JAL-3878 update branch from 2.12 merge from 2.11.2

[jalview.git] / src / jalview / gui / FeatureEditor.java

diff --git a/src/jalview/gui/FeatureEditor.java b/src/jalview/gui/FeatureEditor.java
index 6a7bee6..b53e57c 100644 (file)
--- a/src/jalview/gui/FeatureEditor.java
+++ b/src/jalview/gui/FeatureEditor.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.gui;
 
 import jalview.api.FeatureColourI;
@@ -170,30 +190,30 @@ public class FeatureEditor
     });
 
     description = new JTextArea(3, 25);
-
+    
     start = new JSpinner();
     end = new JSpinner();
     start.setPreferredSize(new Dimension(80, 20));
     end.setPreferredSize(new Dimension(80, 20));
-
+    
     /*
      * ensure that start can never be more than end
      */
-    start.addChangeListener(new ChangeListener()
+    start.addChangeListener(new ChangeListener() 
     {
       @Override
       public void stateChanged(ChangeEvent e)
       {
-        Integer startVal = (Integer) start.getValue();
+        Integer startVal = (Integer) start.getValue(); 
         ((SpinnerNumberModel) end.getModel()).setMinimum(startVal);
       }
     });
-    end.addChangeListener(new ChangeListener()
+    end.addChangeListener(new ChangeListener() 
     {
       @Override
       public void stateChanged(ChangeEvent e)
       {
-        Integer endVal = (Integer) end.getValue();
+        Integer endVal = (Integer) end.getValue(); 
         ((SpinnerNumberModel) start.getModel()).setMaximum(endVal);
       }
     });
@@ -222,7 +242,7 @@ public class FeatureEditor
               updateColourButton(mainPanel, colour, featureColour);
             };
           };
-          JalviewColourChooser.showColourChooser(Desktop.getDesktop(),
+          JalviewColourChooser.showColourChooser(Desktop.getDesktopPane(),
                   title, featureColour.getColour(), listener);
         }
         else
@@ -381,10 +401,8 @@ public class FeatureEditor
 
     start.setValue(new Integer(firstFeature.getBegin()));
     end.setValue(new Integer(firstFeature.getEnd()));
-    ((SpinnerNumberModel) start.getModel())
-            .setMaximum(firstFeature.getEnd());
-    ((SpinnerNumberModel) end.getModel())
-            .setMinimum(firstFeature.getBegin());
+    ((SpinnerNumberModel) start.getModel()).setMaximum(firstFeature.getEnd());
+    ((SpinnerNumberModel) end.getModel()).setMinimum(firstFeature.getBegin());
 
     description.setText(firstFeature.getDescription());
     featureColour = fr.getFeatureStyle(featureType);
@@ -407,14 +425,14 @@ public class FeatureEditor
    */
   public void showDialog()
   {
-    Runnable okAction = forCreate ? getCreateAction() : getAmendAction();
-    Runnable cancelAction = getCancelAction();
+         Runnable okAction = forCreate ? getCreateAction() : getAmendAction();
+         Runnable cancelAction = getCancelAction();
 
     /*
      * set dialog action handlers for OK (create/Amend) and Cancel options
      * also for Delete if applicable (when amending features)
      */
-    JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop)
+    JvOptionPane dialog = JvOptionPane.newOptionDialog(ap.alignFrame)
             .setResponseHandler(0, okAction)
             .setResponseHandler(2, cancelAction);
     if (!forCreate)
@@ -442,8 +460,9 @@ public class FeatureEditor
     }
 
     dialog.showInternalDialog(mainPanel, title,
-            JvOptionPane.YES_NO_CANCEL_OPTION, JvOptionPane.PLAIN_MESSAGE,
-            null, options, MessageManager.getString("action.ok"));
+            JvOptionPane.YES_NO_CANCEL_OPTION,
+            JvOptionPane.PLAIN_MESSAGE, null, options,
+            MessageManager.getString("action.ok"));
   }
 
   /**
@@ -456,7 +475,7 @@ public class FeatureEditor
    */
   protected Runnable getCancelAction()
   {
-    Runnable okAction = new Runnable()
+       Runnable okAction = new Runnable()
     {
       @Override
       public void run()
@@ -480,10 +499,11 @@ public class FeatureEditor
    */
   protected Runnable getCreateAction()
   {
-    Runnable okAction = new Runnable()
+       Runnable okAction = new Runnable()
     {
       boolean useLastDefaults = features.get(0).getType() == null;
 
+      @Override
       public void run()
       {
         final String enteredType = name.getText().trim();
@@ -538,8 +558,9 @@ public class FeatureEditor
    */
   protected Runnable getDeleteAction()
   {
-    Runnable deleteAction = new Runnable()
+         Runnable deleteAction = new Runnable()
     {
+      @Override
       public void run()
       {
         SequenceFeature sf = features.get(featureIndex);
@@ -640,14 +661,14 @@ public class FeatureEditor
    */
   protected Runnable getAmendAction()
   {
-    Runnable okAction = new Runnable()
+       Runnable okAction = new Runnable()
     {
       boolean useLastDefaults = features.get(0).getType() == null;
-
+  
       String featureType = name.getText();
-
+  
       String featureGroup = group.getText();
-
+      @Override
       public void run()
       {
         final String enteredType = name.getText().trim();