Updated geworkbench, geworkbench-web

Jonathan Bell [2012-05-16 16:17:47]
Updated geworkbench, geworkbench-web
Filename
create.sql
genspace-common/src/org/geworkbench/components/genspace/entity/AnalysisEvent.java
genspace-common/src/org/geworkbench/components/genspace/server/stubs/FriendFacadeService.java
genspace-common/src/org/geworkbench/components/genspace/server/stubs/NetworkFacadeService.java
genspace-common/src/org/geworkbench/components/genspace/server/stubs/ObjectFactory.java
genspace-common/src/org/geworkbench/components/genspace/server/stubs/PublicFacadeService.java
genspace-common/src/org/geworkbench/components/genspace/server/stubs/ToolUsageInformation.java
genspace-common/src/org/geworkbench/components/genspace/server/stubs/ToolUsageInformationService.java
genspace-common/src/org/geworkbench/components/genspace/server/stubs/UsageInformation.java
genspace-common/src/org/geworkbench/components/genspace/server/stubs/UsageInformationService.java
genspace-common/src/org/geworkbench/components/genspace/server/stubs/UserFacade.java
genspace-common/src/org/geworkbench/components/genspace/server/stubs/UserFacadeService.java
genspace-common/src/org/geworkbench/components/genspace/server/stubs/WorkflowRepository.java
genspace-common/src/org/geworkbench/components/genspace/server/stubs/WorkflowRepositoryService.java
genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/GenericUsageInformation.java
genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/ToolUsageInformation.java
genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/UsageInformation.java
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geworkbench-core/bin/matrixreduce/.svn/entries
geworkbench-core/build.xml
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geworkbench-web/src/org/geworkbenchweb/interactions/CNKB/.svn/text-base/InteractionsConnectionImpl.java.svn-base
geworkbench-web/src/org/geworkbenchweb/interactions/CNKB/.svn/text-base/VersionDescriptor.java.svn-base
geworkbench-web/src/org/geworkbenchweb/interactions/CNKB/CNKBInteractions.java
geworkbench-web/src/org/geworkbenchweb/interactions/CNKB/CNKBParamForm.java
geworkbench-web/src/org/geworkbenchweb/interactions/CNKB/Constants.java
geworkbench-web/src/org/geworkbenchweb/interactions/CNKB/InteractionParticipant.java
geworkbench-web/src/org/geworkbenchweb/interactions/CNKB/InteractionsConnectionImpl.java
geworkbench-web/src/org/geworkbenchweb/interactions/CNKB/VersionDescriptor.java
geworkbench-web/src/org/geworkbenchweb/layout/.svn/all-wcprops
geworkbench-web/src/org/geworkbenchweb/layout/.svn/entries
geworkbench-web/src/org/geworkbenchweb/layout/.svn/prop-base/DataTab.java.svn-base
geworkbench-web/src/org/geworkbenchweb/layout/.svn/prop-base/MainLayout.java.svn-base
geworkbench-web/src/org/geworkbenchweb/layout/.svn/prop-base/UDataTab.java.svn-base
geworkbench-web/src/org/geworkbenchweb/layout/.svn/prop-base/UMainLayout.java.svn-base
geworkbench-web/src/org/geworkbenchweb/layout/.svn/prop-base/UVisualPlugin.java.svn-base
geworkbench-web/src/org/geworkbenchweb/layout/.svn/prop-base/VisualPlugin.java.svn-base
geworkbench-web/src/org/geworkbenchweb/layout/.svn/text-base/DataTab.java.svn-base
geworkbench-web/src/org/geworkbenchweb/layout/.svn/text-base/MainLayout.java.svn-base
geworkbench-web/src/org/geworkbenchweb/layout/.svn/text-base/UAccordionPanel.java.svn-base
geworkbench-web/src/org/geworkbenchweb/layout/.svn/text-base/UDataTab.java.svn-base
geworkbench-web/src/org/geworkbenchweb/layout/.svn/text-base/UHeatMap.java.svn-base
geworkbench-web/src/org/geworkbenchweb/layout/.svn/text-base/UMainLayout.java.svn-base
geworkbench-web/src/org/geworkbenchweb/layout/.svn/text-base/UMenuBar.java.svn-base
geworkbench-web/src/org/geworkbenchweb/layout/.svn/text-base/USetsTabSheet.java.svn-base
geworkbench-web/src/org/geworkbenchweb/layout/.svn/text-base/UVisualPlugin.java.svn-base
geworkbench-web/src/org/geworkbenchweb/layout/.svn/text-base/VisualPlugin.java.svn-base
geworkbench-web/src/org/geworkbenchweb/layout/DataTab.java
geworkbench-web/src/org/geworkbenchweb/layout/MainLayout.java
geworkbench-web/src/org/geworkbenchweb/layout/UAccordionPanel.java
geworkbench-web/src/org/geworkbenchweb/layout/UDataTab.java
geworkbench-web/src/org/geworkbenchweb/layout/UHeatMap.java
geworkbench-web/src/org/geworkbenchweb/layout/UMainLayout.java
geworkbench-web/src/org/geworkbenchweb/layout/UMenuBar.java
geworkbench-web/src/org/geworkbenchweb/layout/USetsTabSheet.java
geworkbench-web/src/org/geworkbenchweb/layout/UVisualPlugin.java
geworkbench-web/src/org/geworkbenchweb/layout/VisualPlugin.java
geworkbench-web/src/org/geworkbenchweb/pojos/.svn/entries
geworkbench-web/src/org/geworkbenchweb/utils/.svn/all-wcprops
geworkbench-web/src/org/geworkbenchweb/utils/.svn/entries
geworkbench-web/src/org/geworkbenchweb/utils/.svn/text-base/DataSetOperations.java.svn-base
geworkbench-web/src/org/geworkbenchweb/utils/.svn/text-base/SetOperations.java.svn-base
geworkbench-web/src/org/geworkbenchweb/utils/.svn/text-base/SubSetOperations.java.svn-base
geworkbench-web/src/org/geworkbenchweb/utils/DataSetOperations.java
geworkbench-web/src/org/geworkbenchweb/utils/SetOperations.java
geworkbench-web/src/org/geworkbenchweb/utils/SubSetOperations.java
geworkbench-web/src/org/geworkbenchweb/visualizations/.svn/all-wcprops
geworkbench-web/src/org/geworkbenchweb/visualizations/.svn/entries
geworkbench-web/src/org/geworkbenchweb/visualizations/.svn/text-base/Clustergram.java.svn-base
geworkbench-web/src/org/geworkbenchweb/visualizations/.svn/text-base/Cytoscape.java.svn-base
geworkbench-web/src/org/geworkbenchweb/visualizations/.svn/text-base/Dendrogram.java.svn-base
geworkbench-web/src/org/geworkbenchweb/visualizations/.svn/text-base/GeworkbenchWidgetset.gwt.xml.svn-base
geworkbench-web/src/org/geworkbenchweb/visualizations/.svn/text-base/HeatMap.java.svn-base
geworkbench-web/src/org/geworkbenchweb/visualizations/Clustergram.java
geworkbench-web/src/org/geworkbenchweb/visualizations/Cytoscape.java
geworkbench-web/src/org/geworkbenchweb/visualizations/Dendrogram.java
geworkbench-web/src/org/geworkbenchweb/visualizations/GeworkbenchWidgetset.gwt.xml
geworkbench-web/src/org/geworkbenchweb/visualizations/HeatMap.java
geworkbench-web/src/org/geworkbenchweb/visualizations/client/.svn/all-wcprops
geworkbench-web/src/org/geworkbenchweb/visualizations/client/.svn/entries
geworkbench-web/src/org/geworkbenchweb/visualizations/client/ui/.svn/all-wcprops
geworkbench-web/src/org/geworkbenchweb/visualizations/client/ui/.svn/entries
geworkbench-web/src/org/geworkbenchweb/visualizations/client/ui/.svn/text-base/EventCallback.java.svn-base
geworkbench-web/src/org/geworkbenchweb/visualizations/client/ui/.svn/text-base/FilterCallback.java.svn-base
geworkbench-web/src/org/geworkbenchweb/visualizations/client/ui/.svn/text-base/JsBean.java.svn-base
geworkbench-web/src/org/geworkbenchweb/visualizations/client/ui/.svn/text-base/ReadyCallback.java.svn-base
geworkbench-web/src/org/geworkbenchweb/visualizations/client/ui/.svn/text-base/VClustergram.java.svn-base
geworkbench-web/src/org/geworkbenchweb/visualizations/client/ui/.svn/text-base/VCytoscape.java.svn-base
geworkbench-web/src/org/geworkbenchweb/visualizations/client/ui/.svn/text-base/VDendrogram.java.svn-base
geworkbench-web/src/org/geworkbenchweb/visualizations/client/ui/.svn/text-base/VHeatMap.java.svn-base
geworkbench-web/src/org/geworkbenchweb/visualizations/client/ui/.svn/text-base/Visualization.java.svn-base
geworkbench-web/src/org/geworkbenchweb/visualizations/client/ui/EventCallback.java
geworkbench-web/src/org/geworkbenchweb/visualizations/client/ui/FilterCallback.java
geworkbench-web/src/org/geworkbenchweb/visualizations/client/ui/JsBean.java
geworkbench-web/src/org/geworkbenchweb/visualizations/client/ui/ReadyCallback.java
geworkbench-web/src/org/geworkbenchweb/visualizations/client/ui/VClustergram.java
geworkbench-web/src/org/geworkbenchweb/visualizations/client/ui/VCytoscape.java
geworkbench-web/src/org/geworkbenchweb/visualizations/client/ui/VDendrogram.java
geworkbench-web/src/org/geworkbenchweb/visualizations/client/ui/VHeatMap.java
geworkbench-web/src/org/geworkbenchweb/visualizations/client/ui/Visualization.java
geworkbench-web/src/org/geworkbenchweb/visualizations/public/.svn/all-wcprops
geworkbench-web/src/org/geworkbenchweb/visualizations/public/.svn/entries
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/.svn/all-wcprops
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/.svn/entries
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/.svn/text-base/exporting.js.svn-base
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/.svn/text-base/highcharts.js.svn-base
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/.svn/text-base/jquery-1.4.4.min.js.svn-base
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/.svn/text-base/jquery.cytoscapeweb.all.js.svn-base
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/.svn/text-base/jquery.cytoscapeweb.js.svn-base
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/exporting.js
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/extensions/.svn/all-wcprops
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/extensions/.svn/entries
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/extensions/.svn/text-base/jquery.cytoscapeweb.layout.arbor.js.svn-base
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/extensions/.svn/text-base/jquery.cytoscapeweb.layout.grid.js.svn-base
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/extensions/.svn/text-base/jquery.cytoscapeweb.layout.null.js.svn-base
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/extensions/.svn/text-base/jquery.cytoscapeweb.layout.preset.js.svn-base
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/extensions/.svn/text-base/jquery.cytoscapeweb.layout.random.js.svn-base
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/extensions/.svn/text-base/jquery.cytoscapeweb.layout.springy.js.svn-base
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/extensions/.svn/text-base/jquery.cytoscapeweb.renderer.null.js.svn-base
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/extensions/.svn/text-base/jquery.cytoscapeweb.renderer.svg.js.svn-base
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/extensions/jquery.cytoscapeweb.layout.arbor.js
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/extensions/jquery.cytoscapeweb.layout.grid.js
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/extensions/jquery.cytoscapeweb.layout.null.js
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/extensions/jquery.cytoscapeweb.layout.preset.js
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/extensions/jquery.cytoscapeweb.layout.random.js
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/extensions/jquery.cytoscapeweb.layout.springy.js
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/extensions/jquery.cytoscapeweb.renderer.null.js
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/extensions/jquery.cytoscapeweb.renderer.svg.js
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/highcharts.js
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/jquery-1.4.4.min.js
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/jquery.cytoscapeweb.all.js
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/jquery.cytoscapeweb.js
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/lib/.svn/all-wcprops
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/lib/.svn/entries
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/lib/.svn/text-base/2D.js.svn-base
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/lib/.svn/text-base/arbor.js.svn-base
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/lib/.svn/text-base/jquery-1.3.2.min.js.svn-base
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/lib/.svn/text-base/jquery-1.7.2.js.svn-base
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/lib/.svn/text-base/jquery.color.js.svn-base
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/lib/.svn/text-base/jquery.mousewheel.js.svn-base
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/lib/.svn/text-base/jquery.svg.js.svn-base
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/lib/2D.js
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/lib/arbor.js
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/lib/jquery-1.3.2.min.js
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/lib/jquery-1.7.2.js
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/lib/jquery.color.js
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/lib/jquery.mousewheel.js
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/lib/jquery.svg.js
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/min/.svn/all-wcprops
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/min/.svn/entries
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/min/.svn/text-base/AC_OETags.min.js.svn-base
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/min/.svn/text-base/cytoscapeweb.min.js.svn-base
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/min/.svn/text-base/json2.min.js.svn-base
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/min/AC_OETags.min.js
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/min/cytoscapeweb.min.js
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/min/json2.min.js
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/plugins/.svn/all-wcprops
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/plugins/.svn/entries
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/plugins/.svn/text-base/jquery.cytoscapeweb-edgehandles.js.svn-base
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/plugins/.svn/text-base/jquery.cytoscapeweb-panzoom.css.svn-base
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/plugins/.svn/text-base/jquery.cytoscapeweb-panzoom.js.svn-base
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/plugins/jquery.cytoscapeweb-edgehandles.js
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/plugins/jquery.cytoscapeweb-panzoom.css
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/plugins/jquery.cytoscapeweb-panzoom.js
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/src/.svn/all-wcprops
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/src/.svn/entries
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/src/.svn/text-base/AC_OETags.js.svn-base
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/src/.svn/text-base/cytoscapeweb.js.svn-base
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/src/.svn/text-base/json2.js.svn-base
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/src/AC_OETags.js
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/src/cytoscapeweb.js
geworkbench-web/src/org/geworkbenchweb/visualizations/public/js/src/json2.js
geworkbench-web/src/org/geworkbenchweb/visualizations/public/swf/.svn/all-wcprops
geworkbench-web/src/org/geworkbenchweb/visualizations/public/swf/.svn/entries
geworkbench-web/src/org/geworkbenchweb/visualizations/public/swf/.svn/prop-base/CytoscapeWeb.swf.svn-base
geworkbench-web/src/org/geworkbenchweb/visualizations/public/swf/.svn/prop-base/playerProductInstall.swf.svn-base
geworkbench-web/src/org/geworkbenchweb/visualizations/public/swf/.svn/text-base/CytoscapeWeb.swf.svn-base
geworkbench-web/src/org/geworkbenchweb/visualizations/public/swf/.svn/text-base/playerProductInstall.swf.svn-base
geworkbench-web/src/org/geworkbenchweb/visualizations/public/swf/CytoscapeWeb.swf
geworkbench-web/src/org/geworkbenchweb/visualizations/public/swf/playerProductInstall.swf
diff --git a/create.sql b/create.sql
index 297ae53..f64e968 100644
--- a/create.sql
+++ b/create.sql
@@ -1,4 +1,4 @@
-CREATE TABLE ANALYSISEVENT (ID INTEGER AUTO_INCREMENT NOT NULL, CREATEDAT DATETIME, NOTE VARCHAR(255), TRANSACTION_ID INTEGER, TOOL_ID INTEGER, PRIMARY KEY (ID))
+CREATE TABLE ANALYSISEVENT (ID INTEGER AUTO_INCREMENT NOT NULL, CREATEDAT DATETIME, FINISHEDAT DATETIME, NOTE VARCHAR(255), TRANSACTION_ID INTEGER, TOOL_ID INTEGER, PRIMARY KEY (ID))
 CREATE TABLE ANALYSISEVENTPARAMETER (ID INTEGER AUTO_INCREMENT NOT NULL, PARAMETERKEY VARCHAR(255), PARAMETERVALUE VARCHAR(255), EVENT_ID INTEGER, PRIMARY KEY (ID))
 CREATE TABLE Friend (ID INTEGER AUTO_INCREMENT NOT NULL, MUTUAL TINYINT(1) default 0, VISIBLE TINYINT(1) default 0, id_1 INTEGER, id_2 INTEGER, PRIMARY KEY (ID))
 CREATE TABLE INCOMINGWORKFLOW (ID INTEGER AUTO_INCREMENT NOT NULL, CREATEDAT DATETIME, NAME VARCHAR(255), RECEIVER_ID INTEGER, SENDER_ID INTEGER, WORKFLOW_ID INTEGER, PRIMARY KEY (ID))
diff --git a/genspace-common/src/org/geworkbench/components/genspace/entity/AnalysisEvent.java b/genspace-common/src/org/geworkbench/components/genspace/entity/AnalysisEvent.java
index eddbdd6..751ecb1 100644
--- a/genspace-common/src/org/geworkbench/components/genspace/entity/AnalysisEvent.java
+++ b/genspace-common/src/org/geworkbench/components/genspace/entity/AnalysisEvent.java
@@ -22,6 +22,7 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlID;
 import javax.xml.bind.annotation.XmlIDREF;
 import javax.xml.bind.annotation.XmlRootElement;
+import javax.xml.bind.annotation.XmlTransient;

 @Entity
 @XmlRootElement
@@ -35,6 +36,7 @@ public class AnalysisEvent extends LazyCycleBreaker implements Serializable {
 	private Set<AnalysisEventParameter> parameters;
 	private String toolname;
 	private String note;
+	private java.util.Date finishedAt;

 //	@Override
 //	protected Object clone() throws CloneNotSupportedException {
@@ -103,4 +105,12 @@ public class AnalysisEvent extends LazyCycleBreaker implements Serializable {
 	public void setNote(String note) {
 		this.note = note;
 	}
+	@Temporal(TemporalType.TIMESTAMP)
+	@XmlTransient
+	public java.util.Date getFinishedAt() {
+		return finishedAt;
+	}
+	public void setFinishedAt(java.util.Date finishedAt) {
+		this.finishedAt = finishedAt;
+	}
 }
diff --git a/genspace-common/src/org/geworkbench/components/genspace/server/stubs/FriendFacadeService.java b/genspace-common/src/org/geworkbench/components/genspace/server/stubs/FriendFacadeService.java
index 9e7792d..cc37652 100644
--- a/genspace-common/src/org/geworkbench/components/genspace/server/stubs/FriendFacadeService.java
+++ b/genspace-common/src/org/geworkbench/components/genspace/server/stubs/FriendFacadeService.java
@@ -17,7 +17,7 @@ import javax.xml.ws.WebServiceFeature;
  * Generated source version: 2.1
  *
  */
-@WebServiceClient(name = "FriendFacadeService", targetNamespace = "http://server.genspace.components.geworkbench.org/", wsdlLocation = "http://127.0.0.1:8080/FriendFacadeService/FriendFacade?wsdl")
+@WebServiceClient(name = "FriendFacadeService", targetNamespace = "http://server.genspace.components.geworkbench.org/", wsdlLocation = "http://genspace.cs.columbia.edu:8080/FriendFacadeService/FriendFacade?wsdl")
 public class FriendFacadeService
     extends Service
 {
@@ -30,9 +30,9 @@ public class FriendFacadeService
         try {
             URL baseUrl;
             baseUrl = org.geworkbench.components.genspace.server.stubs.FriendFacadeService.class.getResource(".");
-            url = new URL(baseUrl, "http://127.0.0.1:8080/FriendFacadeService/FriendFacade?wsdl");
+            url = new URL(baseUrl, "http://genspace.cs.columbia.edu:8080/FriendFacadeService/FriendFacade?wsdl");
         } catch (MalformedURLException e) {
-            logger.warning("Failed to create URL for the wsdl Location: 'http://127.0.0.1:8080/FriendFacadeService/FriendFacade?wsdl', retrying as a local file");
+            logger.warning("Failed to create URL for the wsdl Location: 'http://genspace.cs.columbia.edu:8080/FriendFacadeService/FriendFacade?wsdl', retrying as a local file");
             logger.warning(e.getMessage());
         }
         FRIENDFACADESERVICE_WSDL_LOCATION = url;
diff --git a/genspace-common/src/org/geworkbench/components/genspace/server/stubs/NetworkFacadeService.java b/genspace-common/src/org/geworkbench/components/genspace/server/stubs/NetworkFacadeService.java
index d19a12e..d336e03 100644
--- a/genspace-common/src/org/geworkbench/components/genspace/server/stubs/NetworkFacadeService.java
+++ b/genspace-common/src/org/geworkbench/components/genspace/server/stubs/NetworkFacadeService.java
@@ -17,7 +17,7 @@ import javax.xml.ws.WebServiceFeature;
  * Generated source version: 2.1
  *
  */
-@WebServiceClient(name = "NetworkFacadeService", targetNamespace = "http://server.genspace.components.geworkbench.org/", wsdlLocation = "http://127.0.0.1:8080/NetworkFacadeService/NetworkFacade?wsdl")
+@WebServiceClient(name = "NetworkFacadeService", targetNamespace = "http://server.genspace.components.geworkbench.org/", wsdlLocation = "http://genspace.cs.columbia.edu:8080/NetworkFacadeService/NetworkFacade?wsdl")
 public class NetworkFacadeService
     extends Service
 {
@@ -30,9 +30,9 @@ public class NetworkFacadeService
         try {
             URL baseUrl;
             baseUrl = org.geworkbench.components.genspace.server.stubs.NetworkFacadeService.class.getResource(".");
-            url = new URL(baseUrl, "http://127.0.0.1:8080/NetworkFacadeService/NetworkFacade?wsdl");
+            url = new URL(baseUrl, "http://genspace.cs.columbia.edu:8080/NetworkFacadeService/NetworkFacade?wsdl");
         } catch (MalformedURLException e) {
-            logger.warning("Failed to create URL for the wsdl Location: 'http://127.0.0.1:8080/NetworkFacadeService/NetworkFacade?wsdl', retrying as a local file");
+            logger.warning("Failed to create URL for the wsdl Location: 'http://genspace.cs.columbia.edu:8080/NetworkFacadeService/NetworkFacade?wsdl', retrying as a local file");
             logger.warning(e.getMessage());
         }
         NETWORKFACADESERVICE_WSDL_LOCATION = url;
diff --git a/genspace-common/src/org/geworkbench/components/genspace/server/stubs/ObjectFactory.java b/genspace-common/src/org/geworkbench/components/genspace/server/stubs/ObjectFactory.java
index fd4f2ba..2373cba 100644
--- a/genspace-common/src/org/geworkbench/components/genspace/server/stubs/ObjectFactory.java
+++ b/genspace-common/src/org/geworkbench/components/genspace/server/stubs/ObjectFactory.java
@@ -56,115 +56,123 @@ public class ObjectFactory {
     }

     /**
-     * Create an instance of {@link JoinNetwork }
+     * Create an instance of {@link GetMyNetworks }
      *
      */
-    public JoinNetwork createJoinNetwork() {
-        return new JoinNetwork();
+    public GetMyNetworks createGetMyNetworks() {
+        return new GetMyNetworks();
     }

     /**
-     * Create an instance of {@link UpdateNetworkVisibilityResponse }
+     * Create an instance of {@link LeaveNetwork }
      *
      */
-    public UpdateNetworkVisibilityResponse createUpdateNetworkVisibilityResponse() {
-        return new UpdateNetworkVisibilityResponse();
+    public LeaveNetwork createLeaveNetwork() {
+        return new LeaveNetwork();
     }

     /**
-     * Create an instance of {@link GetNetworkRequests }
+     * Create an instance of {@link CreateNetwork }
      *
      */
-    public GetNetworkRequests createGetNetworkRequests() {
-        return new GetNetworkRequests();
+    public CreateNetwork createCreateNetwork() {
+        return new CreateNetwork();
     }

     /**
-     * Create an instance of {@link CreateNetworkResponse }
+     * Create an instance of {@link AcceptNetworkRequest }
      *
      */
-    public CreateNetworkResponse createCreateNetworkResponse() {
-        return new CreateNetworkResponse();
+    public AcceptNetworkRequest createAcceptNetworkRequest() {
+        return new AcceptNetworkRequest();
     }

     /**
-     * Create an instance of {@link UpdateNetworkVisibility }
+     * Create an instance of {@link GetNumberOfNetworkRequestsResponse }
      *
      */
-    public UpdateNetworkVisibility createUpdateNetworkVisibility() {
-        return new UpdateNetworkVisibility();
+    public GetNumberOfNetworkRequestsResponse createGetNumberOfNetworkRequestsResponse() {
+        return new GetNumberOfNetworkRequestsResponse();
     }

     /**
-     * Create an instance of {@link RejectNetworkRequest }
+     * Create an instance of {@link UserNetwork }
      *
      */
-    public RejectNetworkRequest createRejectNetworkRequest() {
-        return new RejectNetworkRequest();
+    public UserNetwork createUserNetwork() {
+        return new UserNetwork();
     }

     /**
-     * Create an instance of {@link User }
+     * Create an instance of {@link GetNumberOfNetworkRequests }
      *
      */
-    public User createUser() {
-        return new User();
+    public GetNumberOfNetworkRequests createGetNumberOfNetworkRequests() {
+        return new GetNumberOfNetworkRequests();
     }

     /**
-     * Create an instance of {@link JoinNetworkResponse }
+     * Create an instance of {@link GetNetworkRequests }
      *
      */
-    public JoinNetworkResponse createJoinNetworkResponse() {
-        return new JoinNetworkResponse();
+    public GetNetworkRequests createGetNetworkRequests() {
+        return new GetNetworkRequests();
     }

     /**
-     * Create an instance of {@link Network }
+     * Create an instance of {@link GetMyNetworksResponse }
      *
      */
-    public Network createNetwork() {
-        return new Network();
+    public GetMyNetworksResponse createGetMyNetworksResponse() {
+        return new GetMyNetworksResponse();
     }

     /**
-     * Create an instance of {@link GetAllNetworksResponse }
+     * Create an instance of {@link AcceptNetworkRequestResponse }
      *
      */
-    public GetAllNetworksResponse createGetAllNetworksResponse() {
-        return new GetAllNetworksResponse();
+    public AcceptNetworkRequestResponse createAcceptNetworkRequestResponse() {
+        return new AcceptNetworkRequestResponse();
     }

     /**
-     * Create an instance of {@link GetProfilesByNetwork }
+     * Create an instance of {@link GetProfilesByNetworkResponse }
      *
      */
-    public GetProfilesByNetwork createGetProfilesByNetwork() {
-        return new GetProfilesByNetwork();
+    public GetProfilesByNetworkResponse createGetProfilesByNetworkResponse() {
+        return new GetProfilesByNetworkResponse();
     }

     /**
-     * Create an instance of {@link GetNumberOfNetworkRequestsResponse }
+     * Create an instance of {@link RejectNetworkRequest }
      *
      */
-    public GetNumberOfNetworkRequestsResponse createGetNumberOfNetworkRequestsResponse() {
-        return new GetNumberOfNetworkRequestsResponse();
+    public RejectNetworkRequest createRejectNetworkRequest() {
+        return new RejectNetworkRequest();
     }

     /**
-     * Create an instance of {@link AcceptNetworkRequest }
+     * Create an instance of {@link JoinNetwork }
      *
      */
-    public AcceptNetworkRequest createAcceptNetworkRequest() {
-        return new AcceptNetworkRequest();
+    public JoinNetwork createJoinNetwork() {
+        return new JoinNetwork();
     }

     /**
-     * Create an instance of {@link UserNetwork }
+     * Create an instance of {@link User }
      *
      */
-    public UserNetwork createUserNetwork() {
-        return new UserNetwork();
+    public User createUser() {
+        return new User();
+    }
+
+    /**
+     * Create an instance of {@link Network }
+     *
+     */
+    public Network createNetwork() {
+        return new Network();
     }

     /**
@@ -176,11 +184,11 @@ public class ObjectFactory {
     }

     /**
-     * Create an instance of {@link GetMyNetworks }
+     * Create an instance of {@link GetAllNetworksResponse }
      *
      */
-    public GetMyNetworks createGetMyNetworks() {
-        return new GetMyNetworks();
+    public GetAllNetworksResponse createGetAllNetworksResponse() {
+        return new GetAllNetworksResponse();
     }

     /**
@@ -192,51 +200,43 @@ public class ObjectFactory {
     }

     /**
-     * Create an instance of {@link LeaveNetworkResponse }
-     *
-     */
-    public LeaveNetworkResponse createLeaveNetworkResponse() {
-        return new LeaveNetworkResponse();
-    }
-
-    /**
-     * Create an instance of {@link GetNumberOfNetworkRequests }
+     * Create an instance of {@link JoinNetworkResponse }
      *
      */
-    public GetNumberOfNetworkRequests createGetNumberOfNetworkRequests() {
-        return new GetNumberOfNetworkRequests();
+    public JoinNetworkResponse createJoinNetworkResponse() {
+        return new JoinNetworkResponse();
     }

     /**
-     * Create an instance of {@link GetMyNetworksResponse }
+     * Create an instance of {@link UpdateNetworkVisibility }
      *
      */
-    public GetMyNetworksResponse createGetMyNetworksResponse() {
-        return new GetMyNetworksResponse();
+    public UpdateNetworkVisibility createUpdateNetworkVisibility() {
+        return new UpdateNetworkVisibility();
     }

     /**
-     * Create an instance of {@link LeaveNetwork }
+     * Create an instance of {@link LeaveNetworkResponse }
      *
      */
-    public LeaveNetwork createLeaveNetwork() {
-        return new LeaveNetwork();
+    public LeaveNetworkResponse createLeaveNetworkResponse() {
+        return new LeaveNetworkResponse();
     }

     /**
-     * Create an instance of {@link CreateNetwork }
+     * Create an instance of {@link UpdateNetworkVisibilityResponse }
      *
      */
-    public CreateNetwork createCreateNetwork() {
-        return new CreateNetwork();
+    public UpdateNetworkVisibilityResponse createUpdateNetworkVisibilityResponse() {
+        return new UpdateNetworkVisibilityResponse();
     }

     /**
-     * Create an instance of {@link AcceptNetworkRequestResponse }
+     * Create an instance of {@link CreateNetworkResponse }
      *
      */
-    public AcceptNetworkRequestResponse createAcceptNetworkRequestResponse() {
-        return new AcceptNetworkRequestResponse();
+    public CreateNetworkResponse createCreateNetworkResponse() {
+        return new CreateNetworkResponse();
     }

     /**
@@ -248,11 +248,11 @@ public class ObjectFactory {
     }

     /**
-     * Create an instance of {@link GetProfilesByNetworkResponse }
+     * Create an instance of {@link GetProfilesByNetwork }
      *
      */
-    public GetProfilesByNetworkResponse createGetProfilesByNetworkResponse() {
-        return new GetProfilesByNetworkResponse();
+    public GetProfilesByNetwork createGetProfilesByNetwork() {
+        return new GetProfilesByNetwork();
     }

     /**
diff --git a/genspace-common/src/org/geworkbench/components/genspace/server/stubs/PublicFacadeService.java b/genspace-common/src/org/geworkbench/components/genspace/server/stubs/PublicFacadeService.java
index 2d1e39e..f33dab4 100644
--- a/genspace-common/src/org/geworkbench/components/genspace/server/stubs/PublicFacadeService.java
+++ b/genspace-common/src/org/geworkbench/components/genspace/server/stubs/PublicFacadeService.java
@@ -17,7 +17,7 @@ import javax.xml.ws.WebServiceFeature;
  * Generated source version: 2.1
  *
  */
-@WebServiceClient(name = "PublicFacadeService", targetNamespace = "http://server.genspace.components.geworkbench.org/", wsdlLocation = "http://127.0.0.1:8080/PublicFacadeService/PublicFacade?wsdl")
+@WebServiceClient(name = "PublicFacadeService", targetNamespace = "http://server.genspace.components.geworkbench.org/", wsdlLocation = "http://genspace.cs.columbia.edu:8080/PublicFacadeService/PublicFacade?wsdl")
 public class PublicFacadeService
     extends Service
 {
@@ -30,9 +30,9 @@ public class PublicFacadeService
         try {
             URL baseUrl;
             baseUrl = org.geworkbench.components.genspace.server.stubs.PublicFacadeService.class.getResource(".");
-            url = new URL(baseUrl, "http://127.0.0.1:8080/PublicFacadeService/PublicFacade?wsdl");
+            url = new URL(baseUrl, "http://genspace.cs.columbia.edu:8080/PublicFacadeService/PublicFacade?wsdl");
         } catch (MalformedURLException e) {
-            logger.warning("Failed to create URL for the wsdl Location: 'http://127.0.0.1:8080/PublicFacadeService/PublicFacade?wsdl', retrying as a local file");
+            logger.warning("Failed to create URL for the wsdl Location: 'http://genspace.cs.columbia.edu:8080/PublicFacadeService/PublicFacade?wsdl', retrying as a local file");
             logger.warning(e.getMessage());
         }
         PUBLICFACADESERVICE_WSDL_LOCATION = url;
diff --git a/genspace-common/src/org/geworkbench/components/genspace/server/stubs/ToolUsageInformation.java b/genspace-common/src/org/geworkbench/components/genspace/server/stubs/ToolUsageInformation.java
index 8e7139a..75bcfad 100644
--- a/genspace-common/src/org/geworkbench/components/genspace/server/stubs/ToolUsageInformation.java
+++ b/genspace-common/src/org/geworkbench/components/genspace/server/stubs/ToolUsageInformation.java
@@ -281,4 +281,35 @@ public interface ToolUsageInformation {
         @WebParam(name = "arg0", targetNamespace = "")
         int arg0);

+    /**
+     *
+     * @param arg1
+     * @param arg0
+     */
+    @WebMethod
+    @RequestWrapper(localName = "analysisEventCompleted", targetNamespace = "http://server.genspace.components.geworkbench.org/", className = "org.geworkbench.components.genspace.server.stubs.AnalysisEventCompleted")
+    @ResponseWrapper(localName = "analysisEventCompletedResponse", targetNamespace = "http://server.genspace.components.geworkbench.org/", className = "org.geworkbench.components.genspace.server.stubs.AnalysisEventCompletedResponse")
+    public void analysisEventCompleted(
+        @WebParam(name = "arg0", targetNamespace = "")
+        Transaction arg0,
+        @WebParam(name = "arg1", targetNamespace = "")
+        String arg1);
+
+    /**
+     *
+     * @param arg1
+     * @param arg0
+     * @return
+     *     returns org.geworkbench.components.genspace.server.stubs.Transaction
+     */
+    @WebMethod
+    @WebResult(targetNamespace = "")
+    @RequestWrapper(localName = "popAnalysisFromTransaction", targetNamespace = "http://server.genspace.components.geworkbench.org/", className = "org.geworkbench.components.genspace.server.stubs.PopAnalysisFromTransaction")
+    @ResponseWrapper(localName = "popAnalysisFromTransactionResponse", targetNamespace = "http://server.genspace.components.geworkbench.org/", className = "org.geworkbench.components.genspace.server.stubs.PopAnalysisFromTransactionResponse")
+    public Transaction popAnalysisFromTransaction(
+        @WebParam(name = "arg0", targetNamespace = "")
+        Transaction arg0,
+        @WebParam(name = "arg1", targetNamespace = "")
+        String arg1);
+
 }
diff --git a/genspace-common/src/org/geworkbench/components/genspace/server/stubs/ToolUsageInformationService.java b/genspace-common/src/org/geworkbench/components/genspace/server/stubs/ToolUsageInformationService.java
index 224233d..a3c6fab 100644
--- a/genspace-common/src/org/geworkbench/components/genspace/server/stubs/ToolUsageInformationService.java
+++ b/genspace-common/src/org/geworkbench/components/genspace/server/stubs/ToolUsageInformationService.java
@@ -17,7 +17,7 @@ import javax.xml.ws.WebServiceFeature;
  * Generated source version: 2.1
  *
  */
-@WebServiceClient(name = "ToolUsageInformationService", targetNamespace = "http://server.genspace.components.geworkbench.org/", wsdlLocation = "http://127.0.0.1:8080/ToolUsageInformationService/ToolUsageInformation?wsdl")
+@WebServiceClient(name = "ToolUsageInformationService", targetNamespace = "http://server.genspace.components.geworkbench.org/", wsdlLocation = "http://genspace.cs.columbia.edu:8080/ToolUsageInformationService/ToolUsageInformation?wsdl")
 public class ToolUsageInformationService
     extends Service
 {
@@ -30,9 +30,9 @@ public class ToolUsageInformationService
         try {
             URL baseUrl;
             baseUrl = org.geworkbench.components.genspace.server.stubs.ToolUsageInformationService.class.getResource(".");
-            url = new URL(baseUrl, "http://127.0.0.1:8080/ToolUsageInformationService/ToolUsageInformation?wsdl");
+            url = new URL(baseUrl, "http://genspace.cs.columbia.edu:8080/ToolUsageInformationService/ToolUsageInformation?wsdl");
         } catch (MalformedURLException e) {
-            logger.warning("Failed to create URL for the wsdl Location: 'http://127.0.0.1:8080/ToolUsageInformationService/ToolUsageInformation?wsdl', retrying as a local file");
+            logger.warning("Failed to create URL for the wsdl Location: 'http://genspace.cs.columbia.edu:8080/ToolUsageInformationService/ToolUsageInformation?wsdl', retrying as a local file");
             logger.warning(e.getMessage());
         }
         TOOLUSAGEINFORMATIONSERVICE_WSDL_LOCATION = url;
diff --git a/genspace-common/src/org/geworkbench/components/genspace/server/stubs/UsageInformation.java b/genspace-common/src/org/geworkbench/components/genspace/server/stubs/UsageInformation.java
index 4e5f851..3fd91f0 100644
--- a/genspace-common/src/org/geworkbench/components/genspace/server/stubs/UsageInformation.java
+++ b/genspace-common/src/org/geworkbench/components/genspace/server/stubs/UsageInformation.java
@@ -141,6 +141,20 @@ public interface UsageInformation {

     /**
      *
+     * @param arg0
+     * @return
+     *     returns java.util.List<org.geworkbench.components.genspace.server.stubs.AnalysisEventParameter>
+     */
+    @WebMethod
+    @WebResult(targetNamespace = "")
+    @RequestWrapper(localName = "getParametersForEvent", targetNamespace = "http://server.genspace.components.geworkbench.org/", className = "org.geworkbench.components.genspace.server.stubs.GetParametersForEvent")
+    @ResponseWrapper(localName = "getParametersForEventResponse", targetNamespace = "http://server.genspace.components.geworkbench.org/", className = "org.geworkbench.components.genspace.server.stubs.GetParametersForEventResponse")
+    public List<AnalysisEventParameter> getParametersForEvent(
+        @WebParam(name = "arg0", targetNamespace = "")
+        AnalysisEvent arg0);
+
+    /**
+     *
      * @param arg1
      * @param arg0
      * @return
@@ -156,4 +170,18 @@ public interface UsageInformation {
         @WebParam(name = "arg1", targetNamespace = "")
         String arg1);

+    /**
+     *
+     * @param arg0
+     * @return
+     *     returns java.util.List<org.geworkbench.components.genspace.server.stubs.AnalysisEventParameter>
+     */
+    @WebMethod
+    @WebResult(targetNamespace = "")
+    @RequestWrapper(localName = "getAnalysisParameters", targetNamespace = "http://server.genspace.components.geworkbench.org/", className = "org.geworkbench.components.genspace.server.stubs.GetAnalysisParameters")
+    @ResponseWrapper(localName = "getAnalysisParametersResponse", targetNamespace = "http://server.genspace.components.geworkbench.org/", className = "org.geworkbench.components.genspace.server.stubs.GetAnalysisParametersResponse")
+    public List<AnalysisEventParameter> getAnalysisParameters(
+        @WebParam(name = "arg0", targetNamespace = "")
+        int arg0);
+
 }
diff --git a/genspace-common/src/org/geworkbench/components/genspace/server/stubs/UsageInformationService.java b/genspace-common/src/org/geworkbench/components/genspace/server/stubs/UsageInformationService.java
index 79584b6..ae89e42 100644
--- a/genspace-common/src/org/geworkbench/components/genspace/server/stubs/UsageInformationService.java
+++ b/genspace-common/src/org/geworkbench/components/genspace/server/stubs/UsageInformationService.java
@@ -17,7 +17,7 @@ import javax.xml.ws.WebServiceFeature;
  * Generated source version: 2.1
  *
  */
-@WebServiceClient(name = "UsageInformationService", targetNamespace = "http://server.genspace.components.geworkbench.org/", wsdlLocation = "http://127.0.0.1:8080/UsageInformationService/UsageInformation?wsdl")
+@WebServiceClient(name = "UsageInformationService", targetNamespace = "http://server.genspace.components.geworkbench.org/", wsdlLocation = "http://genspace.cs.columbia.edu:8080/UsageInformationService/UsageInformation?wsdl")
 public class UsageInformationService
     extends Service
 {
@@ -30,9 +30,9 @@ public class UsageInformationService
         try {
             URL baseUrl;
             baseUrl = org.geworkbench.components.genspace.server.stubs.UsageInformationService.class.getResource(".");
-            url = new URL(baseUrl, "http://127.0.0.1:8080/UsageInformationService/UsageInformation?wsdl");
+            url = new URL(baseUrl, "http://genspace.cs.columbia.edu:8080/UsageInformationService/UsageInformation?wsdl");
         } catch (MalformedURLException e) {
-            logger.warning("Failed to create URL for the wsdl Location: 'http://127.0.0.1:8080/UsageInformationService/UsageInformation?wsdl', retrying as a local file");
+            logger.warning("Failed to create URL for the wsdl Location: 'http://genspace.cs.columbia.edu:8080/UsageInformationService/UsageInformation?wsdl', retrying as a local file");
             logger.warning(e.getMessage());
         }
         USAGEINFORMATIONSERVICE_WSDL_LOCATION = url;
diff --git a/genspace-common/src/org/geworkbench/components/genspace/server/stubs/UserFacade.java b/genspace-common/src/org/geworkbench/components/genspace/server/stubs/UserFacade.java
index 59bf7f2..07bee90 100644
--- a/genspace-common/src/org/geworkbench/components/genspace/server/stubs/UserFacade.java
+++ b/genspace-common/src/org/geworkbench/components/genspace/server/stubs/UserFacade.java
@@ -37,17 +37,6 @@ public interface UserFacade {

     /**
      *
-     * @return
-     *     returns org.geworkbench.components.genspace.server.stubs.User
-     */
-    @WebMethod
-    @WebResult(targetNamespace = "")
-    @RequestWrapper(localName = "getMe", targetNamespace = "http://server.genspace.components.geworkbench.org/", className = "org.geworkbench.components.genspace.server.stubs.GetMe")
-    @ResponseWrapper(localName = "getMeResponse", targetNamespace = "http://server.genspace.components.geworkbench.org/", className = "org.geworkbench.components.genspace.server.stubs.GetMeResponse")
-    public User getMe();
-
-    /**
-     *
      * @param arg0
      */
     @WebMethod
@@ -61,20 +50,6 @@ public interface UserFacade {
      *
      * @param arg0
      * @return
-     *     returns org.geworkbench.components.genspace.server.stubs.User
-     */
-    @WebMethod
-    @WebResult(targetNamespace = "")
-    @RequestWrapper(localName = "getProfile", targetNamespace = "http://server.genspace.components.geworkbench.org/", className = "org.geworkbench.components.genspace.server.stubs.GetProfile")
-    @ResponseWrapper(localName = "getProfileResponse", targetNamespace = "http://server.genspace.components.geworkbench.org/", className = "org.geworkbench.components.genspace.server.stubs.GetProfileResponse")
-    public User getProfile(
-        @WebParam(name = "arg0", targetNamespace = "")
-        String arg0);
-
-    /**
-     *
-     * @param arg0
-     * @return
      *     returns boolean
      */
     @WebMethod
@@ -96,4 +71,29 @@ public interface UserFacade {
     @ResponseWrapper(localName = "getMyNetworksResponse", targetNamespace = "http://server.genspace.components.geworkbench.org/", className = "org.geworkbench.components.genspace.server.stubs.GetMyNetworksResponse")
     public List<UserNetwork> getMyNetworks();

+    /**
+     *
+     * @return
+     *     returns org.geworkbench.components.genspace.server.stubs.User
+     */
+    @WebMethod
+    @WebResult(targetNamespace = "")
+    @RequestWrapper(localName = "getMe", targetNamespace = "http://server.genspace.components.geworkbench.org/", className = "org.geworkbench.components.genspace.server.stubs.GetMe")
+    @ResponseWrapper(localName = "getMeResponse", targetNamespace = "http://server.genspace.components.geworkbench.org/", className = "org.geworkbench.components.genspace.server.stubs.GetMeResponse")
+    public User getMe();
+
+    /**
+     *
+     * @param arg0
+     * @return
+     *     returns org.geworkbench.components.genspace.server.stubs.User
+     */
+    @WebMethod
+    @WebResult(targetNamespace = "")
+    @RequestWrapper(localName = "getProfile", targetNamespace = "http://server.genspace.components.geworkbench.org/", className = "org.geworkbench.components.genspace.server.stubs.GetProfile")
+    @ResponseWrapper(localName = "getProfileResponse", targetNamespace = "http://server.genspace.components.geworkbench.org/", className = "org.geworkbench.components.genspace.server.stubs.GetProfileResponse")
+    public User getProfile(
+        @WebParam(name = "arg0", targetNamespace = "")
+        String arg0);
+
 }
diff --git a/genspace-common/src/org/geworkbench/components/genspace/server/stubs/UserFacadeService.java b/genspace-common/src/org/geworkbench/components/genspace/server/stubs/UserFacadeService.java
index 3e21abe..7e91788 100644
--- a/genspace-common/src/org/geworkbench/components/genspace/server/stubs/UserFacadeService.java
+++ b/genspace-common/src/org/geworkbench/components/genspace/server/stubs/UserFacadeService.java
@@ -17,7 +17,7 @@ import javax.xml.ws.WebServiceFeature;
  * Generated source version: 2.1
  *
  */
-@WebServiceClient(name = "UserFacadeService", targetNamespace = "http://server.genspace.components.geworkbench.org/", wsdlLocation = "http://127.0.0.1:8080/UserFacadeService/UserFacade?wsdl")
+@WebServiceClient(name = "UserFacadeService", targetNamespace = "http://server.genspace.components.geworkbench.org/", wsdlLocation = "http://genspace.cs.columbia.edu:8080/UserFacadeService/UserFacade?wsdl")
 public class UserFacadeService
     extends Service
 {
@@ -30,9 +30,9 @@ public class UserFacadeService
         try {
             URL baseUrl;
             baseUrl = org.geworkbench.components.genspace.server.stubs.UserFacadeService.class.getResource(".");
-            url = new URL(baseUrl, "http://127.0.0.1:8080/UserFacadeService/UserFacade?wsdl");
+            url = new URL(baseUrl, "http://genspace.cs.columbia.edu:8080/UserFacadeService/UserFacade?wsdl");
         } catch (MalformedURLException e) {
-            logger.warning("Failed to create URL for the wsdl Location: 'http://127.0.0.1:8080/UserFacadeService/UserFacade?wsdl', retrying as a local file");
+            logger.warning("Failed to create URL for the wsdl Location: 'http://genspace.cs.columbia.edu:8080/UserFacadeService/UserFacade?wsdl', retrying as a local file");
             logger.warning(e.getMessage());
         }
         USERFACADESERVICE_WSDL_LOCATION = url;
diff --git a/genspace-common/src/org/geworkbench/components/genspace/server/stubs/WorkflowRepository.java b/genspace-common/src/org/geworkbench/components/genspace/server/stubs/WorkflowRepository.java
index 8966c4d..657af4e 100644
--- a/genspace-common/src/org/geworkbench/components/genspace/server/stubs/WorkflowRepository.java
+++ b/genspace-common/src/org/geworkbench/components/genspace/server/stubs/WorkflowRepository.java
@@ -28,20 +28,6 @@ public interface WorkflowRepository {
      *
      * @param arg0
      * @return
-     *     returns org.geworkbench.components.genspace.server.stubs.WorkflowComment
-     */
-    @WebMethod
-    @WebResult(targetNamespace = "")
-    @RequestWrapper(localName = "addComment", targetNamespace = "http://server.genspace.components.geworkbench.org/", className = "org.geworkbench.components.genspace.server.stubs.AddComment")
-    @ResponseWrapper(localName = "addCommentResponse", targetNamespace = "http://server.genspace.components.geworkbench.org/", className = "org.geworkbench.components.genspace.server.stubs.AddCommentResponse")
-    public WorkflowComment addComment(
-        @WebParam(name = "arg0", targetNamespace = "")
-        WorkflowComment arg0);
-
-    /**
-     *
-     * @param arg0
-     * @return
      *     returns boolean
      */
     @WebMethod
@@ -127,6 +113,20 @@ public interface WorkflowRepository {

     /**
      *
+     * @param arg0
+     * @return
+     *     returns org.geworkbench.components.genspace.server.stubs.WorkflowComment
+     */
+    @WebMethod
+    @WebResult(targetNamespace = "")
+    @RequestWrapper(localName = "addComment", targetNamespace = "http://server.genspace.components.geworkbench.org/", className = "org.geworkbench.components.genspace.server.stubs.AddComment")
+    @ResponseWrapper(localName = "addCommentResponse", targetNamespace = "http://server.genspace.components.geworkbench.org/", className = "org.geworkbench.components.genspace.server.stubs.AddCommentResponse")
+    public WorkflowComment addComment(
+        @WebParam(name = "arg0", targetNamespace = "")
+        WorkflowComment arg0);
+
+    /**
+     *
      * @param arg1
      * @param arg0
      * @return
diff --git a/genspace-common/src/org/geworkbench/components/genspace/server/stubs/WorkflowRepositoryService.java b/genspace-common/src/org/geworkbench/components/genspace/server/stubs/WorkflowRepositoryService.java
index e0f90e2..ecc2364 100644
--- a/genspace-common/src/org/geworkbench/components/genspace/server/stubs/WorkflowRepositoryService.java
+++ b/genspace-common/src/org/geworkbench/components/genspace/server/stubs/WorkflowRepositoryService.java
@@ -17,7 +17,7 @@ import javax.xml.ws.WebServiceFeature;
  * Generated source version: 2.1
  *
  */
-@WebServiceClient(name = "WorkflowRepositoryService", targetNamespace = "http://server.genspace.components.geworkbench.org/", wsdlLocation = "http://127.0.0.1:8080/WorkflowRepositoryService/WorkflowRepository?wsdl")
+@WebServiceClient(name = "WorkflowRepositoryService", targetNamespace = "http://server.genspace.components.geworkbench.org/", wsdlLocation = "http://genspace.cs.columbia.edu:8080/WorkflowRepositoryService/WorkflowRepository?wsdl")
 public class WorkflowRepositoryService
     extends Service
 {
@@ -30,9 +30,9 @@ public class WorkflowRepositoryService
         try {
             URL baseUrl;
             baseUrl = org.geworkbench.components.genspace.server.stubs.WorkflowRepositoryService.class.getResource(".");
-            url = new URL(baseUrl, "http://127.0.0.1:8080/WorkflowRepositoryService/WorkflowRepository?wsdl");
+            url = new URL(baseUrl, "http://genspace.cs.columbia.edu:8080/WorkflowRepositoryService/WorkflowRepository?wsdl");
         } catch (MalformedURLException e) {
-            logger.warning("Failed to create URL for the wsdl Location: 'http://127.0.0.1:8080/WorkflowRepositoryService/WorkflowRepository?wsdl', retrying as a local file");
+            logger.warning("Failed to create URL for the wsdl Location: 'http://genspace.cs.columbia.edu:8080/WorkflowRepositoryService/WorkflowRepository?wsdl', retrying as a local file");
             logger.warning(e.getMessage());
         }
         WORKFLOWREPOSITORYSERVICE_WSDL_LOCATION = url;
diff --git a/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/GenericUsageInformation.java b/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/GenericUsageInformation.java
index c777c11..bf1aa97 100644
--- a/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/GenericUsageInformation.java
+++ b/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/GenericUsageInformation.java
@@ -349,7 +349,22 @@ public abstract class GenericUsageInformation extends AbstractFacade<Tool>
 		}
 		return ret;
 	}
-
+	public void analysisEventCompleted(Transaction transaction, String toolName)
+	{
+		Transaction tr = getEntityManager().find(Transaction.class, transaction.getId());
+		if(!tr.getClientID().equals(transaction.getClientID())) //A basic security check
+			return;
+		Query q = getEntityManager().createNativeQuery("select a.* FROM analysisEvent a " +
+				"inner join transaction tr on tr.id=a.transaction_id " +
+				"inner join tool t on t.id=a.tool_id " +
+				"where tr.id=? AND t.name=? " +
+				"group by t.name HAVING max(a.createdat)", AnalysisEvent.class);
+		q.setParameter(1, tr.getId());
+		q.setParameter(2, toolName);
+		AnalysisEvent ev = (AnalysisEvent) q.getSingleResult();
+		ev.setFinishedAt(new Date());
+		getEntityManager().merge(ev);
+	}
 	@Override
 	public Transaction sendUsageEvent(AnalysisEvent e) {
 		e.setCreatedAt(new Date());
@@ -357,6 +372,58 @@ public abstract class GenericUsageInformation extends AbstractFacade<Tool>
 		e.setTransaction(createOrFindTransaction(e.getTransaction()));
 		return handleSingleUsageEvent(e);
 	}
+	public Transaction popAnalysisFromTransaction(Transaction transaction, String toolName)
+	{
+		if(transaction == null)
+			return null;
+		Transaction tr = getEntityManager().find(Transaction.class, transaction.getId());
+		if(!tr.getClientID().equals(transaction.getClientID())) //A basic security check
+			return null;
+		Query q = getEntityManager().createNativeQuery("select a.* FROM analysisEvent a " +
+				"inner join transaction tr on tr.id=a.transaction_id " +
+				"inner join tool t on t.id=a.tool_id " +
+				"where tr.id=? AND t.name=? " +
+				"group by t.name HAVING max(a.createdat)", AnalysisEvent.class);
+		q.setParameter(1, tr.getId());
+		q.setParameter(2, toolName);
+		AnalysisEvent ev = (AnalysisEvent) q.getSingleResult();
+
+
+		ev.getTransaction()
+		.getWorkflow()
+		.setUsageCount(
+				ev.getTransaction().getWorkflow().getUsageCount() - 1);
+
+		ev.getTool().setUsageCount(ev.getTool().getUsageCount() - 1);
+		getEntityManager().merge(ev.getTool());
+		getEntityManager().merge(ev.getTransaction().getWorkflow());
+
+		tr.getAnalysisEvents().remove(ev);
+		if(ev != null)
+			getEntityManager().remove(ev);
+		getEntityManager().flush();
+		recalculateTransactionWorkflow(tr);
+		getEntityManager().merge(tr);
+
+		if(tr.getWorkflow() != null)
+		{
+			getEntityManager().detach(tr.getWorkflow());
+			tr.getWorkflow().setParent(null);
+			tr.getWorkflow().setChildren(new ArrayList<Workflow>());
+		}
+		return tr;
+	}
+	private void recalculateTransactionWorkflow(Transaction tr) {
+		tr.setWorkflow(null);
+		getEntityManager().flush();
+		for(AnalysisEvent ev : tr.getAnalysisEvents())
+		{
+			System.out.println("Building up from " + ev);
+			tr.setWorkflow(getExtendedWorkflow(tr, ev.getTool()));
+			getEntityManager().flush();
+		}
+
+	}

 	private Transaction handleSingleUsageEvent(AnalysisEvent e) {
 //		System.out.println(e.getTool() + " -> " + e.getToolname());
@@ -402,6 +469,7 @@ public abstract class GenericUsageInformation extends AbstractFacade<Tool>
 					getEntityManager().merge(p);
 				}
 			}
+
 		// Update the workflow for the transaction
 		e.getTransaction().setWorkflow(
 				getExtendedWorkflow(e.getTransaction(), e.getTool()));
@@ -459,6 +527,8 @@ public abstract class GenericUsageInformation extends AbstractFacade<Tool>
 	 * @return
 	 */
 	private Workflow getExtendedWorkflow(Transaction t, Tool tool) {
+		getEntityManager().getEntityManagerFactory().getCache().evictAll();
+
 		if (t.getWorkflow() == null) {
 			Query q = getEntityManager()
 					.createNativeQuery(
diff --git a/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/ToolUsageInformation.java b/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/ToolUsageInformation.java
index 651d4c7..fc6b731 100644
--- a/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/ToolUsageInformation.java
+++ b/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/ToolUsageInformation.java
@@ -124,7 +124,19 @@ public class ToolUsageInformation extends GenericUsageInformation{
 	public void refreshMahoutRecommender() {
 		super.refreshMahoutRecommender();
 	}
-
+	@Override
+	@WebMethod
+	public void analysisEventCompleted(Transaction transaction, String toolName) {
+		// TODO Auto-generated method stub
+		super.analysisEventCompleted(transaction, toolName);
+	}
+	@Override
+	@WebMethod
+	public Transaction popAnalysisFromTransaction(Transaction transaction, String toolName) {
+		// TODO Auto-generated method stub
+		return super.popAnalysisFromTransaction(transaction, toolName);
+	}
+
 	@WebMethod(exclude=true)
 	@Override
 	public byte[] sendUsageSingleEvent(byte[] analysisEvent) {
diff --git a/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/UsageInformation.java b/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/UsageInformation.java
index c6cb527..8065b78 100644
--- a/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/UsageInformation.java
+++ b/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/UsageInformation.java
@@ -185,7 +185,8 @@ public class UsageInformation extends GenericUsageInformation implements
 	@WebMethod
 	@RolesAllowed("user")
 	public List<AnalysisEvent> getMyNotes(String filter, String sortOn) {
-		Query q = getEntityManager().createQuery("SELECT ev FROM AnalysisEvent ev join ev.transaction tr where tr.user=:user "+(filter != null ? "AND (ev.note LIKE :filter1 OR ev.tool.name LIKE :filter2)" : "")+" ORDER BY " + ("tool".equals(sortOn) ? "ev.tool.name" : "ev.createdAt"));
+		getEntityManager().getEntityManagerFactory().getCache().evictAll();
+		Query q = getEntityManager().createQuery("SELECT ev FROM AnalysisEvent ev join ev.transaction tr where tr.user=:user "+(filter != null ? "AND (ev.note LIKE :filter1 OR ev.tool.name LIKE :filter2)" : "")+" ORDER BY " + ("tool".equals(sortOn) ? "ev.tool.name" : "ev.createdAt DESC"));
 		q.setParameter("user", getUser());
 		if(filter != null)
 		{
@@ -205,4 +206,23 @@ public class UsageInformation extends GenericUsageInformation implements
 		System.out.println(ret.size() +"being ret");
 		return ret;
 	}
+
+	@WebMethod
+	@RolesAllowed("user")
+	public List<AnalysisEventParameter> getAnalysisParameters(int analysisId)
+	{
+		Query q = getEntityManager().createNativeQuery("select parm.* from analysiseventparameter parm " +
+				"inner join analysisevent ev on ev.id=parm.EVENT_ID " +
+				"inner join transaction tr on tr.id=ev.transaction_id where parm.event_id=? and tr.USER_ID=?;",AnalysisEventParameter.class);
+			q.setParameter(1,analysisId);
+			q.setParameter(2, getUser().getId());
+		ArrayList<AnalysisEventParameter> ret = new ArrayList<AnalysisEventParameter>();
+		for(Object o :q.getResultList())
+		{
+			getEntityManager().detach(o);
+			((AnalysisEventParameter) o).setEvent(null);
+			ret.add(((AnalysisEventParameter) o));
+		}
+		return ret;
+	}
 }
diff --git a/geworkbench-core/.settings/.svn/entries b/geworkbench-core/.settings/.svn/entries
index 04a13bd..b47320c 100644
--- a/geworkbench-core/.settings/.svn/entries
+++ b/geworkbench-core/.settings/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-9328
+9479
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/.settings
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/.svn/all-wcprops b/geworkbench-core/.svn/all-wcprops
index 9ffb086..ee88002 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/9328/trunk/geworkbench
+/svn/geworkbench/!svn/ver/9478/trunk/geworkbench
 END
 java.policy
 K 25
@@ -151,7 +151,7 @@ build.xml
 K 25
 svn:wc:ra_dav:version-url
 V 58
-/svn/geworkbench/!svn/ver/9255/trunk/geworkbench/build.xml
+/svn/geworkbench/!svn/ver/9380/trunk/geworkbench/build.xml
 END
 .classpath
 K 25
diff --git a/geworkbench-core/.svn/entries b/geworkbench-core/.svn/entries
index be5ed1d..911354f 100644
--- a/geworkbench-core/.svn/entries
+++ b/geworkbench-core/.svn/entries
@@ -1,15 +1,15 @@
 10

 dir
-9328
+9479
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2012-04-18T21:43:35.865140Z
-9328
-zji
+2012-05-16T15:22:23.801429Z
+9478
+wangmen
 has-props


@@ -271,10 +271,10 @@ file



-f676d9714b82ad538767d4050e00439e
-2012-04-02T17:57:29.620294Z
-9255
-maz
+93b55cc80f37842af17f28f6de99fce6
+2012-04-24T15:14:18.904238Z
+9380
+zji
 has-props

 .classpath
@@ -883,12 +883,6 @@ has-props

 25858

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

@@ -923,17 +917,23 @@ has-props

 26231

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




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


@@ -955,19 +955,19 @@ has-props



-26638
+35965

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




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


@@ -989,22 +989,19 @@ has-props



-35965
-
-src
-dir
+26638

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




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


@@ -1026,19 +1023,19 @@ has-props



-2574
+44234

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




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


@@ -1060,7 +1057,10 @@ has-props



-44234
+2574
+
+src
+dir

 ReleaseNotes_2.2.2.txt
 file
@@ -1198,17 +1198,17 @@ keshav

 19453

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




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



@@ -1230,19 +1230,19 @@ keshav



-18940
+21345

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




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



@@ -1264,20 +1264,20 @@ jiz



-21345
+18940

-ReleaseNotes1.6.3.txt
+YG_cDNA_annot.csv
 file




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



@@ -1298,20 +1298,19 @@ ksmith



-19053
+1529229

-YG_cDNA_annot.csv
+ReleaseNotes1.6.3.txt
 file




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



@@ -1332,7 +1331,8 @@ has-props



-1529229
+
+19053

 build-component.xml
 file
diff --git a/geworkbench-core/.svn/text-base/build.xml.svn-base b/geworkbench-core/.svn/text-base/build.xml.svn-base
index c6d545a..8bd1173 100644
--- a/geworkbench-core/.svn/text-base/build.xml.svn-base
+++ b/geworkbench-core/.svn/text-base/build.xml.svn-base
@@ -113,6 +113,7 @@
 				<include name="filtering" />
 				<include name="foldchange" />
 				<include name="geneontology2" />
+				<include name="genomespace" />
 				<include name="genspace" />
 				<include name="geworkbench-core" />
 				<include name="gpmodule_v3_0" />
@@ -515,15 +516,17 @@
 		</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-->
@@ -569,6 +572,7 @@
 				<include name="${components}/filtering/**/*" />
 				<include name="${components}/foldchange/**/*" />
 				<include name="${components}/geneontology2/**/*" />
+				<include name="${components}/genomespace/**/*" />
 				<include name="${components}/genspace/**/*" />
 				<include name="${components}/gpmodule_v3_0/**/*" />
 				<include name="${components}/hierarchicalclustering/**/*" />
@@ -646,4 +650,36 @@
 		</copy>
 		<copy file="build_runDirect.xml" tofile="${cleanFolder}/build.xml" />
 	</target>
+	<!-- ====================================================================== -->
+	<!-- CREATE DISTRIBUTABLE JARS, e.g. for Web version -->
+	<!-- ====================================================================== -->
+	<target name="jarForWeb" depends="compile" description="Creating geWorkbench jars">
+		<property name="jarForWeb" value="../jarForWeb" />
+		<!-- one jar for core -->
+		<jar destfile="geworkbench-core.jar" basedir="${classes}" includes="org/geworkbench/**">
+			<manifest>
+				<attribute name="Built-By" value="${user.name}" />
+			</manifest>
+		</jar>
+
+		<!-- components jars -->
+		<subant target="jar" genericantfile="build-component.xml">
+			<dirset dir="components">
+				<include name="analysis" />
+				<include name="ttest" />
+				<include name="hierarchicalclustering" />
+				<include name="aracne-java" />
+				<include name="interactions" />
+			</dirset>
+		</subant>
+		<mkdir dir="${jarForWeb}" />
+		<!-- geworkbenh core jar -->
+		<move todir="${jarForWeb}" file="geworkbench-core.jar" />
+		<!-- component jars -->
+		<move todir="${jarForWeb}" file="components/analysis/analysis.jar" />
+		<move todir="${jarForWeb}" file="components/aracne-java/aracne-java.jar" />
+		<move todir="${jarForWeb}" file="components/hierarchicalclustering/hierarchicalclustering.jar" />
+		<move todir="${jarForWeb}" file="components/interactions/interactions.jar" />
+		<move todir="${jarForWeb}" file="components/ttest/ttest.jar" />
+	</target>
 </project>
diff --git a/geworkbench-core/.svn/tmp/build.xml.tmp b/geworkbench-core/.svn/tmp/build.xml.tmp
new file mode 100644
index 0000000..d6e0b2c
--- /dev/null
+++ b/geworkbench-core/.svn/tmp/build.xml.tmp
@@ -0,0 +1,687 @@
+<?xml version="1.0"?>
+<project name="geWorkBench" default="run">
+	<!-- ===================================================================== -->
+	<!-- INIT  -->
+	<!-- ===================================================================== -->
+	<target name="init" description="Initializes the build environment.">
+		<!-- Project-wide properties -->
+		<!-- App name -->
+		<property name="app" value="geWorkbench" />
+		<property name="version" value="development" />
+		<!-- DEBUG setting -->
+		<property name="debug" value="on" />
+		<!-- Paths -->
+		<property name="classes" value="classes" />
+		<property name="conf" value="conf" />
+		<property name="temp" value="temp" />
+		<property name="testing" value="testing" />
+		<property name="test.reports" value="${testing}/junitreport" />
+		<!-- Java Source -->
+		<property name="src" value="src" />
+		<property name="test" value="test" />
+		<property name="conf" value="conf" />
+		<!-- Directory for releases -->
+		<property name="dist" value="dist" />
+		<!-- Directory for releases -->
+		<property name="cleanFolder" value="../cleanFolder" />
+		<!-- Directory for developer kit releases -->
+		<property name="dev" value="devkit" />
+		<!-- Source directory for resources -->
+		<property name="res" value="res" />
+		<!-- Directory for Javadoc -->
+		<property name="docs" value="web/api" />
+		<!-- The executable libs -->
+		<property name="lib" value="lib" />
+		<!-- The executable 64bit libs -->
+		<property name="lib64" value="lib64" />
+		<!-- The components directory -->
+		<property name="components" value="components" />
+		<!-- Release info -->
+		<property name="release.file" value="${dist}/${app}-${version}" />
+		<!-- Release info -->
+		<property name="devkit.file" value="${dist}/${app}_v${version}-SDK" />
+		<!-- Location to write reports -->
+		<property name="reports" value="reports" />
+		<condition property="32bit">
+			<equals arg1="${sun.arch.data.model}" arg2="32" />
+		</condition>
+		<condition property="64bit">
+			<equals arg1="${sun.arch.data.model}" arg2="64" />
+		</condition>
+	</target>
+	<target name="classpath.32" depends="init" if="32bit">
+		<property name="Dlib" value="${lib}" />
+		<echo message="32bit: ${32bit}" />
+	</target>
+	<target name="classpath.64" depends="init" if="64bit">
+		<property name="Dlib" value="${lib64};${lib}" />
+		<echo message="64bit: ${64bit}" />
+	</target>
+	<!-- ===================================================================== -->
+	<!-- PREPARE  -->
+	<!-- ===================================================================== -->
+	<target name="prepare" depends="init, classpath.32, classpath.64" description="Prepares for compilation.">
+		<mkdir dir="${classes}" />
+		<path id="classpath">
+			<fileset dir="${lib}">
+				<include name="**/*.jar" />
+			</fileset>
+		</path>
+		<!-- Classpath for running -->
+		<path id="run.classpath">
+			<pathelement location="${classes}" />
+			<pathelement location="${conf}" />
+			<path refid="classpath" />
+		</path>
+		<!-- BootClasspath for running jdic on mac -->
+		<path id="bootclasspath">
+			<pathelement path="/Library/Java/Home/lib/plugin.jar:/Library/Java/Home/lib/deploy.jar"/>
+		</path>
+		<property name="bootclasspath" refid="bootclasspath"/>
+	</target>
+	<!-- ===================================================================== -->
+	<!-- COMPILE  -->
+	<!-- ===================================================================== -->
+	<target name="compile" depends="prepare" description="Compiles core and component .java source code.">
+		<javac srcdir="${src}" destdir="${classes}" debug="${debug}" source="1.6" target="1.6" memorymaximumsize="256M" fork="true">
+			<classpath>
+				<path refid="classpath" />
+			</classpath>
+		</javac>
+		<copy todir="${classes}">
+			<fileset dir="${src}">
+				<exclude name="CVS" />
+				<exclude name="**/*.java" />
+			</fileset>
+		</copy>
+		<!-- Compile components -->
+		<subant target="compile" genericantfile="build-component.xml">
+			<dirset dir="components" >
+				<include name="alignment" />
+				<include name="analysis" />
+				<include name="annotations" />
+				<include name="anova" />
+				<include name="aracne-java" />
+				<include name="caarray" />
+				<include name="celprocessing" />
+				<include name="cgems" />
+				<include name="colormosaic" />
+				<include name="cupid" />
+				<include name="cytoscape" />
+				<include name="discovery" />
+				<include name="evidenceintegration" />
+				<include name="filtering" />
+				<include name="foldchange" />
+				<include name="geneontology2" />
+				<include name="genomespace" />
+				<include name="genspace" />
+				<include name="geworkbench-core" />
+				<!--
+				<include name="gpmodule_v3_0" />
+				-->
+				<include name="hierarchicalclustering" />
+				<include name="idea" />
+				<include name="sam" />
+				<include name="interactions" />
+				<include name="jmol" />
+				<include name="markus" />
+				<include name="masterregulator" />
+				<include name="matrixreduce" />
+				<include name="medusa" />
+				<include name="microarrays" />
+				<include name="mindy" />
+				<include name="netboost" />
+				<include name="normalization" />
+				<include name="plots" />
+				<include name="poshistogram" />
+				<include name="promoter" />
+				<include name="pudge" />
+				<include name="selectors" />
+				<include name="sequenceretriever" />
+				<include name="sequences" />
+				<include name="skybase" />
+				<include name="skybaseview" />
+				<include name="skyline" />
+				<!-- include name="skylinecontour" / -->
+				<include name="skylineview" />
+				<include name="somclustering" />
+				<include name="ttest" />
+				<include name="versioninfo" />
+				<include name="viewers" />
+			</dirset>
+		</subant>
+		<chmod file="./bin/matrixreduce/FitModelMac" perm="700"/>
+		<chmod file="./bin/matrixreduce/FitModel" perm="700"/>
+	</target>
+	<!-- ===================================================================== -->
+	<!-- DIST  -->
+	<!-- ===================================================================== -->
+	<target name="dist" depends="compile" description="Builds a zip file distribution.">
+		<delete dir="${dist}" />
+		<mkdir dir="${dist}" />
+		<zip destfile="${release.file}.zip">
+			<fileset dir=".">
+				<include name="${classes}/**/*" />
+				<include name="${components}/**/*" />
+				<exclude name="${components}/**/src/*" />
+				<include name="annotation/**/*" />
+				<include name="${lib}/**/*" />
+				<include name="caWorkbenchLicense.txt" />
+				<include name="java.policy" />
+				<include name="*annot.csv" />
+			</fileset>
+			<fileset dir="bin">
+				<include name="build.xml" />
+			</fileset>
+		</zip>
+	</target>
+	<!-- ===================================================================== -->
+	<!-- DEV  -->
+	<!-- ===================================================================== -->
+	<target name="dev" depends="compile,javadoc" description="Builds a developer kit (zip file).">
+		<mkdir dir="${dist}" />
+		<delete dir="${dev}" />
+		<mkdir dir="${dev}" />
+		<mkdir dir="${dev}/components" />
+		<mkdir dir="${dev}/conf" />
+		<mkdir dir="${dev}/core" />
+		<mkdir dir="${dev}/sampleData" />
+		<copy todir="${dev}/libraries">
+			<fileset dir="${lib}" />
+		</copy>
+		<copy todir="${dev}/components">
+			<fileset dir="${components}">
+				<include name="analysis/**/*" />
+				<include name="somclustering/**/*" />
+				<include name="colormosaic/**/*" />
+				<include name="example/**/*" />
+				<include name="filtering/**/*" />
+				<include name="hierarchicalclustering/**/*" />
+				<include name="microarrays/**/*" />
+				<include name="normalization/**/*" />
+				<include name="plots/**/*" />
+				<include name="selectors/**/*" />
+				<include name="sequences/**/*" />
+				<include name="versioninfo/**/*" />
+				<include name="viewers/**/*" />
+			</fileset>
+		</copy>
+		<copy todir="${dev}/sampleData">
+			<fileset dir="data">
+				<include name="web100.exp" />
+				<include name="rmaExpressSample.txt" />
+				<include name="histoall.fa" />
+				<include name="aml8_924_ab_hu68_4000markers.txt" />
+				<include name="aml8_965_ab_hu68_4000markers.txt" />
+				<include name="21161 neu10-4000markers.gpr" />
+				<include name="21162 ras7-4000markers.gpr" />
+			</fileset>
+		</copy>
+		<copy todir="${dev}/docs">
+			<fileset dir="${docs}" />
+		</copy>
+		<copy todir="${dev}/conf" file="${conf}/minimal.xml" />
+		<copy todir="${dev}/conf" file="${conf}/application.properties" />
+		<copy file="devBuild.xml" tofile="${dev}/build.xml" />
+		<copy file="devReadme.txt" tofile="${dev}/readme.txt" />
+		<copy file="devSource.txt" tofile="${dev}/src/readme.txt" />
+		<copy file="devLib.txt" tofile="${dev}/lib/readme.txt" />
+		<copy todir="${dev}" file="java.policy" />
+		<mkdir dir="${dev}/src" />
+		<mkdir dir="${dev}/lib" />
+		<jar destfile="${dev}/core/geworkbench-core.jar">
+			<fileset dir="${classes}" />
+			<manifest>
+				<attribute name="core-version" value="${version}" />
+			</manifest>
+		</jar>
+		<zip destfile="${devkit.file}.zip">
+			<fileset dir="devkit" />
+		</zip>
+	</target>
+	<!-- ===================================================================== -->
+	<!-- SRC-DIST  -->
+	<!-- ===================================================================== -->
+	<target name="src-dist" depends="compile" description="Builds a zip file distribution, including source.">
+		<delete dir="${dist}" />
+		<mkdir dir="${dist}" />
+		<zip destfile="${release.file}.zip">
+			<fileset dir=".">
+				<include name="${classes}/**/*" />
+				<include name="${src}/**/*" />
+				<include name="${docs}/**/*" />
+				<include name="${components}/**/*" />
+				<!-- Leave out the following components due to prohibitive size -->
+				<exclude name="${components}/sequenceretriever/**/*" />
+				<exclude name="${components}/goterms/**/*" />
+				<exclude name="${components}/gsea/**/*" />
+				<exclude name="${components}/gominer/**/*" />
+				<!-- Leave out the following components due to Windows native calls -->
+				<exclude name="${components}/associationdiscovery/**/*" />
+				<exclude name="${components}/cytoscape/**/*" />
+				<!-- Leave out the following components due to dependence on one of the above components -->
+				<exclude name="${components}/pathwaydecoder/**/*" />
+				<include name="annotation/**/*" />
+				<include name="${lib}/**/*" />
+				<include name="caWorkbenchLicense.txt" />
+				<include name="java.policy" />
+				<!-- <include name="*annot.csv"/> -->
+			</fileset>
+			<fileset dir="bin">
+				<include name="build.xml" />
+			</fileset>
+		</zip>
+	</target>
+	<!-- ===================================================================== -->
+	<!-- CLEAN  -->
+	<!-- ===================================================================== -->
+	<target name="clean" description="Clean all build products." depends="init">
+		<delete dir="${classes}" />
+		<delete dir="${temp}" />
+		<!-- Compile components -->
+		<subant target="clean" genericantfile="build-component.xml">
+			<dirset dir="components" includes="*" />
+		</subant>
+		<delete dir="components/genspace/conf" />
+		<delete dir="components/analysis/conf" />
+		<property file="conf/application.properties" />
+		<antcall target="cleanSettingFromDefaultLocation" />
+		<antcall target="cleanSettingFromUserLocation" />
+	</target>
+	<target name="cleanSettingFromDefaultLocation" unless="user.setting.directory">
+		<echo message="clean settings from default location"/>
+		<delete verbose="true">
+			<fileset dir="components" includes="*/*.ccmproperties"/>
+			<fileset dir="components" includes="*/savedParams/*"/>
+		</delete>
+	</target>
+	<target name="cleanSettingFromUserLocation" if="user.setting.directory">
+		<echo message="clean settings from user location ${user.home}${file.separator}${user.setting.directory} "/>
+		<delete verbose="true">
+			<fileset dir="${user.home}${file.separator}${user.setting.directory}" />
+		</delete>
+	</target>
+	<!-- ====================================================================== -->
+	<!-- JAVADOC -->
+	<!-- ====================================================================== -->
+	<target name="javadoc" depends="prepare" description="Creates javadocs for core only.">
+		<javadoc maxmemory="256M" destdir="${docs}" packagenames="*">
+			<classpath refid="classpath" />
+			<packageset dir="${src}" defaultexcludes="yes">
+				<include name="org/geworkbench/**" />
+			</packageset>
+		</javadoc>
+	</target>
+	<!-- ====================================================================== -->
+	<!-- RUN -->
+	<!-- ====================================================================== -->
+	<target name="run" depends="compile" description="Runs geWorkbench.">
+		<java fork="true" classname="org.geworkbench.engine.config.UILauncher">
+			<jvmarg value="-Xss1024k" />
+			<jvmarg value="-Xmx1024M" />
+			<jvmarg value="-XX:MaxPermSize=128m" />
+			<jvmarg value="-Djava.library.path=${Dlib}" />
+			<jvmarg value="-Xbootclasspath/p:${bootclasspath}" />
+			<classpath refid="run.classpath" />
+		</java>
+	</target>
+	<target name="run-mindy" depends="compile" description="Runs mindy test application.">
+		<path id="mindy.classpath">
+			<pathelement location="components/mindy/${classes}" />
+			<pathelement location="components/mindy/lib/swingx-2006_10_27.jar" />
+			<path refid="run.classpath" />
+		</path>
+		<java fork="true" classname="org.geworkbench.components.mindy.test.MindyTest">
+			<jvmarg value="-Xmx640M" />
+			<jvmarg value="-Djava.library.path=lib" />
+			<classpath refid="mindy.classpath" />
+		</java>
+	</target>
+	<!-- ====================================================================== -->
+	<!-- RUN PRODUCTION-->
+	<!-- ====================================================================== -->
+	<target name="run-prod" depends="compile" description="Runs geWorkbench.">
+		<java fork="true" classname="org.geworkbench.engine.config.UILauncher">
+			<jvmarg value="-Xmx640M" />
+			<jvmarg value="-XX:MaxPermSize=128m" />
+			<jvmarg value="-Djava.library.path=lib" />
+			<arg value="all.xml" />
+			<classpath refid="run.classpath" />
+		</java>
+	</target>
+	<!-- ====================================================================== -->
+	<!-- RUN SILENT -->
+	<!-- ====================================================================== -->
+	<target name="run-silent" depends="compile" description="Runs geWorkbench.">
+		<java fork="true" classname="org.geworkbench.engine.config.UILauncher">
+			<jvmarg value="-Xmx640M" />
+			<jvmarg value="-Djava.library.path=lib" />
+			<redirector output="NUL" />
+			<classpath refid="run.classpath" />
+		</java>
+	</target>
+	<!-- ====================================================================== -->
+	<!-- RUN ComboxBox Flavor-->
+	<!-- ====================================================================== -->
+	<target name="runNewFlavor" depends="compile" description="Runs geWorkbench.">
+		<java fork="true" classname="org.geworkbench.engine.config.UILauncher">
+			<jvmarg value="-Xmx640M" />
+			<jvmarg value="-Djava.library.path=lib" />
+			<arg value="all_combobox.xml" />
+			<classpath refid="run.classpath" />
+		</java>
+	</target>
+	<!-- ====================================================================== -->
+	<!-- TEST -->
+	<!-- ====================================================================== -->
+	<target name="test" depends="compile" description="Runs all tests with source of the form **/test/Test*.java">
+		<!--<taskdef name="junit" classname="org.apache.tools.ant.taskdefs.optional.junit.JUnitTask">-->
+		<!--<classpath>-->
+		<!--<pathelement location="lib/junit.jar"/>-->
+		<!--</classpath>-->
+		<!--</taskdef>-->
+		<delete dir="testResults" />
+		<mkdir dir="testResults" />
+		<junit printsummary="yes" haltonfailure="false">
+			<classpath refid="run.classpath" />
+			<formatter type="xml" />
+			<!--
+                        <test name="org.geworkbench.bison.testing.TestAll" haltonfailure="no" todir="testResults">
+                            <formatter type="xml"/>
+                        </test>
+            -->
+			<batchtest fork="yes" todir="testResults">
+				<formatter type="xml" />
+				<fileset dir="${src}">
+					<include name="org/geworkbench/**/test/Test*.java" />
+					<include name="org/geworkbench/bison/testing/TestCSPanel.java" />
+				</fileset>
+			</batchtest>
+		</junit>
+		<property name="junitreport" value="${reports}/junitreport" />
+		<delete dir="${junitreport}" />
+		<mkdir dir="${junitreport}" />
+		<junitreport todir="${reports}">
+			<fileset dir="testResults">
+				<include name="TEST-*.xml" />
+			</fileset>
+			<report format="frames" todir="${junitreport}" />
+		</junitreport>
+	</target>
+	<!-- ====================================================================== -->
+	<!-- Prepare a clean file for depositing to NCI CVS -->
+	<!-- ====================================================================== -->
+	<target name="createCleanSource" depends="compile" description="Creating a new folder for depositing...">
+		<delete dir="../cleanResource" />
+		<mkdir dir="../cleanResource" />
+		<copy todir="../cleanResource">
+			<fileset dir=".">
+				<exclude name="CVS" />
+				<exclude name="**/*.cvsignore" />
+			</fileset>
+		</copy>
+	</target>
+	<target name="gear" depends="init" description="Create a .gear file out of a component. Specify a directory containing a component like -Dcomponent=name">
+		<property name="component" value="" />
+		<echo message="Going to create .gear file out of directory: ${components}/${component}" />
+		<jar destfile="${component}.gear" basedir="${components}/${component}" includes="classes/**,lib/**">
+			<manifest>
+				<attribute name="core-version" value="${version}" />
+			</manifest>
+		</jar>
+	</target>
+	<!-- JUnit Run and Report -->
+	<target name="junit-run" depends="compile" description="Run JUnit tests and produce success report.">
+		<taskdef name="junit" classname="org.apache.tools.ant.taskdefs.optional.junit.JUnitTask" />
+		<delete dir="${testing}" />
+		<mkdir dir="${testing}" />
+		<junit fork="yes" dir="${basedir}" failureProperty="test.failed" printsummary="yes">
+			<jvmarg value="-Xmx640M" />
+			<jvmarg value="-Djava.awt.headless=true" />
+			<classpath refid="run.classpath" />
+			<formatter type="xml" />
+			<!--<test name="wb.test.TestAll" todir="${testing}"/>-->
+			<batchtest todir="${testing}" unless="testcase">
+				<fileset dir="${test}">
+					<include name="**/*Test.java" />
+					<exclude name="**/BulkTest.java" />
+					<exclude name="**/*GuiTest.java" />
+				</fileset>
+			</batchtest>
+		</junit>
+		<mkdir dir="${test.reports}" />
+		<junitreport todir="${test.reports}">
+			<fileset dir="${testing}">
+				<include name="TEST-*.xml" />
+			</fileset>
+			<report todir="${test.reports}" />
+		</junitreport>
+		<subant target="junit-run" genericantfile="build-component.xml">
+			<dirset dir="components" includes="*" />
+		</subant>
+		<fail>
+			<condition>
+				<isset property="test.failed" />
+			</condition>
+		</fail>
+	</target>
+	<!-- ====================================================================== -->
+	<!-- CLEAR   DISTRIBUTION-->
+	<!-- ====================================================================== -->
+	<target name="cleanDist" depends="init" description="Clean the folder for depositing...">
+		<delete dir="${cleanFolder}" />
+	</target>
+	<!-- ====================================================================== -->
+	<!-- CREATE CLEAN DISTRIBUTION-->
+	<!-- ====================================================================== -->
+	<target name="createCleanDist" depends="cleanDist, createDist" description="Creating a new folder for depositing...">
+
+	</target>
+	<!-- ====================================================================== -->
+	<!-- CREATE CORE JARS-->
+	<!-- ====================================================================== -->
+	<target name="jar" depends="compile" description="Creating geWorkbench core jars">
+		<jar destfile="geworkbench-parsers.jar" basedir="${classes}" includes="org/geworkbench/parsers/**">
+			<manifest>
+				<attribute name="Built-By" value="${user.name}" />
+
+				<!-- attribute name="Class-Path" value="" / -->
+				<!-- attribute name="Main-Class" value="" / -->
+			</manifest>
+		</jar>
+		<jar destfile="geworkbench-engine.jar" basedir="${classes}" includes="org/geworkbench/engine/**">
+			<manifest>
+				<attribute name="Built-By" value="${user.name}" />
+			</manifest>
+		</jar>
+		<jar destfile="geworkbench-events.jar" basedir="${classes}" includes="org/geworkbench/events/**">
+			<manifest>
+				<attribute name="Built-By" value="${user.name}" />
+			</manifest>
+		</jar>
+		<jar destfile="geworkbench-builtin.jar" basedir="${classes}" includes="org/geworkbench/builtin/**">
+			<manifest>
+				<attribute name="Built-By" value="${user.name}" />
+			</manifest>
+		</jar>
+		<jar destfile="geworkbench-util.jar" basedir="${classes}" includes="org/geworkbench/util/**">
+			<manifest>
+				<attribute name="Built-By" value="${user.name}" />
+			</manifest>
+		</jar>
+		<jar destfile="geworkbench-bison.jar" basedir="${classes}" includes="org/geworkbench/bison/**">
+			<manifest>
+				<attribute name="Built-By" value="${user.name}" />
+			</manifest>
+		</jar>
+		<jar destfile="geworkbench-others.jar" basedir="${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 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="./components/versioninfo/classes/org/geworkbench/components/versioninfo/" />
+			<classpath>
+				<path refid="classpath" />
+				<pathelement location="./components/versioninfo/classes" />
+			</classpath>
+		</java>
+
+		<mkdir dir="${cleanFolder}" />
+		<mkdir dir="${cleanFolder}/log" />
+		<echo>Begin to create a new source, which is located at ${cleanFolder}, please wait...</echo>
+		<move todir="${cleanFolder}" >
+			<fileset dir=".">
+				<!-- geworkbenh core jars -->
+				<include name="*.jar" />
+			</fileset>
+		</move>
+		<copy todir="${cleanFolder}" includeEmptyDirs="NO">
+			<fileset dir=".">
+
+				<exclude name="CVS" />
+				<exclude name="${conf}/**/*" />
+
+				<!-- Include the following components for distribution -->
+				<include name="bin/matrixreduce/*" />
+				<include name="${components}/alignment/**/*" />
+				<include name="${components}/analysis/**/*" />
+				<include name="${components}/annotations/**/*" />
+				<include name="${components}/anova/**/*" />
+				<include name="${components}/aracne-java/**/*" />
+				<include name="${components}/caarray/**/*" />
+				<include name="${components}/celprocessing/**/*" />
+
+				<include name="${components}/somclustering/**/*" />
+				<include name="${components}/colormosaic/**/*" />
+				<include name="${components}/cytoscape/**/*" />
+				<include name="${components}/discovery/**/*" />
+				<include name="${components}/filtering/**/*" />
+				<include name="${components}/foldchange/**/*" />
+				<include name="${components}/geneontology2/**/*" />
+				<include name="${components}/genomespace/**/*" />
+				<include name="${components}/genspace/**/*" />
+				<include name="${components}/gpmodule_v3_0/**/*" />
+				<include name="${components}/hierarchicalclustering/**/*" />
+				<include name="${components}/idea/**/*" />
+				<include name="${components}/sam/**/*" />
+				<include name="${components}/interactions/**/*" />
+				<include name="${components}/jmol/**/*" />
+				<include name="${components}/masterregulator/**/*" />
+				<include name="${components}/matrixreduce/**/*" />
+				<include name="${components}/microarrays/**/*" />
+				<include name="${components}/mindy/**/*" />
+
+				<include name="${components}/normalization/**/*" />
+
+				<include name="${components}/plots/**/*" />
+				<include name="${components}/poshistogram/**/*" />
+				<include name="${components}/promoter/**/*" />
+				<include name="${components}/pudge/**/*" />
+				<include name="${components}/selectors/**/*" />
+				<include name="${components}/sequenceretriever/**/*" />
+				<include name="${components}/sequences/**/*" />
+
+				<include name="${components}/versioninfo/**/*" />
+				<include name="${components}/viewers/**/*" />
+				<include name="${components}/markus/**/*" />
+
+				<include name="${components}/skyline/**/*" />
+				<include name="${components}/skylineview/**/*" />
+				<include name="${components}/skybase/**/*" />
+				<include name="${components}/skybaseview/**/*" />
+
+				<include name="${components}/ttest/**/*" />
+
+				<!-- Leave out the following components for release -->
+				<exclude name="**/synteny/*" />
+				<exclude name="**/src/**" />
+				<exclude name="**/test/**" />
+
+				<include name="annotation/**/*" />
+				<include name="${lib}/**/*" />
+				<include name="${lib64}/**/*" />
+				<include name="geWorkbenchLicense.txt" />
+				<include name="ReleaseNotes_2.3.0.txt" />
+				<include name="welcometext.html" />
+				<include name="java.policy" />
+
+				<include name="Bcell-100.exp_ARACNe_AP_threshold.txt" />
+				<include name="Bcell-100.exp_ARACNe_FBW_kernel.txt" />
+				<include name="Bcell-100.exp_ARACNe_FBW_threshold.txt" />
+
+				<include name="launch_geworkbench.bat" />
+				<include name="launch_geworkbench.sh" />
+				<exclude name="**/*.cvsignore" />
+				<exclude name="data" />
+				<exclude name="nbproject" />
+				<include name="data/cardiogenomics.med.harvard.edu/**" />
+				<include name="data/public_data/**" />
+				<include name="data/jaspar_CORE/**" />
+				<include name="data/gene_ontology.1_2.obo"/>
+			</fileset>
+		</copy>
+		<copy todir="${cleanFolder}/conf" includeEmptyDirs="NO">
+			<fileset dir="./conf">
+				<include name="application.properties" />
+				<include name="all.xml" />
+				<include name="client-config.wsdd" />
+				<include name="*.xsd" />
+				<include name="*.dtd" />
+				<include name="xml-mapping.xml" />
+				<include name="unmarshaller-xml-mapping.xml" />
+				<include name="application-config-client.xml" />
+				<include name="jdic.properties" />
+				<include name="log4j.properties" />
+			</fileset>
+		</copy>
+		<copy file="build_runDirect.xml" tofile="${cleanFolder}/build.xml" />
+	</target>
+	<!-- ====================================================================== -->
+	<!-- CREATE DISTRIBUTABLE JARS, e.g. for Web version -->
+	<!-- ====================================================================== -->
+	<target name="jarForWeb" depends="compile" description="Creating geWorkbench jars">
+		<property name="jarForWeb" value="../jarForWeb" />
+		<!-- one jar for core -->
+		<jar destfile="geworkbench-core.jar" basedir="${classes}" includes="org/geworkbench/**">
+			<manifest>
+				<attribute name="Built-By" value="${user.name}" />
+			</manifest>
+		</jar>
+
+		<!-- components jars -->
+		<subant target="jar" genericantfile="build-component.xml">
+			<dirset dir="components">
+				<include name="analysis" />
+				<include name="ttest" />
+				<include name="hierarchicalclustering" />
+				<include name="aracne-java" />
+				<include name="interactions" />
+			</dirset>
+		</subant>
+		<mkdir dir="${jarForWeb}" />
+		<!-- geworkbenh core jar -->
+		<move todir="${jarForWeb}" file="geworkbench-core.jar" />
+		<!-- component jars -->
+		<move todir="${jarForWeb}" file="components/analysis/analysis.jar" />
+		<move todir="${jarForWeb}" file="components/aracne-java/aracne-java.jar" />
+		<move todir="${jarForWeb}" file="components/hierarchicalclustering/hierarchicalclustering.jar" />
+		<move todir="${jarForWeb}" file="components/interactions/interactions.jar" />
+		<move todir="${jarForWeb}" file="components/ttest/ttest.jar" />
+	</target>
+</project>
diff --git a/geworkbench-core/bin/.svn/entries b/geworkbench-core/bin/.svn/entries
index 3b5a78e..a5ef9b5 100644
--- a/geworkbench-core/bin/.svn/entries
+++ b/geworkbench-core/bin/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-9328
+9479
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/bin
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/bin/matrixreduce/.svn/entries b/geworkbench-core/bin/matrixreduce/.svn/entries
index 74f82b3..bc03a39 100644
--- a/geworkbench-core/bin/matrixreduce/.svn/entries
+++ b/geworkbench-core/bin/matrixreduce/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-9328
+9479
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/bin/matrixreduce
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/build.xml b/geworkbench-core/build.xml
index de6bfb6..d6e0b2c 100755
--- a/geworkbench-core/build.xml
+++ b/geworkbench-core/build.xml
@@ -113,6 +113,7 @@
 				<include name="filtering" />
 				<include name="foldchange" />
 				<include name="geneontology2" />
+				<include name="genomespace" />
 				<include name="genspace" />
 				<include name="geworkbench-core" />
 				<!--
@@ -517,15 +518,17 @@
 		</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-->
@@ -571,6 +574,7 @@
 				<include name="${components}/filtering/**/*" />
 				<include name="${components}/foldchange/**/*" />
 				<include name="${components}/geneontology2/**/*" />
+				<include name="${components}/genomespace/**/*" />
 				<include name="${components}/genspace/**/*" />
 				<include name="${components}/gpmodule_v3_0/**/*" />
 				<include name="${components}/hierarchicalclustering/**/*" />
@@ -648,4 +652,36 @@
 		</copy>
 		<copy file="build_runDirect.xml" tofile="${cleanFolder}/build.xml" />
 	</target>
+	<!-- ====================================================================== -->
+	<!-- CREATE DISTRIBUTABLE JARS, e.g. for Web version -->
+	<!-- ====================================================================== -->
+	<target name="jarForWeb" depends="compile" description="Creating geWorkbench jars">
+		<property name="jarForWeb" value="../jarForWeb" />
+		<!-- one jar for core -->
+		<jar destfile="geworkbench-core.jar" basedir="${classes}" includes="org/geworkbench/**">
+			<manifest>
+				<attribute name="Built-By" value="${user.name}" />
+			</manifest>
+		</jar>
+
+		<!-- components jars -->
+		<subant target="jar" genericantfile="build-component.xml">
+			<dirset dir="components">
+				<include name="analysis" />
+				<include name="ttest" />
+				<include name="hierarchicalclustering" />
+				<include name="aracne-java" />
+				<include name="interactions" />
+			</dirset>
+		</subant>
+		<mkdir dir="${jarForWeb}" />
+		<!-- geworkbenh core jar -->
+		<move todir="${jarForWeb}" file="geworkbench-core.jar" />
+		<!-- component jars -->
+		<move todir="${jarForWeb}" file="components/analysis/analysis.jar" />
+		<move todir="${jarForWeb}" file="components/aracne-java/aracne-java.jar" />
+		<move todir="${jarForWeb}" file="components/hierarchicalclustering/hierarchicalclustering.jar" />
+		<move todir="${jarForWeb}" file="components/interactions/interactions.jar" />
+		<move todir="${jarForWeb}" file="components/ttest/ttest.jar" />
+	</target>
 </project>
diff --git a/geworkbench-core/cascripts/.svn/entries b/geworkbench-core/cascripts/.svn/entries
index 4e61aed..bbebfd7 100644
--- a/geworkbench-core/cascripts/.svn/entries
+++ b/geworkbench-core/cascripts/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-9328
+9479
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/cascripts
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/.svn/all-wcprops b/geworkbench-core/classes/.svn/all-wcprops
index 27598a5..5fc1f31 100644
--- a/geworkbench-core/classes/.svn/all-wcprops
+++ b/geworkbench-core/classes/.svn/all-wcprops
@@ -1,7 +1,7 @@
 K 25
 svn:wc:ra_dav:version-url
 V 53
-/svn/geworkbench/!svn/ver/8924/trunk/geworkbench/conf
+/svn/geworkbench/!svn/ver/9164/trunk/geworkbench/conf
 END
 client-config.wsdd
 K 25
@@ -25,7 +25,7 @@ all.xml
 K 25
 svn:wc:ra_dav:version-url
 V 61
-/svn/geworkbench/!svn/ver/8434/trunk/geworkbench/conf/all.xml
+/svn/geworkbench/!svn/ver/9164/trunk/geworkbench/conf/all.xml
 END
 log4j.properties
 K 25
diff --git a/geworkbench-core/classes/.svn/entries b/geworkbench-core/classes/.svn/entries
index 76a3f6e..ac022d6 100644
--- a/geworkbench-core/classes/.svn/entries
+++ b/geworkbench-core/classes/.svn/entries
@@ -1,15 +1,15 @@
 10

 dir
-9024
+9328
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/conf
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2012-02-27T22:42:50.953800Z
-8924
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 has-props


@@ -26,16 +26,16 @@ has-props

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

-.cvsignore
+client-config.wsdd
 file




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-1f0e698e6ea28e2e6f42e158c681f0e3
-2007-04-16T17:08:58.000000Z
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 has-props

@@ -58,20 +58,19 @@ has-props



-18
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-ConfigurationFile Schema.xsd
+jdic.properties
 file




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@@ -92,19 +91,20 @@ has-props



-5861
+
+39

-Descriptor Schema.xsd
+ConfigurationFile Schema.xsd
 file




 2011-08-17T00:10:46.000000Z
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 has-props


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



-9253
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 all.xml
 file
@@ -134,11 +134,11 @@ file



-2012-01-10T19:15:27.000000Z
-28104fc616ab64ae32280509e083f329
-2011-10-19T21:34:53.145523Z
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 has-props


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



-3127
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-application.properties
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 zji
 has-props

@@ -194,19 +194,22 @@ has-props



-4419
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-client-config.wsdd
+cruisecontrol
+dir
+
+Descriptor Schema.xsd
 file




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@@ -228,23 +231,20 @@ has-props



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-
-cruisecontrol
-dir
+9253

-jdic.properties
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 2011-08-17T00:10:46.000000Z
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@@ -265,18 +265,18 @@ wangm



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-log4j.properties
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-2011-08-17T00:19:06.000000Z
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-7925
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 zji
 has-props

@@ -299,5 +299,5 @@ has-props



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diff --git a/geworkbench-core/classes/.svn/text-base/all.xml.svn-base b/geworkbench-core/classes/.svn/text-base/all.xml.svn-base
index 89dc1b6..25559fa 100644
--- a/geworkbench-core/classes/.svn/text-base/all.xml.svn-base
+++ b/geworkbench-core/classes/.svn/text-base/all.xml.svn-base
@@ -3,8 +3,19 @@
 	xsi:noNamespaceSchemaLocation="ConfigurationFile Schema.xsd">

 	<gui-window name="Main GUI" class="org.geworkbench.engine.skin.Skin" />
-
-    <plugin id="SoftFileFilter" name="soft. Format"
+	<!-- Preferences is only loaded here so that its help file appears -->
+	<plugin id="Preferences" name="for Preferences Help"
+		class="org.geworkbench.engine.preferences.Preferences" />
+
+	<!-- FileFormatHelp is a dummy class used only to load the help file. -->
+	<plugin id="fileFormatHelp" name="for File Format Help"
+		class="org.geworkbench.parsers.FileFormatHelp" />
+
+	<!-- LocalDataFilesHelp is a dummy class used only to load the help file-->
+	<plugin id="localDataFilesHelp" name="for Local Data File Help"
+		class="org.geworkbench.builtin.projects.LocalDataFilesHelp" />
+
+	<plugin id="SoftFileFilter" name="soft. Format"
 		class="org.geworkbench.parsers.SOFTFileFormat" />

 	<plugin id="MageTabFileFilter" name="MAGE-TAB. Format"
diff --git a/geworkbench-core/classes/all.xml b/geworkbench-core/classes/all.xml
index 89dc1b6..25559fa 100755
--- a/geworkbench-core/classes/all.xml
+++ b/geworkbench-core/classes/all.xml
@@ -3,8 +3,19 @@
 	xsi:noNamespaceSchemaLocation="ConfigurationFile Schema.xsd">

 	<gui-window name="Main GUI" class="org.geworkbench.engine.skin.Skin" />
-
-    <plugin id="SoftFileFilter" name="soft. Format"
+	<!-- Preferences is only loaded here so that its help file appears -->
+	<plugin id="Preferences" name="for Preferences Help"
+		class="org.geworkbench.engine.preferences.Preferences" />
+
+	<!-- FileFormatHelp is a dummy class used only to load the help file. -->
+	<plugin id="fileFormatHelp" name="for File Format Help"
+		class="org.geworkbench.parsers.FileFormatHelp" />
+
+	<!-- LocalDataFilesHelp is a dummy class used only to load the help file-->
+	<plugin id="localDataFilesHelp" name="for Local Data File Help"
+		class="org.geworkbench.builtin.projects.LocalDataFilesHelp" />
+
+	<plugin id="SoftFileFilter" name="soft. Format"
 		class="org.geworkbench.parsers.SOFTFileFormat" />

 	<plugin id="MageTabFileFilter" name="MAGE-TAB. Format"
diff --git a/geworkbench-core/classes/cruisecontrol/.svn/entries b/geworkbench-core/classes/cruisecontrol/.svn/entries
index f06af05..13fc74f 100644
--- a/geworkbench-core/classes/cruisecontrol/.svn/entries
+++ b/geworkbench-core/classes/cruisecontrol/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
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 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/conf/cruisecontrol
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diff --git a/geworkbench-core/classes/images/.svn/entries b/geworkbench-core/classes/images/.svn/entries
index 2ffc430..4f037ef 100644
--- a/geworkbench-core/classes/images/.svn/entries
+++ b/geworkbench-core/classes/images/.svn/entries
@@ -1,7 +1,7 @@
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@@ -26,14 +26,14 @@ wangmen

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

-Back.png
+Right.gif
 file




 2011-08-17T00:10:49.000000Z
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@@ -92,16 +92,16 @@ has-props



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 mkustagi
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diff --git a/geworkbench-core/classes/org/.svn/all-wcprops b/geworkbench-core/classes/org/.svn/all-wcprops
index 8d577aa..1ed356e 100644
--- a/geworkbench-core/classes/org/.svn/all-wcprops
+++ b/geworkbench-core/classes/org/.svn/all-wcprops
@@ -1,5 +1,5 @@
 K 25
 svn:wc:ra_dav:version-url
-V 57
-/svn/geworkbench/!svn/ver/8965/trunk/geworkbench/test/org
+V 56
+/svn/geworkbench/!svn/ver/9328/trunk/geworkbench/src/org
 END
diff --git a/geworkbench-core/classes/org/.svn/entries b/geworkbench-core/classes/org/.svn/entries
index a03e180..ce0af74 100644
--- a/geworkbench-core/classes/org/.svn/entries
+++ b/geworkbench-core/classes/org/.svn/entries
@@ -1,14 +1,14 @@
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 dir
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 zji


diff --git a/geworkbench-core/classes/org/geworkbench/.svn/all-wcprops b/geworkbench-core/classes/org/geworkbench/.svn/all-wcprops
index 4e80bfc..a30df0b 100644
--- a/geworkbench-core/classes/org/geworkbench/.svn/all-wcprops
+++ b/geworkbench-core/classes/org/geworkbench/.svn/all-wcprops
@@ -1,5 +1,5 @@
 K 25
 svn:wc:ra_dav:version-url
-V 69
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+V 68
+/svn/geworkbench/!svn/ver/9328/trunk/geworkbench/src/org/geworkbench
 END
diff --git a/geworkbench-core/classes/org/geworkbench/.svn/entries b/geworkbench-core/classes/org/geworkbench/.svn/entries
index 1b74978..f69e434 100644
--- a/geworkbench-core/classes/org/geworkbench/.svn/entries
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@@ -1,14 +1,14 @@
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@@ -26,22 +26,22 @@ zji

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diff --git a/geworkbench-core/classes/org/geworkbench/analysis/.svn/all-wcprops b/geworkbench-core/classes/org/geworkbench/analysis/.svn/all-wcprops
index 215893d..a78f5d8 100644
--- a/geworkbench-core/classes/org/geworkbench/analysis/.svn/all-wcprops
+++ b/geworkbench-core/classes/org/geworkbench/analysis/.svn/all-wcprops
@@ -1,7 +1,7 @@
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 svn:wc:ra_dav:version-url
 V 77
-/svn/geworkbench/!svn/ver/8990/trunk/geworkbench/src/org/geworkbench/analysis
+/svn/geworkbench/!svn/ver/9244/trunk/geworkbench/src/org/geworkbench/analysis
 END
 AbstractAnalysisLabelComparator.java
 K 25
@@ -25,7 +25,7 @@ AbstractAnalysis.java
 K 25
 svn:wc:ra_dav:version-url
 V 99
-/svn/geworkbench/!svn/ver/8990/trunk/geworkbench/src/org/geworkbench/analysis/AbstractAnalysis.java
+/svn/geworkbench/!svn/ver/9244/trunk/geworkbench/src/org/geworkbench/analysis/AbstractAnalysis.java
 END
 AbstractSaveableParameterPanel.java
 K 25
diff --git a/geworkbench-core/classes/org/geworkbench/analysis/.svn/entries b/geworkbench-core/classes/org/geworkbench/analysis/.svn/entries
index a16de53..94783dc 100644
--- a/geworkbench-core/classes/org/geworkbench/analysis/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/analysis/.svn/entries
@@ -1,14 +1,14 @@
 10

 dir
-9024
+9328
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/analysis
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2012-03-07T19:21:35.661934Z
-8990
+2012-03-30T20:50:22.917946Z
+9244
 zji


@@ -26,18 +26,17 @@ zji

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

-AbstractAnalysis.java
+AbstractAnalysisLabelComparator.java
 file




-2012-03-08T18:51:46.000000Z
-f68fff73048d34b6a68b8c7853bda193
-2012-03-07T19:21:35.661934Z
-8990
+2011-08-17T00:10:49.000000Z
+3833c4721fd3a60ac6f06ab9d5bde6ac
+2010-02-26T21:15:07.709772Z
+6085
 zji
-has-props



@@ -58,19 +57,20 @@ has-props



-24546
+
+475

-AbstractAnalysisLabelComparator.java
+ReHighlightable.java
 file




 2011-08-17T00:10:49.000000Z
-3833c4721fd3a60ac6f06ab9d5bde6ac
-2010-02-26T21:15:07.709772Z
-6085
-zji
+e50d8d2b53f984cb6539b3b4145358a4
+2009-05-27T21:36:54.000000Z
+5144
+jiz



@@ -92,20 +92,19 @@ zji



-475
+340

-AbstractGridAnalysis.java
+HighlightCurrentParameterThread.java
 file




 2011-08-17T00:10:49.000000Z
-599708e9177a8d443e82ff7f8ba2c9dd
-2010-11-28T01:06:12.895894Z
-7231
-zji
-has-props
+f0b767724d9006cb3bb49651cd19cf12
+2009-05-27T21:36:54.000000Z
+5144
+jiz



@@ -126,18 +125,19 @@ has-props



-3237
+
+522

-AbstractSaveableParameterPanel.java
+AbstractAnalysis.java
 file




-2011-08-17T00:10:49.000000Z
-797bb5598cea2e47b13b476741433166
-2011-02-24T04:32:15.323159Z
-7483
+2012-04-19T14:07:32.000000Z
+6b3fbc1fa4e7eabf8601a7bb0b46969a
+2012-03-30T20:50:22.917946Z
+9244
 zji
 has-props

@@ -160,20 +160,20 @@ has-props



-5794
+24424

-HighlightCurrentParameterThread.java
+AbstractSaveableParameterPanel.java
 file




 2011-08-17T00:10:49.000000Z
-f0b767724d9006cb3bb49651cd19cf12
-2009-05-27T21:36:54.000000Z
-5144
-jiz
-
+797bb5598cea2e47b13b476741433166
+2011-02-24T04:32:15.323159Z
+7483
+zji
+has-props



@@ -194,7 +194,7 @@ jiz



-522
+5794

 ParameterKey.java
 file
@@ -230,18 +230,18 @@ keshav

 1371

-ReHighlightable.java
+AbstractGridAnalysis.java
 file




 2011-08-17T00:10:49.000000Z
-e50d8d2b53f984cb6539b3b4145358a4
-2009-05-27T21:36:54.000000Z
-5144
-jiz
-
+599708e9177a8d443e82ff7f8ba2c9dd
+2010-11-28T01:06:12.895894Z
+7231
+zji
+has-props



@@ -262,5 +262,5 @@ jiz



-340
+3237

diff --git a/geworkbench-core/classes/org/geworkbench/analysis/.svn/text-base/AbstractAnalysis.java.svn-base b/geworkbench-core/classes/org/geworkbench/analysis/.svn/text-base/AbstractAnalysis.java.svn-base
index 404cad7..033d1a6 100644
--- a/geworkbench-core/classes/org/geworkbench/analysis/.svn/text-base/AbstractAnalysis.java.svn-base
+++ b/geworkbench-core/classes/org/geworkbench/analysis/.svn/text-base/AbstractAnalysis.java.svn-base
@@ -34,7 +34,6 @@ import org.geworkbench.bison.model.analysis.ParameterPanel;
 import org.geworkbench.engine.config.PluginRegistry;
 import org.geworkbench.engine.management.ComponentClassLoader;
 import org.geworkbench.util.FilePathnameUtils;
-import org.ginkgo.labs.util.FileTools;

 /**
  * <p>
@@ -63,6 +62,8 @@ public abstract class AbstractAnalysis implements Analysis, Serializable,

 	private static final String XML = "xml";
 	private static final String FILE_EXTENSION_SEPARATOR = ".";
+	private static final String NEWLINE = "\n";
+	private static final String TAB = "\t";

 	private static final String ERR_TXT = FilePathnameUtils
 			.getUserSettingDirectoryPath() + "err.txt";
@@ -692,7 +693,7 @@ public abstract class AbstractAnalysis implements Analysis, Serializable,
 		StringBuilder ans = new StringBuilder(
 				"=The MicroarraySetView used for analysis: ");
 		/* Generate text for microarrays/groups */
-		ans.append(FileTools.NEWLINE);
+		ans.append(NEWLINE);
 		try {
 			log.debug("We got a " + maSetView.items().getClass().toString());
 			if (maSetView.items().getClass() == CSPanel.class) {
@@ -702,29 +703,29 @@ public abstract class AbstractAnalysis implements Analysis, Serializable,

 				ans.append("==Used Microarray Sets [")
 						.append(paneltest.size() + "]==")
-						.append(FileTools.NEWLINE);
+						.append(NEWLINE);
 				for (DSPanel<DSMicroarray> temp : paneltest) {
-					ans.append(FileTools.TAB + temp.toString()).append(
-							FileTools.NEWLINE);
+					ans.append(TAB + temp.toString()).append(
+							NEWLINE);
 					for (DSMicroarray temp2 : temp) {
-						ans.append(FileTools.TAB).append(FileTools.TAB)
+						ans.append(TAB).append(TAB)
 								.append(temp2.toString())
-								.append(FileTools.NEWLINE);
+								.append(NEWLINE);
 					}
 				}
 			} else if (maSetView.items().getClass() == CSMicroarraySet.class) {
 				log.debug("situation 2: microarraySets not selected");
 				CSMicroarraySet exprSet = (CSMicroarraySet) maSetView.items();
 				ans.append("==Used Microarrays [").append(exprSet.size())
-						.append("]==").append(FileTools.NEWLINE);
+						.append("]==").append(NEWLINE);
 				for (Iterator<DSMicroarray> iterator = exprSet.iterator(); iterator
 						.hasNext();) {
 					DSMicroarray array = iterator.next();
-					ans.append(FileTools.TAB).append(array.getLabel())
-							.append(FileTools.NEWLINE);
+					ans.append(TAB).append(array.getLabel())
+							.append(NEWLINE);
 				}
 			}
-			ans.append("==End of Microarray Sets==").append(FileTools.NEWLINE);
+			ans.append("==End of Microarray Sets==").append(NEWLINE);
 			/* Generate text for markers */

 			if (useMarkersFromSelector) {
@@ -750,15 +751,15 @@ public abstract class AbstractAnalysis implements Analysis, Serializable,
 					log.debug("situation 5: All Markers selected.");
 					DSItemList<DSGeneMarker> markers = maSetView.allMarkers();
 					ans .append( "==Used Markers [" ).append( markers.size() ).append( "]==" )
-							.append( FileTools.NEWLINE );
+							.append( NEWLINE );
 					for (DSGeneMarker marker : markers) {
-						ans .append( FileTools.TAB ).append( marker.getLabel()
-						).append( FileTools.NEWLINE );
+						ans .append( TAB ).append( marker.getLabel()
+						).append( NEWLINE );
 					}
 				}


-				ans.append("==End of Used Markers==").append(FileTools.NEWLINE);
+				ans.append("==End of Used Markers==").append(NEWLINE);
 			}
 		} catch (ClassCastException cce) {
 			/* it's not a DSPanel, we generate nothing for panel part */
@@ -771,14 +772,14 @@ public abstract class AbstractAnalysis implements Analysis, Serializable,
 	@SuppressWarnings("rawtypes")
 	public String generateHistoryStringForGeneralDataSet(DSDataSet dataset) {
 		if (dataset == null) {
-			return "No information on the data set." + FileTools.NEWLINE;
+			return "No information on the data set." + NEWLINE;
 		} else {
 			StringBuilder sb = new StringBuilder();
 			sb.append("The data set used for analysis is [ ");
 			sb.append(dataset.getDataSetName());
 			sb.append(" ] from file [ ");
 			sb.append(dataset.getFile());
-			sb.append(" ]." + FileTools.NEWLINE);
+			sb.append(" ]." + NEWLINE);
 			return sb.toString();
 		}
 	}
diff --git a/geworkbench-core/classes/org/geworkbench/bison/.svn/all-wcprops b/geworkbench-core/classes/org/geworkbench/bison/.svn/all-wcprops
index 5801e09..dd51772 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/.svn/all-wcprops
+++ b/geworkbench-core/classes/org/geworkbench/bison/.svn/all-wcprops
@@ -1,5 +1,5 @@
 K 25
 svn:wc:ra_dav:version-url
 V 74
-/svn/geworkbench/!svn/ver/8955/trunk/geworkbench/src/org/geworkbench/bison
+/svn/geworkbench/!svn/ver/9288/trunk/geworkbench/src/org/geworkbench/bison
 END
diff --git a/geworkbench-core/classes/org/geworkbench/bison/.svn/entries b/geworkbench-core/classes/org/geworkbench/bison/.svn/entries
index 11d7277..bee27b8 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/bison/.svn/entries
@@ -1,15 +1,15 @@
 10

 dir
-9024
+9328
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/bison
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2012-03-05T17:45:18.759987Z
-8955
-zji
+2012-04-07T01:05:03.331060Z
+9288
+maz



@@ -26,19 +26,19 @@ zji

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

-algorithm
+parsers
 dir

-annotation
+model
 dir

-datastructure
+algorithm
 dir

-model
+annotation
 dir

-parsers
+datastructure
 dir

 util
diff --git a/geworkbench-core/classes/org/geworkbench/bison/algorithm/.svn/entries b/geworkbench-core/classes/org/geworkbench/bison/algorithm/.svn/entries
index cdfe89a..2c611c3 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/algorithm/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/bison/algorithm/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-9024
+9328
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/bison/algorithm
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/bison/algorithm/classification/.svn/entries b/geworkbench-core/classes/org/geworkbench/bison/algorithm/classification/.svn/entries
index ecef810..459b2c4 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/algorithm/classification/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/bison/algorithm/classification/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-9024
+9328
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/bison/algorithm/classification
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/bison/annotation/.svn/entries b/geworkbench-core/classes/org/geworkbench/bison/annotation/.svn/entries
index 189a66e..cc9a89d 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/annotation/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/bison/annotation/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-9024
+9328
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/bison/annotation
 https://ncisvn.nci.nih.gov/svn/geworkbench

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

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

-CSAnnotationContext.java
+CSAnnotationContextManager.java
 file




-2011-08-17T00:10:49.000000Z
-41e1112d59762ea6739dd25c6caa822b
-2010-10-15T22:52:00.856412Z
-7129
+2012-01-10T19:15:27.000000Z
+768395cda43573fb5ba4705178f671b8
+2011-10-03T21:38:59.636724Z
+8357
 zji
 has-props

@@ -58,16 +58,16 @@ has-props



-20869
+7111

-CSAnnotationContextManager.java
+DSAnnotationContextManager.java
 file




 2012-01-10T19:15:27.000000Z
-768395cda43573fb5ba4705178f671b8
+844a9976aaead4bd8f293738704c5171
 2011-10-03T21:38:59.636724Z
 8357
 zji
@@ -92,18 +92,18 @@ has-props



-7111
+4375

-DSAnnotationContext.java
+CSAnnotationContext.java
 file




 2011-08-17T00:10:49.000000Z
-6200fd2973a368422fe2088b1016009b
-2010-10-15T21:07:02.633731Z
-7126
+41e1112d59762ea6739dd25c6caa822b
+2010-10-15T22:52:00.856412Z
+7129
 zji
 has-props

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



-12695
+20869

-DSAnnotationContextManager.java
+DSAnnotationContext.java
 file




-2012-01-10T19:15:27.000000Z
-844a9976aaead4bd8f293738704c5171
-2011-10-03T21:38:59.636724Z
-8357
+2011-08-17T00:10:49.000000Z
+6200fd2973a368422fe2088b1016009b
+2010-10-15T21:07:02.633731Z
+7126
 zji
 has-props

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



-4375
+12695

diff --git a/geworkbench-core/classes/org/geworkbench/bison/datastructure/.svn/all-wcprops b/geworkbench-core/classes/org/geworkbench/bison/datastructure/.svn/all-wcprops
index 83e4927..b34edbe 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/datastructure/.svn/all-wcprops
+++ b/geworkbench-core/classes/org/geworkbench/bison/datastructure/.svn/all-wcprops
@@ -1,5 +1,5 @@
 K 25
 svn:wc:ra_dav:version-url
 V 88
-/svn/geworkbench/!svn/ver/8955/trunk/geworkbench/src/org/geworkbench/bison/datastructure
+/svn/geworkbench/!svn/ver/9288/trunk/geworkbench/src/org/geworkbench/bison/datastructure
 END
diff --git a/geworkbench-core/classes/org/geworkbench/bison/datastructure/.svn/entries b/geworkbench-core/classes/org/geworkbench/bison/datastructure/.svn/entries
index 3a82e65..48c6cd6 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/datastructure/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/bison/datastructure/.svn/entries
@@ -1,15 +1,15 @@
 10

 dir
-9024
+9328
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/bison/datastructure
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2012-03-05T17:45:18.759987Z
-8955
-zji
+2012-04-07T01:05:03.331060Z
+9288
+maz



@@ -26,15 +26,15 @@ zji

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

-biocollections
-dir
-
 bioobjects
 dir

 complex
 dir

+biocollections
+dir
+
 properties
 dir

diff --git a/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/.svn/all-wcprops b/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/.svn/all-wcprops
index 4fd10de..724da60 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/.svn/all-wcprops
+++ b/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/.svn/all-wcprops
@@ -1,13 +1,13 @@
 K 25
 svn:wc:ra_dav:version-url
 V 103
-/svn/geworkbench/!svn/ver/8761/trunk/geworkbench/src/org/geworkbench/bison/datastructure/biocollections
+/svn/geworkbench/!svn/ver/9265/trunk/geworkbench/src/org/geworkbench/bison/datastructure/biocollections
 END
 AdjacencyMatrix.java
 K 25
 svn:wc:ra_dav:version-url
 V 124
-/svn/geworkbench/!svn/ver/8424/trunk/geworkbench/src/org/geworkbench/bison/datastructure/biocollections/AdjacencyMatrix.java
+/svn/geworkbench/!svn/ver/9265/trunk/geworkbench/src/org/geworkbench/bison/datastructure/biocollections/AdjacencyMatrix.java
 END
 GoAnalysisResult.java
 K 25
diff --git a/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/.svn/entries b/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/.svn/entries
index aca3c4e..665b7d8 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/.svn/entries
@@ -1,15 +1,15 @@
 10

 dir
-9024
+9328
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/bison/datastructure/biocollections
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2012-01-25T17:34:14.733766Z
-8761
-zji
+2012-04-04T16:04:58.112473Z
+9265
+youmi



@@ -26,17 +26,23 @@ zji

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

+gsea
+dir
+
+pca
+dir
+
 AdjacencyMatrix.java
 file




-2012-01-10T19:15:27.000000Z
-159ca6b228e894302037743d650959b5
-2011-10-19T16:34:53.735246Z
-8424
-zji
+2012-04-19T14:07:37.000000Z
+2f356c679bfc4f80942e79cc0d396081
+2012-04-04T16:04:58.112473Z
+9265
+youmi
 has-props


@@ -58,19 +64,19 @@ has-props



-8341
+9817

-AdjacencyMatrixDataSet.java
+GoAnalysisResult.java
 file




-2012-01-10T21:28:37.000000Z
-fa9193ebfc68a232ad769233774dbdda
-2012-01-06T17:16:16.839429Z
-8665
-youmi
+2012-01-10T19:15:27.000000Z
+c37d8a97b16a5a8e093b9dc296f669ed
+2011-11-02T15:43:58.696033Z
+8481
+zji
 has-props


@@ -92,7 +98,7 @@ has-props



-9308
+7068

 CSAncillaryDataSet.java
 file
@@ -128,16 +134,16 @@ has-props

 1101

-CSDataSet.java
+CSMarkerVector.java
 file




 2012-01-10T19:15:27.000000Z
-4c9592c8241a19f296a64bd33fe4bfb7
-2011-11-02T13:48:00.049131Z
-8478
+57dafbfa3f882bf292ad0a4ee08e3e3f
+2011-10-27T20:30:19.075377Z
+8466
 zji
 has-props

@@ -160,18 +166,18 @@ has-props



-8321
+8097

-CSMarkerVector.java
+CSDataSet.java
 file




 2012-01-10T19:15:27.000000Z
-57dafbfa3f882bf292ad0a4ee08e3e3f
-2011-10-27T20:30:19.075377Z
-8466
+4c9592c8241a19f296a64bd33fe4bfb7
+2011-11-02T13:48:00.049131Z
+8478
 zji
 has-props

@@ -194,7 +200,7 @@ has-props



-8097
+8321

 DSAncillaryDataSet.java
 file
@@ -230,17 +236,23 @@ has-props

 433

-DSDataSet.java
+microarrays
+dir
+
+sequences
+dir
+
+AdjacencyMatrixDataSet.java
 file




-2012-01-10T19:15:27.000000Z
-d459b1ef0a1fa55928c4f49f797b304f
-2011-10-17T18:11:10.752549Z
-8410
-zji
+2012-01-10T21:28:37.000000Z
+fa9193ebfc68a232ad769233774dbdda
+2012-01-06T17:16:16.839429Z
+8665
+youmi
 has-props


@@ -262,18 +274,18 @@ has-props



-3334
+9308

-GoAnalysisResult.java
+DSDataSet.java
 file




 2012-01-10T19:15:27.000000Z
-c37d8a97b16a5a8e093b9dc296f669ed
-2011-11-02T15:43:58.696033Z
-8481
+d459b1ef0a1fa55928c4f49f797b304f
+2011-10-17T18:11:10.752549Z
+8410
 zji
 has-props

@@ -296,23 +308,11 @@ has-props



-7068
+3334

-gsea
+views
 dir

 medusa
 dir

-microarrays
-dir
-
-pca
-dir
-
-sequences
-dir
-
-views
-dir
-
diff --git a/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/.svn/text-base/AdjacencyMatrix.java.svn-base b/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/.svn/text-base/AdjacencyMatrix.java.svn-base
index 7cf77ae..0fea791 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/.svn/text-base/AdjacencyMatrix.java.svn-base
+++ b/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/.svn/text-base/AdjacencyMatrix.java.svn-base
@@ -30,10 +30,18 @@ public class AdjacencyMatrix implements Serializable {
 		private static final long serialVersionUID = 8884626375173162244L;
 		public float value;
 		public String type;
+		public Short evidenceId;

 		EdgeInfo(float value, String type) {
 			this.value = value;
 			this.type = type;
+			this.evidenceId = 0;
+		}
+
+		EdgeInfo(float value, String type, Short evidenceId) {
+			this.value = value;
+			this.type = type;
+			this.evidenceId = evidenceId;
 		}

 		@Override
@@ -46,9 +54,9 @@ public class AdjacencyMatrix implements Serializable {
 			if (type == null || edgeInfo.type == null)
 				return true;

-			if (edgeInfo.type.equals(this.type)	)
+			if (edgeInfo.type.equals(this.type))
 				return true;
-		    else
+		    else
 				return false;
 		}

@@ -162,6 +170,7 @@ public class AdjacencyMatrix implements Serializable {
 	private final String name;

 	private final Map<String, String> interactionTypeSifMap; // TODO check ?
+	private final Map<String, String> interactionEvidenceMap;

     private Set<Node> nodeSet = new HashSet<Node>();

@@ -171,6 +180,7 @@ public class AdjacencyMatrix implements Serializable {
 		this.name = name;
 		maSet = microarraySet;
 		interactionTypeSifMap = null;
+		interactionEvidenceMap = null;
 		log.debug("AdjacencyMatrix created with label " + name
 				+ " and microarray set " + maSet.getDataSetName());
 	}
@@ -181,11 +191,25 @@ public class AdjacencyMatrix implements Serializable {
 		this.name = name;
 		maSet = microarraySet;
 		this.interactionTypeSifMap = interactionTypeSifMap;
+		interactionEvidenceMap = null;
+		log.debug("AdjacencyMatrix created with label " + name
+				+ " and microarray set " + maSet.getDataSetName()
+				+ ", with interaction type map");
+	}
+
+	public AdjacencyMatrix(String name,
+			final DSMicroarraySet microarraySet,
+			Map<String, String> interactionTypeSifMap, Map<String, String> interactionEvidenceMap) {
+		this.name = name;
+		maSet = microarraySet;
+		this.interactionTypeSifMap = interactionTypeSifMap;
+		this.interactionEvidenceMap = interactionEvidenceMap;
 		log.debug("AdjacencyMatrix created with label " + name
 				+ " and microarray set " + maSet.getDataSetName()
 				+ ", with interaction type map");
 	}

+
 	/**
 	 * Returns a map with all the edges to geneId. This is only used by
 	 * master regulator analysis.
@@ -230,6 +254,34 @@ public class AdjacencyMatrix implements Serializable {
 	public String getLabel() {
 		return name;
 	}
+
+	/**
+	 * Adds and edge between geneId1 and geneId2.
+	 *
+	 */
+	public void add(Node node1, Node node2, float edge, String interaction, Short evidenceId) {
+
+		HashMap<Node, Set<EdgeInfo>> row = geneRows.get(node1);
+		if (row == null) {
+			row = new HashMap<Node, Set<EdgeInfo>>();
+			geneRows.put(node1, row);
+			nodeSet.add(node1);
+		}
+
+		Set<EdgeInfo> edgeSet = row.get(node2);
+		if (edgeSet == null)
+		{
+			edgeSet = new HashSet<EdgeInfo>();
+			nodeSet.add(node2);
+		}
+
+	    edgeSet.add(new EdgeInfo(edge, interaction, evidenceId));
+
+
+		row.put(node2, edgeSet);
+
+	}
+

 	/**
 	 * Adds and edge between geneId1 and geneId2.
@@ -298,6 +350,10 @@ public class AdjacencyMatrix implements Serializable {
 		return interactionTypeSifMap;
 	}

+	public Map<String, String> getInteractionEvidenceMap() {
+		return interactionEvidenceMap;
+	}
+
 	public static class Edge {
 		public Node node1;
 		public Node node2;
diff --git a/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/gsea/.svn/entries b/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/gsea/.svn/entries
index ddc49b9..2639c92 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/gsea/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/gsea/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-9024
+9328
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/bison/datastructure/biocollections/gsea
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/medusa/.svn/entries b/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/medusa/.svn/entries
index 9bbaebf..f989a92 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/medusa/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/medusa/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-9024
+9328
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/bison/datastructure/biocollections/medusa
 https://ncisvn.nci.nih.gov/svn/geworkbench

@@ -26,18 +26,18 @@ zji

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

-MedusaCommand.java
+MedusaDataSet.java
 file




-2011-12-29T06:13:04.000000Z
-f660ea1560bf45f6e22f9d301a184f30
-2010-03-11T20:48:36.492576Z
-6128
-wangmen
-
+2012-01-10T19:15:27.000000Z
+0e8490bacaf5f4c08914f450569b5408
+2011-11-02T15:43:58.696033Z
+8481
+zji
+has-props



@@ -58,7 +58,7 @@ wangmen



-2998
+1193

 MedusaData.java
 file
@@ -94,18 +94,17 @@ zji

 1736

-MedusaDataSet.java
+MedusaCommand.java
 file




-2012-01-10T19:15:27.000000Z
-0e8490bacaf5f4c08914f450569b5408
-2011-11-02T15:43:58.696033Z
-8481
-zji
-has-props
+2011-12-29T06:13:04.000000Z
+f660ea1560bf45f6e22f9d301a184f30
+2010-03-11T20:48:36.492576Z
+6128
+wangmen



@@ -126,5 +125,6 @@ has-props



-1193
+
+2998

diff --git a/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/microarrays/.svn/entries b/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/microarrays/.svn/entries
index 869e815..4dff461 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/microarrays/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/microarrays/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-9024
+9328
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/bison/datastructure/biocollections/microarrays
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/pca/.svn/entries b/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/pca/.svn/entries
index 65ca23e..5a0190d 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/pca/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/pca/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-9024
+9328
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/bison/datastructure/biocollections/pca
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/sequences/.svn/entries b/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/sequences/.svn/entries
index 2b30184..de78a8e 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/sequences/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/sequences/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-9024
+9328
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/bison/datastructure/biocollections/sequences
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/views/.svn/entries b/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/views/.svn/entries
index cca721f..219b554 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/views/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/views/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-9024
+9328
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/bison/datastructure/biocollections/views
 https://ncisvn.nci.nih.gov/svn/geworkbench

@@ -60,16 +60,16 @@ has-props

 7210

-DSDataSetView.java
+DSMicroarraySetView.java
 file




-2011-12-29T06:13:04.000000Z
-8f0746c7731fa1e8cd5d91eefb8ca01e
-2011-01-25T19:36:05.950308Z
-7385
+2012-01-10T19:15:27.000000Z
+76d624296f9ca1f58ff744f5abaa43c2
+2011-10-19T16:34:53.735246Z
+8424
 zji
 has-props

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



-1001
+3062

-DSMicroarraySetView.java
+DSDataSetView.java
 file




-2012-01-10T19:15:27.000000Z
-76d624296f9ca1f58ff744f5abaa43c2
-2011-10-19T16:34:53.735246Z
-8424
+2011-12-29T06:13:04.000000Z
+8f0746c7731fa1e8cd5d91eefb8ca01e
+2011-01-25T19:36:05.950308Z
+7385
 zji
 has-props

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



-3062
+1001

diff --git a/geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/.svn/all-wcprops b/geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/.svn/all-wcprops
index 0bbacc9..fd3d8b9 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/.svn/all-wcprops
+++ b/geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/.svn/all-wcprops
@@ -1,7 +1,7 @@
 K 25
 svn:wc:ra_dav:version-url
 V 99
-/svn/geworkbench/!svn/ver/8818/trunk/geworkbench/src/org/geworkbench/bison/datastructure/bioobjects
+/svn/geworkbench/!svn/ver/9288/trunk/geworkbench/src/org/geworkbench/bison/datastructure/bioobjects
 END
 DSClassification.java
 K 25
@@ -31,7 +31,7 @@ IdeaEdge.java
 K 25
 svn:wc:ra_dav:version-url
 V 113
-/svn/geworkbench/!svn/ver/7296/trunk/geworkbench/src/org/geworkbench/bison/datastructure/bioobjects/IdeaEdge.java
+/svn/geworkbench/!svn/ver/9240/trunk/geworkbench/src/org/geworkbench/bison/datastructure/bioobjects/IdeaEdge.java
 END
 IdeaGLoc.java
 K 25
@@ -69,6 +69,12 @@ svn:wc:ra_dav:version-url
 V 118
 /svn/geworkbench/!svn/ver/7305/trunk/geworkbench/src/org/geworkbench/bison/datastructure/bioobjects/IdeaProbeGene.java
 END
+SamResultData.java
+K 25
+svn:wc:ra_dav:version-url
+V 118
+/svn/geworkbench/!svn/ver/9286/trunk/geworkbench/src/org/geworkbench/bison/datastructure/bioobjects/SamResultData.java
+END
 KMeansResult.java
 K 25
 svn:wc:ra_dav:version-url
diff --git a/geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/.svn/entries b/geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/.svn/entries
index 561ddd4..b326fbf 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/.svn/entries
@@ -1,14 +1,14 @@
 10

 dir
-9024
+9328
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/bison/datastructure/bioobjects
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2012-01-31T22:07:39.967902Z
-8818
+2012-04-07T01:05:03.331060Z
+9288
 maz


@@ -26,17 +26,17 @@ maz

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

-DSBioObject.java
+KMeansResultMarkers.java
 file




-2011-08-17T00:10:50.000000Z
-b4881ef5121d9cf4578d4ee789299b4a
-2006-03-03T18:05:24.000000Z
-1317
-mhall
+2012-01-10T19:15:28.000000Z
+209e761e2d371e2d83e942eebb7a9ad4
+2011-10-19T16:34:53.735246Z
+8424
+zji
 has-props


@@ -58,20 +58,19 @@ has-props



-377
+2398

-DSClassification.java
+IdeaResultDataSet.java
 file




-2011-08-17T00:10:50.000000Z
-4d86b64d8591358fc3538a8237fff7b6
-2006-01-13T17:35:07.000000Z
-1115
-watkin
-has-props
+2012-01-10T19:15:27.000000Z
+995a6ccbb9a5f44c403072b2de6ea6a1
+2011-11-02T15:43:58.696033Z
+8481
+zji



@@ -92,20 +91,20 @@ has-props



-724
+
+1438

-DSPValued.java
+IdeaGLoc.java
 file




-2011-08-17T00:10:50.000000Z
-c8f83949b536e6eebebee9583a59bd28
-2006-01-13T17:35:07.000000Z
-1115
-watkin
-has-props
+2012-01-10T19:15:27.000000Z
+dda175d92cb80ed50818890750f26209
+2011-09-06T22:30:11.516277Z
+8254
+maz



@@ -126,20 +125,20 @@ has-props



-395
+
+1869

-FoldChangeResult.java
+IdeaNode.java
 file




 2012-01-10T19:15:27.000000Z
-d8f035a61df88cb3ce2b9e1537d0dd05
-2011-11-02T15:43:58.696033Z
-8481
-zji
-has-props
+f584cb4d22b0f0c7dd7e953a4c6802b0
+2011-09-06T22:30:11.516277Z
+8254
+maz



@@ -160,20 +159,21 @@ has-props



-700
+
+2025

-IdeaEdge.java
+IdeaModule.java
 file




-2011-08-17T00:10:50.000000Z
-ea57aa0c85ebc8839222acf2d25f3b38
-2010-12-06T22:31:56