X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=190f15cf811164411174a79b2044c7c7d54acf0e;hb=623d576bab61337289656eab9e4e26cf63e0afc0;hp=1b01606251cab1d3a8dffdd4fa9652cb8f360e63;hpb=6efee133896c4f98ffafc68cf165bfc44a596580;p=jalview.git

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 1b01606..190f15c 100755
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -49,11 +49,8 @@ import java.beans.PropertyChangeEvent;
  */
 public class TreePanel extends GTreePanel
 {
-    SequenceI[] seq;
     String type;
     String pwtype;
-    int start;
-    int end;
     TreeCanvas treeCanvas;
     NJTree tree;
     AlignViewport av;
@@ -68,11 +65,10 @@ public class TreePanel extends GTreePanel
      * @param s DOCUMENT ME!
      * @param e DOCUMENT ME!
      */
-    public TreePanel(AlignViewport av, Vector seqVector, String type,
-                     String pwtype, int s, int e)
+    public TreePanel(AlignViewport av, String type, String pwtype)
     {
       super();
-      initTreePanel(av, seqVector, type, pwtype, s, e, null);
+      initTreePanel(av, type, pwtype, null);
 
       // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default
       showDistances(true);
@@ -87,11 +83,13 @@ public class TreePanel extends GTreePanel
      * @param type DOCUMENT ME!
      * @param pwtype DOCUMENT ME!
      */
-    public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,
-                     String type, String pwtype)
+    public TreePanel(AlignViewport av,
+                     String type,
+                     String pwtype,
+                     NewickFile newtree)
     {
       super();
-      initTreePanel(av, seqVector, type, pwtype, 0, seqVector.size(), newtree);
+      initTreePanel(av, type, pwtype, newtree);
     }
 
     public AlignmentI getAlignment()
@@ -100,20 +98,13 @@ public class TreePanel extends GTreePanel
     }
 
 
-    void initTreePanel(AlignViewport av, Vector seqVector, String type,
-                       String pwtype, int s, int e, NewickFile newTree)
+    void initTreePanel(AlignViewport av, String type,  String pwtype,
+                       NewickFile newTree)
     {
 
       this.type = type;
       this.pwtype = pwtype;
 
-      start = s;
-      end = e;
-
-      seq = new Sequence[seqVector.size()];
-      seqVector.toArray(seq);
-
-
       treeCanvas = new TreeCanvas(av, scrollPane);
       scrollPane.setViewportView(treeCanvas);
 
@@ -161,10 +152,36 @@ public class TreePanel extends GTreePanel
 
       public void run()
       {
+
         if(newtree!=null)
-          tree = new NJTree(seq, newtree);
+          tree = new NJTree(av.alignment.getSequencesArray(),
+                            newtree);
         else
-          tree = new NJTree(seq, type, pwtype, start, end);
+        {
+          int start, end;
+          SequenceI [] seqs;
+          String [] seqStrings = null;
+          if (av.hasHiddenColumns)
+          {
+            seqStrings = av.getSelectionAsString();
+          }
+
+          if(av.getSelectionGroup()==null)
+          {
+            start = 0;
+            end = av.alignment.getWidth();
+            seqs = av.alignment.getSequencesArray();
+          }
+          else
+          {
+            start = av.getSelectionGroup().getStartRes();
+            end = av.getSelectionGroup().getEndRes()+1;
+            seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
+          }
+
+          tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
+        }
+
 
         tree.reCount(tree.getTopNode());
         tree.findHeight(tree.getTopNode());
@@ -292,6 +309,16 @@ public class TreePanel extends GTreePanel
         treeCanvas.startPrinting();
     }
 
+
+    public void originalSeqData_actionPerformed(ActionEvent e)
+    {
+      CutAndPasteTransfer cap = new CutAndPasteTransfer();
+      cap.setText(tree.printOriginalSequenceData());
+      Desktop.addInternalFrame(cap, "Original Data",
+          400, 400);
+    }
+
+
     /**
      * DOCUMENT ME!
      *