X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqPanel.java;h=f9304cf562f6b6ef5cef349df5f6606c8a2a86ba;hb=ae45339b760492fc71cadf5a52b0b386942a4bd4;hp=89e2086a1ebbd81a81e2f2286dc7071a3fc7455c;hpb=0452450533728e478ef8c893ea2cb3483c740fb3;p=jalview.git

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 89e2086..f9304cf 100755
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -19,17 +19,19 @@
 
 package jalview.appletgui;
 
+import java.util.*;
+
 import java.awt.*;
 import java.awt.event.*;
 
+import jalview.commands.*;
 import jalview.datamodel.*;
 import jalview.schemes.*;
-import jalview.commands.*;
-
-import java.util.Vector;
+import jalview.structure.SequenceListener;
+import jalview.structure.StructureSelectionManager;
 
 public class SeqPanel
-    extends Panel implements MouseMotionListener, MouseListener
+    extends Panel implements MouseMotionListener, MouseListener, SequenceListener
 {
 
   public SeqCanvas seqCanvas;
@@ -63,6 +65,9 @@ public class SeqPanel
 
   EditCommand editCommand;
 
+  StructureSelectionManager ssm;
+
+
   public SeqPanel(AlignViewport avp, AlignmentPanel p)
   {
     this.av = avp;
@@ -75,13 +80,15 @@ public class SeqPanel
 
     seqCanvas.addMouseMotionListener(this);
     seqCanvas.addMouseListener(this);
+    ssm = StructureSelectionManager.getStructureSelectionManager();
+    ssm.addStructureViewerListener(this);
 
     seqCanvas.repaint();
   }
 
   void endEditing()
   {
-    if (editCommand!=null && editCommand.getSize() > 0)
+    if (editCommand != null && editCommand.getSize() > 0)
     {
       ap.alignFrame.addHistoryItem(editCommand);
       av.firePropertyChange("alignment", null,
@@ -94,400 +101,492 @@ public class SeqPanel
     groupEditing = false;
     keyboardNo1 = null;
     keyboardNo2 = null;
-     editCommand = null;
-   }
-
-   void setCursorRow()
-   {
-     seqCanvas.cursorY = getKeyboardNo(keyboardNo1)-1;
-     scrollToVisible();
-   }
-
-   void setCursorColumn()
-   {
-     seqCanvas.cursorX = getKeyboardNo(keyboardNo1)-1;
-     scrollToVisible();
-   }
-
-   void setCursorRowAndColumn()
-   {
-     if(keyboardNo2==null)
-     {
-       keyboardNo2 = new StringBuffer();
-     }
-     else
-     {
-       seqCanvas.cursorX = getKeyboardNo(keyboardNo1) - 1;
-       seqCanvas.cursorY = getKeyboardNo(keyboardNo2) - 1;
-       scrollToVisible();
-     }
-   }
-
-   void setCursorPosition()
-   {
-     SequenceI sequence =
-         (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
-
-     seqCanvas.cursorX = sequence.findIndex(
-         getKeyboardNo(keyboardNo1)-1
-         );
-     scrollToVisible();
-   }
-
-   void moveCursor(int dx, int dy)
-   {
-     seqCanvas.cursorX += dx;
-     seqCanvas.cursorY += dy;
-     if (av.hasHiddenColumns && !av.colSel.isVisible(seqCanvas.cursorX))
-     {
-       int original = seqCanvas.cursorX - dx;
-       int maxWidth = av.alignment.getWidth();
-
-       while(!av.colSel.isVisible(seqCanvas.cursorX)
-             && seqCanvas.cursorX<maxWidth
-             && seqCanvas.cursorX>0)
-       {
-         seqCanvas.cursorX += dx;
-       }
-
-       if(seqCanvas.cursorX>=maxWidth
-          || !av.colSel.isVisible(seqCanvas.cursorX) )
-       {
-         seqCanvas.cursorX = original;
-       }
-      }
-     scrollToVisible();
-   }
-
-   void scrollToVisible()
-   {
-     if (seqCanvas.cursorX < 0)
-       seqCanvas.cursorX = 0;
-     else if (seqCanvas.cursorX > av.alignment.getWidth() - 1)
-       seqCanvas.cursorX = av.alignment.getWidth() - 1;
-
-     if (seqCanvas.cursorY < 0)
-       seqCanvas.cursorY = 0;
-     else if (seqCanvas.cursorY > av.alignment.getHeight() - 1)
-       seqCanvas.cursorY = av.alignment.getHeight() - 1;
-
-
-     endEditing();
-     if (av.wrapAlignment)
-     {
-       ap.scrollToWrappedVisible(seqCanvas.cursorX);
-     }
-     else
-     {
-       while (seqCanvas.cursorY < av.startSeq)
-       {
-         ap.scrollUp(true);
-       }
-       while (seqCanvas.cursorY + 1 > av.endSeq)
-       {
-         ap.scrollUp(false);
-       }
-       while (seqCanvas.cursorX < av.colSel.adjustForHiddenColumns(av.startRes))
-       {
-
-         if (!ap.scrollRight(false))
-           break;
-       }
-       while (seqCanvas.cursorX > av.colSel.adjustForHiddenColumns(av.endRes))
-       {
-         if (!ap.scrollRight(true))
-           break;
-       }
-     }
-     setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY),
-                      seqCanvas.cursorX, seqCanvas.cursorY);
-
-     seqCanvas.repaint();
-   }
-
-   void setSelectionAreaAtCursor(boolean topLeft)
-   {
-     SequenceI sequence =
-         (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
-
-     if(av.getSelectionGroup()!=null)
-     {
-       SequenceGroup sg = av.selectionGroup;
-       //Find the top and bottom of this group
-       int min = av.alignment.getHeight(), max = 0;
-       for(int i=0; i<sg.getSize(); i++)
-       {
-         int index = av.alignment.findIndex( sg.getSequenceAt(i) );
-         if(index > max)
-           max = index;
-         if(index < min)
-           min = index;
-       }
-
-       max ++;
-
-       if(topLeft)
-       {
-         sg.setStartRes(seqCanvas.cursorX);
-         if(sg.getEndRes()<seqCanvas.cursorX)
-           sg.setEndRes(seqCanvas.cursorX);
-
-         min = seqCanvas.cursorY;
-       }
-       else
-       {
-         sg.setEndRes(seqCanvas.cursorX);
-         if(sg.getStartRes()>seqCanvas.cursorX)
-           sg.setStartRes(seqCanvas.cursorX);
-
-         max = seqCanvas.cursorY+1;
-       }
-
-       if(min>max)
-       {
-         // Only the user can do this
-         av.setSelectionGroup(null);
-       }
-       else
-       {
-         // Now add any sequences between min and max
-         sg.getSequences(null).removeAllElements();
-         for (int i = min; i < max; i++)
-         {
-           sg.addSequence(av.alignment.getSequenceAt(i), false);
-         }
-       }
-     }
-
-     if (av.getSelectionGroup() == null)
-     {
-       SequenceGroup sg = new SequenceGroup();
-       sg.setStartRes(seqCanvas.cursorX);
-       sg.setEndRes(seqCanvas.cursorX);
-       sg.addSequence(sequence, false);
-       av.setSelectionGroup(sg);
-     }
-
-
-     ap.repaint();
-   }
-
-   void insertGapAtCursor(boolean group)
-   {
-     groupEditing = group;
-     startseq = seqCanvas.cursorY;
-     lastres = seqCanvas.cursorX;
-     editSequence(true, seqCanvas.cursorX+getKeyboardNo(keyboardNo1));
-     endEditing();
-   }
-
-   void deleteGapAtCursor(boolean group)
-   {
-     groupEditing = group;
-     startseq = seqCanvas.cursorY;
-     lastres = seqCanvas.cursorX+getKeyboardNo(keyboardNo1);
-     editSequence(false, seqCanvas.cursorX);
-     endEditing();
-   }
-
-   void numberPressed(char value)
-   {
-     if(keyboardNo1==null)
-       keyboardNo1 = new StringBuffer();
-
-     if(keyboardNo2!=null)
-       keyboardNo2.append(value);
-     else
-       keyboardNo1.append(value);
-   }
-
-   int getKeyboardNo(StringBuffer kb)
-   {
-     if(kb==null)
-       return 1;
-     else
-       return Integer.parseInt(kb.toString());
-   }
-
-   void setStatusMessage(SequenceI sequence, int res, int seq)
-   {
-     StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
-                                          sequence.getName());
-
-     Object obj = null;
-     if (av.alignment.isNucleotide())
-     {
-       obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
-                                                  "");
-       if (obj != null)
-         text.append(" Nucleotide: ");
-     }
-     else
-     {
-       obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
-       if (obj != null)
-         text.append("  Residue: ");
-     }
-
-     if (obj != null)
-     {
-
-       if (obj != "")
-       {
-         text.append(obj + " (" + sequence.findPosition(res) +
-                     ")");
-       }
-     }
-
-     ap.alignFrame.statusBar.setText(text.toString());
-
-    }
-     public void mousePressed(MouseEvent evt)
-     {
-       lastMousePress = evt.getPoint();
-
-       //For now, ignore the mouseWheel font resizing on Macs
-       //As the Button2_mask always seems to be true
-       if ( (evt.getModifiers() & InputEvent.BUTTON2_MASK) ==
-         InputEvent.BUTTON2_MASK && !av.MAC)
-       {
-         mouseWheelPressed = true;
-         return;
-       }
-
-       if (evt.isShiftDown()
-           || evt.isControlDown()
-           || evt.isAltDown())
-       {
-         if (evt.isControlDown() || evt.isAltDown())
-         {
-           groupEditing = true;
-         }
-         editingSeqs = true;
-       }
-       else
-       {
-         doMousePressedDefineMode(evt);
-         return;
-       }
-
-
-       int seq = findSeq(evt);
-       int res = findRes(evt);
-
-       if(seq<0 || res<0)
-         return;
-
-
-         if ((seq < av.getAlignment().getHeight()) &&
-                 (res < av.getAlignment().getSequenceAt(seq).getLength()))
-         {
-             startseq = seq;
-             lastres = res;
-         }
-         else
-         {
-             startseq = -1;
-             lastres = -1;
-         }
+    editCommand = null;
+  }
 
-        return;
-     }
+  void setCursorRow()
+  {
+    seqCanvas.cursorY = getKeyboardNo1() - 1;
+    scrollToVisible();
+  }
+
+  void setCursorColumn()
+  {
+    seqCanvas.cursorX = getKeyboardNo1() - 1;
+    scrollToVisible();
+  }
+
+  void setCursorRowAndColumn()
+  {
+    if (keyboardNo2 == null)
+    {
+      keyboardNo2 = new StringBuffer();
+    }
+    else
+    {
+      seqCanvas.cursorX = getKeyboardNo1() - 1;
+      seqCanvas.cursorY = getKeyboardNo2() - 1;
+      scrollToVisible();
+    }
+  }
+
+  void setCursorPosition()
+  {
+    SequenceI sequence =
+        (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
+
+    seqCanvas.cursorX = sequence.findIndex(
+        getKeyboardNo1() - 1
+        );
+    scrollToVisible();
+  }
+
+  void moveCursor(int dx, int dy)
+  {
+    seqCanvas.cursorX += dx;
+    seqCanvas.cursorY += dy;
+    if (av.hasHiddenColumns && !av.colSel.isVisible(seqCanvas.cursorX))
+    {
+      int original = seqCanvas.cursorX - dx;
+      int maxWidth = av.alignment.getWidth();
+
+      while (!av.colSel.isVisible(seqCanvas.cursorX)
+             && seqCanvas.cursorX < maxWidth
+             && seqCanvas.cursorX > 0)
+      {
+        seqCanvas.cursorX += dx;
+      }
+
+      if (seqCanvas.cursorX >= maxWidth
+          || !av.colSel.isVisible(seqCanvas.cursorX))
+      {
+        seqCanvas.cursorX = original;
+      }
+    }
+    scrollToVisible();
+  }
+
+  void scrollToVisible()
+  {
+    if (seqCanvas.cursorX < 0)
+    {
+      seqCanvas.cursorX = 0;
+    }
+    else if (seqCanvas.cursorX > av.alignment.getWidth() - 1)
+    {
+      seqCanvas.cursorX = av.alignment.getWidth() - 1;
+    }
+
+    if (seqCanvas.cursorY < 0)
+    {
+      seqCanvas.cursorY = 0;
+    }
+    else if (seqCanvas.cursorY > av.alignment.getHeight() - 1)
+    {
+      seqCanvas.cursorY = av.alignment.getHeight() - 1;
+    }
+
+    endEditing();
+    if (av.wrapAlignment)
+    {
+      ap.scrollToWrappedVisible(seqCanvas.cursorX);
+    }
+    else
+    {
+      while (seqCanvas.cursorY < av.startSeq)
+      {
+        ap.scrollUp(true);
+      }
+      while (seqCanvas.cursorY + 1 > av.endSeq)
+      {
+        ap.scrollUp(false);
+      }
+      while (seqCanvas.cursorX < av.colSel.adjustForHiddenColumns(av.startRes))
+      {
+
+        if (!ap.scrollRight(false))
+        {
+          break;
+        }
+      }
+      while (seqCanvas.cursorX > av.colSel.adjustForHiddenColumns(av.endRes))
+      {
+        if (!ap.scrollRight(true))
+        {
+          break;
+        }
+      }
+    }
+    setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY),
+                     seqCanvas.cursorX, seqCanvas.cursorY);
+
+    seqCanvas.repaint();
+  }
+
+  void setSelectionAreaAtCursor(boolean topLeft)
+  {
+    SequenceI sequence =
+        (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
+
+    if (av.getSelectionGroup() != null)
+    {
+      SequenceGroup sg = av.selectionGroup;
+      //Find the top and bottom of this group
+      int min = av.alignment.getHeight(), max = 0;
+      for (int i = 0; i < sg.getSize(); i++)
+      {
+        int index = av.alignment.findIndex(sg.getSequenceAt(i));
+        if (index > max)
+        {
+          max = index;
+        }
+        if (index < min)
+        {
+          min = index;
+        }
+      }
+
+      max++;
+
+      if (topLeft)
+      {
+        sg.setStartRes(seqCanvas.cursorX);
+        if (sg.getEndRes() < seqCanvas.cursorX)
+        {
+          sg.setEndRes(seqCanvas.cursorX);
+        }
+
+        min = seqCanvas.cursorY;
+      }
+      else
+      {
+        sg.setEndRes(seqCanvas.cursorX);
+        if (sg.getStartRes() > seqCanvas.cursorX)
+        {
+          sg.setStartRes(seqCanvas.cursorX);
+        }
+
+        max = seqCanvas.cursorY + 1;
+      }
+
+      if (min > max)
+      {
+        // Only the user can do this
+        av.setSelectionGroup(null);
+      }
+      else
+      {
+        // Now add any sequences between min and max
+        sg.getSequences(null).removeAllElements();
+        for (int i = min; i < max; i++)
+        {
+          sg.addSequence(av.alignment.getSequenceAt(i), false);
+        }
+      }
+    }
+
+    if (av.getSelectionGroup() == null)
+    {
+      SequenceGroup sg = new SequenceGroup();
+      sg.setStartRes(seqCanvas.cursorX);
+      sg.setEndRes(seqCanvas.cursorX);
+      sg.addSequence(sequence, false);
+      av.setSelectionGroup(sg);
+    }
+
+    ap.paintAlignment(false);
+  }
+
+  void insertGapAtCursor(boolean group)
+  {
+    groupEditing = group;
+    startseq = seqCanvas.cursorY;
+    lastres = seqCanvas.cursorX;
+    editSequence(true, seqCanvas.cursorX + getKeyboardNo1());
+    endEditing();
+  }
+
+  void deleteGapAtCursor(boolean group)
+  {
+    groupEditing = group;
+    startseq = seqCanvas.cursorY;
+    lastres = seqCanvas.cursorX + getKeyboardNo1();
+    editSequence(false, seqCanvas.cursorX);
+    endEditing();
+  }
+
+  void numberPressed(char value)
+  {
+    if (keyboardNo1 == null)
+    {
+      keyboardNo1 = new StringBuffer();
+    }
+
+    if (keyboardNo2 != null)
+    {
+      keyboardNo2.append(value);
+    }
+    else
+    {
+      keyboardNo1.append(value);
+    }
+  }
+
+  int getKeyboardNo1()
+  {
+    if (keyboardNo1 == null)
+      return 1;
+    else
+    {
+      int value = Integer.parseInt(keyboardNo1.toString());
+      keyboardNo1 = null;
+      return value;
+    }
+  }
+
+  int getKeyboardNo2()
+  {
+    if (keyboardNo2 == null)
+      return 1;
+    else
+    {
+      int value = Integer.parseInt(keyboardNo2.toString());
+      keyboardNo2 = null;
+      return value;
+    }
+  }
+
+
+  void setStatusMessage(SequenceI sequence, int res, int seq)
+  {
+    StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
+                                         sequence.getName());
+
+    Object obj = null;
+    if (av.alignment.isNucleotide())
+    {
+      obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
+                                                 "");
+      if (obj != null)
+      {
+        text.append(" Nucleotide: ");
+      }
+    }
+    else
+    {
+      obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
+      if (obj != null)
+      {
+        text.append("  Residue: ");
+      }
+    }
+
+    if (obj != null)
+    {
+
+      if (obj != "")
+      {
+        text.append(obj + " (" + sequence.findPosition(res) +
+                    ")");
+      }
+    }
+
+    ap.alignFrame.statusBar.setText(text.toString());
+
+  }
+
+  public void mousePressed(MouseEvent evt)
+  {
+    lastMousePress = evt.getPoint();
+
+    //For now, ignore the mouseWheel font resizing on Macs
+    //As the Button2_mask always seems to be true
+    if ( (evt.getModifiers() & InputEvent.BUTTON2_MASK) ==
+        InputEvent.BUTTON2_MASK && !av.MAC)
+    {
+      mouseWheelPressed = true;
+      return;
+    }
+
+    if (evt.isShiftDown()
+        || evt.isControlDown()
+        || evt.isAltDown())
+    {
+      if (evt.isControlDown() || evt.isAltDown())
+      {
+        groupEditing = true;
+      }
+      editingSeqs = true;
+    }
+    else
+    {
+      doMousePressedDefineMode(evt);
+      return;
+    }
+
+    int seq = findSeq(evt);
+    int res = findRes(evt);
+
+    if (seq < 0 || res < 0)
+    {
+      return;
+    }
+
+    if ( (seq < av.getAlignment().getHeight()) &&
+        (res < av.getAlignment().getSequenceAt(seq).getLength()))
+    {
+      startseq = seq;
+      lastres = res;
+    }
+    else
+    {
+      startseq = -1;
+      lastres = -1;
+    }
 
-     public void mouseClicked(MouseEvent evt){}
+    return;
+  }
+
+  public void mouseClicked(MouseEvent evt)
+  {
+    SequenceI sequence = av.alignment.getSequenceAt(findSeq(evt));
+    if (evt.getClickCount() > 1)
+    {
+      if (av.getSelectionGroup().getSize() == 1
+          && av.getSelectionGroup().getEndRes()
+          - av.getSelectionGroup().getStartRes() < 2)
+      {
+        av.setSelectionGroup(null);
+      }
+
+      SequenceFeature[] features = findFeaturesAtRes(
+          sequence,
+          sequence.findPosition(findRes(evt))
+          );
+
+      if (features != null && features.length > 0)
+      {
+        SearchResults highlight = new SearchResults();
+        highlight.addResult(sequence,
+                            features[0].getBegin(),
+                            features[0].getEnd());
+        seqCanvas.highlightSearchResults(highlight);
+      }
+      if (features != null && features.length > 0)
+      {
+        seqCanvas.getFeatureRenderer().amendFeatures(
+            new SequenceI[]
+            {sequence}, features, false, ap);
 
+        seqCanvas.highlightSearchResults(null);
+      }
+    }
+  }
 
   public void mouseReleased(MouseEvent evt)
   {
     mouseDragging = false;
     mouseWheelPressed = false;
+    ap.paintAlignment(true);
 
     if (!editingSeqs)
     {
-       doMouseReleasedDefineMode(evt);
-       return;
+      doMouseReleasedDefineMode(evt);
+      return;
     }
 
-     endEditing();
-     ap.repaint();
+    endEditing();
+
   }
 
-  int startWrapBlock=-1;
-  int wrappedBlock=-1;
+  int startWrapBlock = -1;
+  int wrappedBlock = -1;
   int findRes(MouseEvent evt)
- {
-   int res = 0;
-   int x = evt.getX();
-
-  if (av.wrapAlignment)
   {
+    int res = 0;
+    int x = evt.getX();
 
-    int hgap = av.charHeight;
-    if (av.scaleAboveWrapped)
-      hgap += av.charHeight;
+    if (av.wrapAlignment)
+    {
+
+      int hgap = av.charHeight;
+      if (av.scaleAboveWrapped)
+      {
+        hgap += av.charHeight;
+      }
 
-    int cHeight = av.getAlignment().getHeight() * av.charHeight
-        + hgap + seqCanvas.getAnnotationHeight();
+      int cHeight = av.getAlignment().getHeight() * av.charHeight
+          + hgap + seqCanvas.getAnnotationHeight();
 
       int y = evt.getY();
       y -= hgap;
       x -= seqCanvas.LABEL_WEST;
 
-
       int cwidth = seqCanvas.getWrappedCanvasWidth(getSize().width);
-      if(cwidth<1)
+      if (cwidth < 1)
+      {
         return 0;
+      }
 
       wrappedBlock = y / cHeight;
       wrappedBlock += av.getStartRes() / cwidth;
 
       res = wrappedBlock * cwidth + x / av.getCharWidth();
 
-  }
-  else
-  {
+    }
+    else
+    {
       res = (x / av.getCharWidth()) + av.getStartRes();
-  }
+    }
 
-  if(av.hasHiddenColumns)
-          res = av.getColumnSelection().adjustForHiddenColumns(res);
+    if (av.hasHiddenColumns)
+    {
+      res = av.getColumnSelection().adjustForHiddenColumns(res);
+    }
 
-  return res;
+    return res;
 
- }
+  }
 
- int findSeq(MouseEvent evt)
- {
+  int findSeq(MouseEvent evt)
+  {
 
-   int seq = 0;
-   int y = evt.getY();
+    int seq = 0;
+    int y = evt.getY();
 
-   if (av.wrapAlignment)
-   {
-     int hgap = av.charHeight;
-     if (av.scaleAboveWrapped)
-       hgap += av.charHeight;
+    if (av.wrapAlignment)
+    {
+      int hgap = av.charHeight;
+      if (av.scaleAboveWrapped)
+      {
+        hgap += av.charHeight;
+      }
 
-     int cHeight = av.getAlignment().getHeight() * av.charHeight
-         + hgap + seqCanvas.getAnnotationHeight();
+      int cHeight = av.getAlignment().getHeight() * av.charHeight
+          + hgap + seqCanvas.getAnnotationHeight();
 
-       y -= hgap;
+      y -= hgap;
+
+      seq = Math.min( (y % cHeight) / av.getCharHeight(),
+                     av.alignment.getHeight() - 1);
+      if (seq < 0)
+      {
+        seq = 0;
+      }
+    }
+    else
+    {
+      seq = Math.min( (y / av.getCharHeight()) + av.getStartSeq(),
+                     av.alignment.getHeight() - 1);
+      if (seq < 0)
+      {
+        seq = 0;
+      }
+    }
 
-     seq = Math.min( (y % cHeight) / av.getCharHeight(),
-                     av.alignment.getHeight() -1);
-     if(seq<0)
-       seq = 0;
-   }
-   else
-   {
-     seq = Math.min( (y / av.getCharHeight()) + av.getStartSeq(),
-                     av.alignment.getHeight() -1);
-     if(seq<0)
-       seq = 0;
-   }
+    return seq;
+  }
 
-   return seq;
- }
 
 
   public void doMousePressed(MouseEvent evt)
@@ -515,38 +614,83 @@ public class SeqPanel
     return;
   }
 
+
+  String lastMessage;
+  public void mouseOverSequence(SequenceI sequence, int index)
+  {
+    String tmp = sequence.hashCode()+index+"";
+    if (lastMessage == null || !lastMessage.equals(tmp))
+      ssm.mouseOverSequence(sequence, index);
+
+    lastMessage = tmp;
+  }
+
+
+  public void highlightSequence(jalview.datamodel.SequenceI seq, int index)
+  {
+    if(av.alignment.findIndex(seq)>-1)
+    {
+      SearchResults highlight = new SearchResults();
+      highlight.addResult(seq,index,index);
+      seqCanvas.highlightSearchResults(highlight);
+    }
+  }
+
+  public void updateColours(SequenceI seq, int index)
+  {
+    System.out.println("update the seqPanel colours");
+    //repaint();
+  }
+
   public void mouseMoved(MouseEvent evt)
   {
     int res = findRes(evt);
     int seq = findSeq(evt);
 
-    if (seq >= av.getAlignment().getHeight() || seq<0 || res<0)
+    if (seq >= av.getAlignment().getHeight() || seq < 0 || res < 0)
     {
+      if (tooltip != null)
+      {
+        tooltip.setTip("");
+      }
       return;
     }
 
     SequenceI sequence = av.getAlignment().getSequenceAt(seq);
     if (res > sequence.getLength())
     {
+      if (tooltip != null)
+      {
+        tooltip.setTip("");
+      }
       return;
     }
 
+
+    if (ssm != null)
+      mouseOverSequence(sequence, sequence.findPosition(res));
+
+
     StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
-            sequence.getName());
+                                         sequence.getName());
 
     Object obj = null;
     if (av.alignment.isNucleotide())
     {
       obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
-          "");
-      if(obj!=null)
+                                                 "");
+      if (obj != null)
+      {
         text.append(" Nucleotide: ");
+      }
     }
     else
     {
       obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
-      if(obj!=null)
+      if (obj != null)
+      {
         text.append("  Residue: ");
+      }
     }
 
     if (obj != null)
@@ -557,81 +701,98 @@ public class SeqPanel
       }
     }
 
-    if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence)
-    {
-      seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));
-    }
-
     ap.alignFrame.statusBar.setText(text.toString());
 
+    StringBuffer tooltipText = new StringBuffer();
+    SequenceGroup[] groups = av.alignment.findAllGroups(sequence);
+    if (groups != null)
+    {
+      for (int g = 0; g < groups.length; g++)
+      {
+        if (groups[g].getStartRes() <= res && groups[g].getEndRes() >= res)
+        {
+          if (!groups[g].getName().startsWith("JTreeGroup") &&
+              !groups[g].getName().startsWith("JGroup"))
+          {
+            tooltipText.append(groups[g].getName() + " ");
+          }
+          if (groups[g].getDescription() != null)
+          {
+            tooltipText.append(groups[g].getDescription());
+          }
+          tooltipText.append("\n");
+        }
+      }
+    }
 
     // use aa to see if the mouse pointer is on a
-    if (av.showSequenceFeatures
-        && sequence.getSequenceFeatures()!=null
-        && av.featuresDisplayed!=null)
-    {
-      StringBuffer featureText = new StringBuffer();
-      Vector allFeatures = getAllFeaturesAtRes(sequence, sequence.findPosition(res));
+    SequenceFeature [] allFeatures = findFeaturesAtRes(sequence,
+                                               sequence.findPosition(res));
 
       int index = 0;
-      while (index < allFeatures.size())
+      while (index < allFeatures.length)
       {
-        SequenceFeature sf = (SequenceFeature) allFeatures.elementAt(index);
+        SequenceFeature sf = allFeatures[index];
 
-        featureText.append(sf.getType()+" "+sf.begin+":"+sf.end);
+        tooltipText.append(sf.getType() + " " + sf.begin + ":" + sf.end);
 
         if (sf.getDescription() != null)
-          featureText.append(" " + sf.getDescription());
+        {
+          tooltipText.append(" " + sf.getDescription());
+        }
 
-        if (sf.getValue("status") != null )
+        if (sf.getValue("status") != null)
         {
           String status = sf.getValue("status").toString();
-          if(status.length()>0)
-            featureText.append(" (" + sf.getValue("status") + ")");
+          if (status.length() > 0)
+          {
+            tooltipText.append(" (" + sf.getValue("status") + ")");
+          }
         }
-        featureText.append("\n");
+        tooltipText.append("\n");
 
         index++;
       }
 
-
-        if (tooltip == null)
-          tooltip = new Tooltip(featureText.toString(), seqCanvas);
-        else
-          tooltip.setTip(featureText.toString());
-
-        tooltip.repaint();
-
+    if (tooltip == null)
+    {
+      tooltip = new Tooltip(tooltipText.toString(), seqCanvas);
+    }
+    else
+    {
+      tooltip.setTip(tooltipText.toString());
     }
-    else if (tooltip != null)
-     {
-       tooltip.setTip("");
-     }
   }
 
-  Vector getAllFeaturesAtRes(SequenceI seq, int res)
+  SequenceFeature[] findFeaturesAtRes(SequenceI sequence, int res)
   {
-    Vector allFeatures = new Vector();
-    int index = 0;
-    if(seq.getSequenceFeatures()!=null)
+    Vector tmp = new Vector();
+    SequenceFeature[] features = sequence.getSequenceFeatures();
+    if (features != null)
     {
-      while (index < seq.getSequenceFeatures().length)
+      for (int i = 0; i < features.length; i++)
       {
-        SequenceFeature sf = seq.getSequenceFeatures()[index];
-        if (sf.getBegin() <= res &&
-            sf.getEnd() >= res)
+        if (av.featuresDisplayed == null
+            || !av.featuresDisplayed.containsKey(features[i].getType()))
         {
-          if (av.featuresDisplayed.containsKey(sf.getType()))
-          {
-            allFeatures.addElement(sf);
-          }
+          continue;
+        }
+
+        if ( (features[i].getBegin() <= res) &&
+            (features[i].getEnd() >= res))
+        {
+          tmp.addElement(features[i]);
         }
-        index++;
       }
     }
-    return allFeatures;
+
+    features = new SequenceFeature[tmp.size()];
+    tmp.copyInto(features);
+
+    return features;
   }
 
+
   Tooltip tooltip;
 
   public void mouseDragged(MouseEvent evt)
@@ -655,9 +816,10 @@ public class SeqPanel
           fontSize++;
         }
 
-
-        if(fontSize<1)
+        if (fontSize < 1)
+        {
           fontSize = 1;
+        }
 
         av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
         av.charWidth = oldWidth;
@@ -673,7 +835,7 @@ public class SeqPanel
           av.charWidth++;
         }
 
-        if(av.charWidth<1)
+        if (av.charWidth < 1)
         {
           av.charWidth = 1;
         }
@@ -686,40 +848,44 @@ public class SeqPanel
 
       lastMousePress = evt.getPoint();
 
-      ap.repaint();
+      ap.paintAlignment(false);
       ap.annotationPanel.image = null;
       return;
-      }
+    }
 
-      if (!editingSeqs)
-      {
-        doMouseDraggedDefineMode(evt);
-        return;
-      }
+    if (!editingSeqs)
+    {
+      doMouseDraggedDefineMode(evt);
+      return;
+    }
 
-  int res = findRes(evt);
+    int res = findRes(evt);
 
-  if (res < 0)
-  {
+    if (res < 0)
+    {
       res = 0;
-  }
+    }
 
-  if ((lastres == -1) || (lastres == res))
-  {
+    if ( (lastres == -1) || (lastres == res))
+    {
       return;
-  }
+    }
 
-  if ( (res < av.getAlignment().getWidth()) && (res < lastres))
-  {
-    // dragLeft, delete gap
-    editSequence(false, res);
-  }
-  else
-    editSequence(true, res);
+    if ( (res < av.getAlignment().getWidth()) && (res < lastres))
+    {
+      // dragLeft, delete gap
+      editSequence(false, res);
+    }
+    else
+    {
+      editSequence(true, res);
+    }
 
-  mouseDragging = true;
-  if(scrollThread!=null)
-    scrollThread.setEvent(evt);
+    mouseDragging = true;
+    if (scrollThread != null)
+    {
+      scrollThread.setEvent(evt);
+    }
 
   }
 
@@ -732,324 +898,348 @@ public class SeqPanel
 
     SequenceI seq = av.alignment.getSequenceAt(startseq);
 
-      if (!groupEditing && av.hasHiddenRows)
+    if (!groupEditing && av.hasHiddenRows)
+    {
+      if (av.hiddenRepSequences != null
+          && av.hiddenRepSequences.containsKey(seq))
       {
-        if (av.hiddenRepSequences!=null
-            && av.hiddenRepSequences.containsKey(seq))
-        {
-          sg = (SequenceGroup)av.hiddenRepSequences.get(seq);
-          groupEditing = true;
-          }
+        sg = (SequenceGroup) av.hiddenRepSequences.get(seq);
+        groupEditing = true;
       }
+    }
 
-      StringBuffer message = new StringBuffer();
-      if (groupEditing)
+    StringBuffer message = new StringBuffer();
+    if (groupEditing)
+    {
+      message.append("Edit group:");
+      if (editCommand == null)
       {
-        message.append("Edit group:");
-        if (editCommand == null)
-          editCommand = new EditCommand("Edit Group");
+        editCommand = new EditCommand("Edit Group");
       }
-      else
-       {
-         message.append("Edit sequence: " + seq.getName());
-         String label = seq.getName();
-         if(label.length()>10)
-           label = label.substring(0,10);
-         if(editCommand==null)
-           editCommand = new EditCommand("Edit "+label);
-       }
+    }
+    else
+    {
+      message.append("Edit sequence: " + seq.getName());
+      String label = seq.getName();
+      if (label.length() > 10)
+      {
+        label = label.substring(0, 10);
+      }
+      if (editCommand == null)
+      {
+        editCommand = new EditCommand("Edit " + label);
+      }
+    }
+
+    if (insertGap)
+    {
+      message.append(" insert ");
+    }
+    else
+    {
+      message.append(" delete ");
+    }
 
-     if(insertGap)
-       message.append(" insert ");
-     else
-       message.append(" delete ");
+    message.append(Math.abs(startres - lastres) + " gaps.");
+    ap.alignFrame.statusBar.setText(message.toString());
 
-     message.append(Math.abs(startres-lastres)+" gaps.");
-     ap.alignFrame.statusBar.setText(message.toString());
+    //Are we editing within a selection group?
+    if (groupEditing
+        || (sg != null && sg.getSequences(av.hiddenRepSequences).contains(seq)))
+    {
+      fixedColumns = true;
 
+      //sg might be null as the user may only see 1 sequence,
+      //but the sequence represents a group
+      if (sg == null)
+      {
+        if (av.hiddenRepSequences == null
+            || !av.hiddenRepSequences.containsKey(seq))
+        {
+          endEditing();
+          return;
+        }
+
+        sg = (SequenceGroup) av.hiddenRepSequences.get(seq);
+      }
+
+      fixedLeft = sg.getStartRes();
+      fixedRight = sg.getEndRes();
+
+      if ( (startres < fixedLeft && lastres >= fixedLeft)
+          || (startres >= fixedLeft && lastres < fixedLeft)
+          || (startres > fixedRight && lastres <= fixedRight)
+          || (startres <= fixedRight && lastres > fixedRight))
+      {
+        endEditing();
+        return;
+      }
 
-      //Are we editing within a selection group?
-      if (groupEditing
-          || (sg != null && sg.getSequences(av.hiddenRepSequences).contains(seq)))
+      if (fixedLeft > startres)
       {
-        fixedColumns = true;
-
-        //sg might be null as the user may only see 1 sequence,
-        //but the sequence represents a group
-        if (sg == null)
-        {
-          sg = (SequenceGroup) av.hiddenRepSequences.get(seq);
-        }
+        fixedRight = fixedLeft - 1;
+        fixedLeft = 0;
+      }
+      else if (fixedRight < startres)
+      {
+        fixedLeft = fixedRight;
+        fixedRight = -1;
+      }
+    }
 
-        fixedLeft = sg.getStartRes();
-        fixedRight = sg.getEndRes();
+    if (av.hasHiddenColumns)
+    {
+      fixedColumns = true;
+      int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
+      int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);
 
-        if (   (startres < fixedLeft && lastres >= fixedLeft)
-            || (startres >= fixedLeft && lastres < fixedLeft)
-            || (startres > fixedRight && lastres <=fixedRight)
-            || (startres <= fixedRight && lastres > fixedRight))
-        {
-          endEditing();
-          return;
-        }
+      if ( (insertGap && startres > y1 && lastres < y1)
+          || (!insertGap && startres < y2 && lastres > y2))
+      {
+        endEditing();
+        return;
+      }
 
-        if (fixedLeft > startres)
+      //System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
+      //Selection spans a hidden region
+      if (fixedLeft < y1 && (fixedRight > y2 || fixedRight == -1))
+      {
+        if (startres >= y2)
         {
-          fixedRight = fixedLeft - 1;
-          fixedLeft = 0;
+          fixedLeft = y2;
         }
-        else if (fixedRight < startres)
+        else
         {
-          fixedLeft = fixedRight;
-          fixedRight = -1;
+          fixedRight = y2 - 1;
         }
       }
+    }
 
-
-      if(av.hasHiddenColumns )
+    if (groupEditing)
+    {
+      Vector vseqs = sg.getSequences(av.hiddenRepSequences);
+      int g, groupSize = vseqs.size();
+      SequenceI[] groupSeqs = new SequenceI[groupSize];
+      for (g = 0; g < groupSeqs.length; g++)
       {
-          fixedColumns = true;
-          int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
-          int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);
-
-          if ( (insertGap && startres > y1 && lastres < y1)
-              || (!insertGap && startres < y2 && lastres > y2))
-          {
-            endEditing();
-            return;
-          }
-
-          //System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
-          //Selection spans a hidden region
-          if(fixedLeft<y1 && (fixedRight>y2 || fixedRight==-1))
-          {
-            if(startres>=y2)
-            {
-              fixedLeft = y2;
-            }
-            else
-            {
-             fixedRight = y2 - 1;
-           }
-          }
+        groupSeqs[g] = (SequenceI) vseqs.elementAt(g);
       }
 
-
-      if (groupEditing)
+      // drag to right
+      if (insertGap)
       {
-        Vector vseqs = sg.getSequences(av.hiddenRepSequences);
-        int g, groupSize = vseqs.size();
-        SequenceI[] groupSeqs = new SequenceI[groupSize];
-        for (g = 0; g < groupSeqs.length; g++)
-          groupSeqs[g] = (SequenceI) vseqs.elementAt(g);
+        //If the user has selected the whole sequence, and is dragging to
+        // the right, we can still extend the alignment and selectionGroup
+        if (sg.getStartRes() == 0
+            && sg.getEndRes() == fixedRight
+            && sg.getEndRes() == av.alignment.getWidth() - 1
+            )
+        {
+          sg.setEndRes(av.alignment.getWidth() + startres - lastres);
+          fixedRight = sg.getEndRes();
+        }
 
-        // drag to right
-        if (insertGap)
+        // Is it valid with fixed columns??
+        // Find the next gap before the end
+        // of the visible region boundary
+        boolean blank = false;
+        for (fixedRight = fixedRight;
+             fixedRight > lastres;
+             fixedRight--)
         {
-            //If the user has selected the whole sequence, and is dragging to
-            // the right, we can still extend the alignment and selectionGroup
-            if(   sg.getStartRes() == 0
-                  && sg.getEndRes() == fixedRight
-                  && sg.getEndRes() == av.alignment.getWidth()-1
-               )
-            {
-              sg.setEndRes(av.alignment.getWidth() + startres - lastres);
-              fixedRight = sg.getEndRes();
-            }
+          blank = true;
 
-          // Is it valid with fixed columns??
-          // Find the next gap before the end
-          // of the visible region boundary
-          boolean blank = false;
-          for (fixedRight = fixedRight;
-               fixedRight > lastres;
-               fixedRight--)
+          for (g = 0; g < groupSize; g++)
           {
-            blank = true;
-
-            for (g = 0; g < groupSize; g++)
+            for (int j = 0; j < startres - lastres; j++)
             {
-              for (int j = 0; j < startres - lastres; j++)
+              if (!jalview.util.Comparison.isGap(
+                  groupSeqs[g].getCharAt(fixedRight - j)))
               {
-                if (!jalview.util.Comparison.isGap(
-                    groupSeqs[g].getCharAt(fixedRight - j)))
-                {
-                  blank = false;
-                  break;
-                }
+                blank = false;
+                break;
               }
             }
-            if (blank)
-              break;
           }
-
-          if (!blank)
+          if (blank)
           {
-            if(sg.getSize() == av.alignment.getHeight()  )
-            {
-              if((av.hasHiddenColumns
-                  && startres<av.getColumnSelection().getHiddenBoundaryRight(startres)))
-              {
-                endEditing();
-                return;
-              }
-
-              int alWidth = av.alignment.getWidth();
-              if(av.hasHiddenRows)
-              {
-                int hwidth = av.alignment.getHiddenSequences().getWidth();
-                if(hwidth>alWidth)
-                  alWidth = hwidth;
-              }
-              //We can still insert gaps if the selectionGroup
-              //contains all the sequences
-              sg.setEndRes(sg.getEndRes()+startres-lastres);
-              fixedRight = alWidth+startres-lastres;
-            }
-            else
-            {
-              endEditing();
-              return;
-            }
+            break;
           }
         }
 
-
-        // drag to left
-        else if(!insertGap)
+        if (!blank)
         {
-          /// Are we able to delete?
-          // ie are all columns blank?
-
-          for (g = 0; g < groupSize; g++)
+          if (sg.getSize() == av.alignment.getHeight())
           {
-            for (int j = startres; j < lastres; j++)
+            if ( (av.hasHiddenColumns
+                  &&
+                  startres < av.getColumnSelection().getHiddenBoundaryRight(startres)))
             {
-              if (groupSeqs[g].getLength() <= j)
-              {
-                continue;
-              }
+              endEditing();
+              return;
+            }
 
-              if (!jalview.util.Comparison.isGap(
-                  groupSeqs[g].getCharAt(j)))
+            int alWidth = av.alignment.getWidth();
+            if (av.hasHiddenRows)
+            {
+              int hwidth = av.alignment.getHiddenSequences().getWidth();
+              if (hwidth > alWidth)
               {
-                // Not a gap, block edit not valid
-                endEditing();
-                return;
+                alWidth = hwidth;
               }
             }
+            //We can still insert gaps if the selectionGroup
+            //contains all the sequences
+            sg.setEndRes(sg.getEndRes() + startres - lastres);
+            fixedRight = alWidth + startres - lastres;
+          }
+          else
+          {
+            endEditing();
+            return;
           }
         }
+      }
+
+      // drag to left
+      else if (!insertGap)
+      {
+        /// Are we able to delete?
+        // ie are all columns blank?
 
-          if (insertGap)
+        for (g = 0; g < groupSize; g++)
+        {
+          for (int j = startres; j < lastres; j++)
           {
-            // dragging to the right
-            if (fixedColumns && fixedRight != -1)
+            if (groupSeqs[g].getLength() <= j)
             {
-              for (int j = lastres; j < startres; j++)
-              {
-                  insertChar(j, groupSeqs, fixedRight);
-              }
+              continue;
             }
-            else
+
+            if (!jalview.util.Comparison.isGap(
+                groupSeqs[g].getCharAt(j)))
             {
-              editCommand.appendEdit(EditCommand.INSERT_GAP,
-                                     groupSeqs,
-                                     startres, startres-lastres,
-                                     av.getGapCharacter(),
-                                     true);
+              // Not a gap, block edit not valid
+              endEditing();
+              return;
             }
           }
-          else
-          {
-            // dragging to the left
-            if (fixedColumns && fixedRight != -1)
-            {
-              for (int j = lastres; j > startres; j--)
-              {
-                deleteChar(startres, groupSeqs, fixedRight);
-              }
-            }
-            else
-              editCommand.appendEdit(EditCommand.DELETE_GAP,
-                                     groupSeqs,
-                                     startres, lastres - startres,
-                                     av.getGapCharacter(),
-                                     true);
+        }
+      }
 
+      if (insertGap)
+      {
+        // dragging to the right
+        if (fixedColumns && fixedRight != -1)
+        {
+          for (int j = lastres; j < startres; j++)
+          {
+            insertChar(j, groupSeqs, fixedRight);
           }
+        }
+        else
+        {
+          editCommand.appendEdit(EditCommand.INSERT_GAP,
+                                 groupSeqs,
+                                 startres, startres - lastres,
+                                 av.alignment,
+                                 true);
+        }
       }
-      else /////Editing a single sequence///////////
+      else
       {
-        if (insertGap)
+        // dragging to the left
+        if (fixedColumns && fixedRight != -1)
         {
-          // dragging to the right
-          if (fixedColumns && fixedRight != -1)
+          for (int j = lastres; j > startres; j--)
           {
-            for (int j = lastres; j < startres; j++)
-            {
-              insertChar(j, new SequenceI[]{seq}, fixedRight);
-            }
+            deleteChar(startres, groupSeqs, fixedRight);
           }
-          else
+        }
+        else
+        {
+          editCommand.appendEdit(EditCommand.DELETE_GAP,
+                                 groupSeqs,
+                                 startres, lastres - startres,
+                                 av.alignment,
+                                 true);
+        }
+
+      }
+    }
+    else /////Editing a single sequence///////////
+    {
+      if (insertGap)
+      {
+        // dragging to the right
+        if (fixedColumns && fixedRight != -1)
+        {
+          for (int j = lastres; j < startres; j++)
           {
-            editCommand.appendEdit(EditCommand.INSERT_GAP,
-                                   new SequenceI[]
-                                   {seq},
-                                   lastres, startres-lastres,
-                                   av.getGapCharacter(),
-                                   true);
+            insertChar(j, new SequenceI[]
+                       {seq}, fixedRight);
           }
         }
         else
         {
-          // dragging to the left
-          if (fixedColumns && fixedRight != -1)
+          editCommand.appendEdit(EditCommand.INSERT_GAP,
+                                 new SequenceI[]
+                                 {seq},
+                                 lastres, startres - lastres,
+                                 av.alignment,
+                                 true);
+        }
+      }
+      else
+      {
+        // dragging to the left
+        if (fixedColumns && fixedRight != -1)
+        {
+          for (int j = lastres; j > startres; j--)
           {
-            for (int j = lastres; j > startres; j--)
+            if (!jalview.util.Comparison.isGap(seq.getCharAt(startres)))
             {
-              if (!jalview.util.Comparison.isGap(seq.getCharAt(startres)))
-              {
-                endEditing();
-                break;
-              }
-              deleteChar(startres, new SequenceI[]{seq}, fixedRight);
+              endEditing();
+              break;
             }
+            deleteChar(startres, new SequenceI[]
+                       {seq}, fixedRight);
           }
-          else
+        }
+        else
+        {
+          //could be a keyboard edit trying to delete none gaps
+          int max = 0;
+          for (int m = startres; m < lastres; m++)
           {
-            //could be a keyboard edit trying to delete none gaps
-            int max=0;
-            for(int m = startres; m<lastres; m++)
+            if (!jalview.util.Comparison.isGap(seq.getCharAt(m)))
             {
-              if(!jalview.util.Comparison.isGap(seq.getCharAt(m)))
-                break;
-              max++;
+              break;
             }
+            max++;
+          }
 
-            if (max>0)
-            {
-              editCommand.appendEdit(EditCommand.DELETE_GAP,
-                                     new SequenceI[]
-                                     {seq},
-                                     startres, max,
-                                     av.getGapCharacter(),
-                                     true);
-            }
+          if (max > 0)
+          {
+            editCommand.appendEdit(EditCommand.DELETE_GAP,
+                                   new SequenceI[]
+                                   {seq},
+                                   startres, max,
+                                   av.alignment,
+                                   true);
           }
         }
       }
+    }
 
-      lastres = startres;
-      seqCanvas.repaint();
+    lastres = startres;
+    seqCanvas.repaint();
   }
 
-
-
-  void insertChar(int j, SequenceI [] seq, int fixedColumn)
+  void insertChar(int j, SequenceI[] seq, int fixedColumn)
   {
     int blankColumn = fixedColumn;
-    for(int s=0; s<seq.length; s++)
+    for (int s = 0; s < seq.length; s++)
     {
       //Find the next gap before the end of the visible region boundary
       //If lastCol > j, theres a boundary after the gap insertion
@@ -1073,28 +1263,27 @@ public class SeqPanel
 
     editCommand.appendEdit(EditCommand.DELETE_GAP,
                            seq,
-                           blankColumn, 1, av.getGapCharacter(), true);
+                           blankColumn, 1, av.alignment, true);
 
     editCommand.appendEdit(EditCommand.INSERT_GAP,
                            seq,
-                           j, 1, av.getGapCharacter(),
+                           j, 1, av.alignment,
                            true);
 
   }
 
-  void deleteChar(int j, SequenceI [] seq, int fixedColumn)
+  void deleteChar(int j, SequenceI[] seq, int fixedColumn)
   {
 
     editCommand.appendEdit(EditCommand.DELETE_GAP,
                            seq,
-                           j, 1, av.getGapCharacter(), true);
+                           j, 1, av.alignment, true);
 
     editCommand.appendEdit(EditCommand.INSERT_GAP,
                            seq,
-                           fixedColumn, 1, av.getGapCharacter(), true);
+                           fixedColumn, 1, av.alignment, true);
   }
 
-
 //////////////////////////////////////////
 /////Everything below this is for defining the boundary of the rubberband
 //////////////////////////////////////////
@@ -1109,10 +1298,12 @@ public class SeqPanel
     int res = findRes(evt);
     int seq = findSeq(evt);
     oldSeq = seq;
-    startWrapBlock=wrappedBlock;
+    startWrapBlock = wrappedBlock;
 
-    if(seq==-1)
+    if (seq == -1)
+    {
       return;
+    }
 
     SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
 
@@ -1160,26 +1351,24 @@ public class SeqPanel
       av.setSelectionGroup(stretchGroup);
     }
 
-
     // DETECT RIGHT MOUSE BUTTON IN AWT
     if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK) ==
-             InputEvent.BUTTON3_MASK)
+        InputEvent.BUTTON3_MASK)
     {
-      Vector allFeatures = getAllFeaturesAtRes(sequence,
+      SequenceFeature [] allFeatures = findFeaturesAtRes(sequence,
                                                sequence.findPosition(res));
 
       Vector links = null;
-      if(allFeatures!=null)
+      if (allFeatures != null)
       {
-        for (int i = 0; i < allFeatures.size(); i++)
+        for (int i = 0; i < allFeatures.length; i++)
         {
-          SequenceFeature sf = (SequenceFeature) allFeatures.elementAt(i);
-          if (sf.links != null)
+          if (allFeatures[i].links != null)
           {
             links = new Vector();
-            for (int j = 0; j < sf.links.size(); j++)
+            for (int j = 0; j < allFeatures[i].links.size(); j++)
             {
-              links.addElement(sf.links.elementAt(j));
+              links.addElement(allFeatures[i].links.elementAt(j));
             }
           }
         }
@@ -1187,7 +1376,6 @@ public class SeqPanel
       APopupMenu popup = new APopupMenu(ap, null, links);
       this.add(popup);
       popup.show(this, evt.getX(), evt.getY());
-      ap.repaint();
       return;
     }
 
@@ -1199,40 +1387,40 @@ public class SeqPanel
       return;
     }
 
-      //Only if left mouse button do we want to change group sizes
+    //Only if left mouse button do we want to change group sizes
 
-      if (stretchGroup == null)
+    if (stretchGroup == null)
+    {
+      // define a new group here
+      SequenceGroup sg = new SequenceGroup();
+      sg.setStartRes(res);
+      sg.setEndRes(res);
+      sg.addSequence(sequence, false);
+      av.setSelectionGroup(sg);
+      stretchGroup = sg;
+
+      if (av.getConservationSelected())
       {
-        // define a new group here
-        SequenceGroup sg = new SequenceGroup();
-        sg.setStartRes(res);
-        sg.setEndRes(res);
-        sg.addSequence(sequence, false);
-        av.setSelectionGroup(sg);
-        stretchGroup = sg;
-
-        if (av.getConservationSelected())
-        {
-          SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(),
-                                            "Background");
-        }
-        if (av.getAbovePIDThreshold())
-        {
-          SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
-                                         "Background");
-        }
-
+        SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(),
+                                          "Background");
+      }
+      if (av.getAbovePIDThreshold())
+      {
+        SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
+                                       "Background");
       }
+
+    }
   }
 
   public void doMouseReleasedDefineMode(MouseEvent evt)
   {
     if (stretchGroup == null)
     {
-        return;
+      return;
     }
 
-    if(stretchGroup.cs!=null)
+    if (stretchGroup.cs != null)
     {
       if (stretchGroup.cs instanceof ClustalxColourScheme)
       {
@@ -1245,8 +1433,9 @@ public class SeqPanel
           || stretchGroup.cs instanceof PIDColourScheme
           || stretchGroup.cs.conservationApplied()
           || stretchGroup.cs.getThreshold() > 0)
+      {
         stretchGroup.recalcConservation();
-
+      }
 
       if (stretchGroup.cs.conservationApplied())
       {
@@ -1264,7 +1453,7 @@ public class SeqPanel
     changeStartRes = false;
     stretchGroup = null;
     PaintRefresher.Refresh(ap, av.getSequenceSetId());
-    ap.repaint();
+    ap.paintAlignment(true);
   }
 
   public void doMouseDraggedDefineMode(MouseEvent evt)
@@ -1272,125 +1461,132 @@ public class SeqPanel
     int res = findRes(evt);
     int y = findSeq(evt);
 
-    if(wrappedBlock!=startWrapBlock)
+    if (wrappedBlock != startWrapBlock)
+    {
       return;
+    }
 
-     if (stretchGroup == null)
-     {
-          return;
-     }
+    if (stretchGroup == null)
+    {
+      return;
+    }
+
+    mouseDragging = true;
 
-     mouseDragging = true;
+    if (y > av.alignment.getHeight())
+    {
+      y = av.alignment.getHeight() - 1;
+    }
 
+    if (res >= av.alignment.getWidth())
+    {
+      res = av.alignment.getWidth() - 1;
+    }
 
-      if(y > av.alignment.getHeight())
-      {
-        y = av.alignment.getHeight() -1;
-      }
+    if (stretchGroup.getEndRes() == res)
+    {
+      // Edit end res position of selected group
+      changeEndRes = true;
+    }
+    else if (stretchGroup.getStartRes() == res)
+    {
+      // Edit start res position of selected group
+      changeStartRes = true;
+    }
 
-      if(res>=av.alignment.getWidth())
-        res = av.alignment.getWidth()-1;
+    if (res < 0)
+    {
+      res = 0;
+    }
 
-      if (stretchGroup.getEndRes() == res)
+    if (changeEndRes)
+    {
+      if (res > (stretchGroup.getStartRes() - 1))
       {
-          // Edit end res position of selected group
-          changeEndRes = true;
+        stretchGroup.setEndRes(res);
       }
-      else if (stretchGroup.getStartRes() == res)
+    }
+    else if (changeStartRes)
+    {
+      if (res < (stretchGroup.getEndRes() + 1))
       {
-          // Edit start res position of selected group
-          changeStartRes = true;
+        stretchGroup.setStartRes(res);
       }
+    }
 
-      if (res < 0)
-      {
-          res = 0;
-      }
+    int dragDirection = 0;
 
-      if (changeEndRes)
-      {
-          if (res > (stretchGroup.getStartRes() - 1))
-          {
-              stretchGroup.setEndRes(res);
-          }
-      }
-      else if (changeStartRes)
-      {
-          if (res < (stretchGroup.getEndRes() + 1))
-          {
-              stretchGroup.setStartRes(res);
-          }
-      }
+    if (y > oldSeq)
+    {
+      dragDirection = 1;
+    }
+    else if (y < oldSeq)
+    {
+      dragDirection = -1;
+    }
+
+    while ( (y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))
+    {
+      // This routine ensures we don't skip any sequences, as the
+      // selection is quite slow.
+      Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
 
-      int dragDirection = 0;
+      oldSeq += dragDirection;
 
-      if (y > oldSeq)
-      {
-          dragDirection = 1;
-      }
-      else if (y < oldSeq)
+      if (oldSeq < 0)
       {
-          dragDirection = -1;
+        break;
       }
 
+      Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
 
-      while ((y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))
+      if (stretchGroup.getSequences(null).contains(nextSeq))
       {
-          // This routine ensures we don't skip any sequences, as the
-          // selection is quite slow.
-          Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
-
-          oldSeq += dragDirection;
-
-          if(oldSeq<0)
-            break;
-
-          Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
-
-          if (stretchGroup.getSequences(null).contains(nextSeq))
-          {
-              stretchGroup.deleteSequence(seq, false);
-          }
-          else
-          {
-              if (seq != null)
-              {
-                  stretchGroup.addSequence(seq, false);
-              }
+        stretchGroup.deleteSequence(seq, false);
+      }
+      else
+      {
+        if (seq != null)
+        {
+          stretchGroup.addSequence(seq, false);
+        }
 
-              stretchGroup.addSequence(nextSeq, false);
-          }
+        stretchGroup.addSequence(nextSeq, false);
       }
+    }
 
-      if(oldSeq < 0)
-        oldSeq = -1;
+    if (oldSeq < 0)
+    {
+      oldSeq = -1;
+    }
 
+    if (res > av.endRes || res < av.startRes
+        || y < av.startSeq || y > av.endSeq)
+    {
+      mouseExited(evt);
+    }
 
-      if(res>av.endRes || res<av.startRes
-          || y<av.startSeq || y>av.endSeq)
-      {
-        mouseExited(evt);
-      }
+    if (scrollThread != null)
+    {
+      scrollThread.setEvent(evt);
+    }
 
-      if (scrollThread != null)
-      {
-        scrollThread.setEvent(evt);
-      }
+    seqCanvas.repaint();
+  }
 
-      seqCanvas.repaint();
+  public void mouseEntered(MouseEvent e)
+  {
+    if (oldSeq < 0)
+    {
+      oldSeq = 0;
     }
 
-    public void mouseEntered(MouseEvent e)
+    if (scrollThread != null)
     {
-      if (oldSeq < 0)
-        oldSeq = 0;
-
-      if (scrollThread != null)
-      {
-        scrollThread.running = false;
-        scrollThread = null;
-      }
+      scrollThread.running = false;
+      scrollThread = null;
     }
+  }
 
   public void mouseExited(MouseEvent e)
   {
@@ -1399,7 +1595,7 @@ public class SeqPanel
       return;
     }
 
-    if (mouseDragging && scrollThread==null)
+    if (mouseDragging && scrollThread == null)
     {
       scrollThread = new ScrollThread();
     }
@@ -1407,9 +1603,9 @@ public class SeqPanel
 
   void scrollCanvas(MouseEvent evt)
   {
-    if(evt==null)
+    if (evt == null)
     {
-      if(scrollThread!=null)
+      if (scrollThread != null)
       {
         scrollThread.running = false;
         scrollThread = null;
@@ -1419,13 +1615,15 @@ public class SeqPanel
     else
     {
       if (scrollThread == null)
+      {
         scrollThread = new ScrollThread();
+      }
 
       mouseDragging = true;
       scrollThread.setEvent(evt);
     }
 
-    }
+  }
 
   // this class allows scrolling off the bottom of the visible alignment
   class ScrollThread