Merge branch 'develop' into features/JAL-2068groovyAnnotationWorker

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

diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java
index 4536b1a..d774131 100644 (file)
--- a/src/jalview/appletgui/FeatureRenderer.java
+++ b/src/jalview/appletgui/FeatureRenderer.java
@@ -20,6 +20,14 @@
  */
 package jalview.appletgui;
 
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.GraduatedColor;
+import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
+
 import java.awt.BorderLayout;
 import java.awt.Button;
 import java.awt.Choice;
@@ -35,15 +43,6 @@ import java.awt.TextArea;
 import java.awt.TextField;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
-import java.util.Hashtable;
-
-import jalview.datamodel.SearchResults;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
-import jalview.schemes.AnnotationColourGradient;
-import jalview.schemes.GraduatedColor;
-import jalview.util.MessageManager;
-import jalview.viewmodel.AlignmentViewport;
 
 /**
  * DOCUMENT ME!
@@ -54,11 +53,6 @@ import jalview.viewmodel.AlignmentViewport;
 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.
    * 
@@ -67,11 +61,8 @@ public class FeatureRenderer extends
    */
   public FeatureRenderer(AlignmentViewport av)
   {
-    super();
-    this.av = av;
+    super(av);
 
-    setTransparencyAvailable(!System.getProperty("java.version")
-            .startsWith("1.1"));
   }
 
   static String lastFeatureAdded;
@@ -154,6 +145,7 @@ public class FeatureRenderer extends
       super(null);
     }
 
+    @Override
     public void paint(Graphics g)
     {
       Dimension d = getSize();
@@ -227,6 +219,7 @@ public class FeatureRenderer extends
 
       overlaps.addItemListener(new java.awt.event.ItemListener()
       {
+        @Override
         public void itemStateChanged(java.awt.event.ItemEvent e)
         {
           int index = overlaps.getSelectedIndex();
@@ -326,8 +319,7 @@ public class FeatureRenderer extends
     String title = newFeatures ? MessageManager
             .getString("label.create_new_sequence_features")
             : MessageManager.formatMessage("label.amend_delete_features",
-                    new String[]
-                    { sequences[0].getName() });
+                    new String[] { sequences[0].getName() });
 
     final JVDialog dialog = new JVDialog(ap.alignFrame, title, true, 385,
             240);
@@ -345,6 +337,7 @@ public class FeatureRenderer extends
       dialog.buttonPanel.add(deleteButton, 1);
       deleteButton.addActionListener(new ActionListener()
       {
+        @Override
         public void actionPerformed(ActionEvent evt)
         {
           deleteFeature = true;
@@ -358,12 +351,6 @@ public class FeatureRenderer extends
     start.setText(features[0].getBegin() + "");
     end.setText(features[0].getEnd() + "");
     description.setText(features[0].getDescription());
-    Color col = getColour(name.getText());
-    if (col == null)
-    {
-      col = new jalview.schemes.UserColourScheme()
-              .createColourFromName(name.getText());
-    }
     Object fcol = getFeatureStyle(name.getText());
     // simply display the feature color in a box
     colourPanel.updateColor(fcol);
@@ -371,6 +358,7 @@ public class FeatureRenderer extends
     // TODO: render the graduated color in the box.
     colourPanel.addMouseListener(new java.awt.event.MouseAdapter()
     {
+      @Override
       public void mousePressed(java.awt.event.MouseEvent evt)
       {
         if (!colourPanel.isGcol)