X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureEditor.java;h=880a1b22d9aaac0734cfb6c8aff84840445b522d;hb=ba1f9fee25b87bdac0c535019252b787939a8f80;hp=d547c5882bc4e61f23da6733a9da3676713efd72;hpb=2afa9987e7d3276b4525abb28767617732e6e7cf;p=jalview.git

diff --git a/src/jalview/gui/FeatureEditor.java b/src/jalview/gui/FeatureEditor.java
index d547c58..880a1b2 100644
--- a/src/jalview/gui/FeatureEditor.java
+++ b/src/jalview/gui/FeatureEditor.java
@@ -1,16 +1,25 @@
+/*
+ * 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;
-import jalview.datamodel.SearchResults;
-import jalview.datamodel.SearchResultsI;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
-import jalview.gui.JalviewColourChooser.ColourChooserListener;
-import jalview.io.FeaturesFile;
-import jalview.schemes.FeatureColour;
-import jalview.util.ColorUtils;
-import jalview.util.MessageManager;
-
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.Dimension;
@@ -39,6 +48,17 @@ import javax.swing.event.ChangeListener;
 import javax.swing.event.DocumentEvent;
 import javax.swing.event.DocumentListener;
 
+import jalview.api.FeatureColourI;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResultsI;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.gui.JalviewColourChooser.ColourChooserListener;
+import jalview.io.FeaturesFile;
+import jalview.schemes.FeatureColour;
+import jalview.util.ColorUtils;
+import jalview.util.MessageManager;
+
 /**
  * Provides a dialog allowing the user to add new features, or amend or delete
  * existing features
@@ -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);
       }
     });
@@ -233,7 +253,7 @@ public class FeatureEditor
            */
           final String ft = features.get(featureIndex).getType();
           final String type = ft == null ? lastFeatureAdded : ft;
-          FeatureTypeSettings fcc = new FeatureTypeSettings(fr, type);
+          FeatureTypeSettings fcc = new FeatureTypeSettings(fr, type, true);
           fcc.setRequestFocusEnabled(true);
           fcc.requestFocus();
           fcc.addActionListener(new ActionListener()
@@ -381,8 +401,10 @@ 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);
@@ -405,15 +427,16 @@ 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)
-            .setResponseHandler(0, okAction).setResponseHandler(2, cancelAction);
+    JvOptionPane dialog = JvOptionPane.newOptionDialog(ap.alignFrame)
+            .setResponseHandler(0, okAction)
+            .setResponseHandler(2, cancelAction);
     if (!forCreate)
     {
       dialog.setResponseHandler(1, getDeleteAction());
@@ -439,9 +462,8 @@ 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"));
   }
 
   /**
@@ -454,14 +476,9 @@ public class FeatureEditor
    */
   protected Runnable getCancelAction()
   {
-	Runnable okAction = new Runnable()
-    {
-      @Override
-      public void run()
-      {
-        ap.highlightSearchResults(null);
-        ap.paintAlignment(false, false);
-      }
+    Runnable okAction = () -> {
+      ap.highlightSearchResults(null);
+      ap.paintAlignment(false, false);
     };
     return okAction;
   }
@@ -478,10 +495,11 @@ 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();
@@ -536,16 +554,12 @@ public class FeatureEditor
    */
   protected Runnable getDeleteAction()
   {
-	  Runnable deleteAction = new Runnable()
-    {
-      public void run()
-      {
-        SequenceFeature sf = features.get(featureIndex);
-        sequences.get(0).getDatasetSequence().deleteFeature(sf);
-        fr.featuresAdded();
-        ap.getSeqPanel().seqCanvas.highlightSearchResults(null);
-        ap.paintAlignment(true, true);
-      }
+    Runnable deleteAction = () -> {
+      SequenceFeature sf = features.get(featureIndex);
+      sequences.get(0).getDatasetSequence().deleteFeature(sf);
+      fr.featuresAdded();
+      ap.getSeqPanel().seqCanvas.highlightSearchResults(null);
+      ap.paintAlignment(true, true);
     };
     return deleteAction;
   }
@@ -638,14 +652,15 @@ 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();