Removed global GMT. Refactored mastermap dialog.

Author: mikekucera

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

@@ -20,9 +20,9 @@
 import org.baderlab.csplugins.enrichmentmap.view.heatmap.HeatMapMainPanel;
 import org.baderlab.csplugins.enrichmentmap.view.heatmap.HeatMapParentPanel;
 import org.baderlab.csplugins.enrichmentmap.view.heatmap.table.ColumnHeaderRankOptionRenderer;
-import org.baderlab.csplugins.enrichmentmap.view.mastermap.EditCommonPropertiesPanel;
 import org.baderlab.csplugins.enrichmentmap.view.mastermap.EditDataSetPanel;
 import org.baderlab.csplugins.enrichmentmap.view.mastermap.ErrorMessageDialog;
+import org.baderlab.csplugins.enrichmentmap.view.mastermap.PathTextField;
 import org.baderlab.csplugins.enrichmentmap.view.postanalysis.PostAnalysisInputPanel;
 import org.baderlab.csplugins.enrichmentmap.view.postanalysis.PostAnalysisKnownSignaturePanel;
 import org.baderlab.csplugins.enrichmentmap.view.postanalysis.PostAnalysisSignatureDiscoveryPanel;
@@ -86,9 +86,9 @@ protected void configure() {
 		installFactory(ExportTXTAction.Factory.class);
 		installFactory(AddRanksDialog.Factory.class);
 		installFactory(EditDataSetPanel.Factory.class);
-		installFactory(EditCommonPropertiesPanel.Factory.class);
 		installFactory(ErrorMessageDialog.Factory.class);
 		installFactory(ColumnHeaderRankOptionRenderer.Factory.class);
+		installFactory(PathTextField.Factory.class);
 	}
 
 	private void installFactory(Class<?> factoryInterface) {

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/model/EMCreationParameters.java

@@ -1,6 +1,5 @@
 package org.baderlab.csplugins.enrichmentmap.model;
 
-import java.nio.file.Path;
 import java.util.HashSet;
 import java.util.Optional;
 import java.util.Set;
@@ -40,8 +39,6 @@ public static enum GreatFilter {
 	private boolean createDistinctEdges;
 	private String enrichmentEdgeType = "Geneset_Overlap";
 
-	private Path globalGmtFile;
-	
 	private final Set<String> pValueColumnNames = new HashSet<>();
 	private final Set<String> qValueColumnNames = new HashSet<>();
 	private final Set<String> similarityCutoffColumnNames = new HashSet<>();
@@ -67,14 +64,6 @@ public EMCreationParameters(
 		this.combinedConstant = combinedConstant;
 	}
 
-	public void setGlobalGmtFile(Path path) {
-		this.globalGmtFile = path;
-	}
-	
-	public Path getGlobalGmtFile() {
-		return globalGmtFile;
-	}
-	
 	public String getAttributePrefix() {
 		return attributePrefix;
 	}

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/model/EnrichmentMap.java

@@ -45,8 +45,6 @@ public class EnrichmentMap {
 	/** Post analysis signature genesets associated with this map.*/
 	private Map<String, EMSignatureDataSet> signatureDataSets = new HashMap<>();
 
-	private SetOfGeneSets globalGenesets = new SetOfGeneSets();
-
 	private int NumberOfGenes = 0;
 	private boolean isLegacy = false;
 	private boolean isDistinctExpressionSets = false;
@@ -222,8 +220,6 @@ public Map<String, GeneSet> getAllGeneSets() {
 		Map<String, GeneSet> allGeneSets = new HashMap<>();
 
 		synchronized (lock) {
-			allGeneSets.putAll(globalGenesets.getGeneSets());
-		
 			// If a GeneSet appears in more than one DataSet, then its totally arbitrary which version of it gets picked
 			// If a GeneSet appears in an enrichment file it will override the one with the same name in the global GMT file
 			for (EMDataSet ds : dataSets.values()) {
@@ -300,20 +296,14 @@ public Set<String> getAllGeneSetOfInterestNames() {
 	}
 
 	public String findGeneSetDescription(String genesetName) {
-		GeneSet gs = globalGenesets.getGeneSets().get(genesetName);
-		if(gs != null)
-			return gs.getDescription();
 		for(EMDataSet ds : dataSets.values()) {
-			gs = ds.getGeneSetsOfInterest().getGeneSets().get(genesetName);
+			GeneSet gs = ds.getGeneSetsOfInterest().getGeneSets().get(genesetName);
 			if(gs != null)
 				return gs.getDescription();
 		}
 		return null;
 	}
 
-	public SetOfGeneSets getGlobalGenesets() {
-		return globalGenesets;
-	}
 
 	public Map<String, EMDataSet> getDataSets() {
 		return dataSets;

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/parsers/ParseGenericEnrichmentResults.java

@@ -28,7 +28,7 @@ public void parseLines(List<String> lines, EMDataSet dataset, TaskMonitor taskMo
 
 		//Get the current genesets so we can check that all the results are in the geneset list
 		//and put the size of the genesets into the visual style
-		Map<String, GeneSet> genesets = dataset.getMap().getGlobalGenesets().getGeneSets();
+		Map<String, GeneSet> genesets = dataset.getSetOfGeneSets().getGeneSets();
 
 		int currentProgress = 0;
 		int maxValue = lines.size();

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/task/CreateEnrichmentMapTaskFactory.java

@@ -57,11 +57,6 @@ public TaskIterator createTaskIterator() {
 
 		EnrichmentMap map = new EnrichmentMap(params, serviceRegistrar);
 
-		// Load global GMT file into each dataset
-		if(params.getGlobalGmtFile() != null) {
-			tasks.append(new GMTFileReaderTask(map, params.getGlobalGmtFile().toString(), map.getGlobalGenesets()));
-		}
-
 		for(DataSetParameters dataSetParameters : dataSets) {
 			String datasetName = dataSetParameters.getName();
 			Method method = dataSetParameters.getMethod();

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/mastermap/EditCommonPanel.java

@@ -0,0 +1,108 @@
+package org.baderlab.csplugins.enrichmentmap.view.mastermap;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.swing.GroupLayout;
+import javax.swing.GroupLayout.Alignment;
+import javax.swing.JPanel;
+
+import org.baderlab.csplugins.enrichmentmap.AfterInjection;
+import org.baderlab.csplugins.enrichmentmap.view.util.FileBrowser;
+import org.cytoscape.util.swing.IconManager;
+import org.cytoscape.util.swing.LookAndFeelUtil;
+
+import com.google.inject.Inject;
+
+@SuppressWarnings("serial")
+public class EditCommonPanel extends JPanel implements DetailPanel {
+
+	@Inject private PathTextField.Factory pathTextFactory;
+	
+	private PathTextField gmtText;
+	private PathTextField expressionsText;
+	
+	
+	@Override
+	public String getIcon() {
+		return IconManager.ICON_FILE_O;
+	}
+
+	@Override
+	public String getDisplayName() {
+		return "Common Files";
+	}
+
+	@Override
+	public JPanel getPanel() {
+		return this;
+	}
+	
+	@AfterInjection
+	private void createContents() {
+		gmtText = pathTextFactory.create("GMT File:", FileBrowser.Filter.GMT);
+		expressionsText = pathTextFactory.create("Expressions:", FileBrowser.Filter.EXPRESSION);
+		
+		GroupLayout layout = new GroupLayout(this);
+		setLayout(layout);
+		layout.setAutoCreateContainerGaps(true);
+		layout.setAutoCreateGaps(true);
+	   		
+		layout.setHorizontalGroup(
+			layout.createSequentialGroup()
+				.addGroup(layout.createParallelGroup(Alignment.TRAILING)
+					.addComponent(gmtText.getLabel())
+					.addComponent(expressionsText.getLabel())
+				)
+				.addGroup(layout.createParallelGroup(Alignment.LEADING, true)
+					.addComponent(gmtText.getTextField())
+					.addComponent(expressionsText.getTextField())
+				)
+				.addGroup(layout.createParallelGroup()
+					.addComponent(gmtText.getBrowseButton())
+					.addComponent(expressionsText.getBrowseButton())
+				)
+		);
+		
+		layout.setVerticalGroup(
+			layout.createSequentialGroup()
+				.addGroup(layout.createParallelGroup(Alignment.BASELINE)
+					.addComponent(gmtText.getLabel())
+					.addComponent(gmtText.getTextField())
+					.addComponent(gmtText.getBrowseButton())
+				)
+				.addGroup(layout.createParallelGroup(Alignment.BASELINE)
+					.addComponent(expressionsText.getLabel())
+					.addComponent(expressionsText.getTextField())
+					.addComponent(expressionsText.getBrowseButton())
+				)
+		);
+		
+   		if(LookAndFeelUtil.isAquaLAF())
+   			setOpaque(false);
+	}
+	
+
+	@Override
+	public List<String> validateInput() {
+		gmtText.hideError();
+		expressionsText.hideError();
+		
+		List<String> err = new ArrayList<>(2);
+		if(!gmtText.emptyOrReadable())
+			err.add(gmtText.showError("Enrichments file path is not valid."));
+		if(!expressionsText.emptyOrReadable())
+			err.add(expressionsText.showError("Enrichments 2 file path is not valid."));
+		return err;
+	}
+	
+	
+	public String getGmtFile() {
+		return gmtText.getText();
+	}
+	
+	public String getExpressionFile() {
+		return expressionsText.getText();
+	}
+	
+}