Merge branch 'develop' into trialMerge

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

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index bc668fd..5ef2568 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -708,16 +708,20 @@ public class AlignViewport extends AlignmentViewport
     {
       if (AlignmentUtils.isMappable(toAdd, getAlignment()))
       {
-        if (openLinkedAlignment(toAdd, title))
-        {
-          return;
-        }
+        openLinkedAlignment(toAdd, title);
+        return;
       }
     }
+    addDataToAlignment(toAdd);
+  }
 
-    /*
-     * No mappings, or offer declined - add sequences to this alignment
-     */
+  /**
+   * adds sequences to this alignment
+   * 
+   * @param toAdd
+   */
+  void addDataToAlignment(AlignmentI toAdd)
+  {
     // TODO: JAL-407 regardless of above - identical sequences (based on ID and
     // provenance) should share the same dataset sequence
 
@@ -752,30 +756,58 @@ public class AlignViewport extends AlignmentViewport
    * @param al
    * @param title
    */
-  protected boolean openLinkedAlignment(AlignmentI al, String title)
+  protected void openLinkedAlignment(AlignmentI al, String title)
   {
     String[] options = new String[] { MessageManager.getString("action.no"),
         MessageManager.getString("label.split_window"),
         MessageManager.getString("label.new_window"), };
     final String question = JvSwingUtils.wrapTooltip(true,
             MessageManager.getString("label.open_split_window?"));
-    int response = JvOptionPane.showOptionDialog(Desktop.desktop, question,
+    final AlignViewport us = this;
+    
+    /*
+     * options No, Split Window, New Window correspond to
+     * dialog responses 0, 1, 2 (even though JOptionPane shows them
+     * in reverse order)
+     */
+    JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop)
+            .setResponseHandler(0, new Runnable()
+            {
+              @Override
+              public void run()
+              {
+                  addDataToAlignment(al);
+              }
+            }).setResponseHandler(1, new Runnable()
+            {
+              @Override
+              public void run()
+              {
+                us.openLinkedAlignmentAs(al, title, true);
+              }
+            }).setResponseHandler(2, new Runnable()
+            {
+              @Override
+              public void run()
+              {
+                us.openLinkedAlignmentAs(al, title, false);
+              }
+            });
+       dialog.showDialog(question,
             MessageManager.getString("label.open_split_window"),
             JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
             options, options[0]);
+  }
 
-    if (response != 1 && response != 2)
+  protected void openLinkedAlignmentAs(AlignmentI al, String title,
+          boolean newWindowOrSplitPane)
     {
-      return false;
-    }
-    final boolean openSplitPane = (response == 1);
-    final boolean openInNewWindow = (response == 2);
-
     /*
      * Identify protein and dna alignments. Make a copy of this one if opening
      * in a new split pane.
      */
-    AlignmentI thisAlignment = openSplitPane ? new Alignment(getAlignment())
+    AlignmentI thisAlignment = newWindowOrSplitPane
+            ? new Alignment(getAlignment())
             : getAlignment();
     AlignmentI protein = al.isNucleotide() ? thisAlignment : al;
     final AlignmentI cdna = al.isNucleotide() ? al : thisAlignment;
@@ -807,7 +839,7 @@ public class AlignViewport extends AlignmentViewport
     // alignFrame.setFileName(file, format);
     // }
 
-    if (openInNewWindow)
+    if (!newWindowOrSplitPane)
     {
       Desktop.addInternalFrame(newAlignFrame, title,
               AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
@@ -821,13 +853,11 @@ public class AlignViewport extends AlignmentViewport
     {
     }
 
-    if (openSplitPane)
+    if (newWindowOrSplitPane)
     {
       al.alignAs(thisAlignment);
       protein = openSplitFrame(newAlignFrame, thisAlignment);
     }
-
-    return true;
   }
 
   /**