coloring wasn't applied to center

CHANGELOG

@@ -7,6 +7,8 @@ minerva (14.0.6) stable; urgency=medium
     displayed at all (regresion 14.0.5, #1045)
   * Bug fix: when there is a problem with database during removing project, 
     project removal doesn't hang (#1058)
+  * Bug fix: coloring of the reaction wasn't applied to center of reaction
+    (#1057)
 
  -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 18 Dec 2019 12:00:00 +0200
 

converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverter.java

@@ -296,8 +296,15 @@ public class ReactionConverter extends BioEntityConverter<Reaction> {
    *          {@link ColorSchema} to modify reaction
    */
   private void applyColorSchema(Reaction reaction, ColorSchema colorSchema) {
+    PolylineData pd = new PolylineData(reaction.getLine());
+    pd.setColor(colorExtractor.getNormalizedColor(colorSchema));
+    if (colorSchema.getLineWidth() != null) {
+      pd.setWidth(colorSchema.getLineWidth());
+    }
+    reaction.setLine(pd);
+
     for (AbstractNode node : reaction.getNodes()) {
-      PolylineData pd = new PolylineData(node.getLine());
+      pd = new PolylineData(node.getLine());
       pd.setColor(colorExtractor.getNormalizedColor(colorSchema));
       if (colorSchema.getLineWidth() != null) {
         pd.setWidth(colorSchema.getLineWidth());

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

@@ -81,13 +81,17 @@ public class ColorModelCommand extends ModelCommand {
    * @throws InvalidColorSchemaException
    *           thrown when {@link Reaction} was already colored by other schema
    */
-  private void applyColor(Reaction reaction, ColorSchema schema) throws InvalidColorSchemaException {
+  void applyColor(Reaction reaction, ColorSchema schema) throws InvalidColorSchemaException {
     if (!reaction.getReactants().get(0).getLine().getColor().equals(Color.BLACK)) {
       throw new InvalidColorSchemaException(
           "At least two rows try to set color to reaction: " + reaction.getIdReaction());
     }
 
     Color color = colorExtractor.getNormalizedColor(schema);
+    reaction.getLine().setColor(color);
+    if (schema.getLineWidth() != null) {
+      reaction.getLine().setWidth(schema.getLineWidth());
+    }
     for (AbstractNode node : reaction.getNodes()) {
       node.getLine().setColor(color);
       if (schema.getLineWidth() != null) {
@@ -342,6 +346,7 @@ public class ColorModelCommand extends ModelCommand {
       element.setGlyph(null);
     }
     for (Reaction reaction : result.getReactions()) {
+      reaction.getLine().setColor(Color.BLACK);
       for (AbstractNode node : reaction.getNodes()) {
         node.getLine().setColor(Color.BLACK);
       }

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

@@ -2,9 +2,8 @@ package lcsb.mapviewer.commands;
 
 import static org.junit.Assert.*;
 
-import java.awt.*;
+import java.awt.Color;
 import java.util.*;
-import java.util.List;
 
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
@@ -460,4 +459,21 @@ public class ColorModelCommandTest extends CommandTestFunctions {
     assertNotNull(factory.getModifiedElements().get(reaction));
   }
 
+  @Test
+  public void testApplyColorToReaction() throws Exception {
+    Model model = getModelForFile("testFiles/sample.xml", false);
+    Reaction re4 = model.getReactionByReactionId("re1");
+
+    ColorSchema schema = new GenericColorSchema();
+    schema.setElementId("re1");
+    schema.setColor(Color.YELLOW);
+    schema.setName(null);
+
+    ColorModelCommand factory = new ColorModelCommand(model, new ArrayList<>(), colorExtractor);
+
+    factory.applyColor(re4, schema);
+
+    assertEquals(Color.YELLOW, re4.getLine().getColor());
+  }
+
 }