Added web version of geworkbench and a stubby genspace

Jonathan Bell [2012-04-12 20:57:19]
Added web version of geworkbench and a stubby genspace
Filename
genspace-authPlugin/src/org/geworkbench/components/genspace/server/auth/GELoginModule.java
genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/GenericUsageInformation.java
genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/MahoutRecommender.java
genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/mahout/GenspaceMySQLJDBCDataModel.java
genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/mahout/GenspaceUserSimilarity.java
geworkbench-core/.DS_Store
geworkbench-core/.classpath
geworkbench-core/.settings/.svn/entries
geworkbench-core/.svn/all-wcprops
geworkbench-core/.svn/entries
geworkbench-core/.svn/tmp/.classpath.tmp
geworkbench-core/.svn/tmp/build.xml.tmp
geworkbench-core/bin/.svn/entries
geworkbench-core/bin/matrixreduce/.svn/entries
geworkbench-core/cascripts/.svn/entries
geworkbench-core/classes/.svn/entries
geworkbench-core/classes/.svn/tmp/application.properties.tmp
geworkbench-core/classes/cruisecontrol/.svn/entries
geworkbench-core/classes/images/.svn/entries
geworkbench-core/classes/org/.svn/all-wcprops
geworkbench-core/classes/org/.svn/entries
geworkbench-core/classes/org/geworkbench/.svn/all-wcprops
geworkbench-core/classes/org/geworkbench/.svn/entries
geworkbench-core/classes/org/geworkbench/analysis/.svn/all-wcprops
geworkbench-core/classes/org/geworkbench/analysis/.svn/entries
geworkbench-core/classes/org/geworkbench/analysis/.svn/text-base/AbstractAnalysis.java.svn-base
geworkbench-core/classes/org/geworkbench/bison/.svn/entries
geworkbench-core/classes/org/geworkbench/bison/algorithm/.svn/entries
geworkbench-core/classes/org/geworkbench/bison/algorithm/classification/.svn/entries
geworkbench-core/classes/org/geworkbench/bison/annotation/.svn/entries
geworkbench-core/classes/org/geworkbench/bison/datastructure/.svn/entries
geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/.svn/entries
geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/gsea/.svn/entries
geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/medusa/.svn/entries
geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/microarrays/.svn/entries
geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/pca/.svn/entries
geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/sequences/.svn/entries
geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/views/.svn/entries
geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/.svn/entries
geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/markers/.svn/entries
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geworkbench-web/src/org/geworkbenchweb/components/genspace/ui/GenSpaceWindow.java
geworkbench-web/src/org/geworkbenchweb/components/genspace/ui/component/GenSpaceLogin.java
geworkbench-web/src/org/geworkbenchweb/components/genspace/ui/component/GenSpaceProfile.java
geworkbench-web/src/org/geworkbenchweb/components/genspace/ui/component/GenSpaceTab.java
geworkbench-web/src/org/geworkbenchweb/components/genspace/ui/component/RealTimeWorkflowSuggestion.java
geworkbench-web/src/org/geworkbenchweb/components/genspace/ui/component/WorkflowStatistics.java
geworkbench-web/src/org/geworkbenchweb/components/genspace/ui/component/WorkflowVisualization.java
geworkbench-web/src/org/geworkbenchweb/components/genspace/wrapper/ToolWrapper.java
geworkbench-web/src/org/geworkbenchweb/components/genspace/wrapper/UserWrapper.java
geworkbench-web/src/org/geworkbenchweb/components/genspace/wrapper/WorkflowWrapper.java
geworkbench-web/src/org/geworkbenchweb/dataset/.svn/all-wcprops
geworkbench-web/src/org/geworkbenchweb/dataset/.svn/entries
geworkbench-web/src/org/geworkbenchweb/dataset/.svn/prop-base/DataSetParser.java.svn-base
geworkbench-web/src/org/geworkbenchweb/dataset/.svn/prop-base/DataSetUpload.java.svn-base
geworkbench-web/src/org/geworkbenchweb/dataset/.svn/text-base/DataSetParser.java.svn-base
geworkbench-web/src/org/geworkbenchweb/dataset/.svn/text-base/DataSetUpload.java.svn-base
geworkbench-web/src/org/geworkbenchweb/dataset/DataSetParser.java
geworkbench-web/src/org/geworkbenchweb/dataset/DataSetUpload.java
geworkbench-web/src/org/geworkbenchweb/interactions/.svn/all-wcprops
geworkbench-web/src/org/geworkbenchweb/interactions/.svn/entries
geworkbench-web/src/org/geworkbenchweb/interactions/CNKB/.svn/all-wcprops
geworkbench-web/src/org/geworkbenchweb/interactions/CNKB/.svn/entries
geworkbench-web/src/org/geworkbenchweb/interactions/CNKB/.svn/text-base/CNKBInteractions.java.svn-base
geworkbench-web/src/org/geworkbenchweb/interactions/CNKB/.svn/text-base/CNKBParamForm.java.svn-base
geworkbench-web/src/org/geworkbenchweb/interactions/CNKB/.svn/text-base/Constants.java.svn-base
geworkbench-web/src/org/geworkbenchweb/interactions/CNKB/.svn/text-base/InteractionParticipant.java.svn-base
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/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/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/VisualPlugin.java
geworkbench-web/src/org/geworkbenchweb/pojos/.svn/all-wcprops
geworkbench-web/src/org/geworkbenchweb/pojos/.svn/entries
geworkbench-web/src/org/geworkbenchweb/pojos/.svn/prop-base/DataSet.java.svn-base
geworkbench-web/src/org/geworkbenchweb/pojos/.svn/text-base/DataSet.java.svn-base
geworkbench-web/src/org/geworkbenchweb/pojos/.svn/text-base/ResultSet.java.svn-base
geworkbench-web/src/org/geworkbenchweb/pojos/.svn/text-base/SubSet.java.svn-base
geworkbench-web/src/org/geworkbenchweb/pojos/DataSet.java
geworkbench-web/src/org/geworkbenchweb/pojos/ResultSet.java
geworkbench-web/src/org/geworkbenchweb/pojos/SubSet.java
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/SetOperations.java.svn-base
geworkbench-web/src/org/geworkbenchweb/utils/SetOperations.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/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/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/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/TreeData.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/TreeData.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/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/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/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/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/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
diff --git a/genspace-authPlugin/src/org/geworkbench/components/genspace/server/auth/GELoginModule.java b/genspace-authPlugin/src/org/geworkbench/components/genspace/server/auth/GELoginModule.java
index ff9332f..eacf939 100644
--- a/genspace-authPlugin/src/org/geworkbench/components/genspace/server/auth/GELoginModule.java
+++ b/genspace-authPlugin/src/org/geworkbench/components/genspace/server/auth/GELoginModule.java
@@ -61,22 +61,27 @@ public class GELoginModule extends AppservPasswordLoginModule {

 		try {
             Connection conn = getConnection();
-			PreparedStatement s = conn.prepareStatement("SELECT id FROM registration where username=? and password=?");
+			PreparedStatement s = conn.prepareStatement("SELECT id,password FROM registration where username=?");
 			s.setString(1, _username);
+			String password;
 			if(_password.length() == 40)
-				s.setString(2, _password);
+				password =  _password;
 			else
-				s.setString(2, getEncryptedPassword(_password));
+				password = getEncryptedPassword(_password);
 			s.execute();
 			ResultSet rs = s.getResultSet();
 			if(rs.next())
 			{
-				String[] groups = new String[1];
-				groups[0] = "users";
-
-				commitUserAuthentication(groups);
-				conn.close();
-				return;
+				String dbPass = rs.getString(2);
+				if(dbPass.equalsIgnoreCase(password))
+				{
+					String[] groups = new String[1];
+					groups[0] = "users";
+
+					commitUserAuthentication(groups);
+					conn.close();
+					return;
+				}
 			}
         } catch (Exception ex) {
             LoginException le = new LoginException("Unable to read username/password or connect to database");
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 a398d60..c777c11 100644
--- a/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/GenericUsageInformation.java
+++ b/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/GenericUsageInformation.java
@@ -426,6 +426,8 @@ public abstract class GenericUsageInformation extends AbstractFacade<Tool>
 		for (WorkflowTool t : e.getTransaction().getWorkflow().getTools()) {
 			t.getTool();
 		}
+
+		getEntityManager().detach(e.getTransaction().getWorkflow());
 		e.getTransaction().getWorkflow().setParent(null);
 		e.getTransaction().getWorkflow().setChildren(new ArrayList<Workflow>());
 		return e.getTransaction();
diff --git a/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/MahoutRecommender.java b/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/MahoutRecommender.java
index 64151c6..62216d9 100644
--- a/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/MahoutRecommender.java
+++ b/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/MahoutRecommender.java
@@ -7,9 +7,11 @@ import java.util.Map;
 import java.util.Set;
 import java.util.Vector;

+import javax.ejb.EJB;
 import javax.ejb.LocalBean;
 import javax.ejb.Stateful;
 import javax.ejb.Schedule;
+import javax.ejb.Stateless;
 import javax.jws.WebMethod;
 import javax.jws.WebService;
 import javax.persistence.EntityManager;
@@ -44,254 +46,46 @@ import org.geworkbench.components.genspace.server.mahout.GenspaceItemSimilarity;
 import org.geworkbench.components.genspace.server.mahout.GenspaceMySQLJDBCDataModel;
 import org.geworkbench.components.genspace.server.mahout.GenspaceSimilarWorkflowRecommender;
 import org.geworkbench.components.genspace.server.mahout.GenspaceUserSimilarity;
+import org.geworkbench.components.genspace.server.mahout.MahoutSingleton;
 import org.geworkbench.components.genspace.server.stubs.GetAllWorkflowsIncluding;

 /**
  * Session Bean implementation class MahoutRecommender
  */
 //@WebService
-@Stateful
+@Stateless
 public class MahoutRecommender implements MahoutRecommenderLocal {
+	@EJB MahoutSingleton mahoutSingleton;

-	@PersistenceContext(unitName="genspace_persist") private EntityManager em;
-
-    public MahoutRecommender() {
-
-    }
-
-    @Resource(name="jdbc/GenSpaceDB")
-	DataSource dataSource;
-
-    private CachingItemSimilarity cachingItemSimilarity;
-    private CachingUserSimilarity cachingUserSimilarity;
-    private CachingUserSimilarity cachingUserNetworkSimilarity;
-    private CachingRecommender cachingItemRecommender;
-    private GenspaceMySQLJDBCDataModel mysqlModel;
-    private ReloadFromJDBCDataModel model;
-
-    private static int RECOMMENDATIONS = 5;
-    private static int NEIGHBORHOOD = 5;
-
-    @PostConstruct
-    public void initialize() {
-    	try {
-			mysqlModel =
-				new GenspaceMySQLJDBCDataModel(dataSource, "mahout_view", "taste_users_id", "workflow_id", "preference", "timestamp", "network_id");
-			model = new ReloadFromJDBCDataModel(mysqlModel);
-
-			HashMap<Long, Vector<Integer>> networkMap;
-			HashMap<Long, Long> parentMap;
-			networkMap = mysqlModel.getUserNetworks();
-			parentMap = mysqlModel.getParentMap();
-
-			ItemSimilarity genspaceItemSimilarity = new GenspaceItemSimilarity(model, parentMap);
-
-			UserSimilarity userSimilarity = new GenspaceUserSimilarity(model, 0, networkMap);
-			UserSimilarity userNetworkSimilarity = new GenspaceUserSimilarity(model, 1, networkMap);
-
-			cachingItemSimilarity = new CachingItemSimilarity(genspaceItemSimilarity, model);
-			cachingItemRecommender =
-				new CachingRecommender(new GenspaceItemRecommender(model, cachingItemSimilarity));
-
-			cachingUserSimilarity = new CachingUserSimilarity(userSimilarity, model);
-			cachingUserNetworkSimilarity = new CachingUserSimilarity(userNetworkSimilarity, model);
-
-		} catch (TasteException e) {
-			e.printStackTrace();
-		}
-    }
-
-    @WebMethod
 	@Override
 	public void refresh() {
-    	try {
-			model.refresh(null);
-
-			HashMap<Long, Vector<Integer>> networkMap;
-			HashMap<Long, Long> parentMap;
-			networkMap = mysqlModel.getUserNetworks();
-			parentMap = mysqlModel.getParentMap();
-
-			ItemSimilarity genspaceItemSimilarity = new GenspaceItemSimilarity(model, parentMap);
-
-			UserSimilarity userSimilarity = new GenspaceUserSimilarity(model, 0, networkMap);
-			UserSimilarity userNetworkSimilarity = new GenspaceUserSimilarity(model, 1, networkMap);
-
-			cachingItemSimilarity = new CachingItemSimilarity(genspaceItemSimilarity, model);
-			cachingItemRecommender =
-				new CachingRecommender(new GenspaceItemRecommender(model, cachingItemSimilarity));
-
-			cachingUserSimilarity = new CachingUserSimilarity(userSimilarity, model);
-			cachingUserNetworkSimilarity = new CachingUserSimilarity(userNetworkSimilarity, model);
-
-		} catch (TasteException e) {
-			e.printStackTrace();
-		}
+		mahoutSingleton.refresh();
 	}

-    @WebMethod
 	@Override
 	public List<Workflow> getToolSuggestions(int userId, int filterMethod) {
-
-    	List<Workflow> ret = new ArrayList<Workflow>();
-		try {
-
-			List<RecommendedItem> recommendations = cachingItemRecommender.recommend(userId, RECOMMENDATIONS);
-			if (recommendations != null) {
-				for (RecommendedItem recommendedItem : recommendations) {
-					Workflow wf = em.find(Workflow.class, new Integer(new Long (recommendedItem.getItemID()).toString()));
-					ret.add(wf.slimDown());
-	        	}
-			}
-		} catch (Exception e) {
-			e.printStackTrace();
-		}
-		return ret;
+		return mahoutSingleton.getToolsSuggestionsForUser(userId, filterMethod);
 	}

-    @WebMethod
 	@Override
 	public List<TasteUser> getUserSuggestions(int userId, int filterMethod) {
-		List<TasteUser> ret = new ArrayList<TasteUser>();
-		try {
-
-			if (filterMethod == 0) {
-				UserNeighborhood neighborhood = new NearestNUserNeighborhood(NEIGHBORHOOD, cachingUserSimilarity, model);
-
-				long[] ids = neighborhood.getUserNeighborhood(userId);
-				for (Long id : ids) {
-					ret.add(em.find(TasteUser.class, new Integer(id.toString())));
-				}
-			} else {
-				UserNeighborhood neighborhood = new NearestNUserNeighborhood(NEIGHBORHOOD, cachingUserNetworkSimilarity, model);
-
-				long[] ids = neighborhood.getUserNeighborhood(userId);
-				for (Long id : ids) {
-					ret.add(em.find(TasteUser.class, new Integer(id.toString())));
-				}
-			}
-		} catch (Exception e) {
-			e.printStackTrace();
-		}
-		return ret;
-	}
-
-    @WebMethod
-	@Override
-    public List<Workflow> getToolsSuggestionsForUser(int userId, int filterMethod) {
-		List<Workflow> ret = new ArrayList<Workflow>();
-
-		try {
-
-			if (filterMethod == 0) {
-				UserNeighborhood neighborhood = new NearestNUserNeighborhood(NEIGHBORHOOD, cachingUserSimilarity, model);
-
-				Recommender toolsRecommender =
-		        	new GenericUserBasedRecommender(model, neighborhood, cachingUserSimilarity);
-				List<RecommendedItem> recommendations = toolsRecommender.recommend(userId, RECOMMENDATIONS);
-				if (recommendations != null) {
-					for (RecommendedItem recommendedItem : recommendations) {
-						Workflow wf = em.find(Workflow.class, new Integer(new Long (recommendedItem.getItemID()).toString()));
-						ret.add(wf.slimDown());
-		        	}
-				}
-			} else {
-				UserNeighborhood neighborhood = new NearestNUserNeighborhood(NEIGHBORHOOD, cachingUserNetworkSimilarity, model);
-				Recommender toolsRecommender =
-		        	new GenericUserBasedRecommender(model, neighborhood, cachingUserNetworkSimilarity);
-
-				List<RecommendedItem> recommendations = toolsRecommender.recommend(userId, RECOMMENDATIONS);
-				if (recommendations != null) {
-					for (RecommendedItem recommendedItem : recommendations) {
-						Workflow wf = em.find(Workflow.class, new Integer(new Long (recommendedItem.getItemID()).toString()));
-						ret.add(wf.slimDown());
-		        	}
-				}
-			}
-		} catch (Exception e) {
-			e.printStackTrace();
-		}
-		return ret;
+		return mahoutSingleton.getUserSuggestions(userId, filterMethod);
 	}

 	@Override
 	public List<Workflow> getSimilarWorkflows(List<Tool> tools) {
-
-		String criteriaString = "(";
-		List<Integer> toolsIds = new ArrayList<Integer>();
-		for (Tool t : tools) {
-			toolsIds.add(t.getId());
-			criteriaString += "wt.tool_id=" + t.getId() + " or ";
-		}
-		criteriaString = criteriaString.substring(0, criteriaString.length()-4);
-		criteriaString += ") ";
-
-		System.out.println(criteriaString);
-
-		List<Workflow> ret = new ArrayList<Workflow>();
-
-		Query q = em.createNativeQuery(
-				"select tu.* " +
-				"from " +
-				"(select taste_users_id, workflow_id " +
-				"from TRANSACTION " +
-				"group by taste_users_id, workflow_id) as t, WORKFLOWTOOL wt, TASTE_USERS tu " +
-				"where t.workflow_id = wt.workflow_id and " +
-				"tu.id = t.taste_users_id and "+ criteriaString +
-				"group by t.taste_users_id order by count(*) desc limit 1 ",
-				TasteUser.class);
-		TasteUser tu = null;
-		try {
-			tu = (TasteUser) q.getSingleResult();
-		} catch (NoResultException e) {
-
-		}
-
-		if (tu == null)
-			return null;
-		else {
-			Integer tasteUserId = tu.getId();
-			ret = getToolsSuggestionsForUser(tasteUserId, 0);
-			return ret;
-		}
-
+		return mahoutSingleton.getSimilarWorkflows(tools);
 	}
-
+
 	@Override
 	public List<Workflow> getSimilarUserWorkflows(int userId, int filterMethod) {
-
-		List<Workflow> ret = new ArrayList<Workflow>();
-		try {
-
-			// No Filtering
-			if (filterMethod == 0) {
-
-				UserNeighborhood neighborhood = new NearestNUserNeighborhood(NEIGHBORHOOD, cachingUserSimilarity, model);
-				CachingRecommender cachingRecommender =
-		        	new CachingRecommender(new GenericUserBasedRecommender(model, neighborhood, cachingUserSimilarity));
-				List<RecommendedItem> recommendations = cachingRecommender.recommend(userId, RECOMMENDATIONS);
-				if (recommendations != null) {
-					for (RecommendedItem recommendedItem : recommendations) {
-						Workflow wf = em.find(Workflow.class, new Integer(new Long (recommendedItem.getItemID()).toString()));
-						ret.add(wf.slimDown());
-					}
-				}
-			} else { // Filtering within network
-
-				UserNeighborhood neighborhood = new NearestNUserNeighborhood(NEIGHBORHOOD, cachingUserNetworkSimilarity, model);
-				CachingRecommender cachingRecommender =
-		        	new CachingRecommender(new GenericUserBasedRecommender(model, neighborhood, cachingUserNetworkSimilarity));
-				List<RecommendedItem> recommendations = cachingRecommender.recommend(userId, RECOMMENDATIONS);
-				if (recommendations != null) {
-					for (RecommendedItem recommendedItem : recommendations) {
-						Workflow wf = em.find(Workflow.class, new Integer(new Long (recommendedItem.getItemID()).toString()));
-						ret.add(wf.slimDown());
-					}
-				}
-			}
-		} catch (Exception e) {
-			e.printStackTrace();
-		}
-		return ret;
+		return mahoutSingleton.getSimilarUserWorkflows(userId, filterMethod);
 	}
+
+	@Override
+	public List<Workflow> getToolsSuggestionsForUser(int userId,
+			int filterMethod) {
+		return mahoutSingleton.getToolsSuggestionsForUser(userId, filterMethod);
+	}
+
 }
diff --git a/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/mahout/GenspaceMySQLJDBCDataModel.java b/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/mahout/GenspaceMySQLJDBCDataModel.java
index 3c5ed0a..70c7f6c 100644
--- a/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/mahout/GenspaceMySQLJDBCDataModel.java
+++ b/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/mahout/GenspaceMySQLJDBCDataModel.java
@@ -94,7 +94,30 @@ public class GenspaceMySQLJDBCDataModel extends AbstractJDBCDataModel{
 	    	IOUtils.quietClose(rs, stmt, conn);
 	    }
 	}
-
+	public HashMap<Long, Integer> getUserVisibility() throws TasteException {
+
+	    Connection conn = null;
+	    PreparedStatement stmt = null;
+	    ResultSet rs = null;
+	    HashMap<Long, Integer> hashMap = new HashMap<Long, Integer>();
+	    try {
+	      conn = super.getDataSource().getConnection();
+	      stmt = conn.prepareStatement("SELECT t.ID,case when r.DATAVISIBILITY is null then 2 else r.DATAVISIBILITY end as DATAVISIBILITY FROM taste_users t left join registration r on r.id=t.registration_id");
+
+	      rs = stmt.executeQuery();
+	      while (rs.next()) {
+	        long userId = rs.getLong(1);
+	        int visible = rs.getInt(2);
+	        hashMap.put(userId, visible);
+	      }
+	        return hashMap;
+	    } catch (SQLException sqle) {
+	      throw new TasteException(sqle);
+	    } finally {
+	      IOUtils.quietClose(rs, stmt, conn);
+	    }
+	  }
+
 	public HashMap<Long, Vector<Integer>> getUserNetworks() throws TasteException {

 	    Connection conn = null;
diff --git a/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/mahout/GenspaceUserSimilarity.java b/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/mahout/GenspaceUserSimilarity.java
index 45dad67..597cd9f 100644
--- a/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/mahout/GenspaceUserSimilarity.java
+++ b/genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/mahout/GenspaceUserSimilarity.java
@@ -18,12 +18,14 @@ public class GenspaceUserSimilarity implements UserSimilarity{
 	private UserSimilarity spearmanDistance;
 	private int filtering;
 	private HashMap<Long, Vector<Integer>> networkMap;
+	private HashMap<Long, Integer> visibilityMap;

-	public GenspaceUserSimilarity(DataModel model, int filtering, HashMap<Long, Vector<Integer>> networkMap) throws TasteException {
+	public GenspaceUserSimilarity(DataModel model, int filtering, HashMap<Long, Vector<Integer>> networkMap, HashMap<Long, Integer> visibilityMap) throws TasteException {
 		//euclideanDistance = new EuclideanDistanceSimilarity(model);
 		spearmanDistance = new SpearmanCorrelationSimilarity(model);
 		this.filtering = filtering;
 		this.networkMap = networkMap;
+		this.visibilityMap = visibilityMap;
 	}

 	@Override
@@ -43,11 +45,11 @@ public class GenspaceUserSimilarity implements UserSimilarity{
 		double spearmanSimilarity = spearmanDistance.userSimilarity(userID1, userID2);
 		Vector<Integer> networks1;
 		Vector<Integer> networks2;
-		if (filtering == 0)
-			return spearmanSimilarity;
-
-		else if (filtering == 1) {
-			double r = 0;
+		if(visibilityMap.get(userID1) == 0 || visibilityMap.get(userID2) == 0)
+		{
+			return Double.NaN;
+		}
+			double r = 0;
 			networks1 = networkMap.get(userID1);
 			networks2 = networkMap.get(userID2);

@@ -67,15 +69,18 @@ public class GenspaceUserSimilarity implements UserSimilarity{
 					}
 				}
 			}
-			if (equalItems != 0) {
-				double n = (double) equalItems / size;
-				r = 2*n - 1; // r is within [-1;1]
-				double similarity = spearmanSimilarity *3/4 + r*1/4;
-				return similarity;
-			} else
+			if( (visibilityMap.get(userID1) == 1 || visibilityMap.get(userID2) == 1) && equalItems == 0)
 				return Double.NaN;
-		}
-		else
+			if(filtering == 1)
+				if (equalItems != 0) {
+					double n = (double) equalItems / size;
+					r = 2*n - 1; // r is within [-1;1]
+					double similarity = spearmanSimilarity *3/4 + r*1/4;
+					return similarity;
+				} else
+					return Double.NaN;
+//			System.out.println("Checking " + userID1 + ", " + userID2 +"->" + spearmanSimilarity);
+
 			return spearmanSimilarity;
 	}
 }
diff --git a/geworkbench-core/.DS_Store b/geworkbench-core/.DS_Store
index 9477d3e..ffecf2b 100644
Binary files a/geworkbench-core/.DS_Store and b/geworkbench-core/.DS_Store differ
diff --git a/geworkbench-core/.classpath b/geworkbench-core/.classpath
index 8406c32..d99a412 100755
--- a/geworkbench-core/.classpath
+++ b/geworkbench-core/.classpath
@@ -1,61 +1,73 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
-	<classpathentry kind="src" path="conf"/>
-	<classpathentry kind="src" path="src"/>
-	<classpathentry kind="src" path="test"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER">
-		<attributes>
-			<attribute name="org.eclipse.jdt.launching.CLASSPATH_ATTR_LIBRARY_PATH_ENTRY" value="geworkbench-core/lib"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry exported="true" kind="lib" path="lib/AffxFusion.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/ant.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/ant-launcher.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/bcel-5.1.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/cglib-nodep-2.1.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/collections-generic-4.0.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/commons-beanutils.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/commons-collections.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/commons-digester.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/commons-discovery.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/commons-logging.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/docking.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/forms-1.0.5.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/jai_codec.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/jai_core.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/jaxb-rt-1.0-ea.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/jaxrpc.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/jcommon-1.0.5.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/jdom.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/jfreechart-1.0.2.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/jhall.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/jsr173_api.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/log4j-1.2.8.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/mail.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/ostermillerutils_1_04_03_for_kaffe.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/stax-1.2.0_rc1-dev.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/xml-apis.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/commons-codec-1.3.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/j3dcore.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/j3dutils.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/vecmath.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/commons-lang-2.4.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/ginkgo-0.1-SNAPSHOT.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/commons-math-2.2.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/commons-httpclient-3.1.jar"/>
-	<classpathentry kind="lib" path="lib/xalan.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/junit.jar"/>
-	<classpathentry kind="lib" path="lib/jaxen.jar"/>
-	<classpathentry kind="lib" path="lib/axis2-kernel-1.5.3.jar"/>
-	<classpathentry kind="lib" path="lib/axiom-api-1.2.10.jar"/>
-	<classpathentry kind="lib" path="lib/axiom-impl-1.2.10.jar"/>
-	<classpathentry kind="lib" path="lib/axis2-adb-1.5.3.jar"/>
-	<classpathentry kind="lib" path="lib/wsdl4j-1.6.2.jar"/>
-	<classpathentry kind="lib" path="lib/XmlSchema-1.4.3.jar"/>
-	<classpathentry kind="lib" path="lib/neethi-2.0.4.jar"/>
-	<classpathentry kind="lib" path="lib/axis2-transport-local-1.5.3.jar"/>
-	<classpathentry kind="lib" path="lib/axis2-transport-http-1.5.3.jar"/>
-	<classpathentry kind="lib" path="lib/httpcore-4.0.jar"/>
-	<classpathentry kind="lib" path="lib/axis2-upload-client.jar"/>
-	<classpathentry kind="output" path="classes"/>
-</classpath>
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="src" path="conf"/>
+	<classpathentry kind="src" path="src"/>
+	<classpathentry kind="src" path="test"/>
+	<classpathentry kind="src" path="components/genspace/src"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER">
+		<attributes>
+			<attribute name="org.eclipse.jdt.launching.CLASSPATH_ATTR_LIBRARY_PATH_ENTRY" value="geworkbench-core/lib"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry exported="true" kind="lib" path="lib/AffxFusion.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/ant.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/ant-launcher.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/bcel-5.1.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/cglib-nodep-2.1.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/collections-generic-4.0.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/commons-beanutils.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/commons-collections.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/commons-digester.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/commons-discovery.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/commons-logging.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/docking.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/forms-1.0.5.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/jai_codec.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/jai_core.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/jaxb-rt-1.0-ea.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/jaxrpc.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/jcommon-1.0.5.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/jdom.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/jfreechart-1.0.2.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/jhall.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/jsr173_api.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/log4j-1.2.8.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/mail.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/ostermillerutils_1_04_03_for_kaffe.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/stax-1.2.0_rc1-dev.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/xml-apis.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/commons-codec-1.3.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/j3dcore.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/j3dutils.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/vecmath.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/commons-lang-2.4.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/ginkgo-0.1-SNAPSHOT.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/commons-math-2.2.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/commons-httpclient-3.1.jar"/>
+	<classpathentry kind="lib" path="lib/xalan.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/junit.jar"/>
+	<classpathentry kind="lib" path="lib/jaxen.jar"/>
+	<classpathentry kind="lib" path="lib/axis2-kernel-1.5.3.jar"/>
+	<classpathentry kind="lib" path="lib/axiom-api-1.2.10.jar"/>
+	<classpathentry kind="lib" path="lib/axiom-impl-1.2.10.jar"/>
+	<classpathentry kind="lib" path="lib/axis2-adb-1.5.3.jar"/>
+	<classpathentry kind="lib" path="lib/wsdl4j-1.6.2.jar"/>
+	<classpathentry kind="lib" path="lib/XmlSchema-1.4.3.jar"/>
+	<classpathentry kind="lib" path="lib/neethi-2.0.4.jar"/>
+	<classpathentry kind="lib" path="lib/axis2-transport-local-1.5.3.jar"/>
+	<classpathentry kind="lib" path="lib/axis2-transport-http-1.5.3.jar"/>
+	<classpathentry kind="lib" path="lib/httpcore-4.0.jar"/>
+	<classpathentry kind="lib" path="lib/axis2-upload-client.jar"/>
+	<classpathentry kind="lib" path="components/genspace/lib/axis2-saaj-1.5.4.jar"/>
+	<classpathentry kind="lib" path="components/genspace/lib/genspace-common.jar"/>
+	<classpathentry kind="lib" path="components/genspace/lib/ha-api.jar"/>
+	<classpathentry kind="lib" path="components/genspace/lib/intellij.jar"/>
+	<classpathentry kind="lib" path="components/genspace/lib/jgraphx.jar"/>
+	<classpathentry kind="lib" path="components/genspace/lib/jimi.jar"/>
+	<classpathentry kind="lib" path="components/genspace/lib/mina-core-1.1.7.jar"/>
+	<classpathentry kind="lib" path="components/genspace/lib/persistence-common.jar"/>
+	<classpathentry kind="lib" path="components/genspace/lib/smack.jar"/>
+	<classpathentry kind="lib" path="components/genspace/lib/smackx.jar"/>
+	<classpathentry kind="lib" path="components/genspace/lib/swing-layout-1.0.3.jar"/>
+	<classpathentry kind="output" path="classes"/>
+</classpath>
diff --git a/geworkbench-core/.settings/.svn/entries b/geworkbench-core/.settings/.svn/entries
index 61208be..882ef4d 100644
--- a/geworkbench-core/.settings/.svn/entries
+++ b/geworkbench-core/.settings/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8955
+9024
 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 33bea38..addad8d 100644
--- a/geworkbench-core/.svn/all-wcprops
+++ b/geworkbench-core/.svn/all-wcprops
@@ -1,43 +1,81 @@
+END
+caWorkbenchLicense.txt
 K 25
 svn:wc:ra_dav:version-url
-V 48
-/svn/geworkbench/!svn/ver/8955/trunk/geworkbench
+V 70
+/svn/geworkbench/!svn/ver/971/trunk/geworkbench/caWorkbenchLicense.txt
 END
-java.policy
+tests.sh
 K 25
 svn:wc:ra_dav:version-url
-V 58
-/svn/geworkbench/!svn/ver/50/trunk/geworkbench/java.policy
+V 57
+/svn/geworkbench/!svn/ver/1909/trunk/geworkbench/tests.sh
 END
-buildremotecomponents.xml
+geWorkbenchLicense.txt
 K 25
 svn:wc:ra_dav:version-url
-V 74
-/svn/geworkbench/!svn/ver/6424/trunk/geworkbench/buildremotecomponents.xml
+V 71
+/svn/geworkbench/!svn/ver/6786/trunk/geworkbench/geWorkbenchLicense.txt
 END
-deploycomponents.txt
+devBuild.xml
 K 25
 svn:wc:ra_dav:version-url
-V 69
-/svn/geworkbench/!svn/ver/6424/trunk/geworkbench/deploycomponents.txt
+V 61
+/svn/geworkbench/!svn/ver/5737/trunk/geworkbench/devBuild.xml
 END
-devLib.txt
+.cvsignore
 K 25
 svn:wc:ra_dav:version-url
 V 59
-/svn/geworkbench/!svn/ver/1317/trunk/geworkbench/devLib.txt
+/svn/geworkbench/!svn/ver/5187/trunk/geworkbench/.cvsignore
 END
-ReleaseNotes_2.0.0.txt
+makeGear.bat
 K 25
 svn:wc:ra_dav:version-url
-V 71
-/svn/geworkbench/!svn/ver/6969/trunk/geworkbench/ReleaseNotes_2.0.0.txt
+V 61
+/svn/geworkbench/!svn/ver/1160/trunk/geworkbench/makeGear.bat
 END
-.project
+build-component.xml
 K 25
 svn:wc:ra_dav:version-url
-V 57
-/svn/geworkbench/!svn/ver/2393/trunk/geworkbench/.project
+V 68
+/svn/geworkbench/!svn/ver/7318/trunk/geworkbench/build-component.xml
+END
+Bcell-100.exp_ARACNe_AP_threshold.txt
+K 25
+svn:wc:ra_dav:version-url
+V 86
+/svn/geworkbench/!svn/ver/5271/trunk/geworkbench/Bcell-100.exp_ARACNe_AP_threshold.txt
+END
+tests.xml
+K 25
+svn:wc:ra_dav:version-url
+V 58
+/svn/geworkbench/!svn/ver/1893/trunk/geworkbench/tests.xml
+END
+launch_geworkbench.sh
+K 25
+svn:wc:ra_dav:version-url
+V 70
+/svn/geworkbench/!svn/ver/1658/trunk/geworkbench/launch_geworkbench.sh
+END
+Bcell-100.exp_ARACNe_FBW_kernel.txt
+K 25
+svn:wc:ra_dav:version-url
+V 84
+/svn/geworkbench/!svn/ver/5271/trunk/geworkbench/Bcell-100.exp_ARACNe_FBW_kernel.txt
+END
+devSource.txt
+K 25
+svn:wc:ra_dav:version-url
+V 62
+/svn/geworkbench/!svn/ver/1317/trunk/geworkbench/devSource.txt
+END
+ReleaseNotes_2.0.0.txt
+K 25
+svn:wc:ra_dav:version-url
+V 71
+/svn/geworkbench/!svn/ver/6969/trunk/geworkbench/ReleaseNotes_2.0.0.txt
 END
 ReleaseNotes_2.0.1.txt
 K 25
@@ -51,6 +89,12 @@ svn:wc:ra_dav:version-url
 V 71
 /svn/geworkbench/!svn/ver/7051/trunk/geworkbench/ReleaseNotes_2.1.0.txt
 END
+caWorkbench_Readme_v3.0.txt
+K 25
+svn:wc:ra_dav:version-url
+V 75
+/svn/geworkbench/!svn/ver/798/trunk/geworkbench/caWorkbench_Readme_v3.0.txt
+END
 ReleaseNotes_2.0.2.txt
 K 25
 svn:wc:ra_dav:version-url
@@ -63,12 +107,6 @@ svn:wc:ra_dav:version-url
 V 71
 /svn/geworkbench/!svn/ver/7925/trunk/geworkbench/ReleaseNotes_2.2.0.txt
 END
-caWorkbench_Readme_v3.0.txt
-K 25
-svn:wc:ra_dav:version-url
-V 75
-/svn/geworkbench/!svn/ver/798/trunk/geworkbench/caWorkbench_Readme_v3.0.txt
-END
 ReleaseNotes_2.2.1.txt
 K 25
 svn:wc:ra_dav:version-url
@@ -87,17 +125,23 @@ svn:wc:ra_dav:version-url
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-	<classpathentry exported="true" kind="lib" path="lib/jaxb-rt-1.0-ea.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/jaxrpc.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/jcommon-1.0.5.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/jdom.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/jfreechart-1.0.2.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/jhall.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/jsr173_api.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/log4j-1.2.8.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/mail.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/ostermillerutils_1_04_03_for_kaffe.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/stax-1.2.0_rc1-dev.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/xml-apis.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/commons-codec-1.3.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/j3dcore.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/j3dutils.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/vecmath.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/commons-lang-2.4.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/ginkgo-0.1-SNAPSHOT.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/commons-math-2.2.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/commons-httpclient-3.1.jar"/>
-	<classpathentry kind="lib" path="lib/xalan.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/junit.jar"/>
-	<classpathentry kind="lib" path="lib/jaxen.jar"/>
-	<classpathentry kind="lib" path="lib/axis2-kernel-1.5.3.jar"/>
-	<classpathentry kind="lib" path="lib/axiom-api-1.2.10.jar"/>
-	<classpathentry kind="lib" path="lib/axiom-impl-1.2.10.jar"/>
-	<classpathentry kind="lib" path="lib/axis2-adb-1.5.3.jar"/>
-	<classpathentry kind="lib" path="lib/wsdl4j-1.6.2.jar"/>
-	<classpathentry kind="lib" path="lib/XmlSchema-1.4.3.jar"/>
-	<classpathentry kind="lib" path="lib/neethi-2.0.4.jar"/>
-	<classpathentry kind="lib" path="lib/axis2-transport-local-1.5.3.jar"/>
-	<classpathentry kind="lib" path="lib/axis2-transport-http-1.5.3.jar"/>
-	<classpathentry kind="lib" path="lib/httpcore-4.0.jar"/>
-	<classpathentry kind="lib" path="lib/axis2-upload-client.jar"/>
-	<classpathentry kind="output" path="classes"/>
-</classpath>
->>>>>>> .r8955
diff --git a/geworkbench-core/.svn/tmp/build.xml.tmp b/geworkbench-core/.svn/tmp/build.xml.tmp
deleted file mode 100644
index 156a9d0..0000000
--- a/geworkbench-core/.svn/tmp/build.xml.tmp
+++ /dev/null
@@ -1,649 +0,0 @@
-<?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="genspace" />
-				<include name="geworkbench-core" />
-				<!--
-				<include name="gpmodule_v3_0" />
-				-->
-				<include name="hierarchicalclustering" />
-				<include name="idea" />
-				<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 the dead projets -->
-				<exclude name="skylinecontour" />
-			</dirset>
-		</subant>
-	</target>
-	<!-- ====================================================================== -->
-	<!-- CREATE   DISTRIBUTION-->
-	<!-- ====================================================================== -->
-	<target name="createDist" depends="compile, jar" description="Creating a new folder for depositing...">
-		<java classname="org.geworkbench.components.versioninfo.VersionInfoDialog" failonerror="true" >
-			<arg value="./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="${components}/genspace/**/*" />
-				<include name="${components}/gpmodule_v3_0/**/*" />
-				<include name="${components}/hierarchicalclustering/**/*" />
-				<include name="${components}/idea/**/*" />
-				<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>
-</project>
diff --git a/geworkbench-core/bin/.svn/entries b/geworkbench-core/bin/.svn/entries
index eed9178..8364724 100644
--- a/geworkbench-core/bin/.svn/entries
+++ b/geworkbench-core/bin/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8955
+9024
 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 92412f8..17d37a1 100644
--- a/geworkbench-core/bin/matrixreduce/.svn/entries
+++ b/geworkbench-core/bin/matrixreduce/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8955
+9024
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/bin/matrixreduce
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/cascripts/.svn/entries b/geworkbench-core/cascripts/.svn/entries
index fa3f6b5..3f802f7 100644
--- a/geworkbench-core/cascripts/.svn/entries
+++ b/geworkbench-core/cascripts/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8955
+9024
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/cascripts
 https://ncisvn.nci.nih.gov/svn/geworkbench

@@ -26,17 +26,17 @@ xiaoqing

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

-workflow2.script
+gridbasic.script
 file




 2011-08-17T00:10:35.000000Z
-9831cd21fa385ec4ce97a3744d19fc72
-2007-06-21T18:52:02.000000Z
-3033
-xiaoqing
+23ee1fb373ca32a06711a8f080fe5310
+2007-05-10T17:37:53.000000Z
+2801
+mhall
 has-props


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



-1205
+896

-gridbasic.script
+workflow1.script
 file




 2011-08-17T00:10:35.000000Z
-23ee1fb373ca32a06711a8f080fe5310
-2007-05-10T17:37:53.000000Z
-2801
-mhall
+7b81b0a496613cfb3165d7c9d02aa73f
+2007-06-21T17:19:43.000000Z
+3029
+xiaoqing
 has-props


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



-896
+2333

-workflow1.script
+workflow2.script
 file




 2011-08-17T00:10:35.000000Z
-7b81b0a496613cfb3165d7c9d02aa73f
-2007-06-21T17:19:43.000000Z
-3029
+9831cd21fa385ec4ce97a3744d19fc72
+2007-06-21T18:52:02.000000Z
+3033
 xiaoqing
 has-props

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



-2333
+1205

diff --git a/geworkbench-core/classes/.svn/entries b/geworkbench-core/classes/.svn/entries
index f8d860f..76a3f6e 100644
--- a/geworkbench-core/classes/.svn/entries
+++ b/geworkbench-core/classes/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8955
+9024
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/conf
 https://ncisvn.nci.nih.gov/svn/geworkbench

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

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

-client-config.wsdd
+.cvsignore
 file




-2012-01-10T18:25:38.000000Z
-55fbd4c6f381a12079f184b8dbbdf9db
-2007-01-11T15:24:36.000000Z
-2201
+2011-08-17T00:10:46.000000Z
+1f0e698e6ea28e2e6f42e158c681f0e3
+2007-04-16T17:08:58.000000Z
+2683
 keshav
 has-props

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



-6954
+18

-jdic.properties
+ConfigurationFile Schema.xsd
 file




 2011-08-17T00:10:46.000000Z
-7690eeda2362b576a4194f3b987ec36f
-2009-05-11T19:10:11.000000Z
-5104
-wangm
-
+bfc038fcb40d61c20b0422c636abbfac
+2006-01-12T20:06:11.000000Z
+1109
+watkin
+has-props



@@ -92,19 +92,19 @@ wangm



-39
+5861

-ConfigurationFile Schema.xsd
+Descriptor Schema.xsd
 file




 2011-08-17T00:10:46.000000Z
-bfc038fcb40d61c20b0422c636abbfac
-2006-01-12T20:06:11.000000Z
-1109
-watkin
+f3895ec116d9797752da2ea5b20ce009
+2010-03-10T18:05:11.708079Z
+6114
+maz
 has-props


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



-5861
+9253

 all.xml
 file
@@ -162,16 +162,16 @@ has-props

 3127

-log4j.properties
+application.properties
 file




-2011-08-17T00:19:06.000000Z
-0d8902552aed687e66fe82f456984b32
-2011-05-25T14:25:11.688972Z
-7925
+2012-03-05T20:23:31.000000Z
+11fa199565bf0f48f655523b02ffd5ef
+2012-02-27T22:42:50.953800Z
+8924
 zji
 has-props

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



-898
-
-cruisecontrol
-dir
+4419

-Descriptor Schema.xsd
+client-config.wsdd
 file




-2011-08-17T00:10:46.000000Z
-f3895ec116d9797752da2ea5b20ce009
-2010-03-10T18:05:11.708079Z
-6114
-maz
+2012-01-10T18:25:38.000000Z
+55fbd4c6f381a12079f184b8dbbdf9db
+2007-01-11T15:24:36.000000Z
+2201
+keshav
 has-props


@@ -231,20 +228,22 @@ has-props



-9253
+6954

-.cvsignore
+cruisecontrol
+dir
+
+jdic.properties
 file




 2011-08-17T00:10:46.000000Z
-1f0e698e6ea28e2e6f42e158c681f0e3
-2007-04-16T17:08:58.000000Z
-2683
-keshav
-has-props
+7690eeda2362b576a4194f3b987ec36f
+2009-05-11T19:10:11.000000Z
+5104
+wangm



@@ -265,18 +264,40 @@ has-props



-18
+
+39

-application.properties
+log4j.properties
 file




-
-11fa199565bf0f48f655523b02ffd5ef
-2012-02-27T22:42:50.953800Z
-8924
+2011-08-17T00:19:06.000000Z
+0d8902552aed687e66fe82f456984b32
+2011-05-25T14:25:11.688972Z
+7925
 zji
 has-props
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
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+898

diff --git a/geworkbench-core/classes/.svn/tmp/application.properties.tmp b/geworkbench-core/classes/.svn/tmp/application.properties.tmp
deleted file mode 100644
index 039e1bf..0000000
--- a/geworkbench-core/classes/.svn/tmp/application.properties.tmp
+++ /dev/null
@@ -1,118 +0,0 @@
-# The security policy for running the JVM needs to be modified for
-# performing caBIO queries
-java.security.policy=java.policy
-
-# Required for caBIO
-gov.nih.nci.caBIO.manager.dir=coreMgrDir.txt
-
-# Please modify to set path to your browser executable
-browser.path="C\:\\Program Files\\Internet Explorer\\IEXPLORE.EXE"
-
-# This is the file name where analyses parameter indices are stored
-analyses.parameter.file.name=parameterDB.index
-
-# This is the directory where temporary files are created
-temporary.files.directory=temp/GEAW
-
-# This is the application configuration file that the application will
-# default to if none is provided as a command line argument.
-component.configuration.file=all.xml
-
-# This has the Class definitions of components used in the application
-class.definition.file=class-def.xml
-
-# Directory where datafiles are stored that come with distribution, not for temporary files
-data.files.dir=data
-
-# URL where the master help set file is located. It is necessary that
-# this file is present, in order for the online help system to operate
-# properly. If this file is not found, then attempts to dynamically remove
-# components from the application (after the application has been started)
-# may incapacitate the online help.
-master.help.set=org/geworkbench/engine/help/master.hs
-
-# Flag to specify if the "exp" formatted expression dataset needs to
-# have a p-value column
-expressionMA.usePValue=false
-
-#Content of the File is a directory where datafiles are stored
-userSettings=userSettings.config
-
-#Content of the File is a directory where housekeeping genes config file is stored
-housekeepingnormalizerSettings=temp/GEAW/housekeepingnormalizerSettings.config
-# MySQL database Affy probes and GO bindings
-affy.data.manager.db=jdbc:mysql://localhost/c2b2pnp
-
-# The title string shown on the application framework
-application.title=geWorkbench {0} - An Open Extensible Platform for BioMedical Informatics
-application.version=Development
-
-# The URL where sequence alignment SOAP server located.
-sequence.server.endpoint=http://adparacel.cu-genome.org/axis/servlet/AxisServlet
-
-# The URL where columbia globus is located.
-globus.url=http://gridgate.genomecenter.columbia.edu:18080
-caarray.indexservice=/ogsa/services/edu/columbia/CaARRAYIndexService
-
-# The URL where dispatcher service is located.
-
-## production
-
-### nci
-
-<<<<<<< .mine
-## production URL for 2.2.1
-indexServer.url=http://cagridnode.c2b2.columbia.edu:8080/v2.2.1/wsrf/services/DefaultIndexService
-dispatcher.url=http://cagridnode.c2b2.columbia.edu:8080/v2.2.1/wsrf/services/cagrid/Dispatcher
-=======
-## production URL for 2.3.0
-#indexServer.url=http://cagridnode.c2b2.columbia.edu:8080/v2.3.0/wsrf/services/DefaultIndexService
-#dispatcher.url=http://cagridnode.c2b2.columbia.edu:8080/v2.3.0/wsrf/services/cagrid/Dispatcher
->>>>>>> .r8955
-
-## luna
-#dispatcher.url=http://luna.bioc.columbia.edu:8081/wsrf/services/cagrid/Dispatcher
-#indexServer.url=http://luna.bioc.columbia.edu:8081/wsrf/services/DefaultIndexService
-
-## development
-#indexServer.url=http://afdev.c2b2.columbia.edu:8080/wsrf/services/DefaultIndexService
-#dispatcher.url=http://afdev.c2b2.columbia.edu:8080/wsrf/services/cagrid/Dispatcher
-
-#supported host types
-supported.host.type=splash blast
-
-# The responding Class name of QueryFactory for different server
-blast=org.geworkbench.util.session.server.BlastSessionQueryFactory
-splash=org.geworkbench.util.session.server.SplashSessionQueryFactory
-
-# caBIO stuff
-DefaultPersistenceManagerClass=REMOTE
-DefaultObjectManagerClass=REMOTE
-
-# Default utility file download site
-data.download.site=http://amdec-bioinfo.cu-genome.org/html/caWorkBench/data/
-
-# For dynamic instantiation of Expression Markers
-expression.marker.type=org.geworkbench.bison.datastructure.bioobjects.markers.CSExpressionMarker
-
-# For SOAP based ARACNe invocation
-aracne.nonmpi.host=reverse-eng.cu-genome.org
-aracne.mpi.host=reverse-eng-mpi.cu-genome.org
-
-# Axis SOAP URL that links to a web service to obtain Protein-Protein and Protein-DNA interactions in Human
-interactions.endpoint=http://interactions.cu-genome.org/axis/services/interactions
-
-#cnkb interactions servlet url
-interactions_servlet_url=http://cagridnode.c2b2.columbia.edu:8080/cknb/InteractionsServlet_new/InteractionsServlet
-
-# 3000 milliseconds
-interactions_servlet_connection_timeout=3000
-# reasonable number of interactions for create cytoscape network
-max_interaction_number=2000
-# Cnkb interaction flag. If value is set to 0, then draw pair interactions use cnkb version1 method.
-# If value is set to 1, the draw interactions use cnkb version2 method.
-interaction_flag=1
-
-
-# user setting directory
-user.setting.directory=.geworkbench
diff --git a/geworkbench-core/classes/cruisecontrol/.svn/entries b/geworkbench-core/classes/cruisecontrol/.svn/entries
index e91f457..f06af05 100644
--- a/geworkbench-core/classes/cruisecontrol/.svn/entries
+++ b/geworkbench-core/classes/cruisecontrol/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8955
+9024
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/conf/cruisecontrol
 https://ncisvn.nci.nih.gov/svn/geworkbench

diff --git a/geworkbench-core/classes/images/.svn/entries b/geworkbench-core/classes/images/.svn/entries
index a4c3c2a..2ffc430 100644
--- a/geworkbench-core/classes/images/.svn/entries
+++ b/geworkbench-core/classes/images/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8955
+9024
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/images
 https://ncisvn.nci.nih.gov/svn/geworkbench

@@ -26,14 +26,14 @@ wangmen

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

-Right.gif
+Back.png
 file




 2011-08-17T00:10:49.000000Z
-5fa54896cf7a55e892cbf6ca73280057
+0a7b372947cff61f523f559833d8545f
 2009-06-12T21:57:51.000000Z
 5224
 wangm
@@ -58,19 +58,19 @@ has-props



-82
+407

-start.gif
+ButtonClose.png
 file




 2011-08-17T00:10:49.000000Z
-18140a4a2fbc0dfd3aa41a63e24634bc
-2005-07-28T22:36:56.000000Z
-50
-watkin
+808b6a176d21e4d67fec2e9a631d30dc
+2010-11-10T20:35:42.089935Z
+7180
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 has-props


@@ -92,16 +92,16 @@ has-props



-239
+717

-Back.png
+Forward.png
 file




 2011-08-17T00:10:49.000000Z
-0a7b372947cff61f523f559833d8545f
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 2009-06-12T21:57:51.000000Z
 5224
 wangm
@@ -126,19 +126,19 @@ has-props



-407
+390

-load.gif
+Reload.png
 file




 2011-08-17T00:10:49.000000Z
-adbe8a131677d7124c9940f7f963db80
-2005-07-28T22:36:56.000000Z
-50
-watkin
+16df894a37d801956452f953f94013ad
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 has-props


@@ -160,19 +160,19 @@ has-props



-462
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-ButtonClose.png
+Right.gif
 file




 2011-08-17T00:10:49.000000Z
-808b6a176d21e4d67fec2e9a631d30dc
-2010-11-10T20:35:42.089935Z
-7180
-wangmen
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 has-props


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



-717
+82

-back.gif
+Stop.png
 file




 2011-08-17T00:10:49.000000Z
-965d8e877fcf64772da7a619be10cb8e
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-1612
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 has-props


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



-183
+765

-Forward.png
+back.gif
 file




 2011-08-17T00:10:49.000000Z
-e6358eb836a9780608066bce737142fd
-2009-06-12T21:57:51.000000Z
-5224
-wangm
+965d8e877fcf64772da7a619be10cb8e
+2006-07-06T14:37:51.000000Z
+1612
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 has-props


@@ -262,19 +262,19 @@ has-props



-390
+183

-Stop.png
+down.gif
 file




 2011-08-17T00:10:49.000000Z
-b5e5c1826ca686c4a10d3da712d739e0
-2009-06-12T21:57:51.000000Z
-5224
-wangm
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 has-props


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



-765
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 forward.gif
 file
@@ -332,17 +332,17 @@ has-props

 183

-up.gif
+load.gif
 file




 2011-08-17T00:10:49.000000Z
-1ff4c3aeb15434088a8c976d5faaebf1
-2006-10-11T00:22:06.000000Z
-1923
-mkustagi
+adbe8a131677d7124c9940f7f963db80
+2005-07-28T22:36:56.000000Z
+50
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 has-props


@@ -364,19 +364,19 @@ has-props



-858
+462

-Reload.png
+start.gif
 file




 2011-08-17T00:10:49.000000Z
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-5224
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 has-props


@@ -398,7 +398,7 @@ has-props



-555
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 stop.gif
 file
@@ -434,14 +434,14 @@ has-props

 313

-down.gif
+up.gif
 file




 2011-08-17T00:10:49.000000Z
-033ac2554ced75708e0f74c63a7df749
+1ff4c3aeb15434088a8c976d5faaebf1
 2006-10-11T00:22:06.000000Z
 1923
 mkustagi
@@ -466,5 +466,5 @@ has-props



-860
+858

diff --git a/geworkbench-core/classes/org/.svn/all-wcprops b/geworkbench-core/classes/org/.svn/all-wcprops
index 0c2dc5a..8d577aa 100644
--- a/geworkbench-core/classes/org/.svn/all-wcprops
+++ b/geworkbench-core/classes/org/.svn/all-wcprops
@@ -1,5 +1,5 @@
 K 25
 svn:wc:ra_dav:version-url
-V 56
-/svn/geworkbench/!svn/ver/8955/trunk/geworkbench/src/org
+V 57
+/svn/geworkbench/!svn/ver/8965/trunk/geworkbench/test/org
 END
diff --git a/geworkbench-core/classes/org/.svn/entries b/geworkbench-core/classes/org/.svn/entries
index a1aa131..a03e180 100644
--- a/geworkbench-core/classes/org/.svn/entries
+++ b/geworkbench-core/classes/org/.svn/entries
@@ -1,14 +1,14 @@
 10

 dir
-8955
+9024
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org
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-2012-03-05T17:45:18.759987Z
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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 618cba7..4e80bfc 100644
--- a/geworkbench-core/classes/org/geworkbench/.svn/all-wcprops
+++ b/geworkbench-core/classes/org/geworkbench/.svn/all-wcprops
@@ -1,5 +1,5 @@
 K 25
 svn:wc:ra_dav:version-url
-V 68
-/svn/geworkbench/!svn/ver/8955/trunk/geworkbench/src/org/geworkbench
+V 69
+/svn/geworkbench/!svn/ver/8965/trunk/geworkbench/test/org/geworkbench
 END
diff --git a/geworkbench-core/classes/org/geworkbench/.svn/entries b/geworkbench-core/classes/org/geworkbench/.svn/entries
index 781567b..1b74978 100644
--- a/geworkbench-core/classes/org/geworkbench/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/.svn/entries
@@ -1,14 +1,14 @@
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 dir
-8955
+9024
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-2012-03-05T17:45:18.759987Z
-8955
+2012-03-08T20:05:59.637361Z
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 zji


@@ -26,22 +26,22 @@ zji

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

-parsers
+analysis
 dir

-analysis
+bison
 dir

-events
+builtin
 dir

 engine
 dir

-builtin
+events
 dir

-bison
+parsers
 dir

 util
diff --git a/geworkbench-core/classes/org/geworkbench/analysis/.svn/all-wcprops b/geworkbench-core/classes/org/geworkbench/analysis/.svn/all-wcprops
index e8997ac..215893d 100644
--- a/geworkbench-core/classes/org/geworkbench/analysis/.svn/all-wcprops
+++ b/geworkbench-core/classes/org/geworkbench/analysis/.svn/all-wcprops
@@ -1,7 +1,7 @@
 K 25
 svn:wc:ra_dav:version-url
 V 77
-/svn/geworkbench/!svn/ver/8743/trunk/geworkbench/src/org/geworkbench/analysis
+/svn/geworkbench/!svn/ver/8990/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/8743/trunk/geworkbench/src/org/geworkbench/analysis/AbstractAnalysis.java
+/svn/geworkbench/!svn/ver/8990/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 a35bef8..a16de53 100644
--- a/geworkbench-core/classes/org/geworkbench/analysis/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/analysis/.svn/entries
@@ -1,15 +1,15 @@
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 dir
-8955
+9024
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/analysis
 https://ncisvn.nci.nih.gov/svn/geworkbench



-2012-01-20T16:26:44.505648Z
-8743
-youmi
+2012-03-07T19:21:35.661934Z
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@@ -26,17 +26,18 @@ youmi

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

-AbstractAnalysisLabelComparator.java
+AbstractAnalysis.java
 file




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-2010-02-26T21:15:07.709772Z
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+2012-03-07T19:21:35.661934Z
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 zji
+has-props



@@ -57,20 +58,19 @@ zji



-
-475
+24546

-ReHighlightable.java
+AbstractAnalysisLabelComparator.java
 file




 2011-08-17T00:10:49.000000Z
-e50d8d2b53f984cb6539b3b4145358a4
-2009-05-27T21:36:54.000000Z
-5144
-jiz
+3833c4721fd3a60ac6f06ab9d5bde6ac
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+zji



@@ -92,20 +92,20 @@ jiz



-340
+475

-HighlightCurrentParameterThread.java
+AbstractGridAnalysis.java
 file




 2011-08-17T00:10:49.000000Z
-f0b767724d9006cb3bb49651cd19cf12
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-
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+zji
+has-props



@@ -126,19 +126,19 @@ jiz



-522
+3237

-AbstractAnalysis.java
+AbstractSaveableParameterPanel.java
 file




-2012-01-31T19:12:35.000000Z
-35abdf721fe296ac75336aba0ac9b5ae
-2012-01-20T16:26:44.505648Z
-8743
-youmi
+2011-08-17T00:10:49.000000Z
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+2011-02-24T04:32:15.323159Z
+7483
+zji
 has-props


@@ -160,20 +160,19 @@ has-props



-24671
+5794

-AbstractSaveableParameterPanel.java
+HighlightCurrentParameterThread.java
 file




 2011-08-17T00:10:49.000000Z
-797bb5598cea2e47b13b476741433166
-2011-02-24T04:32:15.323159Z
-7483
-zji
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+5144
+jiz



@@ -194,7 +193,8 @@ has-props



-5794
+
+522

 ParameterKey.java
 file
@@ -230,18 +230,17 @@ keshav

 1371

-AbstractGridAnalysis.java
+ReHighlightable.java
 file




 2011-08-17T00:10:49.000000Z
-599708e9177a8d443e82ff7f8ba2c9dd
-2010-11-28T01:06:12.895894Z
-7231
-zji
-has-props
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+5144
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@@ -262,5 +261,6 @@ has-props



-3237
+
+340

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 288ea21..404cad7 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
@@ -453,9 +453,10 @@ public abstract class AbstractAnalysis implements Analysis, Serializable,
 	 */
 	public void setDefaultPanel(AbstractSaveableParameterPanel panel) {
 		aspp = panel;
-		if (aspp != null)
+		if (aspp != null) {
 			aspp.setVisible(true);
-		setParameterFilesPath(aspp);
+			setParameterFilesPath(aspp);
+		}
 		loadSavedParameterSets();
 	}

@@ -558,13 +559,6 @@ public abstract class AbstractAnalysis implements Analysis, Serializable,
 	}

 	/**
-	 * Return a code identifying the type of the analysis.
-	 *
-	 * @return
-	 */
-	public abstract int getAnalysisType();
-
-	/**
 	 *
 	 * @return
 	 */
diff --git a/geworkbench-core/classes/org/geworkbench/bison/.svn/entries b/geworkbench-core/classes/org/geworkbench/bison/.svn/entries
index ba00b55..11d7277 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/bison/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8955
+9024
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/bison
 https://ncisvn.nci.nih.gov/svn/geworkbench

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

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

-parsers
+algorithm
 dir

-model
+annotation
 dir

-algorithm
+datastructure
 dir

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+model
 dir

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diff --git a/geworkbench-core/classes/org/geworkbench/bison/algorithm/.svn/entries b/geworkbench-core/classes/org/geworkbench/bison/algorithm/.svn/entries
index 40c5764..cdfe89a 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 @@
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 dir
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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 dd67a36..ecef810 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 @@
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 dir
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 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/bison/algorithm/classification
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diff --git a/geworkbench-core/classes/org/geworkbench/bison/annotation/.svn/entries b/geworkbench-core/classes/org/geworkbench/bison/annotation/.svn/entries
index dd8cdd3..189a66e 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 @@
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 dir
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 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

-CSAnnotationContextManager.java
+CSAnnotationContext.java
 file




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 zji
 has-props

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



-7111
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-DSAnnotationContextManager.java
+CSAnnotationContextManager.java
 file




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



-4375
+7111

-CSAnnotationContext.java
+DSAnnotationContext.java
 file




 2011-08-17T00:10:49.000000Z
-41e1112d59762ea6739dd25c6caa822b
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 zji
 has-props

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



-20869
+12695

-DSAnnotationContext.java
+DSAnnotationContextManager.java
 file




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 zji
 has-props

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



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diff --git a/geworkbench-core/classes/org/geworkbench/bison/datastructure/.svn/entries b/geworkbench-core/classes/org/geworkbench/bison/datastructure/.svn/entries
index 84fe6dc..3a82e65 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/datastructure/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/bison/datastructure/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8955
+9024
 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/bison/datastructure
 https://ncisvn.nci.nih.gov/svn/geworkbench

@@ -26,13 +26,13 @@ zji

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

-bioobjects
+biocollections
 dir

-complex
+bioobjects
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-biocollections
+complex
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 properties
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 fb3e8fa..aca3c4e 100644
--- a/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/bison/datastructure/biocollections/.svn/entries
@@ -1,7 +1,7 @@
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 dir
-8955
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 https://ncisvn.nci.nih.gov/svn/geworkbench/trunk/geworkbench/src/org/geworkbench/bison/datastructure/biocollections
 https://ncisvn.nci.nih.gov/svn/geworkbench

@@ -26,12 +26,6 @@ zji

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

-gsea
-dir
-
-pca
-dir
-
 AdjacencyMatrix.java
 file

@@ -66,17 +60,17 @@ has-props

 8341

-GoAnalysisResult.java
+AdjacencyMatrixDataSet.java
 file




-2012-01-10T19:15:27.000000Z
-c37d8a97b16a5a8e093b9dc296f669ed
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 has-props


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



-7068
+9308

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

 1101

-CSMarkerVector.java
+CSDataSet.java
 file




 2012-01-10T19:15:27.000000Z
-57dafbfa3f882bf292ad0a4ee08e3e3f
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-8466
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 zji
 has-props

@@ -166,24 +160,18 @@ has-props



-8097
-
-microarrays
-dir
-
-sequences
-dir
+8321

-CSDataSet.java
+CSMarkerVector.java
 file




 2012-01-10T19:15:27.000000Z
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-8478
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 zji
 has-props

@@ -206,7 +194,7 @@ has-props



-8321
+8097

 DSAncillaryDataSet.java
 file
@@ -242,17 +230,17 @@ has-props

 433

-AdjacencyMatrixDataSet.java
+DSDataSet.java
 file




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-fa9193ebfc68a232ad769233774dbdda
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 has-props


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



-9308
+3334

-DSDataSet.java
+GoAnalysisResult.java
 file




 2012-01-10T19:15:27.000000Z
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 zji
 has-props

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



-3334
+7068

-views
+gsea
 dir

 medusa
 dir

+microarrays
+dir
+
+pca
+dir
+
+sequences
+dir
+
+views
+dir
+
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 adbb910..ddc49b9 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
-8955
+9024
 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 a3de24b..9bbaebf 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
-8955
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 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 +26,17 @@ zji

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

-MedusaDataSet.java
+MedusaCommand.java
 file




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-0e8490bacaf5f4c08914f450569b5408
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-8481
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-has-props
+2011-12-29T06:13:04.000000Z
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@@ -58,7 +57,8 @@ has-props



-1193
+
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 MedusaData.java
 file
@@ -94,18 +94,18 @@ zji

 1736

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+MedusaDataSet.java
 file




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@@ -126,5 +126,5 @@ wangmen



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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
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diff --git a/geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/sequence/.svn/entries b/geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/sequence/.svn/entries
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diff --git a/geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/structure/.svn/entries b/geworkbench-core/classes/org/geworkbench/bison/datastructure/bioobjects/structure/.svn/entries
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diff --git a/geworkbench-core/classes/org/geworkbench/bison/datastructure/complex/pattern/sequence/.svn/entries b/geworkbench-core/classes/org/geworkbench/bison/datastructure/complex/pattern/sequence/.svn/entries
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diff --git a/geworkbench-core/classes/org/geworkbench/bison/model/clusters/.svn/entries b/geworkbench-core/classes/org/geworkbench/bison/model/clusters/.svn/entries
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diff --git a/geworkbench-core/classes/org/geworkbench/bison/parsers/.svn/entries b/geworkbench-core/classes/org/geworkbench/bison/parsers/.svn/entries
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 OboSourcePreference.java
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diff --git a/geworkbench-core/classes/org/geworkbench/builtin/projects/comments/.svn/entries b/geworkbench-core/classes/org/geworkbench/builtin/projects/comments/.svn/entries
index c5a05ee..6ca93ed 100644
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diff --git a/geworkbench-core/classes/org/geworkbench/builtin/projects/comments/help/.svn/entries b/geworkbench-core/classes/org/geworkbench/builtin/projects/comments/help/.svn/entries
index d3d1756..f45c59b 100644
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@@ -126,19 +126,19 @@ has-props



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 file




 2011-08-17T00:10:50.000000Z
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@@ -160,19 +160,19 @@ has-props



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 file




 2011-08-17T00:10:50.000000Z
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 2011-08-17T00:10:50.000000Z
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 has-props


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 2011-08-17T00:10:50.000000Z
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 has-props


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



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diff --git a/geworkbench-core/classes/org/geworkbench/builtin/projects/help/projects area_overviewed_files/.svn/entries b/geworkbench-core/classes/org/geworkbench/builtin/projects/help/projects area_overviewed_files/.svn/entries
index bf90e73..1647caf 100644
--- a/geworkbench-core/classes/org/geworkbench/builtin/projects/help/projects area_overviewed_files/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/builtin/projects/help/projects area_overviewed_files/.svn/entries
@@ -1,7 +1,7 @@
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 dir
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diff --git a/geworkbench-core/classes/org/geworkbench/builtin/projects/help/remote_files/.svn/entries b/geworkbench-core/classes/org/geworkbench/builtin/projects/help/remote_files/.svn/entries
index ee3a69a..4e8063f 100644
--- a/geworkbench-core/classes/org/geworkbench/builtin/projects/help/remote_files/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/builtin/projects/help/remote_files/.svn/entries
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@@ -26,14 +26,14 @@ mhall

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-image001.jpg
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 file




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



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 edaly
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@@ -92,16 +92,16 @@ has-props



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



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 image001.png
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@@ -162,16 +162,16 @@ has-props

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 edaly
 has-props

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



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diff --git a/geworkbench-core/classes/org/geworkbench/builtin/projects/help/rename_dataset_files/.svn/entries b/geworkbench-core/classes/org/geworkbench/builtin/projects/help/rename_dataset_files/.svn/entries
index 38bd09f..6e0efad 100644
--- a/geworkbench-core/classes/org/geworkbench/builtin/projects/help/rename_dataset_files/.svn/entries
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diff --git a/geworkbench-core/classes/org/geworkbench/builtin/projects/help/user preference_files/.svn/entries b/geworkbench-core/classes/org/geworkbench/builtin/projects/help/user preference_files/.svn/entries
index 064f25a..be64a2c 100644
--- a/geworkbench-core/classes/org/geworkbench/builtin/projects/help/user preference_files/.svn/entries
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diff --git a/geworkbench-core/classes/org/geworkbench/builtin/projects/history/.svn/entries b/geworkbench-core/classes/org/geworkbench/builtin/projects/history/.svn/entries
index a1db4f8..0d6bb47 100644
--- a/geworkbench-core/classes/org/geworkbench/builtin/projects/history/.svn/entries
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@@ -26,17 +26,17 @@ youmi

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

-HistoryPanel.java
+HistoryPanel.cwb.xml
 file




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 has-props


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diff --git a/geworkbench-core/classes/org/geworkbench/builtin/projects/history/help/.svn/entries b/geworkbench-core/classes/org/geworkbench/builtin/projects/history/help/.svn/entries
index ffdfc3c..53933cb 100644
--- a/geworkbench-core/classes/org/geworkbench/builtin/projects/history/help/.svn/entries
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@@ -26,14 +26,14 @@ edaly

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

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 file




 2011-08-17T00:10:50.000000Z
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 has-props


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-datasetHistory.gif
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 watkin
@@ -234,5 +234,5 @@ has-props



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diff --git a/geworkbench-core/classes/org/geworkbench/builtin/projects/history/help/historyPanel_files/.svn/entries b/geworkbench-core/classes/org/geworkbench/builtin/projects/history/help/historyPanel_files/.svn/entries
index d13c6e9..81b5297 100644
--- a/geworkbench-core/classes/org/geworkbench/builtin/projects/history/help/historyPanel_files/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/builtin/projects/history/help/historyPanel_files/.svn/entries
@@ -1,7 +1,7 @@
 10

 dir
-8955
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diff --git a/geworkbench-core/classes/org/geworkbench/builtin/projects/history/help/images/.svn/entries b/geworkbench-core/classes/org/geworkbench/builtin/projects/history/help/images/.svn/entries
index 219228f..8e25e86 100644
--- a/geworkbench-core/classes/org/geworkbench/builtin/projects/history/help/images/.svn/entries
+++ b/geworkbench-core/classes/org/geworkbench/builtin/projects/history/help/images/.svn/entries
@@ -1,7 +1,7 @@
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diff --git a/geworkbench-core/classes/org/geworkbench/builtin/projects/remoteresources/.svn/all-wcprops b/geworkbench-core/classes/org/geworkbench/builtin/projects/remoteresources/.svn/all-wcprops
index 5e34b3d..c8143db 100644
--- a/geworkbench-core/classes/org/geworkbench/builtin/projects/remoteresources/.svn/all-wcprops
+++ b/geworkbench-core/classes/org/geworkbench/builtin/projects/remoteresources/.svn/all-wcprops
@@ -1,7 +1,7 @@
 K 25
 svn:wc:ra_dav:version-url
 V 101
-/svn/geworkbench/!svn/ver/8924/trunk/geworkbench/src/org/geworkbench/builtin/projects/remoteresources
+/svn/geworkbench/!svn/ver/8974/trunk/geworkbench/src/org/geworkbench/builtin/projects/remoteresources
 END
 RemoteResource.java
 K 25
@@ -19,7 +19,7 @@ CaArrayFilteringDialog.java
 K 25
 svn:wc:ra_dav:version-url
 V 129
-/svn/geworkbench/!svn/ver/8278/trunk/geworkbench/src/org/geworkbench/builtin/projects/remoteresources/CaArrayFilteringDialog.java
+/svn/geworkbench/!svn/ver/8974/trunk/geworkbench/src/org/geworkbench/builtin/projects/remoteresources/CaArrayFilteringDialog.java
 END
 RemoteResourceManager.java
 K 25
diff --git a/geworkbench-core/classes/org/geworkbench/builtin/projects/remoteresources/.svn/entries b/geworkbench-core/classes/org/geworkbench/builtin/projects/remoteresources/.svn/entries
index fe55c70..c6c40f9 100644
--- a/geworkbench-core/classes/org/geworkbench/builtin/projects/remoteresources/.svn/entries
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@@ -1,14 +1,14 @@
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 dir
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-2012-02-27T22:42:50.953800Z
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 zji


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

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

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 file




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