X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=b48861a0d34130ece6a660e774363376a6d994bf;hb=2ba9716bbffe4b35f640f8a85be4b60fe5fb2fdd;hp=3df1dac84d44dd425b3a974e6975f9b136e8a8e7;hpb=f288996f4b49bfb065e167f18639c5941dbfcef2;p=jalview.git

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 3df1dac..b48861a 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -4,49 +4,101 @@ import java.awt.*;
 import java.awt.event.*;
 import jalview.datamodel.*;
 import javax.swing.*;
+import java.util.*;
 import jalview.schemes.*;
-import jalview.analysis.*;
-
+import jalview.analysis.Conservation;
 
 public class SeqPanel extends JPanel
 {
 
   public    SeqCanvas         seqCanvas;
-  public    AlignmentPanel    parent;
+  public    AlignmentPanel    ap;
 
-  protected int startres;
   protected int lastres;
-  protected int endres;
-
   protected int startseq;
-  protected int padseq;
+  int startEdit=-1;
+  int endEdit=-1;
 
-  public    boolean editFlag;
   protected AlignViewport av;
 
-  public SeqPanel(AlignViewport av, AlignmentPanel p) {
-    this.av         = 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;
+
+
+  public SeqPanel(AlignViewport avp, AlignmentPanel p) {
+    this.av         = avp;
 
-    seqCanvas  = new SeqCanvas(av);
+    seqCanvas  = new SeqCanvas(avp);
     setLayout(new BorderLayout());
     add(seqCanvas, BorderLayout.CENTER);
 
-    parent = p;
+    ap = p;
 
     addMouseMotionListener( new MouseMotionAdapter()
     {
       public void mouseMoved(MouseEvent evt)
-      {  doMouseMoved(evt);   }
+      {
+       if(av.getWrapAlignment())
+         return;
+        doMouseMoved(evt);    }
+
       public void mouseDragged(MouseEvent evt)
-      {      doMouseDragged(evt);  }
+      {
+        if(av.getWrapAlignment())
+         return;
+        if( editingSeqs )
+          doMouseDragged(evt);
+        else
+          doMouseDraggedDefineMode(evt);
+      }
     });
 
     addMouseListener( new MouseAdapter()
     {
       public void mouseReleased(MouseEvent evt)
-      {  doMouseReleased(evt);  }
+      {
+        if(av.getWrapAlignment())
+         return;
+        if(editingSeqs)
+          doMouseReleased(evt);
+        else
+          doMouseReleasedDefineMode(evt);
+
+      }
       public void mousePressed(MouseEvent evt)
-      {  doMousePressed(evt);   }
+      {
+        if(av.getWrapAlignment())
+         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 (av.getWrapAlignment() || editingSeqs)
+                return;
+              doMouseExitedDefineMode(evt);
+
+      }
+      public void mouseEntered(MouseEvent evt)
+      {
+        if (av.getWrapAlignment() || editingSeqs)
+          return;
+        doMouseEnteredDefineMode(evt);
+      }
 
     });
     repaint();
@@ -55,56 +107,47 @@ public class SeqPanel extends JPanel
 
   public void doMouseReleased(MouseEvent evt) {
 
-    int x = evt.getX();
-      int res = (int)(x/av.getCharWidth()) + av.getStartRes();
-
-      endres = res;
-
-      // This is to detect edits - we're at the end of an edit if mouse is up
-      editFlag = false;
-      startseq = -1;
-      startres = -1;
-      lastres  = -1;
+    if(seqEditOccurred>-1)
+      editOccurred(seqEditOccurred);
 
-    parent.RefreshPanels();
-    repaint();
+    startseq = -1;
+    lastres  = -1;
+    seqEditOccurred = -1;
+    editingSeqs  = false;
+    groupEditing = false;
 
+    ap.repaint();
   }
 
   public void doMousePressed(MouseEvent evt) {
-  parent.alignFrame.addHistoryItem("sequence edit");
+
+    ap.alignFrame.addHistoryItem( new HistoryItem(
+        "Edit Sequence",av.alignment, HistoryItem.EDIT));
+
     int seq;
     int res;
 
     int x = evt.getX();
     int y = evt.getY();
 
-    res = (int)(x/av.getCharWidth()) + av.getStartRes();
-    seq = (y)/av.getCharHeight() + av.getStartSeq();
+    res = x/av.getCharWidth() + av.getStartRes();
+    seq = y/av.getCharHeight() + av.getStartSeq();
 
-    if (seq < av.getAlignment().getHeight() && res < av.getAlignment().getSequenceAt(seq).getLength())
+    if (seq < av.getAlignment().getHeight() &&
+        res < av.getAlignment().getSequenceAt(seq).getLength())
     {
-      //char resstr = align.getSequenceAt(seq).getSequence().charAt(res);
-      // Find the residue's position in the sequence (res is the position
-      // in the alignment
-
       startseq = seq;
-
-      if (startseq == (av.getAlignment().getHeight()-1)) {
-        padseq = 1;
-      } else {
-        padseq = 1;
-      }
-
-      startres = res;
       lastres = res;
-
-      } else {
+    }
+    else
+    {
       startseq = -1;
-      startres = -1;
       lastres = -1;
     }
 
+    startEdit = lastres;
+    endEdit = lastres;
+
     return;
   }
 
@@ -119,18 +162,15 @@ public class SeqPanel extends JPanel
       int chunkHeight = (av.getAlignment().getHeight()+2)*av.charHeight;
 
 
-      res =   (int)((y/chunkHeight)*(getWidth()/av.charWidth)) +  (int)(x/av.getCharWidth()) + av.getStartRes();
+      res =   (int)((y/chunkHeight)*(getWidth()/av.charWidth)) +  x/av.getCharWidth() + av.getStartRes();
 
-      System.out.println( ((y/chunkHeight)*(getWidth()/av.charWidth)) +" "+((x / av.getCharWidth()) + av.getStartRes()) );
       y %= chunkHeight;
       seq =     y / av.getCharHeight() + av.getStartSeq();
 
-      //   chunkHeight =  (da.getHeight() + 2)*charHeight;
-      //  startx += chunkWidth;
     }
     else
     {
-      res = (int) (x / av.getCharWidth()) + av.getStartRes();
+      res = x / av.getCharWidth()  + av.getStartRes();
       seq = y / av.getCharHeight() + av.getStartSeq();
     }
 
@@ -138,125 +178,169 @@ public class SeqPanel extends JPanel
     if(seq>=av.getAlignment().getHeight())
       return;
 
-    Object obj = ResidueProperties.aa2Triplet.get( av.getAlignment().getSequenceAt(seq).getCharAt(res)+"" ) ;
+    SequenceI sequence = av.getAlignment().getSequenceAt(seq);
+    if(res>sequence.getLength())
+      return;
+
+    Object obj = ResidueProperties.aa2Triplet.get( sequence.getCharAt(res)+"" ) ;
     String aa = "";
     if(obj!=null)
          aa = obj.toString();
 
-    StringBuffer text = new StringBuffer("Sequence " +(seq+1)+" ID: "+av.getAlignment().getSequenceAt(seq).getName());
+    StringBuffer text = new StringBuffer("Sequence " +(seq+1)+" ID: "+sequence.getName());
     if(aa!="")
       text.append("  Residue: "+aa+" ("+  av.getAlignment().getSequenceAt(seq).findPosition(res)+")");
 
-    parent.alignFrame.statusBar.setText(text.toString());
+    ap.alignFrame.statusBar.setText(text.toString());
+
+    // use aa to see if the mouse pointer is on a
+    if(  av.showSequenceFeatures)
+    {
+      Vector features = sequence.getSequenceFeatures();
+      Enumeration e = features.elements();
+      StringBuffer sbuffer = new StringBuffer();
+
+
+      while (e.hasMoreElements())
+      {
+        SequenceFeature sf = (SequenceFeature) e.nextElement();
+        if (sf.getStart() <= sequence.findPosition(res) &&
+            sf.getEnd() >= sequence.findPosition(res))
+        {
+          if(sbuffer.length()>0)
+            sbuffer.append("; ");
+          sbuffer.append(sf.getType() + " " + sf.getDescription());
+          if(sf.getStatus().length()>0)
+            sbuffer.append(" ("+sf.getStatus()+")");
+        }
+
+      }
+
+      ToolTipManager.sharedInstance().registerComponent(this);
+      this.setToolTipText(sbuffer.toString());
+    }
+
 
   }
 
   public void doMouseDragged(MouseEvent evt) {
+
     // If we're dragging we're editing
-    editFlag = true;
-    int x = evt.getX();
+    int res = evt.getX() / av.getCharWidth() + av.getStartRes();
+    if (res < 0)
+      res = 0;
 
-    int res = (int)(x/av.getCharWidth()) + av.getStartRes();
-    if (res < 0) {res = 0;}
+    if (lastres == -1 || lastres == res)
+      return;
 
-    if (res  != lastres) {
-      if (startseq != -1) {
+    boolean dragRight = true;
+    if (res < av.getAlignment().getWidth() && res < lastres)
+      dragRight = false;
 
-	// Group editing
-	if (av.getGroupEdit()) {
-	  SequenceGroup sg = av.getAlignment().findGroup(startseq);
 
-          if(sg!=null)
-	  if (res < av.getAlignment().getWidth() && res < lastres)
+    if (res != lastres)
+    {
+        // Group editing
+        if (groupEditing)
+        {
+          SequenceGroup sg = av.getSelectionGroup();
+          if(sg==null)
           {
-	    boolean flag = false;
-	    for (int i= 0 ; i < sg.getSize(); i++)
+            lastres=-1;
+            return;
+          }
+
+            // drag to right
+            if(dragRight)
+                sg.setEndRes(sg.getEndRes() + (res-lastres));
+
+            // drag to left
+            else
             {
-	      SequenceI s = (SequenceI)sg.getSequenceAt(i);
-	      for (int j=lastres-1; j >= res; j--)
+               /// Are we able to delete?
+               // ie are all columns blank?
+               boolean deleteAllowed = false;
+              for (int s = 0; s < sg.getSize(); s++)
               {
-		if (!flag)
+                SequenceI seq = sg.getSequenceAt(s);
+                for (int j=res; j<lastres; j++)
                 {
-		  if (!s.getSequence().substring(j,j+1).equals(av.getAlignment().getGapCharacter()) &&
-		      !s.getSequence().substring(j,j+1).equals(" "))
+                  if(seq.getSequence().length()<=j)
+                    continue;
+
+                  if(!jalview.util.Comparison.isGap(seq.getSequence().charAt(j)))
                   {
-		    res = j+1;
-		    flag = true;
-		  }
-		}
-	      }
-	    }
-	  }
-
-          if(sg!=null)
-	  for (int i= 0 ; i < sg.getSize(); i++)
-          {
-	    SequenceI s = (SequenceI)sg.getSequenceAt(i);
-	    boolean found = false;
-	    int sno = -1;
-	    for (int k = 0; k < av.getAlignment().getHeight(); k++)
-            {
-	      if (av.getAlignment().getSequenceAt(k) == s)
+                    // Not a gap, block edit not valid
+                    res=j+1;
+                    deleteAllowed = false;
+                    continue;
+                  }
+                  deleteAllowed = true;
+                }
+              }
+
+              if(!deleteAllowed)
               {
-		found = true;
-		sno = k;
-		break;
-	      }
-	    }
-	    if (found && sno != -1) {
-	      if (res < av.getAlignment().getWidth() && res > lastres)
-              {
-		for (int j = lastres; j < res; j++)
-		  insertChar(j,sno);
-
-		int index = av.getAlignment().findIndex(s);
-		if (index != -1)
-		  drawChars(index,index+1,lastres);
-
+                lastres = -1;
+                return;
+              }
 
-	      } else if (res < av.getAlignment().getWidth() && res < lastres)
-              {
-		for (int j = res; j < lastres; j++)
-                {
-		  deleteChar(j,res,sno);
-		  startres = res;
-		}
-		int index = av.getAlignment().findIndex(s);
-		if (index != -1)
-		  drawChars(index,index+1,res);
+              sg.setEndRes(sg.getEndRes() - (lastres-res));
+            }
 
-	      }
-	    }
 
-	  }
-	  lastres = res;
-	} else {
+            for (int i = 0; i < sg.getSize(); i++)
+            {
+              SequenceI s = sg.getSequenceAt(i);
+              int k = av.alignment.findIndex(s);
 
+              // drag to right
+              if (dragRight)
+                for (int j = lastres; j < res; j++)
+                  insertChar(j, k);
 
-	  if (res < av.getAlignment().getWidth() && res > lastres) {
+              // drag to left
+              else
+              {
+                for (int j = res; j < lastres; j++)
+                {
+                  if(s.getLength()>j)
+                    deleteChar(res, k);
+                }
+              }
+            }
+        }
+        else /////Editing a single sequence///////////
+        {
+          if (res < av.getAlignment().getWidth() && res > lastres)
+          {
             // dragging to the right
-	    for (int j = lastres; j < res; j++)
-	      insertChar(j,startseq);
+            for (int j = lastres; j < res; j++)
+              insertChar(j, startseq);
+          }
+          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)))
 
-	    drawChars(startseq,startseq+1,lastres);
+              deleteChar(res, startseq);
+              else
+              {
 
-	  } else if (res < av.getAlignment().getWidth() && res < lastres)
-          {
+                break;
+              }
+            }
+          }
 
-            // dragging to the left
-	    for (int j = res; j < lastres; j++) {
-	      deleteChar(j,res,startseq);
-	      startres = res;
-	    }
-	    drawChars(startseq,startseq+1,res);
-	  }
-	}
-      }
-      lastres = res;
+        }
     }
 
+    endEdit = res;
+    lastres = res;
     repaint();
-    return;
   }
 
   public void drawChars(int seqstart, int seqend, int start) {
@@ -266,146 +350,324 @@ public class SeqPanel extends JPanel
 
   public void insertChar(int j, int seq)
   {
-    av.getAlignment().getSequenceAt(seq).insertCharAt(j, av.getGapCharacter().charAt(0));
-    updateConservation(seq);
+    av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());
+    seqEditOccurred=seq;
   }
 
-  public void deleteChar(int j, int res, int sno)
+  public void deleteChar(int j, int seq)
   {
+    av.alignment.getSequenceAt(seq).deleteCharAt(j);
+    seqEditOccurred=seq;
 
-    if (av.getAlignment().getSequenceAt(sno).getSequence().substring(j,j+1).equals(".") ||
-        av.getAlignment().getSequenceAt(sno).getSequence().substring(j,j+1).equals("-") ||
-        av.getAlignment().getSequenceAt(sno).getSequence().substring(j,j+1).equals(" ") )
+    av.alignment.getWidth();
+    repaint();
+  }
+
+
+  void editOccurred(int i)
+  {
+    if(endEdit==startEdit)
     {
-        av.getAlignment().getSequenceAt(sno).deleteCharAt(j);
+      ap.alignFrame.historyList.pop();
+      ap.alignFrame.updateEditMenuBar();
     }
-    updateConservation(sno);
-    av.getAlignment().getWidth();
+
+    av.updateConservation();
+    av.updateConsensus();
+
+    // Y O Y CLUSTALX
+    ColourSchemeI cs = av.getGlobalColourScheme();
+    if(cs instanceof ConservationColourScheme)
+    {
+      ConservationColourScheme ccs =  (ConservationColourScheme) cs;
+      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(cs instanceof ClustalxColourScheme)
+    {
+      ((ClustalxColourScheme)cs).resetClustalX(av.alignment.getSequences(),
+                                    av.alignment.getWidth());
+      av.setGlobalColourScheme(cs);
+    }
+
+  }
+
+//////////////////////////////////////////
+/////Everything below this is for defining the boundary of the rubberband
+//////////////////////////////////////////
+  int oldSeq = -1;
+  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(sequence==null || res>sequence.getLength())
+      return;
+
+    stretchGroup = av.getSelectionGroup();
+
+    if(stretchGroup == null)
+     {
+       stretchGroup = av.alignment.findGroup( sequence );
+       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;
+
+       SequenceGroup[] allGroups = av.alignment.findAllGroups( sequence );
+
+       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(stretchGroup==null)
+    {
+      // 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())
+        SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(), "Background");
+      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());
+
+    // edit the properties of existing group
+    }
+
+    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();
+
     repaint();
+
   }
 
+  boolean changeEndSeq = false;
+  boolean changeStartSeq = false;
+  boolean changeEndRes = false;
+  boolean changeStartRes = false;
+  SequenceGroup stretchGroup = null;
 
-  void updateConservation(int i)
+  public void doMouseReleasedDefineMode(MouseEvent evt)
   {
+    mouseDragging = false;
 
-    Alignment al = (Alignment) av.getAlignment();
-    SequenceGroup sg = av.alignment.findGroup( al.getSequenceAt(i));
-    if(sg==null || !(sg.cs instanceof ConservationColourScheme))
+    if(stretchGroup==null)
       return;
 
-    Conservation c = sg.getConservation();
+    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()) ;
+
+       repaint();
+    }
+    else
+        SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup.getName());
+
 
-    c = new Conservation("All", al.cons,
-                         ResidueProperties.propHash, 3, sg.sequences, 0,
-                         al.getWidth());
-    c.calculate();
-    c.verdict(false, 100);
-    sg.setConservation(c);
-    ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;
-    ccs.conserve = c;
+    changeEndRes = false;
+    changeStartRes = false;
+    stretchGroup = null;
+    ap.idPanel.repaint();
   }
 
 
-  public void setColourScheme(ColourSchemeI cs, boolean showConservation)
+  boolean remove = false;
+  public void doMouseDraggedDefineMode(MouseEvent evt)
   {
-    if (av.getSelection().size() == 0)
+    int res = evt.getX()/av.getCharWidth() + av.getStartRes();
+    int y = evt.getY()/av.getCharHeight() + av.getStartSeq();
+
+    if(stretchGroup==null)
+      return;
+
+    if(res>av.alignment.getWidth())
+      res = av.alignment.getWidth()-1;
+
+
+    if(stretchGroup.getEndRes()==res)
+      // Edit end res position of selected group
+      changeEndRes = true;
+
+    else if(stretchGroup.getStartRes()==res)
+      // Edit start res position of selected group
+      changeStartRes = true;
+
+
+    if(res<av.getStartRes())
+      res = av.getStartRes();
+    else if(res>av.getEndRes())
+      res = av.getEndRes();
+
+    if(changeEndRes)
     {
-      seqCanvas.cs = cs;
-      for (int i = 0; i < av.alignment.getGroups().size();i++)
-      {
-        SequenceGroup sg = (SequenceGroup)av.alignment.getGroups().elementAt(i);
-        sg.cs = cs;
-        if(!showConservation
-            && !(sg.cs instanceof Blosum62ColourScheme)
-            && sg.cs instanceof ConservationColourScheme)
-         {
-           // remove ConservationColouring from existing Conservation group
-           ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;
-           sg.cs = ccs.cs;
-         }
-         else if(showConservation && !(sg.cs instanceof ConservationColourScheme))
-         {
-           // add ConservationColouring to new group
-           Conservation c = sg.getConservation();
-           Alignment al = (Alignment) av.getAlignment();
-           c = new Conservation("All", al.cons,
-                                ResidueProperties.propHash, 3, sg.sequences, 0,
-                                al.getWidth() );
-           c.calculate();
-           c.verdict(false, 100);
-           sg.setConservation(c);
-           sg.cs = new ConservationColourScheme(sg);
-         }
-      }
+      if(res>stretchGroup.getStartRes()-1)
+        stretchGroup.setEndRes( res );
     }
-    else
+    else if(changeStartRes)
+    {
+      if(res<stretchGroup.getEndRes()+1)
+        stretchGroup.setStartRes( res );
+    }
+
+    int dragDirection = 0;
+    if (y > oldSeq)
+      dragDirection = 1;
+    else if (y < oldSeq)
+      dragDirection = -1;
+
+    while (y != oldSeq && oldSeq>0 && y<av.alignment.getHeight())
     {
-      SequenceGroup sg = av.alignment.findGroup((Sequence)av.sel.sequenceAt(0));
+      // This routine ensures we don't skip any sequences, as the
+      // selection is quite slow.
+      Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
 
-      if( isNewSelection(sg) )
+      oldSeq += dragDirection;
+      Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
+
+      if (stretchGroup.sequences.contains(nextSeq))
       {
-        sg = av.getAlignment().addGroup();
-        for (int i=0; i < av.getSelection().size(); i++)
-        {
-          av.alignment.removeFromGroup(av.alignment.findGroup( (Sequence) av.
-              sel.sequenceAt(i)),
-                                       (Sequence) av.sel.sequenceAt(i));
-          av.alignment.addToGroup(sg, (Sequence) av.sel.sequenceAt(i));
-        }
+        stretchGroup.deleteSequence(seq);
+        stretchGroup.deleteSequence(nextSeq);
+      }
+      else
+      {
+       if(seq!=null)
+        stretchGroup.addSequence(seq);
+        stretchGroup.addSequence(nextSeq);
       }
+    }
+    oldSeq = y;
+    mouseDragging = true;
+    if(scrollThread!=null)
+      scrollThread.setEvent(evt);
 
+    repaint();
+  }
 
-      sg.cs = cs;
+  public void doMouseEnteredDefineMode(MouseEvent e)
+  {
+    if (scrollThread != null)
+      scrollThread.running = false;
+  }
 
-      // Selection is made, we only want to change the conservationColour for selected group
-      if(  showConservation
-           && !(sg.cs instanceof ConservationColourScheme)
-           && !(sg.cs instanceof Blosum62ColourScheme))
-      {
-        Conservation c = sg.getConservation();
-        Alignment al = (Alignment) av.getAlignment();
+  public void doMouseExitedDefineMode(MouseEvent e)
+  {
+    if (av.getWrapAlignment())
+      return;
 
-        c = new Conservation("All", al.cons,
-                             ResidueProperties.propHash, 3, sg.sequences, 0,
-                             al.getWidth() );
-        c.calculate();
-        c.verdict(false, 100);
-        sg.setConservation(c);
-        sg.cs = new ConservationColourScheme(sg);
+    if(mouseDragging)
+      scrollThread = new ScrollThread();
+
+  }
+  // this class allows scrolling off the bottom of the visible alignment
+  class ScrollThread extends Thread
+  {
+    MouseEvent evt;
+    boolean running = false;
+    public ScrollThread()
+    {
+      start();
     }
-    else  if( !showConservation && sg.cs instanceof ConservationColourScheme)
+
+    public void setEvent(MouseEvent e)
     {
-      ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;
-      sg.cs = ccs.cs;
+      evt = e;
     }
 
+    public void stopScrolling()
+    {
+      running = false;
+    }
 
+    public void run()
+    {
+      running = true;
+      while (running)
+      {
+        if(evt!=null)
+        {
 
-   }
-   seqCanvas.paintFlag = true;
-   repaint();
-  }
+          if (mouseDragging && evt.getY() < 0 && av.getStartSeq() > 0)
+            running = ap.scrollUp(true);
 
-  boolean isNewSelection(SequenceGroup sg)
-  {
-    if(sg.getSize()!=av.getSelection().size())
-      return true;
+          if (mouseDragging && evt.getY() >= getHeight() &&
+              av.alignment.getHeight() > av.getEndSeq())
+            running = ap.scrollUp(false);
 
-    for(int i=0; i<sg.getSize(); i++)
-     if( !av.getSelection().contains( sg.getSequenceAt(i) ))
-       return true;
+          if (mouseDragging && evt.getX() < 0)
+            running = ap.scrollRight(true);
+
+          else if (mouseDragging && evt.getX() >= getWidth())
+            running = ap.scrollRight(false);
+        }
+
+        try
+        {
+          Thread.sleep(75);
+        }
+        catch (Exception ex)
+        {}
+      }
+    }
+}
 
-    return false;
-  }
 
 
-  public ColourSchemeI getColourScheme()
-  {
-    if(av.getSelection().size()>0)
-       return av.alignment.findGroup((Sequence)av.sel.sequenceAt(0)).cs;
-    else
-      return seqCanvas.cs;
-  }
 }