Fix NPE in GSEALeadingEdgeRankingOption.

Author: mikekucera

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/heatmap/GSEALeadingEdgeRankingOption.java

@@ -10,7 +10,6 @@
 
 import org.baderlab.csplugins.enrichmentmap.model.EMDataSet;
 import org.baderlab.csplugins.enrichmentmap.model.EMDataSet.Method;
-import org.baderlab.csplugins.enrichmentmap.model.EnrichmentResult;
 import org.baderlab.csplugins.enrichmentmap.model.GSEAResult;
 import org.baderlab.csplugins.enrichmentmap.model.GeneExpression;
 import org.baderlab.csplugins.enrichmentmap.model.Rank;
@@ -26,16 +25,16 @@ public class GSEALeadingEdgeRankingOption implements RankingOption {
 
 	private final String rankingName;
 	private final EMDataSet dataset;
-	private final String geneSetName;
+	private final GSEAResult result;
 
 	private double scoreAtMax;
 	private int rankAtMax;
 
 
-	public GSEALeadingEdgeRankingOption(EMDataSet dataset, String geneSetName, String rankingName) {
+	public GSEALeadingEdgeRankingOption(EMDataSet dataset, GSEAResult result, String rankingName) {
 		assert dataset.getMethod() == Method.GSEA;
+		this.result = result;
 		this.dataset = dataset;
-		this.geneSetName = geneSetName;
 		this.rankingName = rankingName;
 	}
 
@@ -123,8 +122,6 @@ else if (ranksSubset[m] >= topRank && isNegative && topRank != 0 && topRank != -
 	 * sets (both if there are two datasets)
 	 */
 	private void initializeLeadingEdge() {
-		Map<String,EnrichmentResult> results = dataset.getEnrichments().getEnrichments();
-		GSEAResult result = (GSEAResult) results.get(geneSetName);
 		scoreAtMax = result.getScoreAtMax();
 		if(scoreAtMax == DetermineEnrichmentResultFileReader.DefaultScoreAtMax) {
 			scoreAtMax = result.getNES();

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/heatmap/HeatMapMediator.java

@@ -14,6 +14,8 @@
 import org.baderlab.csplugins.enrichmentmap.model.EMDataSet.Method;
 import org.baderlab.csplugins.enrichmentmap.model.EnrichmentMap;
 import org.baderlab.csplugins.enrichmentmap.model.EnrichmentMapManager;
+import org.baderlab.csplugins.enrichmentmap.model.EnrichmentResult;
+import org.baderlab.csplugins.enrichmentmap.model.GSEAResult;
 import org.baderlab.csplugins.enrichmentmap.model.Ranking;
 import org.baderlab.csplugins.enrichmentmap.style.EMStyleBuilder;
 import org.baderlab.csplugins.enrichmentmap.util.CoalesceTimerStore;
@@ -200,10 +202,20 @@ private List<RankingOption> getDataSetRankOptions(EnrichmentMap map, CyNetwork n
 		for(EMDataSet dataset : map.getDataSetList()) {
 			if(nodes.size() == 1 && edges.isEmpty() && dataset.getMethod() == Method.GSEA) {
 				String geneSetName = network.getRow(nodes.get(0)).get(CyNetwork.NAME, String.class);
-				Map<String,Ranking> ranks = dataset.getRanks();
-				ranks.forEach((name, ranking) -> {
-					options.add(new GSEALeadingEdgeRankingOption(dataset, geneSetName, name));
-				});
+				Map<String,EnrichmentResult> results = dataset.getEnrichments().getEnrichments();
+				EnrichmentResult result = results.get(geneSetName);
+				if(result instanceof GSEAResult) {
+					GSEAResult gseaResult = (GSEAResult) result; 
+					Map<String,Ranking> ranks = dataset.getRanks();
+					ranks.forEach((name, ranking) -> {
+						options.add(new GSEALeadingEdgeRankingOption(dataset, gseaResult, name));
+					});
+				} else {
+					Map<String,Ranking> ranks = dataset.getRanks();
+					ranks.forEach((name, ranking) -> {
+						options.add(new BasicRankingOption(ranking, dataset, name));
+					});
+				}
 			} else {
 				Map<String,Ranking> ranks = dataset.getRanks();
 				ranks.forEach((name, ranking) -> {

EnrichmentMapPlugin/src/test/java/org/baderlab/csplugins/enrichmentmap/heatmap/HeatMapRanksTest.java

@@ -19,7 +19,9 @@
 import org.baderlab.csplugins.enrichmentmap.model.EMDataSet.Method;
 import org.baderlab.csplugins.enrichmentmap.model.EnrichmentMap;
 import org.baderlab.csplugins.enrichmentmap.model.EnrichmentMapManager;
+import org.baderlab.csplugins.enrichmentmap.model.EnrichmentResult;
 import org.baderlab.csplugins.enrichmentmap.model.EnrichmentResultFilterParams.NESFilter;
+import org.baderlab.csplugins.enrichmentmap.model.GSEAResult;
 import org.baderlab.csplugins.enrichmentmap.model.GeneSet;
 import org.baderlab.csplugins.enrichmentmap.model.LegacySupport;
 import org.baderlab.csplugins.enrichmentmap.model.Ranking;
@@ -91,7 +93,9 @@ public void testLeadingEdge(EnrichmentMapManager emManager) throws Exception {
 		assertNotNull(gs);
 
 		// Run the ranking
-		RankingOption rankingOption = new GSEALeadingEdgeRankingOption(dataset, geneSetName, Ranking.GSEARanking);
+		Map<String,EnrichmentResult> results = dataset.getEnrichments().getEnrichments();
+		GSEAResult result = (GSEAResult) results.get(geneSetName);
+		RankingOption rankingOption = new GSEALeadingEdgeRankingOption(dataset, result, Ranking.GSEARanking);
 		Map<Integer,RankValue> ranks = rankingOption.computeRanking(gs.getGenes()).get().get();
 		assertEquals(454, ranks.size());