Create package for tunables, move CommandModule into base package, refs

#348

Author: mikekucera

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/commands/CommandModule.java renamed to EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/CommandModule.java

@@ -1,10 +1,18 @@
-package org.baderlab.csplugins.enrichmentmap.commands;
+package org.baderlab.csplugins.enrichmentmap;
 
 import static java.lang.annotation.RetentionPolicy.RUNTIME;
 
 import java.lang.annotation.Retention;
 
 import org.baderlab.csplugins.enrichmentmap.actions.OpenEnrichmentMapAction;
+import org.baderlab.csplugins.enrichmentmap.commands.DatasetShowCommandTask;
+import org.baderlab.csplugins.enrichmentmap.commands.EMBuildCommandTask;
+import org.baderlab.csplugins.enrichmentmap.commands.EMGseaCommandTask;
+import org.baderlab.csplugins.enrichmentmap.commands.ExportModelJsonCommandTask;
+import org.baderlab.csplugins.enrichmentmap.commands.PAKnownSignatureCommandTask;
+import org.baderlab.csplugins.enrichmentmap.commands.ResolverCommandTask;
+import org.baderlab.csplugins.enrichmentmap.commands.TableCommandTask;
+import org.baderlab.csplugins.enrichmentmap.commands.DatasetShowCommandTask.Factory;
 import org.cytoscape.work.AbstractTaskFactory;
 import org.cytoscape.work.Task;
 import org.cytoscape.work.TaskFactory;

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/CyActivator.java

@@ -8,18 +8,17 @@
 import java.util.Properties;
 
 import org.baderlab.csplugins.enrichmentmap.ApplicationModule.Headless;
+import org.baderlab.csplugins.enrichmentmap.CommandModule.BuildCommand;
+import org.baderlab.csplugins.enrichmentmap.CommandModule.BuildTableCommand;
+import org.baderlab.csplugins.enrichmentmap.CommandModule.DatasetHide;
+import org.baderlab.csplugins.enrichmentmap.CommandModule.DatasetShow;
+import org.baderlab.csplugins.enrichmentmap.CommandModule.GSEACommand;
+import org.baderlab.csplugins.enrichmentmap.CommandModule.JsonCommand;
+import org.baderlab.csplugins.enrichmentmap.CommandModule.PACommand;
+import org.baderlab.csplugins.enrichmentmap.CommandModule.ResolveCommand;
 import org.baderlab.csplugins.enrichmentmap.actions.OpenEnrichmentMapAction;
 import org.baderlab.csplugins.enrichmentmap.actions.OpenPathwayCommonsTaskFactory;
-import org.baderlab.csplugins.enrichmentmap.commands.CommandModule;
-import org.baderlab.csplugins.enrichmentmap.commands.CommandModule.BuildCommand;
-import org.baderlab.csplugins.enrichmentmap.commands.CommandModule.BuildTableCommand;
-import org.baderlab.csplugins.enrichmentmap.commands.CommandModule.DatasetHide;
-import org.baderlab.csplugins.enrichmentmap.commands.CommandModule.DatasetShow;
-import org.baderlab.csplugins.enrichmentmap.commands.CommandModule.GSEACommand;
-import org.baderlab.csplugins.enrichmentmap.commands.CommandModule.JsonCommand;
-import org.baderlab.csplugins.enrichmentmap.commands.CommandModule.PACommand;
-import org.baderlab.csplugins.enrichmentmap.commands.CommandModule.ResolveCommand;
-import org.baderlab.csplugins.enrichmentmap.commands.MannWhitRanksTunableHandlerFactory;
+import org.baderlab.csplugins.enrichmentmap.commands.tunables.MannWhitRanksTunableHandlerFactory;
 import org.baderlab.csplugins.enrichmentmap.model.EnrichmentMapManager;
 import org.baderlab.csplugins.enrichmentmap.model.io.SessionListener;
 import org.baderlab.csplugins.enrichmentmap.rest.EnrichmentMapResource;

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/commands/DatasetShowCommandTask.java

@@ -4,6 +4,8 @@
 import java.util.Map;
 import java.util.Set;
 
+import org.baderlab.csplugins.enrichmentmap.commands.tunables.DatasetListTunable;
+import org.baderlab.csplugins.enrichmentmap.commands.tunables.NetworkTunable;
 import org.baderlab.csplugins.enrichmentmap.model.EnrichmentMap;
 import org.baderlab.csplugins.enrichmentmap.view.control.ControlPanelMediator;
 import org.baderlab.csplugins.enrichmentmap.view.control.io.ViewParams;

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/commands/EMBuildCommandTask.java

@@ -51,6 +51,7 @@
 import java.util.ArrayList;
 import java.util.List;
 
+import org.baderlab.csplugins.enrichmentmap.commands.tunables.FilterTunablesLegacy;
 import org.baderlab.csplugins.enrichmentmap.model.DataSetFiles;
 import org.baderlab.csplugins.enrichmentmap.model.DataSetParameters;
 import org.baderlab.csplugins.enrichmentmap.model.EMCreationParameters;

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/commands/ExportModelJsonCommandTask.java

@@ -3,6 +3,7 @@
 import java.io.File;
 import java.io.FileWriter;
 
+import org.baderlab.csplugins.enrichmentmap.commands.tunables.NetworkTunable;
 import org.baderlab.csplugins.enrichmentmap.model.EnrichmentMap;
 import org.baderlab.csplugins.enrichmentmap.model.io.ModelSerializer;
 import org.cytoscape.work.AbstractTask;

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/commands/PAKnownSignatureCommandTask.java

@@ -6,6 +6,9 @@
 import java.util.List;
 import java.util.Set;
 
+import org.baderlab.csplugins.enrichmentmap.commands.tunables.FilterTunables;
+import org.baderlab.csplugins.enrichmentmap.commands.tunables.MannWhitRanks;
+import org.baderlab.csplugins.enrichmentmap.commands.tunables.NetworkTunable;
 import org.baderlab.csplugins.enrichmentmap.model.EMDataSet;
 import org.baderlab.csplugins.enrichmentmap.model.EnrichmentMap;
 import org.baderlab.csplugins.enrichmentmap.model.PostAnalysisFilterType;

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/commands/ResolverCommandTask.java

@@ -3,6 +3,7 @@
 import java.io.File;
 import java.util.List;
 
+import org.baderlab.csplugins.enrichmentmap.commands.tunables.FilterTunables;
 import org.baderlab.csplugins.enrichmentmap.model.DataSetParameters;
 import org.baderlab.csplugins.enrichmentmap.model.EMCreationParameters;
 import org.baderlab.csplugins.enrichmentmap.resolver.ResolverTask;

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/commands/TableCommandTask.java

@@ -3,6 +3,8 @@
 import java.util.Collections;
 import java.util.List;
 
+import org.baderlab.csplugins.enrichmentmap.commands.tunables.FilterTunables;
+import org.baderlab.csplugins.enrichmentmap.commands.tunables.TableTunables;
 import org.baderlab.csplugins.enrichmentmap.model.DataSetParameters;
 import org.baderlab.csplugins.enrichmentmap.model.EMCreationParameters;
 import org.baderlab.csplugins.enrichmentmap.model.EMDataSet.Method;

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/commands/DatasetListTunable.java renamed to EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/commands/tunables/DatasetListTunable.java

@@ -1,4 +1,4 @@
-package org.baderlab.csplugins.enrichmentmap.commands;
+package org.baderlab.csplugins.enrichmentmap.commands.tunables;
 
 import java.util.Collection;
 import java.util.Collections;

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/commands/FilterTunables.java renamed to EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/commands/tunables/FilterTunables.java

@@ -1,4 +1,4 @@
-package org.baderlab.csplugins.enrichmentmap.commands;
+package org.baderlab.csplugins.enrichmentmap.commands.tunables;
 
 
 import static org.baderlab.csplugins.enrichmentmap.model.EMCreationParameters.SimilarityMetric.COMBINED;