X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=2fe27b381bf84bffe35aac5fb94700b32ef764fa;hb=2959d102cb701ba58489e7222cd101d0eb02ead6;hp=f4d77c3345e955d91b8d2defe54aec9c19296d16;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index f4d77c3..2fe27b3 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -18,814 +18,1110 @@
  */
 package jalview.gui;
 
-import java.util.*;
+import jalview.datamodel.*;
+
+import jalview.schemes.*;
 
 import java.awt.*;
 import java.awt.event.*;
+
 import javax.swing.*;
 
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.schemes.*;
 
-public class SeqPanel
-    extends JPanel
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class SeqPanel extends JPanel implements MouseListener,
+    MouseMotionListener, MouseWheelListener
+
 {
-  public SeqCanvas seqCanvas;
-  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;
-  ScrollThread scrollThread = null;
-  boolean mouseDragging = false;
-  boolean editingSeqs = false;
-  boolean groupEditing = false;
-
-  //////////////////////////////////////////
-  /////Everything below this is for defining the boundary of the rubberband
-  //////////////////////////////////////////
-  int oldSeq = -1;
-  boolean changeEndSeq = false;
-  boolean changeStartSeq = false;
-  boolean changeEndRes = false;
-  boolean changeStartRes = false;
-  SequenceGroup stretchGroup = null;
-  boolean remove = false;
-
-  public SeqPanel(AlignViewport avp, AlignmentPanel p)
-  {
-    this.av = avp;
-
-    seqCanvas = new SeqCanvas(avp);
-    setLayout(new BorderLayout());
-    add(seqCanvas, BorderLayout.CENTER);
-
-    ap = p;
-
-    addMouseMotionListener(new MouseMotionAdapter()
+    /** DOCUMENT ME!! */
+    public SeqCanvas seqCanvas;
+
+    /** DOCUMENT ME!! */
+    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
+    boolean seqEditOccurred = false;
+    ScrollThread scrollThread = null;
+    boolean mouseDragging = false;
+    boolean editingSeqs = false;
+    boolean groupEditing = false;
+
+    //////////////////////////////////////////
+    /////Everything below this is for defining the boundary of the rubberband
+    //////////////////////////////////////////
+    int oldSeq = -1;
+    boolean changeEndSeq = false;
+    boolean changeStartSeq = false;
+    boolean changeEndRes = false;
+    boolean changeStartRes = false;
+    SequenceGroup stretchGroup = null;
+    boolean remove = false;
+
+    boolean mouseWheelPressed = false;
+
+    /**
+     * Creates a new SeqPanel object.
+     *
+     * @param avp DOCUMENT ME!
+     * @param p DOCUMENT ME!
+     */
+    public SeqPanel(AlignViewport avp, AlignmentPanel p)
     {
-      public void mouseMoved(MouseEvent evt)
-      {
-        if (av.getWrapAlignment())
-        {
-          return;
-        }
+        ToolTipManager.sharedInstance().registerComponent(this);
+        ToolTipManager.sharedInstance().setInitialDelay(0);
+        ToolTipManager.sharedInstance().setDismissDelay(10000);
+        this.av = avp;
+        setBackground(Color.white);
 
-        doMouseMoved(evt);
-      }
+        seqCanvas = new SeqCanvas(avp);
+        setLayout(new BorderLayout());
+        add(seqCanvas, BorderLayout.CENTER);
 
-      public void mouseDragged(MouseEvent evt)
-      {
-        if (av.getWrapAlignment())
-        {
-          return;
-        }
+        ap = p;
 
-        if (editingSeqs)
+        if(!av.isDataset())
         {
-          doMouseDragged(evt);
+          addMouseMotionListener(this);
+          addMouseListener(this);
+          addMouseWheelListener(this);
         }
-        else
-        {
-          doMouseDraggedDefineMode(evt);
-        }
-      }
-    });
+    }
 
-    addMouseListener(new MouseAdapter()
-    {
-      public void mouseReleased(MouseEvent evt)
-      {
-        if (av.getWrapAlignment())
-        {
-          return;
-        }
+    int startWrapBlock=-1;
+    int wrappedBlock=-1;
+    int findRes(MouseEvent evt)
+   {
+     int res = 0;
+     int x = evt.getX();
 
-        if (editingSeqs)
-        {
-          doMouseReleased(evt);
-        }
-        else
-        {
-          doMouseReleasedDefineMode(evt);
-        }
-      }
+    if (av.wrapAlignment)
+    {
 
-      public void mousePressed(MouseEvent evt)
-      {
-        if (av.getWrapAlignment())
-        {
-          return;
-        }
+      int hgap = av.charHeight;
+      if (av.scaleAboveWrapped)
+        hgap += av.charHeight;
 
-        if (evt.isShiftDown() || evt.isAltDown() ||
-            evt.isControlDown())
-        {
-          if (evt.isAltDown() || evt.isControlDown())
-          {
-            groupEditing = true;
-          }
+      int cHeight = av.getAlignment().getHeight() * av.charHeight
+          + hgap + seqCanvas.getAnnotationHeight();
 
-          editingSeqs = true;
-          doMousePressed(evt);
-        }
-        else
-        {
-          doMousePressedDefineMode(evt);
-        }
-      }
+        int y = evt.getY();
+        y -= hgap;
+        x -= seqCanvas.LABEL_WEST;
 
-      public void mouseExited(MouseEvent evt)
-      {
-        if (av.getWrapAlignment() || editingSeqs)
-        {
-          return;
-        }
 
-        doMouseExitedDefineMode(evt);
-      }
+        int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());
 
-      public void mouseEntered(MouseEvent evt)
-      {
-        if (av.getWrapAlignment() || editingSeqs)
-        {
-          return;
-        }
+        wrappedBlock = y / cHeight;
+        wrappedBlock += av.getStartRes() / cwidth;
 
-        doMouseEnteredDefineMode(evt);
-      }
-    });
-    repaint();
-  }
+        res = wrappedBlock * cwidth + x / av.getCharWidth();
 
-  public void doMouseReleased(MouseEvent evt)
-  {
-    if (seqEditOccurred > -1)
+    }
+    else
     {
-      editOccurred(seqEditOccurred);
+        res = (x / av.getCharWidth()) + av.getStartRes();
     }
 
-    startseq = -1;
-    lastres = -1;
-    seqEditOccurred = -1;
-    editingSeqs = false;
-    groupEditing = false;
+    if(av.hasHiddenColumns)
+          res = av.getColumnSelection().adjustForHiddenColumns(res);
 
-    ap.repaint();
-  }
+    return res;
 
-  public void doMousePressed(MouseEvent evt)
-  {
-    ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
-                                                 av.alignment, HistoryItem.EDIT));
+   }
 
-    int seq;
-    int res;
+   int findSeq(MouseEvent evt)
+   {
 
-    int x = evt.getX();
-    int y = evt.getY();
+     int seq = 0;
+     int y = evt.getY();
 
-    res = (x / av.getCharWidth()) + av.getStartRes();
-    seq = (y / av.getCharHeight()) + av.getStartSeq();
+     if (av.wrapAlignment)
+     {
+       int hgap = av.charHeight;
+       if (av.scaleAboveWrapped)
+         hgap += av.charHeight;
 
-    if ( (seq < av.getAlignment().getHeight()) &&
-        (res < av.getAlignment().getSequenceAt(seq).getLength()))
-    {
-      startseq = seq;
-      lastres = res;
-    }
-    else
-    {
-      startseq = -1;
-      lastres = -1;
-    }
+       int cHeight = av.getAlignment().getHeight() * av.charHeight
+           + hgap + seqCanvas.getAnnotationHeight();
 
-    startEdit = lastres;
-    endEdit = lastres;
-
-    return;
-  }
-
-  public void doMouseMoved(MouseEvent evt)
-  {
-    int res = 0;
-    int seq = 0;
-    int x = evt.getX();
-    int y = evt.getY();
-
-    if (av.wrapAlignment)
-    {
-      y -= (2 * av.charHeight);
+         y -= hgap;
 
-      int chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;
+       seq = ( (y % cHeight) / av.getCharHeight());
+     }
+     else
+     {
+       seq = (y / av.getCharHeight()) + av.getStartSeq();
+     }
 
-      res = (int) ( (y / chunkHeight) * (getWidth() / av.charWidth)) +
-          (x / av.getCharWidth()) + av.getStartRes();
+     return seq;
+   }
 
-      y %= chunkHeight;
-      seq = (y / av.getCharHeight()) + av.getStartSeq();
-    }
-    else
-    {
-      res = (x / av.getCharWidth()) + av.getStartRes();
-      seq = (y / av.getCharHeight()) + av.getStartSeq();
+   void endEditing()
+   {
+     startseq = -1;
+     lastres = -1;
+     seqEditOccurred = false;
+     editingSeqs = false;
+     groupEditing = false;
     }
 
-    if (seq >= av.getAlignment().getHeight())
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mouseReleased(MouseEvent evt)
     {
-      return;
-    }
-
-    SequenceI sequence = av.getAlignment().getSequenceAt(seq);
+      mouseDragging = false;
 
-    if (res > sequence.getLength())
-    {
-      return;
-    }
+      if (!editingSeqs)
+      {
+         doMouseReleasedDefineMode(evt);
+         return;
+      }
 
-    Object obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) +
-                                                  "");
-    String aa = "";
+        if (seqEditOccurred)
+        {
+            editOccurred();
+        }
 
-    if (obj != null)
-    {
-      aa = obj.toString();
+        endEditing();
+        ap.repaint();
     }
 
-    StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
-                                         sequence.getName());
 
-    if (aa != "")
-    {
-      text.append("  Residue: " + aa + " (" +
-                  av.getAlignment().getSequenceAt(seq).findPosition(res) + ")");
-    }
-
-    ap.alignFrame.statusBar.setText(text.toString());
 
-    // use aa to see if the mouse pointer is on a
-    if (av.showSequenceFeatures)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mousePressed(MouseEvent evt)
     {
-      Vector features = sequence.getSequenceFeatures();
-      Enumeration e = features.elements();
-      StringBuffer sbuffer = new StringBuffer();
-
-      while (e.hasMoreElements())
+      if (javax.swing.SwingUtilities.isMiddleMouseButton(evt))
       {
-        SequenceFeature sf = (SequenceFeature) e.nextElement();
+        mouseWheelPressed = true;
+        return;
+      }
 
-        if ( (sf.getStart() <= sequence.findPosition(res)) &&
-            (sf.getEnd() >= sequence.findPosition(res)))
+      if (evt.isShiftDown() || evt.isAltDown() ||
+          evt.isControlDown())
+      {
+        if (evt.isAltDown() || evt.isControlDown())
         {
-          if (sbuffer.length() > 0)
-          {
-            sbuffer.append("; ");
-          }
-
-          sbuffer.append(sf.getType() + " " + sf.getDescription());
-
-          if (sf.getStatus().length() > 0)
-          {
-            sbuffer.append(" (" + sf.getStatus() + ")");
-          }
+          groupEditing = true;
         }
+        editingSeqs = true;
+      }
+      else
+      {
+        doMousePressedDefineMode(evt);
+        return;
       }
 
-      ToolTipManager.sharedInstance().registerComponent(this);
-      this.setToolTipText(sbuffer.toString());
-    }
-  }
 
-  public void doMouseDragged(MouseEvent evt)
-  {
-    // If we're dragging we're editing
-    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+      ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
+                                                   av.alignment, HistoryItem.EDIT));
 
-    if (res < 0)
-    {
-      res = 0;
-    }
+      int seq = findSeq(evt);
+      int res = findRes(evt);
 
-    if ( (lastres == -1) || (lastres == res))
-    {
-      return;
-    }
+      if(seq<0 || res<0)
+        return;
 
-    boolean dragRight = true;
+        if ((seq < av.getAlignment().getHeight()) &&
+                (res < av.getAlignment().getSequenceAt(seq).getLength()))
+        {
+            startseq = seq;
+            lastres = res;
+        }
+        else
+        {
+            startseq = -1;
+            lastres = -1;
+        }
 
-    if ( (res < av.getAlignment().getWidth()) && (res < lastres))
-    {
-      dragRight = false;
+        startEdit = lastres;
+        endEdit = lastres;
+
+        return;
     }
 
-    if (res != lastres)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mouseMoved(MouseEvent evt)
     {
-      // Group editing
-      if (groupEditing)
+      if (editingSeqs)
       {
-        SequenceGroup sg = av.getSelectionGroup();
+       // This is because MacOSX creates a mouseMoved
+       // If control is down, other platforms will not.
+       mouseDragged(evt);
+      }
 
-        if (sg == null)
-        {
-          lastres = -1;
+      int res = findRes(evt);
+      int seq = findSeq(evt);
+
+      if(res<0 || seq<0 || seq >= av.getAlignment().getHeight())
+            return;
+
+      SequenceI sequence = av.getAlignment().getSequenceAt(seq);
+
+      if (res > sequence.getLength())
+      {
+        return;
+      }
+
+      if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence)
+      {
+        seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));
+      }
 
-          return;
-        }
 
-        // drag to right
-        if (dragRight)
+        StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
+                sequence.getName());
+
+        Object obj = null;
+        if (av.alignment.isNucleotide())
         {
-          sg.setEndRes(sg.getEndRes() + (res - lastres));
+          obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
+              "");
+          if(obj!=null)
+            text.append(" Nucleotide: ");
         }
-        // drag to left
         else
         {
-          /// Are we able to delete?
-          // ie are all columns blank?
-          boolean deleteAllowed = false;
+          obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
+          if(obj!=null)
+            text.append("  Residue: ");
+        }
+
+        if (obj != null)
+        {
 
-          for (int s = 0; s < sg.getSize(); s++)
+          if (obj != "")
           {
-            SequenceI seq = sg.getSequenceAt(s);
+            text.append( obj + " (" +
+                        av.getAlignment().getSequenceAt(seq).findPosition(res) + ")");
+          }
+        }
 
-            for (int j = res; j < lastres; j++)
+        ap.alignFrame.statusBar.setText(text.toString());
+
+        // use aa to see if the mouse pointer is on a
+        if (av.showSequenceFeatures)
+        {
+            SequenceFeature [] features = sequence.getDatasetSequence().getSequenceFeatures();
+            if(features!=null)
             {
-              if (seq.getSequence().length() <= j)
-              {
-                continue;
-              }
+              StringBuffer sbuffer = new StringBuffer("<html>");
 
-              if (!jalview.util.Comparison.isGap(
-                  seq.getSequence().charAt(j)))
+              for (int i = 0; i < features.length; i++)
               {
-                // Not a gap, block edit not valid
-                res = j + 1;
-                deleteAllowed = false;
 
-                continue;
+                if ( (features[i].getBegin() <= sequence.findPosition(res)) &&
+                    (features[i].getEnd() >= sequence.findPosition(res)))
+                {
+                  if(!av.featuresDisplayed.containsKey(features[i].getType()))
+                  continue;
+
+
+                  if (features[i].getType().equals("disulfide bond"))
+                  {
+                    if (features[i].getBegin() == sequence.findPosition(res)
+                        || features[i].getEnd() == sequence.findPosition(res))
+                    {
+                      if (sbuffer.length() > 6)
+                        sbuffer.append("<br>");
+                      sbuffer.append("disulfide bond " + features[i].getBegin() + ":" +
+                                     features[i].getEnd());
+                    }
+                  }
+                  else
+                  {
+                    if (sbuffer.length() > 6)
+                      sbuffer.append("<br>");
+                    if(features[i].featureGroup!=null)
+                      sbuffer.append(features[i].featureGroup+";");
+
+                    sbuffer.append(features[i].getType());
+
+                    if (features[i].getDescription() != null
+                        && !features[i].description.equals(features[i].getType()))
+                      sbuffer.append("; " + features[i].getDescription());
+
+                    if (features[i].getStatus() != null && features[i].getStatus().length()>0)
+                    {
+                      sbuffer.append("; (" + features[i].getStatus() + ")");
+                    }
+                  }
+                }
+
               }
 
-              deleteAllowed = true;
+              sbuffer.append("</html>");
+              if(sbuffer.length()==13) // <html></html>
+                setToolTipText("");
+              else
+               setToolTipText(sbuffer.toString());
             }
-          }
+            else
+              setToolTipText("");
+        }
+    }
 
-          if (!deleteAllowed)
-          {
-            lastres = -1;
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mouseDragged(MouseEvent evt)
+    {
+      if (!editingSeqs)
+      {
+        doMouseDraggedDefineMode(evt);
+        return;
+      }
 
-            return;
-          }
+        int res = findRes(evt);
 
-          sg.setEndRes(sg.getEndRes() - (lastres - res));
+        if (res < 0)
+        {
+            res = 0;
         }
 
-        for (int i = 0; i < sg.getSize(); i++)
+        if ((lastres == -1) || (lastres == res))
         {
-          SequenceI s = sg.getSequenceAt(i);
-          int k = av.alignment.findIndex(s);
+            return;
+        }
 
-          // drag to right
-          if (dragRight)
-          {
-            for (int j = lastres; j < res; j++)
-            {
-              insertChar(j, k);
-            }
-          }
-          // drag to left
-          else
+        boolean dragRight = true;
+
+        if ((res < av.getAlignment().getWidth()) && (res < lastres))
+        {
+            dragRight = false;
+        }
+        else if(av.hasHiddenColumns)
+        {
+          //Stop editing if the user has dragged beyond hiddenBoundary
+          int lastCol = av.getColumnSelection().getHiddenRegionBoundary(lastres);
+          if( lastCol < res)
           {
-            for (int j = res; j < lastres; j++)
+            if(lastres!=lastCol)
             {
-              if (s.getLength() > j)
-              {
-                deleteChar(res, k);
-              }
+              endEditing();
+              return;
             }
           }
         }
-      }
-      else /////Editing a single sequence///////////
-      {
-        if ( (res < av.getAlignment().getWidth()) && (res > lastres))
+
+        if(!groupEditing && av.hasHiddenRows)
         {
-          // dragging to the right
-          for (int j = lastres; j < res; j++)
+          if(av.alignment.getSequenceAt(startseq).getHiddenSequences()!=null)
           {
-            insertChar(j, startseq);
+            groupEditing = true;
           }
         }
-        else if ( (res < av.getAlignment().getWidth()) &&
-                 (res < lastres))
+
+
+        if (res != lastres)
         {
-          // dragging to the left
-          for (int j = lastres; j > res; j--)
-          {
-            if (jalview.util.Comparison.isGap(
-                av.alignment.getSequenceAt(startseq)
-                .getSequence().charAt(res)))
+            SequenceI seq;
+            // Group editing
+            if (groupEditing)
             {
-              deleteChar(res, startseq);
+                SequenceGroup sg = av.getSelectionGroup();
+
+                if (av.hasHiddenRows)
+                {
+                  //sg might be null as the user may only see 1 sequence
+                  if(sg==null)
+                  {
+                    sg = new SequenceGroup();
+                    sg.addSequence(av.alignment.getSequenceAt(startseq), false);
+                  }
+
+                  SequenceGroup tmp = new SequenceGroup();
+
+                  //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;
+                }
+
+
+                if (sg == null)
+                {
+                    endEditing();
+                    return;
+                }
+
+                int blankColumn = -1;
+
+                // drag to right
+                if (dragRight)
+                {
+
+                  // Is it valid??
+                  // Find the next gap before the end
+                  // of the visible region boundary
+                  if (av.hasHiddenColumns)
+                  {
+                    if(res-lastres > 1)
+                    {
+                      res = lastres+1;
+                    }
+
+
+                    int lastCol = av.getColumnSelection().
+                          getHiddenRegionBoundary(res);
+
+                    if(lastCol!=res)
+                    {
+                      for (blankColumn = lastCol;
+                           blankColumn > lastres;
+                           blankColumn--)
+                      {
+                        boolean blank = true;
+                        for (int s = 0; s < sg.getSize(); s++)
+                        {
+                          seq = sg.getSequenceAt(s);
+
+                          if (seq.getSequence().length() <= blankColumn)
+                          {
+                            continue;
+                          }
+
+                          if (!jalview.util.Comparison.isGap(
+                              seq.getSequence().charAt(blankColumn)))
+                          {
+                            blank = false;
+                            continue;
+                          }
+                        }
+                        if (blank)
+                          break;
+                      }
+
+
+                      if (blankColumn <= lastres)
+                      {
+                        endEditing();
+                        return;
+                      }
+                    }
+                    else
+                      blankColumn = -1;
+
+                  }
+
+                  sg.setEndRes(sg.getEndRes() + (res - lastres));
+                }
+
+                // drag to left
+                else
+                {
+                    /// Are we able to delete?
+                    // ie are all columns blank?
+
+                    for (int s = 0; s < sg.getSize(); s++)
+                    {
+                        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
+                                endEditing();
+                                return;
+                            }
+                        }
+                    }
+
+                    if(res<sg.getStartRes())
+                    {
+                      sg.setStartRes(sg.getStartRes() - 1);
+                    }
+                    sg.setEndRes(sg.getEndRes() - (lastres - res));
+                }
+
+                for (int i = 0; i < sg.getSize(); i++)
+                {
+                    seq = sg.getSequenceAt(i);
+
+                    // drag to right
+                    if (dragRight)
+                    {
+                        for (int j = lastres; j < res; j++)
+                        {
+                            insertChar(j, seq, blankColumn);
+                        }
+                    }
+
+                    // drag to left
+                    else
+                    {
+                        for (int j = res; j < lastres; j++)
+                        {
+                            if (seq.getLength()-1 > res)
+                            {
+                                deleteChar(res, seq);
+                            }
+                        }
+                    }
+                }
             }
-            else
+            else /////Editing a single sequence///////////
             {
-              break;
+                seq = av.alignment.getSequenceAt(startseq);
+                if ((res < av.getAlignment().getWidth()) && (res > lastres))
+                {
+                    // dragging to the right
+                    for (int j = lastres; j < res; j++)
+                    {
+                        insertChar(j, seq, j);
+                    }
+                }
+                else if ((res < av.getAlignment().getWidth()) &&
+                        (res < lastres))
+                {
+                    // 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, seq);
+                        }
+                        else
+                        {
+                            break;
+                        }
+                    }
+                }
             }
-          }
         }
-      }
-    }
-
-    endEdit = res;
-    lastres = res;
-    repaint();
-  }
-
-  public void drawChars(int seqstart, int seqend, int start)
-  {
-    seqCanvas.drawPanel(seqCanvas.gg, start, av.getEndRes(), seqstart,
-                        seqend, av.getStartRes(), av.getStartSeq(), 0);
-    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)
-  {
-    av.alignment.getSequenceAt(seq).deleteCharAt(j);
-    seqEditOccurred = seq;
-
-    av.alignment.getWidth();
-    repaint();
-  }
-
-  void editOccurred(int i)
-  {
-    if (endEdit == startEdit)
-    {
-      ap.alignFrame.historyList.pop();
-      ap.alignFrame.updateEditMenuBar();
-    }
 
-    av.updateConservation();
-    av.updateConsensus();
+        mouseDragging = true;
+        if(scrollThread!=null)
+          scrollThread.setEvent(evt);
 
-    // Y O Y CLUSTALX
-    ColourSchemeI cs = av.getGlobalColourScheme();
+        endEdit = res;
+        lastres = res;
+        seqCanvas.repaint();
+    }
 
-    if (cs instanceof ConservationColourScheme)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void mouseEntered(MouseEvent e)
     {
-      ConservationColourScheme ccs = (ConservationColourScheme) cs;
+        if(oldSeq < 0)
+          oldSeq = 0;
 
-      if (ccs.cs instanceof ClustalxColourScheme)
-      {
-        Conservation c = new Conservation("All",
-                                          ResidueProperties.propHash, 3,
-                                          av.alignment.getSequences(), 0,
-                                          av.alignment.getWidth() - 1);
-        c.calculate();
-        c.verdict(false, av.ConsPercGaps);
-
-        ClustalxColourScheme cxs = (ClustalxColourScheme) ccs.cs;
-        cxs.resetClustalX(av.alignment.getSequences(),
-                          av.alignment.getWidth());
-        ccs = new ConservationColourScheme(c, cxs);
-        av.setGlobalColourScheme(ccs);
-      }
+        if (scrollThread != null)
+        {
+            scrollThread.running = false;
+            scrollThread = null;
+        }
     }
 
-    if (cs instanceof ClustalxColourScheme)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void mouseExited(MouseEvent e)
     {
-      ( (ClustalxColourScheme) cs).resetClustalX(av.alignment.getSequences(),
-                                                 av.alignment.getWidth());
-      av.setGlobalColourScheme(cs);
-    }
-  }
-
-  public void doMousePressedDefineMode(MouseEvent evt)
-  {
-    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
-    int seq = (evt.getY() / av.getCharHeight()) + av.getStartSeq();
-    oldSeq = seq;
-
-    SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
+        if (av.getWrapAlignment())
+        {
+            return;
+        }
 
-    if ( (sequence == null) || (res > sequence.getLength()))
-    {
-      return;
+        if (mouseDragging)
+        {
+            scrollThread = new ScrollThread();
+        }
     }
 
-    stretchGroup = av.getSelectionGroup();
+    public void mouseClicked(MouseEvent evt)
+    {}
 
-    if (stretchGroup == null)
+    public void mouseWheelMoved(MouseWheelEvent e)
     {
-      stretchGroup = av.alignment.findGroup(sequence);
-
-      if ( (stretchGroup != null) && (res > stretchGroup.getStartRes()) &&
-          (res < stretchGroup.getEndRes()))
+      if (mouseWheelPressed)
       {
-        av.setSelectionGroup(stretchGroup);
+        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
       {
-        stretchGroup = null;
+        if (e.getWheelRotation() > 0)
+          ap.scrollUp(false);
+        else
+          ap.scrollUp(true);
       }
+
     }
-    else if (!stretchGroup.sequences.contains(sequence) ||
-             (stretchGroup.getStartRes() > res) ||
-             (stretchGroup.getEndRes() < res))
-    {
-      stretchGroup = null;
 
-      SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
 
-      if (allGroups != null)
-      {
-        for (int i = 0; i < allGroups.length; i++)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param j DOCUMENT ME!
+     * @param seq DOCUMENT ME!
+     */
+    void insertChar(int j, SequenceI seq, int blankColumn)
+    {
+        if(av.hasHiddenColumns)
         {
-          if ( (allGroups[i].getStartRes() <= res) &&
-              (allGroups[i].getEndRes() >= res))
+          //Find the next gap before the end of the visible region boundary
+          int lastCol = av.getColumnSelection().getHiddenRegionBoundary(j);
+          if(lastCol != j)
           {
-            stretchGroup = allGroups[i];
-            av.setSelectionGroup(stretchGroup);
+            if (!groupEditing || lastCol <= j)
+            {
+              blankColumn = lastCol;
+              //If lastCol > j, theres a boundary after the gap insertion
+              if (lastCol > j)
+              {
+                for (blankColumn = lastCol; 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;
+                }
+              }
+
+            }
 
-            break;
+            // Editing with hidden regions only!!
+            seq.deleteCharAt(blankColumn);
           }
-        }
       }
+
+        seq.insertCharAt(j, av.getGapCharacter());
+        seqEditOccurred = true;
     }
 
-    if (stretchGroup == null)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param j DOCUMENT ME!
+     * @param seq DOCUMENT ME!
+     */
+    public void deleteChar(int j, SequenceI seq)
     {
-      // define a new group here
-      SequenceGroup sg = new SequenceGroup();
-      sg.setStartRes(res);
-      sg.setEndRes(res);
-      sg.addSequence(sequence);
-      av.setSelectionGroup(sg);
-      stretchGroup = sg;
-
-      if (av.getConservationSelected())
+      if (av.hasHiddenColumns)
       {
-        SliderPanel.setConservationSlider(ap,
-                                          av.getGlobalColourScheme(),
-                                          "Background");
-      }
+        //Find the next gap before the end of the visible region boundary
+        int lastCol = av.getColumnSelection().getHiddenRegionBoundary(j);
 
-      if (av.getAbovePIDThreshold())
-      {
-        SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
-                                       "Background");
+        //If lastCol > j, theres a boundary after the gap insertion
+        if (lastCol > j)
+        {
+          seq.insertCharAt(lastCol, av.getGapCharacter());
+        }
       }
-    }
-    else if (javax.swing.SwingUtilities.isRightMouseButton(evt))
-    {
-      jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null);
-      pop.show(this, evt.getX(), evt.getY());
 
-      // edit the properties of existing group
+        seq.deleteCharAt(j);
+        seqEditOccurred = true;
+
+        seqCanvas.repaint();
     }
 
-    if ( (stretchGroup != null) && (stretchGroup.getEndRes() == res))
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     */
+    void editOccurred()
     {
-      // Edit end res position of selected group
-      changeEndRes = true;
+      if (endEdit == startEdit)
+      {
+        ap.alignFrame.historyList.pop();
+        ap.alignFrame.updateEditMenuBar();
+      }
+
+      av.firePropertyChange("alignment", null,av.getAlignment().getSequences());
+
     }
-    else if ( (stretchGroup != null) && (stretchGroup.getStartRes() == res))
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void doMousePressedDefineMode(MouseEvent evt)
     {
-      // Edit end res position of selected group
-      changeStartRes = true;
-    }
+      int res = findRes(evt);
+      int seq = findSeq(evt);
+      oldSeq = seq;
 
-    stretchGroup.getWidth();
+      startWrapBlock=wrappedBlock;
 
-    repaint();
-  }
+      if(av.wrapAlignment && seq>av.alignment.getHeight())
+      {
+          JOptionPane.showInternalMessageDialog(Desktop.desktop,
+              "Cannot edit annotations in wrapped view.",
+              "Wrapped view - no edit",
+              JOptionPane.WARNING_MESSAGE);
+        return;
+      }
 
-  public void doMouseReleasedDefineMode(MouseEvent evt)
-  {
-    mouseDragging = false;
+      if(seq<0 || res<0)
+            return;
 
-    if (stretchGroup == null)
-    {
-      return;
-    }
 
-    if (stretchGroup.cs instanceof ClustalxColourScheme)
-    {
-      stretchGroup.cs = new ClustalxColourScheme(stretchGroup.sequences,
-                                                 av.alignment.getWidth());
-      repaint();
-    }
-    else if (stretchGroup.cs instanceof ConservationColourScheme)
-    {
-      ConservationColourScheme ccs = (ConservationColourScheme) stretchGroup.cs;
-      stretchGroup.cs = ccs;
-      SliderPanel.setConservationSlider(ap, stretchGroup.cs,
-                                        stretchGroup.getName());
+        SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
 
-      repaint();
-    }
-    else
-    {
-      SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
-                                     stretchGroup.getName());
-    }
+        if ((sequence == null) || (res > sequence.getLength()))
+        {
+            return;
+        }
 
-    changeEndRes = false;
-    changeStartRes = false;
-    stretchGroup = null;
-    ap.idPanel.repaint();
-  }
+        stretchGroup = av.getSelectionGroup();
 
-  public void doMouseDraggedDefineMode(MouseEvent evt)
-  {
-    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
-    int y = (evt.getY() / av.getCharHeight()) + av.getStartSeq();
+        if (stretchGroup == null)
+        {
+            stretchGroup = av.alignment.findGroup(sequence);
 
-    if (stretchGroup == null)
-    {
-      return;
-    }
+            if ((stretchGroup != null) && (res > stretchGroup.getStartRes()) &&
+                    (res < stretchGroup.getEndRes()))
+            {
+                av.setSelectionGroup(stretchGroup);
+            }
+            else
+            {
+                stretchGroup = null;
+            }
+        }
+        else if (!stretchGroup.sequences.contains(sequence) ||
+                (stretchGroup.getStartRes() > res) ||
+                (stretchGroup.getEndRes() < res))
+        {
+            stretchGroup = null;
 
-    if (res > av.alignment.getWidth())
-    {
-      res = av.alignment.getWidth() - 1;
-    }
+            SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
 
-    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 (allGroups != null)
+            {
+                for (int i = 0; i < allGroups.length; i++)
+                {
+                    if ((allGroups[i].getStartRes() <= res) &&
+                            (allGroups[i].getEndRes() >= res))
+                    {
+                        stretchGroup = allGroups[i];
+                        av.setSelectionGroup(stretchGroup);
+
+                        break;
+                    }
+                }
+            }
+        }
 
-    if (res < av.getStartRes())
-    {
-      res = av.getStartRes();
-    }
-    else if (res > av.getEndRes())
-    {
-      res = av.getEndRes();
-    }
+        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 (changeEndRes)
-    {
-      if (res > (stretchGroup.getStartRes() - 1))
-      {
-        stretchGroup.setEndRes(res);
-      }
-    }
-    else if (changeStartRes)
-    {
-      if (res < (stretchGroup.getEndRes() + 1))
-      {
-        stretchGroup.setStartRes(res);
-      }
-    }
+            if (av.getAbovePIDThreshold())
+            {
+                SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
+                    "Background");
+            }
+        }
+        else if (javax.swing.SwingUtilities.isRightMouseButton(evt))
+        {
+            jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null);
+            pop.show(this, evt.getX(), evt.getY());
 
-    int dragDirection = 0;
+            // edit the properties of existing group
+        }
 
-    if (y > oldSeq)
-    {
-      dragDirection = 1;
+        if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))
+        {
+            // Edit end res position of selected group
+            changeEndRes = true;
+        }
+        else if ((stretchGroup != null) && (stretchGroup.getStartRes() == res))
+        {
+            // Edit end res position of selected group
+            changeStartRes = true;
+        }
+
+        stretchGroup.getWidth();
+
+        seqCanvas.repaint();
     }
-    else if (y < oldSeq)
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void doMouseReleasedDefineMode(MouseEvent evt)
     {
-      dragDirection = -1;
+        if (stretchGroup == null)
+        {
+            return;
+        }
+
+
+        if(stretchGroup.cs!=null)
+        {
+          if (stretchGroup.cs instanceof ClustalxColourScheme)
+          {
+            ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup.
+                sequences,
+                stretchGroup.getWidth());
+          }
+
+          if (stretchGroup.cs.conservationApplied())
+          {
+            SliderPanel.setConservationSlider(ap, stretchGroup.cs,
+                                              stretchGroup.getName());
+            stretchGroup.recalcConservation();
+          }
+          else
+          {
+            SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
+                                           stretchGroup.getName());
+          }
+        }
+        changeEndRes = false;
+        changeStartRes = false;
+        stretchGroup = null;
+        PaintRefresher.Refresh(av.alignment);
     }
 
-    while ( (y != oldSeq) && (oldSeq > 0) && (y < av.alignment.getHeight()))
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void doMouseDraggedDefineMode(MouseEvent evt)
     {
-      // This routine ensures we don't skip any sequences, as the
-      // selection is quite slow.
-      Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
+      int res = findRes(evt);
+      int y = findSeq(evt);
 
-      oldSeq += dragDirection;
+      if(wrappedBlock!=startWrapBlock)
+        return;
 
-      Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
+       if (stretchGroup == null)
+       {
+            return;
+       }
 
-      if (stretchGroup.sequences.contains(nextSeq))
-      {
-        stretchGroup.deleteSequence(seq);
-        stretchGroup.deleteSequence(nextSeq);
-      }
-      else
-      {
-        if (seq != null)
+
+        if(y > av.alignment.getHeight())
         {
-          stretchGroup.addSequence(seq);
+          y = av.alignment.getHeight() -1;
         }
 
-        stretchGroup.addSequence(nextSeq);
-      }
-    }
+        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;
+        }
 
-    oldSeq = y;
-    mouseDragging = true;
+        if (res < av.getStartRes())
+        {
+            res = av.getStartRes();
+        }
 
-    if (scrollThread != null)
-    {
-      scrollThread.setEvent(evt);
-    }
+        if (changeEndRes)
+        {
+            if (res > (stretchGroup.getStartRes() - 1))
+            {
+                stretchGroup.setEndRes(res);
+            }
+        }
+        else if (changeStartRes)
+        {
+            if (res < (stretchGroup.getEndRes() + 1))
+            {
+                stretchGroup.setStartRes(res);
+            }
+        }
 
-    repaint();
-  }
+        int dragDirection = 0;
 
-  public void doMouseEnteredDefineMode(MouseEvent e)
-  {
-    if (scrollThread != null)
-    {
-      scrollThread.running = false;
-    }
-  }
+        if (y > oldSeq)
+        {
+            dragDirection = 1;
+        }
+        else if (y < oldSeq)
+        {
+            dragDirection = -1;
+        }
 
-  public void doMouseExitedDefineMode(MouseEvent e)
-  {
-    if (av.getWrapAlignment())
-    {
-      return;
-    }
 
-    if (mouseDragging)
-    {
-      scrollThread = new ScrollThread();
-    }
-  }
+        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);
 
-  // this class allows scrolling off the bottom of the visible alignment
-  class ScrollThread
-      extends Thread
-  {
-    MouseEvent evt;
-    boolean running = false;
+            oldSeq += dragDirection;
 
-    public ScrollThread()
-    {
-      start();
-    }
+            if(oldSeq<0)
+              break;
 
-    public void setEvent(MouseEvent e)
-    {
-      evt = e;
-    }
+            Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
 
-    public void stopScrolling()
-    {
-      running = false;
+            if (stretchGroup.sequences.contains(nextSeq))
+            {
+                stretchGroup.deleteSequence(seq, false);
+            }
+            else
+            {
+                if (seq != null)
+                {
+                    stretchGroup.addSequence(seq, false);
+                }
+
+                stretchGroup.addSequence(nextSeq, false);
+            }
+        }
+
+        if(oldSeq < 0)
+          oldSeq = -1;
+
+        mouseDragging = true;
+
+        if (scrollThread != null)
+        {
+            scrollThread.setEvent(evt);
+        }
+
+        seqCanvas.repaint();
     }
 
-    public void run()
+
+
+    // this class allows scrolling off the bottom of the visible alignment
+    class ScrollThread extends Thread
     {
-      running = true;
+        MouseEvent evt;
+        boolean running = false;
 
-      while (running)
-      {
-        if (evt != null)
+        public ScrollThread()
         {
-          if (mouseDragging && (evt.getY() < 0) &&
-              (av.getStartSeq() > 0))
-          {
-            running = ap.scrollUp(true);
-          }
-
-          if (mouseDragging && (evt.getY() >= getHeight()) &&
-              (av.alignment.getHeight() > av.getEndSeq()))
-          {
-            running = ap.scrollUp(false);
-          }
+            start();
+        }
 
-          if (mouseDragging && (evt.getX() < 0))
-          {
-            running = ap.scrollRight(true);
-          }
-          else if (mouseDragging && (evt.getX() >= getWidth()))
-          {
-            running = ap.scrollRight(false);
-          }
+        public void setEvent(MouseEvent e)
+        {
+            evt = e;
         }
 
-        try
+        public void stopScrolling()
         {
-          Thread.sleep(75);
+            running = false;
         }
-        catch (Exception ex)
+
+        public void run()
         {
+            running = true;
+
+            while (running)
+            {
+                if (evt != null)
+                {
+                    if (mouseDragging && (evt.getY() < 0) &&
+                            (av.getStartSeq() > 0))
+                    {
+                        running = ap.scrollUp(true);
+                    }
+
+                    if (mouseDragging && (evt.getY() >= getHeight()) &&
+                            (av.alignment.getHeight() > av.getEndSeq()))
+                    {
+                        running = ap.scrollUp(false);
+                    }
+
+                    if (mouseDragging && (evt.getX() < 0))
+                    {
+                        running = ap.scrollRight(true);
+                    }
+                    else if (mouseDragging && (evt.getX() >= getWidth()))
+                    {
+                        running = ap.scrollRight(false);
+                    }
+                }
+
+                try
+                {
+                    Thread.sleep(20);
+                }
+                catch (Exception ex)
+                {
+                }
+            }
         }
-      }
     }
-  }
 }