X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=d3b8afc948f58c4a1f190e22c7a31525f3218618;hb=d616b0e1ac213a82591cece50ea25c5bfbfa865f;hp=3f923348bedf78f5b6e31cc2d018ee82a4cfd132;hpb=5e3ef593f6032b49eb41b962badf1ee36403184e;p=jalview.git

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 3f92334..d3b8afc 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -23,6 +23,7 @@ package jalview.gui;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.bin.Cache;
+import jalview.bin.Jalview;
 import jalview.io.FileLoader;
 import jalview.io.FormatAdapter;
 import jalview.io.IdentifyFile;
@@ -2381,6 +2382,12 @@ public class Desktop extends jalview.jbgui.GDesktop implements
    */
   public static AlignFrame[] getAlignFrames()
   {
+    if (Jalview.isHeadlessMode())
+    {
+      // Desktop.desktop is null in headless mode
+      return new AlignFrame[] { currentAlignFrame };
+    }
+
     JInternalFrame[] frames = Desktop.desktop.getAllFrames();
 
     if (frames == null)
@@ -2976,25 +2983,39 @@ public class Desktop extends jalview.jbgui.GDesktop implements
        * AlignmentPanel objects, including their AlignmentViewports, so the
        * cdna/protein relationships between the viewports is carried over to the
        * new split frames.
+       * 
+       * explodedGeometry holds the (x, y) position of the previously exploded
+       * SplitFrame, and the (width, height) of the AlignFrame component
        */
       AlignmentPanel topPanel = (AlignmentPanel) topPanels.get(i);
       AlignFrame newTopFrame = new AlignFrame(topPanel);
       newTopFrame.setSize(oldTopFrame.getSize());
       newTopFrame.setVisible(true);
+      Rectangle geometry = ((AlignViewport) topPanel.getAlignViewport())
+              .getExplodedGeometry();
+      if (geometry != null)
+      {
+        newTopFrame.setSize(geometry.getSize());
+      }
+
       AlignmentPanel bottomPanel = (AlignmentPanel) bottomPanels.get(i);
       AlignFrame newBottomFrame = new AlignFrame(bottomPanel);
       newBottomFrame.setSize(oldBottomFrame.getSize());
       newBottomFrame.setVisible(true);
+      geometry = ((AlignViewport) bottomPanel.getAlignViewport())
+              .getExplodedGeometry();
+      if (geometry != null)
+      {
+        newBottomFrame.setSize(geometry.getSize());
+      }
+
       topPanel.av.setGatherViewsHere(false);
       bottomPanel.av.setGatherViewsHere(false);
       JInternalFrame splitFrame = new SplitFrame(newTopFrame,
               newBottomFrame);
-      // either panel may hold previous exploded frame geometry
-      Rectangle geometry = ((AlignViewport) topPanel.getAlignViewport())
-              .getExplodedGeometry();
       if (geometry != null)
       {
-        splitFrame.setBounds(geometry);
+        splitFrame.setLocation(geometry.getLocation());
       }
       Desktop.addInternalFrame(splitFrame, sf.getTitle(), -1, -1);
     }
@@ -3017,10 +3038,18 @@ public class Desktop extends jalview.jbgui.GDesktop implements
    */
   public void gatherViews(GSplitFrame source)
   {
+    /*
+     * special handling of explodedGeometry for a view within a SplitFrame: - it
+     * holds the (x, y) position of the enclosing SplitFrame, and the (width,
+     * height) of the AlignFrame component
+     */
     AlignFrame myTopFrame = (AlignFrame) source.getTopFrame();
     AlignFrame myBottomFrame = (AlignFrame) source.getBottomFrame();
-    myTopFrame.viewport.setExplodedGeometry(source.getBounds());
-    myBottomFrame.viewport.setExplodedGeometry(source.getBounds());
+    myTopFrame.viewport.setExplodedGeometry(new Rectangle(source.getX(),
+            source.getY(), myTopFrame.getWidth(), myTopFrame.getHeight()));
+    myBottomFrame.viewport.setExplodedGeometry(new Rectangle(source.getX(),
+            source.getY(), myBottomFrame.getWidth(), myBottomFrame
+                    .getHeight()));
     myTopFrame.viewport.setGatherViewsHere(true);
     myBottomFrame.viewport.setGatherViewsHere(true);
     String topViewId = myTopFrame.viewport.getSequenceSetId();
@@ -3045,10 +3074,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements
             gatherThis = true;
             topPanel.av.setGatherViewsHere(false);
             bottomPanel.av.setGatherViewsHere(false);
-            // both panels refer to the same split frame geometry
-            Rectangle position = sf.getBounds();
-            topPanel.av.setExplodedGeometry(position);
-            bottomPanel.av.setExplodedGeometry(position);
+            topPanel.av.setExplodedGeometry(new Rectangle(sf.getLocation(),
+                    topFrame.getSize()));
+            bottomPanel.av.setExplodedGeometry(new Rectangle(sf
+                    .getLocation(), bottomFrame.getSize()));
             myTopFrame.addAlignmentPanel(topPanel, false);
             myBottomFrame.addAlignmentPanel(bottomPanel, false);
           }