X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=933ca0457d88fb9572c23589ee6ae9d2dd73c9fe;hb=6fc9aca27f606f6e3a0121597896e1a5dae35c36;hp=b9ba9f344c7fa4aaebc5af7be02b2d08a0b725bc;hpb=171f3813518871b1e2b1a2255a481866b4e7cd70;p=jalview.git

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index b9ba9f3..933ca04 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -25,8 +25,6 @@ import jalview.schemes.*;
 import java.awt.*;
 import java.awt.event.*;
 
-import java.util.*;
-
 import javax.swing.*;
 
 
@@ -36,7 +34,9 @@ import javax.swing.*;
  * @author $author$
  * @version $Revision$
  */
-public class SeqPanel extends JPanel
+public class SeqPanel extends JPanel implements MouseListener,
+    MouseMotionListener, MouseWheelListener
+
 {
     /** DOCUMENT ME!! */
     public SeqCanvas seqCanvas;
@@ -45,12 +45,10 @@ public class SeqPanel extends JPanel
     public AlignmentPanel ap;
     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;
@@ -68,6 +66,8 @@ public class SeqPanel extends JPanel
     boolean remove = false;
 
     boolean mouseWheelPressed = false;
+    StringBuffer keyboardNo1;
+    StringBuffer keyboardNo2;
 
     /**
      * Creates a new SeqPanel object.
@@ -89,130 +89,12 @@ public class SeqPanel extends JPanel
 
         ap = p;
 
-
-        addMouseMotionListener(new MouseMotionAdapter()
-            {
-                public void mouseMoved(MouseEvent evt)
-                {
-                    doMouseMoved(evt);
-                    if (editingSeqs)
-                    {
-                      // This is because MacOSX creates a mouseMoved
-                      // If control is down
-                      if(!av.isDataset())
-                        doMouseDragged(evt);
-                    }
-                }
-
-                public void mouseDragged(MouseEvent evt)
-                {
-                    if (editingSeqs)
-                    {
-                      if(!av.isDataset())
-                        doMouseDragged(evt);
-                    }
-                    else
-                    {
-                      if(!av.isDataset())
-                        doMouseDraggedDefineMode(evt);
-                    }
-                }
-            });
-
-       addMouseWheelListener(new MouseWheelListener()
-       {
-         public void mouseWheelMoved(MouseWheelEvent e)
-         {
-
-           if (mouseWheelPressed)
-           {
-             Font font = av.getFont();
-             int fontSize = font.getSize();
-             if (e.getWheelRotation() > 0 && fontSize < 51)
-               fontSize++;
-             else if (fontSize > 1)
-               fontSize--;
-
-             av.setFont(new Font(font.getName(), font.getStyle(), fontSize));
-             ap.fontChanged();
-           }
-           else
-           {
-             if (e.getWheelRotation() > 0)
-               ap.scrollUp(false);
-             else
-               ap.scrollUp(true);
-           }
-
-         }
-       });
-
-
-       if(!av.isDataset())
-       {
-         addMouseListener(new MouseAdapter()
-         {
-           public void mouseReleased(MouseEvent evt)
-           {
-             mouseWheelPressed = false;
-
-             if (editingSeqs)
-             {
-               doMouseReleased(evt);
-             }
-             else
-             {
-               doMouseReleasedDefineMode(evt);
-             }
-           }
-
-           public void mousePressed(MouseEvent evt)
-           {
-             if (javax.swing.SwingUtilities.isMiddleMouseButton(evt))
-             {
-               mouseWheelPressed = true;
-               return;
-             }
-
-             if (evt.isShiftDown() || evt.isAltDown() ||
-                 evt.isControlDown())
-             {
-               if (evt.isAltDown() || evt.isControlDown())
-               {
-                 groupEditing = true;
-
-               }
-
-               editingSeqs = true;
-               doMousePressed(evt);
-             }
-             else
-             {
-               doMousePressedDefineMode(evt);
-             }
-           }
-
-           public void mouseExited(MouseEvent evt)
-           {
-             if (editingSeqs)
-             {
-               return;
-             }
-
-             doMouseExitedDefineMode(evt);
-           }
-
-           public void mouseEntered(MouseEvent evt)
-           {
-             if (editingSeqs)
-             {
-               return;
-             }
-
-             doMouseEnteredDefineMode(evt);
-           }
-         });
-       }
+        if(!av.isDataset())
+        {
+          addMouseMotionListener(this);
+          addMouseListener(this);
+          addMouseWheelListener(this);
+        }
     }
 
     int startWrapBlock=-1;
@@ -284,37 +166,271 @@ public class SeqPanel extends JPanel
      return seq;
    }
 
+   void endEditing()
+   {
+     startseq = -1;
+     lastres = -1;
+     seqEditOccurred = false;
+     editingSeqs = false;
+     groupEditing = false;
+     keyboardNo1 = null;
+     keyboardNo2 = 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;
+      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);
+        }
+        if (!av.wrapAlignment)
+        {
+          while (seqCanvas.cursorX < av.startRes)
+          {
+            if (!ap.scrollRight(false))
+              break;
+          }
+          while (seqCanvas.cursorX > 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.sequences.clear();
+          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)
+    {
+      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();
+    }
+
+    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();
+    }
+
+    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());
+    }
+
 
     /**
      * DOCUMENT ME!
      *
      * @param evt DOCUMENT ME!
      */
-    public void doMouseReleased(MouseEvent evt)
+    public void mouseReleased(MouseEvent evt)
     {
-        if (seqEditOccurred > -1)
-        {
-            editOccurred(seqEditOccurred);
-        }
+      mouseDragging = false;
+      mouseWheelPressed = false;
 
-        startseq = -1;
-        lastres = -1;
-        seqEditOccurred = -1;
-        editingSeqs = false;
-        groupEditing = false;
+      if (!editingSeqs)
+      {
+         doMouseReleasedDefineMode(evt);
+         return;
+      }
 
-        ap.repaint();
+       editOccurred();
+
+       endEditing();
+       ap.repaint();
     }
 
+
+
     /**
      * DOCUMENT ME!
      *
      * @param evt DOCUMENT ME!
      */
-    public void doMousePressed(MouseEvent evt)
+    public void mousePressed(MouseEvent evt)
     {
-      ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
-                                                   av.alignment, HistoryItem.EDIT));
+      if (javax.swing.SwingUtilities.isMiddleMouseButton(evt))
+      {
+        mouseWheelPressed = true;
+        return;
+      }
+
+      if (evt.isShiftDown() || evt.isAltDown() ||
+          evt.isControlDown())
+      {
+        if (evt.isAltDown() || evt.isControlDown())
+        {
+          groupEditing = true;
+        }
+        editingSeqs = true;
+      }
+      else
+      {
+        doMousePressedDefineMode(evt);
+        return;
+      }
+
+
 
       int seq = findSeq(evt);
       int res = findRes(evt);
@@ -322,6 +438,9 @@ public class SeqPanel extends JPanel
       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()))
         {
@@ -334,9 +453,6 @@ public class SeqPanel extends JPanel
             lastres = -1;
         }
 
-        startEdit = lastres;
-        endEdit = lastres;
-
         return;
     }
 
@@ -345,11 +461,19 @@ public class SeqPanel extends JPanel
      *
      * @param evt DOCUMENT ME!
      */
-    public void doMouseMoved(MouseEvent evt)
+    public void mouseMoved(MouseEvent evt)
     {
+      if (editingSeqs)
+      {
+       // This is because MacOSX creates a mouseMoved
+       // If control is down, other platforms will not.
+       mouseDragged(evt);
+      }
+
       int res = findRes(evt);
       int seq = findSeq(evt);
 
+
       if(res<0 || seq<0 || seq >= av.getAlignment().getHeight())
             return;
 
@@ -365,36 +489,7 @@ public class SeqPanel extends JPanel
         seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));
       }
 
-
-        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 + " (" +
-                        av.getAlignment().getSequenceAt(seq).findPosition(res) + ")");
-          }
-        }
-
-        ap.alignFrame.statusBar.setText(text.toString());
+      setStatusMessage(sequence, res, seq);
 
         // use aa to see if the mouse pointer is on a
         if (av.showSequenceFeatures)
@@ -410,7 +505,8 @@ public class SeqPanel extends JPanel
                 if ( (features[i].getBegin() <= sequence.findPosition(res)) &&
                     (features[i].getEnd() >= sequence.findPosition(res)))
                 {
-                  if(!av.featuresDisplayed.containsKey(features[i].getType()))
+                  if(av.featuresDisplayed==null
+                    || !av.featuresDisplayed.containsKey(features[i].getType()))
                   continue;
 
 
@@ -458,14 +554,52 @@ public class SeqPanel extends JPanel
         }
     }
 
+    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());
+
+    }
+
     /**
      * DOCUMENT ME!
      *
      * @param evt DOCUMENT ME!
      */
-    public void doMouseDragged(MouseEvent evt)
+    public void mouseDragged(MouseEvent evt)
     {
-        // If we're dragging we're editing
+      if (!editingSeqs)
+      {
+        doMouseDraggedDefineMode(evt);
+        return;
+      }
+
         int res = findRes(evt);
 
         if (res < 0)
@@ -478,135 +612,301 @@ public class SeqPanel extends JPanel
             return;
         }
 
-        boolean dragRight = true;
+        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();
+
+      if(groupEditing && sg==null)
+        return;
 
-        if ((res < av.getAlignment().getWidth()) && (res < lastres))
+        if (!groupEditing && av.hasHiddenRows)
         {
-            dragRight = false;
+          //This needs to check all the sequences in a group edit,m
+          // not just the startseq
+          if (av.alignment.getSequenceAt(startseq).getHiddenSequences() != null)
+          {
+            groupEditing = true;
+          }
+        }
+
+        SequenceI seq = av.alignment.getSequenceAt(startseq);
+        StringBuffer message = new StringBuffer();
+        if (groupEditing)
+           message.append("Edit group:");
+        else
+            message.append("Edit sequence: "+seq.getName());
+
+       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.sequences.contains(seq)))
+        {
+          fixedColumns = true;
+
+          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(fixedRight<y2 && fixedRight==-1 && y2!=startres)
+            fixedRight = y2 -1;
+          if(y1>fixedLeft && fixedLeft==-1)
+            fixedLeft = y1;
         }
 
-        if (res != lastres)
+        if (groupEditing)
         {
-            // Group editing
-            if (groupEditing)
+
+          /*if (av.hasHiddenRows)
+          {
+            //sg might be null as the user may only see 1 sequence
+            if (sg == null)
             {
-                SequenceGroup sg = av.getSelectionGroup();
+              sg = new SequenceGroup();
+              sg.addSequence(av.alignment.getSequenceAt(startseq), false);
+            }
 
-                if (sg == null)
-                {
-                    lastres = -1;
+            SequenceGroup tmp = new SequenceGroup();
 
-                    return;
-                }
+            //Do any of the sequences have hidden associates?
+            for (int s = 0; s < sg.getSize(); s++)
+            {
+              seq = sg.getSequenceAt(s);
+              tmp.addSequence(seq, false);
+              if (seq.getHiddenSequences() != null)
+              {
+                for (int h = 0; h < seq.getHiddenSequences().getSize(); h++)
+                  tmp.addSequence(seq.getHiddenSequences().getSequenceAt(h),
+                                  false);
+              }
+            }
+
+            sg = tmp;
+          }*/
+          // int blankColumn = -1;
 
-                // drag to right
-                if (dragRight)
+
+          // 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() + 1 == av.alignment.getWidth())
+              {
+                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 (int s = 0; s < sg.getSize(); s++)
+              {
+                seq = sg.getSequenceAt(s);
+                for (int j = 0; j < startres - lastres; j++)
                 {
-                    sg.setEndRes(sg.getEndRes() + (res - lastres));
+                  if (!jalview.util.Comparison.isGap(
+                      seq.getCharAt(fixedRight - j)))
+                  {
+                    blank = false;
+                    break;
+                  }
                 }
+              }
+              if (blank)
+                break;
+            }
 
-                // drag to left
-                else
-                {
-                    /// Are we able to delete?
-                    // ie are all columns blank?
-                    boolean deleteAllowed = false;
+            if (!blank)
+            {
+              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
+              {
+                endEditing();
+                return;
+              }
+            }
+          }
 
-                    for (int s = 0; s < sg.getSize(); s++)
-                    {
-                        SequenceI seq = sg.getSequenceAt(s);
-
-                        for (int j = res; j < lastres; j++)
-                        {
-                            if (seq.getSequence().length() <= j)
-                            {
-                                continue;
-                            }
-
-                            if (!jalview.util.Comparison.isGap(
-                                        seq.getSequence().charAt(j)))
-                            {
-                                // Not a gap, block edit not valid
-                                res = j + 1;
-                                deleteAllowed = false;
-
-                                continue;
-                            }
-
-                            deleteAllowed = true;
-                        }
-                    }
 
-                    if (!deleteAllowed)
-                    {
-                        lastres = -1;
+          // drag to left
+          else if(!insertGap)
+          {
+            /// Are we able to delete?
+            // ie are all columns blank?
 
-                        return;
-                    }
+            for (int s = 0; s < sg.getSize(); s++)
+            {
+              seq = sg.getSequenceAt(s);
 
-                    sg.setEndRes(sg.getEndRes() - (lastres - res));
+              for (int j = startres; j < lastres; j++)
+              {
+                if (seq.getSequence().length() <= j)
+                {
+                  continue;
                 }
 
-                for (int i = 0; i < sg.getSize(); i++)
+                if (!jalview.util.Comparison.isGap(
+                    seq.getSequence().charAt(j)))
                 {
-                    SequenceI s = sg.getSequenceAt(i);
-                    int k = av.alignment.findIndex(s);
+                  // Not a gap, block edit not valid
+                  endEditing();
+                  return;
+                }
+              }
+            }
+          }
 
-                    // drag to right
-                    if (dragRight)
-                    {
-                        for (int j = lastres; j < res; j++)
-                        {
-                            insertChar(j, k);
-                        }
-                    }
 
-                    // drag to left
-                    else
-                    {
-                        for (int j = res; j < lastres; j++)
-                        {
-                            if (s.getLength() > j)
-                            {
-                                deleteChar(res, k);
-                            }
-                        }
-                    }
+          for (int i = 0; i < sg.getSize(); i++)
+          {
+            seq = sg.getSequenceAt(i);
+
+            if (insertGap)
+            {
+              // dragging to the right
+              for (int j = lastres; j < startres; j++)
+              {
+                if (fixedColumns && fixedRight != -1)
+                {
+                  insertChar(j, seq, fixedRight);
                 }
+                else
+                  insertChar(j, seq);
+              }
             }
-            else /////Editing a single sequence///////////
+            else
             {
-                if ((res < av.getAlignment().getWidth()) && (res > lastres))
+              // dragging to the left
+              for (int j = lastres; j > startres; j--)
+              {
+                if (fixedColumns && fixedRight != -1)
                 {
-                    // dragging to the right
-                    for (int j = lastres; j < res; j++)
-                    {
-                        insertChar(j, startseq);
-                    }
+                  deleteChar(startres, seq, fixedRight);
                 }
-                else if ((res < av.getAlignment().getWidth()) &&
-                        (res < lastres))
+                else
                 {
-                    // dragging to the left
-                    for (int j = lastres; j > res; j--)
-                    {
-                        if (jalview.util.Comparison.isGap(
-                                    av.alignment.getSequenceAt(startseq)
-                                                    .getSequence().charAt(res)))
-                        {
-                            deleteChar(res, startseq);
-                        }
-                        else
-                        {
-                            break;
-                        }
-                    }
+                  deleteChar(startres, seq);
                 }
+              }
             }
+          }
+        }
+        else /////Editing a single sequence///////////
+        {
+          if (insertGap)
+          {
+            // 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);
+            }
+          }
+          else
+          {
+            // dragging to the left
+            for (int j = lastres; j > startres; j--)
+            {
+              if (fixedColumns && fixedRight != -1)
+              {
+                deleteChar(startres, seq, fixedRight);
+              }
+              else
+              {
+                deleteChar(startres, seq);
+              }
+            }
+          }
         }
 
-        endEdit = res;
-        lastres = res;
+        lastres = startres;
         seqCanvas.repaint();
     }
 
@@ -617,10 +917,56 @@ public class SeqPanel extends JPanel
      * @param j DOCUMENT ME!
      * @param seq DOCUMENT ME!
      */
-    public void insertChar(int j, int seq)
+    void insertChar(int j, SequenceI seq)
+    {
+        seq.insertCharAt(j, av.getGapCharacter());
+        seqEditOccurred = true;
+    }
+
+    void insertChar(int j, SequenceI seq, int fixedColumn)
+    {
+      //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)))
+        {
+          //Theres a space, so break and insert the gap
+          break;
+        }
+      }
+
+      if (blankColumn <= j)
+      {
+        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)
     {
-        av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());
-        seqEditOccurred = 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);
+      seq.insertCharAt(fixedColumn, av.getGapCharacter());
+      seqEditOccurred = true;
     }
 
     /**
@@ -629,28 +975,99 @@ public class SeqPanel extends JPanel
      * @param j DOCUMENT ME!
      * @param seq DOCUMENT ME!
      */
-    public void deleteChar(int j, int seq)
+    void deleteChar(int j, SequenceI seq)
     {
-        av.alignment.getSequenceAt(seq).deleteCharAt(j);
-        seqEditOccurred = seq;
+      if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))
+      {
+        ap.alignFrame.statusBar.setText(
+            "End editing: Tried removing residue " + seq.getCharAt(j));
+        return;
+      }
 
-        av.alignment.getWidth();
+        seq.deleteCharAt(j);
+        seqEditOccurred = true;
         seqCanvas.repaint();
     }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void mouseEntered(MouseEvent e)
+    {
+        if(oldSeq < 0)
+          oldSeq = 0;
+
+        if (scrollThread != null)
+        {
+            scrollThread.running = false;
+            scrollThread = null;
+        }
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void mouseExited(MouseEvent e)
+    {
+        if (av.getWrapAlignment())
+        {
+            return;
+        }
+
+        if (mouseDragging)
+        {
+            scrollThread = new ScrollThread();
+        }
+    }
+
+    public void mouseClicked(MouseEvent evt)
+    {}
+
+    public void mouseWheelMoved(MouseWheelEvent e)
+    {
+      e.consume();
+      if (mouseWheelPressed)
+      {
+        Font font = av.getFont();
+        int fontSize = font.getSize();
+        if (e.getWheelRotation() > 0 && fontSize < 51)
+          fontSize++;
+        else if (fontSize > 1)
+          fontSize--;
+
+        av.setFont(new Font(font.getName(), font.getStyle(), fontSize));
+        ap.fontChanged();
+      }
+      else
+      {
+        if (e.getWheelRotation() > 0)
+          ap.scrollUp(false);
+        else
+          ap.scrollUp(true);
+      }
+
+    }
+
+
 
     /**
      * DOCUMENT ME!
      *
      * @param i DOCUMENT ME!
      */
-    void editOccurred(int i)
+    void editOccurred()
     {
-      if (endEdit == startEdit)
+      if (!seqEditOccurred)
       {
         ap.alignFrame.historyList.pop();
         ap.alignFrame.updateEditMenuBar();
       }
 
+      endEditing();
+
       av.firePropertyChange("alignment", null,av.getAlignment().getSequences());
 
     }
@@ -680,7 +1097,6 @@ public class SeqPanel extends JPanel
       if(seq<0 || res<0)
             return;
 
-
         SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
 
         if ((sequence == null) || (res > sequence.getLength()))
@@ -728,6 +1144,15 @@ public class SeqPanel extends JPanel
             }
         }
 
+        if (av.cursorMode)
+        {
+          seqCanvas.cursorX = findRes(evt);
+          seqCanvas.cursorY = findSeq(evt);
+          seqCanvas.repaint();
+          return;
+        }
+
+
         if (stretchGroup == null)
         {
             // define a new group here
@@ -781,17 +1206,12 @@ public class SeqPanel extends JPanel
      */
     public void doMouseReleasedDefineMode(MouseEvent evt)
     {
-        if (mouseDragging)
-        {
-            stretchGroup.recalcConservation();
-            mouseDragging = false;
-        }
-
         if (stretchGroup == null)
         {
             return;
         }
 
+
         if(stretchGroup.cs!=null)
         {
           if (stretchGroup.cs instanceof ClustalxColourScheme)
@@ -805,6 +1225,7 @@ public class SeqPanel extends JPanel
           {
             SliderPanel.setConservationSlider(ap, stretchGroup.cs,
                                               stretchGroup.getName());
+            stretchGroup.recalcConservation();
           }
           else
           {
@@ -831,14 +1252,19 @@ public class SeqPanel extends JPanel
       if(wrappedBlock!=startWrapBlock)
         return;
 
-      if (stretchGroup == null)
-      {
+       if (stretchGroup == null)
+       {
             return;
-        }
+       }
+
 
-        if (res > av.alignment.getWidth())
+        if(y > av.alignment.getHeight())
         {
-            res = av.alignment.getWidth() - 1;
+          y = av.alignment.getHeight() -1;
+        }
+        if(res> av.alignment.getWidth())
+        {
+          res = av.alignment.getWidth()-1;
         }
 
         if (stretchGroup.getEndRes() == res)
@@ -856,10 +1282,6 @@ public class SeqPanel extends JPanel
         {
             res = av.getStartRes();
         }
-        else if (res > av.getEndRes() && !av.getWrapAlignment())
-        {
-            res = av.getEndRes();
-        }
 
         if (changeEndRes)
         {
@@ -887,7 +1309,8 @@ public class SeqPanel extends JPanel
             dragDirection = -1;
         }
 
-        while ((y != oldSeq) && (oldSeq > 0) && (y < av.alignment.getHeight()))
+
+        while ((y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))
         {
             // This routine ensures we don't skip any sequences, as the
             // selection is quite slow.
@@ -895,6 +1318,9 @@ public class SeqPanel extends JPanel
 
             oldSeq += dragDirection;
 
+            if(oldSeq<0)
+              break;
+
             Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
 
             if (stretchGroup.sequences.contains(nextSeq))
@@ -912,7 +1338,9 @@ public class SeqPanel extends JPanel
             }
         }
 
-        oldSeq = y;
+        if(oldSeq < 0)
+          oldSeq = -1;
+
         mouseDragging = true;
 
         if (scrollThread != null)
@@ -923,37 +1351,29 @@ public class SeqPanel extends JPanel
         seqCanvas.repaint();
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void doMouseEnteredDefineMode(MouseEvent e)
+    void scrollCanvas(MouseEvent evt)
     {
-        if (scrollThread != null)
+      if(evt==null)
+      {
+        if(scrollThread!=null)
         {
-            scrollThread.running = false;
+          scrollThread.running = false;
+          scrollThread = null;
         }
-    }
+        mouseDragging = false;
+      }
+      else
+      {
+        if (scrollThread == null)
+          scrollThread = new ScrollThread();
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void doMouseExitedDefineMode(MouseEvent e)
-    {
-        if (av.getWrapAlignment())
-        {
-            return;
-        }
+        mouseDragging = true;
+        scrollThread.setEvent(evt);
+      }
 
-        if (mouseDragging)
-        {
-            scrollThread = new ScrollThread();
-        }
     }
 
+
     // this class allows scrolling off the bottom of the visible alignment
     class ScrollThread extends Thread
     {
@@ -997,11 +1417,11 @@ public class SeqPanel extends JPanel
 
                     if (mouseDragging && (evt.getX() < 0))
                     {
-                        running = ap.scrollRight(true);
+                        running = ap.scrollRight(false);
                     }
                     else if (mouseDragging && (evt.getX() >= getWidth()))
                     {
-                        running = ap.scrollRight(false);
+                        running = ap.scrollRight(true);
                     }
                 }