Had speed issue when launching EM directly from GSEA because command tool printed out task status updates to command tool. Got rid of all all iterative status update statements and changed it to one statement at the top so that the user can still see the progress of the build from the command tool (They can’t see them anymore when being built from the interface but the progress bar is still being updated.

risserlin · risserlin · commit dd3275491143 · 2015-10-01T12:20:38.000-04:00
diff --git a/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/parsers/ExpressionFileReaderTask.java b/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/parsers/ExpressionFileReaderTask.java
@@ -112,7 +112,8 @@ public GeneExpressionMatrix parse() throws IOException {
     			//expression
 
     			boolean twoColumns = false;
-
+    			
+					
 
     			HashSet<Integer> datasetGenes = dataset.getDatasetGenes();
     			HashMap genes = dataset.getMap().getGenes();
@@ -126,6 +127,9 @@ public GeneExpressionMatrix parse() throws IOException {
     			maxValue = lines.length;
     			int expressionUniverse = 0;
     		
+    			if (taskMonitor != null) 					
+                    taskMonitor.setStatusMessage("Parsing GCT file - " + maxValue + " rows");
+    			
     			GeneExpressionMatrix expressionMatrix = dataset.getExpressionSets();
     			//GeneExpressionMatrix expressionMatrix = new GeneExpressionMatrix(lines[0].split("\t"));
     			//HashMap<Integer,GeneExpression> expression = new HashMap<Integer, GeneExpression>();
@@ -241,7 +245,6 @@ public GeneExpressionMatrix parse() throws IOException {
     					// Calculate Percentage.  This must be a value between 0..100.
         				int percentComplete = (int) (((double) currentProgress / maxValue) * 100);
 	                    taskMonitor.setProgress(percentComplete);
-	                    taskMonitor.setStatusMessage("Parsing GCT file " + currentProgress + " of " + maxValue);
     				}	
     				currentProgress++;
 
diff --git a/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/parsers/GMTFileReaderTask.java b/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/parsers/GMTFileReaderTask.java
@@ -153,6 +153,8 @@ public void parse(TaskMonitor taskMonitor) throws IOException {
 
         int currentProgress = 0;
         int maxValue = lines.length;
+        
+        taskMonitor.setStatusMessage("Parsing GMT file - " + maxValue + " rows");   
         try {
             for (int i = 0; i < lines.length; i++) {
                 if (cancelled)
@@ -179,8 +181,7 @@ public void parse(TaskMonitor taskMonitor) throws IOException {
 
                     // Calculate Percentage.  This must be a value between 0..100.
                     int percentComplete = (int) (((double) currentProgress / maxValue) * 100);
-                    taskMonitor.setProgress(percentComplete);
-                    taskMonitor.setStatusMessage("Parsing GMT file " + currentProgress + " of " + maxValue);                      
+                    taskMonitor.setProgress(percentComplete);                   
                     currentProgress++;
 
                     //All subsequent fields in the list are the geneset associated with this geneset.
diff --git a/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/parsers/ParseBingoEnrichmentResults.java b/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/parsers/ParseBingoEnrichmentResults.java
@@ -128,7 +128,8 @@ public void parseBingoFile(String [] lines){
         int currentProgress = 0;
         int maxValue = lines.length;
         boolean FDR = true;
-
+        if(taskMonitor != null)
+        	taskMonitor.setStatusMessage("Parsing Generic Results file -" + maxValue + " rows");   
          //skip the first l9 which just has the field names (start i=1)
         //check to see how many columns the data has
 
@@ -245,8 +246,7 @@ public void parseBingoFile(String [] lines){
             //  Estimate Time Remaining
             long timeRemaining = maxValue - currentProgress;
             if (taskMonitor != null) {
-                    taskMonitor.setProgress(percentComplete);
-                    taskMonitor.setStatusMessage("Parsing Generic Results file " + currentProgress + " of " + maxValue);              
+                    taskMonitor.setProgress(percentComplete);           
                 }
             currentProgress++;
 
diff --git a/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/parsers/ParseDavidEnrichmentResults.java b/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/parsers/ParseDavidEnrichmentResults.java
@@ -124,6 +124,9 @@ public void parseDavidFile(String [] lines){
 
         int currentProgress = 0;
         int maxValue = lines.length;
+        if(taskMonitor != null)
+        	taskMonitor.setStatusMessage("Parsing Generic Results file - " + maxValue + " rows");
+        
         boolean FDR = true;
 
          //skip the first line which just has the field names (start i=1)
@@ -229,8 +232,7 @@ public void parseDavidFile(String [] lines){
             //  Estimate Time Remaining
             long timeRemaining = maxValue - currentProgress;
             if (taskMonitor != null) {
-                    taskMonitor.setProgress(percentComplete);
-                    taskMonitor.setStatusMessage("Parsing Generic Results file " + currentProgress + " of " + maxValue);
+                    taskMonitor.setProgress(percentComplete);                    
                 }
             currentProgress++;
 
diff --git a/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/parsers/ParseGREATEnrichmentResults.java b/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/parsers/ParseGREATEnrichmentResults.java
@@ -118,6 +118,8 @@ public void parseGreatFile(String [] lines){
 
         int currentProgress = 0;
         int maxValue = lines.length;
+        if(taskMonitor != null)
+            taskMonitor.setStatusMessage("Parsing Great Results file - " + maxValue + " rows");
         //for great files there is an FDR
     		dataset.getMap().getParams().setFDR(true);   
 
@@ -287,10 +289,9 @@ else if ((hasBackground) && (!tokens[15].equalsIgnoreCase("")))
             int percentComplete = (int) (((double) currentProgress / maxValue) * 100);
             //  Estimate Time Remaining
             long timeRemaining = maxValue - currentProgress;
-            if (taskMonitor != null) {
+            if (taskMonitor != null) 
                     taskMonitor.setProgress(percentComplete);
-                    taskMonitor.setStatusMessage("Parsing Great Results file " + currentProgress + " of " + maxValue);
-                }
+                
             currentProgress++;
           
             //check to see if the gene set has already been entered in the results
diff --git a/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/parsers/ParseGSEAEnrichmentResults.java b/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/parsers/ParseGSEAEnrichmentResults.java
@@ -103,6 +103,9 @@ public void parseGSEAFile(String[] lines){
 
          int currentProgress = 0;
          int maxValue = lines.length;
+         if(taskMonitor!=null)
+        	taskMonitor.setStatusMessage("Parsing Enrichment Results file - " + maxValue + " rows");
+         
          for (int i = 1; i < lines.length; i++) {
                 String line = lines[i];
 
@@ -172,11 +175,9 @@ public void parseGSEAFile(String[] lines){
                 int percentComplete = (int) (((double) currentProgress / maxValue) * 100);
                 //  Estimate Time Remaining
                 long timeRemaining = maxValue - currentProgress;
-                if (taskMonitor != null) {
+                if (taskMonitor != null) 
                         taskMonitor.setProgress(percentComplete);
-                        taskMonitor.setStatusMessage("Parsing Enrichment Results file " + currentProgress + " of " + maxValue);
-                        
-                    }
+ 
                 currentProgress++;
 
                 results.put(Name, result);
diff --git a/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/parsers/ParseGenericEnrichmentResults.java b/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/parsers/ParseGenericEnrichmentResults.java
@@ -106,6 +106,8 @@ public void parseGenericFile(String [] lines){
 
         int currentProgress = 0;
         int maxValue = lines.length;
+        if(taskMonitor != null)
+        	taskMonitor.setStatusMessage("Parsing Generic Results file - " + maxValue + " rows");
         boolean FDR = false;
 
          //skip the first line which just has the field names (start i=1)
@@ -295,10 +297,9 @@ else if(tokens[4].equalsIgnoreCase(downPhenotype))
             int percentComplete = (int) (((double) currentProgress / maxValue) * 100);
             //  Estimate Time Remaining
             long timeRemaining = maxValue - currentProgress;
-            if (taskMonitor != null) {
+            if (taskMonitor != null) 
                     taskMonitor.setProgress(percentComplete);
-                    taskMonitor.setStatusMessage("Parsing Generic Results file " + currentProgress + " of " + maxValue);
-                }
+                
             currentProgress++;
 
              //check to see if the gene set has already been entered in the results
diff --git a/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/parsers/RanksFileReaderTask.java b/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/parsers/RanksFileReaderTask.java
@@ -152,6 +152,8 @@ public void parse(TaskMonitor taskMonitor) throws IOException {
         String[] lines = fullText.split("\r\n?|\n");
         int currentProgress = 0;
         maxValue = lines.length;
+        if(taskMonitor != null)
+            taskMonitor.setStatusMessage("Parsing Rank file - " + maxValue + " rows");  
 
         HashMap<String,Integer> genes = dataset.getMap().getGenes();
         // we don't know the number of scores in the rank file yet, but it can't be more than the number of lines.
@@ -266,8 +268,7 @@ else if(tokens.length == 2){
             // Calculate Percentage.  This must be a value between 0..100.
             if (taskMonitor != null) {
             	int percentComplete = (int) (((double) currentProgress / maxValue) * 100);
-                taskMonitor.setProgress(percentComplete);
-                taskMonitor.setStatusMessage("Parsing Rank file " + currentProgress + " of " + maxValue);                    
+                taskMonitor.setProgress(percentComplete);                  
             }
             currentProgress++;
 
diff --git a/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/task/BuildDiseaseSignatureTask.java b/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/task/BuildDiseaseSignatureTask.java
@@ -180,6 +180,8 @@ public void buildDiseaseSignature(TaskMonitor taskMonitor) {
          * and Enrichment Genesets.                         *
          ****************************************************/
         int maxValue = SelectedSignatureGenesets.size() * EnrichmentGenesets.size();
+        if(taskMonitor != null)
+            taskMonitor.setStatusMessage("Computing Geneset similarity - " + maxValue + " rows");
         int currentProgress = 0;
         double currentNodeY_offset = paParams.getCurrentNodePlacementY_Offset();
         double currentNodeY_increment = 150.0;
@@ -240,7 +242,6 @@ public void buildDiseaseSignature(TaskMonitor taskMonitor) {
                     // Estimate Time Remaining
                     if (taskMonitor != null) {
                        taskMonitor.setProgress(percentComplete);
-                       taskMonitor.setStatusMessage("Computing Geneset similarity " + currentProgress + " of " + maxValue);
                        taskMonitor.setTitle("Post Analysis");
                     }
                     currentProgress++;
diff --git a/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/task/ComputeSimilarityTask.java b/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/task/ComputeSimilarityTask.java
@@ -136,6 +136,8 @@ else if (type == SIGNATURE ){
             
             int currentProgress = 0;
             int maxValue = genesetsOfInterest.size();
+            if(taskMonitor != null)
+                taskMonitor.setStatusMessage("Computing Geneset similarity - " + maxValue + " similarities"); 
 
             //figure out if we need to compute edges for two different expression sets or one.
             int enrichment_set =0;
@@ -153,10 +155,9 @@ else if (type == SIGNATURE ){
                 //int percentComplete = (int) (((double) currentProgress / maxValue) * 100);
                 //  Estimate Time Remaining
                 long timeRemaining = maxValue - currentProgress;
-                if (taskMonitor != null) {
-                   taskMonitor.setProgress((double) currentProgress / maxValue);
-                   taskMonitor.setStatusMessage("Computing Geneset similarity " + currentProgress + " of " + maxValue);                
-                }
+                if (taskMonitor != null) 
+                   taskMonitor.setProgress((double) currentProgress / maxValue);             
+                
                 currentProgress++;
 
                 String geneset1_name = i.next().toString();
@@ -239,18 +240,18 @@ else if(geneset_similarities.containsKey(similarity_key1) || geneset_similaritie
                 genesetsInnerLoop = genesetsOfInterest_set2;
                 
                 maxValue = genesetsOfInterest.size() + genesetsOfInterest_set2.size();
-                
+                if(taskMonitor != null)
+                    taskMonitor.setStatusMessage("Computing Geneset similarity - " + maxValue + " similarities");   
                //iterate through the each of the GSEA Results of interest - for the second set.
                 for(Iterator i = genesetsOfInterest_set2.keySet().iterator(); i.hasNext(); ){
 
                     // Calculate Percentage.  This must be a value between 0..100.
                     int percentComplete = (int) (((double) currentProgress / maxValue) * 100);
                     //  Estimate Time Remaining
                     long timeRemaining = maxValue - currentProgress;
-                    if (taskMonitor != null) {
-                        taskMonitor.setProgress((double) currentProgress / maxValue);
-                        taskMonitor.setStatusMessage("Computing Geneset similarity " + currentProgress + " of " + maxValue);                       
-                    }
+                    if (taskMonitor != null) 
+                        taskMonitor.setProgress((double) currentProgress / maxValue);                       
+                    
                     currentProgress++;
 
                     String geneset1_name = i.next().toString();
diff --git a/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/task/CreateEnrichmentMapNetworkTask.java b/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/task/CreateEnrichmentMapNetworkTask.java
@@ -232,6 +232,8 @@ public boolean computeMap(){
              
             int currentProgress = 0;
             int maxValue = genesetsOfInterest.size();
+            if(taskMonitor != null)
+                taskMonitor.setStatusMessage("Building Enrichment Map - " + maxValue + " genesets"); 
 
             //create the nodes
             //Each geneset of interest is a node
@@ -321,10 +323,9 @@ public boolean computeMap(){
                 int percentComplete = (int) (((double) currentProgress / maxValue) * 100);
                 //  Estimate Time Remaining
                 long timeRemaining = maxValue - currentProgress;
-                if (taskMonitor != null) {
+                if (taskMonitor != null) 
                     taskMonitor.setProgress(percentComplete);
-                    taskMonitor.setStatusMessage("Building Enrichment Map " + currentProgress + " of " + maxValue);                    
-                }
+
                 currentProgress++;
 
             }
diff --git a/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/task/FilterSignatureGSTask.java b/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/task/FilterSignatureGSTask.java
@@ -39,7 +39,7 @@ private void filterSignatureGS(TaskMonitor taskMonitor) {
 			DefaultListModel<String> signatureSetNames = paParams.getSignatureSetNames();
 	        DefaultListModel<String> selectedSignatureSetNames = paParams.getSelectedSignatureSetNames();
 	        signatureSetNames.clear(); // clear, that we don't have duplicates afterwards - Bug #103 a
-	        
+	        	        
 	        //filter the signature genesets to only include genesets that overlap with the genesets in our current map.
 	        
 	        // Use the same genesets that are saved to the session file (bug #66)
@@ -49,13 +49,17 @@ private void filterSignatureGS(TaskMonitor taskMonitor) {
 	        String[] setNamesArray = paParams.getSignatureGenesets().getGenesets().keySet().toArray(new String[0]);
 	        Arrays.sort(setNamesArray);
 	        
+	        if(taskMonitor != null)
+	        	taskMonitor.setStatusMessage("Analyzing "+ setNamesArray.length+ " genesets"  );
+	        
+	        
 	        FilterMetric filterMetric = null;
         	
 	        for (int i = 0; i < setNamesArray.length; i++) {  
 	        	
 	        	int percentComplete = (int) (((double) i / setNamesArray.length) * 100);
-	            taskMonitor.setStatusMessage("Analyzing geneset " + (i + 1) + " of " + setNamesArray.length);
-	            taskMonitor.setProgress(percentComplete);
+	            if(taskMonitor != null)
+	            	taskMonitor.setProgress(percentComplete);
 	            if (cancelled)
 	                throw new InterruptedException();
 	            String signatureGeneset = setNamesArray[i];
diff --git a/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/task/InitializeGenesetsOfInterestTask.java b/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/task/InitializeGenesetsOfInterestTask.java
@@ -106,7 +106,7 @@ public boolean initializeSets(){
  
         //create subset of genesets that contains only the genesets of interest with pvalue and qbalue less than values
         //specified by the user.
-               
+       	
         //Go through each Dataset populating the Gene set of interest in each dataset object
         HashMap<String,DataSet> datasets = map.getDatasets();
         for(Iterator<String> j = datasets.keySet().iterator();j.hasNext();){
@@ -136,6 +136,10 @@ public boolean initializeSets(){
         		int currentProgress = 0;
         		int maxValue = enrichmentResults.size() ;
         		
+        	  	if(taskMonitor!=null)
+        			taskMonitor.setStatusMessage("Initializing " + maxValue + " genesets");
+            
+        		
         		//if there are no enrichment Results then do nothing
         		if(enrichmentResults == null || enrichmentResults.isEmpty())
         			return false;
@@ -147,11 +151,9 @@ public boolean initializeSets(){
         			int percentComplete = (int) (((double) currentProgress / maxValue) * 100);
         			//  Estimate Time Remaining
         			long timeRemaining = maxValue - currentProgress;
-        			if (taskMonitor != null) {
+        			if (taskMonitor != null) 
         				taskMonitor.setProgress(percentComplete);
-        				taskMonitor.setStatusMessage("Parsing GMT file " + currentProgress + " of " + maxValue);
-        				
-        			}
+
         			currentProgress++;
 
         			String current_name = i.next().toString();
