAlgo!=null) {
-        	if(!blastAlgo.cancel(true)) {
-        		log.error("blast job was not able to be cancelled.");
-        	}
-        }
-    }
-
-    public void updateProgressBar(final double percent, final String text) {
-        Runnable r = new Runnable() {
-            public void run() {
-                try {
-                    serviceProgressBar.setString(text);
-                    serviceProgressBar.setValue((int) (percent * 100));
-                } catch (Exception e) {
-                }
-            }
-        };
-        SwingUtilities.invokeLater(r);
-    }
-
-    public void updateProgressBar(final String text) {
-        Runnable r = new Runnable() {
-            public void run() {
-                try {
-                    serviceProgressBar.setString(text);
-                    serviceProgressBar.setIndeterminate(true);
-                } catch (Exception e) {
-                }
-            }
-        };
-        SwingUtilities.invokeLater(r);
-    }
-
-    public void updateProgressBar(final boolean boo, final String text) {
-        Runnable r = new Runnable() {
-            public void run() {
-                try {
-                    serviceProgressBar.setString(text);
-                    serviceProgressBar.setIndeterminate(boo);
-                } catch (Exception e) {
-                }
-            }
-        };
-        SwingUtilities.invokeLater(r);
-    }
-
-    public BlastAppComponent getBlastAppComponent() {
-        return blastAppComponent;
-    }
-
-    public boolean isStopButtonPushed() {
-        return stopButtonPushed;
-    }
-
-    /**
-     * publishProjectNodeAddedEvent
-     *
-     * @param event ProjectNodeAddedEvent
-     */
-    @Publish public org.geworkbench.events.ProjectNodeAddedEvent
-            publishProjectNodeAddedEvent(org.geworkbench.events.
-                                         ProjectNodeAddedEvent event) {
-        return event;
-    }
-
-	/**
-	 * getComponent
-	 *
-	 * @return Component
-	 */
-	public Component getComponent() {
-		return mainPanel;
-	}
-
-	private void init1() throws Exception {
-		mainPanel = new JPanel();
-
-		displayToolBar = new JToolBar();
-		displayToolBar
-				.setLayout(new BoxLayout(displayToolBar, BoxLayout.X_AXIS));
-		chkAllMarkers.setToolTipText("Use All Markers.");
-		chkAllMarkers.setSelected(false);
-		chkAllMarkers.addActionListener(new ActionListener() {
-
-			public void actionPerformed(ActionEvent e) {
-				activateMarkers = !((JCheckBox) e.getSource()).isSelected();
-				refreshMaSetView();
-			}
-
-		});
-
-		BorderLayout borderLayout2 = new BorderLayout();
-		mainPanel.setLayout(borderLayout2);
-		sequenceNumberField = new JTextField(20);
-		sequenceNumberField.setMaximumSize(sequenceNumberField.getPreferredSize());
-		sequenceNumberField.setEditable(false);
-
-		sequenceNumberField.setText("Total Sequence Number:");
-		displayToolBar.add(chkAllMarkers, null);
-		displayToolBar.add(Box.createHorizontalStrut(5), null);
-		displayToolBar.add(sequenceNumberField);
-		mainPanel.add(displayToolBar, java.awt.BorderLayout.SOUTH);
-
-		activateMarkers = !chkAllMarkers.isSelected();
-
-	}
-
-	@SuppressWarnings("rawtypes")
-	private void refreshMaSetView() {
-		activateMarkers = !chkAllMarkers.isSelected();
-		if (activateMarkers) {
-			if (activatedMarkers != null && activatedMarkers.size() > 0) {
-
-				if (activateMarkers && (sequenceDB != null)) {
-					activeSequenceDB = (CSSequenceSet) ((CSSequenceSet) sequenceDB)
-							.getActiveSequenceSet(activatedMarkers);
-					sequenceNumberField.setText("Activated Sequence Number: "
-							+ activeSequenceDB.size());
-				}
-
-			} else if (sequenceDB != null) {
-				sequenceNumberField.setText("Total Sequence Number: "
-						+ sequenceDB.size());
-
-				activeSequenceDB = (CSSequenceSet) sequenceDB;
-			}
-
-		} else if (sequenceDB != null) {
-			sequenceNumberField.setText("Total Sequence Number: "
-					+ sequenceDB.size());
-		}
-
-	}
-
-	/**
-	 * receiveProjectSelection
-	 *
-	 * @param e -
-	 *            ProjectEvent
-	 */
-	@SuppressWarnings("rawtypes")
-	@Subscribe
-	public void receive(org.geworkbench.events.ProjectEvent e, Object source) {
-		DSDataSet dataSet = e.getDataSet();
-		if (dataSet instanceof DSSequenceSet) {
-			if (sequenceDB != dataSet) {
-				this.sequenceDB = (DSSequenceSet) dataSet;
-
-				activatedMarkers = null;
-			}
-			refreshMaSetView();
-		}
-	}
-
-	/**
-	 * geneSelectorAction
-	 *
-	 * @param e
-	 *            GeneSelectorEvent
-	 */
-	@Subscribe(Asynchronous.class)
-	public void receive(GeneSelectorEvent e, Object source) {
-		if(e.getGenericMarker()!=null && e.getPanel() == null) // do nothing for single marker selection
-			return;
-
-		if (e.getPanel() != null && e.getPanel().size() > 0) {
-			activatedMarkers = e.getPanel().activeSubset();
-		} else {
-			activatedMarkers = null;
-		}
-		refreshMaSetView();
-	}
-
-	// following are a group of listener classes
-    private class BlastAppComponent_jMatrixBox_actionAdapter implements
-			java.awt.event.ActionListener {
-
-		public void actionPerformed(ActionEvent e) {
-			jMatrixBox_actionPerformed(e);
-		}
-	}
-
-    private class BlastAppComponent_jProgramBox_actionAdapter implements
-			java.awt.event.ActionListener {
-
-		public void actionPerformed(ActionEvent e) {
-			jProgramBox_actionPerformed(e);
-		}
-	}
-
-    private class BlastAppComponent_default_actionAdapter implements
-			java.awt.event.ActionListener {
-
-    	public void actionPerformed(ActionEvent e) {
-    		jDefaultButton_actionPerformed(e);
-    	}
-    }
-
-
-    private class BlastAppComponent_megablastBtn_actionAdapter implements
-			java.awt.event.ActionListener {
-    		public void actionPerformed(ActionEvent e) {
-    		jMegaBlastBtn_actionPerformed(e);
-    	}
-    }
-
-    private class BlastAppComponent_discontiguousBtn_actionAdapter implements
-	java.awt.event.ActionListener {
-	public void actionPerformed(ActionEvent e) {
-	jDiscontiguousBtn_actionPerformed(e);
-}
-}
-
-
-
-    private class BlastAppComponent_blastButton_actionAdapter implements
-			java.awt.event.ActionListener {
-
-		public void actionPerformed(ActionEvent e) {
-			blastButton_actionPerformed(e);
-		}
-	}
-
-    private class BlastAppComponent_blastStopButton_actionAdapter implements
-			java.awt.event.ActionListener {
-		public void actionPerformed(ActionEvent e) {
-			blastStopButton_actionPerformed(e);
-		}
-	}
-
-    private class BlastAppComponent_jDBList_listSelectionListener implements
-			ListSelectionListener {
-
-		public void valueChanged(ListSelectionEvent e) {
-			if (e.getValueIsAdjusting()) {
-				return;
-			}
-
-	        String program = (String) jProgramBox.getSelectedItem();
-	        int selectedRow = databaseTable.getSelectedRow();
-	        String dbDetails = "";
-	        if(selectedRow!=-1) {
-		        String dbName = (String)databaseTable.getModel().getValueAt(selectedRow, DATABASE_NAME_INDEX);
-		        dbDetails = algorithmMatcher.getDatabaseDetail(program, dbName);
-		       	jSpeciesBox.setSelectedIndex(0);
-	        }
-
-	        textArea.setText( dbDetails );
-		}
-	}
-
-}
diff --git a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/.svn/text-base/BlastViewComponent.cwb.xml.svn-base b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/.svn/text-base/BlastViewComponent.cwb.xml.svn-base
index 871c2dd..0fc8345 100644
--- a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/.svn/text-base/BlastViewComponent.cwb.xml.svn-base
+++ b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/.svn/text-base/BlastViewComponent.cwb.xml.svn-base
@@ -15,7 +15,7 @@
 		mustAccept="false"
 		category="visualizer" loadByDefault="true">
 		<required-component
-			class="org.geworkbench.components.alignment.panels.BlastAppComponent" />
+			class="org.geworkbench.components.alignment.blast.BlastAnalysis" />
 		<license><![CDATA[
 			<html><head><meta http-equiv=Content-Type content="text/html; charset=windows-1252"></head>
 				<body>----</body>
diff --git a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/.svn/text-base/BlastViewComponent.java.svn-base b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/.svn/text-base/BlastViewComponent.java.svn-base
index d528db7..bac35bf 100644
--- a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/.svn/text-base/BlastViewComponent.java.svn-base
+++ b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/.svn/text-base/BlastViewComponent.java.svn-base
@@ -2,6 +2,8 @@ package org.geworkbench.components.alignment.panels;

 import java.awt.Component;
 import java.awt.Container;
+import java.util.ArrayList;
+import java.util.Vector;

 import javax.swing.JTabbedPane;

@@ -11,108 +13,115 @@ import org.geworkbench.bison.datastructure.biocollections.DSAncillaryDataSet;
 import org.geworkbench.bison.datastructure.biocollections.DSDataSet;
 import org.geworkbench.bison.datastructure.biocollections.sequences.CSSequenceSet;
 import org.geworkbench.bison.datastructure.bioobjects.DSBioObject;
-import org.geworkbench.bison.datastructure.bioobjects.sequence.CSAlignmentResultSet;
+import org.geworkbench.bison.datastructure.bioobjects.sequence.BlastObj;
 import org.geworkbench.bison.datastructure.bioobjects.sequence.DSAlignmentResultSet;
 import org.geworkbench.bison.datastructure.bioobjects.sequence.DSSequence;
 import org.geworkbench.builtin.projects.ProjectPanel;
-import org.geworkbench.builtin.projects.ProjectSelection;
-import org.geworkbench.components.alignment.blast.NCBIBlastParser;
+import org.geworkbench.builtin.projects.ProjectSelection;
 import org.geworkbench.engine.config.VisualPlugin;
 import org.geworkbench.engine.management.AcceptTypes;
 import org.geworkbench.engine.management.Publish;
 import org.geworkbench.engine.management.Subscribe;

 /**
- * <p>Title: Bioworks</p>
- * <p>Description: Modular Application Framework for Gene Expession, Sequence and Genotype Analysis</p>
- * <p>Copyright: Copyright (c) 2003 -2004</p>
- * <p>Company: Columbia University</p>
- *
+ * <p>
+ * Title: Bioworks
+ * </p>
+ * <p>
+ * Description: Modular Application Framework for Gene Expession, Sequence and
+ * Genotype Analysis
+ * </p>
+ * <p>
+ * Copyright: Copyright (c) 2003 -2004
+ * </p>
+ * <p>
+ * Company: Columbia University
+ * </p>
+ *
  * @author XZ
  * @version $Id$
  */
-@AcceptTypes( {DSAlignmentResultSet.class})
-public class BlastViewComponent implements
-        VisualPlugin {
+@AcceptTypes( { DSAlignmentResultSet.class })
+public class BlastViewComponent implements VisualPlugin {
 	private static Log log = LogFactory.getLog(BlastViewComponent.class);

-    private BlastViewPanel blastViewPanel;
-
-    @Publish public org.geworkbench.events.ProjectNodeAddedEvent
-            publishProjectNodeAddedEvent(org.geworkbench.events.
-                                         ProjectNodeAddedEvent event) {
-        return event;
-    }
-
-    public BlastViewComponent() {
-        try {
-            blastViewPanel = new BlastViewPanel();
-            blastViewPanel.setBlastViewComponent(this);
-
-        } catch (Exception e) {
-            e.printStackTrace();
-        }
-    }
-
-    /**
-     * getComponent
-     *
-     * @return Component
-     */
-    public Component getComponent() {
-        return blastViewPanel;
-    }
-
-    /**
-     * receiveProjectSelection
-     *
-     * @param e ProjectEvent
-     */
-    @SuppressWarnings("unchecked")
-	@Subscribe public void receive(org.geworkbench.events.ProjectEvent e,
-                                   Object source) {
-
-        Container parent = blastViewPanel.getParent();
-        if (parent instanceof JTabbedPane) {
-            ((JTabbedPane) parent).setSelectedComponent(blastViewPanel);
-        }
-
-        ProjectSelection selection = ((ProjectPanel) source).getSelection();
-        DSAncillaryDataSet<DSBioObject> df = selection.getDataSubSet();
-        //Get the sequenceDb from DAncillaryDataset not from project.
-        DSDataSet<? extends DSSequence> sequenceDB = selection.getDataSet();
-        if (df != null && df instanceof CSAlignmentResultSet) {
-          //  sequenceDB = df.getParentDataSet();
-            sequenceDB = ((CSAlignmentResultSet)df).getBlastedParentDataSet();
-        }
-        if (sequenceDB instanceof CSSequenceSet && df != null) {
-            if (df instanceof DSAlignmentResultSet) {
-            	log.debug("update blast result view panel");
-               	int totalSequenceNumber = ((CSSequenceSet<? extends DSSequence>) sequenceDB)
-						.size();
-				NCBIBlastParser nbp = new NCBIBlastParser(totalSequenceNumber,
-						((DSAlignmentResultSet) df).getResultFilePath());
+	private BlastViewPanel blastViewPanel;
+
+	@Publish
+	public org.geworkbench.events.ProjectNodeAddedEvent publishProjectNodeAddedEvent(
+			org.geworkbench.events.ProjectNodeAddedEvent event) {
+		return event;
+	}
+
+	public BlastViewComponent() {
+		try {
+			blastViewPanel = new BlastViewPanel();
+			blastViewPanel.setBlastViewComponent(this);
+
+		} catch (Exception e) {
+			e.printStackTrace();
+		}
+	}
+
+	/**
+	 * getComponent
+	 *
+	 * @return Component
+	 */
+	public Component getComponent() {
+		return blastViewPanel;
+	}
+
+	/**
+	 * receiveProjectSelection
+	 *
+	 * @param e
+	 *            ProjectEvent
+	 */
+	@SuppressWarnings("unchecked")
+	@Subscribe
+	public void receive(org.geworkbench.events.ProjectEvent e, Object source) {
+
+		Container parent = blastViewPanel.getParent();
+		if (parent instanceof JTabbedPane) {
+			((JTabbedPane) parent).setSelectedComponent(blastViewPanel);
+		}
+
+		ProjectSelection selection = ((ProjectPanel) source).getSelection();
+		DSAncillaryDataSet<DSBioObject> df = selection.getDataSubSet();
+		// Get the sequenceDb from DAncillaryDataset not from project.
+		DSDataSet<? extends DSSequence> sequenceDB = selection.getDataSet();
+		if (df != null && df instanceof DSAlignmentResultSet) {
+			// sequenceDB = df.getParentDataSet();
+			sequenceDB = ((DSAlignmentResultSet) df).getBlastedParentDataSet();
+		}
+		if (sequenceDB instanceof CSSequenceSet && df != null) {
+			if (df instanceof DSAlignmentResultSet) {
+				log.debug("update blast result view panel");
+				DSAlignmentResultSet resultSet = (DSAlignmentResultSet) df;
+				ArrayList<Vector<BlastObj>> blastDataSet = resultSet
+						.getBlastDataSet();

 				blastViewPanel
 						.setSequenceDB((CSSequenceSet<DSSequence>) sequenceDB);
-				blastViewPanel.setBlastDataSet(nbp.parseResults());
+				blastViewPanel.setBlastDataSet(blastDataSet);

-				String summary = nbp.getSummary();
+				String summary = resultSet.getSummary();
 				blastViewPanel.setSummary(summary);
-				df.addDescription(summary);
-				if (nbp.getHitCount()==0){
+				df.setDescription(summary);
+
+				if (resultSet.getHitCount() == 0) {
 					blastViewPanel.resetToWhite("No alignment hit is found.");
 					blastViewPanel.setSummaryPanelOff();
+				} else {
+					blastViewPanel.setSummaryPanelOn();
 				}
-				else {
-					blastViewPanel.setSummaryPanelOn();
-				}
-            } else {
-                blastViewPanel.resetToWhite();
-            }
+			} else {
+				blastViewPanel.resetToWhite();
+			}

-        }
+		}

-    }
+	}

 }
diff --git a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/.svn/text-base/BlastViewPanel.java.svn-base b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/.svn/text-base/BlastViewPanel.java.svn-base
index 19f6435..3de85ac 100644
--- a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/.svn/text-base/BlastViewPanel.java.svn-base
+++ b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/.svn/text-base/BlastViewPanel.java.svn-base
@@ -31,11 +31,10 @@ import javax.swing.event.ListSelectionListener;
 import javax.swing.table.AbstractTableModel;

 import org.geworkbench.bison.datastructure.biocollections.sequences.CSSequenceSet;
+import org.geworkbench.bison.datastructure.bioobjects.sequence.BlastObj;
 import org.geworkbench.bison.datastructure.bioobjects.sequence.CSSequence;
 import org.geworkbench.bison.datastructure.bioobjects.sequence.DSSequence;
 import org.geworkbench.bison.util.RandomNumberGenerator;
-import org.geworkbench.components.alignment.blast.BlastObj;
-import org.geworkbench.engine.management.Subscribe;
 import org.geworkbench.util.BrowserLauncher;
 import org.geworkbench.util.FilePathnameUtils;
 import org.geworkbench.util.JAutoList;
@@ -93,17 +92,6 @@ public class BlastViewPanel extends JPanel implements HyperlinkListener {
 		blastViewComponent = bc;
 	}

-	@Subscribe
-	public void receive(org.geworkbench.events.ProjectNodeAddedEvent pnae,
-			Object source) {
-		/**
-		 * TODO Implement this
-		 * medusa.components.listeners.ProjectNodeAddedListener method
-		 */
-		throw new java.lang.UnsupportedOperationException(
-				"Method projectNodeAdded() not yet implemented.");
-	}
-
 	public void hyperlinkUpdate(HyperlinkEvent event) {
 		if (event.getEventType() == HyperlinkEvent.EventType.ACTIVATED) {
 			try {
@@ -229,11 +217,11 @@ public class BlastViewPanel extends JPanel implements HyperlinkListener {

 		summaryLabel.setText(s);
 		double propLoc = .8D;
-		rightPanel.setDividerLocation(propLoc);
+	    rightPanel.setDividerLocation(propLoc);
 		rightPanel.setResizeWeight(0.95);
-		jSplitPane1.setDividerLocation(jSplitPane1DividerLocation);
-		jSplitPane1.setResizeWeight(0.4);
-		revalidate();
+	    jSplitPane1.setDividerLocation(jSplitPane1DividerLocation);
+		jSplitPane1.setResizeWeight(0.4);
+		revalidate();
 	}

 	/**
@@ -289,7 +277,7 @@ public class BlastViewPanel extends JPanel implements HyperlinkListener {
 		JTable table = new JTable(myModel);

 		// setting the size of the table and its columns
-		table.setPreferredScrollableViewportSize(new Dimension(800, 100));
+		table.setPreferredScrollableViewportSize(new Dimension(800, 100));
 		table.getColumnModel().getColumn(0).setPreferredWidth(35);
 		table.getColumnModel().getColumn(1).setPreferredWidth(50);
 		table.getColumnModel().getColumn(2).setPreferredWidth(300);
diff --git a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/.svn/text-base/ParameterSetting.java.svn-base b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/.svn/text-base/ParameterSetting.java.svn-base
deleted file mode 100644
index 1dd7b44..0000000
--- a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/.svn/text-base/ParameterSetting.java.svn-base
+++ /dev/null
@@ -1,302 +0,0 @@
-package org.geworkbench.components.alignment.panels;
-
-/**
- *
- * @author zji
- * @version $Id$
- */
-public class ParameterSetting {
-        /**
-         * Database name, a required parameter.
-         */
-        private String dbName;
-        /**
-         * Blast program name, a required parameter.
-         */
-        private String programName;
-        /**
-         * Whether launch Web browser to view the  result. Default is yes.
-         */
-        private boolean viewInBrowser;
-        /**
-         * Matrix name, a optional parameter. For BLASTN, dna.mat, for others default is blossum62
-         */
-        private String matrix;
-        /**
-         * Frame shift penalty, optional parameter. Default is no OOP.
-         */
-        private String penalty;
-
-        private final double DEFAULTEXPECT = 10;
-        /**
-         * Expect value.
-         */
-        private double expect = DEFAULTEXPECT;
-
-        /**
-         * Low complexity filter. Default is on.
-         */
-        private boolean lowComplexityFilterOn = true;
-        /**
-         * Human Repeat Filter, only for blastn program
-         */
-        private boolean humanRepeatFilterOn = false;
-
-        /**
-         * Filter the low case.
-         */
-
-        private boolean maskLowCase = false;
-
-        /**
-         * Whether use NCBI Blast Server
-         */
-        private boolean useNCBI = false;
-        private boolean maskLookupTable = false;
-        private String wordsize = "11";
-        private String gapCost;
-        /**
-         * For subsequence information.
-         */
-        private int startPoint = -1;
-        private int endPoint = -1;
-
-        private boolean excludeModelsOn;
-        private boolean excludeUncultureOn;
-        private boolean megaBlastOn;
-        private boolean discontiguousOn;
-        private boolean blastnBtnOn;
-        private boolean shortQueriesOn;
-        private String matchScores;
-        private String compositionalAdjustment;
-        private String speciesRepeat;
-        private String templateLength;
-        private String templateType;
-        private String geneticCode;
-        private String maxTargetNumber;
-        private String entrezQuery;
-        private String fromQuery;
-        private String toQuery;
-        private String hspRange;
-
-    /**
-     * No public constructor because this is only used in this package.
-     *
-     * @param dbName
-     * @param programName
-     * @param viewInBrowser
-     * @param expect
-     * @param lowComplexityFilterOn
-     * @param humanRepeatFilterOn
-     * @param maskLowCase
-     * @param matrix
-     * @param maskLookupTable
-     *
-     * @param excludeModelsOn
-     * @param excludeUncultureOn
-     * @param megaBlastOn
-     * @param discontiguousOn
-     * @param blastnBtnOn
-     * @param shortQueriesOn
-     * @param matchScores
-     * @param compositionalAdjustment
-     * @param speciesRepeat
-     * @param geneticCode
-     * @param maxTargetNumber
-     * @param entrezQuery
-     * @param fromQuery
-     * @param toQuery
-     * @param hspRange
-     *
-     */
-    ParameterSetting(String dbName, String programName, boolean viewInBrowser,
-			double expect, boolean lowComplexityFilterOn,
-			boolean humanRepeatFilterOn, boolean maskLowCase, String matrix,
-			boolean maskLookupTable, boolean excludeModelsOn, boolean excludeUncultureOn, String entrezQuery,
-			String fromQuery, String toQuery, boolean megaBlastOn, boolean discontiguousOn, boolean blastnBtnOn, boolean shortQueriesOn,
-			String matchScores, String compositionalAdjustment, String speciesRepeat, String templateLength,
-			String templateType, String geneticCode, String maxTargetNumber, String hspRange) {
-        this.dbName = dbName;
-        this.programName = programName;
-        this.viewInBrowser = viewInBrowser;
-        this.expect = expect;
-        this.lowComplexityFilterOn = lowComplexityFilterOn;
-        this.humanRepeatFilterOn = humanRepeatFilterOn;
-        this.maskLowCase=maskLowCase;
-        this.matrix = matrix;
-		this.maskLookupTable = maskLookupTable;
-
-		this.excludeModelsOn=excludeModelsOn;
-		this.excludeUncultureOn=excludeUncultureOn;
-		this.megaBlastOn=megaBlastOn;
-		this.discontiguousOn=discontiguousOn;
-		this.blastnBtnOn=blastnBtnOn;
-		this.shortQueriesOn=shortQueriesOn;
-		this.matchScores=matchScores;
-		this.compositionalAdjustment=compositionalAdjustment;
-		this.speciesRepeat=speciesRepeat;
-		this.templateLength=templateLength;
-		this.templateType=templateType;
-		this.geneticCode=geneticCode;
-		this.maxTargetNumber=maxTargetNumber;
-		this.entrezQuery=entrezQuery;
-		this.fromQuery=fromQuery;
-		this.toQuery=toQuery;
-		this.hspRange=hspRange;
-    }
-
-    public void setPenalty(String penalty) {
-        this.penalty = penalty;
-    }
-
-    public void setUseNCBI(boolean useNCBI) {
-        this.useNCBI = useNCBI;
-    }
-
-    public void setEndPoint(int endPoint) {
-        this.endPoint = endPoint;
-    }
-
-    public void setStartPoint(int startPoint) {
-        this.startPoint = startPoint;
-    }
-
-    public void setWordsize(String wordsize) {
-        this.wordsize = wordsize;
-    }
-
-    public void setGapCost(String gapCost) {
-        this.gapCost = gapCost;
-    }
-
-    // following are the getters
-    public String getDbName() {
-        return dbName;
-    }
-
-    public String getProgramName() {
-        return programName;
-    }
-
-    public boolean isViewInBrowser() {
-        return viewInBrowser;
-    }
-
-    public String getMatrix() {
-        return matrix;
-    }
-
-    public String getPenalty() {
-        return penalty;
-    }
-
-    public double getExpect() {
-        return expect;
-    }
-
-    public boolean isHumanRepeatFilterOn() {
-        return humanRepeatFilterOn;
-    }
-
-    public boolean isLowComplexityFilterOn() {
-        return lowComplexityFilterOn;
-    }
-
-    public boolean isUseNCBI() {
-        return useNCBI;
-    }
-
-    public int getEndPoint() {
-        return endPoint;
-    }
-
-    public int getStartPoint() {
-        return startPoint;
-    }
-
-    public boolean isMaskLowCase() {
-        return maskLowCase;
-    }
-
-    public String getWordsize() {
-        return wordsize;
-    }
-
-    public String getGapCost() {
-        return gapCost;
-    }
-
-	/**
-	 * @return the maskLookupTable
-	 */
-	public boolean isMaskLookupTable() {
-		return maskLookupTable;
-	}
-
-	public boolean isExcludeModelsOn() {
-		return excludeModelsOn;
-	}
-
-	public boolean isExcludeUncultureOn() {
-		return excludeUncultureOn;
-	}
-
-	public boolean isMegaBlastOn() {
-		return megaBlastOn;
-	}
-
-
-	public boolean isDiscontiguousOn() {
-		return discontiguousOn;
-	}
-
-
-	public boolean isShortQueriesOn() {
-		return shortQueriesOn;
-	}
-
-	public String getMatchScores() {
-		return matchScores;
-	}
-
-	public String getSpeciesRepeat() {
-		return speciesRepeat;
-	}
-
-	public boolean isBlastnBtnOn() {
-		return blastnBtnOn;
-	}
-
-	public String getTemplateLength() {
-		return templateLength;
-	}
-
-	public String getTemplateType() {
-		return templateType;
-	}
-
-	public String getGeneticCode() {
-		return geneticCode;
-	}
-
-	public String getMaxTargetNumber() {
-		return maxTargetNumber;
-	}
-
-	public String getCompositionalAdjustment() {
-		return compositionalAdjustment;
-	}
-
-	public String getEntrezQuery() {
-		return entrezQuery;
-	}
-	public String getFromQuery() {
-		return fromQuery;
-	}
-	public String getToQuery() {
-		return toQuery;
-	}
-	public String getHspRange() {
-		return hspRange;
-	}
-}
diff --git a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/AlgorithmMatcher.java b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/AlgorithmMatcher.java
deleted file mode 100755
index e66b31c..0000000
--- a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/AlgorithmMatcher.java
+++ /dev/null
@@ -1,666 +0,0 @@
-package org.geworkbench.components.alignment.panels;
-
-import java.io.File;
-import java.io.IOException;
-import java.io.UnsupportedEncodingException;
-import java.net.URLEncoder;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import org.apache.commons.digester.Digester;
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-import org.geworkbench.engine.management.ComponentClassLoader;
-import org.geworkbench.engine.management.ComponentResource;
-import org.xml.sax.SAXException;
-
-/**
- * Utility used by BlastAppComponent and BlastAlgorithm.
- *
- * <p>Company: Columbia University</p>
- *
- * @author zji
- * @version $Id: AlgorithmMatcher.java 7629 2011-03-24 18:57:49Z youmi $
- */
-public class AlgorithmMatcher {
-	Log log = LogFactory.getLog(AlgorithmMatcher.class);
-
-	private static AlgorithmMatcher instance;
-	private List<DatabaseInfo> databaseList = null;
-
-	@SuppressWarnings("unchecked")
-	private AlgorithmMatcher() {
-        String componentDirectory = null;
-		ClassLoader classLoader = AlgorithmMatcher.class.getClassLoader();
-        if (classLoader instanceof ComponentClassLoader) {
-            ComponentClassLoader ccl = (ComponentClassLoader) classLoader;
-            ComponentResource componentResource = ccl.getComponentResource();
-            componentDirectory = componentResource.getDir();
-        } else {
-        	log.error("not loaded by ComponentClassLoader");
-        }
-
-		Digester digester = new Digester();
-		digester.setValidating( false );
-
-		digester.setUseContextClassLoader(true);
-		digester.addObjectCreate("database_list", ArrayList.class);
-		digester.addObjectCreate("database_list/database", DatabaseInfo.class);
-		digester.addSetProperties( "database_list/database", "name", "abbreviation" );
-		digester.addSetProperties( "database_list/database", "type", "type" );
-		digester.addBeanPropertySetter( "database_list/database/description", "description" );
-        digester.addBeanPropertySetter( "database_list/database/detail", "detail" );
-        digester.addSetNext("database_list/database", "add" );
-
-        File input = new File( componentDirectory+"/classes/databaseInfo.xml" );
-
-		try {
-			databaseList = (List<DatabaseInfo>)digester.parse( input );
-		} catch (IOException e) {
-			// TODO Auto-generated catch block
-			e.printStackTrace();
-		} catch (SAXException e) {
-			// TODO Auto-generated catch block
-			e.printStackTrace();
-		}
-
-    	List<DatabaseInfo> proteinList = new ArrayList<DatabaseInfo>();
-    	List<DatabaseInfo> nucleotideList = new ArrayList<DatabaseInfo>();
-    	for(DatabaseInfo d: databaseList) {
-    		if(d.getType().equals("protein"))proteinList.add(d);
-    		else if(d.getType().equals("nucleotide"))nucleotideList.add(d);
-    		else {
-    			log.error("wrong type "+d.getType()+" "+d.abbreviation);
-    		}
-    	}
-    	proteinDBdescriptionArray  = new String[proteinList.size()][2];
-    	int i = 0;
-		for(DatabaseInfo d: proteinList) {
-			proteinDBdescriptionArray[i][1] = d.getAbbreviation();
-			proteinDBdescriptionArray[i][0] = d.getDescription();
-			i++;
-		}
-		nucleotideDBdescriptionArray = new String[nucleotideList.size()][2];
-    	i = 0;
-		for(DatabaseInfo d: nucleotideList) {
-			nucleotideDBdescriptionArray[i][1] = d.getAbbreviation();
-			nucleotideDBdescriptionArray[i][0] = d.getDescription();
-			i++;
-		}
-	} // end of constructor
-
-	private String[][] nucleotideDBdescriptionArray = null;
-	private String[][] proteinDBdescriptionArray = null;
-
-	static AlgorithmMatcher getInstance() {
-		if(instance==null) {
-			instance = new AlgorithmMatcher();
-		}
-		return instance;
-	}
-
-	static public class DatabaseInfo {
-		private String abbreviation;
-		private String description;
-		private String detail;
-		private String type;
-
-		public DatabaseInfo() {
-		}
-
-		public void setAbbreviation(String abbreviation) {
-			this.abbreviation = abbreviation;
-		}
-
-		public void setDescription(String description) {
-			this.description = description;
-		}
-
-		public void setDetail(String detail) {
-			this.detail = detail;
-		}
-
-		public void setType(String type) {
-			this.type = type;
-		}
-
-		String getAbbreviation() {
-			return abbreviation;
-		}
-
-		String getDescription() {
-			return description;
-		}
-
-		String getDetail() {
-			return detail;
-		}
-
-		String getType() {
-			return type;
-		}
-	}
-
-	static private Map<String, String> program2type = new HashMap<String, String>();
-	static {
-		program2type.put("blastn", "nucleotide");
-		program2type.put("blastp", "protein");
-		program2type.put("blastx", "protein");
-		program2type.put("tblastn", "nucleotide");
-		program2type.put("tblastx", "nucleotide");
-	}
-
-	static private Map<String, String> template2number= new HashMap<String, String>();
-	static{
-		template2number.put("None", "0");
-		template2number.put("16", "16");
-		template2number.put("18", "18");
-		template2number.put("21", "21");
-		template2number.put("Coding", "0");
-		template2number.put("Maximal", "1");
-		template2number.put("Two template", "2");
-	}
-
-	static private Map<String, String> compositional2number= new HashMap<String, String>();
-	static{
-		compositional2number.put("No adjustment", "0");
-		compositional2number.put("Composition-based statistics", "1");
-		compositional2number.put("Conditional compositional score matrix adjustment", "2");
-		compositional2number.put("Universal compositional score matrix adjustment", "3");
-	}
-
-	static private Map<String, String> geneticCode2number=new HashMap<String, String>();
-	static{
-		geneticCode2number.put("Standard (1)","1");
-		geneticCode2number.put("Vertebrate Mitochondrial (2)","2");
-		geneticCode2number.put("Yeast Mitochondrial (3)","3");
-		geneticCode2number.put("Mold Mitochondrial (4)","4");
-		geneticCode2number.put("Invertebrate Mitochondrial (5)","5");
-		geneticCode2number.put("Ciliate Nuclear (6)","6");
-		geneticCode2number.put("Echinoderm Mitochondrial (9)","9");
-		geneticCode2number.put("Euplotid Nuclear (10)","10");
-		geneticCode2number.put("Bacteria and Archaea (11)","11");
-		geneticCode2number.put("Alternative Yeast Nuclear (12)","12");
-		geneticCode2number.put("Ascidian Mitochondrial (13)","13");
-		geneticCode2number.put("Flatworm Mitochondrial (14)","14");
-		geneticCode2number.put("Blepharisma Macronuclear (15)","15");
-	}
-
-	private static final String GAPB0_1 = "Linear";
-    private static final String GAPB0_2 = "Existence: 5 Extension: 2";
-    private static final String GAPB0_3 = "Existence: 2 Extension: 2";
-    private static final String GAPB0_4 = "Existence: 1 Extension: 2";
-    private static final String GAPB0_5 = "Existence: 0 Extension: 2";
-    private static final String GAPB0_6 = "Existence: 3 Extension: 1";
-    private static final String GAPB0_7 = "Existence: 2 Extension: 1";
-    private static final String GAPB0_8 = "Existence: 1 Extension: 1";
-
-    private static final String GAPB1_1 = "Existence: 4 Extension: 4";
-    private static final String GAPB1_2 = "Existence: 2 Extension: 4";
-    private static final String GAPB1_3 = "Existence: 0 Extension: 4";
-    private static final String GAPB1_4 = "Existence: 3 Extension: 3";
-    private static final String GAPB1_5 = "Existence: 6 Extension: 2";
-    private static final String GAPB1_6 = "Existence: 5 Extension: 2";
-    private static final String GAPB1_7 = "Existence: 4 Extension: 2";
-    private static final String GAPB1_8 = "Existence: 2 Extension: 2";
-
-	private static final String GAP0 = "Existence: 11 Extension: 1";
-    private static final String GAP1 = "Existence: 9 Extension: 2";
-    private static final String GAP2 = "Existence: 8 Extension: 2";
-    private static final String GAP3 = "Existence: 7 Extension: 2";
-    private static final String GAP4 = "Existence: 12 Extension: 1";
-    private static final String GAP5 = "Existence: 10 Extension: 1";
-
-    private static final String GAPB45_1 = "Existence: 15 Extension: 2";
-    private static final String GAPB45_2 = "Existence: 13 Extension: 3";
-    private static final String GAPB45_3 = "Existence: 12 Extension: 3";
-    private static final String GAPB45_4 = "Existence: 11 Extension: 3";
-    private static final String GAPB45_5 = "Existence: 10 Extension: 3";
-    private static final String GAPB45_6 = "Existence: 14 Extension: 2";
-    private static final String GAPB45_7 = "Existence: 13 Extension: 2";
-    private static final String GAPB45_8 = "Existence: 12 Extension: 2";
-    private static final String GAPB45_9 = "Existence: 19 Extension: 1";
-    private static final String GAPB45_10 = "Existence: 18 Extension: 1";
-    private static final String GAPB45_11 = "Existence: 17 Extension: 1";
-    private static final String GAPB45_12 = "Existence: 16 Extension: 1";
-    private static final String GAPB80_1 = "Existence: 10 Extension: 1";
-    private static final String GAPB80_2 = "Existence: 8 Extension: 2";
-    private static final String GAPB80_3 = "Existence: 7 Extension: 2";
-    private static final String GAPB80_4 = "Existence: 6 Extension: 2";
-    private static final String GAPB80_5 = "Existence: 11 Extension: 1";
-    private static final String GAPB80_6 = "Existence: 9 Extension: 1";
-    private static final String GAPP30_1 = "Existence: 9 Extension: 1";
-    private static final String GAPP30_2 = "Existence: 7 Extension: 2";
-    private static final String GAPP30_3 = "Existence: 6 Extension: 2";
-    private static final String GAPP30_4 = "Existence: 5 Extension: 2";
-    private static final String GAPP30_5 = "Existence: 8 Extension: 1";
-    private static final String GAPP30_6 = "Existence: 10 Extension: 1";
-    private static final String GAPP70_1 = "Existence: 10 Extension: 1";
-    private static final String GAPP70_2 = "Existence: 7 Extension: 2";
-    private static final String GAPP70_3 = "Existence: 6 Extension: 2";
-    private static final String GAPP70_4 = "Existence: 8 Extension: 2";
-    private static final String GAPP70_5 = "Existence: 9 Extension: 1";
-    private static final String GAPP70_6 = "Existence: 11 Extension: 1";
-
-    private static final String MATRIX1 = "BLOSUM62";
-    private static final String MATRIX2 = "BLOSUM45";
-    private static final String MATRIX3 = "BLOSUM80";
-    private static final String MATRIX4 = "PAM30";
-    private static final String MATRIX5 = "PAM70";
-    private static final String MATRIX0 = "dna.mat";
-
-    /**
-     * Match to correct database.
-     *
-     */
-    String[][] translateToArray(String programName) {
-    	String type = program2type.get(programName);
-		if (type==null) {
-			log.error("no database type for program "+programName);
-			return null;
-		} else if (type.equalsIgnoreCase("protein")) {
-			return proteinDBdescriptionArray;
-		} else if (type.equalsIgnoreCase("nucleotide")) {
-			return nucleotideDBdescriptionArray;
-		} else {
-			log.error("wrong database type "+type+" for program "+programName);
-			return null;
-		}
-	}
-
-    /**
-     * Given program + the index of database, return the detail
-     * @param programName
-     * @param selection
-     * @return
-     */
-    String getDatabaseDetail(String programName, String databaseName) {
-    	String type = program2type.get(programName);
-    	for(DatabaseInfo d: databaseList) {
-    		if (d.getType().equals(type)
-					&& d.getAbbreviation().equals(databaseName))
-				return d.getDetail();
-    	}
-    	log.error("no matching database for program "+programName);
-    	return null;
-	}
-
-    /**
-     * Static utility used in BlastAppComponent: Match to correct matrix.
-     * @param programName String
-     * @return String[]
-     */
-    static String[] translateToMatrices(String programName) {
-        if (programName.equalsIgnoreCase("blastn")) {
-            return new String[] {MATRIX0};
-        } else {
-            return new String[] {MATRIX4,MATRIX5, MATRIX3, MATRIX1, MATRIX2
-            };
-        }
-    }
-
-    /**
-     * Static utility used in BlastAppComponent: Match matrix name with gap costs.
-     * @param programName String
-     * @return String[]
-     */
-    static String[] translateToGapcosts(String programName) {
-    	if (programName.equalsIgnoreCase(MATRIX0)) {
-            return new String[] {GAPB0_1, GAPB0_2, GAPB0_3, GAPB0_4, GAPB0_5, GAPB0_6,GAPB0_7,GAPB0_8};
-
-        } else if (programName.equalsIgnoreCase(MATRIX1)) {
-            return new String[] {GAP1, GAP2, GAP3, GAP4, GAP0, GAP5};
-
-        } else if (programName.equalsIgnoreCase(MATRIX2)) {
-            return new String[] { GAPB45_2, GAPB45_3, GAPB45_4,
-                    GAPB45_5, GAPB45_1, GAPB45_6, GAPB45_7, GAPB45_8, GAPB45_9, GAPB45_10,
-                    GAPB45_11, GAPB45_12
-            };
-        } else if (programName.equalsIgnoreCase(MATRIX3)) {
-            return new String[] {GAPB80_2, GAPB80_3, GAPB80_4,
-                    GAPB80_5, GAPB80_1, GAPB80_6};
-        } else if (programName.equalsIgnoreCase(MATRIX4)) {
-            return new String[] {GAPP30_2, GAPP30_3, GAPP30_4,
-            		GAPP30_6,GAPP30_1, GAPP30_5};
-        } else if (programName.equalsIgnoreCase(MATRIX5)) {
-            return new String[] {GAPP70_4, GAPP70_2, GAPP70_3,
-            		GAPP70_6, GAPP70_1, GAPP70_5, };
-        }
-
-        String[] defaultGAPCOSTS = new String[] {GAP1, GAP2, GAP3, GAP4, GAP0, GAP5};
-        return defaultGAPCOSTS;
-
-    }
-
-    static String[] translateToGapcosts(String selectedProgramName, String optimizeFor) {
-    	if (selectedProgramName.equalsIgnoreCase("blastn")) {
-    		if (optimizeFor.equalsIgnoreCase("megablast")){
-    			return new String[] {GAPB0_1, GAPB0_2, GAPB0_3, GAPB0_4, GAPB0_5, GAPB0_6,GAPB0_7,GAPB0_8};
-    		}
-    		else {
-    			return new String[] {GAPB1_1, GAPB1_2, GAPB1_3, GAPB1_4, GAPB1_5, GAPB1_6,GAPB1_7,GAPB1_8};
-    		}
-
-    	}
-    	String[] defaultGAPCOSTS = new String[] {GAP1, GAP2, GAP3, GAP4, GAP0, GAP5};
-        return defaultGAPCOSTS;
-    }
-
-
-    static Map<String, Integer> defaultGapcostIndex = new HashMap<String, Integer>();
-    static {
-    	defaultGapcostIndex.put(MATRIX1, 4);
-    	defaultGapcostIndex.put(MATRIX2, 4);
-    	defaultGapcostIndex.put(MATRIX3, 4);
-    	defaultGapcostIndex.put(MATRIX4, 4);
-    	defaultGapcostIndex.put(MATRIX5, 4);
-    	defaultGapcostIndex.put("megablast", 0);
-    	defaultGapcostIndex.put("discontiguous", 5);
-    }
-
-    /**
-     * Static utility ussed in BlastAppComponent: translate program name to word size.
-     *
-     * @param selectedProgramName String
-     * @return String[]
-     */
-
-    static String[] translateToWordSize(String selectedProgramName, String optimizeFor) {
-        if (selectedProgramName.trim().equalsIgnoreCase("blastn")) {
-            if(optimizeFor.trim().equalsIgnoreCase("megablast")){
-            	return new String[]{"16","20","24","28","32","48","64","128","256"};
-            }
-            else
-            	return new String[] {"11", "12"};
-        } else {
-            return new String[] {"2", "3"};
-        }
-
-    }
-
-
-    /**
-     * Utility to create command-line parameter, only used by BlastAlgorithm.execute();
-     *
-     * @param ps
-     * @return
-     */
-    public static String translateToCommandline(ParameterSetting ps) {
-        String cmd = null;
-        if (ps != null) {
-            if (!ps.isUseNCBI()) {
-                cmd = "pb blastall -p " + ps.getProgramName() + "   -d   " +
-                      ps.getDbName() + " -e " + ps.getExpect() + " -M " +
-                      ps.getMatrix();
-                if (ps.isLowComplexityFilterOn()) {
-                    cmd += " -F T ";
-                } else {
-                    cmd += " -F F ";
-                }
-                if (ps.isMaskLowCase()) {
-                    cmd += " -U T ";
-                } else {
-                    cmd += " -U F ";
-                }
-                if (ps.getWordsize() != null) {
-                    cmd += " -W " + ps.getWordsize() + " ";
-                }
-                if (!ps.getProgramName().equals("blastn")) {
-
-                    String gapCost = ps.getGapCost();
-                    if (gapCost.equals(GAP1)) {
-                        cmd += " -G 9 -E 2 ";
-                    } else if (gapCost.equals(GAP2)) {
-                        cmd += " -G 8 -E 2 ";
-                    } else if (gapCost.equals(GAP3)) {
-                        cmd += " -G 7 -E 2 ";
-                    } else if (gapCost.equals(GAP4)) {
-                        cmd += " -G 12 -E 1 ";
-                    } else if (gapCost.equals(GAP5)) {
-                        cmd += " -G 10 -E 1 ";
-                    } else if (gapCost.equals(GAPB45_1)) {
-                        cmd += " -G 15 -E 2 ";
-                    } else if (gapCost.equals(GAPB45_2)) {
-                        cmd += " -G 13 -E 3 ";
-                    } else if (gapCost.equals(GAPB45_3)) {
-                        cmd += " -G 12 -E 3 ";
-                    } else if (gapCost.equals(GAPB45_4)) {
-                        cmd += " -G 11 -E 3 ";
-                    } else if (gapCost.equals(GAPB45_5)) {
-                        cmd += " -G 10 -E 3 ";
-                    } else if (gapCost.equals(GAPB45_6)) {
-                        cmd += " -G 14 -E 2 ";
-                    } else if (gapCost.equals(GAPB45_7)) {
-                        cmd += " -G 13 -E 2 ";
-                    } else if (gapCost.equals(GAPB45_8)) {
-                        cmd += " -G 12 -E 2 ";
-                    } else if (gapCost.equals(GAPB45_9)) {
-                        cmd += " -G 19 -E 1 ";
-                    } else if (gapCost.equals(GAPB45_10)) {
-                        cmd += " -G 18 -E 1 ";
-                    } else if (gapCost.equals(GAPB45_11)) {
-                        cmd += " -G 17 -E 1 ";
-                    } else if (gapCost.equals(GAPB45_12)) {
-                        cmd += " -G 16 -E 1 ";
-                    } else if (gapCost.equals(GAPB45_6)) {
-                        cmd += " -G 11 -E 1 ";
-                    } else if (gapCost.equals(GAPP30_1)) {
-                        cmd += " -G 9 -E 1 ";
-                    } else if (gapCost.equals(GAPP30_4)) {
-                        cmd += " -G 5 -E 2 ";
-                    } else if (gapCost.equals(GAPP30_2)) {
-                        cmd += " -G 7 -E 2 ";
-                    } else if (gapCost.equals(GAPP30_3)) {
-                        cmd += " -G 6 -E 2 ";
-                    } else if (gapCost.equals(GAPP30_5)) {
-                        cmd += " -G 8 -E 1 ";
-                    } else if (gapCost.equals(GAPB80_1)) {
-                        cmd += " -G 10 -E 1 ";
-                    } else if (gapCost.equals(GAPB80_2)) {
-                        cmd += " -G 8 -E 2 ";
-                    } else if (gapCost.equals(GAPB80_3)) {
-                        cmd += " -G 7 -E 2 ";
-                    } else if (gapCost.equals(GAPB80_4)) {
-                        cmd += " -G 6 -E 2 ";
-                    } else if (gapCost.equals(GAPB80_5)) {
-                        cmd += " -G 11 -E 1 ";
-                    } else if (gapCost.equals(GAPB80_6)) {
-                        cmd += " -G 9 -E 1 ";
-                    }  else if (gapCost.equalsIgnoreCase("Linear")) {
-                        cmd += " -G 0 -E 0 ";
-                    } else if (gapCost.equals(GAPB0_2)) {
-                        cmd += " -G 5 -E 2 ";
-                    } else if (gapCost.equals(GAPB0_3)) {
-                        cmd += " -G 2 -E 2 ";
-                    } else if (gapCost.equals(GAPB0_4)) {
-                        cmd += " -G 1 -E 2 ";
-                    } else if (gapCost.equals(GAPB0_5)) {
-                        cmd += " -G 0 -E 2 ";
-                    } else if (gapCost.equals(GAPB0_6)) {
-                        cmd += " -G 3 -E 1 ";
-                    } else if (gapCost.equals(GAPB0_7)) {
-                        cmd += " -G 2 -E 1 ";
-                    } else if (gapCost.equals(GAPB0_8)) {
-                        cmd += " -G 1 -E 1 ";
-                    } else if (gapCost.equals(GAPB1_1)) {
-                        cmd += " -G 4 -E 4 ";
-                    } else if (gapCost.equals(GAPB1_2)) {
-                        cmd += " -G 2 -E 4 ";
-                    } else if (gapCost.equals(GAPB1_3)) {
-                        cmd += " -G 0 -E 4 ";
-                    } else if (gapCost.equals(GAPB1_4)) {
-                        cmd += " -G 3 -E 3 ";
-                    } else if (gapCost.equals(GAPB1_5)) {
-                        cmd += " -G 6 -E 2 ";
-                    } else if (gapCost.equals(GAPB1_6)) {
-                        cmd += " -G 5 -E 2 ";
-                    } else if (gapCost.equals(GAPB1_7)) {
-                        cmd += " -G 4 -E 2 ";
-                    } else if (gapCost.equals(GAPB1_8)) {
-                        cmd += " -G 2 -E 2 ";
-                    }
-                }
-
-            } 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";
-                }
-                if (ps.isHumanRepeatFilterOn()) {
-                    cmd += "&FILTER=R";
-                }
-
-                if (ps.isExcludeModelsOn()){
-                	cmd += "&EXCLUDE_MODELS=yes";
-                }
-                if (ps.isExcludeUncultureOn()){
-                	cmd += "&EXCLUDE_SEQ_UNCULT=yes";
-                }
-                if (!(ps.getEntrezQuery()==null)||(ps.getEntrezQuery().trim()!="")){
-                	String entrezQuery = ps.getEntrezQuery();
-                	try {
-                		entrezQuery = URLEncoder.encode(entrezQuery, "UTF-8");
-        		    } catch (UnsupportedEncodingException ex) {
-        			    throw new RuntimeException("UTF-8 not supported", ex);
-        		    }
-                	cmd += "&EQ_TEXT="+entrezQuery;
-                }
-                if (!(ps.getFromQuery()==null)||(ps.getFromQuery().trim()!="")){
-                	cmd += "&QUERY_FROM="+ps.getFromQuery();
-                }
-                if (!(ps.getToQuery()==null)||(ps.getToQuery().trim()!="")){
-                	cmd += "&QUERY_TO="+ps.getToQuery();
-                }
-
-                if(ps.getProgramName().equalsIgnoreCase("blastn")){
-                	cmd +="&PAGE=MegaBlast";
-	                if (ps.isMegaBlastOn()){
-	                	cmd += "&BLAST_PROGRAMS=megaBlast";
-	                	cmd+="&MEGABLAST=on";
-	            		cmd+="&SELECTED_PROG_TYPE=megaBlast";
-	                }
-	                else if (ps.isDiscontiguousOn()){
-	                	cmd += "&BLAST_PROGRAMS=discoMegablast";
-	                	cmd+="&SELECTED_PROG_TYPE=discoMegablast";
-	                	cmd+="&MEGABLAST=on";
-
-	                    if (ps.getTemplateLength() != null) {
-	                       cmd += "&TEMPLATE_LENGTH=" + template2number.get(ps.getTemplateLength());
-	                    }
-	                    if (ps.getTemplateType() != null) {
-	                        cmd += "&TEMPLATE_TYPE=" + template2number.get(ps.getTemplateType());
-	                    }
-
-	                }
-	                else if (ps.isBlastnBtnOn()){
-	                	cmd += "&BLAST_PROGRAMS=blastn";
-	                }
-                }
-                else cmd += "&BLAST_PROGRAMS="+ps.getProgramName();
-                if (ps.getProgramName().equalsIgnoreCase("blastp"))
-                	cmd +="&PAGE=Proteins";
-                if(ps.getProgramName().equalsIgnoreCase("blastx")||ps.getProgramName().equalsIgnoreCase("tblastn")||ps.getProgramName().equalsIgnoreCase("tblastx")){
-                	cmd +="&PAGE=Translations";
-                	cmd +="&PAGE_TYPE=BlastSearch";
-                }
-                if (ps.getProgramName().equalsIgnoreCase("blastx")||ps.getProgramName().equalsIgnoreCase("tblastx")){
-                	cmd +="&GENETIC_CODE="+ geneticCode2number.get(ps.getGeneticCode());
-                }
-                if (ps.getProgramName().equalsIgnoreCase("blastp")||ps.getProgramName().equalsIgnoreCase("tblastn")){
-                	cmd +="&COMPOSITION_BASED_STATISTICS="+ compositional2number.get(ps.getCompositionalAdjustment());
-                }
-
-                if (ps.getProgramName().equalsIgnoreCase("blastp")||ps.getProgramName().equalsIgnoreCase("blastn")){
-	                if (ps.isShortQueriesOn()){
-	                	cmd += "&SHORT_QUERY_ADJUST=yes";
-	                }
-	            	else cmd += "&SHORT_QUERY_ADJUST=";
-                }
-
-                if (ps.isMaskLowCase()) {
-                    cmd += "&LCASE_MASK=yes";
-                }
-
-                if (ps.isMaskLookupTable()) {
-                    cmd += "&FILTER=m";
-                }
-                if (!ps.getMatrix().startsWith("dna")) {
-                    cmd += "&MATRIX_NAME=" + ps.getMatrix().trim();
-                }
-                if (ps.getWordsize() != null) {
-                    cmd += "&WORD_SIZE=" + ps.getWordsize().trim();
-                }
-                cmd+="&HSP_RANGE_MAX=" + ps.getHspRange().trim();
-                String gapCost = ps.getGapCost();
-                if (gapCost != null) {
-                	if(gapCost.equalsIgnoreCase("Linear")) gapCost="Existence: 0 Extension: 0";
-                    String[] s = gapCost.split(" ");
-                    if (s.length > 3) {
-                        cmd += "&GAPCOSTS=" + s[1].trim() + "%20" +
-                                s[3].trim();
-                    }
-                }
-
-                if(ps.getProgramName().equalsIgnoreCase("blastn")){
-	                String matchScores=ps.getMatchScores();
-	                if(matchScores!=null){
-	                	String[] s=matchScores.split(",");
-	                	if(s.length>1){
-	                		cmd+="&MATCH_SCORES=" + s[0].trim() + "%2C" + s[1].trim();
-	                	}
-	                }
-                }
-        		cmd+="&PAGE_TYPE=BlastSearch";
-
-                Map<String, String> specie_repeat=new HashMap<String,String>();
-                specie_repeat.put("Human","repeat_9606");
-                specie_repeat.put("Rodents","repeat_9989");
-                specie_repeat.put("Arabidopsis","repeat_3702");
-                specie_repeat.put("Rice","repeat_4530");
-                specie_repeat.put("Mammals","repeat_40674");
-                specie_repeat.put("Fungi","repeat_4751");
-                specie_repeat.put("C.elegans","repeat_6239");
-                specie_repeat.put("A.gambiae","repeat_7165");
-                specie_repeat.put("Zebrafish","repeat_7955");
-                specie_repeat.put("Fruit fly","repeat_7227");
-                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
-                	cmd += "&EXPECT=" + ps.getExpect() + "&AUTO_FORMAT=Semiauto&SHOW_OVERVIEW=on&SERVICE=plain\r\n\r\n";
-            }
-
-        }
-
-        return cmd;
-    }
-}
diff --git a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/BlastAppComponent.cwb.xml b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/BlastAppComponent.cwb.xml
deleted file mode 100644
index a6f9c89..0000000
--- a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/BlastAppComponent.cwb.xml
+++ /dev/null
@@ -1,34 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<component-descriptor xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-	xsi:noNamespaceSchemaLocation="Descriptor Schema.xsd">
-
-	<component name="BLAST Analysis"
-		class="org.geworkbench.components.alignment.panels.BlastAppComponent"
-		version="1.0"
-		author="geWorkbench Development Team"
-		authorURL="http://wiki.c2b2.columbia.edu/workbench/index.php/Home"
-		toolURL="http://wiki.c2b2.columbia.edu/workbench/index.php/Home"
-		tutorialURL="http://wiki.c2b2.columbia.edu/workbench/index.php/BLAST"
-		description="The Sequence Alignment component allows amino-acid (protein)
- or nucleotide (DNA) sequences to be submitted to the NCBI BLAST server
- for sequence similarity search against various databases."
-		category="analysis" loadByDefault="true">
-		<required-component
-			class="org.geworkbench.components.alignment.panels.BlastViewComponent" />
-		<required-component
-			class="org.geworkbench.components.sequences.SequenceViewAppComponent" />
-		<related-component class="org.geworkbench.components.promoter.PromoterView" />
-		<license><![CDATA[
-			<html><head><meta http-equiv=Content-Type content="text/html; charset=windows-1252"></head>
-				<body>----</body>
-			</html>
-		]]></license>
-
-	</component>
-
-	<plugin id="BlastAppComponent" name="Sequence Alignment"
-		class="org.geworkbench.components.alignment.panels.BlastAppComponent"
-		source="alignment">
-		<gui-area name="CommandArea" />
-	</plugin>
-</component-descriptor>
diff --git a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/BlastAppComponent.java b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/BlastAppComponent.java
deleted file mode 100755
index 07ea08d..0000000
--- a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/BlastAppComponent.java
+++ /dev/null
@@ -1,1473 +0,0 @@
-package org.geworkbench.components.alignment.panels;
-
-import java.awt.BorderLayout;
-import java.awt.Color;
-import java.awt.Component;
-import java.awt.Container;
-import java.awt.Dimension;
-import java.awt.FlowLayout;
-import java.awt.Font;
-import java.awt.GridBagConstraints;
-import java.awt.GridBagLayout;
-import java.awt.Insets;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.util.Date;
-
-import javax.swing.BorderFactory;
-import javax.swing.Box;
-import javax.swing.BoxLayout;
-import javax.swing.ButtonGroup;
-import javax.swing.DefaultComboBoxModel;
-import javax.swing.ImageIcon;
-import javax.swing.JButton;
-import javax.swing.JCheckBox;
-import javax.swing.JComboBox;
-import javax.swing.JFileChooser;
-import javax.swing.JLabel;
-import javax.swing.JOptionPane;
-import javax.swing.JPanel;
-import javax.swing.JProgressBar;
-import javax.swing.JRadioButton;
-import javax.swing.JScrollPane;
-import javax.swing.JTabbedPane;
-import javax.swing.JTable;
-import javax.swing.JTextArea;
-import javax.swing.JTextField;
-import javax.swing.JToolBar;
-import javax.swing.JViewport;
-import javax.swing.ListSelectionModel;
-import javax.swing.SwingConstants;
-import javax.swing.SwingUtilities;
-import javax.swing.UIManager;
-import javax.swing.border.Border;
-import javax.swing.border.TitledBorder;
-import javax.swing.event.ListSelectionEvent;
-import javax.swing.event.ListSelectionListener;
-import javax.swing.table.AbstractTableModel;
-import javax.swing.table.TableColumn;
-import javax.swing.table.TableModel;
-
-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.sequences.CSSequenceSet;
-import org.geworkbench.bison.datastructure.biocollections.sequences.DSSequenceSet;
-import org.geworkbench.bison.datastructure.bioobjects.markers.DSGeneMarker;
-import org.geworkbench.bison.datastructure.bioobjects.sequence.CSSequence;
-import org.geworkbench.bison.datastructure.bioobjects.sequence.DSSequence;
-import org.geworkbench.bison.datastructure.complex.panels.DSPanel;
-import org.geworkbench.components.alignment.blast.BlastAlgorithm;
-import org.geworkbench.engine.config.VisualPlugin;
-import org.geworkbench.engine.management.AcceptTypes;
-import org.geworkbench.engine.management.Asynchronous;
-import org.geworkbench.engine.management.Publish;
-import org.geworkbench.engine.management.Subscribe;
-import org.geworkbench.events.GeneSelectorEvent;
-
-/**
- *
- * @author not attributable
- * @version $Id: BlastAppComponent.java 7338 2010-12-16 16:46:53Z maz $
- */
-//test
-@SuppressWarnings("unchecked")
-@AcceptTypes( {CSSequenceSet.class})
-public class BlastAppComponent implements VisualPlugin {
-	private static final String SELECT_A_PROGRAM_PROMPT = "Select a program";
-
-	private static final int DATABASE_NAME_INDEX = 1;
-
-	Log log = LogFactory.getLog(BlastAppComponent.class);
-
-	private static AlgorithmMatcher algorithmMatcher = AlgorithmMatcher.getInstance();
-
-	// members from the base class in the previous version
-	private DSSequenceSet<DSSequence> sequenceDB = null;
-	private CSSequenceSet<? extends DSSequence> activeSequenceDB = null;
-	private boolean activateMarkers = true;
-	private DSPanel<? extends DSGeneMarker> activatedMarkers = null;
-
-	private JPanel mainPanel;
-	private JToolBar displayToolBar;
-	private JCheckBox chkAllMarkers = new JCheckBox("All Markers");
-	private JTextField sequenceNumberField;
-
-	// members from originally in this class
-	private JPanel jBasicPane = new JPanel();
-    private JTabbedPane jTabbedPane1 = new JTabbedPane();
-    private JTabbedPane jTabbedBlastPane = new JTabbedPane();
-
-    //boxes for bug2019
-    private JCheckBox excludeModels = null;
-    private JCheckBox excludeUnculture = null;
-    private JLabel jexcludeLabel = new JLabel("Exclude: ");
-    private JLabel jEntrezQueryLabel=new JLabel("Entrez Query: ");
-    private JTextField jEntrezQueryText=new JTextField(10);
-    private JTextField jQueryFromText=new JTextField(5);
-    private JTextField jQueryToText=new JTextField(5);
-
-    private JRadioButton megablastBtn=null;
-    private JLabel jmegablastLabel = new JLabel("Optimize for: ");
-    private JRadioButton discontiguousBtn=null;
-    private JRadioButton blastnBtn=null;
-    private ButtonGroup programBtnGroup=new ButtonGroup();
-
-    private JLabel jgeneticCodeLabel = new JLabel("Genetic Code: ");
-    private JComboBox jgeneticCodeBox=new JComboBox();
-
-    // five check boxes in filter panel+...
-    private JCheckBox shortQueriesBox =null;
-    private JCheckBox lowComplexFilterBox = null;
-    private JCheckBox speciesRepeatFilter = null;
-    private JLabel jMaskLabel =new JLabel("Mask:");
-    private JCheckBox maskLowCaseBox = null;
-    private JCheckBox maskLookupOnlyBox = null;
-    private JLabel jDisplayLabel =new JLabel("Browser:");
-    private JCheckBox jDisplayInWebBox = null;
-
-    JPanel jAdvancedPane = new JPanel();
-    JFileChooser jFileChooser1 = new JFileChooser();
-
-    static final int BLAST = 0;//keep unchanged
-
-    public static final String NCBILABEL = "NCBI BLAST Result";
-    public static final String ERROR1 = "Interrupted";
-    public static final String ERROR2 = "The connection to the Columbia Blast Server cannot be established, please try NCBI Blast Server.";
-
-    private JTable databaseTable = null;
-    private JButton blastButton = new JButton();
-    private JScrollPane jScrollPane1 = new JScrollPane();
-
-    private JComboBox jProgramBox = new JComboBox();
-
-    private JPanel speciesRepeatPanel = new JPanel();
-    private JButton defaultButton = new JButton();
-
-    // pairs of label and combo box on blastxSettingPanel
-    private JLabel jMatrixLabel= new JLabel("Matrix:");
-    private JComboBox jMatrixBox = new JComboBox();
-    private JLabel maxTargetLabel= new JLabel("Max target sequences:");
-    private JComboBox jMaxTargetBox=new JComboBox();
-
-    private JComboBox jExpectBox = new JComboBox();
-    private JComboBox jWordsizeBox = new JComboBox();
-    private JTextField jHspRangeBox=new JTextField(5);
-
-    private JLabel jScoresLabel= new JLabel("Match/mismatch Scores:");
-    private JComboBox jScoresBox=new JComboBox();
-    private JLabel jGapcostsLabel = new JLabel("Gap costs:");
-    private JComboBox jGapcostsBox = new JComboBox();
-    private JLabel jCompositionalLabel= new JLabel("Compositional Adjustments:");
-    private JComboBox jCompositionalBox=new JComboBox();
-    private JComboBox jSpeciesBox=new JComboBox();
-    private JLabel jTemplateLengthLabel = new JLabel("Template Length:");
-    private JComboBox jTemplateLengthBox=new JComboBox();
-    private JLabel jTemplateTypeLabel = new JLabel("Template Type:");
-    private JComboBox jTemplateTypeBox=new JComboBox();
-
-    private BlastAppComponent blastAppComponent = null;
-    private JPanel subSeqPanel;
-    private JPanel subSeqPanel2;
-
-    private JTextField jstartPointField = new JTextField();
-    private JTextField jendPointField = new JTextField();
-    private JProgressBar serviceProgressBar = new JProgressBar();
-
-    private JButton blastStopButton = new JButton();
-
-    private JToolBar jToolBar2 = new JToolBar();
-
-    private Border border1 = BorderFactory.createEtchedBorder(Color.white,
-            new Color(165, 163, 151));
-    private Border border2 = new TitledBorder(border1,
-                                      "Please specify Program and Database");
-    private Border border3 = new TitledBorder(border1, "Database Details");
-    private JTextArea textArea = new JTextArea();
-
-    private ImageIcon startButtonIcon = new ImageIcon(this.getClass().getResource(
-            "start.gif"));
-    private ImageIcon stopButtonIcon = new ImageIcon(this.getClass().getResource(
-            "stop.gif"));
-
-    private JPanel jPanel3 = new JPanel();
-    private BorderLayout borderLayout2 = new BorderLayout();
-
-    private BorderLayout borderLayout3 = new BorderLayout();
-    private JScrollPane jScrollPane4 = new JScrollPane();
-    private static final int MAIN = 0;
-    private static final int SERVER = 2;
-
-    private boolean stopButtonPushed;
-
-	private JPanel discontiguousWordOptionsPanel;
-
-	private JPanel geneticCodePanel;
-
-    private static JLabel DatabaseLabel = new JLabel("Database:");
-
-    private String programForDefaultButton="blastn";
-
-    private JPanel chooseSearchPanel=new JPanel();
-
-    public BlastAppComponent() {
-        try {
-        	init1();
-        	init2();
-        } catch (Exception e) {
-            e.printStackTrace();
-        }
-    }
-
-    private void init2() throws Exception {
-
-        jBasicPane = new JPanel();
-        jTabbedPane1 = new JTabbedPane();
-        jTabbedBlastPane = new JTabbedPane();
-
-        jScrollPane4 = new JScrollPane();
-
-        databaseTable = new JTable() // customized only to hide the header
-        {
-			private static final long serialVersionUID = -7546361375519248646L;
-
-			protected void configureEnclosingScrollPane() {
-                Container p = getParent();
-                if (p instanceof JViewport) {
-                    Container gp = p.getParent();
-                    if (gp instanceof JScrollPane) {
-                        JScrollPane scrollPane = (JScrollPane)gp;
-                        // Make certain we are the viewPort's view and not, for
-                        // example, the rowHeaderView of the scrollPane -
-                        // an implementor of fixed columns might do this.
-                        JViewport viewport = scrollPane.getViewport();
-                        if (viewport == null || viewport.getView() != this) {
-                            return;
-                        }
-//                        scrollPane.setColumnHeaderView(getTableHeader());
-                        scrollPane.getViewport().setScrollMode(JViewport.BACKINGSTORE_SCROLL_MODE );
-                        scrollPane.setBorder(UIManager.getBorder("Table.scrollPaneBorder"));
-                    }
-                }
-            }
-        };
-
-        blastButton = new JButton();
-        jScrollPane1 = new JScrollPane();
-        jProgramBox = new JComboBox();
-
-        jstartPointField = new JTextField();
-        jendPointField = new JTextField();
-        serviceProgressBar = new JProgressBar();
-
-        blastStopButton = new JButton();
-
-        jToolBar2 = new JToolBar();
-
-        border1 = BorderFactory.createEtchedBorder(Color.white,
-                new Color(165, 163, 151));
-        border2 = new TitledBorder(border1,
-                                   "Please specify Program and Database");
-
-        startButtonIcon = new ImageIcon(this.getClass().getResource(
-                "start.gif"));
-        stopButtonIcon = new ImageIcon(this.getClass().getResource(
-                "stop.gif"));
-
-        jPanel3 = new JPanel();
-        borderLayout2 = new BorderLayout();
-
-        borderLayout3 = new BorderLayout();
-
-        geneticCodePanel = new JPanel();
-
-        //above is part of code to get rid of npe.
-        //sgePanel.setPv(this);
-        subSeqPanel = new JPanel();
-        subSeqPanel.setBorder(border2);
-        subSeqPanel2 = new JPanel();
-        subSeqPanel2.setBorder(border3);
-
-        jBasicPane.setPreferredSize(new Dimension(364, 250));
-        jBasicPane.setLayout(borderLayout2);
-
-        jPanel3.setLayout(borderLayout3);
-
-        databaseTable.setToolTipText("Select a database");
-        databaseTable.setVerifyInputWhenFocusTarget(true);
-        databaseTable.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
-        jProgramBox.addItem(SELECT_A_PROGRAM_PROMPT);
-        jProgramBox.addItem("blastn");
-        jProgramBox.addItem("blastp");
-        jProgramBox.addItem("blastx");
-        jProgramBox.addItem("tblastn");
-        jProgramBox.addItem("tblastx");
-
-        defaultButton.setText("Restore Defaults");
-        defaultButton.addActionListener(new
-                BlastAppComponent_default_actionAdapter());
-
-        blastButton.setFont(new java.awt.Font("Arial Black", 0, 11));
-        blastButton.setHorizontalAlignment(SwingConstants.LEFT);
-        blastButton.setHorizontalTextPosition(SwingConstants.CENTER);
-        //blastButton.setText("BLAST");
-        blastButton.setIcon(startButtonIcon);
-
-        blastButton.setToolTipText("Start BLAST");
-
-        blastButton.addActionListener(new
-                                      BlastAppComponent_blastButton_actionAdapter());
-        jTabbedPane1.setDebugGraphicsOptions(0);
-        jTabbedPane1.setMinimumSize(new Dimension(5, 5));
-        jProgramBox.addActionListener(new
-                                      BlastAppComponent_jProgramBox_actionAdapter());
-        databaseTable.getSelectionModel().addListSelectionListener(new BlastAppComponent_jDBList_listSelectionListener() );
-
-        // details of four combo boxes on plastx panel
-        // (1)
-        jMatrixBox
-				.addActionListener(new BlastAppComponent_jMatrixBox_actionAdapter());
-        jMatrixBox.addItem("dna.mat");
-        jMatrixBox.setVerifyInputWhenFocusTarget(true);
-        jMatrixBox.setSelectedIndex(0);
-        // (2)
-
-        jExpectBox.setVerifyInputWhenFocusTarget(true);
-        jExpectBox.addItem("0.000000001");
-        jExpectBox.addItem("0.01");
-        jExpectBox.addItem("0.1");
-        jExpectBox.addItem("1");
-        jExpectBox.addItem("10");
-        jExpectBox.addItem("100");
-        jExpectBox.addItem("1000");
-        jExpectBox.setEditable(true);
-
-        // (3)
-        jGapcostsBox.setVerifyInputWhenFocusTarget(true);
-    	String defaulMatrixName = "BLOSUM62";
-        String[] model = AlgorithmMatcher.translateToGapcosts(defaulMatrixName);
-       	jGapcostsBox.setModel(new DefaultComboBoxModel(model));
-       	Integer index = AlgorithmMatcher.defaultGapcostIndex.get(defaulMatrixName);
-       	if(index==null) index = 0;
-       	jGapcostsBox.setSelectedIndex(index);
-
-        // (4)
-        jWordsizeBox.addItem("3");
-        jWordsizeBox.addItem("2");
-        jWordsizeBox.addItem("7");
-        jWordsizeBox.addItem("11");
-        jWordsizeBox.addItem("15");
-        jWordsizeBox.setMaximumRowCount(10);
-
-        //(5)
-        jScoresBox.addItem("1,-2");
-        jScoresBox.addItem("1,-3");
-        jScoresBox.addItem("1,-4");
-        jScoresBox.addItem("2,-3");
-        jScoresBox.addItem("4,-5");
-        jScoresBox.addItem("1,-1");
-
-        jCompositionalBox.addItem("No adjustment");
-        jCompositionalBox.addItem("Composition-based statistics");
-        jCompositionalBox.addItem("Conditional compositional score matrix adjustment");
-        jCompositionalBox.addItem("Universal compositional score matrix adjustment");
-
-        jSpeciesBox.addItem("Human");
-        jSpeciesBox.addItem("Rodents");
-        jSpeciesBox.addItem("Arabidopsis");
-        jSpeciesBox.addItem("Rice");
-        jSpeciesBox.addItem("Mammals");
-        jSpeciesBox.addItem("Fungi");
-        jSpeciesBox.addItem("C.elegans");
-        jSpeciesBox.addItem("A.gambiae");
-        jSpeciesBox.addItem("Zebrafish");
-        jSpeciesBox.addItem("Fruit fly");
-        jSpeciesBox.setMaximumRowCount(10);
-
-        jTemplateLengthBox.addItem("None");
-        jTemplateLengthBox.addItem("16");
-        jTemplateLengthBox.addItem("18");
-        jTemplateLengthBox.addItem("21");
-
-        jTemplateTypeBox.addItem("Coding");
-        jTemplateTypeBox.addItem("Maximal");
-        jTemplateTypeBox.addItem("Two template");
-
-        jgeneticCodeBox.addItem("Standard (1)");
-        jgeneticCodeBox.addItem("Vertebrate Mitochondrial (2)");
-        jgeneticCodeBox.addItem("Yeast Mitochondrial (3)");
-        jgeneticCodeBox.addItem("Mold Mitochondrial (4)");
-        jgeneticCodeBox.addItem("Invertebrate Mitochondrial (5)");
-        jgeneticCodeBox.addItem("Ciliate Nuclear(6)");
-        jgeneticCodeBox.addItem("Echinoderm Mitochondrial (9)");
-        jgeneticCodeBox.addItem("Euplotid Nuclear (10)");
-        jgeneticCodeBox.addItem("Bacteria and Archaea (11)");
-        jgeneticCodeBox.addItem("Alternative Yeast Nuclear (12)");
-        jgeneticCodeBox.addItem("Ascidian Mitochondrial (13)");
-        jgeneticCodeBox.addItem("Flatworm Mitochondrial (14)");
-        jgeneticCodeBox.addItem("Blepharisma Macronuclear (15)");
-        jgeneticCodeBox.setMaximumRowCount(13);
-
-        jMaxTargetBox.addItem("10");
-        jMaxTargetBox.addItem("50");
-        jMaxTargetBox.addItem("100");
-        jMaxTargetBox.addItem("250");
-        jMaxTargetBox.addItem("500");
-        jMaxTargetBox.addItem("1000");
-        jMaxTargetBox.addItem("5000");
-        jMaxTargetBox.addItem("10000");
-        jMaxTargetBox.addItem("20000");
-        jMaxTargetBox.setMaximumRowCount(10);
-
-        jAdvancedPane.setLayout(new GridBagLayout());
-
-        jProgramBox.setAutoscrolls(false);
-        subSeqPanel.setLayout(new BoxLayout(subSeqPanel, BoxLayout.Y_AXIS));
-        subSeqPanel2.setLayout(new BoxLayout(subSeqPanel2, BoxLayout.Y_AXIS));
-
-        jstartPointField.setText("1");
-        jendPointField.setText("");
-
-        blastStopButton.setFont(new java.awt.Font("Arial Black", 0, 11));
-        blastStopButton.setVerifyInputWhenFocusTarget(true);
-        //blastStopButton.setText("STOP");
-        blastStopButton.setIcon(stopButtonIcon);
-        blastStopButton.setToolTipText("Stop the Query");
-
-        blastStopButton.addActionListener(new
-                                          BlastAppComponent_blastStopButton_actionAdapter());
-
-        jToolBar2.setLayout(new BoxLayout(jToolBar2, BoxLayout.LINE_AXIS));
-        jToolBar2.add(serviceProgressBar);
-        serviceProgressBar.setOrientation(JProgressBar.HORIZONTAL);
-        serviceProgressBar.setBorder(BorderFactory.createEtchedBorder());
-        serviceProgressBar.setStringPainted(true);
-
-        jTabbedPane1.add(jTabbedBlastPane, "BLAST");
-
-        excludeModels = new JCheckBox();
-        excludeModels.setMinimumSize(new Dimension(10, 23));
-        excludeModels.setMnemonic(0);
-        excludeModels.setSelected(false);
-        excludeModels.setText("Models(XM/XP)");
-
-        excludeUnculture = new JCheckBox();
-        excludeUnculture.setMinimumSize(new Dimension(10, 23));
-        excludeUnculture.setMnemonic(0);
-        excludeUnculture.setSelected(false);
-        excludeUnculture.setText("Uncultured/environmental sequences");
-
-        megablastBtn=new JRadioButton();
-        megablastBtn.setMinimumSize(new Dimension(10,23));
-        megablastBtn.setMnemonic(0);
-        megablastBtn.setSelected(true);
-        megablastBtn.setText("Highly similar sequences (megablast)");
-        megablastBtn.addActionListener(new BlastAppComponent_megablastBtn_actionAdapter());
-
-        discontiguousBtn=new JRadioButton();
-        discontiguousBtn.setMinimumSize(new Dimension(10,23));
-        discontiguousBtn.setMnemonic(0);
-        discontiguousBtn.setText("More dissimilar sequences (discontiguous megablast)");
-        discontiguousBtn.addActionListener(new BlastAppComponent_discontiguousBtn_actionAdapter());
-
-        blastnBtn=new JRadioButton();
-        blastnBtn.setMinimumSize(new Dimension(10,23));
-        blastnBtn.setMnemonic(0);
-        blastnBtn.setText("Somewhat similar sequences (blastn)");
-        blastnBtn.addActionListener(new BlastAppComponent_discontiguousBtn_actionAdapter());
-
-        programBtnGroup.add(megablastBtn);
-        programBtnGroup.add(discontiguousBtn);
-        programBtnGroup.add(blastnBtn);
-
-        // 5 check boxes on filter panel+...
-        shortQueriesBox=new JCheckBox();
-        shortQueriesBox.setMnemonic('0');
-        shortQueriesBox.setSelected(true);
-        shortQueriesBox.setText("Automatically adjust parameters for short input sequences");
-
-        lowComplexFilterBox = new JCheckBox();
-        lowComplexFilterBox.setMnemonic('0');
-        lowComplexFilterBox.setSelected(false);
-        lowComplexFilterBox.setText("Low Complexity");
-
-        maskLowCaseBox = new JCheckBox();
-        maskLowCaseBox.setToolTipText("Filterl lower case sequences.");
-        maskLowCaseBox.setText("Mask lower case letter");
-
-        maskLookupOnlyBox = new JCheckBox();
-        maskLookupOnlyBox.setText("Mask for lookup table only");
-        maskLookupOnlyBox.setMnemonic('0');
-        maskLookupOnlyBox.setSelected(false);
-
-        speciesRepeatFilter = new JCheckBox();
-        speciesRepeatFilter.setToolTipText("Species_specific Repeat Filter");
-        speciesRepeatFilter.setSelected(false);
-        speciesRepeatFilter.setText("Species-specific repeats for");
-
-        jDisplayInWebBox = new JCheckBox();
-        jDisplayInWebBox.setSelected(true);
-        jDisplayInWebBox.setText("Display result in your web browser");
-
-        // speciesRepeatPanel: including 2 items
-        speciesRepeatPanel = new JPanel();
-        speciesRepeatPanel.setLayout(new FlowLayout(FlowLayout.LEADING));
-        speciesRepeatPanel.add(new JLabel("          "));
-        speciesRepeatPanel.add(speciesRepeatFilter);
-        speciesRepeatPanel.add(jSpeciesBox);
-
-        // update tooltip text
-        // based on information from http://blast.ncbi.nlm.nih.gov/Blast.cgi and http://www.ncbi.nlm.nih.gov/BLAST/matrix_info.html
-        jMaxTargetBox.setToolTipText("Select the maximum number of aligned sequences to display");
-        jExpectBox.setToolTipText("Random background noise");
-        jWordsizeBox.setToolTipText("The length of the words governing the sensitivity");
-        jHspRangeBox.setToolTipText("Limit the number of matches to a query range");
-        jMatrixBox.setToolTipText("Assigns a score for aligning any possible pair of residues");
-        jGapcostsBox.setToolTipText("Score subtracted due to the gaps");
-        excludeModels.setToolTipText("Models(XM/XP)");
-        excludeUnculture.setToolTipText("Uncultured/environmental sample sequences");
-        jEntrezQueryText.setToolTipText("Enter an Entrez query to limit search ");
-        jQueryFromText.setToolTipText("Sequence coordinates are from 1 to the sequence length");
-        jQueryToText.setToolTipText("Sequence coordinates are from 1 to the sequence length");
-        megablastBtn.setToolTipText("Highly similar sequences (megablast)");
-        discontiguousBtn.setToolTipText("More dissimilar sequences (discontiguous megablast)");
-        blastnBtn.setToolTipText("Somewhat similar sequences (blastn)");
-
-		// jTabbedBlastPane contains two panels
-		jTabbedBlastPane.add(jBasicPane, "Main");
-        jTabbedBlastPane.add(new JScrollPane(jAdvancedPane), "Algorithm Parameters");
-        jAdvancedPane.setEnabled(false);
-
-        // mainPanel contains one tabbed pane
-        mainPanel.add(jTabbedPane1, java.awt.BorderLayout.CENTER);
-
-        JPanel programPanel = new JPanel();
-        programPanel.setLayout(new FlowLayout(FlowLayout.LEADING) );
-        programPanel.add(new JLabel("Program: "));
-        programPanel.add(jProgramBox);
-        programPanel.setAlignmentX(Component.LEFT_ALIGNMENT);
-        subSeqPanel.add(programPanel);
-
-        JPanel discontinguousPanel = new JPanel();
-        discontinguousPanel.setLayout(new BoxLayout(discontinguousPanel, BoxLayout.X_AXIS) );
-        discontinguousPanel.setBorder(BorderFactory.createEmptyBorder(10,10,10,10));
-        jmegablastLabel.setAlignmentY(Component.TOP_ALIGNMENT);
-        discontinguousPanel.add(jmegablastLabel);
-        JPanel discontinguousOptionsPanel = new JPanel();
-        discontinguousOptionsPanel.setLayout(new BoxLayout(discontinguousOptionsPanel, BoxLayout.Y_AXIS));
-        discontinguousOptionsPanel.add(megablastBtn);
-        discontinguousOptionsPanel.add(discontiguousBtn);
-        discontinguousOptionsPanel.add(blastnBtn);
-        discontinguousOptionsPanel.setAlignmentY(Component.TOP_ALIGNMENT);
-        discontinguousPanel.add(discontinguousOptionsPanel);
-        discontinguousPanel.setAlignmentX(Component.LEFT_ALIGNMENT);
-        subSeqPanel.add(discontinguousPanel);
-        enableBlastnRelateOptions(false);
-
-        geneticCodePanel.setLayout(new FlowLayout(FlowLayout.LEADING));
-        geneticCodePanel.add(jgeneticCodeLabel);
-        geneticCodePanel.add(jgeneticCodeBox);
-        geneticCodePanel.setAlignmentX(Component.LEFT_ALIGNMENT);
-        subSeqPanel.add(geneticCodePanel);
-        geneticCodePanel.setVisible(false);
-
-        DatabaseLabel.setAlignmentX(Component.LEFT_ALIGNMENT);
-        subSeqPanel.add(DatabaseLabel);
-        jScrollPane1.setPreferredSize(new Dimension(300, 100));
-        jScrollPane1.setAlignmentX(Component.LEFT_ALIGNMENT);
-        subSeqPanel.add(jScrollPane1);
-
-        textArea.setBackground(subSeqPanel2.getBackground());
-        textArea.setEditable(false);
-        textArea.setLineWrap(true); //wrap text around
-        textArea.setFont(new Font("Monospaced", Font.PLAIN, 12));
-        textArea.setPreferredSize(new Dimension(350, 100));
-        subSeqPanel2.add(textArea);
-
-        chooseSearchPanel.setLayout(new GridBagLayout());
-
-        JPanel excludePanel = new JPanel();
-        excludePanel.setLayout(new BoxLayout(excludePanel, BoxLayout.Y_AXIS) );
-        excludePanel.setBorder(new TitledBorder(border1, "Search Choice (optional)"));
-
-        JPanel excludeOptions1Panel = new JPanel();
-        excludeOptions1Panel.setLayout(new FlowLayout(FlowLayout.LEADING) );
-        excludeOptions1Panel.add(jexcludeLabel);
-        excludeOptions1Panel.add(excludeModels);
-        excludePanel.add(excludeOptions1Panel);
-        JPanel excludeOptions2Panel = new JPanel();
-        excludeOptions2Panel.setLayout(new FlowLayout(FlowLayout.LEADING) );
-        excludeOptions2Panel.add(new JLabel("                "));
-        excludeOptions2Panel.add(excludeUnculture);
-        excludePanel.add(excludeOptions2Panel);
-
-        JPanel entrezQueryPanel = new JPanel();
-        entrezQueryPanel.setLayout(new FlowLayout(FlowLayout.LEADING) );
-        entrezQueryPanel.add(jEntrezQueryLabel);
-        entrezQueryPanel.add(jEntrezQueryText);
-
-        jEntrezQueryText.setText("");
-        jEntrezQueryLabel.setVisible(false);
-		jEntrezQueryText.setVisible(false);
-        excludePanel.add(entrezQueryPanel);
-
-        GridBagConstraints b = new GridBagConstraints(0, 0, 1, 1,
-				0.0, 0.0, GridBagConstraints.WEST,
-				GridBagConstraints.NONE, new Insets(2, 2, 2, 2), 0, 0);
-        b.gridx = 0;
-        b.gridy = 0;
-        chooseSearchPanel.add(excludePanel,b);
-
-		JPanel querySubrangePanel=new JPanel();
-		querySubrangePanel.setBorder(new TitledBorder(border1, "Query Subrange"));
-		querySubrangePanel.setLayout(new BoxLayout(querySubrangePanel, BoxLayout.Y_AXIS) );
-		//querySubrangePanel.setBorder(BorderFactory.createEmptyBorder(10,10,10,10));
-
-		JPanel queryFromPanel = new JPanel();
-		queryFromPanel.setLayout(new FlowLayout(FlowLayout.LEADING));
-		queryFromPanel.add(new JLabel("From:"));
-		queryFromPanel.add(jQueryFromText);
-		querySubrangePanel.add(queryFromPanel);
-
-		JPanel queryToPanel = new JPanel();
-		queryToPanel.setLayout(new FlowLayout(FlowLayout.LEADING));
-		queryToPanel.add(new JLabel("To:     "));
-		queryToPanel.add(jQueryToText);
-		querySubrangePanel.add(queryToPanel);
-        b.gridx = 1;
-        b.gridy = 0;
-        chooseSearchPanel.add(querySubrangePanel,b);
-        chooseSearchPanel.setAlignmentX(Component.LEFT_ALIGNMENT);
-		subSeqPanel.add(chooseSearchPanel);
-		chooseSearchPanel.setVisible(false);
-
-        displayToolBar.add(Box.createHorizontalStrut(10), null);
-        displayToolBar.add(blastButton);
-        displayToolBar.add(Box.createHorizontalStrut(5), null);
-        displayToolBar.add(blastStopButton);
-        jScrollPane4.getViewport().add(jPanel3);
-        jPanel3.add(subSeqPanel, BorderLayout.CENTER);
-        jPanel3.add(subSeqPanel2, BorderLayout.EAST);
-        jBasicPane.add(jScrollPane4, java.awt.BorderLayout.CENTER);
-        jBasicPane.add(jToolBar2, java.awt.BorderLayout.NORTH);
-
-        jTabbedPane1.setSelectedComponent(jTabbedBlastPane);
-        jTabbedBlastPane.setSelectedComponent(jBasicPane);
-    }
-
-    static private class UneditableTableModel extends AbstractTableModel {
-		private static final long serialVersionUID = 1231350431097267149L;
-
-		private String[][] data;
-
-    	UneditableTableModel(String[][] data) {
-    		this.data = data;
-    	}
-
-		@Override
-		public int getColumnCount() {
-			return 2;
-		}
-
-		@Override
-		public int getRowCount() {
-			return data.length;
-		}
-
-		@Override
-		public Object getValueAt(int rowIndex, int columnIndex) {
-			return data[rowIndex][columnIndex];
-		}
-
-		@Override
-		public boolean isCellEditable(int rowIndex,
-                int columnIndex) {
-			return false;
-		}
-    }
-
-    private void enableBlastnRelateOptions(Boolean b){
-    	geneticCodePanel.setVisible(false);
-    	if(((String) jProgramBox.getSelectedItem()).equalsIgnoreCase("blastn")&&b){
-    		megablastBtn.setVisible(b);
-    		discontiguousBtn.setVisible(b);
-    		blastnBtn.setVisible(b);
-    		jmegablastLabel.setVisible(b);
-    	}
-    	else{
-    		megablastBtn.setVisible(false);
-    		discontiguousBtn.setVisible(false);
-    		blastnBtn.setVisible(false);
-    		jmegablastLabel.setVisible(false);
-    	}
-    	jexcludeLabel.setVisible(b);
-		excludeModels.setVisible(b);
-		excludeUnculture.setVisible(b);
-    }
-
-    private void setAdvancedOptions(){
-    	String selectedProgramName = programForDefaultButton;
-		jAdvancedPane.removeAll();
-		jEntrezQueryLabel.setVisible(true);
-		jEntrezQueryText.setVisible(true);
-		enableBlastnRelateOptions(true);
-		if(selectedProgramName.equalsIgnoreCase("blastx")||selectedProgramName.equalsIgnoreCase("tblastx")){
-			geneticCodePanel.setVisible(true);
-		}
-
-        JPanel generalParametersPanel = new JPanel();
-        generalParametersPanel.setBorder( new TitledBorder(border1, "General Parameters"));
-        generalParametersPanel.setLayout(new BoxLayout(generalParametersPanel, BoxLayout.Y_AXIS));
-        JPanel maxTargetPanel = new JPanel();
-        maxTargetPanel.setLayout(new FlowLayout(FlowLayout.LEADING) );
-        maxTargetPanel.add(maxTargetLabel);
-        maxTargetPanel.add(jMaxTargetBox);
-        maxTargetPanel.setAlignmentX(Component.LEFT_ALIGNMENT);
-        generalParametersPanel.add(maxTargetPanel);
-        shortQueriesBox.setAlignmentX(Component.LEFT_ALIGNMENT);
-        generalParametersPanel.add(shortQueriesBox);
-        JPanel expectThresholdPanel = new JPanel();
-        expectThresholdPanel.setLayout(new FlowLayout(FlowLayout.LEADING) );
-		expectThresholdPanel.add(new JLabel("Expect threshold:"));
-        expectThresholdPanel.add(jExpectBox);
-        expectThresholdPanel.setAlignmentX(Component.LEFT_ALIGNMENT);
-        generalParametersPanel.add(expectThresholdPanel);
-        JPanel wordSizePanel = new JPanel();
-        wordSizePanel.setLayout(new FlowLayout(FlowLayout.LEADING) );
-        wordSizePanel.add(new JLabel("Word size:"));
-        wordSizePanel.add(jWordsizeBox);
-        wordSizePanel.setAlignmentX(Component.LEFT_ALIGNMENT);
-        generalParametersPanel.add(wordSizePanel);
-        JPanel hspRangePanel = new JPanel();
-        hspRangePanel.setLayout(new FlowLayout(FlowLayout.LEADING) );
-        hspRangePanel.add(new JLabel("Max matches in a query range:"));
-        hspRangePanel.add(jHspRangeBox);
-        hspRangePanel.setAlignmentX(Component.LEFT_ALIGNMENT);
-        generalParametersPanel.add(hspRangePanel);
-        jHspRangeBox.setText("0");
-
-        GridBagConstraints c = new GridBagConstraints(0, 0, 1, 1,
-				0.0, 0.0, GridBagConstraints.WEST,
-				GridBagConstraints.NONE, new Insets(2, 2, 2, 2), 0, 0);
-        jAdvancedPane.add(generalParametersPanel, c);
-
-        JPanel scoringParametersPanel = new JPanel();
-        scoringParametersPanel.setBorder(new TitledBorder(border1, "Scoring Paremeters"));
-        scoringParametersPanel.setLayout(new BoxLayout(scoringParametersPanel, BoxLayout.Y_AXIS));
-        JPanel maxtrixPanel = new JPanel();
-        maxtrixPanel.setLayout(new FlowLayout(FlowLayout.LEADING) );
-        maxtrixPanel.add(jMatrixLabel);
-        maxtrixPanel.add(jMatrixBox);
-        maxtrixPanel.setAlignmentX(Component.LEFT_ALIGNMENT);
-        scoringParametersPanel.add(maxtrixPanel);
-        JPanel scoresPanel = new JPanel();
-        scoresPanel.setLayout(new FlowLayout(FlowLayout.LEADING));
-        scoresPanel.add(jScoresLabel);
-        scoresPanel.add(jScoresBox);
-        scoresPanel.setAlignmentX(Component.LEFT_ALIGNMENT);
-        scoringParametersPanel.add(scoresPanel);
-        JPanel gapCostsPanel = new JPanel();
-        gapCostsPanel.setLayout(new FlowLayout(FlowLayout.LEADING));
-        gapCostsPanel.add(jGapcostsLabel);
-        gapCostsPanel.add(jGapcostsBox);
-        gapCostsPanel.setAlignmentX(Component.LEFT_ALIGNMENT);
-        scoringParametersPanel.add(gapCostsPanel);
-        JPanel compositionalPanel = new JPanel();
-        compositionalPanel.setLayout(new FlowLayout(FlowLayout.LEADING));
-        compositionalPanel.add(jCompositionalLabel);
-        compositionalPanel.add(jCompositionalBox);
-        compositionalPanel.setAlignmentX(Component.LEFT_ALIGNMENT);
-        scoringParametersPanel.add(compositionalPanel);
-        c.gridy = 1;
-        jAdvancedPane.add(scoringParametersPanel, c);
-
-        JPanel filterAndMaskPanel = new JPanel();
-        filterAndMaskPanel.setBorder(new TitledBorder(border1, "Filters and Masking"));
-        filterAndMaskPanel.setLayout(new BoxLayout(filterAndMaskPanel, BoxLayout.Y_AXIS));
-        JPanel filter1Panel = new JPanel();
-        filter1Panel.setLayout(new FlowLayout(FlowLayout.LEADING));
-        filter1Panel.add(new JLabel("Filter:"));
-        filter1Panel.add(lowComplexFilterBox);
-        filterAndMaskPanel.add(filter1Panel);
-        filterAndMaskPanel.add(speciesRepeatPanel);
-        JPanel mask1Panel = new JPanel();
-        mask1Panel.setLayout(new FlowLayout(FlowLayout.LEADING));
-        mask1Panel.add(jMaskLabel);
-        mask1Panel.add(maskLookupOnlyBox);
-        filterAndMaskPanel.add(mask1Panel);
-        JPanel mask2Panel = new JPanel();
-        mask2Panel.setLayout(new FlowLayout(FlowLayout.LEADING));
-        mask2Panel.add(new JLabel("          "));
-        mask2Panel.add(maskLowCaseBox);
-        filterAndMaskPanel.add(mask2Panel);
-        c.gridx = 1;
-        c.gridy = 0;
-        jAdvancedPane.add(filterAndMaskPanel, c);
-
-        JPanel browserPanel = new JPanel();
-        browserPanel.setLayout(new FlowLayout(FlowLayout.LEADING) );
-        browserPanel.add(jDisplayLabel);
-        browserPanel.add(jDisplayInWebBox);
-        browserPanel.setAlignmentX(Component.LEFT_ALIGNMENT);
-        c.gridx = 0;
-        c.gridy = 2;
-        jAdvancedPane.add(browserPanel, c);
-
-        JPanel defaultButtonPanel = new JPanel();
-        defaultButtonPanel.setLayout(new FlowLayout(FlowLayout.LEADING) );
-        defaultButtonPanel.add(defaultButton);
-        defaultButtonPanel.setAlignmentX(Component.LEFT_ALIGNMENT);
-        c.gridx = 1;
-        c.gridy = 2;
-        jAdvancedPane.add(defaultButtonPanel, c);
-
-        discontiguousWordOptionsPanel = new JPanel();
-        discontiguousWordOptionsPanel.setBorder(new TitledBorder(border1, "Discontiguous Word Options"));
-        discontiguousWordOptionsPanel.setLayout( new BoxLayout(discontiguousWordOptionsPanel, BoxLayout.Y_AXIS) );
-        JPanel templeateLengthPanel = new JPanel();
-        templeateLengthPanel.setLayout(new FlowLayout(FlowLayout.LEADING) );
-        templeateLengthPanel.add(jTemplateLengthLabel);
-        templeateLengthPanel.add(jTemplateLengthBox);
-        jTemplateLengthBox.setSelectedIndex(2);
-        discontiguousWordOptionsPanel.add(templeateLengthPanel);
-        JPanel templeateTypePanel = new JPanel();
-        templeateTypePanel.setLayout(new FlowLayout(FlowLayout.LEADING) );
-        templeateTypePanel.add(jTemplateTypeLabel);
-        templeateTypePanel.add(jTemplateTypeBox);
-        jTemplateTypeBox.setSelectedIndex(0);
-        discontiguousWordOptionsPanel.add(templeateTypePanel);
-        c.gridx = 1;
-        c.gridy = 1;
-        jAdvancedPane.add(discontiguousWordOptionsPanel, c);
-
-        discontiguousWordOptionsPanel.setVisible(false);
-
-		jCompositionalLabel.setVisible(false);
-		jCompositionalBox.setVisible(false);
-
-		shortQueriesBox.setVisible(false);
-
-		jAdvancedPane.setEnabled(true);
-
-		String[] model = AlgorithmMatcher
-				.translateToMatrices(selectedProgramName);
-		jMatrixBox.setModel(new DefaultComboBoxModel(model));
-
-		jWordsizeBox.setVerifyInputWhenFocusTarget(true);
-       	String defaultOptimizeFor="megablast";
-		String[] model2 = AlgorithmMatcher
-				.translateToWordSize(selectedProgramName,defaultOptimizeFor);
-		jWordsizeBox.setModel(new DefaultComboBoxModel(model2));
-		jMaxTargetBox.setSelectedIndex(2);
-		jExpectBox.setSelectedIndex(4);
-		jSpeciesBox.setSelectedIndex(0);
-		shortQueriesBox.setSelected(true);
-		jDisplayInWebBox.setSelected(true);
-
-		if (selectedProgramName.equalsIgnoreCase("blastn")) {
-			String[] capModel = AlgorithmMatcher.translateToGapcosts("blastn","megablast");
-	       	jGapcostsBox.setModel(new DefaultComboBoxModel(capModel));
-	       	Integer index = AlgorithmMatcher.defaultGapcostIndex.get("megablast");
-	       	if(index==null) index = 0;
-	       	jGapcostsBox.setSelectedIndex(index);
-			jWordsizeBox.setSelectedIndex(3);//default selection
-			jScoresLabel.setVisible(true);
-			jScoresBox.setVisible(true);
-			jScoresBox.setSelectedIndex(0);
-			speciesRepeatPanel.setVisible(true);
-			jGapcostsBox.setEditable(false);
-			jGapcostsBox.setVisible(true);
-			jGapcostsLabel.setVisible(true);
-			maskLookupOnlyBox.setSelected(true);
-			shortQueriesBox.setVisible(true);
-			jMatrixLabel.setVisible(false);
-			jMatrixBox.setVisible(false);
-			if (megablastBtn.isSelected())
-				megaBlastSet();
-			else
-				discontiguosSet();
-
-		} else {
-			jScoresLabel.setVisible(false);
-			jScoresBox.setVisible(false);
-			jMatrixBox.setSelectedIndex(3);
-			jWordsizeBox.setSelectedIndex(1);
-			speciesRepeatPanel.setVisible(false);
-			jGapcostsBox.setEditable(false);
-			jGapcostsBox.setVisible(true);
-			jGapcostsLabel.setVisible(true);
-			maskLookupOnlyBox.setSelected(false);
-			maskLowCaseBox.setSelected(false);
-			jMatrixLabel.setVisible(true);
-			jMatrixBox.setVisible(true);
-			if (selectedProgramName.equalsIgnoreCase("blastp")||selectedProgramName.equalsIgnoreCase("tblastn")){
-				jCompositionalLabel.setVisible(true);
-				jCompositionalBox.setVisible(true);
-				jCompositionalBox.setSelectedIndex(2);
-
-			}
-			if (selectedProgramName.equalsIgnoreCase("blastp")){
-				lowComplexFilterBox.setSelected(false);
-				shortQueriesBox.setVisible(true);
-			}
-			else{
-				lowComplexFilterBox.setSelected(true);
-			}
-		}
-    }
-
-    private void jDefaultButton_actionPerformed(ActionEvent e) {
-    	setAdvancedOptions();
-    }
-
-    private void jProgramBox_actionPerformed(ActionEvent e) {
-
-        JComboBox cb = (JComboBox) e.getSource();
-		// Get the new item
-		String selectedProgramName = (String) cb.getSelectedItem();
-		programForDefaultButton=selectedProgramName;
-		jAdvancedPane.removeAll();
-		if (selectedProgramName == null
-				|| selectedProgramName
-						.equalsIgnoreCase(SELECT_A_PROGRAM_PROMPT)) {
-			jScrollPane1.getViewport().removeAll();
-			textArea.setText( "" );
-			jAdvancedPane.setEnabled(false);
-			enableBlastnRelateOptions(false);
-			jEntrezQueryLabel.setVisible(false);
-			jEntrezQueryText.setVisible(false);
-			chooseSearchPanel.setVisible(false);
-			return;
-		}
-
-		String[][] arrayT = algorithmMatcher
-				.translateToArray((String) selectedProgramName);
-		String[][] array = null;
-		/*though blastn, tblastn, tblastx are all type "nucleotide", however, their database choices are different.
-		 * for tblastn, tblastx, there are no database choices:dbindex/9606/rna and dbindex/10090/rna
-		 */
-		if(arrayT!=null){
-			if(selectedProgramName.equalsIgnoreCase("tblastn")||selectedProgramName.equalsIgnoreCase("tblastx")){
-				int num=0;
-				for(int i=0;i<arrayT.length;i++){
-					if(arrayT[i][1].equalsIgnoreCase("dbindex/9606/allcontig_and_rna")||arrayT[i][1].equalsIgnoreCase("dbindex/10090/allcontig_and_rna")){
-						num++;
-					}
-				}
-				array=new String[arrayT.length-num][2];
-				int i=0;
-				for(int j=0;j<arrayT.length;j++){
-					if (!(arrayT[j][1].equalsIgnoreCase("dbindex/9606/allcontig_and_rna")||arrayT[j][1].equalsIgnoreCase("dbindex/10090/allcontig_and_rna"))){
-						array[i]=arrayT[j];
-						i++;
-					}
-				}
-			}
-			else {
-				array=arrayT;
-			}
-		}
-		else
-			return;
-
-		TableModel listModel = new UneditableTableModel(array);
-		databaseTable.setModel(listModel);
-		databaseTable.setAutoResizeMode(JTable.AUTO_RESIZE_LAST_COLUMN);
-		// make the first column large enough
-		int vColIndex = 0;
-		TableColumn col = databaseTable.getColumnModel().getColumn(vColIndex);
-		int width = 250;
-		col.setPreferredWidth(width);
-		(jScrollPane1.getViewport()).add(databaseTable, null);
-		excludeModels.setSelected(false);
-	    excludeUnculture.setSelected(false);
-	    jEntrezQueryText.setText("");
-	    jQueryFromText.setText("");
-		jQueryToText.setText("");
-	    megablastBtn.setSelected(true);
-	    chooseSearchPanel.setVisible(true);
-
-		setAdvancedOptions();
-    }
-
-    private void jMegaBlastBtn_actionPerformed(ActionEvent e) {
-    	megaBlastSet();
-    }
-    private void megaBlastSet(){
-    	String[] model2 = AlgorithmMatcher
-		.translateToWordSize("blastn","megablast");
-		jWordsizeBox.setModel(new DefaultComboBoxModel(model2));
-		jWordsizeBox.setSelectedIndex(3);
-		jScoresBox.setSelectedIndex(0);
-		String[] capModel = AlgorithmMatcher.translateToGapcosts("blastn","megablast");
-		jGapcostsBox.setModel(new DefaultComboBoxModel(capModel));
-		Integer index = AlgorithmMatcher.defaultGapcostIndex.get("megablast");
-		if(index==null) index = 0;
-		jGapcostsBox.setSelectedIndex(index);
-		lowComplexFilterBox.setSelected(true);
-		speciesRepeatFilter.setSelected(false);
-		maskLookupOnlyBox.setSelected(true);
-		maskLowCaseBox.setSelected(false);
-
-		discontiguousWordOptionsPanel.setVisible(false);
-    }
-
-    private void jDiscontiguousBtn_actionPerformed(ActionEvent e) {
-    	discontiguosSet();
-    }
-
-    private void discontiguosSet(){
-    	String[] model2 = AlgorithmMatcher
-		.translateToWordSize("blastn","discontiguous");
-    	jWordsizeBox.setModel(new DefaultComboBoxModel(model2));
-    	jWordsizeBox.setSelectedIndex(0);
-    	jScoresBox.setSelectedIndex(3);
-    	String[] capModel = AlgorithmMatcher.translateToGapcosts("blastn","discontiguous");
-		jGapcostsBox.setModel(new DefaultComboBoxModel(capModel));
-		Integer index = AlgorithmMatcher.defaultGapcostIndex.get("discontiguous");
-		if(index==null) index = 0;
-		jGapcostsBox.setSelectedIndex(index);
-		lowComplexFilterBox.setSelected(true);
-		speciesRepeatFilter.setSelected(false);
-		maskLookupOnlyBox.setSelected(true);
-		maskLowCaseBox.setSelected(false);
-
-		if (discontiguousBtn.isSelected()){
-			discontiguousWordOptionsPanel.setVisible(true);
-		}
-		else{
-			discontiguousWordOptionsPanel.setVisible(false);
-		}
-    }
-
-    private void jMatrixBox_actionPerformed(ActionEvent e) {
-    	String matrixName = jMatrixBox.getSelectedItem().toString();
-        String[] model = AlgorithmMatcher.translateToGapcosts(matrixName
-                );
-       	jGapcostsBox.setModel(new DefaultComboBoxModel(model));
-       	Integer index = AlgorithmMatcher.defaultGapcostIndex.get(matrixName);
-       	if(index==null) index = 0;
-       	jGapcostsBox.setSelectedIndex(index);
-    }
-
-    public void reportError(String message, String title) {
-        JOptionPane.showMessageDialog(null, message, title,
-                                      JOptionPane.ERROR_MESSAGE);
-    }
-
-    private BlastAlgorithm blastAlgo = null;
-    private void runBlastAlgorithm() {
-        ParameterSetting parameterSetting = collectParameters();
-        if (parameterSetting == null) {
-            return;
-        }
-        parameterSetting.setUseNCBI(true);
-        if (activeSequenceDB != null) {
-            if (sequenceDB == null) {
-                reportError("Please select a sequence file first!",
-                            "Parameter Error");
-                return;
-            } else { //to handle new sequenceDB.
-
-                try {
-
-                    serviceProgressBar.setForeground(Color.BLACK);
-                    serviceProgressBar.setBackground(Color.WHITE);
-
-                    updateProgressBar(10, "Wait...");
-
-                    blastAlgo = new BlastAlgorithm();
-                    blastAlgo.setParameterSetting(parameterSetting);
-
-                    blastAlgo.setBlastAppComponent(this);
-
-                    blastAlgo.setSequenceDB( (CSSequenceSet<CSSequence>) activeSequenceDB);
-                    blastAlgo.setParentSequenceDB(sequenceDB);
-
-                    blastAlgo.execute();
-                } catch (Exception e) {
-                    e.printStackTrace();
-                }
-
-            }
-        }
-    }
-
-    /**
-     * Collect all selected parameters and save it to a ParameterSetting object.
-     * @return ParameterSetting
-     */
-    @SuppressWarnings("rawtypes")
-	private ParameterSetting collectParameters() {
-        String programName = (String) jProgramBox.getSelectedItem();
-        if (programName == null ||
-            programName.equalsIgnoreCase(SELECT_A_PROGRAM_PROMPT)) {
-            reportError("Please select a PROGRAM to search!", "Parameter Error");
-            return null;
-        }
-        int selectedRow = databaseTable.getSelectedRow();
-        String dbName = null;
-        if(selectedRow!=-1) {
-        	dbName = (String)databaseTable.getModel().getValueAt(selectedRow, DATABASE_NAME_INDEX);
-        }
-        if (dbName == null) {
-            reportError("Please select a DATABASE to search!",
-                        "Parameter Error");
-            return null;
-        }
-
-        boolean lowComplexFilterOn = lowComplexFilterBox.isSelected();
-        boolean maskLowCaseOn = maskLowCaseBox.isSelected();
-        String expectString = (String) jExpectBox.getSelectedItem();
-        double expectValue = 10;
-        if (expectString != null) {
-            expectValue = Double.parseDouble(expectString.trim());
-        }
-        String endPoint = jendPointField.getSelectedText();
-        String startPoint = jstartPointField.getSelectedText();
-        DSSequenceSet fastaFile = null;
-		if (activeSequenceDB != null) {
-            fastaFile = activeSequenceDB;
-        } else if (fastaFile == null && sequenceDB != null) {
-            fastaFile = sequenceDB;
-        }
-
-        int endValue = -1;
-        int startValue = 1;
-        if (endPoint != null) {
-            try {
-                endValue = Integer.parseInt(endPoint.trim());
-                startValue = Integer.parseInt(startPoint.trim());
-            } catch (NumberFormatException e) {
-
-            }
-        }
-        String wordsize = (String) jWordsizeBox.getSelectedItem();
-
-        boolean humanRepeatFilterOn = speciesRepeatFilter.isSelected();
-
-        boolean excludeModelsOn = excludeModels.isSelected();
-        boolean excludeUncultureOn = excludeUnculture.isSelected();
-        boolean megaBlastOn=megablastBtn.isSelected();
-        boolean discontiguousOn=discontiguousBtn.isSelected();
-        boolean blastnBtnOn=blastnBtn.isSelected();
-        boolean shortQueriesOn=shortQueriesBox.isSelected();
-        String matchScores=(String) jScoresBox.getSelectedItem();
-        String compositionalAdjustment=(String) jCompositionalBox.getSelectedItem();
-        String speciesRepeat=(String) jSpeciesBox.getSelectedItem();
-        String templateLength=(String) jTemplateLengthBox.getSelectedItem();
-        String templateType=(String) jTemplateTypeBox.getSelectedItem();
-        String geneticCode=(String) jgeneticCodeBox.getSelectedItem();
-        String maxTargetNumber=(String) jMaxTargetBox.getSelectedItem();
-        String entrezQuery=jEntrezQueryText.getText().trim();
-        String fromQuery=jQueryFromText.getText().trim();
-        String toQuery=jQueryToText.getText().trim();
-        String hspRange=jHspRangeBox.getText().trim();
-
-        ParameterSetting ps = new ParameterSetting(dbName, programName,
-				jDisplayInWebBox.isSelected(), expectValue, lowComplexFilterOn,
-				humanRepeatFilterOn, maskLowCaseOn, (String) jMatrixBox
-						.getSelectedItem(), maskLookupOnlyBox.isSelected(),
-						excludeModelsOn,excludeUncultureOn, entrezQuery, fromQuery, toQuery, megaBlastOn,
-						discontiguousOn,blastnBtnOn,shortQueriesOn,matchScores,compositionalAdjustment,
-						speciesRepeat, templateLength, templateType, geneticCode, maxTargetNumber, hspRange);
-        if (startValue <= 1 && endValue >= fastaFile.getMaxLength()) {
-            //just use whole sequence. No end to reset.
-        } else {
-            ps.setStartPoint(startValue);
-            ps.setEndPoint(endValue);
-        }
-        if (wordsize != null) {
-            ps.setWordsize(wordsize);
-        }
-        String gapCost = (String) jGapcostsBox.getSelectedItem();
-        if (gapCost != null) {
-            ps.setGapCost(gapCost);
-        }
-
-        return ps;
-    }
-
-    private void blastButton_actionPerformed(ActionEvent e) {
-        stopButtonPushed = false;
-        if (jTabbedPane1.getSelectedIndex() == BlastAppComponent.BLAST) {
-            jTabbedBlastPane.setSelectedIndex(BlastAppComponent.MAIN);
-
-			// only support NCBI server now
-			runBlastAlgorithm();
-        } else {
-            log.warn("unexpected selectedIndex of jTabbedPane1 "+jTabbedPane1.getSelectedIndex());
-        }
-
-    }
-
-    public void setBlastDisplayPanel(int selectedPanel) {
-        if (selectedPanel == BlastAppComponent.SERVER) {
-            jTabbedBlastPane.setSelectedIndex(BlastAppComponent.SERVER);
-
-        } else {
-            jTabbedBlastPane.setSelectedIndex(BlastAppComponent.MAIN);
-        }
-
-    }
-
-    private void blastStopButton_actionPerformed(ActionEvent e) {
-        stopButtonPushed = true;
-        if (this.jTabbedPane1.getSelectedIndex() == BlastAppComponent.BLAST) {
-			serviceProgressBar.setForeground(Color.ORANGE);
-			serviceProgressBar.setBackground(Color.ORANGE);
-			updateProgressBar(false, "Stopped on " + new Date());
-		}
-
-        if(blastAlgo!=null) {
-        	if(!blastAlgo.cancel(true)) {
-        		log.error("blast job was not able to be cancelled.");
-        	}
-        }
-    }
-
-    public void updateProgressBar(final double percent, final String text) {
-        Runnable r = new Runnable() {
-            public void run() {
-                try {
-                    serviceProgressBar.setString(text);
-                    serviceProgressBar.setValue((int) (percent * 100));
-                } catch (Exception e) {
-                }
-            }
-        };
-        SwingUtilities.invokeLater(r);
-    }
-
-    public void updateProgressBar(final String text) {
-        Runnable r = new Runnable() {
-            public void run() {
-                try {
-                    serviceProgressBar.setString(text);
-                    serviceProgressBar.setIndeterminate(true);
-                } catch (Exception e) {
-                }
-            }
-        };
-        SwingUtilities.invokeLater(r);
-    }
-
-    public void updateProgressBar(final boolean boo, final String text) {
-        Runnable r = new Runnable() {
-            public void run() {
-                try {
-                    serviceProgressBar.setString(text);
-                    serviceProgressBar.setIndeterminate(boo);
-                } catch (Exception e) {
-                }
-            }
-        };
-        SwingUtilities.invokeLater(r);
-    }
-
-    public BlastAppComponent getBlastAppComponent() {
-        return blastAppComponent;
-    }
-
-    public boolean isStopButtonPushed() {
-        return stopButtonPushed;
-    }
-
-    /**
-     * publishProjectNodeAddedEvent
-     *
-     * @param event ProjectNodeAddedEvent
-     */
-    @Publish public org.geworkbench.events.ProjectNodeAddedEvent
-            publishProjectNodeAddedEvent(org.geworkbench.events.
-                                         ProjectNodeAddedEvent event) {
-        return event;
-    }
-
-	/**
-	 * getComponent
-	 *
-	 * @return Component
-	 */
-	public Component getComponent() {
-		return mainPanel;
-	}
-
-	private void init1() throws Exception {
-		mainPanel = new JPanel();
-
-		displayToolBar = new JToolBar();
-		displayToolBar
-				.setLayout(new BoxLayout(displayToolBar, BoxLayout.X_AXIS));
-		chkAllMarkers.setToolTipText("Use All Markers.");
-		chkAllMarkers.setSelected(false);
-		chkAllMarkers.addActionListener(new ActionListener() {
-
-			public void actionPerformed(ActionEvent e) {
-				activateMarkers = !((JCheckBox) e.getSource()).isSelected();
-				refreshMaSetView();
-			}
-
-		});
-
-		BorderLayout borderLayout2 = new BorderLayout();
-		mainPanel.setLayout(borderLayout2);
-		sequenceNumberField = new JTextField(20);
-		sequenceNumberField.setMaximumSize(sequenceNumberField.getPreferredSize());
-		sequenceNumberField.setEditable(false);
-
-		sequenceNumberField.setText("Total Sequence Number:");
-		displayToolBar.add(chkAllMarkers, null);
-		displayToolBar.add(Box.createHorizontalStrut(5), null);
-		displayToolBar.add(sequenceNumberField);
-		mainPanel.add(displayToolBar, java.awt.BorderLayout.SOUTH);
-
-		activateMarkers = !chkAllMarkers.isSelected();
-
-	}
-
-	@SuppressWarnings("rawtypes")
-	private void refreshMaSetView() {
-		activateMarkers = !chkAllMarkers.isSelected();
-		if (activateMarkers) {
-			if (activatedMarkers != null && activatedMarkers.size() > 0) {
-
-				if (activateMarkers && (sequenceDB != null)) {
-					activeSequenceDB = (CSSequenceSet) ((CSSequenceSet) sequenceDB)
-							.getActiveSequenceSet(activatedMarkers);
-					sequenceNumberField.setText("Activated Sequence Number: "
-							+ activeSequenceDB.size());
-				}
-
-			} else if (sequenceDB != null) {
-				sequenceNumberField.setText("Total Sequence Number: "
-						+ sequenceDB.size());
-
-				activeSequenceDB = (CSSequenceSet) sequenceDB;
-			}
-
-		} else if (sequenceDB != null) {
-			sequenceNumberField.setText("Total Sequence Number: "
-					+ sequenceDB.size());
-		}
-
-	}
-
-	/**
-	 * receiveProjectSelection
-	 *
-	 * @param e -
-	 *            ProjectEvent
-	 */
-	@SuppressWarnings("rawtypes")
-	@Subscribe
-	public void receive(org.geworkbench.events.ProjectEvent e, Object source) {
-		DSDataSet dataSet = e.getDataSet();
-		if (dataSet instanceof DSSequenceSet) {
-			if (sequenceDB != dataSet) {
-				this.sequenceDB = (DSSequenceSet) dataSet;
-
-				activatedMarkers = null;
-			}
-			refreshMaSetView();
-		}
-	}
-
-	/**
-	 * geneSelectorAction
-	 *
-	 * @param e
-	 *            GeneSelectorEvent
-	 */
-	@Subscribe(Asynchronous.class)
-	public void receive(GeneSelectorEvent e, Object source) {
-		if(e.getGenericMarker()!=null && e.getPanel() == null) // do nothing for single marker selection
-			return;
-
-		if (e.getPanel() != null && e.getPanel().size() > 0) {
-			activatedMarkers = e.getPanel().activeSubset();
-		} else {
-			activatedMarkers = null;
-		}
-		refreshMaSetView();
-	}
-
-	// following are a group of listener classes
-    private class BlastAppComponent_jMatrixBox_actionAdapter implements
-			java.awt.event.ActionListener {
-
-		public void actionPerformed(ActionEvent e) {
-			jMatrixBox_actionPerformed(e);
-		}
-	}
-
-    private class BlastAppComponent_jProgramBox_actionAdapter implements
-			java.awt.event.ActionListener {
-
-		public void actionPerformed(ActionEvent e) {
-			jProgramBox_actionPerformed(e);
-		}
-	}
-
-    private class BlastAppComponent_default_actionAdapter implements
-			java.awt.event.ActionListener {
-
-    	public void actionPerformed(ActionEvent e) {
-    		jDefaultButton_actionPerformed(e);
-    	}
-    }
-
-
-    private class BlastAppComponent_megablastBtn_actionAdapter implements
-			java.awt.event.ActionListener {
-    		public void actionPerformed(ActionEvent e) {
-    		jMegaBlastBtn_actionPerformed(e);
-    	}
-    }
-
-    private class BlastAppComponent_discontiguousBtn_actionAdapter implements
-	java.awt.event.ActionListener {
-	public void actionPerformed(ActionEvent e) {
-	jDiscontiguousBtn_actionPerformed(e);
-}
-}
-
-
-
-    private class BlastAppComponent_blastButton_actionAdapter implements
-			java.awt.event.ActionListener {
-
-		public void actionPerformed(ActionEvent e) {
-			blastButton_actionPerformed(e);
-		}
-	}
-
-    private class BlastAppComponent_blastStopButton_actionAdapter implements
-			java.awt.event.ActionListener {
-		public void actionPerformed(ActionEvent e) {
-			blastStopButton_actionPerformed(e);
-		}
-	}
-
-    private class BlastAppComponent_jDBList_listSelectionListener implements
-			ListSelectionListener {
-
-		public void valueChanged(ListSelectionEvent e) {
-			if (e.getValueIsAdjusting()) {
-				return;
-			}
-
-	        String program = (String) jProgramBox.getSelectedItem();
-	        int selectedRow = databaseTable.getSelectedRow();
-	        String dbDetails = "";
-	        if(selectedRow!=-1) {
-		        String dbName = (String)databaseTable.getModel().getValueAt(selectedRow, DATABASE_NAME_INDEX);
-		        dbDetails = algorithmMatcher.getDatabaseDetail(program, dbName);
-		       	jSpeciesBox.setSelectedIndex(0);
-	        }
-
-	        textArea.setText( dbDetails );
-		}
-	}
-
-}
diff --git a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/BlastViewComponent.cwb.xml b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/BlastViewComponent.cwb.xml
index 871c2dd..0fc8345 100644
--- a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/BlastViewComponent.cwb.xml
+++ b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/BlastViewComponent.cwb.xml
@@ -15,7 +15,7 @@
 		mustAccept="false"
 		category="visualizer" loadByDefault="true">
 		<required-component
-			class="org.geworkbench.components.alignment.panels.BlastAppComponent" />
+			class="org.geworkbench.components.alignment.blast.BlastAnalysis" />
 		<license><![CDATA[
 			<html><head><meta http-equiv=Content-Type content="text/html; charset=windows-1252"></head>
 				<body>----</body>
diff --git a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/BlastViewComponent.java b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/BlastViewComponent.java
index 22c7e82..207302a 100755
--- a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/BlastViewComponent.java
+++ b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/BlastViewComponent.java
@@ -2,6 +2,8 @@ package org.geworkbench.components.alignment.panels;

 import java.awt.Component;
 import java.awt.Container;
+import java.util.ArrayList;
+import java.util.Vector;

 import javax.swing.JTabbedPane;

@@ -11,108 +13,115 @@ import org.geworkbench.bison.datastructure.biocollections.DSAncillaryDataSet;
 import org.geworkbench.bison.datastructure.biocollections.DSDataSet;
 import org.geworkbench.bison.datastructure.biocollections.sequences.CSSequenceSet;
 import org.geworkbench.bison.datastructure.bioobjects.DSBioObject;
-import org.geworkbench.bison.datastructure.bioobjects.sequence.CSAlignmentResultSet;
+import org.geworkbench.bison.datastructure.bioobjects.sequence.BlastObj;
 import org.geworkbench.bison.datastructure.bioobjects.sequence.DSAlignmentResultSet;
 import org.geworkbench.bison.datastructure.bioobjects.sequence.DSSequence;
 import org.geworkbench.builtin.projects.ProjectPanel;
-import org.geworkbench.builtin.projects.ProjectSelection;
-import org.geworkbench.components.alignment.blast.NCBIBlastParser;
+import org.geworkbench.builtin.projects.ProjectSelection;
 import org.geworkbench.engine.config.VisualPlugin;
 import org.geworkbench.engine.management.AcceptTypes;
 import org.geworkbench.engine.management.Publish;
 import org.geworkbench.engine.management.Subscribe;

 /**
- * <p>Title: Bioworks</p>
- * <p>Description: Modular Application Framework for Gene Expession, Sequence and Genotype Analysis</p>
- * <p>Copyright: Copyright (c) 2003 -2004</p>
- * <p>Company: Columbia University</p>
- *
+ * <p>
+ * Title: Bioworks
+ * </p>
+ * <p>
+ * Description: Modular Application Framework for Gene Expession, Sequence and
+ * Genotype Analysis
+ * </p>
+ * <p>
+ * Copyright: Copyright (c) 2003 -2004
+ * </p>
+ * <p>
+ * Company: Columbia University
+ * </p>
+ *
  * @author XZ
- * @version $Id: BlastViewComponent.java 8187 2011-07-30 04:31:30Z zji $
+ * @version $Id: BlastViewComponent.java 8479 2011-11-02 15:39:37Z zji $
  */
-@AcceptTypes( {DSAlignmentResultSet.class})
-public class BlastViewComponent implements
-        VisualPlugin {
+@AcceptTypes( { DSAlignmentResultSet.class })
+public class BlastViewComponent implements VisualPlugin {
 	private static Log log = LogFactory.getLog(BlastViewComponent.class);

-    private BlastViewPanel blastViewPanel;
-
-    @Publish public org.geworkbench.events.ProjectNodeAddedEvent
-            publishProjectNodeAddedEvent(org.geworkbench.events.
-                                         ProjectNodeAddedEvent event) {
-        return event;
-    }
-
-    public BlastViewComponent() {
-        try {
-            blastViewPanel = new BlastViewPanel();
-            blastViewPanel.setBlastViewComponent(this);
-
-        } catch (Exception e) {
-            e.printStackTrace();
-        }
-    }
-
-    /**
-     * getComponent
-     *
-     * @return Component
-     */
-    public Component getComponent() {
-        return blastViewPanel;
-    }
-
-    /**
-     * receiveProjectSelection
-     *
-     * @param e ProjectEvent
-     */
-    @SuppressWarnings("unchecked")
-	@Subscribe public void receive(org.geworkbench.events.ProjectEvent e,
-                                   Object source) {
-
-        Container parent = blastViewPanel.getParent();
-        if (parent instanceof JTabbedPane) {
-            ((JTabbedPane) parent).setSelectedComponent(blastViewPanel);
-        }
-
-        ProjectSelection selection = ((ProjectPanel) source).getSelection();
-        DSAncillaryDataSet<DSBioObject> df = selection.getDataSubSet();
-        //Get the sequenceDb from DAncillaryDataset not from project.
-        DSDataSet<? extends DSSequence> sequenceDB = selection.getDataSet();
-        if (df != null && df instanceof CSAlignmentResultSet) {
-          //  sequenceDB = df.getParentDataSet();
-            sequenceDB = ((CSAlignmentResultSet)df).getBlastedParentDataSet();
-        }
-        if (sequenceDB instanceof CSSequenceSet && df != null) {
-            if (df instanceof DSAlignmentResultSet) {
-            	log.debug("update blast result view panel");
-               	int totalSequenceNumber = ((CSSequenceSet<? extends DSSequence>) sequenceDB)
-						.size();
-				NCBIBlastParser nbp = new NCBIBlastParser(totalSequenceNumber,
-						((DSAlignmentResultSet) df).getResultFilePath());
+	private BlastViewPanel blastViewPanel;
+
+	@Publish
+	public org.geworkbench.events.ProjectNodeAddedEvent publishProjectNodeAddedEvent(
+			org.geworkbench.events.ProjectNodeAddedEvent event) {
+		return event;
+	}
+
+	public BlastViewComponent() {
+		try {
+			blastViewPanel = new BlastViewPanel();
+			blastViewPanel.setBlastViewComponent(this);
+
+		} catch (Exception e) {
+			e.printStackTrace();
+		}
+	}
+
+	/**
+	 * getComponent
+	 *
+	 * @return Component
+	 */
+	public Component getComponent() {
+		return blastViewPanel;
+	}
+
+	/**
+	 * receiveProjectSelection
+	 *
+	 * @param e
+	 *            ProjectEvent
+	 */
+	@SuppressWarnings("unchecked")
+	@Subscribe
+	public void receive(org.geworkbench.events.ProjectEvent e, Object source) {
+
+		Container parent = blastViewPanel.getParent();
+		if (parent instanceof JTabbedPane) {
+			((JTabbedPane) parent).setSelectedComponent(blastViewPanel);
+		}
+
+		ProjectSelection selection = ((ProjectPanel) source).getSelection();
+		DSAncillaryDataSet<DSBioObject> df = selection.getDataSubSet();
+		// Get the sequenceDb from DAncillaryDataset not from project.
+		DSDataSet<? extends DSSequence> sequenceDB = selection.getDataSet();
+		if (df != null && df instanceof DSAlignmentResultSet) {
+			// sequenceDB = df.getParentDataSet();
+			sequenceDB = ((DSAlignmentResultSet) df).getBlastedParentDataSet();
+		}
+		if (sequenceDB instanceof CSSequenceSet && df != null) {
+			if (df instanceof DSAlignmentResultSet) {
+				log.debug("update blast result view panel");
+				DSAlignmentResultSet resultSet = (DSAlignmentResultSet) df;
+				ArrayList<Vector<BlastObj>> blastDataSet = resultSet
+						.getBlastDataSet();

 				blastViewPanel
 						.setSequenceDB((CSSequenceSet<DSSequence>) sequenceDB);
-				blastViewPanel.setBlastDataSet(nbp.parseResults());
+				blastViewPanel.setBlastDataSet(blastDataSet);

-				String summary = nbp.getSummary();
+				String summary = resultSet.getSummary();
 				blastViewPanel.setSummary(summary);
-				df.addDescription(summary);
-				if (nbp.getHitCount()==0){
+				df.setDescription(summary);
+
+				if (resultSet.getHitCount() == 0) {
 					blastViewPanel.resetToWhite("No alignment hit is found.");
 					blastViewPanel.setSummaryPanelOff();
+				} else {
+					blastViewPanel.setSummaryPanelOn();
 				}
-				else {
-					blastViewPanel.setSummaryPanelOn();
-				}
-            } else {
-                blastViewPanel.resetToWhite();
-            }
+			} else {
+				blastViewPanel.resetToWhite();
+			}

-        }
+		}

-    }
+	}

 }
diff --git a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/BlastViewPanel.java b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/BlastViewPanel.java
index 0a93d25..6503c6e 100755
--- a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/BlastViewPanel.java
+++ b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/BlastViewPanel.java
@@ -31,11 +31,10 @@ import javax.swing.event.ListSelectionListener;
 import javax.swing.table.AbstractTableModel;

 import org.geworkbench.bison.datastructure.biocollections.sequences.CSSequenceSet;
+import org.geworkbench.bison.datastructure.bioobjects.sequence.BlastObj;
 import org.geworkbench.bison.datastructure.bioobjects.sequence.CSSequence;
 import org.geworkbench.bison.datastructure.bioobjects.sequence.DSSequence;
 import org.geworkbench.bison.util.RandomNumberGenerator;
-import org.geworkbench.components.alignment.blast.BlastObj;
-import org.geworkbench.engine.management.Subscribe;
 import org.geworkbench.util.BrowserLauncher;
 import org.geworkbench.util.FilePathnameUtils;
 import org.geworkbench.util.JAutoList;
@@ -43,7 +42,7 @@ import org.geworkbench.util.JAutoList;
 /**
  *
  * @author XZ
- * @version $Id: BlastViewPanel.java 8187 2011-07-30 04:31:30Z zji $
+ * @version $Id: BlastViewPanel.java 8455 2011-10-24 22:06:10Z youmi $
  */
 public class BlastViewPanel extends JPanel implements HyperlinkListener {
 	private static final long serialVersionUID = -5271804907456553741L;
@@ -93,17 +92,6 @@ public class BlastViewPanel extends JPanel implements HyperlinkListener {
 		blastViewComponent = bc;
 	}

-	@Subscribe
-	public void receive(org.geworkbench.events.ProjectNodeAddedEvent pnae,
-			Object source) {
-		/**
-		 * TODO Implement this
-		 * medusa.components.listeners.ProjectNodeAddedListener method
-		 */
-		throw new java.lang.UnsupportedOperationException(
-				"Method projectNodeAdded() not yet implemented.");
-	}
-
 	public void hyperlinkUpdate(HyperlinkEvent event) {
 		if (event.getEventType() == HyperlinkEvent.EventType.ACTIVATED) {
 			try {
@@ -229,11 +217,11 @@ public class BlastViewPanel extends JPanel implements HyperlinkListener {

 		summaryLabel.setText(s);
 		double propLoc = .8D;
-		rightPanel.setDividerLocation(propLoc);
+	    rightPanel.setDividerLocation(propLoc);
 		rightPanel.setResizeWeight(0.95);
-		jSplitPane1.setDividerLocation(jSplitPane1DividerLocation);
-		jSplitPane1.setResizeWeight(0.4);
-		revalidate();
+	    jSplitPane1.setDividerLocation(jSplitPane1DividerLocation);
+		jSplitPane1.setResizeWeight(0.4);
+		revalidate();
 	}

 	/**
@@ -289,7 +277,7 @@ public class BlastViewPanel extends JPanel implements HyperlinkListener {
 		JTable table = new JTable(myModel);

 		// setting the size of the table and its columns
-		table.setPreferredScrollableViewportSize(new Dimension(800, 100));
+		table.setPreferredScrollableViewportSize(new Dimension(800, 100));
 		table.getColumnModel().getColumn(0).setPreferredWidth(35);
 		table.getColumnModel().getColumn(1).setPreferredWidth(50);
 		table.getColumnModel().getColumn(2).setPreferredWidth(300);
diff --git a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/ParameterSetting.java b/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/ParameterSetting.java
deleted file mode 100755
index 92553af..0000000
--- a/geworkbench-core/components/alignment/src/org/geworkbench/components/alignment/panels/ParameterSetting.java
+++ /dev/null
@@ -1,302 +0,0 @@
-package org.geworkbench.components.alignment.panels;
-
-/**
- *
- * @author zji
- * @version $Id: ParameterSetting.java 7316 2010-12-09 19:57:45Z maz $
- */
-public class ParameterSetting {
-        /**
-         * Database name, a required parameter.
-         */
-        private String dbName;
-        /**
-         * Blast program name, a required parameter.
-         */
-        private String programName;
-        /**
-         * Whether launch Web browser to view the  result. Default is yes.
-         */
-        private boolean viewInBrowser;
-        /**
-         * Matrix name, a optional parameter. For BLASTN, dna.mat, for others default is blossum62
-         */
-        private String matrix;
-        /**
-         * Frame shift penalty, optional parameter. Default is no OOP.
-         */
-        private String penalty;
-
-        private final double DEFAULTEXPECT = 10;
-        /**
-         * Expect value.
-         */
-        private double expect = DEFAULTEXPECT;
-
-        /**
-         * Low complexity filter. Default is on.
-         */
-        private boolean lowComplexityFilterOn = true;
-        /**
-         * Human Repeat Filter, only for blastn program
-         */
-        private boolean humanRepeatFilterOn = false;
-
-        /**
-         * Filter the low case.
-         */
-
-        private boolean maskLowCase = false;
-
-        /**
-         * Whether use NCBI Blast Server
-         */
-        private boolean useNCBI = false;
-        private boolean maskLookupTable = false;
-        private String wordsize = "11";
-        private String gapCost;
-        /**
-         * For subsequence information.
-         */
-        private int startPoint = -1;
-        private int endPoint = -1;
-
-        private boolean excludeModelsOn;
-        private boolean excludeUncultureOn;
-        private boolean megaBlastOn;
-        private boolean discontiguousOn;
-        private boolean blastnBtnOn;
-        private boolean shortQueriesOn;
-        private String matchScores;
-        private String compositionalAdjustment;
-        private String speciesRepeat;
-        private String templateLength;
-        private String templateType;
-        private String geneticCode;
-        private String maxTargetNumber;
-        private String entrezQuery;
-        private String fromQuery;
-        private String toQuery;
-        private String hspRange;
-
-    /**
-     * No public constructor because this is only used in this package.
-     *
-     * @param dbName
-     * @param programName
-     * @param viewInBrowser
-     * @param expect
-     * @param lowComplexityFilterOn
-     * @param humanRepeatFilterOn
-     * @param maskLowCase
-     * @param matrix
-     * @param maskLookupTable
-     *
-     * @param excludeModelsOn
-     * @param excludeUncultureOn
-     * @param megaBlastOn
-     * @param discontiguousOn
-     * @param blastnBtnOn
-     * @param shortQueriesOn
-     * @param matchScores
-     * @param compositionalAdjustment
-     * @param speciesRepeat
-     * @param geneticCode
-     * @param maxTargetNumber
-     * @param entrezQuery
-     * @param fromQuery
-     * @param toQuery
-     * @param hspRange
-     *
-     */
-    ParameterSetting(String dbName, String programName, boolean viewInBrowser,
-			double expect, boolean lowComplexityFilterOn,
-			boolean humanRepeatFilterOn, boolean maskLowCase, String matrix,
-			boolean maskLookupTable, boolean excludeModelsOn, boolean excludeUncultureOn, String entrezQuery,
-			String fromQuery, String toQuery, boolean megaBlastOn, boolean discontiguousOn, boolean blastnBtnOn, boolean shortQueriesOn,
-			String matchScores, String compositionalAdjustment, String speciesRepeat, String templateLength,
-			String templateType, String geneticCode, String maxTargetNumber, String hspRange) {
-        this.dbName = dbName;
-        this.programName = programName;
-        this.viewInBrowser = viewInBrowser;
-        this.expect = expect;
-        this.lowComplexityFilterOn = lowComplexityFilterOn;
-        this.humanRepeatFilterOn = humanRepeatFilterOn;
-        this.maskLowCase=maskLowCase;
-        this.matrix = matrix;
-		this.maskLookupTable = maskLookupTable;
-
-		this.excludeModelsOn=excludeModelsOn;
-		this.excludeUncultureOn=excludeUncultureOn;
-		this.megaBlastOn=megaBlastOn;
-		this.discontiguousOn=discontiguousOn;
-		this.blastnBtnOn=blastnBtnOn;
-		this.shortQueriesOn=shortQueriesOn;
-		this.matchScores=matchScores;
-		this.compositionalAdjustment=compositionalAdjustment;
-		this.speciesRepeat=speciesRepeat;
-		this.templateLength=templateLength;
-		this.templateType=templateType;
-		this.geneticCode=geneticCode;
-		this.maxTargetNumber=maxTargetNumber;
-		this.entrezQuery=entrezQuery;
-		this.fromQuery=fromQuery;
-		this.toQuery=toQuery;
-		this.hspRange=hspRange;
-    }
-
-    public void setPenalty(String penalty) {
-        this.penalty = penalty;
-    }
-
-    public void setUseNCBI(boolean useNCBI) {
-        this.useNCBI = useNCBI;
-    }
-
-    public void setEndPoint(int endPoint) {
-        this.endPoint = endPoint;
-    }
-
-    public void setStartPoint(int startPoint) {
-        this.startPoint = startPoint;
-    }
-
-    public void setWordsize(String wordsize) {
-        this.wordsize = wordsize;
-    }
-
-    public void setGapCost(String gapCost) {
-        this.gapCost = gapCost;
-    }
-
-    // following are the getters
-    public String getDbName() {
-        return dbName;
-    }
-
-    public String getP