X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqPanel.java;h=89e2086a1ebbd81a81e2f2286dc7071a3fc7455c;hb=7724430e3293cbb862d0c50c5308a3b3b0417cac;hp=fb11579f29a9cfc3d20ec42a333baed76b583f12;hpb=8da7acff9214ddaf0e6d28e76219ab51bd38e62d;p=jalview.git

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index fb11579..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
@@ -19,16 +19,17 @@
 
 package jalview.appletgui;
 
-import java.util.*;
-
 import java.awt.*;
 import java.awt.event.*;
 
 import jalview.datamodel.*;
 import jalview.schemes.*;
+import jalview.commands.*;
+
+import java.util.Vector;
 
 public class SeqPanel
-    extends Panel
+    extends Panel implements MouseMotionListener, MouseListener
 {
 
   public SeqCanvas seqCanvas;
@@ -36,20 +37,32 @@ public class SeqPanel
 
   protected int lastres;
   protected int startseq;
-  int startEdit = -1;
-  int endEdit = -1;
 
   protected AlignViewport av;
 
   // if character is inserted or deleted, we will need to recalculate the conservation
-  int seqEditOccurred = -1;
+  boolean seqEditOccurred = false;
 
   ScrollThread scrollThread = null;
   boolean mouseDragging = false;
-
   boolean editingSeqs = false;
   boolean groupEditing = false;
 
+  int oldSeq = -1;
+  boolean changeEndSeq = false;
+  boolean changeStartSeq = false;
+  boolean changeEndRes = false;
+  boolean changeStartRes = false;
+  SequenceGroup stretchGroup = null;
+
+  StringBuffer keyboardNo1;
+  StringBuffer keyboardNo2;
+
+  boolean mouseWheelPressed = false;
+  Point lastMousePress;
+
+  EditCommand editCommand;
+
   public SeqPanel(AlignViewport avp, AlignmentPanel p)
   {
     this.av = avp;
@@ -60,96 +73,343 @@ public class SeqPanel
 
     ap = p;
 
-    seqCanvas.addMouseMotionListener(new MouseMotionAdapter()
-    {
-      public void mouseMoved(MouseEvent evt)
-      {
-        doMouseMoved(evt);
-      }
+    seqCanvas.addMouseMotionListener(this);
+    seqCanvas.addMouseListener(this);
 
-      public void mouseDragged(MouseEvent evt)
-      {
-        if (editingSeqs)
-        {
-          doMouseDragged(evt);
-        }
-        else
-        {
-          doMouseDraggedDefineMode(evt);
-        }
-      }
-    });
+    seqCanvas.repaint();
+  }
 
-    seqCanvas.addMouseListener(new MouseAdapter()
+  void endEditing()
+  {
+    if (editCommand!=null && editCommand.getSize() > 0)
     {
-      public void mouseReleased(MouseEvent evt)
-      {
-        if (editingSeqs)
-        {
-          doMouseReleased(evt);
-        }
-        else
-        {
-          doMouseReleasedDefineMode(evt);
-        }
+      ap.alignFrame.addHistoryItem(editCommand);
+      av.firePropertyChange("alignment", null,
+                            av.getAlignment().getSequences());
+    }
 
-      }
+    startseq = -1;
+    lastres = -1;
+    editingSeqs = false;
+    groupEditing = false;
+    keyboardNo1 = null;
+    keyboardNo2 = null;
+     editCommand = null;
+   }
 
-      public void mousePressed(MouseEvent evt)
-      {
-        if (evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
-        {
-          if (evt.isAltDown() || evt.isControlDown())
-          {
-            groupEditing = true;
-          }
+   void setCursorRow()
+   {
+     seqCanvas.cursorY = getKeyboardNo(keyboardNo1)-1;
+     scrollToVisible();
+   }
 
-          editingSeqs = true;
-          doMousePressed(evt);
-        }
-        else
-        {
-          doMousePressedDefineMode(evt);
-        }
-      }
+   void setCursorColumn()
+   {
+     seqCanvas.cursorX = getKeyboardNo(keyboardNo1)-1;
+     scrollToVisible();
+   }
 
-      public void mouseExited(MouseEvent evt)
-      {
-        if (editingSeqs)
-        {
-          return;
-        }
-        doMouseExitedDefineMode(evt);
+   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);
 
-      public void mouseEntered(MouseEvent evt)
-      {
-        if (editingSeqs)
-        {
-          return;
-        }
-        doMouseEnteredDefineMode(evt);
+     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();
+   }
 
-    });
-    seqCanvas.repaint();
-  }
+   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);
+     }
 
-  public void doMouseReleased(MouseEvent evt)
+
+     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;
+         }
+
+        return;
+     }
+
+     public void mouseClicked(MouseEvent evt){}
+
+
+  public void mouseReleased(MouseEvent evt)
   {
+    mouseDragging = false;
+    mouseWheelPressed = false;
 
-    if (seqEditOccurred > -1)
+    if (!editingSeqs)
     {
-      editOccurred(seqEditOccurred);
+       doMouseReleasedDefineMode(evt);
+       return;
     }
 
-    startseq = -1;
-    lastres = -1;
-    seqEditOccurred = -1;
-    editingSeqs = false;
-    groupEditing = false;
-    ap.repaint();
+     endEditing();
+     ap.repaint();
   }
 
   int startWrapBlock=-1;
@@ -161,40 +421,69 @@ public class SeqPanel
 
   if (av.wrapAlignment)
   {
+
+    int hgap = av.charHeight;
+    if (av.scaleAboveWrapped)
+      hgap += av.charHeight;
+
+    int cHeight = av.getAlignment().getHeight() * av.charHeight
+        + hgap + seqCanvas.getAnnotationHeight();
+
       int y = evt.getY();
-      y -= (2 * av.charHeight);
+      y -= hgap;
       x -= seqCanvas.LABEL_WEST;
 
-      int chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;
-      int cwidth = seqCanvas.getWrappedCanvasWidth(this.getSize().width);
-      wrappedBlock = y/chunkHeight;
-      wrappedBlock += av.getStartRes()/cwidth;
 
-      res = wrappedBlock*cwidth   +   x / av.getCharWidth();
+      int cwidth = seqCanvas.getWrappedCanvasWidth(getSize().width);
+      if(cwidth<1)
+        return 0;
+
+      wrappedBlock = y / cHeight;
+      wrappedBlock += av.getStartRes() / cwidth;
+
+      res = wrappedBlock * cwidth + x / av.getCharWidth();
+
   }
   else
   {
       res = (x / av.getCharWidth()) + av.getStartRes();
   }
 
+  if(av.hasHiddenColumns)
+          res = av.getColumnSelection().adjustForHiddenColumns(res);
+
   return res;
 
  }
 
  int findSeq(MouseEvent evt)
  {
+
    int seq = 0;
    int y = evt.getY();
 
    if (av.wrapAlignment)
    {
-     y -= (2 * av.charHeight);
-     int chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;
-     seq = ( (y % chunkHeight) / av.getCharHeight());
+     int hgap = av.charHeight;
+     if (av.scaleAboveWrapped)
+       hgap += av.charHeight;
+
+     int cHeight = av.getAlignment().getHeight() * av.charHeight
+         + hgap + seqCanvas.getAnnotationHeight();
+
+       y -= hgap;
+
+     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;
@@ -203,8 +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);
@@ -228,7 +515,7 @@ public class SeqPanel
     return;
   }
 
-  public void doMouseMoved(MouseEvent evt)
+  public void mouseMoved(MouseEvent evt)
   {
     int res = findRes(evt);
     int seq = findSeq(evt);
@@ -244,235 +531,589 @@ public class SeqPanel
       return;
     }
 
-    Object obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
-    String aa = "";
+    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)
     {
-      aa = obj.toString();
+      if (obj != "")
+      {
+        text.append(obj + " (" + sequence.findPosition(res) + ")");
+      }
     }
 
-    StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
-                                         sequence.getName());
-    if (aa != "")
+    if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence)
     {
-      text.append("  Residue: " + aa + " (" +
-                  av.getAlignment().getSequenceAt(seq).findPosition(res) + ")");
+      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)
+    if (av.showSequenceFeatures
+        && sequence.getSequenceFeatures()!=null
+        && av.featuresDisplayed!=null)
     {
-      Vector features = sequence.getSequenceFeatures();
-      Enumeration e = features.elements();
-      StringBuffer sbuffer = new StringBuffer();
+      StringBuffer featureText = new StringBuffer();
+      Vector allFeatures = getAllFeaturesAtRes(sequence, sequence.findPosition(res));
 
-      while (e.hasMoreElements())
+      int index = 0;
+      while (index < allFeatures.size())
       {
-        SequenceFeature sf = (SequenceFeature) e.nextElement();
-        if (sf.getStart() <= 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 (sbuffer.length() > 0)
-          {
-            sbuffer.append("; ");
-          }
-          sbuffer.append(sf.getType() + " " + sf.getDescription());
-          if (sf.getStatus().length() > 0)
-          {
-            sbuffer.append(" (" + sf.getStatus() + ")");
-          }
+          String status = sf.getValue("status").toString();
+          if(status.length()>0)
+            featureText.append(" (" + sf.getValue("status") + ")");
         }
+        featureText.append("\n");
 
+        index++;
       }
-    }
 
+
+        if (tooltip == null)
+          tooltip = new Tooltip(featureText.toString(), seqCanvas);
+        else
+          tooltip.setTip(featureText.toString());
+
+        tooltip.repaint();
+
+    }
+    else if (tooltip != null)
+     {
+       tooltip.setTip("");
+     }
   }
 
-  public void doMouseDragged(MouseEvent evt)
+  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()))
+          {
+            allFeatures.addElement(sf);
+          }
+        }
+        index++;
+      }
+    }
+    return allFeatures;
+  }
 
-    // If we're dragging we're editing
-    int res = findRes(evt);
-    if (res < 0)
+  Tooltip tooltip;
+
+  public void mouseDragged(MouseEvent evt)
+  {
+    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);
+
+  if (res < 0)
+  {
       res = 0;
-    }
+  }
+
+  if ((lastres == -1) || (lastres == res))
+  {
+      return;
+  }
+
+  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);
+
+  }
+
+  synchronized void editSequence(boolean insertGap, int startres)
+  {
+    int fixedLeft = -1;
+    int fixedRight = -1;
+    boolean fixedColumns = false;
+    SequenceGroup sg = av.getSelectionGroup();
+
+    SequenceI seq = av.alignment.getSequenceAt(startseq);
+
+      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());
+
+
+      //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);
+        }
+
+        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;
+        }
+
+        if (fixedLeft > startres)
+        {
+          fixedRight = fixedLeft - 1;
+          fixedLeft = 0;
+        }
+        else if (fixedRight < startres)
+        {
+          fixedLeft = fixedRight;
+          fixedRight = -1;
+        }
+      }
+
+
+      if(av.hasHiddenColumns )
+      {
+          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;
+          }
 
-    if (lastres == -1 || lastres == res)
-    {
-      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;
+           }
+          }
+      }
 
-    boolean dragRight = true;
-    if (res < av.getAlignment().getWidth() && res < lastres)
-    {
-      dragRight = false;
-    }
 
-    if (res != lastres)
-    {
-      // Group editing
       if (groupEditing)
       {
-        SequenceGroup sg = av.getSelectionGroup();
-        if (sg == null)
-        {
-          lastres = -1;
-          return;
-        }
+        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 (dragRight)
+        if (insertGap)
         {
-          sg.setEndRes(sg.getEndRes() + (res - lastres));
+            //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--)
+          {
+            blank = true;
+
+            for (g = 0; g < groupSize; g++)
+            {
+              for (int j = 0; j < startres - lastres; j++)
+              {
+                if (!jalview.util.Comparison.isGap(
+                    groupSeqs[g].getCharAt(fixedRight - j)))
+                {
+                  blank = false;
+                  break;
+                }
+              }
+            }
+            if (blank)
+              break;
+          }
+
+          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;
+            }
+          }
         }
 
+
         // drag to left
-        else
+        else if(!insertGap)
         {
           /// Are we able to delete?
           // ie are all columns blank?
-          boolean deleteAllowed = false;
-          for (int s = 0; s < sg.getSize(); s++)
+
+          for (g = 0; g < groupSize; g++)
           {
-            SequenceI seq = sg.getSequenceAt(s);
-            for (int j = res; j < lastres; j++)
+            for (int j = startres; j < lastres; j++)
             {
-              if (seq.getSequence().length() <= j)
+              if (groupSeqs[g].getLength() <= j)
               {
                 continue;
               }
 
-              if (!jalview.util.Comparison.isGap(seq.getSequence().charAt(j)))
+              if (!jalview.util.Comparison.isGap(
+                  groupSeqs[g].getCharAt(j)))
               {
                 // Not a gap, block edit not valid
-                res = j + 1;
-                deleteAllowed = false;
-                continue;
+                endEditing();
+                return;
               }
-              deleteAllowed = true;
             }
           }
-
-          if (!deleteAllowed)
-          {
-            lastres = -1;
-            return;
-          }
-
-          sg.setEndRes(sg.getEndRes() - (lastres - res));
         }
 
-        for (int i = 0; i < sg.getSize(); i++)
-        {
-          SequenceI s = sg.getSequenceAt(i);
-          int k = av.alignment.findIndex(s);
-
-          // drag to right
-          if (dragRight)
+          if (insertGap)
           {
-            for (int j = lastres; j < res; j++)
+            // dragging to the right
+            if (fixedColumns && fixedRight != -1)
+            {
+              for (int j = lastres; j < startres; j++)
+              {
+                  insertChar(j, groupSeqs, fixedRight);
+              }
+            }
+            else
             {
-              insertChar(j, k);
+              editCommand.appendEdit(EditCommand.INSERT_GAP,
+                                     groupSeqs,
+                                     startres, startres-lastres,
+                                     av.getGapCharacter(),
+                                     true);
             }
           }
-
-          // drag to left
           else
           {
-            for (int j = res; j < lastres; j++)
+            // dragging to the left
+            if (fixedColumns && fixedRight != -1)
             {
-              if (s.getLength() > j)
+              for (int j = lastres; j > startres; j--)
               {
-                deleteChar(res, k);
+                deleteChar(startres, groupSeqs, fixedRight);
               }
             }
+            else
+              editCommand.appendEdit(EditCommand.DELETE_GAP,
+                                     groupSeqs,
+                                     startres, lastres - startres,
+                                     av.getGapCharacter(),
+                                     true);
+
           }
-        }
       }
       else /////Editing a single sequence///////////
       {
-        if (res < av.getAlignment().getWidth() && res > lastres)
+        if (insertGap)
         {
           // dragging to the right
-          for (int j = lastres; j < res; j++)
+          if (fixedColumns && fixedRight != -1)
+          {
+            for (int j = lastres; j < startres; j++)
+            {
+              insertChar(j, new SequenceI[]{seq}, fixedRight);
+            }
+          }
+          else
           {
-            insertChar(j, startseq);
+            editCommand.appendEdit(EditCommand.INSERT_GAP,
+                                   new SequenceI[]
+                                   {seq},
+                                   lastres, startres-lastres,
+                                   av.getGapCharacter(),
+                                   true);
           }
         }
-        else if (res < av.getAlignment().getWidth() && res < lastres)
+        else
         {
           // dragging to the left
-          for (int j = lastres; j > res; j--)
+          if (fixedColumns && fixedRight != -1)
           {
-            if (jalview.util.Comparison.isGap(
-                av.alignment.getSequenceAt(startseq).getSequence().charAt(res)))
+            for (int j = lastres; j > startres; j--)
             {
-
-              deleteChar(res, startseq);
+              if (!jalview.util.Comparison.isGap(seq.getCharAt(startres)))
+              {
+                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++)
             {
+              if(!jalview.util.Comparison.isGap(seq.getCharAt(m)))
+                break;
+              max++;
+            }
 
-              break;
+            if (max>0)
+            {
+              editCommand.appendEdit(EditCommand.DELETE_GAP,
+                                     new SequenceI[]
+                                     {seq},
+                                     startres, max,
+                                     av.getGapCharacter(),
+                                     true);
             }
           }
         }
-
       }
-    }
 
-    endEdit = res;
-    lastres = res;
-    seqCanvas.repaint();
+      lastres = startres;
+      seqCanvas.repaint();
   }
 
-  public void drawChars(int seqstart, int seqend, int start)
-  {
-    seqCanvas.drawPanel(seqCanvas.gg, start, av.getEndRes(), seqstart, seqend,
-                        av.getStartRes(), av.getStartSeq(), 0);
-    seqCanvas.repaint();
-  }
 
-  public void insertChar(int j, int seq)
-  {
-    av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());
-    seqEditOccurred = seq;
-  }
 
-  public void deleteChar(int j, int seq)
+  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
+
+      for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
+      {
+        if (jalview.util.Comparison.isGap(seq[s].getCharAt(blankColumn)))
+        {
+          //Theres a space, so break and insert the gap
+          break;
+        }
+      }
+
+      if (blankColumn <= j)
+      {
+        blankColumn = fixedColumn;
+        endEditing();
+        return;
+      }
+    }
+
+    editCommand.appendEdit(EditCommand.DELETE_GAP,
+                           seq,
+                           blankColumn, 1, av.getGapCharacter(), true);
+
+    editCommand.appendEdit(EditCommand.INSERT_GAP,
+                           seq,
+                           j, 1, av.getGapCharacter(),
+                           true);
 
-    av.alignment.getSequenceAt(seq).deleteCharAt(j);
-    seqEditOccurred = seq;
-    av.alignment.getWidth();
-    repaint();
   }
 
-  void editOccurred(int i)
+  void deleteChar(int j, SequenceI [] seq, int fixedColumn)
   {
-    if (endEdit == startEdit)
-    {
-        ap.alignFrame.historyList.pop();
-        ap.alignFrame.updateEditMenuBar();
-    }
 
-    av.firePropertyChange("alignment", null,av.getAlignment().getSequences());
+    editCommand.appendEdit(EditCommand.DELETE_GAP,
+                           seq,
+                           j, 1, av.getGapCharacter(), true);
+
+    editCommand.appendEdit(EditCommand.INSERT_GAP,
+                           seq,
+                           fixedColumn, 1, av.getGapCharacter(), true);
   }
 
+
 //////////////////////////////////////////
 /////Everything below this is for defining the boundary of the rubberband
 //////////////////////////////////////////
-  int oldSeq = -1;
   public void doMousePressedDefineMode(MouseEvent evt)
   {
+    if (scrollThread != null)
+    {
+      scrollThread.running = false;
+      scrollThread = null;
+    }
+
     int res = findRes(evt);
     int seq = findSeq(evt);
     oldSeq = seq;
     startWrapBlock=wrappedBlock;
 
+    if(seq==-1)
+      return;
+
     SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
 
     if (sequence == null || res > sequence.getLength())
@@ -496,7 +1137,7 @@ public class SeqPanel
       }
     }
 
-    else if (!stretchGroup.sequences.contains(sequence)
+    else if (!stretchGroup.getSequences(null).contains(sequence)
              || stretchGroup.getStartRes() > res
              || stretchGroup.getEndRes() < res)
     {
@@ -512,84 +1153,106 @@ 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");
+        }
 
-  boolean changeEndSeq = false;
-  boolean changeStartSeq = false;
-  boolean changeEndRes = false;
-  boolean changeStartRes = false;
-  SequenceGroup stretchGroup = null;
+      }
+  }
 
   public void doMouseReleasedDefineMode(MouseEvent evt)
   {
-    if(mouseDragging)
-     {
-       stretchGroup.recalcConservation();
-       mouseDragging = false;
-     }
-
     if (stretchGroup == null)
     {
-      return;
+        return;
     }
 
     if(stretchGroup.cs!=null)
     {
+      if (stretchGroup.cs instanceof ClustalxColourScheme)
+      {
+        ( (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,
                                           stretchGroup.getName());
+        stretchGroup.recalcConservation();
       }
       else
       {
@@ -600,126 +1263,170 @@ public class SeqPanel
     changeEndRes = false;
     changeStartRes = false;
     stretchGroup = null;
-    seqCanvas.repaint();
+    PaintRefresher.Refresh(ap, av.getSequenceSetId());
     ap.repaint();
   }
 
-  boolean remove = false;
   public void doMouseDraggedDefineMode(MouseEvent evt)
   {
     int res = findRes(evt);
     int y = findSeq(evt);
 
     if(wrappedBlock!=startWrapBlock)
-        return;
+      return;
+
+     if (stretchGroup == null)
+     {
+          return;
+     }
 
-    if(y>=av.alignment.getHeight())
-      y = av.alignment.getHeight()-1;
+     mouseDragging = true;
 
-    if (stretchGroup == null)
-    {
-      return;
-    }
 
-    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;
-    }
+      if(res>=av.alignment.getWidth())
+        res = av.alignment.getWidth()-1;
 
-    else if (stretchGroup.getStartRes() == res)
-    {
-      // Edit start res position of selected group
-      changeStartRes = true;
-    }
+      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.getStartRes())
-    {
-      res = av.getStartRes();
-    }
-    else if (res > av.getEndRes() && !av.getWrapAlignment())
-    {
-      res = av.getEndRes();
-    }
+      if (res < 0)
+      {
+          res = 0;
+      }
 
-    if (changeEndRes)
-    {
-      if (res > stretchGroup.getStartRes() - 1)
+      if (changeEndRes)
       {
-        stretchGroup.setEndRes(res);
+          if (res > (stretchGroup.getStartRes() - 1))
+          {
+              stretchGroup.setEndRes(res);
+          }
       }
-    }
-    else if (changeStartRes)
-    {
-      if (res < stretchGroup.getEndRes() + 1)
+      else if (changeStartRes)
       {
-        stretchGroup.setStartRes(res);
+          if (res < (stretchGroup.getEndRes() + 1))
+          {
+              stretchGroup.setStartRes(res);
+          }
       }
-    }
 
-    int dragDirection = 0;
-    if (y > oldSeq)
-    {
-      dragDirection = 1;
-    }
-    else if (y < oldSeq)
-    {
-      dragDirection = -1;
-    }
+      int dragDirection = 0;
 
-    while (y != oldSeq && oldSeq > 0 && 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);
+      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);
+
+          oldSeq += dragDirection;
+
+          if(oldSeq<0)
+            break;
+
+          Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
 
-      oldSeq += dragDirection;
-      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.addSequence(nextSeq, false);
+          }
+      }
+
+      if(oldSeq < 0)
+        oldSeq = -1;
 
-      if (stretchGroup.sequences.contains(nextSeq))
+
+      if(res>av.endRes || res<av.startRes
+          || y<av.startSeq || y>av.endSeq)
       {
-        stretchGroup.deleteSequence(seq, false);
+        mouseExited(evt);
       }
-      else
+
+      if (scrollThread != null)
       {
-        if (seq != null)
-        {
-          stretchGroup.addSequence(seq, false);
-        }
-        stretchGroup.addSequence(nextSeq, false);
+        scrollThread.setEvent(evt);
       }
+
+      seqCanvas.repaint();
     }
-    oldSeq = y;
-    mouseDragging = true;
-    if (scrollThread != null)
+
+    public void mouseEntered(MouseEvent e)
     {
-      scrollThread.setEvent(evt);
-    }
+      if (oldSeq < 0)
+        oldSeq = 0;
 
-    seqCanvas.repaint();
-  }
+      if (scrollThread != null)
+      {
+        scrollThread.running = false;
+        scrollThread = null;
+      }
+    }
 
-  public void doMouseEnteredDefineMode(MouseEvent e)
+  public void mouseExited(MouseEvent e)
   {
-    if (scrollThread != null)
+    if (av.getWrapAlignment())
     {
-      scrollThread.running = false;
+      return;
     }
-  }
 
-  public void doMouseExitedDefineMode(MouseEvent e)
-  {
-    if (mouseDragging)
+    if (mouseDragging && scrollThread==null)
     {
       scrollThread = new ScrollThread();
     }
   }
 
+  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
@@ -746,6 +1453,7 @@ public class SeqPanel
       running = true;
       while (running)
       {
+
         if (evt != null)
         {
 
@@ -762,12 +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);
           }
         }