Resolve GSEA time-series files. Fixes #135.

Author: mikekucera

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

@@ -119,4 +119,8 @@ public int size() {
 	public void clear() {
 		geneSets.clear();
 	}
+	
+	public boolean isEmpty() {
+		return geneSets.isEmpty();
+	}
 }

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/resolver/GSEAResolver.java

@@ -193,21 +193,25 @@ private static String[] getRptPhenotypes(Map<String, String> params) {
 		String phenotype1 = "na";
 		String phenotype2 = "na";
 
-		if (classes != null && method.equalsIgnoreCase("Gsea")) {
+		if(classes != null && method.equalsIgnoreCase("Gsea")) {
 			String[] classes_split = classes.split("#");
 			// only and try parse classes out of label if they are there
-			if (classes_split.length >= 2) {
+			if(classes_split.length >= 2) {
 				String phenotypes = classes_split[1];
 				String[] phenotypes_split = phenotypes.split("_versus_");
-				if (phenotypes_split.length >= 2) {
+				if(phenotypes_split.length >= 2) {
 					phenotype1 = phenotypes_split[0];
 					phenotype2 = phenotypes_split[1];
 				}
+				else if(phenotypes_split.length == 1) {
+					phenotype1 = phenotypes_split[0] + "_pos";
+					phenotype2 = phenotypes_split[0] + "_neg";
+				}
 			}
-		} else if (method.equalsIgnoreCase("GseaPreranked")) {
+		} else if(method.equalsIgnoreCase("GseaPreranked")) {
 			phenotype1 = "na_pos";
 			phenotype2 = "na_neg";
-			if (params.containsKey("param phenotypes")) {
+			if(params.containsKey("param phenotypes")) {
 				String phenotypes = params.get("param phenotypes");
 				String[] phenotypes_split = phenotypes.split("_versus_");
 				if (phenotypes_split.length >= 2) {

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

@@ -56,6 +56,7 @@
 import org.baderlab.csplugins.enrichmentmap.model.GSEAResult;
 import org.baderlab.csplugins.enrichmentmap.model.GeneSet;
 import org.baderlab.csplugins.enrichmentmap.model.Ranking;
+import org.baderlab.csplugins.enrichmentmap.model.SetOfGeneSets;
 import org.baderlab.csplugins.enrichmentmap.util.DiscreteTaskMonitor;
 import org.baderlab.csplugins.enrichmentmap.util.NullTaskMonitor;
 import org.cytoscape.work.AbstractTask;
@@ -90,7 +91,7 @@ public void setThrowIfMissing(boolean throwIfMissing) {
 	 * 
 	 * @return true if successful and false otherwise.
 	 */
-	public boolean initializeSets(TaskMonitor tm) {
+	public void initializeSets(TaskMonitor tm) {
 		if(tm == null)
 			tm = new NullTaskMonitor();
 		DiscreteTaskMonitor taskMonitor = new DiscreteTaskMonitor(tm, map.getDataSetCount());
@@ -120,7 +121,7 @@ public boolean initializeSets(TaskMonitor tm) {
 
 			//if there are no enrichment Results then do nothing
 			if(enrichmentResults == null || enrichmentResults.isEmpty()) {
-				return false;
+				continue;
 			}
 
 			//iterate through the GSEA Results to figure out which genesets we want to use
@@ -161,9 +162,12 @@ else if(throwIfMissing) {
 			}
 		}
 
-		// MKTODO clear all the genesets that are not "of interest" just to free up memory
+		boolean empty = datasets.values().stream().map(EMDataSet::getGeneSetsOfInterest).allMatch(SetOfGeneSets::isEmpty);
+		if(empty) {
+			throw new IllegalArgumentException("None of the gene sets have passed the filter. Try relaxing the gene set filter parameters.");
+		}
 
-		return true;
+		// MKTODO clear all the genesets that are not "of interest" just to free up memory
 	}
 
 	private void updateRankAtMax(GSEAResult current_result, Ranking ranks) {

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/creation/MasterDetailDialogPage.java

@@ -147,7 +147,7 @@ public void finish() {
 			}
 		}
 
-		System.out.println(params);
+//		System.out.println(params);
 
 		CreateEnrichmentMapTaskFactory taskFactory = taskFactoryFactory.create(params, dataSets);
 		TaskIterator tasks = taskFactory.createTaskIterator();