X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FTreePanel.java;h=b3fc3b341b27a0592507e2b26d5627428dae5701;hb=4eaa51766c1b8d2a670062696535131bc3907e07;hp=61b0546264108027120db7cfd053e7088d747e18;hpb=de468b0bf50850a89c6a8a7acfa4ff5b689ffed1;p=jalview.git

diff --git a/src/jalview/appletgui/TreePanel.java b/src/jalview/appletgui/TreePanel.java
index 61b0546..b3fc3b3 100755
--- 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;
   TreeCanvas treeCanvas;
   NJTree tree;
+  AlignViewport av;
 
   public NJTree getTree()
   {
@@ -53,8 +54,7 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
    * @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)
   {
     try
     {
@@ -66,7 +66,7 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
       ex.printStackTrace();
     }
 
-    initTreePanel(av, seqVector, type, pwtype, s, e, null);
+    initTreePanel(av, type, pwtype, null);
   }
 
   /**
@@ -78,8 +78,10 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
    * @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)
   {
     try
     {
@@ -91,25 +93,20 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
       e.printStackTrace();
     }
 
-    initTreePanel(av, seqVector, type, pwtype, 0, seqVector.size(), newtree);
+    initTreePanel(av, type, pwtype, newtree);
   }
 
 
-  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.av = av;
     this.type = type;
     this.pwtype = pwtype;
 
-    start = s;
-    end = e;
-
-    seq = new Sequence[seqVector.size()];
-    for(int i=0; i<seqVector.size(); i++)
-      seq[i] = (SequenceI)seqVector.elementAt(i);
-
-
     treeCanvas = new TreeCanvas(av, scrollPane);
     scrollPane.add(treeCanvas);
 
@@ -119,9 +116,31 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
 
   }
 
+  void showOriginalData()
+  {
+    // decide if av alignment is sufficiently different to original data to warrant a new window to be created
+    // create new alignmnt window with hidden regions (unhiding hidden regions yields unaligned seqs)
+    // or create a selection box around columns in alignment view
+    // test Alignment(SeqCigar[])
+    Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(av.
+        getGapCharacter());
+
+    if (alAndColsel != null && alAndColsel[0]!=null)
+     {
+       Alignment al = new Alignment( (SequenceI[]) alAndColsel[0]);
+       AlignFrame af = new AlignFrame(al,
+             av.applet,
+             "Original Data for Tree",
+             false);
+
+      af.viewport.setHiddenColumns( (ColumnSelection) alAndColsel[1] );
+     }
+  }
+
   class TreeLoader extends Thread
   {
     NewickFile newtree;
+    jalview.datamodel.AlignmentView odata=null;
 
     public TreeLoader(NewickFile newtree)
     {
@@ -131,9 +150,34 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
     public void run()
     {
       if(newtree!=null)
-        tree = new NJTree(seq, newtree);
-      else
-        tree = new NJTree(seq, type, pwtype, start, end);
+      {
+        if (odata == null)
+          tree = new NJTree(av.alignment.getSequencesArray(),
+                            newtree);
+        else
+          tree = new NJTree(av.alignment.getSequencesArray(), odata, newtree);
+
+        }
+        else
+        {
+          int start, end;
+          SequenceI [] seqs;
+          AlignmentView seqStrings = av.getAlignmentView(av.getSelectionGroup()!=null);
+          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());
@@ -149,6 +193,8 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
 
       treeCanvas.repaint();
 
+      av.setCurrentTree(tree);
+
     }
   }
 
@@ -158,6 +204,8 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
       newickOutput_actionPerformed();
     else if(evt.getSource()==fontSize)
       fontSize_actionPerformed();
+    else if(evt.getSource()==inputData)
+      showOriginalData();
   }
 
   public void itemStateChanged(ItemEvent evt)
@@ -209,6 +257,8 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
   }
 
 
+
+
   BorderLayout borderLayout1 = new BorderLayout();
   protected ScrollPane scrollPane = new ScrollPane();
   MenuBar jMenuBar1 = new MenuBar();
@@ -220,6 +270,7 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
   protected CheckboxMenuItem fitToWindow = new CheckboxMenuItem();
   Menu fileMenu = new Menu();
   MenuItem newickOutput = new MenuItem();
+  MenuItem inputData = new MenuItem();
 
   private void jbInit() throws Exception {
       setLayout(borderLayout1);
@@ -240,6 +291,7 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
       fileMenu.setLabel("File");
       newickOutput.setLabel("Newick Format");
       newickOutput.addActionListener(this);
+    inputData.setLabel("Input Data...");
 
     add(scrollPane, BorderLayout.CENTER);
       jMenuBar1.add(fileMenu);
@@ -250,6 +302,8 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
       jMenu2.add(bootstrapMenu);
       jMenu2.add(placeholdersMenu);
     fileMenu.add(newickOutput);
+    fileMenu.add(inputData);
+    inputData.addActionListener(this);
   }
 
 }