optimization: model.getBioEntities is computed per call - changing order increase speed by 2

model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java

@@ -4,8 +4,10 @@ import java.awt.Color;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.HashMap;
+import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
+import java.util.Set;
 
 import org.apache.log4j.Logger;
 
@@ -289,9 +291,10 @@ public class ColorModelCommand extends ModelCommand {
     List<Model> models = new ArrayList<>();
     models.add(getModel());
     models.addAll(getModel().getSubmodels());
+
     for (Model model : models) {
-      for (ColorSchema schema : schemas) {
-        for (BioEntity element : model.getBioEntities()) {
+      for (BioEntity element : model.getBioEntities()) {
+        for (ColorSchema schema : schemas) {
           if (match(element, schema)) {
             if (result.get(element) != null
                 && !colorExtractor.getNormalizedColor(result.get(element)).equals(Color.WHITE)) {

model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java

@@ -2,6 +2,7 @@ package lcsb.mapviewer.commands;
 
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
 import static org.junit.Assert.assertTrue;
 
 import java.awt.Color;
@@ -537,4 +538,32 @@ public class ColorModelCommandTest extends CommandTestFunctions {
     }
   }
 
+  @Test
+  public void testGetModifiedElements() throws Exception {
+    try {
+      Reaction reaction = new Reaction();
+      reaction.addMiriamData(new MiriamData(MiriamType.PUBMED, "1234"));
+      
+      Model model = new ModelFullIndexed(null);
+      model.addReaction(reaction);
+
+      GenericColorSchema colorSchema = new GenericColorSchema();
+      colorSchema.addMiriamData(new MiriamData(MiriamType.PUBMED,"1234"));
+
+      List<ColorSchema> schemas = new ArrayList<>();
+      schemas.add(colorSchema);
+
+      ColorModelCommand factory = new ColorModelCommand(model, schemas, colorExtractor);
+
+      assertNotNull(factory.getModifiedElements().get(reaction));
+
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+
+  }
+
+  
+
 }