X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FSeqPanel.java;h=e29f4e15e4c22cf389f97f2a1b3ec8ffc959ae30;hb=9a23ee1cee6a2ef0f797fd8e1a6a950e66ef6e72;hp=3a707de53b16f72dd0293febcba007d6bf17462f;hpb=2ece3719ca3be664ef49768ff8334d1f257720f3;p=jalview.git

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 3a707de..e29f4e1 100755
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -1,22 +1,43 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+
 package jalview.appletgui;
 
+import java.util.*;
+
 import java.awt.*;
 import java.awt.event.*;
+
 import jalview.datamodel.*;
-import java.util.*;
 import jalview.schemes.*;
 
-
-public class SeqPanel extends Panel
+public class SeqPanel
+    extends Panel implements MouseMotionListener, MouseListener
 {
 
-  public    SeqCanvas         seqCanvas;
-  public    AlignmentPanel    ap;
+  public SeqCanvas seqCanvas;
+  public AlignmentPanel ap;
 
   protected int lastres;
   protected int startseq;
-  int startEdit=-1;
-  int endEdit=-1;
+  int startEdit = -1;
+  int endEdit = -1;
 
   protected AlignViewport av;
 
@@ -29,106 +50,140 @@ public class SeqPanel extends Panel
   boolean editingSeqs = false;
   boolean groupEditing = false;
 
+  public SeqPanel(AlignViewport avp, AlignmentPanel p)
+  {
+    this.av = avp;
 
-
-  public SeqPanel(AlignViewport avp, AlignmentPanel p) {
-    this.av         = avp;
-
-    seqCanvas  = new SeqCanvas(avp);
+    seqCanvas = new SeqCanvas(avp);
     setLayout(new BorderLayout());
     add(seqCanvas);
 
     ap = p;
 
-    seqCanvas.addMouseMotionListener( new MouseMotionAdapter()
-    {
-      public void mouseMoved(MouseEvent evt)
-      {
-       if(av.getWrapAlignment())
-         return;
-        doMouseMoved(evt);    }
+    seqCanvas.addMouseMotionListener(this);
+    seqCanvas.addMouseListener(this);
 
-      public void mouseDragged(MouseEvent evt)
-      {
-        if(av.getWrapAlignment())
-         return;
-        if( editingSeqs )
-          doMouseDragged(evt);
-        else
-          doMouseDraggedDefineMode(evt);
-      }
-    });
+    seqCanvas.repaint();
+  }
 
-    seqCanvas.addMouseListener( new MouseAdapter()
-    {
-      public void mouseReleased(MouseEvent evt)
-      {
-        if(av.getWrapAlignment())
-         return;
-        if(editingSeqs)
-          doMouseReleased(evt);
-        else
-          doMouseReleasedDefineMode(evt);
 
-      }
-      public void mousePressed(MouseEvent evt)
-      {
-        if(av.getWrapAlignment())
-         return;
-        if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
-        {
-          if(evt.isAltDown() || evt.isControlDown())
-            groupEditing = true;
+     public void mousePressed(MouseEvent evt)
+     {
+       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);
+         editingSeqs = true;
+         doMousePressed(evt);
+       }
+       else
+       {
+         doMousePressedDefineMode(evt);
+       }
+     }
 
-      }
-      public void mouseEntered(MouseEvent evt)
-      {
-        if (av.getWrapAlignment() || editingSeqs)
-          return;
-        doMouseEnteredDefineMode(evt);
-      }
+     public void mouseClicked(MouseEvent evt){}
 
-    });
-    seqCanvas.repaint();
-  }
 
+  public void mouseReleased(MouseEvent evt)
+  {
+    if (!editingSeqs)
+    {
+      doMouseReleasedDefineMode(evt);
+      return;
+    }
 
-  public void doMouseReleased(MouseEvent evt) {
 
-    if(seqEditOccurred>-1)
+    if (seqEditOccurred > -1)
+    {
       editOccurred(seqEditOccurred);
+    }
 
     startseq = -1;
-    lastres  = -1;
+    lastres = -1;
     seqEditOccurred = -1;
-    editingSeqs  = false;
+    editingSeqs = false;
     groupEditing = false;
     ap.repaint();
   }
 
-  public void doMousePressed(MouseEvent evt) {
-    ap.alignFrame.addHistoryItem( new HistoryItem(
-        "Edit Sequence",av.alignment, HistoryItem.EDIT));
-    int seq;
-    int res;
+  int startWrapBlock=-1;
+  int wrappedBlock=-1;
+  int findRes(MouseEvent evt)
+ {
+   int res = 0;
+   int x = evt.getX();
+
+  if (av.wrapAlignment)
+  {
+
+    int hgap = av.charHeight;
+    if (av.scaleAboveWrapped)
+      hgap += av.charHeight;
+
+    int cHeight = av.getAlignment().getHeight() * av.charHeight
+        + hgap + seqCanvas.getAnnotationHeight();
+
+      int y = evt.getY();
+      y -= hgap;
+      x -= seqCanvas.LABEL_WEST;
+
+
+      int cwidth = seqCanvas.getWrappedCanvasWidth(getSize().width);
 
-    int x = evt.getX();
-    int y = evt.getY();
+      wrappedBlock = y / cHeight;
+      wrappedBlock += av.getStartRes() / cwidth;
 
-    res = x/av.getCharWidth() + av.getStartRes();
-    seq = y/av.getCharHeight() + av.getStartSeq();
+      res = wrappedBlock * cwidth + x / av.getCharWidth();
+
+  }
+  else
+  {
+      res = (x / av.getCharWidth()) + av.getStartRes();
+  }
+
+  return res;
+
+ }
+
+ int findSeq(MouseEvent evt)
+ {
+
+   int seq = 0;
+   int y = evt.getY();
+
+   if (av.wrapAlignment)
+   {
+     int hgap = av.charHeight;
+     if (av.scaleAboveWrapped)
+       hgap += av.charHeight;
+
+     int cHeight = av.getAlignment().getHeight() * av.charHeight
+         + hgap + seqCanvas.getAnnotationHeight();
+
+       y -= hgap;
+
+     seq = ( (y % cHeight) / av.getCharHeight());
+   }
+   else
+   {
+     seq = (y / av.getCharHeight()) + av.getStartSeq();
+   }
+
+   return seq;
+ }
+
+
+  public void doMousePressed(MouseEvent evt)
+  {
+    ap.alignFrame.addHistoryItem(new HistoryItem(
+        "Edit Sequence", av.alignment, HistoryItem.EDIT));
+
+    int seq = findSeq(evt);
+    int res = findRes(evt);
 
     if (seq < av.getAlignment().getHeight() &&
         res < av.getAlignment().getSequenceAt(seq).getLength())
@@ -149,257 +204,285 @@ public class SeqPanel extends Panel
     return;
   }
 
-  public void doMouseMoved(MouseEvent evt)
+  public void mouseMoved(MouseEvent evt)
   {
-    int res=0, seq=0;
-    int x = evt.getX();
-    int y = evt.getY();
-    if(av.wrapAlignment)
-    {
-      y -= 2*av.charHeight;
-      int chunkHeight = (av.getAlignment().getHeight()+2)*av.charHeight;
+    int res = findRes(evt);
+    int seq = findSeq(evt);
 
+    if (seq >= av.getAlignment().getHeight() || seq<0 || res<0)
+    {
+      return;
+    }
 
-      res =   (int)((y/chunkHeight)*(getSize().width/av.charWidth)) +  x/av.getCharWidth() + av.getStartRes();
+    SequenceI sequence = av.getAlignment().getSequenceAt(seq);
+    if (res > sequence.getLength())
+    {
+      return;
+    }
 
-      y %= chunkHeight;
-      seq =     y / av.getCharHeight() + av.getStartSeq();
+    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
     {
-      res = x / av.getCharWidth()  + av.getStartRes();
-      seq = y / av.getCharHeight() + av.getStartSeq();
+      obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
+      if(obj!=null)
+        text.append("  Residue: ");
     }
 
+    if (obj != null)
+    {
 
-    if(seq>=av.getAlignment().getHeight())
-      return;
-
-    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();
+      if (obj != "")
+      {
+        text.append(obj + " (" +
+                    av.getAlignment().getSequenceAt(seq).findPosition(res) + ")");
+      }
+    }
 
-    StringBuffer text = new StringBuffer("Sequence " +(seq+1)+" ID: "+sequence.getName());
-    if(aa!="")
-      text.append("  Residue: "+aa+" ("+  av.getAlignment().getSequenceAt(seq).findPosition(res)+")");
+    if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence)
+    {
+      seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));
+    }
 
-    ap.alignFrame.statusBar.setText(text.toString());
 
     // use aa to see if the mouse pointer is on a
-    if(  av.showSequenceFeatures)
+    if (av.showSequenceFeatures
+        && sequence.getSequenceFeatures()!=null
+        && av.featuresDisplayed!=null)
     {
-      Vector features = sequence.getSequenceFeatures();
-      Enumeration e = features.elements();
-      StringBuffer sbuffer = new StringBuffer();
-
-
-      while (e.hasMoreElements())
+      int index = 0;
+      sequence.getSequenceFeatures();
+      boolean first = true;
+      while (index < sequence.getSequenceFeatures().length)
       {
-        SequenceFeature sf = (SequenceFeature) e.nextElement();
-        if (sf.getStart() <= sequence.findPosition(res) &&
+        SequenceFeature sf = sequence.getSequenceFeatures()[index];
+        if (sf.getBegin() <= 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()+")");
+          if(!av.featuresDisplayed.containsKey(sf.getType()))
+           {
+             index++;
+             continue;
+           }
+
+          if(first)
+          {
+            text.append(" Sequence Feature:");
+            first = false;
+          }
+
+          text.append(" "+sf.getType());
+
+          if(sf.getDescription()!=null)
+            text.append(" "+sf.getDescription());
+
+          if (sf.getStatus()!=null && sf.getStatus().length() > 0)
+          {
+            text.append(" (" + sf.getStatus() + ")");
+          }
+          text.append("; ");
         }
 
+        index++;
+
       }
     }
 
+     ap.alignFrame.statusBar.setText(text.toString());
 
   }
 
-  public void doMouseDragged(MouseEvent evt) {
+  public void mouseDragged(MouseEvent evt)
+  {
+    if (!editingSeqs)
+    {
+      doMouseDraggedDefineMode(evt);
+      return;
+    }
 
-      // If we're dragging we're editing
-      int res = evt.getX() / av.getCharWidth() + av.getStartRes();
-      if (res < 0)
-        res = 0;
+    // If we're dragging we're editing
+    int res = findRes(evt);
+    if (res < 0)
+    {
+      res = 0;
+    }
 
-      if (lastres == -1 || lastres == res)
-        return;
+    if (lastres == -1 || lastres == res)
+    {
+      return;
+    }
 
-      boolean dragRight = true;
-      if (res < av.getAlignment().getWidth() && res < lastres)
-        dragRight = false;
+    boolean dragRight = true;
+    if (res < av.getAlignment().getWidth() && res < lastres)
+    {
+      dragRight = false;
+    }
 
+    if (res != lastres)
+    {
+      // Group editing
+      if (groupEditing)
+      {
+        SequenceGroup sg = av.getSelectionGroup();
+        if (sg == null)
+        {
+          lastres = -1;
+          return;
+        }
 
-      if (res != lastres)
-     {
-         // Group editing
-         if (groupEditing)
-         {
-           SequenceGroup sg = av.getSelectionGroup();
-           if(sg==null)
-           {
-             lastres=-1;
-             return;
-           }
+        // drag to right
+        if (dragRight)
+        {
+          sg.setEndRes(sg.getEndRes() + (res - lastres));
+        }
 
-             // drag to right
-             if(dragRight)
-                 sg.setEndRes(sg.getEndRes() + (res-lastres));
-
-             // drag to left
-             else
-             {
-                /// Are we able to delete?
-                // ie are all columns blank?
-                boolean deleteAllowed = false;
-               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;
-                 return;
-               }
-
-               sg.setEndRes(sg.getEndRes() - (lastres-res));
-             }
-
-
-             for (int i = 0; i < sg.getSize(); i++)
-             {
-               SequenceI s = sg.getSequenceAt(i);
-               int k = av.alignment.findIndex(s);
-
-               // drag to right
-               if (dragRight)
-                 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);
-                 }
-               }
-             }
-         }
-         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);
-           }
-           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, startseq);
-               else
-               {
-
-                 break;
-               }
-             }
-           }
+        // drag to left
+        else
+        {
+          /// Are we able to delete?
+          // ie are all columns blank?
+          boolean deleteAllowed = false;
+          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;
+            return;
+          }
+
+          sg.setEndRes(sg.getEndRes() - (lastres - res));
+        }
 
-         }
-     }
+        for (int i = 0; i < sg.getSize(); i++)
+        {
+          SequenceI s = sg.getSequenceAt(i);
+          int k = av.alignment.findIndex(s);
+
+          // drag to right
+          if (dragRight)
+          {
+            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);
+              }
+            }
+          }
+        }
+      }
+      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);
+          }
+        }
+        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, startseq);
+            }
+            else
+            {
+              if(scrollThread!=null)
+              {
+                scrollThread.running = false;
+                scrollThread = null;
+              }
+              break;
+            }
+          }
+        }
 
-     endEdit = res;
-     lastres = res;
-      seqCanvas.repaint();
-  }
+      }
+    }
+
+    mouseDragging = true;
+    if (res > av.endRes || res < av.startRes)
+    {
+      mouseExited(evt);
+    }
+
+    if (scrollThread != null)
+      scrollThread.setEvent(evt);
 
-  public void drawChars(int seqstart, int seqend, int start) {
-    seqCanvas.drawPanel(seqCanvas.gg, start,av.getEndRes(),seqstart,seqend,av.getStartRes(),av.getStartSeq(),0);
+
+    endEdit = res;
+    lastres = res;
     seqCanvas.repaint();
   }
 
   public void insertChar(int j, int seq)
   {
     av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());
-    seqEditOccurred=seq;
+    seqEditOccurred = seq;
   }
 
   public void deleteChar(int j, int seq)
   {
 
     av.alignment.getSequenceAt(seq).deleteCharAt(j);
-    seqEditOccurred=seq;
+    seqEditOccurred = seq;
     av.alignment.getWidth();
     repaint();
   }
 
-
   void editOccurred(int i)
   {
-    if(endEdit==startEdit)
-    {
-      ap.alignFrame.historyList.pop();
-      ap.alignFrame.updateEditMenuBar();
-    }
-
-    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)
-     {
-        jalview.analysis.Conservation c = new jalview.analysis.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)
+    if (endEdit == startEdit)
     {
-      ((ClustalxColourScheme)cs).resetClustalX(av.alignment.getSequences(),
-                                    av.alignment.getWidth());
-      av.setGlobalColourScheme(cs);
+        ap.alignFrame.historyList.pop();
+        ap.alignFrame.updateEditMenuBar();
     }
 
-
+    av.firePropertyChange("alignment", null,av.getAlignment().getSequences());
   }
 
 //////////////////////////////////////////
@@ -408,78 +491,109 @@ public class SeqPanel extends Panel
   int oldSeq = -1;
   public void doMousePressedDefineMode(MouseEvent evt)
   {
-    int res = evt.getX()/av.getCharWidth() + av.getStartRes();
-    int seq = evt.getY()/av.getCharHeight() + av.getStartSeq();
+    if (scrollThread != null)
+    {
+      scrollThread.running = false;
+      scrollThread = null;
+    }
+
+    int res = findRes(evt);
+    int seq = findSeq(evt);
     oldSeq = seq;
+    startWrapBlock=wrappedBlock;
+
+    if(seq==-1)
+      return;
 
     SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
 
-    if(sequence==null || res>sequence.getLength())
+    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;
-     }
+    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;
+    else if (!stretchGroup.sequences.contains(sequence)
+             || stretchGroup.getStartRes() > res
+             || stretchGroup.getEndRes() < res)
+    {
+      stretchGroup = null;
 
-       SequenceGroup[] allGroups = av.alignment.findAllGroups( sequence );
+      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 (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)
+    if (stretchGroup == null)
     {
       // define a new group here
       SequenceGroup sg = new SequenceGroup();
       sg.setStartRes(res);
       sg.setEndRes(res);
-      sg.addSequence( sequence );
-      av.setSelectionGroup( sg );
+      sg.addSequence(sequence, false);
+      av.setSelectionGroup(sg);
       stretchGroup = sg;
 
-      if(av.getConservationSelected())
-        SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(), "Background");
-      if(av.getAbovePIDThreshold())
-        SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(), "Background");
+      if (av.getConservationSelected())
+      {
+        SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(),
+                                          "Background");
+      }
+      if (av.getAbovePIDThreshold())
+      {
+        SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
+                                       "Background");
+      }
 
     }
 
     // DETECT RIGHT MOUSE BUTTON IN AWT
-    else if( ( evt.getModifiers() & InputEvent .BUTTON3_MASK ) == InputEvent.BUTTON3_MASK )
+    else if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK) ==
+             InputEvent.BUTTON3_MASK)
     {
-      APopupMenu popup = new APopupMenu(ap, null);
+      APopupMenu popup = new APopupMenu(ap, null, null);
       this.add(popup);
       popup.show(this, evt.getX(), evt.getY());
     }
 
-
-    if(stretchGroup!=null && stretchGroup.getEndRes()==res)
+    if (stretchGroup != null && stretchGroup.getEndRes() == res)
+    {
       // Edit end res position of selected group
       changeEndRes = true;
+    }
 
-   else if(stretchGroup!=null && stretchGroup.getStartRes()==res)
+    else if (stretchGroup != null && stretchGroup.getStartRes() == res)
+    {
       // Edit end res position of selected group
       changeStartRes = true;
+    }
 
   }
 
@@ -491,132 +605,180 @@ public class SeqPanel extends Panel
 
   public void doMouseReleasedDefineMode(MouseEvent evt)
   {
-    mouseDragging = false;
-
-    if(stretchGroup==null)
-      return;
-
-    if(stretchGroup.cs instanceof ClustalxColourScheme)
+    if (stretchGroup == null)
     {
-      stretchGroup.cs = new ClustalxColourScheme(stretchGroup.sequences, av.alignment.getWidth());
-      seqCanvas.repaint();
+        return;
     }
 
-    else if(stretchGroup.cs instanceof ConservationColourScheme)
-    {
-       ConservationColourScheme ccs = (ConservationColourScheme)stretchGroup.cs;
-       stretchGroup.cs = ccs;
-       SliderPanel.setConservationSlider(ap, stretchGroup.cs, stretchGroup.getName()) ;
-
-       seqCanvas.repaint();
-    }
-    else
+    if(stretchGroup.cs!=null)
     {
-      if(stretchGroup.cs !=null)
+      if (stretchGroup.cs instanceof ClustalxColourScheme)
       {
-        SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup.getName());
+        ( (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);
     ap.repaint();
   }
 
-
-  boolean remove = false;
   public void doMouseDraggedDefineMode(MouseEvent evt)
   {
-    int res = evt.getX()/av.getCharWidth() + av.getStartRes();
-    int y = evt.getY()/av.getCharHeight() + av.getStartSeq();
+    int res = findRes(evt);
+    int y = findSeq(evt);
 
-    if(stretchGroup==null)
+    if(wrappedBlock!=startWrapBlock)
       return;
 
-    if(res>av.alignment.getWidth())
-      res = av.alignment.getWidth()-1;
+     if (stretchGroup == null)
+     {
+          return;
+     }
 
+     mouseDragging = true;
 
-    if(stretchGroup.getEndRes()==res)
-      // Edit end res position of selected group
-      changeEndRes = true;
 
-    else if(stretchGroup.getStartRes()==res)
-      // Edit start res position of selected group
-      changeStartRes = true;
+      if(y > av.alignment.getHeight())
+      {
+        y = av.alignment.getHeight() -1;
+      }
 
+      if(res>av.alignment.getWidth())
+        res = av.alignment.getWidth()-1;
 
-    if(res<av.getStartRes())
-      res = av.getStartRes();
-    else if(res>av.getEndRes())
-      res = av.getEndRes();
+      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(changeEndRes)
-    {
-      if(res>stretchGroup.getStartRes()-1)
-        stretchGroup.setEndRes( res );
-    }
-    else if(changeStartRes)
-    {
-      if(res<stretchGroup.getEndRes()+1)
-        stretchGroup.setStartRes( res );
-    }
+      if (res < 0)
+      {
+          res = 0;
+      }
 
-    int dragDirection = 0;
-    if (y > oldSeq)
-      dragDirection = 1;
-    else if (y < oldSeq)
-      dragDirection = -1;
+      if (changeEndRes)
+      {
+          if (res > (stretchGroup.getStartRes() - 1))
+          {
+              stretchGroup.setEndRes(res);
+          }
+      }
+      else if (changeStartRes)
+      {
+          if (res < (stretchGroup.getEndRes() + 1))
+          {
+              stretchGroup.setStartRes(res);
+          }
+      }
 
-    while (y != oldSeq && oldSeq>0 && y<av.alignment.getHeight())
-    {
-      // This routine ensures we don't skip any sequences, as the
-      // selection is quite slow.
-      Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
+      int dragDirection = 0;
+
+      if (y > oldSeq)
+      {
+          dragDirection = 1;
+      }
+      else if (y < oldSeq)
+      {
+          dragDirection = -1;
+      }
 
-      oldSeq += dragDirection;
-      Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
 
-      if (stretchGroup.sequences.contains(nextSeq))
+      while ((y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))
       {
-        stretchGroup.deleteSequence(seq);
-        stretchGroup.deleteSequence(nextSeq);
+          // This routine ensures we don't skip any sequences, as the
+          // selection is quite slow.
+          Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
+
+          oldSeq += dragDirection;
+
+          if(oldSeq<0)
+            break;
+
+          Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
+
+          if (stretchGroup.sequences.contains(nextSeq))
+          {
+              stretchGroup.deleteSequence(seq, false);
+          }
+          else
+          {
+              if (seq != null)
+              {
+                  stretchGroup.addSequence(seq, false);
+              }
+
+              stretchGroup.addSequence(nextSeq, false);
+          }
       }
-      else
+
+      if(oldSeq < 0)
+        oldSeq = -1;
+
+
+      if(res>av.endRes || res<av.startRes
+          || y<av.startSeq || y>av.endSeq)
       {
-       if(seq!=null)
-        stretchGroup.addSequence(seq);
-        stretchGroup.addSequence(nextSeq);
+        mouseExited(evt);
       }
+
+      if (scrollThread != null)
+      {
+        scrollThread.setEvent(evt);
+      }
+
+      seqCanvas.repaint();
     }
-    oldSeq = y;
-    mouseDragging = true;
-    if(scrollThread!=null)
-      scrollThread.setEvent(evt);
 
-    seqCanvas.repaint();
-  }
+    public void mouseEntered(MouseEvent e)
+    {
+      if (oldSeq < 0)
+        oldSeq = 0;
 
-  public void doMouseEnteredDefineMode(MouseEvent e)
-  {
-    if (scrollThread != null)
-      scrollThread.running = false;
-  }
+      if (scrollThread != null)
+      {
+        scrollThread.running = false;
+        scrollThread = null;
+      }
+    }
 
-  public void doMouseExitedDefineMode(MouseEvent e)
+  public void mouseExited(MouseEvent e)
   {
     if (av.getWrapAlignment())
+    {
       return;
+    }
 
-    if(mouseDragging)
+    if (mouseDragging && scrollThread==null)
+    {
       scrollThread = new ScrollThread();
-
+    }
   }
+
   // this class allows scrolling off the bottom of the visible alignment
-  class ScrollThread extends Thread
+  class ScrollThread
+      extends Thread
   {
     MouseEvent evt;
     boolean running = false;
@@ -640,21 +802,30 @@ public class SeqPanel extends Panel
       running = true;
       while (running)
       {
-        if(evt!=null)
+
+        if (evt != null)
         {
 
           if (mouseDragging && evt.getY() < 0 && av.getStartSeq() > 0)
+          {
             running = ap.scrollUp(true);
+          }
 
           if (mouseDragging && evt.getY() >= getSize().height &&
               av.alignment.getHeight() > av.getEndSeq())
+          {
             running = ap.scrollUp(false);
+          }
 
           if (mouseDragging && evt.getX() < 0)
+          {
             running = ap.scrollRight(true);
+          }
 
           else if (mouseDragging && evt.getX() >= getSize().width)
+          {
             running = ap.scrollRight(false);
+          }
         }
 
         try
@@ -665,12 +836,6 @@ public class SeqPanel extends Panel
         {}
       }
     }
-}
-
-
+  }
 
 }
-
-
-
-