X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=184944775754cbf8d3cdf53d0de187c00ec02c1e;hb=564c47bdd60cf84046269e45d2f85f39408e4441;hp=140f77e2da23cede327038af2b8e092200808370;hpb=b93f8af382bb2fbdb0c974558bcef57750d1bdd6;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 140f77e..1849447 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -73,6 +73,14 @@ import javax.swing.JInternalFrame;
 public class AlignViewport extends AlignmentViewport
         implements SelectionSource
 {
+
+  public final static int NO_SPLIT = 0;
+
+  public final static int SPLIT_FRAME = 1;
+
+  public final static int NEW_WINDOW = 2;
+
+
   Font font;
 
   boolean cursorMode = false;
@@ -162,7 +170,7 @@ public class AlignViewport extends AlignmentViewport
    * @param hiddenColumns
    * @param seqsetid
    *          (may be null)
-   */
+f   */
   public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns,
           String seqsetid)
   {
@@ -773,47 +781,54 @@ public class AlignViewport extends AlignmentViewport
      * in reverse order)
      */
     JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop)
-            .setResponseHandler(0, new Runnable()
+            .setResponseHandler(NO_SPLIT, new Runnable()
             {
               @Override
               public void run()
               {
                   addDataToAlignment(al);
               }
-            }).setResponseHandler(1, new Runnable()
+            }).setResponseHandler(SPLIT_FRAME, new Runnable()
             {
               @Override
               public void run()
               {
-                us.openLinkedAlignmentAs(al, title, true);
+                openLinkedAlignmentAs(getAlignPanel().alignFrame,
+                        new Alignment(getAlignment()), al, title,
+                        SPLIT_FRAME);
+//                us.openLinkedAlignmentAs(al, title, true);
               }
-            }).setResponseHandler(2, new Runnable()
+            }).setResponseHandler(NEW_WINDOW, new Runnable()
             {
               @Override
               public void run()
               {
-                us.openLinkedAlignmentAs(al, title, false);
+                openLinkedAlignmentAs(null, getAlignment(), al, title,
+                        NEW_WINDOW);
               }
             });
-	dialog.showDialog(question,
+      dialog.showDialog(question,
             MessageManager.getString("label.open_split_window"),
             JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
             options, options[0]);
   }
-
-  protected void openLinkedAlignmentAs(AlignmentI al, String title,
-          boolean newWindowOrSplitPane)
-    {
+  /**
+   * Open a split frame or a new window
+   * 
+   * @param al
+   * @param title
+   * @param mode
+   *          SPLIT_FRAME or NEW_WINDOW
+   */
+  public static void openLinkedAlignmentAs(AlignFrame thisFrame,
+          AlignmentI thisAlignment, AlignmentI al, String title, int mode)
+  {
     /*
      * Identify protein and dna alignments. Make a copy of this one if opening
      * in a new split pane.
      */
-    AlignmentI thisAlignment = newWindowOrSplitPane
-            ? new Alignment(getAlignment())
-            : getAlignment();
     AlignmentI protein = al.isNucleotide() ? thisAlignment : al;
-    final AlignmentI cdna = al.isNucleotide() ? al : thisAlignment;
-
+    AlignmentI cdna = al.isNucleotide() ? al : thisAlignment;
     /*
      * Map sequences. At least one should get mapped as we have already passed
      * the test for 'mappability'. Any mappings made will be added to the
@@ -841,7 +856,7 @@ public class AlignViewport extends AlignmentViewport
     // alignFrame.setFileName(file, format);
     // }
 
-    if (!newWindowOrSplitPane)
+    if (mode == NEW_WINDOW)
     {
       Desktop.addInternalFrame(newAlignFrame, title,
               AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
@@ -855,10 +870,10 @@ public class AlignViewport extends AlignmentViewport
     {
     }
 
-    if (newWindowOrSplitPane)
+    if (mode == SPLIT_FRAME)
     {
       al.alignAs(thisAlignment);
-      protein = openSplitFrame(newAlignFrame, thisAlignment);
+      openSplitFrame(thisFrame, newAlignFrame, thisAlignment);
     }
   }
 
@@ -872,8 +887,8 @@ public class AlignViewport extends AlignmentViewport
    *          cdna/protein complement alignment to show in the other split half
    * @return the protein alignment in the split frame
    */
-  protected AlignmentI openSplitFrame(AlignFrame newAlignFrame,
-          AlignmentI complement)
+  static protected AlignmentI openSplitFrame(AlignFrame thisFrame,
+          AlignFrame newAlignFrame, AlignmentI complement)
   {
     /*
      * Make a new frame with a copy of the alignment we are adding to. If this
@@ -882,7 +897,8 @@ public class AlignViewport extends AlignmentViewport
      */
     AlignFrame copyMe = new AlignFrame(complement, AlignFrame.DEFAULT_WIDTH,
             AlignFrame.DEFAULT_HEIGHT);
-    copyMe.setTitle(getAlignPanel().alignFrame.getTitle());
+    copyMe.setTitle(thisFrame.getTitle());
+
 
     AlignmentI al = newAlignFrame.viewport.getAlignment();
     final AlignFrame proteinFrame = al.isNucleotide() ? copyMe