X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=190f15cf811164411174a79b2044c7c7d54acf0e;hb=623d576bab61337289656eab9e4e26cf63e0afc0;hp=c6c9b5342c5e7e6a1a05f20e855261657b8094ae;hpb=e3cad17c5dba620dafc8459295ecc959cbe52938;p=jalview.git

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index c6c9b53..190f15c 100755
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -38,7 +38,6 @@ import java.util.*;
 
 import javax.imageio.*;
 
-import javax.swing.*;
 import java.beans.PropertyChangeEvent;
 
 
@@ -50,13 +49,11 @@ 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;
 
     /**
      * Creates a new TreePanel object.
@@ -68,15 +65,13 @@ 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
-      treeCanvas.setShowDistances(true);
-      distanceMenu.setSelected(true);
+      showDistances(true);
     }
 
     /**
@@ -88,28 +83,28 @@ 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()
+    {
+      return treeCanvas.av.getAlignment();
     }
 
 
-    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);
 
@@ -131,6 +126,8 @@ public class TreePanel extends GTreePanel
         }
       });
 
+      this.av = av;
+
 
       TreeLoader tl = new TreeLoader(newTree);
       tl.start();
@@ -148,20 +145,43 @@ public class TreePanel extends GTreePanel
         {
           // Must be outside run(), as Jalview2XML tries to
           // update distance/bootstrap visibility at the same time
-          treeCanvas.setShowBootstrap(newtree.HasBootstrap());
-          bootstrapMenu.setSelected(newtree.HasBootstrap());
-
-          treeCanvas.setShowDistances(newtree.HasDistances());
-          distanceMenu.setSelected(newtree.HasDistances());
+          showBootstrap(newtree.HasBootstrap());
+          showDistances(newtree.HasDistances());
         }
       }
 
       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());
@@ -169,9 +189,31 @@ public class TreePanel extends GTreePanel
 
         treeCanvas.repaint();
 
+        av.setCurrentTree(tree);
+
       }
     }
 
+    public void showDistances(boolean b)
+    {
+      treeCanvas.setShowDistances(b);
+      distanceMenu.setSelected(b);
+    }
+
+    public void showBootstrap(boolean b)
+    {
+      treeCanvas.setShowBootstrap(b);
+      bootstrapMenu.setSelected(b);
+    }
+
+    public void showPlaceholders(boolean b)
+    {
+      placeholdersMenu.setState(b);
+      treeCanvas.setMarkPlaceholders(b);
+    }
+
+
+
 
     /**
      * DOCUMENT ME!
@@ -216,7 +258,7 @@ public class TreePanel extends GTreePanel
         Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
 
         jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
-        cap.setText(fout.print(false, true));
+        cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance()));
     }
 
     /**
@@ -243,7 +285,7 @@ public class TreePanel extends GTreePanel
             try
             {
                 jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
-                String output = fout.print(false, true); // distances only
+                String output = fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance());
                 java.io.PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
                             choice));
                 out.println(output);
@@ -267,6 +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!
      *