Fix Hypergeometric distance setting.

Author: mikekucera

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

@@ -25,16 +25,17 @@ public class ClusterRankingOption implements RankingOption {
 	private final TaskManager<?,?> taskManager;
 
 	private final EnrichmentMap map;
-	private Distance distance = Distance.PEARSON;
+	private Distance distance;
 
 	public interface Factory {
-		ClusterRankingOption create(EnrichmentMap map);
+		ClusterRankingOption create(EnrichmentMap map, Distance distance);
 	}
 
 	@Inject
-	public ClusterRankingOption(@Assisted EnrichmentMap map, @Dialog TaskManager<?,?> taskManager) {
+	public ClusterRankingOption(@Assisted EnrichmentMap map, @Assisted Distance distance, @Dialog TaskManager<?,?> taskManager) {
 		this.map = map;
 		this.taskManager = taskManager;
+		this.distance = distance;
 	}
 
 	@Override

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

@@ -291,7 +291,7 @@ private void updateHeatMap(CyNetworkView networkView) {
 
 		List<RankingOption> rankOptions = getDataSetRankOptions(map, network, selectedNodes, selectedEdges);
 		HeatMapParams params = getHeatMapParams(map, network.getSUID(), onlyEdges);
-		ClusterRankingOption clusterRankingOption = getClusterRankingOption(map);
+		ClusterRankingOption clusterRankingOption = clusterRankOptionFactory.create(map, params.getDistanceMetric());
 
 		invokeOnEDT(() -> {
 			HeatMapContentPanel contentPanel = getContentPanel();
@@ -353,7 +353,7 @@ private void updateHeatMapPanel() {
 		EnrichmentMap map = tableModel.getEnrichmentMap();
 		CyNetwork network = networkManager.getNetwork(map.getNetworkID());
 		List<RankingOption> rankOptions = getDataSetRankOptions(map);
-		ClusterRankingOption clusterRankingOption = getClusterRankingOption(map);
+		ClusterRankingOption clusterRankingOption = clusterRankOptionFactory.create(map, params.getDistanceMetric());
 
 		resetWithoutListeners(() -> {
 			getContentPanel().update(network, map, params, rankOptions, getContentPanel().getUnionGenes(), getContentPanel().getInterGenes(), clusterRankingOption);
@@ -392,9 +392,10 @@ private void updateSetting_ShowValues() {
 	}
 
 	private void updateSetting_Distance(Distance distance) {
-		EnrichmentMap map = getContentPanel().getEnrichmentMap();
-		ClusterRankingOption clusterRankingOption = getClusterRankingOption(map);
-		clusterRankingOption.setDistance(distance);
+		RankingOption clusterRankingOption = getContentPanel().getClusterRankingOption();
+		if(clusterRankingOption instanceof ClusterRankingOption) {
+			((ClusterRankingOption)clusterRankingOption).setDistance(distance);
+		}
 		getContentPanel().setSelectedRankingOption(clusterRankingOption);
 		settingChanged();
 	}
@@ -406,10 +407,6 @@ private void settingChanged() {
 		}
 	}
 
-	public ClusterRankingOption getClusterRankingOption(EnrichmentMap map) {
-		return clusterRankOptionFactory.create(map);
-	}
-	
 	public List<RankingOption> getDataSetRankOptions(EnrichmentMap map) {
 		CyNetwork network = networkManager.getNetwork(map.getNetworkID());
 

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

@@ -144,36 +144,22 @@ public JMenuItem getPathwayCommonsButton() {
 	}
 
 	public void update(HeatMapParams params) {
+		updateDistanceMenu(params.getDistanceMetric());
+	}
+
+	private void updateDistanceMenu(Distance dm) {
 		cosineRadio.removeActionListener(cosineListener);
 		euclideanRadio.removeActionListener(euclideanListener);
 		pearsonRadio.removeActionListener(pearsonListener);
 
-		updateDistanceMenu(params.getDistanceMetric());
+		cosineRadio.setSelected(dm == Distance.COSINE);
+		euclideanRadio.setSelected(dm == Distance.EUCLIDEAN);
+		pearsonRadio.setSelected(dm == Distance.PEARSON);
 
 		cosineRadio.addActionListener(cosineListener);
 		euclideanRadio.addActionListener(euclideanListener);
 		pearsonRadio.addActionListener(pearsonListener);
 	}
-
-	private void updateDistanceMenu(Distance dm) {
-		switch (dm) {
-			case COSINE:
-				cosineRadio.setSelected(true);
-				euclideanRadio.setSelected(false);
-				pearsonRadio.setSelected(false);
-				break;
-			case EUCLIDEAN:
-				cosineRadio.setSelected(false);
-				euclideanRadio.setSelected(true);
-				pearsonRadio.setSelected(false);
-				break;
-			case PEARSON:
-				cosineRadio.setSelected(false);
-				euclideanRadio.setSelected(false);
-				pearsonRadio.setSelected(true);
-				break;
-		}
-	}
 
 
 	public Distance getDistance() {