Multiple Views

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

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index d306028..06f8269 100755 (executable)
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -1,6 +1,6 @@
 /*\r
  * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
  *\r
  * This program is free software; you can redistribute it and/or\r
  * modify it under the terms of the GNU General Public License\r
@@ -65,10 +65,10 @@ public class TreePanel extends GTreePanel
      * @param s DOCUMENT ME!\r
      * @param e DOCUMENT ME!\r
      */\r
-    public TreePanel(AlignViewport av, String type, String pwtype)\r
+    public TreePanel(AlignmentPanel ap, String type, String pwtype)\r
     {\r
       super();\r
-      initTreePanel(av, type, pwtype, null);\r
+      initTreePanel(ap, type, pwtype, null);\r
 \r
       // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default\r
       // showDistances(true);\r
@@ -83,13 +83,13 @@ public class TreePanel extends GTreePanel
      * @param type DOCUMENT ME!\r
      * @param pwtype DOCUMENT ME!\r
      */\r
-    public TreePanel(AlignViewport av,\r
+    public TreePanel(AlignmentPanel ap,\r
                      String type,\r
                      String pwtype,\r
                      NewickFile newtree)\r
     {\r
       super();\r
-      initTreePanel(av, type, pwtype, newtree);\r
+      initTreePanel(ap, type, pwtype, newtree);\r
     }\r
 \r
     public AlignmentI getAlignment()\r
@@ -98,14 +98,15 @@ public class TreePanel extends GTreePanel
     }\r
 \r
 \r
-    void initTreePanel(AlignViewport av, String type,  String pwtype,\r
+    void initTreePanel(AlignmentPanel ap, String type,  String pwtype,\r
                        NewickFile newTree)\r
     {\r
 \r
+      av = ap.av;\r
       this.type = type;\r
       this.pwtype = pwtype;\r
 \r
-      treeCanvas = new TreeCanvas(av, scrollPane);\r
+      treeCanvas = new TreeCanvas(ap, scrollPane);\r
       scrollPane.setViewportView(treeCanvas);\r
 \r
       av.addPropertyChangeListener(new java.beans.PropertyChangeListener()\r
@@ -153,8 +154,8 @@ public class TreePanel extends GTreePanel
       public void run()\r
       {\r
 \r
-        if(newtree!=null) {\r
-\r
+        if(newtree!=null)\r
+        {\r
           if (odata==null) {\r
             tree = new NJTree(av.alignment.getSequencesArray(),\r
                               newtree);\r
@@ -213,6 +214,7 @@ public class TreePanel extends GTreePanel
       placeholdersMenu.setState(b);\r
       treeCanvas.setMarkPlaceholders(b);\r
     }\r
+\r
     private void allowOriginalSeqData(boolean b) {\r
       originalSeqData.setVisible(b);\r
     }\r
@@ -343,7 +345,10 @@ public class TreePanel extends GTreePanel
          if (true)\r
          {\r
            // make a new frame!\r
-           AlignFrame af = new AlignFrame(al, (ColumnSelection) alAndColsel[1]);\r
+           AlignFrame af = new AlignFrame(al, (ColumnSelection) alAndColsel[1],\r
+                                           AlignFrame.DEFAULT_WIDTH,\r
+                                           AlignFrame.DEFAULT_HEIGHT\r
+);\r
 \r
            //>>>This is a fix for the moment, until a better solution is found!!<<<\r
            // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());\r
@@ -351,9 +356,9 @@ public class TreePanel extends GTreePanel
        //           af.addSortByOrderMenuItem(ServiceName + " Ordering",\r
        //                                     msaorder);\r
 \r
-           Desktop.addInternalFrame(af, "original Data for " + this.title,\r
-                                    AlignFrame.NEW_WINDOW_WIDTH,\r
-                                    AlignFrame.NEW_WINDOW_HEIGHT);\r
+           Desktop.addInternalFrame(af, "Original Data for " + this.title,\r
+                                    AlignFrame.DEFAULT_WIDTH,\r
+                                    AlignFrame.DEFAULT_HEIGHT);\r
          }\r
        }\r
     }\r