X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureRenderer.java;h=4536b1a754b449e98dea0652aa1d4d69a9f9f0c3;hb=b62d7ddaf034d0bb6b4c347aedd582f69d1119cc;hp=6963ca79f2d653a00637069635635d358bf83e93;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git

diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java
index 6963ca7..4536b1a 100644
--- a/src/jalview/appletgui/FeatureRenderer.java
+++ b/src/jalview/appletgui/FeatureRenderer.java
@@ -20,15 +20,30 @@
  */
 package jalview.appletgui;
 
-import java.util.*;
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.datamodel.*;
+import java.awt.BorderLayout;
+import java.awt.Button;
+import java.awt.Choice;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.Graphics;
+import java.awt.GridLayout;
+import java.awt.Label;
+import java.awt.Panel;
+import java.awt.ScrollPane;
+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.seqfeatures.FeaturesDisplayed;
+import jalview.viewmodel.AlignmentViewport;
 
 /**
  * DOCUMENT ME!
@@ -36,7 +51,8 @@ import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
  * @author $author$
  * @version $Revision$
  */
-public class FeatureRenderer extends jalview.renderer.seqfeatures.FeatureRenderer
+public class FeatureRenderer extends
+        jalview.renderer.seqfeatures.FeatureRenderer
 {
 
   // Holds web links for feature groups and feature types
@@ -49,12 +65,13 @@ public class FeatureRenderer extends jalview.renderer.seqfeatures.FeatureRendere
    * @param av
    *          DOCUMENT ME!
    */
-  public FeatureRenderer(AlignViewport av)
+  public FeatureRenderer(AlignmentViewport av)
   {
     super();
     this.av = av;
 
-    setTransparencyAvailable(!System.getProperty("java.version").startsWith("1.1"));
+    setTransparencyAvailable(!System.getProperty("java.version")
+            .startsWith("1.1"));
   }
 
   static String lastFeatureAdded;
@@ -100,7 +117,9 @@ public class FeatureRenderer extends jalview.renderer.seqfeatures.FeatureRendere
       }
       else
       {
-        throw new Error(MessageManager.getString("error.invalid_colour_for_mycheckbox"));
+        throw new Error(
+                MessageManager
+                        .getString("error.invalid_colour_for_mycheckbox"));
       }
       if (col != null)
       {
@@ -197,7 +216,9 @@ public class FeatureRenderer extends jalview.renderer.seqfeatures.FeatureRendere
                 + "-" + features[i].getEnd();
 
         if (features[i].getFeatureGroup() != null)
+        {
           item += " (" + features[i].getFeatureGroup() + ")";
+        }
 
         overlaps.addItem(item);
       }
@@ -302,8 +323,11 @@ public class FeatureRenderer extends jalview.renderer.seqfeatures.FeatureRendere
       }
     }
 
-    String title = newFeatures ? MessageManager.getString("label.create_new_sequence_features")
-            : MessageManager.formatMessage("label.amend_delete_features", new String[]{sequences[0].getName()});
+    String title = newFeatures ? MessageManager
+            .getString("label.create_new_sequence_features")
+            : MessageManager.formatMessage("label.amend_delete_features",
+                    new String[]
+                    { sequences[0].getName() });
 
     final JVDialog dialog = new JVDialog(ap.alignFrame, title, true, 385,
             240);
@@ -376,7 +400,9 @@ public class FeatureRenderer extends jalview.renderer.seqfeatures.FeatureRendere
     }
 
     if (lastFeatureGroupAdded != null && lastFeatureGroupAdded.length() < 1)
+    {
       lastFeatureGroupAdded = null;
+    }
 
     if (!newFeatures)
     {
@@ -401,7 +427,8 @@ public class FeatureRenderer extends jalview.renderer.seqfeatures.FeatureRendere
         }
 
         ffile.parseDescriptionHTML(sf, false);
-        setVisible(lastFeatureAdded); // if user edited name then make sure new type is visible
+        setVisible(lastFeatureAdded); // if user edited name then make sure new
+                                      // type is visible
       }
       if (deleteFeature)
       {
@@ -422,16 +449,16 @@ public class FeatureRenderer extends jalview.renderer.seqfeatures.FeatureRendere
           ffile.parseDescriptionHTML(features[i], false);
         }
 
-        col = colourPanel.getBackground();
+        Color newColour = colourPanel.getBackground();
         // setColour(lastFeatureAdded, fcol);
 
         if (lastFeatureGroupAdded != null)
         {
           setGroupVisibility(lastFeatureGroupAdded, true);
         }
-        setColour(lastFeatureAdded, fcol);
+        setColour(lastFeatureAdded, newColour); // was fcol
         setVisible(lastFeatureAdded);
-        findAllFeatures(false); // different to original applet behaviour ? 
+        findAllFeatures(false); // different to original applet behaviour ?
         // findAllFeatures();
       }
       else