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

diff --git a/src/jalview/appletgui/TreePanel.java b/src/jalview/appletgui/TreePanel.java
index 61b0546..e770a16 100755 (executable)
--- a/src/jalview/appletgui/TreePanel.java
+++ b/src/jalview/appletgui/TreePanel.java
@@ -37,6 +37,7 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
   int end;\r
   TreeCanvas treeCanvas;\r
   NJTree tree;\r
+  AlignViewport av;\r
 \r
   public NJTree getTree()\r
   {\r
@@ -53,8 +54,7 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
    * @param s DOCUMENT ME!\r
    * @param e DOCUMENT ME!\r
    */\r
-  public TreePanel(AlignViewport av, Vector seqVector, String type,\r
-                   String pwtype, int s, int e)\r
+  public TreePanel(AlignViewport av, String type, String pwtype)\r
   {\r
     try\r
     {\r
@@ -66,7 +66,7 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
       ex.printStackTrace();\r
     }\r
 \r
-    initTreePanel(av, seqVector, type, pwtype, s, e, null);\r
+    initTreePanel(av, type, pwtype, null);\r
   }\r
 \r
   /**\r
@@ -78,8 +78,10 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
    * @param type DOCUMENT ME!\r
    * @param pwtype DOCUMENT ME!\r
    */\r
-  public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,\r
-                   String type, String pwtype)\r
+  public TreePanel(AlignViewport av,\r
+                   String type,\r
+                   String pwtype,\r
+                   NewickFile newtree)\r
   {\r
     try\r
     {\r
@@ -91,25 +93,20 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
       e.printStackTrace();\r
     }\r
 \r
-    initTreePanel(av, seqVector, type, pwtype, 0, seqVector.size(), newtree);\r
+    initTreePanel(av, type, pwtype, newtree);\r
   }\r
 \r
 \r
-  void initTreePanel(AlignViewport av, Vector seqVector, String type,\r
-                     String pwtype, int s, int e, NewickFile newTree)\r
+  void initTreePanel(AlignViewport av,\r
+                     String type,\r
+                     String pwtype,\r
+                     NewickFile newTree)\r
   {\r
 \r
+    this.av = av;\r
     this.type = type;\r
     this.pwtype = pwtype;\r
 \r
-    start = s;\r
-    end = e;\r
-\r
-    seq = new Sequence[seqVector.size()];\r
-    for(int i=0; i<seqVector.size(); i++)\r
-      seq[i] = (SequenceI)seqVector.elementAt(i);\r
-\r
-\r
     treeCanvas = new TreeCanvas(av, scrollPane);\r
     scrollPane.add(treeCanvas);\r
 \r
@@ -130,10 +127,34 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
 \r
     public void run()\r
     {\r
-      if(newtree!=null)\r
-        tree = new NJTree(seq, newtree);\r
+      if (newtree != null)\r
+        tree = new NJTree(av.alignment.getSequencesArray(),\r
+                          newtree);\r
       else\r
-        tree = new NJTree(seq, type, pwtype, start, end);\r
+        {\r
+          int start, end;\r
+          SequenceI [] seqs;\r
+          String [] seqStrings = null;\r
+       //   if (av.hasHiddenColumns)\r
+          {\r
+        //    seqStrings = av.getSelectionAsString();\r
+          }\r
+\r
+          if(av.getSelectionGroup()==null)\r
+          {\r
+            start = 0;\r
+            end = av.alignment.getWidth();\r
+            seqs = av.alignment.getSequencesArray();\r
+          }\r
+          else\r
+          {\r
+            start = av.getSelectionGroup().getStartRes();\r
+            end = av.getSelectionGroup().getEndRes()+1;\r
+            seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);\r
+          }\r
+\r
+          tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);\r
+        }\r
 \r
       tree.reCount(tree.getTopNode());\r
       tree.findHeight(tree.getTopNode());\r
@@ -149,6 +170,8 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
 \r
       treeCanvas.repaint();\r
 \r
+      av.setCurrentTree(tree);\r
+\r
     }\r
   }\r
 \r
@@ -209,6 +232,8 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
   }\r
 \r
 \r
+\r
+\r
   BorderLayout borderLayout1 = new BorderLayout();\r
   protected ScrollPane scrollPane = new ScrollPane();\r
   MenuBar jMenuBar1 = new MenuBar();\r