PA dialog wasn't handling case where there are no ranks. Fixes #304

Author: mikekucera

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

@@ -207,7 +207,7 @@ private FilterMetric.MannWhit processMannWhitneyArgs(EnrichmentMap map, EMDataSe
 		if(mannWhitRanks.isEmpty() && map.isSingleRanksPerDataset()) {
 			String ranksName = dataset.getAllRanksNames().iterator().next();
 			Ranking ranking = dataset.getRanksByName(ranksName);
-			return new FilterMetric.MannWhit(cutoff, ranksName, ranking, type);
+			return new FilterMetric.MannWhit(type, cutoff, ranksName, ranking);
 		} else if(mannWhitRanks.isEmpty()) {
 			throw new IllegalArgumentException("At least one of the data sets you have specified has more than one ranks file. "
 					+ "You must use the 'mannWhitRanks' parameter to specify which ranking to use for each data set.");
@@ -226,10 +226,10 @@ private FilterMetric.MannWhit processMannWhitneyArgs(EnrichmentMap map, EMDataSe
 			if(rankFile == null && ranksNames.size() == 1) {
 				String ranksName = ranksNames.iterator().next();
 				Ranking ranking = dataset.getRanksByName(ranksName);
-				return new FilterMetric.MannWhit(cutoff, ranksName, ranking, type);
+				return new FilterMetric.MannWhit(type, cutoff, ranksName, ranking);
 			} else {
 				Ranking ranking = dataset.getRanksByName(rankFile);
-				return new FilterMetric.MannWhit(cutoff, rankFile, ranking, type);
+				return new FilterMetric.MannWhit(type, cutoff, rankFile, ranking);
 			}
 		}
 	}

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/task/postanalysis/FilterMetric.java

@@ -205,11 +205,11 @@ public String getDisplayString() {
 	class MannWhit extends BaseFilterMetric {
 
 		private final String rankingName;
-		private final Ranking ranks;
+		private final @Nullable Ranking ranks;
 		private final MannWhitneyMemoized mannWhitneyCache = new MannWhitneyMemoized();
+
 
-		
-		public MannWhit(double filter, String rankingName, Ranking ranks, PostAnalysisFilterType type) {
+		public MannWhit(PostAnalysisFilterType type, double filter, String rankingName, Ranking ranks) {
 			super(type, filter);
 			if(!type.isMannWhitney())
 				throw new IllegalArgumentException("FilterType is not Mann Whitney: " + type);
@@ -228,7 +228,7 @@ public double moreSimilar(double x, double y) {
 		public double computeValue(Set<Integer> geneSet, Set<Integer> sigSet, @Nullable SignatureGenesetSimilarity similarity) {
 			Set<Integer> intersection = Sets.intersection(geneSet, sigSet);
 			int size = intersection.size();
-			if(ranks.isEmpty() || size == 0) {
+			if(ranks == null || ranks.isEmpty() || size == 0) {
 				if(similarity != null) {
 					similarity.setMannWhitPValueTwoSided(1.0); // avoid NoDataException
 					similarity.setMannWhitPValueGreater(1.0);

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/postanalysis/PAWeightPanel.java

@@ -17,6 +17,7 @@
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
+import java.util.Set;
 
 import javax.swing.ButtonGroup;
 import javax.swing.DefaultComboBoxModel;
@@ -425,32 +426,35 @@ private JPanel createMannWhittCard() {
 		JPanel body = new JPanel(new GridBagLayout());
 		int y = 0;
 		for(EMDataSet dataset : dataSets) {
-			final String dataSetName = dataset.getName();
-			JLabel label = new JLabel(dataSetName + ":");
-			JComboBox<String> combo = new JComboBox<>();
-			for(String ranksName : dataset.getAllRanksNames()) {
-				combo.addItem(ranksName);
+			Set<String> ranksNames = dataset.getAllRanksNames();
+			if(ranksNames != null && !ranksNames.isEmpty()) {
+				final String dataSetName = dataset.getName();
+				JLabel label = new JLabel(dataSetName + ":");
+				JComboBox<String> combo = new JComboBox<>();
+				for(String ranksName : ranksNames) {
+					combo.addItem(ranksName);
+				}
+				SwingUtil.makeSmall(label, combo);
+				if(combo.getItemCount() <= 1) {
+					combo.setEnabled(false);
+				}
+				
+				String ranksName = mannWhitRanks.get(dataSetName);
+				if(ranksName == null)
+					mannWhitRanks.put(dataSetName, combo.getSelectedItem().toString());
+				else
+					combo.setSelectedItem(ranksName);
+				
+				combo.addActionListener(e -> {
+					String ranks = combo.getSelectedItem().toString();
+					mannWhitRanks.put(dataSetName, ranks);
+					firePropertyChange(PROPERTY_PARAMETERS, false, true);
+				});
+				
+				body.add(label, GBCFactory.grid(0,y).weightx(.5).anchor(EAST).fill(NONE).get());
+				body.add(combo, GBCFactory.grid(1,y).weightx(.5).get());
+				y++;
 			}
-			SwingUtil.makeSmall(label, combo);
-			if(combo.getItemCount() <= 1) {
-				combo.setEnabled(false);
-			}
-			
-			String ranksName = mannWhitRanks.get(dataSetName);
-			if(ranksName == null)
-				mannWhitRanks.put(dataSetName, combo.getSelectedItem().toString());
-			else
-				combo.setSelectedItem(ranksName);
-			
-			combo.addActionListener(e -> {
-				String ranks = combo.getSelectedItem().toString();
-				mannWhitRanks.put(dataSetName, ranks);
-				firePropertyChange(PROPERTY_PARAMETERS, false, true);
-			});
-			
-			body.add(label, GBCFactory.grid(0,y).weightx(.5).anchor(EAST).fill(NONE).get());
-			body.add(combo, GBCFactory.grid(1,y).weightx(.5).get());
-			y++;
 		}
 
 		JPanel container = new JPanel(new BorderLayout());
@@ -611,8 +615,8 @@ public FilterMetric createFilterMetric(String dataset) {
 			case MANN_WHIT_GREATER:
 			case MANN_WHIT_LESS:
 				String rankingName = mannWhitRanks.get(dataset);
-				Ranking ranking = map.getDataSet(dataset).getRanks().get(rankingName);
-				return new FilterMetric.MannWhit(value, rankingName, ranking, type);
+				Ranking ranking = rankingName == null ? null :  map.getDataSet(dataset).getRanks().get(rankingName);
+				return new FilterMetric.MannWhit(type, value, rankingName, ranking);
 			default:
 				return null;
 		}

EnrichmentMapPlugin/src/test/java/org/baderlab/csplugins/enrichmentmap/task/PostAnalysisTaskTest.java

@@ -111,7 +111,7 @@ public void test_2_PostAnalysisMannWhitney(@Continuous VisualMappingFunctionFact
 		PostAnalysisFilterType mannWhitTwoSided = PostAnalysisFilterType.MANN_WHIT_TWO_SIDED;
 
 		FilterMetricSet rankTest = new FilterMetricSet(PostAnalysisFilterType.MANN_WHIT_TWO_SIDED);
-		rankTest.put(LegacySupport.DATASET1, new FilterMetric.MannWhit(mannWhitTwoSided.defaultValue, null, ranking, mannWhitTwoSided));
+		rankTest.put(LegacySupport.DATASET1, new FilterMetric.MannWhit(mannWhitTwoSided, mannWhitTwoSided.defaultValue, null, ranking));
 		builder.setRankTestParameters(rankTest);
 
 		runPostAnalysis(emNetwork, builder, PATH + "PA_top8_middle8_bottom8.gmt", LegacySupport.DATASET1);