X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=2d02e7958513194675c6aef3cb7a39d0e72c95a2;hb=8288438dd58cfc2d1fe18a060afda0d647b85c32;hp=82ec1d2e7e193bda914d529d1c431ae1961cbeb9;hpb=c2e6335a319d61b641fb6fcbb0a4a5dc88a58014;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 82ec1d2..2d02e79 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -2636,6 +2636,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     viewport.invertColumnSelection();
     alignPanel.paintAlignment(true, false);
+    PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
     viewport.sendSelection();
   }
 
@@ -4189,34 +4190,50 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     int x = 4, y = 5;
     int w = 400, h = 500;
+    
     try
     {
       NewickFile fin = new NewickFile(
-              new FileParse(cm.getNewickString(), DataSourceType.PASTE));
-      fin.parse();
-      if (fin.getTree() == null)
-      {
-        return;
-      }
+              new FileParse(cm.getNewick(), DataSourceType.PASTE));
       String title = "PAE Matrix Tree for "
               + cm.getReferenceSeq().getDisplayId(false);
-      TreePanel tp = new TreePanel(alignPanel, fin, aa, title);
-
-      tp.setSize(w, h);
 
-      if (x > 0 && y > 0)
-      {
-        tp.setLocation(x, y);
-      }
-
-      Desktop.addInternalFrame(tp, title, w, h);
+      showColumnWiseTree(fin, aa, title, w,h, x,y);
     } catch (Throwable xx)
     {
       Console.error("Unexpected exception showing tree for contact matrix",
               xx);
     }
+  }
+  public TreePanel showColumnWiseTree(NewickFile nf, AlignmentAnnotation aa, String treeTitle,
+           int w, int h, int x, int y)
+  {
+      try
+      {
+        nf.parse();
+        if (nf.getTree() == null)
+        {
+          return null;
+        }
+        TreePanel tp = new TreePanel(alignPanel, nf, aa, title);
+
+        tp.setSize(w, h);
+
+        if (x > 0 && y > 0)
+        {
+          tp.setLocation(x, y);
+        }
 
+        Desktop.addInternalFrame(tp, title, w, h);
+        return tp;
+      } catch (Throwable xx)
+      {
+        Console.error("Unexpected exception showing tree for contact matrix",
+                xx);
+      }
+      return null;
   }
+  
   private boolean buildingMenu = false;
 
   /**