Scroll implemented for applet editing
[jalview.git] / src / jalview / appletgui / SeqPanel.java
index 6e4a34f..e29f4e1 100755 (executable)
@@ -1,24 +1,43 @@
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
+ */\r
+\r
 package jalview.appletgui;\r
 \r
+import java.util.*;\r
+\r
 import java.awt.*;\r
 import java.awt.event.*;\r
+\r
 import jalview.datamodel.*;\r
-import java.util.*;\r
 import jalview.schemes.*;\r
 \r
-\r
-public class SeqPanel extends Panel\r
+public class SeqPanel\r
+    extends Panel implements MouseMotionListener, MouseListener\r
 {\r
 \r
-  public    SeqCanvas         seqCanvas;\r
-  public    AlignmentPanel    ap;\r
+  public SeqCanvas seqCanvas;\r
+  public AlignmentPanel ap;\r
 \r
-  protected int startres;\r
   protected int lastres;\r
-  protected int endres;\r
-\r
   protected int startseq;\r
-  protected int padseq;\r
+  int startEdit = -1;\r
+  int endEdit = -1;\r
 \r
   protected AlignViewport av;\r
 \r
@@ -28,105 +47,143 @@ public class SeqPanel extends Panel
   ScrollThread scrollThread = null;\r
   boolean mouseDragging = false;\r
 \r
+  boolean editingSeqs = false;\r
+  boolean groupEditing = false;\r
 \r
-  public SeqPanel(AlignViewport avp, AlignmentPanel p) {\r
-    this.av         = avp;\r
+  public SeqPanel(AlignViewport avp, AlignmentPanel p)\r
+  {\r
+    this.av = avp;\r
 \r
-    seqCanvas  = new SeqCanvas(avp);\r
+    seqCanvas = new SeqCanvas(avp);\r
     setLayout(new BorderLayout());\r
     add(seqCanvas);\r
 \r
     ap = p;\r
 \r
-    seqCanvas.addMouseMotionListener( new MouseMotionAdapter()\r
-    {\r
-      public void mouseMoved(MouseEvent evt)\r
-      {\r
-       if(av.getWrapAlignment())\r
-         return;\r
-        doMouseMoved(evt);    }\r
+    seqCanvas.addMouseMotionListener(this);\r
+    seqCanvas.addMouseListener(this);\r
 \r
-      public void mouseDragged(MouseEvent evt)\r
-      {\r
-        if(av.getWrapAlignment())\r
-         return;\r
-        if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())\r
-          doMouseDragged(evt);\r
-        else\r
-          doMouseDraggedDefineMode(evt);\r
-      }\r
-    });\r
+    seqCanvas.repaint();\r
+  }\r
+\r
+\r
+     public void mousePressed(MouseEvent evt)\r
+     {\r
+       if (evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())\r
+       {\r
+         if (evt.isAltDown() || evt.isControlDown())\r
+         {\r
+           groupEditing = true;\r
+         }\r
+\r
+         editingSeqs = true;\r
+         doMousePressed(evt);\r
+       }\r
+       else\r
+       {\r
+         doMousePressedDefineMode(evt);\r
+       }\r
+     }\r
 \r
-    seqCanvas.addMouseListener( new MouseAdapter()\r
+     public void mouseClicked(MouseEvent evt){}\r
+\r
+\r
+  public void mouseReleased(MouseEvent evt)\r
+  {\r
+    if (!editingSeqs)\r
     {\r
-      public void mouseReleased(MouseEvent evt)\r
-      {\r
-        if(av.getWrapAlignment())\r
-         return;\r
-        if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())\r
-          doMouseReleased(evt);\r
-        else\r
-          doMouseReleasedDefineMode(evt);\r
-      }\r
-      public void mousePressed(MouseEvent evt)\r
-      {\r
-        if(av.getWrapAlignment())\r
-         return;\r
-        if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())\r
-          doMousePressed(evt);\r
-        else\r
-          doMousePressedDefineMode(evt);\r
-      }\r
-      public void mouseExited(MouseEvent evt)\r
-      {\r
-        if (av.getWrapAlignment() || evt.isShiftDown() || evt.isAltDown() ||\r
-                  evt.isControlDown())\r
-                return;\r
-              doMouseExitedDefineMode(evt);\r
+      doMouseReleasedDefineMode(evt);\r
+      return;\r
+    }\r
 \r
-      }\r
-      public void mouseEntered(MouseEvent evt)\r
-      {\r
-        if (av.getWrapAlignment() || evt.isShiftDown() || evt.isAltDown() ||\r
-            evt.isControlDown())\r
-          return;\r
-        doMouseEnteredDefineMode(evt);\r
-      }\r
 \r
-    });\r
-    seqCanvas.repaint();\r
+    if (seqEditOccurred > -1)\r
+    {\r
+      editOccurred(seqEditOccurred);\r
+    }\r
+\r
+    startseq = -1;\r
+    lastres = -1;\r
+    seqEditOccurred = -1;\r
+    editingSeqs = false;\r
+    groupEditing = false;\r
+    ap.repaint();\r
   }\r
 \r
+  int startWrapBlock=-1;\r
+  int wrappedBlock=-1;\r
+  int findRes(MouseEvent evt)\r
+ {\r
+   int res = 0;\r
+   int x = evt.getX();\r
 \r
-  public void doMouseReleased(MouseEvent evt) {\r
+  if (av.wrapAlignment)\r
+  {\r
 \r
-    int x = evt.getX();\r
-    int res = x/av.getCharWidth() + av.getStartRes();\r
+    int hgap = av.charHeight;\r
+    if (av.scaleAboveWrapped)\r
+      hgap += av.charHeight;\r
 \r
-    endres = res;\r
+    int cHeight = av.getAlignment().getHeight() * av.charHeight\r
+        + hgap + seqCanvas.getAnnotationHeight();\r
 \r
-    startseq = -1;\r
-    startres = -1;\r
-    lastres  = -1;\r
-    if(seqEditOccurred>-1)\r
-      updateConservation(seqEditOccurred);\r
+      int y = evt.getY();\r
+      y -= hgap;\r
+      x -= seqCanvas.LABEL_WEST;\r
 \r
-    seqEditOccurred = -1;\r
 \r
-    ap.repaint();\r
+      int cwidth = seqCanvas.getWrappedCanvasWidth(getSize().width);\r
+\r
+      wrappedBlock = y / cHeight;\r
+      wrappedBlock += av.getStartRes() / cwidth;\r
 \r
+      res = wrappedBlock * cwidth + x / av.getCharWidth();\r
+\r
+  }\r
+  else\r
+  {\r
+      res = (x / av.getCharWidth()) + av.getStartRes();\r
   }\r
 \r
-  public void doMousePressed(MouseEvent evt) {\r
-    ap.alignFrame.addHistoryItem("sequence edit");\r
-    int seq;\r
-    int res;\r
+  return res;\r
+\r
+ }\r
+\r
+ int findSeq(MouseEvent evt)\r
+ {\r
+\r
+   int seq = 0;\r
+   int y = evt.getY();\r
+\r
+   if (av.wrapAlignment)\r
+   {\r
+     int hgap = av.charHeight;\r
+     if (av.scaleAboveWrapped)\r
+       hgap += av.charHeight;\r
 \r
-    int x = evt.getX();\r
-    int y = evt.getY();\r
+     int cHeight = av.getAlignment().getHeight() * av.charHeight\r
+         + hgap + seqCanvas.getAnnotationHeight();\r
 \r
-    res = x/av.getCharWidth() + av.getStartRes();\r
-    seq = y/av.getCharHeight() + av.getStartSeq();\r
+       y -= hgap;\r
+\r
+     seq = ( (y % cHeight) / av.getCharHeight());\r
+   }\r
+   else\r
+   {\r
+     seq = (y / av.getCharHeight()) + av.getStartSeq();\r
+   }\r
+\r
+   return seq;\r
+ }\r
+\r
+\r
+  public void doMousePressed(MouseEvent evt)\r
+  {\r
+    ap.alignFrame.addHistoryItem(new HistoryItem(\r
+        "Edit Sequence", av.alignment, HistoryItem.EDIT));\r
+\r
+    int seq = findSeq(evt);\r
+    int res = findRes(evt);\r
 \r
     if (seq < av.getAlignment().getHeight() &&\r
         res < av.getAlignment().getSequenceAt(seq).getLength())\r
@@ -136,235 +193,296 @@ public class SeqPanel extends Panel
       // in the alignment\r
 \r
       startseq = seq;\r
-\r
-      if (startseq == (av.getAlignment().getHeight() - 1))\r
-        padseq = 1;\r
-      else\r
-        padseq = 1;\r
-\r
-      startres = res;\r
       lastres = res;\r
-\r
     }\r
     else\r
     {\r
       startseq = -1;\r
-      startres = -1;\r
       lastres = -1;\r
     }\r
 \r
     return;\r
   }\r
 \r
-  public void doMouseMoved(MouseEvent evt)\r
+  public void mouseMoved(MouseEvent evt)\r
   {\r
-    int res=0, seq=0;\r
-    int x = evt.getX();\r
-    int y = evt.getY();\r
-    if(av.wrapAlignment)\r
-    {\r
-      y -= 2*av.charHeight;\r
-      int chunkHeight = (av.getAlignment().getHeight()+2)*av.charHeight;\r
+    int res = findRes(evt);\r
+    int seq = findSeq(evt);\r
 \r
+    if (seq >= av.getAlignment().getHeight() || seq<0 || res<0)\r
+    {\r
+      return;\r
+    }\r
 \r
-      res =   (int)((y/chunkHeight)*(getSize().width/av.charWidth)) +  x/av.getCharWidth() + av.getStartRes();\r
+    SequenceI sequence = av.getAlignment().getSequenceAt(seq);\r
+    if (res > sequence.getLength())\r
+    {\r
+      return;\r
+    }\r
 \r
-      y %= chunkHeight;\r
-      seq =     y / av.getCharHeight() + av.getStartSeq();\r
+    StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +\r
+            sequence.getName());\r
 \r
+    Object obj = null;\r
+    if (av.alignment.isNucleotide())\r
+    {\r
+      obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +\r
+          "");\r
+      if(obj!=null)\r
+        text.append(" Nucleotide: ");\r
     }\r
     else\r
     {\r
-      res = x / av.getCharWidth()  + av.getStartRes();\r
-      seq = y / av.getCharHeight() + av.getStartSeq();\r
+      obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");\r
+      if(obj!=null)\r
+        text.append("  Residue: ");\r
     }\r
 \r
+    if (obj != null)\r
+    {\r
 \r
-    if(seq>=av.getAlignment().getHeight())\r
-      return;\r
-\r
-    SequenceI sequence = av.getAlignment().getSequenceAt(seq);\r
-    if(res>sequence.getLength())\r
-      return;\r
-\r
-    Object obj = ResidueProperties.aa2Triplet.get( sequence.getCharAt(res)+"" ) ;\r
-    String aa = "";\r
-    if(obj!=null)\r
-         aa = obj.toString();\r
+      if (obj != "")\r
+      {\r
+        text.append(obj + " (" +\r
+                    av.getAlignment().getSequenceAt(seq).findPosition(res) + ")");\r
+      }\r
+    }\r
 \r
-    StringBuffer text = new StringBuffer("Sequence " +(seq+1)+" ID: "+sequence.getName());\r
-    if(aa!="")\r
-      text.append("  Residue: "+aa+" ("+  av.getAlignment().getSequenceAt(seq).findPosition(res)+")");\r
+    if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence)\r
+    {\r
+      seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));\r
+    }\r
 \r
-    ap.alignFrame.statusBar.setText(text.toString());\r
 \r
     // use aa to see if the mouse pointer is on a\r
-    if(  av.showSequenceFeatures)\r
+    if (av.showSequenceFeatures\r
+        && sequence.getSequenceFeatures()!=null\r
+        && av.featuresDisplayed!=null)\r
     {\r
-      Vector features = sequence.getSequenceFeatures();\r
-      Enumeration e = features.elements();\r
-      StringBuffer sbuffer = new StringBuffer();\r
-\r
-\r
-      while (e.hasMoreElements())\r
+      int index = 0;\r
+      sequence.getSequenceFeatures();\r
+      boolean first = true;\r
+      while (index < sequence.getSequenceFeatures().length)\r
       {\r
-        SequenceFeature sf = (SequenceFeature) e.nextElement();\r
-        if (sf.getStart() <= sequence.findPosition(res) &&\r
+        SequenceFeature sf = sequence.getSequenceFeatures()[index];\r
+        if (sf.getBegin() <= sequence.findPosition(res) &&\r
             sf.getEnd() >= sequence.findPosition(res))\r
         {\r
-          if(sbuffer.length()>0)\r
-            sbuffer.append("; ");\r
-          sbuffer.append(sf.getType() + " " + sf.getDescription());\r
-          if(sf.getStatus().length()>0)\r
-            sbuffer.append(" ("+sf.getStatus()+")");\r
+          if(!av.featuresDisplayed.containsKey(sf.getType()))\r
+           {\r
+             index++;\r
+             continue;\r
+           }\r
+\r
+          if(first)\r
+          {\r
+            text.append(" Sequence Feature:");\r
+            first = false;\r
+          }\r
+\r
+          text.append(" "+sf.getType());\r
+\r
+          if(sf.getDescription()!=null)\r
+            text.append(" "+sf.getDescription());\r
+\r
+          if (sf.getStatus()!=null && sf.getStatus().length() > 0)\r
+          {\r
+            text.append(" (" + sf.getStatus() + ")");\r
+          }\r
+          text.append("; ");\r
         }\r
 \r
+        index++;\r
+\r
       }\r
     }\r
 \r
+     ap.alignFrame.statusBar.setText(text.toString());\r
 \r
   }\r
 \r
-  public void doMouseDragged(MouseEvent evt) {\r
-    // If we're dragging we're editing\r
-\r
-    if(lastres==-1)\r
+  public void mouseDragged(MouseEvent evt)\r
+  {\r
+    if (!editingSeqs)\r
+    {\r
+      doMouseDraggedDefineMode(evt);\r
       return;\r
+    }\r
 \r
-    int x = evt.getX();\r
-\r
-    int res = x/av.getCharWidth() + av.getStartRes();\r
+    // If we're dragging we're editing\r
+    int res = findRes(evt);\r
     if (res < 0)\r
+    {\r
       res = 0;\r
+    }\r
+\r
+    if (lastres == -1 || lastres == res)\r
+    {\r
+      return;\r
+    }\r
+\r
+    boolean dragRight = true;\r
+    if (res < av.getAlignment().getWidth() && res < lastres)\r
+    {\r
+      dragRight = false;\r
+    }\r
 \r
     if (res != lastres)\r
     {\r
-       // Group editing\r
-       if (evt.isAltDown() || evt.isControlDown())\r
+      // Group editing\r
+      if (groupEditing)\r
+      {\r
+        SequenceGroup sg = av.getSelectionGroup();\r
+        if (sg == null)\r
+        {\r
+          lastres = -1;\r
+          return;\r
+        }\r
+\r
+        // drag to right\r
+        if (dragRight)\r
         {\r
-         SequenceGroup sg = av.getSelectionGroup();\r
-          if(sg==null)\r
-            av.getAlignment().findGroup(startseq);\r
-          if (sg != null)\r
+          sg.setEndRes(sg.getEndRes() + (res - lastres));\r
+        }\r
+\r
+        // drag to left\r
+        else\r
+        {\r
+          /// Are we able to delete?\r
+          // ie are all columns blank?\r
+          boolean deleteAllowed = false;\r
+          for (int s = 0; s < sg.getSize(); s++)\r
           {\r
-            boolean deleteAllowed = false;\r
-            if (res < av.getAlignment().getWidth() && res < lastres)\r
+            SequenceI seq = sg.getSequenceAt(s);\r
+            for (int j = res; j < lastres; j++)\r
             {\r
-              /// Are we able to delete?\r
-              boolean allGaps = true;\r
-              for (int i = 0; i < sg.getSize(); i++)\r
+              if (seq.getSequence().length() <= j)\r
               {\r
-                SequenceI s = sg.getSequenceAt(i);\r
-                for (int j = lastres-1; j >= res && allGaps; j--)\r
-                {\r
-                    if (!jalview.util.Comparison.isGap(s.getSequence().charAt(j)))\r
-                    {\r
-                      res = j + 1;\r
-                      allGaps = false;\r
-                    }\r
-                }\r
-\r
-                if(!deleteAllowed && allGaps)\r
-                  deleteAllowed = true;\r
+                continue;\r
               }\r
-            }\r
-\r
-            // drag to right\r
-            if (res < av.getAlignment().getWidth() && res > lastres)\r
-                sg.setEndRes(sg.getEndRes() + 1);\r
 \r
-            // drag to left\r
-            else if (deleteAllowed && res < av.getAlignment().getWidth() &&\r
-                     res < lastres)\r
-                sg.setEndRes(sg.getEndRes() - 1);\r
+              if (!jalview.util.Comparison.isGap(seq.getSequence().charAt(j)))\r
+              {\r
+                // Not a gap, block edit not valid\r
+                res = j + 1;\r
+                deleteAllowed = false;\r
+                continue;\r
+              }\r
+              deleteAllowed = true;\r
+            }\r
+          }\r
 \r
+          if (!deleteAllowed)\r
+          {\r
+            lastres = -1;\r
+            return;\r
+          }\r
 \r
+          sg.setEndRes(sg.getEndRes() - (lastres - res));\r
+        }\r
 \r
+        for (int i = 0; i < sg.getSize(); i++)\r
+        {\r
+          SequenceI s = sg.getSequenceAt(i);\r
+          int k = av.alignment.findIndex(s);\r
 \r
-            for (int i = 0; i < sg.getSize(); i++)\r
+          // drag to right\r
+          if (dragRight)\r
+          {\r
+            for (int j = lastres; j < res; j++)\r
             {\r
-              SequenceI s = sg.getSequenceAt(i);\r
-              int k = av.alignment.findIndex(s);\r
-\r
-              // drag to right\r
-              if (res < av.getAlignment().getWidth() && res > lastres)\r
-                for (int j = lastres; j < res; j++)\r
-                  insertChar(j, k);\r
+              insertChar(j, k);\r
+            }\r
+          }\r
 \r
-              // drag to left\r
-              else if (deleteAllowed && res < av.getAlignment().getWidth() && res < lastres)\r
+          // drag to left\r
+          else\r
+          {\r
+            for (int j = res; j < lastres; j++)\r
+            {\r
+              if (s.getLength() > j)\r
               {\r
-                for (int j = res; j < lastres; j++)\r
-                {\r
-                  deleteChar(j, k);\r
-                  startres = res;\r
-                }\r
+                deleteChar(res, k);\r
               }\r
             }\r
           }\r
         }\r
-        else /////Editing a single sequence///////////\r
+      }\r
+      else /////Editing a single sequence///////////\r
+      {\r
+        if (res < av.getAlignment().getWidth() && res > lastres)\r
         {\r
-          if (res < av.getAlignment().getWidth() && res > lastres)\r
+          // dragging to the right\r
+          for (int j = lastres; j < res; j++)\r
           {\r
-            // dragging to the right\r
-            for (int j = lastres; j < res; j++)\r
-              insertChar(j, startseq);\r
+            insertChar(j, startseq);\r
           }\r
-          else if (res < av.getAlignment().getWidth() && res < lastres)\r
+        }\r
+        else if (res < av.getAlignment().getWidth() && res < lastres)\r
+        {\r
+          // dragging to the left\r
+          for (int j = lastres; j > res; j--)\r
           {\r
-            // dragging to the left\r
-            for (int j = res; j < lastres; j++)\r
+            if (jalview.util.Comparison.isGap(\r
+                av.alignment.getSequenceAt(startseq).getSequence().charAt(res)))\r
             {\r
-              deleteChar(j, startseq);\r
-              startres = res;\r
+\r
+              deleteChar(res, startseq);\r
             }\r
-         }\r
+            else\r
+            {\r
+              if(scrollThread!=null)\r
+              {\r
+                scrollThread.running = false;\r
+                scrollThread = null;\r
+              }\r
+              break;\r
+            }\r
+          }\r
+        }\r
 \r
-       }\r
+      }\r
+    }\r
 \r
+    mouseDragging = true;\r
+    if (res > av.endRes || res < av.startRes)\r
+    {\r
+      mouseExited(evt);\r
     }\r
 \r
-    lastres = res;\r
-    seqCanvas.repaint();\r
-  }\r
+    if (scrollThread != null)\r
+      scrollThread.setEvent(evt);\r
+\r
 \r
-  public void drawChars(int seqstart, int seqend, int start) {\r
-    seqCanvas.drawPanel(seqCanvas.gg, start,av.getEndRes(),seqstart,seqend,av.getStartRes(),av.getStartSeq(),0);\r
+    endEdit = res;\r
+    lastres = res;\r
     seqCanvas.repaint();\r
   }\r
 \r
   public void insertChar(int j, int seq)\r
   {\r
     av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());\r
-    seqEditOccurred=seq;\r
+    seqEditOccurred = seq;\r
   }\r
 \r
   public void deleteChar(int j, int seq)\r
   {\r
 \r
-    if ( jalview.util.Comparison.isGap( av.alignment.getSequenceAt(seq).getSequence().charAt(j)))\r
-        av.alignment.getSequenceAt(seq).deleteCharAt(j);\r
-\r
+    av.alignment.getSequenceAt(seq).deleteCharAt(j);\r
+    seqEditOccurred = seq;\r
     av.alignment.getWidth();\r
-    seqCanvas.repaint();\r
-    seqEditOccurred=seq;\r
+    repaint();\r
   }\r
 \r
-\r
-  void updateConservation(int i)\r
+  void editOccurred(int i)\r
   {\r
-    av.updateConservation();\r
-    av.updateConsensus();\r
-\r
-    ColourSchemeI cs = av.getGlobalColourScheme();\r
-    if(cs instanceof ConservationColourScheme)\r
-      cs = ( (ConservationColourScheme) cs).cs;\r
-\r
-    if(cs instanceof ClustalxColourScheme)\r
-      cs = new ClustalxColourScheme(av.alignment.getSequences(), av.alignment.getWidth());\r
+    if (endEdit == startEdit)\r
+    {\r
+        ap.alignFrame.historyList.pop();\r
+        ap.alignFrame.updateEditMenuBar();\r
+    }\r
 \r
-    ap.alignFrame.changeColour(cs);\r
+    av.firePropertyChange("alignment", null,av.getAlignment().getSequences());\r
   }\r
 \r
 //////////////////////////////////////////\r
@@ -373,78 +491,109 @@ public class SeqPanel extends Panel
   int oldSeq = -1;\r
   public void doMousePressedDefineMode(MouseEvent evt)\r
   {\r
-    int res = evt.getX()/av.getCharWidth() + av.getStartRes();\r
-    int seq = evt.getY()/av.getCharHeight() + av.getStartSeq();\r
+    if (scrollThread != null)\r
+    {\r
+      scrollThread.running = false;\r
+      scrollThread = null;\r
+    }\r
+\r
+    int res = findRes(evt);\r
+    int seq = findSeq(evt);\r
     oldSeq = seq;\r
+    startWrapBlock=wrappedBlock;\r
+\r
+    if(seq==-1)\r
+      return;\r
 \r
     SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);\r
 \r
-    if(sequence==null || res>sequence.getLength())\r
+    if (sequence == null || res > sequence.getLength())\r
+    {\r
       return;\r
+    }\r
 \r
     stretchGroup = av.getSelectionGroup();\r
 \r
-    if(stretchGroup == null)\r
-     {\r
-       stretchGroup = av.alignment.findGroup( sequence );\r
-       if(stretchGroup!=null && res>stretchGroup.getStartRes() && res<stretchGroup.getEndRes())\r
-         av.setSelectionGroup(stretchGroup);\r
-       else\r
-         stretchGroup = null;\r
-     }\r
+    if (stretchGroup == null)\r
+    {\r
+      stretchGroup = av.alignment.findGroup(sequence);\r
+      if (stretchGroup != null && res > stretchGroup.getStartRes() &&\r
+          res < stretchGroup.getEndRes())\r
+      {\r
+        av.setSelectionGroup(stretchGroup);\r
+      }\r
+      else\r
+      {\r
+        stretchGroup = null;\r
+      }\r
+    }\r
 \r
-    else if(!stretchGroup.sequences.contains(sequence)\r
-            || stretchGroup.getStartRes()>res\r
-            || stretchGroup.getEndRes()<res)\r
-     {\r
-       stretchGroup = null;\r
+    else if (!stretchGroup.sequences.contains(sequence)\r
+             || stretchGroup.getStartRes() > res\r
+             || stretchGroup.getEndRes() < res)\r
+    {\r
+      stretchGroup = null;\r
 \r
-       SequenceGroup[] allGroups = av.alignment.findAllGroups( sequence );\r
+      SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);\r
 \r
-       if (allGroups != null)\r
-         for (int i = 0; i < allGroups.length; i++)\r
-           if (allGroups[i].getStartRes() <= res &&\r
-               allGroups[i].getEndRes() >= res)\r
-           {\r
-             stretchGroup = allGroups[i];\r
-             av.setSelectionGroup(stretchGroup);\r
-             break;\r
-           }\r
-     }\r
+      if (allGroups != null)\r
+      {\r
+        for (int i = 0; i < allGroups.length; i++)\r
+        {\r
+          if (allGroups[i].getStartRes() <= res &&\r
+              allGroups[i].getEndRes() >= res)\r
+          {\r
+            stretchGroup = allGroups[i];\r
+            av.setSelectionGroup(stretchGroup);\r
+            break;\r
+          }\r
+        }\r
+      }\r
+    }\r
 \r
-    if(stretchGroup==null)\r
+    if (stretchGroup == null)\r
     {\r
       // define a new group here\r
       SequenceGroup sg = new SequenceGroup();\r
       sg.setStartRes(res);\r
       sg.setEndRes(res);\r
-      sg.addSequence( sequence );\r
-      av.setSelectionGroup( sg );\r
+      sg.addSequence(sequence, false);\r
+      av.setSelectionGroup(sg);\r
       stretchGroup = sg;\r
 \r
-      if(av.getConservationSelected())\r
-        SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(), "Background");\r
-      if(av.getAbovePIDThreshold())\r
-        SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(), "Background");\r
+      if (av.getConservationSelected())\r
+      {\r
+        SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(),\r
+                                          "Background");\r
+      }\r
+      if (av.getAbovePIDThreshold())\r
+      {\r
+        SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),\r
+                                       "Background");\r
+      }\r
 \r
     }\r
 \r
     // DETECT RIGHT MOUSE BUTTON IN AWT\r
-    else if( ( evt.getModifiers() & InputEvent .BUTTON3_MASK ) == InputEvent.BUTTON3_MASK )\r
+    else if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK) ==\r
+             InputEvent.BUTTON3_MASK)\r
     {\r
-      APopupMenu popup = new APopupMenu(ap, null);\r
+      APopupMenu popup = new APopupMenu(ap, null, null);\r
       this.add(popup);\r
       popup.show(this, evt.getX(), evt.getY());\r
     }\r
 \r
-\r
-    if(stretchGroup!=null && stretchGroup.getEndRes()==res)\r
+    if (stretchGroup != null && stretchGroup.getEndRes() == res)\r
+    {\r
       // Edit end res position of selected group\r
       changeEndRes = true;\r
+    }\r
 \r
-   else if(stretchGroup!=null && stretchGroup.getStartRes()==res)\r
+    else if (stretchGroup != null && stretchGroup.getStartRes() == res)\r
+    {\r
       // Edit end res position of selected group\r
       changeStartRes = true;\r
+    }\r
 \r
   }\r
 \r
@@ -456,133 +605,180 @@ public class SeqPanel extends Panel
 \r
   public void doMouseReleasedDefineMode(MouseEvent evt)\r
   {\r
-    mouseDragging = false;\r
-\r
-    if(stretchGroup==null)\r
-      return;\r
-\r
-    if(stretchGroup.cs instanceof ClustalxColourScheme)\r
+    if (stretchGroup == null)\r
     {\r
-      stretchGroup.cs = new ClustalxColourScheme(stretchGroup.sequences, av.alignment.getWidth());\r
-      seqCanvas.repaint();\r
+        return;\r
     }\r
 \r
-    else if(stretchGroup.cs instanceof ConservationColourScheme)\r
+    if(stretchGroup.cs!=null)\r
     {\r
-       ConservationColourScheme ccs = (ConservationColourScheme)stretchGroup.cs;\r
-       stretchGroup.cs = ccs;\r
-       SliderPanel.setConservationSlider(ap, stretchGroup.cs, stretchGroup.getName()) ;\r
-\r
-       seqCanvas.repaint();\r
-    }\r
-    else\r
-    {\r
-      if(stretchGroup.cs !=null && stretchGroup.cs.canThreshold())\r
+      if (stretchGroup.cs instanceof ClustalxColourScheme)\r
       {\r
-        ResidueColourScheme rcs =  (ResidueColourScheme) stretchGroup.cs;\r
-        SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup.getName());\r
+        ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup.\r
+            sequences,\r
+            stretchGroup.getWidth());\r
       }\r
 \r
+      if (stretchGroup.cs.conservationApplied())\r
+      {\r
+        SliderPanel.setConservationSlider(ap, stretchGroup.cs,\r
+                                          stretchGroup.getName());\r
+        stretchGroup.recalcConservation();\r
+      }\r
+      else\r
+      {\r
+        SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,\r
+                                       stretchGroup.getName());\r
+      }\r
     }\r
-\r
-\r
     changeEndRes = false;\r
     changeStartRes = false;\r
     stretchGroup = null;\r
+    PaintRefresher.Refresh(av.alignment);\r
     ap.repaint();\r
   }\r
 \r
-\r
-  boolean remove = false;\r
   public void doMouseDraggedDefineMode(MouseEvent evt)\r
   {\r
-    int res = evt.getX()/av.getCharWidth() + av.getStartRes();\r
-    int y = evt.getY()/av.getCharHeight() + av.getStartSeq();\r
+    int res = findRes(evt);\r
+    int y = findSeq(evt);\r
 \r
-    if(stretchGroup==null)\r
+    if(wrappedBlock!=startWrapBlock)\r
       return;\r
 \r
-    if(res>av.alignment.getWidth())\r
-      res = av.alignment.getWidth()-1;\r
+     if (stretchGroup == null)\r
+     {\r
+          return;\r
+     }\r
 \r
+     mouseDragging = true;\r
 \r
-    if(stretchGroup.getEndRes()==res)\r
-      // Edit end res position of selected group\r
-      changeEndRes = true;\r
 \r
-    else if(stretchGroup.getStartRes()==res)\r
-      // Edit start res position of selected group\r
-      changeStartRes = true;\r
+      if(y > av.alignment.getHeight())\r
+      {\r
+        y = av.alignment.getHeight() -1;\r
+      }\r
 \r
+      if(res>av.alignment.getWidth())\r
+        res = av.alignment.getWidth()-1;\r
 \r
-    if(res<av.getStartRes())\r
-      res = av.getStartRes();\r
-    else if(res>av.getEndRes())\r
-      res = av.getEndRes();\r
+      if (stretchGroup.getEndRes() == res)\r
+      {\r
+          // Edit end res position of selected group\r
+          changeEndRes = true;\r
+      }\r
+      else if (stretchGroup.getStartRes() == res)\r
+      {\r
+          // Edit start res position of selected group\r
+          changeStartRes = true;\r
+      }\r
 \r
-    if(changeEndRes)\r
-    {\r
-      if(res>stretchGroup.getStartRes()-1)\r
-        stretchGroup.setEndRes( res );\r
-    }\r
-    else if(changeStartRes)\r
-    {\r
-      if(res<stretchGroup.getEndRes()+1)\r
-        stretchGroup.setStartRes( res );\r
-    }\r
+      if (res < 0)\r
+      {\r
+          res = 0;\r
+      }\r
 \r
-    int dragDirection = 0;\r
-    if (y > oldSeq)\r
-      dragDirection = 1;\r
-    else if (y < oldSeq)\r
-      dragDirection = -1;\r
+      if (changeEndRes)\r
+      {\r
+          if (res > (stretchGroup.getStartRes() - 1))\r
+          {\r
+              stretchGroup.setEndRes(res);\r
+          }\r
+      }\r
+      else if (changeStartRes)\r
+      {\r
+          if (res < (stretchGroup.getEndRes() + 1))\r
+          {\r
+              stretchGroup.setStartRes(res);\r
+          }\r
+      }\r
 \r
-    while (y != oldSeq && oldSeq>0 && y<av.alignment.getHeight())\r
-    {\r
-      // This routine ensures we don't skip any sequences, as the\r
-      // selection is quite slow.\r
-      Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);\r
+      int dragDirection = 0;\r
+\r
+      if (y > oldSeq)\r
+      {\r
+          dragDirection = 1;\r
+      }\r
+      else if (y < oldSeq)\r
+      {\r
+          dragDirection = -1;\r
+      }\r
 \r
-      oldSeq += dragDirection;\r
-      Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);\r
 \r
-      if (stretchGroup.sequences.contains(nextSeq))\r
+      while ((y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))\r
       {\r
-        stretchGroup.deleteSequence(seq);\r
-        stretchGroup.deleteSequence(nextSeq);\r
+          // This routine ensures we don't skip any sequences, as the\r
+          // selection is quite slow.\r
+          Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);\r
+\r
+          oldSeq += dragDirection;\r
+\r
+          if(oldSeq<0)\r
+            break;\r
+\r
+          Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);\r
+\r
+          if (stretchGroup.sequences.contains(nextSeq))\r
+          {\r
+              stretchGroup.deleteSequence(seq, false);\r
+          }\r
+          else\r
+          {\r
+              if (seq != null)\r
+              {\r
+                  stretchGroup.addSequence(seq, false);\r
+              }\r
+\r
+              stretchGroup.addSequence(nextSeq, false);\r
+          }\r
       }\r
-      else\r
+\r
+      if(oldSeq < 0)\r
+        oldSeq = -1;\r
+\r
+\r
+      if(res>av.endRes || res<av.startRes\r
+          || y<av.startSeq || y>av.endSeq)\r
       {\r
-       if(seq!=null)\r
-        stretchGroup.addSequence(seq);\r
-        stretchGroup.addSequence(nextSeq);\r
+        mouseExited(evt);\r
       }\r
+\r
+      if (scrollThread != null)\r
+      {\r
+        scrollThread.setEvent(evt);\r
+      }\r
+\r
+      seqCanvas.repaint();\r
     }\r
-    oldSeq = y;\r
-    mouseDragging = true;\r
-    if(scrollThread!=null)\r
-      scrollThread.setEvent(evt);\r
 \r
-    seqCanvas.repaint();\r
-  }\r
+    public void mouseEntered(MouseEvent e)\r
+    {\r
+      if (oldSeq < 0)\r
+        oldSeq = 0;\r
 \r
-  public void doMouseEnteredDefineMode(MouseEvent e)\r
-  {\r
-    if (scrollThread != null)\r
-      scrollThread.running = false;\r
-  }\r
+      if (scrollThread != null)\r
+      {\r
+        scrollThread.running = false;\r
+        scrollThread = null;\r
+      }\r
+    }\r
 \r
-  public void doMouseExitedDefineMode(MouseEvent e)\r
+  public void mouseExited(MouseEvent e)\r
   {\r
     if (av.getWrapAlignment())\r
+    {\r
       return;\r
+    }\r
 \r
-    if(mouseDragging)\r
+    if (mouseDragging && scrollThread==null)\r
+    {\r
       scrollThread = new ScrollThread();\r
-\r
+    }\r
   }\r
+\r
   // this class allows scrolling off the bottom of the visible alignment\r
-  class ScrollThread extends Thread\r
+  class ScrollThread\r
+      extends Thread\r
   {\r
     MouseEvent evt;\r
     boolean running = false;\r
@@ -606,21 +802,30 @@ public class SeqPanel extends Panel
       running = true;\r
       while (running)\r
       {\r
-        if(evt!=null)\r
+\r
+        if (evt != null)\r
         {\r
 \r
           if (mouseDragging && evt.getY() < 0 && av.getStartSeq() > 0)\r
+          {\r
             running = ap.scrollUp(true);\r
+          }\r
 \r
           if (mouseDragging && evt.getY() >= getSize().height &&\r
               av.alignment.getHeight() > av.getEndSeq())\r
+          {\r
             running = ap.scrollUp(false);\r
+          }\r
 \r
           if (mouseDragging && evt.getX() < 0)\r
+          {\r
             running = ap.scrollRight(true);\r
+          }\r
 \r
           else if (mouseDragging && evt.getX() >= getSize().width)\r
+          {\r
             running = ap.scrollRight(false);\r
+          }\r
         }\r
 \r
         try\r
@@ -631,12 +836,6 @@ public class SeqPanel extends Panel
         {}\r
       }\r
     }\r
-}\r
-\r
-\r
+  }\r
 \r
 }\r
-\r
-\r
-\r
-\r