Better expression caching for heatmap. Refs #294

Author: mikekucera

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

@@ -0,0 +1,67 @@
+package org.baderlab.csplugins.enrichmentmap.view.heatmap.table;
+
+import java.util.Map;
+import java.util.Optional;
+import java.util.concurrent.ExecutionException;
+
+import javax.annotation.Nullable;
+
+import org.apache.commons.lang3.tuple.Pair;
+import org.baderlab.csplugins.enrichmentmap.model.EMDataSet;
+import org.baderlab.csplugins.enrichmentmap.model.GeneExpression;
+import org.baderlab.csplugins.enrichmentmap.model.GeneExpressionMatrix;
+import org.baderlab.csplugins.enrichmentmap.view.heatmap.HeatMapParams.Transform;
+
+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;
+
+	public ExpressionCache(Transform transform) {
+		this.transform = transform;
+		this.cache = CacheBuilder.newBuilder().maximumSize(20).build();
+	}
+	
+	public Optional<float[]> getExpressions(EMDataSet dataset, int geneID) {
+		try {
+			return cache.get(Pair.of(geneID, dataset), 
+				() -> Optional.ofNullable(getExpression(dataset, geneID, transform))
+			);
+		} catch (ExecutionException e) {
+			return Optional.empty();
+		}
+	}
+	
+	public float getExpression(EMDataSet dataset, int geneID, int expressionIndex) {
+		Optional<float[]> vals = getExpressions(dataset, geneID);
+		if(vals.isPresent()) {
+			return vals.get()[expressionIndex];
+		} else {
+			return Float.NaN;
+		}
+	}
+	
+
+	public static GeneExpression getGeneExpression(EMDataSet dataset, int geneID) {
+		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);
+		if(expression != null) {
+			switch(transform) {
+				case ROW_NORMALIZE: return expression.rowNormalize();
+				case LOG_TRANSFORM: return expression.rowLogTransform();
+				case AS_IS:         return expression.getExpression();
+			}
+		}
+		return null;
+	}
+	
+}