Fix heat map update bug when changing Transform.

Author: mikekucera

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

@@ -42,7 +42,7 @@ public Optional<String> getPhenotype(int idx) {
 	}
 
 	@Override
-	public double getValue(int geneID, int idx, Compress compress) {
+	public double getValue(int geneID, int idx, Compress compress, Transform transform) {
 		EMDataSet dataset = getDataSet(idx);
 		String pheno = getName(idx);
 
@@ -51,7 +51,7 @@ public double getValue(int geneID, int idx, Compress compress) {
 		if (phenotypes == null || phenotypes.length == 0)
 			return Double.NaN;
 
-		Optional<float[]> optExpr = expressionCache.getExpressions(dataset, geneID);
+		Optional<float[]> optExpr = expressionCache.getExpressions(geneID, dataset, transform);
 
 		if (!optExpr.isPresent())
 			return Double.NaN;

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

@@ -21,9 +21,9 @@ public EMDataSet getDataSet(int idx) {
 	}
 
 	@Override
-	public double getValue(int geneID, int idx, Compress compress) {
+	public double getValue(int geneID, int idx, Compress compress, Transform transform) {
 		EMDataSet dataset = getDataSet(idx);
-		Optional<float[]> expression = expressionCache.getExpressions(dataset, geneID);
+		Optional<float[]> expression = expressionCache.getExpressions(geneID, dataset, transform);
 
 		if (compress == null || !expression.isPresent())
 			return Float.NaN;

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

@@ -6,47 +6,45 @@
 
 import javax.annotation.Nullable;
 
-import org.apache.commons.lang3.tuple.Pair;
+import org.apache.commons.lang3.tuple.Triple;
 
 import com.google.common.cache.Cache;
 import com.google.common.cache.CacheBuilder;
 
 public class ExpressionCache {
 
-	private final Cache<Pair<Integer, EMDataSet>, Optional<float[]>> cache;
-	private final Transform transform;
+	private final Cache<Triple<Integer,EMDataSet,Transform>, Optional<float[]>> cache;
 
-	public ExpressionCache(Transform transform) {
-		this.transform = transform;
+	public ExpressionCache() {
 		this.cache = CacheBuilder.newBuilder().maximumSize(20).build();
 	}
 
-	public Optional<float[]> getExpressions(EMDataSet dataset, int geneID) {
+	public Optional<float[]> getExpressions(int geneID, EMDataSet dataset, Transform transform) {
 		try {
-			return cache.get(Pair.of(geneID, dataset), 
-				() -> Optional.ofNullable(getExpression(dataset, geneID, transform))
+			return cache.get(Triple.of(geneID, dataset, transform), 
+				() -> Optional.ofNullable(getExpression(geneID, dataset, transform))
 			);
 		} catch (ExecutionException e) {
 			return Optional.empty();
 		}
 	}
 
-	public float getExpression(EMDataSet dataset, int geneID, int expressionIndex) {
-		Optional<float[]> vals = getExpressions(dataset, geneID);
+	public float getExpression(int geneID, EMDataSet dataset, Transform transform, int expressionIndex) {
+		Optional<float[]> vals = getExpressions(geneID, dataset, transform);
 
 		return vals.isPresent() ? vals.get()[expressionIndex] : Float.NaN;
 	}
 
-	public static GeneExpression getGeneExpression(EMDataSet dataset, int geneID) {
+	public static GeneExpression getGeneExpression(int geneID, EMDataSet dataset) {
 		GeneExpressionMatrix matrix = dataset.getExpressionSets();
 		Map<Integer, GeneExpression> expressions = matrix.getExpressionMatrix();
 		GeneExpression row = expressions.get(geneID);
 
 		return row;
 	}
 
-	private static @Nullable float[] getExpression(EMDataSet dataset, int geneID, Transform transform) {
-		GeneExpression expression = getGeneExpression(dataset, geneID);
+	private static @Nullable float[] getExpression(int geneID, EMDataSet dataset, Transform transform) {
+		GeneExpression expression = getGeneExpression(geneID, dataset);
 
 		if (expression != null) {
 			switch (transform) {

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

@@ -9,7 +9,7 @@ public interface ExpressionData {
 
 	EMDataSet getDataSet(int col);
 
-	double getValue(int geneID, int col, Compress compress);
+	double getValue(int geneID, int col, Compress compress, Transform transform);
 
 	String getName(int col);
 

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

@@ -37,10 +37,10 @@ private int getIndexInDataSet(int idx) {
 	}
 
 	@Override
-	public double getValue(int geneID, int idx, Compress compress) {
+	public double getValue(int geneID, int idx, Compress compress, Transform transform) {
 		EMDataSet dataset = getDataSet(idx);
 
-		return expressionCache.getExpression(dataset, geneID, getIndexInDataSet(idx));
+		return expressionCache.getExpression(geneID, dataset, transform, getIndexInDataSet(idx));
 	}
 
 	@Override

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

@@ -130,7 +130,7 @@ private void updateExpressionDataColumn() {
 				continue;
 
 			for (int i = 0; i < n; i++) {
-				double value = exp.getValue(id, i, options.getCompress());
+				double value = exp.getValue(id, i, options.getCompress(), options.getTransform());
 				data[i] = value;
 			}
 		}

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/control/ControlPanelMediator.java

@@ -804,7 +804,7 @@ private AssociatedStyleOptions createAssociatedStyleOptions(EnrichmentMap map, A
 
 	private ExpressionData createExpressionData(EnrichmentMap map, List<EMDataSet> datasets, Transform transform, Compress compress) {
 		ExpressionData exp = null;
-		ExpressionCache cache = new ExpressionCache(transform);
+		ExpressionCache cache = new ExpressionCache();
 
 		switch (compress) {
 			case DATASET_MEDIAN:

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

@@ -89,7 +89,7 @@ public void update(
 			datasets = Collections.emptyList();
 		}
 
-		expressionCache = new ExpressionCache(transform);
+		expressionCache = new ExpressionCache();
 
 		ExpressionData uncompressed = new Uncompressed(datasets, expressionCache);
 		ExpressionData compressedDataSet = new CompressedDataSet(datasets, expressionCache, map != null && map.isDistinctExpressionSets());
@@ -120,7 +120,6 @@ public void setTransform(Transform transform, Compress compress) {
 		boolean structureChanged = !this.compress.sameStructure(compress);
 		this.transform = transform;
 		this.compress = compress;
-		this.expressionCache = new ExpressionCache(transform);
 
 		if (structureChanged)
 			fireTableStructureChanged();
@@ -220,7 +219,7 @@ public Object getValueAt(int row, int col) {
 		ExpressionData exp = data.get(compress);
 		if(exp == null || geneID == null)
 			return Double.NaN; // because the DefaultRowSorter doesn't sort null the way we want
-		return exp.getValue(geneID, col - DESC_COL_COUNT, compress);
+		return exp.getValue(geneID, col - DESC_COL_COUNT, compress, transform);
 	}
 
 	public RankValue getRankValue(int row) {