X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqPanel.java;h=89e2086a1ebbd81a81e2f2286dc7071a3fc7455c;hb=7724430e3293cbb862d0c50c5308a3b3b0417cac;hp=55bc65a8c50b63ac899b06287a7a884eb5e19ee4;hpb=94bc21544b9573fdf177c500bdb981e8076a7e7d;p=jalview.git

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 55bc65a..89e2086 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) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 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
@@ -24,6 +24,9 @@ import java.awt.event.*;
 
 import jalview.datamodel.*;
 import jalview.schemes.*;
+import jalview.commands.*;
+
+import java.util.Vector;
 
 public class SeqPanel
     extends Panel implements MouseMotionListener, MouseListener
@@ -55,6 +58,11 @@ public class SeqPanel
   StringBuffer keyboardNo1;
   StringBuffer keyboardNo2;
 
+  boolean mouseWheelPressed = false;
+  Point lastMousePress;
+
+  EditCommand editCommand;
+
   public SeqPanel(AlignViewport avp, AlignmentPanel p)
   {
     this.av = avp;
@@ -73,13 +81,20 @@ public class SeqPanel
 
   void endEditing()
   {
+    if (editCommand!=null && editCommand.getSize() > 0)
+    {
+      ap.alignFrame.addHistoryItem(editCommand);
+      av.firePropertyChange("alignment", null,
+                            av.getAlignment().getSequences());
+    }
+
     startseq = -1;
     lastres = -1;
-    seqEditOccurred = false;
     editingSeqs = false;
     groupEditing = false;
     keyboardNo1 = null;
     keyboardNo2 = null;
+     editCommand = null;
    }
 
    void setCursorRow()
@@ -123,6 +138,24 @@ public class SeqPanel
    {
      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();
    }
 
@@ -140,26 +173,32 @@ public class SeqPanel
 
 
      endEditing();
-     while (seqCanvas.cursorY < av.startSeq)
-     {
-       ap.scrollUp(true);
-     }
-     while (seqCanvas.cursorY + 1 > av.endSeq)
+     if (av.wrapAlignment)
      {
-       ap.scrollUp(false);
+       ap.scrollToWrappedVisible(seqCanvas.cursorX);
      }
-     while (seqCanvas.cursorX < av.startRes)
+     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.endRes)
-     {
-       if(!ap.scrollRight(true))
-         break;
+         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);
 
@@ -212,7 +251,7 @@ public class SeqPanel
        else
        {
          // Now add any sequences between min and max
-         sg.sequences.removeAllElements();
+         sg.getSequences(null).removeAllElements();
          for (int i = min; i < max; i++)
          {
            sg.addSequence(av.alignment.getSequenceAt(i), false);
@@ -235,24 +274,20 @@ public class SeqPanel
 
    void insertGapAtCursor(boolean group)
    {
-     ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
-                                                  av.alignment, HistoryItem.EDIT));
      groupEditing = group;
      startseq = seqCanvas.cursorY;
      lastres = seqCanvas.cursorX;
      editSequence(true, seqCanvas.cursorX+getKeyboardNo(keyboardNo1));
-     editOccurred();
+     endEditing();
    }
 
    void deleteGapAtCursor(boolean group)
    {
-     ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
-                                                  av.alignment, HistoryItem.EDIT));
      groupEditing = group;
      startseq = seqCanvas.cursorY;
      lastres = seqCanvas.cursorX+getKeyboardNo(keyboardNo1);
      editSequence(false, seqCanvas.cursorX);
-     editOccurred();
+     endEditing();
    }
 
    void numberPressed(char value)
@@ -303,15 +338,28 @@ public class SeqPanel
                      ")");
        }
      }
+
      ap.alignFrame.statusBar.setText(text.toString());
 
     }
      public void mousePressed(MouseEvent evt)
      {
-       if (evt.isShiftDown() || evt.isAltDown() ||
-           evt.isControlDown())
+       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)
        {
-         if (evt.isAltDown() || evt.isControlDown())
+         mouseWheelPressed = true;
+         return;
+       }
+
+       if (evt.isShiftDown()
+           || evt.isControlDown()
+           || evt.isAltDown())
+       {
+         if (evt.isControlDown() || evt.isAltDown())
          {
            groupEditing = true;
          }
@@ -330,8 +378,6 @@ public class SeqPanel
        if(seq<0 || res<0)
          return;
 
-       ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
-                                                          av.alignment, HistoryItem.EDIT));
 
          if ((seq < av.getAlignment().getHeight()) &&
                  (res < av.getAlignment().getSequenceAt(seq).getLength()))
@@ -354,6 +400,7 @@ public class SeqPanel
   public void mouseReleased(MouseEvent evt)
   {
     mouseDragging = false;
+    mouseWheelPressed = false;
 
     if (!editingSeqs)
     {
@@ -361,10 +408,8 @@ public class SeqPanel
        return;
     }
 
-     editOccurred();
-
      endEditing();
-       ap.repaint();
+     ap.repaint();
   }
 
   int startWrapBlock=-1;
@@ -390,6 +435,8 @@ public class SeqPanel
 
 
       int cwidth = seqCanvas.getWrappedCanvasWidth(getSize().width);
+      if(cwidth<1)
+        return 0;
 
       wrappedBlock = y / cHeight;
       wrappedBlock += av.getStartRes() / cwidth;
@@ -402,6 +449,9 @@ public class SeqPanel
       res = (x / av.getCharWidth()) + av.getStartRes();
   }
 
+  if(av.hasHiddenColumns)
+          res = av.getColumnSelection().adjustForHiddenColumns(res);
+
   return res;
 
  }
@@ -423,11 +473,17 @@ public class SeqPanel
 
        y -= hgap;
 
-     seq = ( (y % cHeight) / av.getCharHeight());
+     seq = Math.min( (y % cHeight) / av.getCharHeight(),
+                     av.alignment.getHeight() -1);
+     if(seq<0)
+       seq = 0;
    }
    else
    {
-     seq = (y / av.getCharHeight()) + av.getStartSeq();
+     seq = Math.min( (y / av.getCharHeight()) + av.getStartSeq(),
+                     av.alignment.getHeight() -1);
+     if(seq<0)
+       seq = 0;
    }
 
    return seq;
@@ -436,8 +492,6 @@ public class SeqPanel
 
   public void doMousePressed(MouseEvent evt)
   {
-    ap.alignFrame.addHistoryItem(new HistoryItem(
-        "Edit Sequence", av.alignment, HistoryItem.EDIT));
 
     int seq = findSeq(evt);
     int res = findRes(evt);
@@ -497,11 +551,9 @@ public class SeqPanel
 
     if (obj != null)
     {
-
       if (obj != "")
       {
-        text.append(obj + " (" +
-                    av.getAlignment().getSequenceAt(seq).findPosition(res) + ")");
+        text.append(obj + " (" + sequence.findPosition(res) + ")");
       }
     }
 
@@ -510,61 +562,140 @@ public class SeqPanel
       seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));
     }
 
+    ap.alignFrame.statusBar.setText(text.toString());
+
 
     // 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));
+
       int index = 0;
-      sequence.getSequenceFeatures();
-      boolean first = true;
-      while (index < sequence.getSequenceFeatures().length)
+      while (index < allFeatures.size())
       {
-        SequenceFeature sf = sequence.getSequenceFeatures()[index];
-        if (sf.getBegin() <= sequence.findPosition(res) &&
-            sf.getEnd() >= sequence.findPosition(res))
+        SequenceFeature sf = (SequenceFeature) allFeatures.elementAt(index);
+
+        featureText.append(sf.getType()+" "+sf.begin+":"+sf.end);
+
+        if (sf.getDescription() != null)
+          featureText.append(" " + sf.getDescription());
+
+        if (sf.getValue("status") != null )
         {
-          if(!av.featuresDisplayed.containsKey(sf.getType()))
-           {
-             index++;
-             continue;
-           }
+          String status = sf.getValue("status").toString();
+          if(status.length()>0)
+            featureText.append(" (" + sf.getValue("status") + ")");
+        }
+        featureText.append("\n");
 
-          if(first)
-          {
-            text.append(" Sequence Feature:");
-            first = false;
-          }
+        index++;
+      }
+
+
+        if (tooltip == null)
+          tooltip = new Tooltip(featureText.toString(), seqCanvas);
+        else
+          tooltip.setTip(featureText.toString());
 
-          text.append(" "+sf.getType());
+        tooltip.repaint();
 
-          if(sf.getDescription()!=null)
-            text.append(" "+sf.getDescription());
+    }
+    else if (tooltip != null)
+     {
+       tooltip.setTip("");
+     }
+  }
 
-          if (sf.getStatus()!=null && sf.getStatus().length() > 0)
+  Vector getAllFeaturesAtRes(SequenceI seq, int res)
+  {
+    Vector allFeatures = new Vector();
+    int index = 0;
+    if(seq.getSequenceFeatures()!=null)
+    {
+      while (index < seq.getSequenceFeatures().length)
+      {
+        SequenceFeature sf = seq.getSequenceFeatures()[index];
+        if (sf.getBegin() <= res &&
+            sf.getEnd() >= res)
+        {
+          if (av.featuresDisplayed.containsKey(sf.getType()))
           {
-            text.append(" (" + sf.getStatus() + ")");
+            allFeatures.addElement(sf);
           }
-          text.append("; ");
         }
-
         index++;
-
       }
     }
-
-     ap.alignFrame.statusBar.setText(text.toString());
-
+    return allFeatures;
   }
 
+  Tooltip tooltip;
+
   public void mouseDragged(MouseEvent evt)
   {
-    if (!editingSeqs)
-{
-  doMouseDraggedDefineMode(evt);
-  return;
-}
+    if (mouseWheelPressed)
+    {
+      int oldWidth = av.charWidth;
+
+      //Which is bigger, left-right or up-down?
+      if (Math.abs(evt.getY() - lastMousePress.y)
+          > Math.abs(evt.getX() - lastMousePress.x))
+      {
+        int fontSize = av.font.getSize();
+
+        if (evt.getY() < lastMousePress.y && av.charHeight > 1)
+        {
+          fontSize--;
+        }
+        else if (evt.getY() > lastMousePress.y)
+        {
+          fontSize++;
+        }
+
+
+        if(fontSize<1)
+          fontSize = 1;
+
+        av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
+        av.charWidth = oldWidth;
+      }
+      else
+      {
+        if (evt.getX() < lastMousePress.x && av.charWidth > 1)
+        {
+          av.charWidth--;
+        }
+        else if (evt.getX() > lastMousePress.x)
+        {
+          av.charWidth++;
+        }
+
+        if(av.charWidth<1)
+        {
+          av.charWidth = 1;
+        }
+      }
+
+      ap.fontChanged();
+
+      FontMetrics fm = getFontMetrics(av.getFont());
+      av.validCharWidth = fm.charWidth('M') <= av.charWidth;
+
+      lastMousePress = evt.getPoint();
+
+      ap.repaint();
+      ap.annotationPanel.image = null;
+      return;
+      }
+
+      if (!editingSeqs)
+      {
+        doMouseDraggedDefineMode(evt);
+        return;
+      }
 
   int res = findRes(evt);
 
@@ -593,250 +724,339 @@ public class SeqPanel
   }
 
   synchronized void editSequence(boolean insertGap, int startres)
-    {
-      int fixedLeft = -1;
-      int fixedRight = -1;
-      boolean fixedColumns = false;
-      SequenceGroup sg = av.getSelectionGroup();
+  {
+    int fixedLeft = -1;
+    int fixedRight = -1;
+    boolean fixedColumns = false;
+    SequenceGroup sg = av.getSelectionGroup();
 
-      if(groupEditing && sg==null)
-        return;
+    SequenceI seq = av.alignment.getSequenceAt(startseq);
 
-        SequenceI seq = av.alignment.getSequenceAt(startseq);
-        StringBuffer message = new StringBuffer();
-        if (groupEditing)
-           message.append("Edit group:");
-        else
-            message.append("Edit sequence: "+seq.getName());
+      if (!groupEditing && av.hasHiddenRows)
+      {
+        if (av.hiddenRepSequences!=null
+            && av.hiddenRepSequences.containsKey(seq))
+        {
+          sg = (SequenceGroup)av.hiddenRepSequences.get(seq);
+          groupEditing = true;
+          }
+      }
+
+      StringBuffer message = new StringBuffer();
+      if (groupEditing)
+      {
+        message.append("Edit group:");
+        if (editCommand == null)
+          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);
+       }
+
+     if(insertGap)
+       message.append(" insert ");
+     else
+       message.append(" delete ");
+
+     message.append(Math.abs(startres-lastres)+" gaps.");
+     ap.alignFrame.statusBar.setText(message.toString());
 
-       if(insertGap)
-         message.append(" insert ");
-       else
-         message.append(" delete ");
 
-       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)
+        {
+          sg = (SequenceGroup) av.hiddenRepSequences.get(seq);
+        }
 
-        //Are we editing within a selection group?
-        if (groupEditing
-            || (sg != null && sg.sequences.contains(seq)))
+        fixedLeft = sg.getStartRes();
+        fixedRight = sg.getEndRes();
+
+        if (   (startres < fixedLeft && lastres >= fixedLeft)
+            || (startres >= fixedLeft && lastres < fixedLeft)
+            || (startres > fixedRight && lastres <=fixedRight)
+            || (startres <= fixedRight && lastres > fixedRight))
         {
-          fixedColumns = true;
+          endEditing();
+          return;
+        }
+
+        if (fixedLeft > startres)
+        {
+          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))
+          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))
           {
-            fixedRight = fixedLeft - 1;
-            fixedLeft = 0;
-          }
-          else if (fixedRight < startres)
-          {
-            fixedLeft = fixedRight;
-            fixedRight = -1;
+            if(startres>=y2)
+            {
+              fixedLeft = y2;
+            }
+            else
+            {
+             fixedRight = y2 - 1;
+           }
           }
-        }
+      }
 
 
-        if (groupEditing)
+      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++)
+          groupSeqs[g] = (SequenceI) vseqs.elementAt(g);
+
+        // drag to right
+        if (insertGap)
         {
-          // drag to right
-          if (insertGap)
+            //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();
+            }
+
+          // 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() + 1 == av.alignment.getWidth())
-              {
-                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 (int s = 0; s < sg.getSize(); s++)
+              for (int j = 0; j < startres - lastres; j++)
               {
-                seq = sg.getSequenceAt(s);
-                for (int j = 0; j < startres - lastres; j++)
+                if (!jalview.util.Comparison.isGap(
+                    groupSeqs[g].getCharAt(fixedRight - j)))
                 {
-                  if (!jalview.util.Comparison.isGap(
-                      seq.getCharAt(fixedRight - j)))
-                  {
-                    blank = false;
-                    break;
-                  }
+                  blank = false;
+                  break;
                 }
               }
-              if (blank)
-                break;
             }
+            if (blank)
+              break;
+          }
 
-            if (!blank)
+          if (!blank)
+          {
+            if(sg.getSize() == av.alignment.getHeight()  )
             {
-              if(sg.getSize() == av.alignment.getHeight())
-              {
-                //We can still insert gaps if the selectionGroup
-                //contains all the sequences
-                sg.setEndRes(sg.getEndRes()+startres-lastres);
-                fixedRight = av.alignment.getWidth()+startres-lastres;
-              }
-              else
+              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;
             }
           }
+        }
 
 
-          // drag to left
-          else if(!insertGap)
-          {
-            /// Are we able to delete?
-            // ie are all columns blank?
+        // drag to left
+        else if(!insertGap)
+        {
+          /// Are we able to delete?
+          // ie are all columns blank?
 
-            for (int s = 0; s < sg.getSize(); s++)
+          for (g = 0; g < groupSize; g++)
+          {
+            for (int j = startres; j < lastres; j++)
             {
-              seq = sg.getSequenceAt(s);
-
-              for (int j = startres; j < lastres; j++)
+              if (groupSeqs[g].getLength() <= j)
               {
-                if (seq.getSequence().length() <= j)
-                {
-                  continue;
-                }
+                continue;
+              }
 
-                if (!jalview.util.Comparison.isGap(
-                    seq.getSequence().charAt(j)))
-                {
-                  // Not a gap, block edit not valid
-                  endEditing();
-                  return;
-                }
+              if (!jalview.util.Comparison.isGap(
+                  groupSeqs[g].getCharAt(j)))
+              {
+                // Not a gap, block edit not valid
+                endEditing();
+                return;
               }
             }
           }
+        }
 
-
-          for (int i = 0; i < sg.getSize(); i++)
+          if (insertGap)
           {
-            seq = sg.getSequenceAt(i);
-
-            if (insertGap)
+            // dragging to the right
+            if (fixedColumns && fixedRight != -1)
             {
-              // dragging to the right
               for (int j = lastres; j < startres; j++)
               {
-                if (fixedColumns && fixedRight != -1)
-                {
-                  insertChar(j, seq, fixedRight);
-                }
-                else
-                  insertChar(j, seq);
+                  insertChar(j, groupSeqs, fixedRight);
               }
             }
             else
             {
-              // dragging to the left
+              editCommand.appendEdit(EditCommand.INSERT_GAP,
+                                     groupSeqs,
+                                     startres, startres-lastres,
+                                     av.getGapCharacter(),
+                                     true);
+            }
+          }
+          else
+          {
+            // dragging to the left
+            if (fixedColumns && fixedRight != -1)
+            {
               for (int j = lastres; j > startres; j--)
               {
-                if (fixedColumns && fixedRight != -1)
-                {
-                  deleteChar(startres, seq, fixedRight);
-                }
-                else
-                {
-                  deleteChar(startres, seq);
-                }
+                deleteChar(startres, groupSeqs, fixedRight);
               }
             }
+            else
+              editCommand.appendEdit(EditCommand.DELETE_GAP,
+                                     groupSeqs,
+                                     startres, lastres - startres,
+                                     av.getGapCharacter(),
+                                     true);
+
           }
-        }
-        else /////Editing a single sequence///////////
+      }
+      else /////Editing a single sequence///////////
+      {
+        if (insertGap)
         {
-          if (insertGap)
+          // dragging to the right
+          if (fixedColumns && fixedRight != -1)
           {
-            // dragging to the right
             for (int j = lastres; j < startres; j++)
             {
-              if (fixedColumns && fixedRight != -1)
-              {
-                if (sg.getStartRes() == 0
-                    && sg.getEndRes() + 1 == av.alignment.getWidth()
-                    && !jalview.util.Comparison.isGap(seq.getCharAt(fixedRight)))
-                {
-                  //Single sequence edit, whole sequence selected,
-                  //extend the selection group
-                  sg.setEndRes(av.alignment.getWidth() -1 + startres - lastres);
-                  fixedColumns = false;
-                  insertChar(j, seq);
-                }
-                else
-                  insertChar(j, seq, fixedRight);
-              }
-              else
-                insertChar(j, seq);
+              insertChar(j, new SequenceI[]{seq}, fixedRight);
             }
           }
           else
           {
-            // dragging to the left
+            editCommand.appendEdit(EditCommand.INSERT_GAP,
+                                   new SequenceI[]
+                                   {seq},
+                                   lastres, startres-lastres,
+                                   av.getGapCharacter(),
+                                   true);
+          }
+        }
+        else
+        {
+          // dragging to the left
+          if (fixedColumns && fixedRight != -1)
+          {
             for (int j = lastres; j > startres; j--)
             {
-              if (fixedColumns && fixedRight != -1)
-              {
-                deleteChar(startres, seq, fixedRight);
-              }
-              else
+              if (!jalview.util.Comparison.isGap(seq.getCharAt(startres)))
               {
-                deleteChar(startres, seq);
+                endEditing();
+                break;
               }
+              deleteChar(startres, new SequenceI[]{seq}, fixedRight);
+            }
+          }
+          else
+          {
+            //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)))
+                break;
+              max++;
+            }
+
+            if (max>0)
+            {
+              editCommand.appendEdit(EditCommand.DELETE_GAP,
+                                     new SequenceI[]
+                                     {seq},
+                                     startres, max,
+                                     av.getGapCharacter(),
+                                     true);
             }
           }
         }
+      }
 
-        lastres = startres;
-        seqCanvas.repaint();
-    }
+      lastres = startres;
+      seqCanvas.repaint();
+  }
 
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param j DOCUMENT ME!
-     * @param seq DOCUMENT ME!
-     */
-    void insertChar(int j, SequenceI seq)
-    {
-        seq.insertCharAt(j, av.getGapCharacter());
-        seqEditOccurred = true;
-    }
 
-    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++)
     {
       //Find the next gap before the end of the visible region boundary
       //If lastCol > j, theres a boundary after the gap insertion
-      int blankColumn = fixedColumn;
+
       for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
       {
-        if (jalview.util.Comparison.isGap(seq.getCharAt(blankColumn)))
+        if (jalview.util.Comparison.isGap(seq[s].getCharAt(blankColumn)))
         {
           //Theres a space, so break and insert the gap
           break;
@@ -845,74 +1065,35 @@ public class SeqPanel
 
       if (blankColumn <= j)
       {
+        blankColumn = fixedColumn;
         endEditing();
         return;
       }
-
-      if (!jalview.util.Comparison.isGap(seq.getCharAt(blankColumn)))
-      {
-        //Just Checking
-        System.out.println("Tried removing residue (INSERT)"+seq.getCharAt(fixedColumn));
-        return;
-      }
-
-      seq.deleteCharAt(blankColumn);
-      seq.insertCharAt(j, av.getGapCharacter());
-      seqEditOccurred = true;
     }
 
-    void deleteChar(int j, SequenceI seq, int fixedColumn)
-    {
-      if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))
-      {
-        ap.alignFrame.statusBar.setText(
-            "End editing: Tried removing residue " + seq.getCharAt(j));
-        return;
-      }
+    editCommand.appendEdit(EditCommand.DELETE_GAP,
+                           seq,
+                           blankColumn, 1, av.getGapCharacter(), true);
 
-      seq.deleteCharAt(j);
-      seq.insertCharAt(fixedColumn, av.getGapCharacter());
-      seqEditOccurred = true;
-    }
+    editCommand.appendEdit(EditCommand.INSERT_GAP,
+                           seq,
+                           j, 1, av.getGapCharacter(),
+                           true);
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param j DOCUMENT ME!
-     * @param seq DOCUMENT ME!
-     */
-    void deleteChar(int j, SequenceI seq)
-    {
-      if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))
-      {
-        ap.alignFrame.statusBar.setText(
-            "End editing: Tried removing residue " + seq.getCharAt(j));
-        return;
-      }
-
-        seq.deleteCharAt(j);
-        seqEditOccurred = true;
-        seqCanvas.repaint();
-    }
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     */
-    void editOccurred()
-    {
-      if (!seqEditOccurred)
-      {
-        ap.alignFrame.historyList.pop();
-        ap.alignFrame.updateEditMenuBar();
-      }
+  void deleteChar(int j, SequenceI [] seq, int fixedColumn)
+  {
 
-      endEditing();
+    editCommand.appendEdit(EditCommand.DELETE_GAP,
+                           seq,
+                           j, 1, av.getGapCharacter(), true);
 
-      av.firePropertyChange("alignment", null,av.getAlignment().getSequences());
+    editCommand.appendEdit(EditCommand.INSERT_GAP,
+                           seq,
+                           fixedColumn, 1, av.getGapCharacter(), true);
+  }
 
-    }
 
 //////////////////////////////////////////
 /////Everything below this is for defining the boundary of the rubberband
@@ -956,7 +1137,7 @@ public class SeqPanel
       }
     }
 
-    else if (!stretchGroup.sequences.contains(sequence)
+    else if (!stretchGroup.getSequences(null).contains(sequence)
              || stretchGroup.getStartRes() > res
              || stretchGroup.getEndRes() < res)
     {
@@ -972,57 +1153,76 @@ public class SeqPanel
               allGroups[i].getEndRes() >= res)
           {
             stretchGroup = allGroups[i];
-            av.setSelectionGroup(stretchGroup);
             break;
           }
         }
       }
+      av.setSelectionGroup(stretchGroup);
     }
 
-    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())
-      {
-        SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(),
-                                          "Background");
-      }
-      if (av.getAbovePIDThreshold())
-      {
-        SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
-                                       "Background");
-      }
-
-    }
 
     // DETECT RIGHT MOUSE BUTTON IN AWT
-    else if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK) ==
+    if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK) ==
              InputEvent.BUTTON3_MASK)
     {
-      APopupMenu popup = new APopupMenu(ap, null, null);
+      Vector allFeatures = getAllFeaturesAtRes(sequence,
+                                               sequence.findPosition(res));
+
+      Vector links = null;
+      if(allFeatures!=null)
+      {
+        for (int i = 0; i < allFeatures.size(); i++)
+        {
+          SequenceFeature sf = (SequenceFeature) allFeatures.elementAt(i);
+          if (sf.links != null)
+          {
+            links = new Vector();
+            for (int j = 0; j < sf.links.size(); j++)
+            {
+              links.addElement(sf.links.elementAt(j));
+            }
+          }
+        }
+      }
+      APopupMenu popup = new APopupMenu(ap, null, links);
       this.add(popup);
       popup.show(this, evt.getX(), evt.getY());
+      ap.repaint();
+      return;
     }
 
-    if (stretchGroup != null && stretchGroup.getEndRes() == res)
+    if (av.cursorMode)
     {
-      // Edit end res position of selected group
-      changeEndRes = true;
+      seqCanvas.cursorX = findRes(evt);
+      seqCanvas.cursorY = findSeq(evt);
+      seqCanvas.repaint();
+      return;
     }
 
-    else if (stretchGroup != null && stretchGroup.getStartRes() == res)
-    {
-      // Edit end res position of selected group
-      changeStartRes = true;
-    }
+      //Only if left mouse button do we want to change group sizes
 
+      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())
+        {
+          SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(),
+                                            "Background");
+        }
+        if (av.getAbovePIDThreshold())
+        {
+          SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
+                                         "Background");
+        }
+
+      }
   }
 
   public void doMouseReleasedDefineMode(MouseEvent evt)
@@ -1036,11 +1236,18 @@ public class SeqPanel
     {
       if (stretchGroup.cs instanceof ClustalxColourScheme)
       {
-        ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup.
-            sequences,
+        ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(
+            stretchGroup.getSequences(av.hiddenRepSequences),
             stretchGroup.getWidth());
       }
 
+      if (stretchGroup.cs instanceof Blosum62ColourScheme
+          || stretchGroup.cs instanceof PIDColourScheme
+          || stretchGroup.cs.conservationApplied()
+          || stretchGroup.cs.getThreshold() > 0)
+        stretchGroup.recalcConservation();
+
+
       if (stretchGroup.cs.conservationApplied())
       {
         SliderPanel.setConservationSlider(ap, stretchGroup.cs,
@@ -1056,7 +1263,7 @@ public class SeqPanel
     changeEndRes = false;
     changeStartRes = false;
     stretchGroup = null;
-    PaintRefresher.Refresh(av.alignment);
+    PaintRefresher.Refresh(ap, av.getSequenceSetId());
     ap.repaint();
   }
 
@@ -1081,7 +1288,7 @@ public class SeqPanel
         y = av.alignment.getHeight() -1;
       }
 
-      if(res>av.alignment.getWidth())
+      if(res>=av.alignment.getWidth())
         res = av.alignment.getWidth()-1;
 
       if (stretchGroup.getEndRes() == res)
@@ -1140,7 +1347,7 @@ public class SeqPanel
 
           Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
 
-          if (stretchGroup.sequences.contains(nextSeq))
+          if (stretchGroup.getSequences(null).contains(nextSeq))
           {
               stretchGroup.deleteSequence(seq, false);
           }
@@ -1198,6 +1405,28 @@ public class SeqPanel
     }
   }
 
+  void scrollCanvas(MouseEvent evt)
+  {
+    if(evt==null)
+    {
+      if(scrollThread!=null)
+      {
+        scrollThread.running = false;
+        scrollThread = null;
+      }
+      mouseDragging = false;
+    }
+    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
       extends Thread
@@ -1241,12 +1470,12 @@ public class SeqPanel
 
           if (mouseDragging && evt.getX() < 0)
           {
-            running = ap.scrollRight(true);
+            running = ap.scrollRight(false);
           }
 
           else if (mouseDragging && evt.getX() >= getSize().width)
           {
-            running = ap.scrollRight(false);
+            running = ap.scrollRight(true);
           }
         }