Merge branch 'develop' into features/JAL-2094_colourInterface

[jalview.git] / src / jalview / appletgui / FeatureRenderer.java

diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java
index 82736d7..cd9495e 100644 (file)
--- a/src/jalview/appletgui/FeatureRenderer.java
+++ b/src/jalview/appletgui/FeatureRenderer.java
@@ -25,8 +25,10 @@ import jalview.datamodel.SearchResults;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.io.FeaturesFile;
+import jalview.schemes.Colour;
 import jalview.schemes.FeatureColour;
 import jalview.schemes.UserColourScheme;
+import jalview.util.ColorUtils;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
 
@@ -58,22 +60,10 @@ import java.util.Hashtable;
 public class FeatureRenderer extends
         jalview.renderer.seqfeatures.FeatureRenderer
 {
-
   // Holds web links for feature groups and feature types
   // in the form label|link
   Hashtable featureLinks = null;
 
-  /**
-   * Creates a new FeatureRenderer object.
-   * 
-   * @param av
-   */
-  public FeatureRenderer(AlignmentViewport av)
-  {
-    super(av);
-
-  }
-
   static String lastFeatureAdded;
 
   static String lastFeatureGroupAdded;
@@ -86,6 +76,16 @@ public class FeatureRenderer extends
 
   FeatureColourPanel colourPanel;
 
+  /**
+   * Creates a new FeatureRenderer object.
+   * 
+   * @param av
+   */
+  public FeatureRenderer(AlignmentViewport av)
+  {
+    super(av);
+  }
+
   class FeatureColourPanel extends Panel
   {
     String label = "";
@@ -103,7 +103,7 @@ public class FeatureRenderer extends
       String vlabel = "";
       if (newcol.isSimpleColour())
       {
-        bg = newcol.getColour();
+        bg = ColorUtils.getColor(newcol.getColour());
         setBackground(bg);
       }
       else
@@ -124,8 +124,8 @@ public class FeatureRenderer extends
         }
         else
         {
-          setBackground(bg = newcol.getMinColour());
-          maxCol = newcol.getMaxColour();
+          setBackground(bg = ColorUtils.getColor(newcol.getMinColour()));
+          maxCol = ColorUtils.getColor(newcol.getMaxColour());
         }
       }
       label = vlabel;
@@ -237,7 +237,7 @@ public class FeatureRenderer extends
           {
             Color generatedColour = UserColourScheme
                     .createColourFromName(name.getText());
-            col = new FeatureColour(generatedColour);
+            col = new FeatureColour(new Colour(generatedColour));
           }
 
           colourPanel.updateColor(col);
@@ -401,7 +401,9 @@ public class FeatureRenderer extends
         if (!colourPanel.isGcol)
         {
           // update colour - otherwise its already done.
-          setColour(sf.type, new FeatureColour(colourPanel.getBackground()));
+          setColour(
+                  sf.type,
+                  new FeatureColour(new Colour(colourPanel.getBackground())));
         }
         try
         {
@@ -441,7 +443,8 @@ public class FeatureRenderer extends
         {
           setGroupVisibility(lastFeatureGroupAdded, true);
         }
-        setColour(lastFeatureAdded, new FeatureColour(newColour)); // was fcol
+        setColour(lastFeatureAdded,
+                new FeatureColour(new Colour(newColour))); // was fcol
         setVisible(lastFeatureAdded);
         findAllFeatures(false); // different to original applet behaviour ?
         // findAllFeatures();