From 7c05496d1da22f21ce5ae1a199afb9b16c8777ea Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 18 Jul 2006 15:32:16 +0000
Subject: [PATCH] Use selection area with hidden columns in calculations

---
 src/jalview/gui/AlignFrame.java         |  152 ++++++++++++++-----------------
 src/jalview/gui/AlignViewport.java      |  102 +++++++++++++++++++++
 src/jalview/gui/AlignmentPanel.java     |    4 +
 src/jalview/gui/ColumnSelection.java    |   17 ++++
 src/jalview/gui/DasSourceBrowser.java   |    2 +-
 src/jalview/gui/PCAPanel.java           |   61 +++++++------
 src/jalview/gui/PairwiseAlignPanel.java |   36 +++++---
 src/jalview/gui/RedundancyPanel.java    |   73 ++++++++-------
 src/jalview/gui/RotatableCanvas.java    |    2 -
 src/jalview/gui/SeqPanel.java           |   13 ++-
 src/jalview/gui/TreePanel.java          |   67 ++++++++++----
 11 files changed, 339 insertions(+), 190 deletions(-)

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index c1f088b..05ba50c 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -347,9 +347,21 @@ public class AlignFrame
     }
     else
     {
-      String output = new FormatAdapter().formatSequences(format,
-          viewport.getAlignment().
-          getSequences());
+
+      String[] omitHidden = null;
+
+      if (viewport.hasHiddenColumns)
+      {
+        System.out.println("PROMPT USER HERE");
+        omitHidden = viewport.getSelectionAsString();
+      }
+
+      String output = new FormatAdapter().formatSequences(
+          format,
+          viewport.getSelectionAsNewSequence(),
+          omitHidden) ;
+
+
       if (output == null)
       {
         return false;
@@ -381,12 +393,20 @@ public class AlignFrame
   protected void outputText_actionPerformed(ActionEvent e)
   {
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
-    Desktop.addInternalFrame(cap,
-                             "Alignment output - " + e.getActionCommand(), 600,
-                             500);
-    cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
-                                              viewport.getAlignment().
-                                              getSequences()));
+
+
+    String [] omitHidden = null;
+
+    if(viewport.hasHiddenColumns)
+    {
+      System.out.println("PROMPT USER HERE");
+      omitHidden = viewport.getSelectionAsString();
+    }
+
+    cap.setText(new FormatAdapter().formatSequences(
+        e.getActionCommand(),
+        viewport.getSelectionAsNewSequence(),
+        omitHidden));
   }
 
   /**
@@ -647,84 +667,40 @@ public class AlignFrame
     {
       return;
     }
-
-    SequenceGroup sg = viewport.getSelectionGroup();
-
-    Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
-
-    Hashtable orderedSeqs = new Hashtable();
-    SequenceI[] seqs = new SequenceI[sg.getSize(false)];
-
-    for (int i = 0; i < sg.getSize(false); i++)
+    SequenceI [] seqs;
+    if(viewport.getSelectionGroup()==null)
     {
-      SequenceI seq = sg.getSequenceAt(i);
-      int index = viewport.alignment.findIndex(seq);
-      orderedSeqs.put(index + "", seq);
+      seqs = viewport.alignment.getSequencesArray();
     }
-
-    int index = 0, startRes, endRes;
-    char ch;
-
-    for (int i = 0; i < sg.getSize(false); i++)
+    else
     {
-      SequenceI seq = null;
-
-      while (seq == null)
-      {
-        if (orderedSeqs.containsKey(index + ""))
-        {
-          seq = (SequenceI) orderedSeqs.get(index + "");
-          index++;
-
-          break;
-        }
-        else
-        {
-          index++;
-        }
-      }
+      seqs = viewport.getSelectionGroup().getSequencesInOrder(viewport.alignment);
+    }
 
-      //FIND START RES
-      //Returns residue following index if gap
-      startRes = seq.findPosition(sg.getStartRes());
+    Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
 
-      //FIND END RES
-      //Need to find the residue preceeding index if gap
-      endRes = 0;
+    FastaFile ff = new FastaFile();
+    ff.addJVSuffix( viewport.showJVSuffix );
 
-      for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
-      {
-        ch = seq.getCharAt(j);
-        if (!jalview.util.Comparison.isGap( (ch)))
-        {
-          endRes++;
-        }
-      }
+    c.setContents(new StringSelection(ff.print(seqs)), Desktop.instance);
 
-      if (endRes > 0)
+    Vector hiddenColumns = null;
+    if(viewport.hasHiddenColumns && viewport.getSelectionGroup()!=null)
+    {
+      hiddenColumns =new Vector();
+      int hiddenOffset = viewport.getSelectionGroup().getStartRes();
+      for(int i=0; i<viewport.getColumnSelection().getHiddenColumns().size(); i++)
       {
-        endRes += seq.getStart() - 1;
-      }
+        int[] region = (int[])
+            viewport.getColumnSelection().getHiddenColumns().elementAt(i);
 
-      seqs[i] = new Sequence(seq.getName(),
-                             seq.getSequence(sg.getStartRes(), sg.getEndRes() + 1),
-                             startRes,
-                             endRes);
-      seqs[i].setDescription(seq.getDescription());
-      seqs[i].setDBRef(seq.getDBRef());
-      seqs[i].setSequenceFeatures(seq.getSequenceFeatures());
-      seqs[i].setDatasetSequence(seq.getDatasetSequence());
-      if(seq.getAnnotation()!=null)
-      {
-        for(int a=0; a<seq.getAnnotation().length; a++)
-          seqs[i].addAlignmentAnnotation(seq.getAnnotation()[a]);
+        hiddenColumns.addElement(new int[]{region[0]-hiddenOffset,
+                          region[1]-hiddenOffset});
       }
     }
-
-    FastaFile ff = new FastaFile();
-    ff.addJVSuffix( viewport.showJVSuffix );
-    c.setContents(new StringSelection( ff.print(seqs)), Desktop.instance);
-    Desktop.jalviewClipboard = new Object[]{seqs,  viewport.alignment.getDataset()};
+    Desktop.jalviewClipboard = new Object[]{ seqs,
+        viewport.alignment.getDataset(),
+        hiddenColumns};
   }
 
   /**
@@ -848,6 +824,18 @@ public class AlignFrame
        AlignFrame af = new AlignFrame(alignment);
        String newtitle = new String("Copied sequences");
 
+       if(Desktop.jalviewClipboard[2]!=null)
+         {
+           Vector hc = (Vector)Desktop.jalviewClipboard[2];
+           for(int i=0; i<hc.size(); i++)
+           {
+             int [] region = (int[]) hc.elementAt(i);
+             for(int j=region[0]; j<region[1]+1; j++)
+               af.viewport.getColumnSelection().addElement(j);
+             af.viewport.getColumnSelection().hideColumns(region[0], af.viewport);
+           }
+         }
+
 
        //>>>This is a fix for the moment, until a better solution is found!!<<<
        af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings(
@@ -2129,10 +2117,7 @@ public class AlignFrame
       }
 
       title = title + " on region";
-      tp = new TreePanel(viewport,
-                         viewport.getSelectionGroup().getSequences(false),
-                         type, pwType,
-                         sg.getStartRes(), sg.getEndRes());
+      tp = new TreePanel(viewport, type, pwType);
     }
     else
     {
@@ -2149,10 +2134,7 @@ public class AlignFrame
         return;
       }
 
-      tp = new TreePanel(viewport,
-                         viewport.getAlignment().getSequences(), type, pwType,
-                         0,
-                         viewport.alignment.getWidth());
+      tp = new TreePanel(viewport, type, pwType);
     }
 
     addTreeMenuItem(tp, title);
@@ -2403,7 +2385,7 @@ public class AlignFrame
       if (nf.getTree() != null)
       {
         tp = new TreePanel(viewport,
-                           viewport.getAlignment().getSequences(), nf,
+                           nf,
                            "FromFile",
                            title);
 
diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index edbfde5..2e1a4e0 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -1143,4 +1143,106 @@ public class AlignViewport
     {
       return alignment.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex);
     }
+
+    /**
+     * This method returns the a new SequenceI [] with
+     * the selection sequence and start and end points adjusted
+     * @return String[]
+     */
+    public SequenceI[] getSelectionAsNewSequence()
+    {
+      SequenceI[] sequences;
+
+      if (selectionGroup == null)
+        sequences = alignment.getSequencesArray();
+      else
+        sequences = selectionGroup.getSelectionAsNewSequences(alignment);
+
+      return sequences;
+    }
+
+
+    /**
+     * This method returns the visible selected area as text, as
+     * seen on the GUI, ie if columns are hidden they will not
+     * be returned in the result.
+     * Use this for calculating trees, PCA, redundancy etc on views
+     * which contain hidden columns.
+     * @return String[]
+     */
+    public String [] getSelectionAsString()
+    {
+      String [] selection = null;
+      SequenceI [] seqs= null;
+      int i, iSize;
+      int start = 0, end = 0;
+      if(selectionGroup!=null)
+      {
+        iSize = selectionGroup.getSize(false);
+        seqs = selectionGroup.getSequencesInOrder(alignment);
+        start = selectionGroup.getStartRes();
+        end = selectionGroup.getEndRes()+1;
+      }
+      else
+      {
+        iSize = alignment.getHeight();
+        seqs = alignment.getSequencesArray();
+        end = alignment.getWidth();
+      }
+
+      selection = new String[iSize];
+
+
+      for(i=0; i<iSize; i++)
+      {
+        if (hasHiddenColumns)
+        {
+             StringBuffer visibleSeq = new StringBuffer();
+             Vector regions = colSel.getHiddenColumns();
+
+             int blockStart = start, blockEnd=end;
+             int [] region;
+             int hideStart, hideEnd;
+
+             for (int j = 0; j < regions.size(); j++)
+             {
+               region = (int[]) regions.elementAt(j);
+               hideStart = region[0];
+               hideEnd = region[1];
+
+               if(hideStart < start)
+               {
+                 continue;
+               }
+
+               blockStart = Math.min(blockStart, hideEnd+1);
+               blockEnd = Math.min(blockEnd, hideStart);
+
+               if(blockStart>blockEnd)
+               {
+                  break;
+               }
+
+
+               visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));
+
+               blockStart = hideEnd+1;
+               blockEnd = end;
+             }
+
+             if(end>blockStart)
+               visibleSeq.append(seqs[i].getSequence(blockStart, end));
+
+             selection[i] = visibleSeq.toString();
+        }
+        else
+        {
+          selection[i] = seqs[i].getSequence(start, end);
+        }
+
+    //    System.out.println(seqs[i].getName()+"\t"+ selection[i]);
+      }
+
+      return selection;
+    }
 }
diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 2451a96..8a08075 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -117,6 +117,10 @@ public class AlignmentPanel extends GAlignmentPanel
 
             break;
 
+            case KeyEvent.VK_B:
+              av.getSelectionAsString();
+              break;
+
           case KeyEvent.VK_DOWN:
             if(av.cursorMode)
             {
diff --git a/src/jalview/gui/ColumnSelection.java b/src/jalview/gui/ColumnSelection.java
index 55c055c..1032c5b 100755
--- a/src/jalview/gui/ColumnSelection.java
+++ b/src/jalview/gui/ColumnSelection.java
@@ -171,6 +171,23 @@ public class ColumnSelection
                 selected.setElementAt(new Integer(temp - change), i);
             }
         }
+
+        if(hiddenColumns!=null)
+        {
+          for(int i=0; i<hiddenColumns.size(); i++)
+          {
+            int[] region = (int[]) hiddenColumns.elementAt(i);
+            if(region[0] > start)
+            {
+              region[0] -= change;
+              region[1] -= change;
+            }
+            if(region[0]<0)
+              region[0] = 0;
+            if(region[1] <0)
+             region[1] = 0;
+          }
+        }
     }
 
     /**
diff --git a/src/jalview/gui/DasSourceBrowser.java b/src/jalview/gui/DasSourceBrowser.java
index 065fcdf..7875d7b 100755
--- a/src/jalview/gui/DasSourceBrowser.java
+++ b/src/jalview/gui/DasSourceBrowser.java
@@ -240,7 +240,7 @@ public class DasSourceBrowser extends GDasSourceBrowser
 
   public void run()
   {
-    System.out.println("das source browser running");
+
     addLocal.setVisible(false);
     refresh.setVisible(false);
     progressBar.setVisible(true);
diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index 64253b4..8c2ecc9 100755
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -44,7 +44,8 @@ public class PCAPanel extends GPCAPanel implements Runnable
     int top;
     RotatableCanvas rc;
     AlignViewport av;
-    SequenceI [] seqs;
+    String  [] seqstrings;
+    SequenceI  [] seqs;
 
     /**
      * Creates a new PCAPanel object.
@@ -58,36 +59,26 @@ public class PCAPanel extends GPCAPanel implements Runnable
 
         boolean sameLength = true;
 
-        if ((av.getSelectionGroup() != null) &&
-                (av.getSelectionGroup().getSize(false) > 3))
+        seqstrings = av.getSelectionAsString();
+
+        if (av.getSelectionGroup() == null)
         {
-            seqs = new Sequence[av.getSelectionGroup().getSize(false)];
-            int length = av.getSelectionGroup().getSequenceAt(0).getLength();
-            for (int i = 0; i < av.getSelectionGroup().getSize(false); i++)
-            {
-                seqs[i] = av.getSelectionGroup().getSequenceAt(i);
-                if(seqs[i].getLength()!=length)
-                {
-                  sameLength = false;
-                  break;
-                }
-            }
+          seqs = av.alignment.getSequencesArray();
         }
         else
         {
-            seqs = new Sequence[av.getAlignment().getHeight()];
-            int length = av.alignment.getSequenceAt(0).getLength();
-
-            for (int i = 0; i < av.getAlignment().getHeight(); i++)
-            {
-                seqs[i] = av.getAlignment().getSequenceAt(i);
-                if(seqs[i].getLength()!=length)
-               {
-                 sameLength = false;
-                 break;
-               }
-
-            }
+          seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
+        }
+
+        int length = seqs[0].getLength();
+
+        for (int i = 0; i < seqs.length; i++)
+        {
+          if (seqs[i].getLength() != length)
+          {
+            sameLength = false;
+            break;
+          }
         }
 
         if (!sameLength)
@@ -132,7 +123,7 @@ public class PCAPanel extends GPCAPanel implements Runnable
     public void run()
     {
       try{
-        pca = new PCA(seqs);
+        pca = new PCA(seqstrings);
         pca.run();
 
         // Now find the component coordinates
@@ -171,7 +162,6 @@ public class PCAPanel extends GPCAPanel implements Runnable
 
         rc.setPoints(points, pca.getM().rows);
         rc.repaint();
-        seqs = null;
       }
      catch(OutOfMemoryError er)
       { JOptionPane.showInternalMessageDialog(Desktop.desktop,
@@ -265,6 +255,19 @@ public class PCAPanel extends GPCAPanel implements Runnable
       printer.start();
     }
 
+    public void originalSeqData_actionPerformed(ActionEvent e)
+    {
+      CutAndPasteTransfer cap = new CutAndPasteTransfer();
+      for(int i=0; i<seqs.length; i++)
+          cap.appendText(seqs[i].getName()+"\t"
+                         +seqstrings[i]+"\n");
+
+      Desktop.addInternalFrame(cap, "Original Data",
+          400, 400);
+
+    }
+
+
 
     class PCAPrinter extends Thread implements Printable
     {
diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index 5e719f2..f52a1d8 100755
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -37,8 +37,9 @@ import java.util.*;
  */
 public class PairwiseAlignPanel extends GPairwiseAlignPanel
 {
-    Vector sequences = new Vector();
+
     AlignViewport av;
+    Vector sequences;
 
     /**
      * Creates a new PairwiseAlignPanel object.
@@ -50,20 +51,24 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
         super();
         this.av = av;
 
-        Vector selsubset = new Vector();
+        sequences = new Vector();
+
+        SequenceI [] seqs;
+        String []  seqStrings = av.getSelectionAsString();
 
-        for (int i = 0, j = av.getSelectionGroup().getSize(false); i < j; i++)
+        if(av.getSelectionGroup()==null)
         {
-            if (av.getAlignment().getSequences().contains(av.getSelectionGroup()
-                                                                .getSequenceAt(i)))
-            {
-                selsubset.add(av.getSelectionGroup().getSequenceAt(i));
-            }
+          seqs = av.alignment.getSequencesArray();
+        }
+        else
+        {
+          seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
         }
 
-        float[][] scores = new float[selsubset.size()][selsubset.size()];
+
+        float[][] scores = new float[seqs.length][seqs.length];
         double totscore = 0;
-        int count = selsubset.size();
+        int count = seqs.length;
 
         int acount = 0;
         Sequence seq;
@@ -74,8 +79,9 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
             {
                 acount++;
 
-                AlignSeq as = new AlignSeq((SequenceI) selsubset.elementAt(i),
-                        (SequenceI) selsubset.elementAt(j), "pep");
+                AlignSeq as = new AlignSeq(seqs[i], seqStrings[i],
+                        seqs[j], seqStrings[j], "pep");
+
                 as.calcScoreMatrix();
                 as.traceAlignment();
                 as.printAlignment(System.out);
@@ -91,8 +97,8 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
 
                 seq = new Sequence(as.getS2().getName(),
                                    as.getAStr2(),
-                                   as.getS2().getStart(), as.getS2().getEnd()
-                    );
+                                   as.getS2().getStart(),
+                                   as.getS2().getEnd() );
                 sequences.add(seq);
             }
         }
@@ -106,7 +112,7 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
             {
                 jalview.util.Format.print(System.out, "%s \n",
                     ("" + i) + " " +
-                    ((SequenceI) selsubset.elementAt(i)).getName());
+                    seqs[i].getName());
             }
 
             System.out.println("\n");
diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index 78d8424..b248294 100755
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -43,7 +43,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
     AlignmentPanel ap;
     Stack historyList = new Stack(); // simpler than synching with alignFrame.
     float [] redundancy;
-    Vector originalSequences;
+    SequenceI [] originalSequences;
     Hashtable originalColours;
     JInternalFrame frame;
 
@@ -116,63 +116,69 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
 
         validate();
 
-        Vector sel = new Vector();
+        String[] omitHidden = null;
+
         SequenceGroup sg = ap.av.getSelectionGroup();
         int height;
-        originalSequences = new Vector();
+
         originalColours = new Hashtable();
+        int start, end;
 
         if ( (sg != null) && (sg.getSize(false) >= 1))
         {
-           height = sg.getSize(false);
-          for (int i = 0; i < sg.getSize(false); i++)
-          {
-            sel.addElement(sg.getSequenceAt(i));
-          }
+           originalSequences = sg.getSequencesInOrder(ap.av.alignment);
+           start = sg.getStartRes();
+           end = sg.getEndRes();
         }
         else
         {
-          height = ap.av.alignment.getHeight();
-          for (int i = 0; i < ap.av.alignment.getHeight(); i++)
-          {
-            sel.addElement(ap.av.alignment.getSequenceAt(i));
-          }
+          originalSequences = ap.av.alignment.getSequencesArray();
+          start = 0;
+          end = ap.av.alignment.getWidth();
         }
 
+        height = originalSequences.length;
+
         redundancy = new float[height];
         for (int i = 0; i < height; i++)
         {
           redundancy[i] = 0f;
         }
 
+        if (ap.av.hasHiddenColumns)
+        {
+          omitHidden = ap.av.getSelectionAsString();
+        }
+
 
        // long start = System.currentTimeMillis();
 
         float pid;
-        SequenceI seqi, seqj;
-        for (int i = 0; i < sel.size(); i++)
+        String seqi, seqj;
+        for (int i = 0; i < height; i++)
         {
-            originalSequences.addElement(sel.elementAt(i));
-            originalColours.put(sel.elementAt(i),
-                               ((SequenceI) sel.elementAt(i)).getColor());
+            originalColours.put(originalSequences[i],
+                               originalSequences[i].getColor());
 
             for (int j = 0; j < i; j++)
             {
               if(i==j)
                 continue;
 
-              seqi = (SequenceI) sel.elementAt(i);
-              seqj = (SequenceI) sel.elementAt(j);
-
-              if (sg != null)
-                pid = Comparison.PID( seqi,
-                                     seqj,
-                                     sg.getStartRes(), sg.getEndRes());
+              if(omitHidden==null)
+              {
+                seqi = originalSequences[i].getSequence(start, end);
+                seqj = originalSequences[j].getSequence(start, end);
+              }
               else
-                pid = Comparison.PID( seqi,  seqj );
+              {
+                seqi = omitHidden[i];
+                seqj = omitHidden[j];
+              }
 
+              pid = Comparison.PID( seqi,  seqj );
 
-              if(seqj.getLength() < seqi.getLength())
+              if(seqj.length() < seqi.length())
                 redundancy[j] = Math.max(pid, redundancy[j]);
               else
                 redundancy[i] = Math.max(pid, redundancy[i]);
@@ -180,7 +186,6 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
             }
         }
 
-
         progress.setIndeterminate(false);
         progress.setVisible(false);
         progress = null;
@@ -191,7 +196,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
         valueField.setVisible(true);
 
         validate();
-       // System.out.println("blob done "+ (System.currentTimeMillis()-start));
+       // System.out.println((System.currentTimeMillis()-start));
     }
 
     void sliderValueChanged()
@@ -204,9 +209,9 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
       for(int i=0; i<redundancy.length; i++)
       {
         if (value > redundancy[i])
-           ((SequenceI)originalSequences.elementAt(i)).setColor(java.awt.Color.white);
+           originalSequences[i].setColor(java.awt.Color.white);
         else
-           ((SequenceI)originalSequences.elementAt(i)).setColor(java.awt.Color.red);
+          originalSequences[i].setColor(java.awt.Color.red);
       }
 
       PaintRefresher.Refresh(null,ap.av.alignment);
@@ -241,7 +246,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
         {
           if (value <= redundancy[i])
           {
-            SequenceI seq = (SequenceI) originalSequences.elementAt(i);
+            SequenceI seq = originalSequences[i];
             ap.av.alignment.deleteSequence(seq);
             del.add(seq);
             if (sg != null)
@@ -269,9 +274,9 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
 
     void resetColours()
     {
-      for(int i=0; i<originalSequences.size(); i++)
+      for(int i=0; i<originalSequences.length; i++)
       {
-        SequenceI seq = (SequenceI)originalSequences.elementAt(i);
+        SequenceI seq = originalSequences[i];
         seq.setColor( (java.awt.Color)originalColours.get(seq));
       }
 
diff --git a/src/jalview/gui/RotatableCanvas.java b/src/jalview/gui/RotatableCanvas.java
index 8af3d65..ff16b04 100755
--- a/src/jalview/gui/RotatableCanvas.java
+++ b/src/jalview/gui/RotatableCanvas.java
@@ -22,8 +22,6 @@ import jalview.datamodel.*;
 
 import jalview.math.*;
 
-import jalview.util.*;
-
 import java.awt.*;
 import java.awt.event.*;
 
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 4135cb0..9d6b925 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -820,12 +820,10 @@ public class SeqPanel extends JPanel implements MouseListener,
             {
               if(startres>=y2)
               {
-                System.out.println("left of line");
                 fixedLeft = y2;
               }
               else
-             {
-               System.out.println("right of line");
+              {
                fixedRight = y2 - 1;
              }
             }
@@ -876,8 +874,15 @@ public class SeqPanel extends JPanel implements MouseListener,
 
             if (!blank)
             {
-              if(sg.getSize(false) == av.alignment.getHeight())
+              if(sg.getSize(false) == av.alignment.getHeight()  )
               {
+                if((av.hasHiddenColumns
+                    && startres<av.getColumnSelection().getHiddenBoundaryRight(startres)))
+                {
+                  endEditing();
+                  return;
+                }
+
                 //We can still insert gaps if the selectionGroup
                 //contains all the sequences
                 sg.setEndRes(sg.getEndRes()+startres-lastres);
diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 1b01606..a25b01d 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,
+                     NewickFile newtree,
+                     String type,
+                     String pwtype)
     {
       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!
      *
-- 
1.7.10.2