X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;fp=src%2Fjalview%2Fgui%2FDesktop.java;h=d312a25465c31a98757ad38fafc07946fbe99786;hb=55f6f8a9ddd0b8bb4445d1cc582297af1d0aa4c5;hp=a58e22a7ebef1a1e33ac70483192f8290d327548;hpb=9df9ea39635e009b54078c300e8270ca45415410;p=jalview.git

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index a58e22a..d312a25 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -199,7 +199,7 @@ public class Desktop extends GDesktop
 
   public static MyDesktopPane getDesktopPane()
   {
-    Desktop desktop = Desktop.getInstance();
+    Desktop desktop = getInstance();
     return desktop == null ? null : desktop.desktopPane;
   }
 
@@ -799,7 +799,7 @@ public class Desktop extends GDesktop
         FileFormatI format = new IdentifyFile().identify(file,
                 DataSourceType.PASTE);
 
-        new FileLoader().loadFile(file, DataSourceType.PASTE, format);
+        new FileLoader(true).loadFile(file, DataSourceType.PASTE, format);
 
       }
     } catch (Exception ex)
@@ -909,7 +909,7 @@ public class Desktop extends GDesktop
     // A HEADLESS STATE WHEN NO DESKTOP EXISTS. MUST RETURN
     // IF JALVIEW IS RUNNING HEADLESS
     // ///////////////////////////////////////////////
-    if (Desktop.getInstance().instanceOnly || Jalview.isHeadlessMode())
+    if (Jalview.isHeadlessMode() || getInstance().instanceOnly)
     {
       return;
     }
@@ -925,7 +925,7 @@ public class Desktop extends GDesktop
       // The Alignment Frame window could be added from a number of places,
       // hence,
       // I did this here in order not to miss out on any Alignment frame.
-      if (frame instanceof AlignFrame)
+      if (frame instanceof AlignFrame.IFrame)
       {
         frame.setMinimumSize(new Dimension(ALIGN_FRAME_DEFAULT_MIN_WIDTH,
                 ALIGN_FRAME_DEFAULT_MIN_HEIGHT));
@@ -958,9 +958,9 @@ public class Desktop extends GDesktop
         JInternalFrame itf = getDesktopPane().getSelectedFrame();
         if (itf != null)
         {
-          if (itf instanceof AlignFrame)
+          if (itf.getContentPane() instanceof AlignFrame)
           {
-            Jalview.setCurrentAlignFrame((AlignFrame) itf);
+            Jalview.setCurrentAlignFrame((AlignFrame) itf.getContentPane());
           }
           itf.requestFocus();
         }
@@ -987,7 +987,7 @@ public class Desktop extends GDesktop
         {
           menuItem.removeActionListener(menuItem.getActionListeners()[0]);
         }
-        Desktop.getInstance().windowMenu.remove(menuItem);
+        getInstance().windowMenu.remove(menuItem);
       }
     });
 
@@ -1011,7 +1011,7 @@ public class Desktop extends GDesktop
 
     getDesktopPane().add(frame);
 
-    Desktop.getInstance().windowMenu.add(menuItem);
+    getInstance().windowMenu.add(menuItem);
 
     frame.toFront();
     try
@@ -1068,7 +1068,7 @@ public class Desktop extends GDesktop
   {
     if (!internalCopy)
     {
-      Desktop.getInstance().jalviewClipboard = null;
+      getInstance().jalviewClipboard = null;
     }
 
     internalCopy = false;
@@ -1636,9 +1636,9 @@ public class Desktop extends GDesktop
     }
 
     AlignmentViewport source = null, target = null;
-    if (frames[0] instanceof AlignFrame)
+    if (frames[0] instanceof AlignFrame.IFrame)
     {
-      source = ((AlignFrame) frames[0]).getCurrentView();
+      source = ((AlignFrame.IFrame) frames[0]).alignframe.getCurrentView();
     }
     else if (frames[0] instanceof TreePanel)
     {
@@ -1662,9 +1662,10 @@ public class Desktop extends GDesktop
         {
           continue;
         }
-        if (frames[i] instanceof AlignFrame)
+        if (frames[i] instanceof AlignFrame.IFrame)
         {
-          target = ((AlignFrame) frames[i]).getCurrentView();
+          target = ((AlignFrame.IFrame) frames[i]).alignframe
+                  .getCurrentView();
         }
         else if (frames[i] instanceof TreePanel)
         {
@@ -2080,7 +2081,8 @@ public class Desktop extends GDesktop
 
       ap.av.setGatherViewsHere(false);
 
-      addInternalFrame(newaf, af.getTitle(), AlignFrame.DEFAULT_WIDTH,
+      addInternalFrame(newaf, af.getTitle(),
+              AlignFrame.DEFAULT_WIDTH,
               AlignFrame.DEFAULT_HEIGHT);
     }
 
@@ -2106,9 +2108,10 @@ public class Desktop extends GDesktop
 
     for (int t = 0; t < frames.length; t++)
     {
-      if (frames[t] instanceof AlignFrame && frames[t] != source)
+      if (frames[t] instanceof AlignFrame.IFrame
+              && ((AlignFrame.IFrame) frames[t]).alignframe != source)
       {
-        AlignFrame af = (AlignFrame) frames[t];
+        AlignFrame af = ((AlignFrame.IFrame) frames[t]).alignframe;
         boolean gatherThis = false;
         for (int a = 0; a < af.alignPanels.size(); a++)
         {
@@ -2686,6 +2689,7 @@ public class Desktop extends GDesktop
         }
       }
     }
+
   }
 
   /**
@@ -2711,9 +2715,9 @@ public class Desktop extends GDesktop
     // REVERSE ORDER
     for (int i = frames.length - 1; i > -1; i--)
     {
-      if (frames[i] instanceof AlignFrame)
+      if (frames[i].getContentPane() instanceof AlignFrame)
       {
-        avp.add((AlignFrame) frames[i]);
+        avp.add((AlignFrame) frames[i].getContentPane());
       }
       else if (frames[i] instanceof SplitFrame)
       {
@@ -3160,7 +3164,7 @@ public class Desktop extends GDesktop
    */
   public static void showUrl(final String url)
   {
-    showUrl(url, Desktop.getInstance());
+    showUrl(url, getInstance());
   }
 
   /**
@@ -3209,7 +3213,7 @@ public class Desktop extends GDesktop
 
   public static ParamManager getUserParameterStore()
   {
-    Desktop d = Desktop.getInstance();
+    Desktop d = getInstance();
     if (d.wsparamManager == null)
     {
       d.wsparamManager = new WsParamSetManager();
@@ -3500,7 +3504,7 @@ public class Desktop extends GDesktop
 
   public static groovy.ui.Console getGroovyConsole()
   {
-    Desktop desktop = Desktop.getInstance();
+    Desktop desktop = getInstance();
     return desktop == null ? null : desktop.groovyConsole;
   }
 
@@ -3773,4 +3777,10 @@ public class Desktop extends GDesktop
     return result;
   }
 
+  public static void addInternalFrame(AlignFrame af, String title,
+          int width, int height)
+  {
+    addInternalFrame(af.getIFrame(), title, width, height);
+  }
+
 }