X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=9c4b0094dfba47b2deeaf6f703d6336c721ab4fe;hb=106a3890f956e2aa7780b2985f4326655912a558;hp=4d82d7e1e7dacfce9cfcc3f6e09a4a2d020ff3a7;hpb=548577891458e7e9d8afaf30322c93b20de43310;p=jalview.git

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index 4d82d7e..9c4b009 100644
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -64,8 +64,8 @@ import javax.swing.event.DocumentListener;
  * @author $author$
  * @version $Revision$
  */
-public class FeatureRenderer extends
-        jalview.renderer.seqfeatures.FeatureRenderer
+public class FeatureRenderer
+        extends jalview.renderer.seqfeatures.FeatureRenderer
 {
   /*
    * defaults for creating a new feature are the last created
@@ -241,10 +241,9 @@ public class FeatureRenderer extends
        */
       gridPanel = new JPanel(new GridLayout(4, 1));
       JPanel choosePanel = new JPanel();
-      choosePanel.add(new JLabel(MessageManager
-              .getString("label.select_feature")
-              + ":"));
-      final JComboBox<String> overlaps = new JComboBox<String>();
+      choosePanel.add(new JLabel(
+              MessageManager.getString("label.select_feature") + ":"));
+      final JComboBox<String> overlaps = new JComboBox<>();
       List<String> added = new ArrayList<>();
       for (SequenceFeature sf : features)
       {
@@ -281,13 +280,12 @@ public class FeatureRenderer extends
 
             alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(
                     highlight, false);
-
           }
           FeatureColourI col = getFeatureStyle(name.getText());
           if (col == null)
           {
-            col = new FeatureColour(ColorUtils
-                    .createColourFromName(name.getText()));
+            col = new FeatureColour(
+                    ColorUtils.createColourFromName(name.getText()));
           }
           oldcol = fcol = col;
           updateColourButton(mainPanel, colour, col);
@@ -324,9 +322,8 @@ public class FeatureRenderer extends
     mainPanel.add(gridPanel, BorderLayout.NORTH);
 
     JPanel descriptionPanel = new JPanel();
-    descriptionPanel.add(new JLabel(MessageManager
-            .getString("label.description:"),
-            JLabel.RIGHT));
+    descriptionPanel.add(new JLabel(
+            MessageManager.getString("label.description:"), JLabel.RIGHT));
     description.setFont(JvSwingUtils.getTextAreaFont());
     description.setLineWrap(true);
     descriptionPanel.add(new JScrollPane(description));
@@ -380,10 +377,11 @@ public class FeatureRenderer extends
           MessageManager.getString("action.cancel") };
     }
 
-    String title = create ? MessageManager
-            .getString("label.create_new_sequence_features")
+    String title = create
+            ? MessageManager.getString("label.create_new_sequence_features")
             : MessageManager.formatMessage("label.amend_delete_features",
-                    new String[] { sequences.get(0).getName() });
+                    new String[]
+                    { sequences.get(0).getName() });
 
     /*
      * show the dialog
@@ -459,7 +457,7 @@ public class FeatureRenderer extends
         sequences.get(0).deleteFeature(sf);
         SequenceFeature newSf = new SequenceFeature(sf, enteredType,
                 newBegin, newEnd, enteredGroup, sf.getScore());
-        sf.setDescription(enteredDescription);
+        newSf.setDescription(enteredDescription);
         ffile.parseDescriptionHTML(newSf, false);
         // amend features dialog only updates one sequence at a time
         sequences.get(0).addSequenceFeature(newSf);
@@ -489,7 +487,7 @@ public class FeatureRenderer extends
 
         featuresAdded();
 
-        alignPanel.paintAlignment(true);
+        alignPanel.paintAlignment(true, true);
 
         return true;
       }
@@ -499,7 +497,7 @@ public class FeatureRenderer extends
       }
     }
 
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, true);
 
     return true;
   }
@@ -536,7 +534,8 @@ public class FeatureRenderer extends
     {
       String msg = MessageManager.formatMessage("label.warning_hidden",
               MessageManager.getString("label.group"), group);
-      JvOptionPane.showMessageDialog(panel, msg, "", JvOptionPane.OK_OPTION);
+      JvOptionPane.showMessageDialog(panel, msg, "",
+              JvOptionPane.OK_OPTION);
     }
   }