X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqCanvas.java;h=13a0ec82e675bc7c832a35e81e9f10d74b19c9df;hb=32a72d077d2371f4566688fbd103103d8505b27f;hp=fd8330977705d18b7b81a13e6639bdb5c23941c2;hpb=8878681ec11f85c050248236a96ffbcaf2f0497b;p=jalview.git

diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index fd83309..13a0ec8 100755
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 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
@@ -35,25 +35,45 @@ public class SeqCanvas
 
   AlignViewport av;
 
-  boolean displaySearch = false;
-  int[] searchResults = null;
-
-  int chunkHeight;
-  int chunkWidth;
+  SearchResults searchResults = null;
 
   boolean fastPaint = false;
 
-  boolean isOverview = false;
+
+  int cursorX = 0;
+  int cursorY = 0;
+
 
   public SeqCanvas(AlignViewport av)
   {
     this.av = av;
     fr = new FeatureRenderer(av);
     sr = new SequenceRenderer(av);
-    PaintRefresher.Register(this, av.alignment);
+    PaintRefresher.Register(this, av.getSequenceSetId());
+  }
+
+  public AlignViewport getViewport()
+  {
+    return av;
+  }
+
+  public FeatureRenderer getFeatureRenderer()
+  {
+    return fr;
+  }
 
+  MCview.AppletPDBCanvas pdbCanvas;
+  public SequenceRenderer getSequenceRenderer()
+  {
+    return sr;
   }
 
+  public void setPDBCanvas(MCview.AppletPDBCanvas pc)
+  {
+    pdbCanvas = pc;
+  }
+
+
   void drawNorthScale(Graphics g, int startx, int endx, int ypos)
   {
     int scalestartx = startx - startx % 10 + 10;
@@ -63,14 +83,17 @@ public class SeqCanvas
     // NORTH SCALE
     for (int i = scalestartx; i < endx; i += 10)
     {
-      String string = String.valueOf(i);
-      g.drawString(string, (i - startx - 1) * av.charWidth,
-                   ypos - av.charHeight / 2);
+      int value = i;
+      if(av.hasHiddenColumns)
+          value = av.getColumnSelection().adjustForHiddenColumns(value);
 
-      g.drawLine( (i - startx - 1) * av.charWidth + av.charWidth / 2,
-                 ypos + 2 - av.charHeight / 2,
-                 (i - startx - 1) * av.charWidth + av.charWidth / 2, ypos - 2);
+      g.drawString( String.valueOf(value), (i - startx - 1) * av.charWidth,
+          ypos - (av.charHeight / 2));
 
+      g.drawLine(((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
+          (ypos + 2) - (av.charHeight / 2),
+          ((i - startx - 1) * av.charWidth) + (av.charWidth / 2), ypos -
+                2);
     }
   }
 
@@ -78,73 +101,115 @@ public class SeqCanvas
   {
     FontMetrics fm = getFontMetrics(av.getFont());
     ypos += av.charHeight;
-    // EAST SCALE
-    for (int i = 0; i < av.alignment.getHeight(); i++)
+    if (av.hasHiddenColumns)
     {
-      SequenceI seq = av.alignment.getSequenceAt(i);
-      int index = startx;
-      int value = -1;
-      while (index < endx)
+      startx = av.getColumnSelection().adjustForHiddenColumns(startx);
+      endx = av.getColumnSelection().adjustForHiddenColumns(endx);
+    }
+
+    int maxwidth = av.alignment.getWidth();
+    if (av.hasHiddenColumns)
+        maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+
+      // WEST SCALE
+      for (int i = 0; i < av.alignment.getHeight(); i++)
       {
-        if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
+        SequenceI seq = av.alignment.getSequenceAt(i);
+        int index = startx;
+        int value = -1;
+
+        while (index < endx)
         {
-          index++;
-          continue;
+          if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
+          {
+            index++;
+
+            continue;
+          }
+
+          value = av.alignment.getSequenceAt(i).findPosition(index);
+
+          break;
         }
 
-        value = av.alignment.getSequenceAt(i).findPosition(index);
-        break;
-      }
-      if (value != -1)
-      {
-        int x = LABEL_WEST - fm.stringWidth(String.valueOf(value))-av.charWidth/2;
-        g.drawString(value + "", x,
-                     ypos + i * av.charHeight - av.charHeight / 5);
+        if (value != -1)
+        {
+          int x = LABEL_WEST - fm.stringWidth(String.valueOf(value)) -
+              av.charWidth / 2;
+          g.drawString(value + "", x,
+                       (ypos + (i * av.charHeight)) - (av.charHeight / 5));
+        }
       }
     }
-  }
-
   void drawEastScale(Graphics g, int startx, int endx, int ypos)
   {
-    ypos += av.charHeight;
-    // EAST SCALE
-    for (int i = 0; i < av.alignment.getHeight(); i++)
-    {
-      SequenceI seq = av.alignment.getSequenceAt(i);
-      int index = endx;
-      int value = -1;
-      while (index > startx)
-      {
-        if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
+        ypos += av.charHeight;
+
+        if(av.hasHiddenColumns)
+                endx = av.getColumnSelection().adjustForHiddenColumns(endx);
+
+        SequenceI seq;
+        // EAST SCALE
+        for (int i = 0; i < av.alignment.getHeight(); i++)
         {
-          index--;
-          continue;
-        }
+            seq = av.alignment.getSequenceAt(i);
+            int index = endx;
+            int value = -1;
 
-        value = av.alignment.getSequenceAt(i).findPosition(index);
-        break;
-      }
-      if (value != -1)
-      {
-        g.drawString(value + "", av.charWidth/2,
-                     ypos + i * av.charHeight - av.charHeight / 5);
-      }
-    }
+            while (index > startx)
+            {
+                if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
+                {
+                    index--;
 
-  }
+                    continue;
+                }
 
-  public void fastPaint(int horizontal, int vertical)
+                value = seq.findPosition(index);
+
+                break;
+            }
+
+            if (value != -1)
+            {
+                g.drawString(String.valueOf(value), 0,
+                    (ypos + (i * av.charHeight)) - (av.charHeight / 5));
+            }
+        }
+    }
+
+  int lastsr=0;
+  void fastPaint(int horizontal, int vertical)
   {
-    if (gg == null)
+    if ( fastPaint || gg == null)
     {
       return;
     }
 
-    gg.copyArea(0, 0, imgWidth, imgHeight, -horizontal * av.charWidth,
+
+    // Its possible on certain browsers that the call to fastpaint
+    // is faster than it can paint, so this check here catches
+    // this possibility
+    if(lastsr + horizontal != av.startRes)
+    {
+      horizontal = av.startRes - lastsr;
+    }
+
+    lastsr = av.startRes;
+
+    fastPaint = true;
+    gg.copyArea(horizontal * av.charWidth,
+                vertical * av.charHeight,
+                imgWidth - horizontal * av.charWidth,
+                imgHeight - vertical * av.charHeight,
+                -horizontal * av.charWidth,
                 -vertical * av.charHeight);
 
+
+
     int sr = av.startRes, er = av.endRes, ss = av.startSeq, es = av.endSeq,
         transX = 0, transY = 0;
+
     if (horizontal > 0) // scrollbar pulled right, image to the left
     {
       transX = (er - sr - horizontal) * av.charWidth;
@@ -178,12 +243,9 @@ public class SeqCanvas
 
     gg.translate(transX, transY);
 
-    gg.setColor(Color.white);
-    gg.fillRect(0, 0, (er - sr + 1) * av.charWidth, (es - ss) * av.charHeight);
-    drawPanel(gg, sr, er, ss, es, sr, ss, 0);
+    drawPanel(gg, sr, er, ss, es, 0);
     gg.translate( -transX, -transY);
 
-    fastPaint = true;
     repaint();
 
   }
@@ -205,7 +267,15 @@ public class SeqCanvas
 
   public void paint(Graphics g)
   {
-    sr.renderGaps(av.renderGaps);
+
+    if (img != null && (fastPaint
+                        || (getSize().width != g.getClipBounds().width)
+                        || (getSize().height != g.getClipBounds().height)))
+    {
+      g.drawImage(img, 0, 0, this);
+      fastPaint = false;
+      return;
+    }
 
     if (fastPaint)
     {
@@ -237,11 +307,6 @@ public class SeqCanvas
     gg.setColor(Color.white);
     gg.fillRect(0, 0, imgWidth, imgHeight);
 
-    chunkWidth = getWrappedCanvasWidth(getSize().width);
-    chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;
-
-    av.setChunkHeight(chunkHeight);
-    av.setChunkWidth(chunkWidth);
 
     if (av.getWrapAlignment())
     {
@@ -249,17 +314,22 @@ public class SeqCanvas
     }
     else
     {
-      drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, av.startRes,
-                av.startSeq, 0);
+      drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0);
     }
 
     g.drawImage(img, 0, 0, this);
 
+    if (pdbCanvas != null)
+    {
+      pdbCanvas.updateSeqColours();
+    }
   }
 
   int LABEL_WEST, LABEL_EAST;
   public int getWrappedCanvasWidth(int cwidth)
   {
+      cwidth -= cwidth % av.charWidth;
+
       FontMetrics fm = getFontMetrics(av.getFont());
 
       LABEL_EAST = 0;
@@ -267,7 +337,7 @@ public class SeqCanvas
 
       if (av.scaleRightWrapped)
       {
-          LABEL_EAST = fm.stringWidth(getMask()+"0");
+          LABEL_EAST = fm.stringWidth(getMask());
       }
 
       if (av.scaleLeftWrapped)
@@ -286,12 +356,21 @@ public class SeqCanvas
   String getMask()
   {
     String mask = "0";
-    for (int i = av.alignment.getWidth(); i > 0; i /= 10)
+    int maxWidth = 0;
+    int tmp;
+    for (int i = 0; i < av.alignment.getHeight(); i++)
+    {
+      tmp = av.alignment.getSequenceAt(i).getEnd();
+      if (tmp > maxWidth)
+        maxWidth = tmp;
+    }
+
+    for (int i = maxWidth; i > 0; i /= 10)
     {
       mask += "0";
     }
     return mask;
-    }
+  }
 
   public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight,
                                int startRes)
@@ -300,310 +379,418 @@ public class SeqCanvas
 
     FontMetrics fm = getFontMetrics(av.getFont());
 
+
     if (av.scaleRightWrapped)
     {
-        LABEL_EAST = fm.stringWidth(getMask()+"0");
+        LABEL_EAST = fm.stringWidth(getMask());
     }
 
-    int LABEL_WEST = 0;
-
     if (av.scaleLeftWrapped)
     {
         LABEL_WEST = fm.stringWidth(getMask());
     }
 
+    int hgap = av.charHeight;
+    if(av.scaleAboveWrapped)
+      hgap += av.charHeight;
+
     int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
-    int cHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;
+    int cHeight = av.getAlignment().getHeight() * av.charHeight;
+
+    av.setWrappedWidth(cWidth);
 
     av.endRes = av.startRes + cWidth;
 
-    int endx = startRes + cWidth - 1;
-    int ypos = 2 * av.charHeight;
 
-    while (ypos <= canvasHeight && startRes < av.alignment.getWidth())
+    int endx;
+    int ypos = hgap;
+
+    int maxwidth = av.alignment.getWidth();
+
+    if(av.hasHiddenColumns)
+          maxwidth = av.getColumnSelection().findColumnPosition(maxwidth)-1;
+
+    while ((ypos <= canvasHeight) && (startRes < maxwidth))
     {
-      g.setColor(Color.black);
+      endx = startRes + cWidth -1;
 
-      if (av.scaleLeftWrapped)
+      if (endx > maxwidth)
       {
-        drawWestScale(g, startRes, endx, ypos);
+        endx = maxwidth;
       }
 
-      if (av.scaleRightWrapped)
-      {
-        g.translate(canvasWidth - LABEL_EAST, 0);
-        drawEastScale(g, startRes, endx, ypos);
-        g.translate( - (canvasWidth - LABEL_EAST), 0);
-      }
+        g.setColor(Color.black);
 
-      g.translate(LABEL_WEST, 0);
-      if (av.scaleAboveWrapped)
-      {
-        drawNorthScale(g, startRes, endx, ypos);
-      }
+        if (av.scaleLeftWrapped)
+        {
+            drawWestScale(g, startRes, endx, ypos);
+        }
 
+        if (av.scaleRightWrapped)
+        {
+            g.translate(canvasWidth - LABEL_EAST, 0);
+            drawEastScale(g, startRes, endx, ypos);
+            g.translate(-(canvasWidth - LABEL_EAST), 0);
+        }
 
-     if(g.getClip()==null)
-       g.setClip(0, 0, cWidth * av.charWidth, canvasHeight);
+        g.translate(LABEL_WEST, 0);
 
-     if (av.alignment.getWidth() >= av.vconsensus.size())
-     {
-       endx = av.vconsensus.size() - 2;
-     }
-     drawPanel(g, startRes, endx, 0, al.getHeight(), startRes, 0, ypos);
-      g.setClip(null);
-      g.translate( -LABEL_WEST, 0);
+        if (av.scaleAboveWrapped)
+        {
+          drawNorthScale(g, startRes, endx, ypos);
+        }
+        if (av.hasHiddenColumns && av.showHiddenMarkers)
+        {
+          g.setColor(Color.blue);
+          int res;
+          for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size();
+               i++)
+          {
+            res = av.getColumnSelection().findHiddenRegionPosition(i) -
+                startRes;
+
+            if (res < 0 || res > endx - startRes)
+              continue;
+
+            gg.fillPolygon(new int[]
+                           {res * av.charWidth - av.charHeight / 4,
+                           res * av.charWidth + av.charHeight / 4,
+                           res * av.charWidth},
+                           new int[]
+                           {
+                           ypos - (av.charHeight / 2),
+                           ypos - (av.charHeight / 2),
+                           ypos - (av.charHeight / 2) + 8
+            }, 3);
 
-      ypos += cHeight;
-      startRes += cWidth;
-      endx = startRes + cWidth - 1;
+          }
+        }
 
-      if (endx > al.getWidth())
-      {
-        endx = al.getWidth();
-      }
-    }
+        if(g.getClip()==null)
+          g.setClip(0, 0, cWidth * av.charWidth, canvasHeight);
 
-  }
+        drawPanel(g, startRes, endx, 0, al.getHeight(), ypos);
+         g.setClip(null);
 
-  synchronized public void drawPanel(Graphics g, int x1, int x2, int y1, int y2,
-                                     int startx, int starty, int offset)
-  {
 
-    g.setFont(av.getFont());
-    sr.renderGaps(av.renderGaps);
+        if(av.showAnnotation)
+        {
+          g.translate(0, cHeight + ypos+4);
+          if(annotations==null)
+            annotations = new AnnotationPanel(av);
 
-    SequenceI nextSeq;
+          annotations.drawComponent( g, startRes, endx+1 );
+          g.translate(0, -cHeight - ypos-4);
+        }
+        g.translate(-LABEL_WEST, 0);
 
-    /// First draw the sequences
-    /////////////////////////////
-    for (int i = y1; i < y2; i++)
-    {
-      nextSeq = av.alignment.getSequenceAt(i);
+        ypos += cHeight+getAnnotationHeight()+hgap;
 
-      sr.drawSequence(g, nextSeq, av.alignment.findAllGroups(nextSeq), x1, x2,
-                      (x1 - startx) * av.charWidth,
-                      offset +
-                      (i-starty)*av.charHeight,
-                      av.charWidth, av.charHeight);
 
-      if (av.showSequenceFeatures)
-      {
-        fr.drawSequence(g, nextSeq, av.alignment.findAllGroups(nextSeq), x1, x2,
-                        (x1 - startx) * av.charWidth,
-                        offset +
-                        (i-starty)*av.charHeight,
-                        av.charWidth, av.charHeight);
-      }
-    }
-    //
-    /////////////////////////////////////
+        startRes += cWidth;
+        }
 
-    // Now outline any areas if necessary
-    /////////////////////////////////////
-    SequenceGroup group = av.getSelectionGroup();
-    java.util.Vector groups = av.alignment.getGroups();
+  }
 
-    int sx = -1, sy = -1, ex = -1;
-    int groupIndex = -1;
-    if (group == null && groups.size() > 0)
-    {
-      group = (SequenceGroup) groups.elementAt(0);
-      groupIndex = 0;
+  AnnotationPanel annotations;
+  int getAnnotationHeight()
+  {
+    if(!av.showAnnotation)
+      return 0;
+
+    if(annotations==null)
+      annotations = new AnnotationPanel(av);
+
+    return annotations.adjustPanelHeight();
     }
 
-    if (group != null && !isOverview)
+    void drawPanel(Graphics g1, int startRes, int endRes,
+                    int startSeq, int endSeq, int offset)
     {
-      do
+      if(!av.hasHiddenColumns)
+      {
+        draw(g1, startRes, endRes, startSeq, endSeq, offset);
+      }
+      else
       {
-          int oldY = -1;
-          int i = 0;
-          boolean inGroup = false;
-          int top = -1;
-          int bottom = -1;
+        java.util.Vector regions = av.getColumnSelection().getHiddenColumns();
+
+        int screenY = 0;
+        int blockStart = startRes;
+        int blockEnd = endRes;
+
+        for (int i = 0; i < regions.size(); i++)
+        {
+          int[] region = (int[]) regions.elementAt(i);
+          int hideStart = region[0];
+          int hideEnd = region[1];
 
-          for (i = y1; i < y2; i++)
+          if (hideStart <= blockStart)
           {
-              sx = (group.getStartRes() - startx) * av.charWidth;
-              sy = offset + ((i - starty) * av.charHeight);
-              ex = (((group.getEndRes() + 1) - group.getStartRes()) * av.charWidth) -
-                  1;
-
-              if(sx+ex<0 || sx>imgWidth)
-              {
-                continue;
-              }
-
-              if ( (sx <= (x2-x1)*av.charWidth) &&
-                      group.sequences.contains(av.alignment.getSequenceAt(
-                              i)))
-              {
-                  if ((bottom == -1) &&
-                          !group.sequences.contains(
-                              av.alignment.getSequenceAt(i + 1)))
-                  {
-                      bottom = sy + av.charHeight;
-                  }
-
-                  if (!inGroup)
-                  {
-                      if (((top == -1) && (i == 0)) ||
-                              !group.sequences.contains(
-                                  av.alignment.getSequenceAt(i - 1)))
-                      {
-                          top = sy;
-                      }
-
-                      oldY = sy;
-                      inGroup = true;
-
-                      if (group == av.getSelectionGroup())
-                      {
-                          g.setColor(Color.red);
-                      }
-                      else
-                      {
-                          g.setColor(group.getOutlineColour());
-                      }
-                  }
-              }
-              else
-              {
-                if (inGroup)
-                {
-                  if (sx >= 0 && sx < imgWidth)
-                    g.drawLine(sx, oldY, sx, sy);
-
-                  if (sx + ex < imgWidth)
-                    g.drawLine(sx + ex, oldY, sx + ex, sy);
-
-                  if (sx < 0)
-                  {
-                    ex += sx;
-                    sx = 0;
-                  }
-
-                  if (sx + ex > imgWidth)
-                    ex = imgWidth;
-
-                  else if (sx + ex >= (x2 - x1 + 1) * av.charWidth)
-                    ex = (x2 - x1 + 1) * av.charWidth;
-
-                  if (top != -1)
-                  {
-                    g.drawLine(sx, top, sx + ex, top);
-                    top = -1;
-                  }
-
-                  if (bottom != -1)
-                  {
-                    g.drawLine(sx, bottom, sx + ex, bottom);
-                    bottom = -1;
-                  }
-
-                  inGroup = false;
-                  }
-              }
+            blockStart += (hideEnd - hideStart) + 1;
+            continue;
           }
 
-          if (inGroup)
+          blockEnd = hideStart - 1;
+
+          g1.translate(screenY * av.charWidth, 0);
+
+          draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
+
+          if(av.getShowHiddenMarkers())
           {
-            sy = offset + ( (i - starty) * av.charHeight);
-            if (sx >= 0 && sx < imgWidth)
-              g.drawLine(sx, oldY, sx, sy);
+            g1.setColor(Color.blue);
+            g1.drawLine( (blockEnd - blockStart + 1) * av.charWidth - 1,
+                         0 + offset,
+                         (blockEnd - blockStart + 1) * av.charWidth - 1,
+                         (endSeq - startSeq) * av.charHeight + offset);
+          }
 
-            if (sx + ex < imgWidth)
-              g.drawLine(sx + ex, oldY, sx + ex, sy);
+          g1.translate( -screenY * av.charWidth, 0);
+          screenY += blockEnd - blockStart + 1;
+          blockStart = hideEnd + 1;
+        }
 
-            if (sx < 0)
-            {
-              ex += sx;
-              sx = 0;
-            }
+        if (screenY <= (endRes - startRes))
+        {
+          blockEnd = blockStart + (endRes - startRes) - screenY;
+          g1.translate(screenY * av.charWidth, 0);
+          draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
+
+          g1.translate( -screenY * av.charWidth, 0);
+        }
+      }
+
+    }
+
+
+
+
+    //int startRes, int endRes, int startSeq, int endSeq, int x, int y,
+    // int x1, int x2, int y1, int y2, int startx, int starty,
+    void draw(Graphics g,
+                   int startRes, int endRes,
+                   int startSeq, int endSeq,
+                   int offset)
+   {
+      g.setFont(av.getFont());
+      sr.prepare(g, av.renderGaps);
 
-            if (sx + ex > imgWidth)
-              ex = imgWidth;
-            else if (sx + ex >= (x2 - x1 + 1) * av.charWidth)
-              ex = (x2 - x1 + 1) * av.charWidth;
+      SequenceI nextSeq;
 
-            if (top != -1)
+        /// First draw the sequences
+        /////////////////////////////
+        for (int i = startSeq; i < endSeq; i++)
+        {
+            nextSeq = av.alignment.getSequenceAt(i);
+
+            sr.drawSequence(nextSeq, av.alignment.findAllGroups(nextSeq),
+                            startRes, endRes,
+                            offset + ( (i - startSeq) * av.charHeight));
+
+            if (av.showSequenceFeatures)
             {
-              g.drawLine(sx, top, sx + ex, top);
-              top = -1;
+                fr.drawSequence(g, nextSeq, startRes, endRes,
+                    offset + ((i - startSeq) * av.charHeight));
             }
 
-            if (bottom != -1)
+            /// Highlight search Results once all sequences have been drawn
+            //////////////////////////////////////////////////////////
+            if (searchResults != null)
             {
-              g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);
-              bottom = -1;
+              int[] visibleResults = searchResults.getResults(nextSeq, startRes, endRes);
+              if (visibleResults != null)
+                for (int r = 0; r < visibleResults.length; r += 2)
+                {
+                  sr.drawHighlightedText(nextSeq, visibleResults[r],
+                                         visibleResults[r + 1],
+                                         (visibleResults[r] - startRes) * av.charWidth,
+                                         offset + ( (i - startSeq) * av.charHeight));
+                }
             }
 
-              inGroup = false;
-          }
-
-          groupIndex++;
-
-          if (groupIndex >= groups.size())
-          {
-              break;
+            if(av.cursorMode && cursorY==i
+               && cursorX>=startRes && cursorX<=endRes)
+            {
+              sr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * av.charWidth,
+                            offset + ( (i - startSeq) * av.charHeight));
+            }
           }
 
-          group = (SequenceGroup) groups.elementAt(groupIndex);
-      }
-      while (groupIndex < groups.size());
-    }
+          if(av.getSelectionGroup()!=null || av.alignment.getGroups().size()>0)
+            drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset);
 
-    /// Highlight search Results once all sequences have been drawn
-    //////////////////////////////////////////////////////////
-    if (displaySearch)
-    {
-      for (int r = 0; r < searchResults.length; r += 3)
-      {
-        int searchSeq = searchResults[r];
+   }
 
-        if (searchSeq >= y1 && searchSeq < y2)
-        {
-          SequenceI seq = av.getAlignment().getSequenceAt(searchSeq);
+   void drawGroupsBoundaries(Graphics g,
+                   int startRes, int endRes,
+                   int startSeq, int endSeq,
+                   int offset)
+   {
+     //
+     /////////////////////////////////////
+     // Now outline any areas if necessary
+     /////////////////////////////////////
+     SequenceGroup group = av.getSelectionGroup();
 
-          int searchStart = seq.findIndex(searchResults[r + 1]) - 1;
-          int searchEnd = seq.findIndex(searchResults[r + 2]) - 1;
+     int sx = -1;
+     int sy = -1;
+     int ex = -1;
+     int groupIndex = -1;
 
-          SequenceRenderer ssr = (SequenceRenderer) sr;
-          if (searchStart < x1)
-          {
-            searchStart = x1;
-          }
-          if (searchEnd > x2)
-          {
-            searchEnd = x2;
-          }
+     if ( (group == null) && (av.alignment.getGroups().size() > 0))
+     {
+       group = (SequenceGroup) av.alignment.getGroups().elementAt(0);
+       groupIndex = 0;
+     }
 
-          ssr.drawHighlightedText(seq,
-                                  searchStart,
-                                  searchEnd,
-                                  (searchStart - startx) * av.charWidth,
-                                  offset +
-                                  (searchSeq-starty)*av.charHeight,
-                                  av.charWidth,
-                                  av.charHeight);
-        }
-      }
-    }
+     if (group != null)
+     {
+       do
+       {
+         int oldY = -1;
+         int i = 0;
+         boolean inGroup = false;
+         int top = -1;
+         int bottom = -1;
+         int alHeight = av.alignment.getHeight()-1;
+
+         for (i = startSeq; i < endSeq; i++)
+         {
+           sx = (group.getStartRes() - startRes) * av.charWidth;
+           sy = offset + ( (i - startSeq) * av.charHeight);
+           ex = ( ( (group.getEndRes() + 1) - group.getStartRes()) * av.charWidth) -
+               1;
+
+           if (sx + ex < 0 || sx > imgWidth)
+           {
+             continue;
+           }
+
+           if ( (sx <= (endRes - startRes) * av.charWidth) &&
+               group.getSequences(false).
+               contains(av.alignment.getSequenceAt(i)))
+           {
+             if ( (bottom == -1) &&
+             (i >= alHeight ||
+                 !group.getSequences(false).contains(
+                     av.alignment.getSequenceAt(i + 1))))
+             {
+               bottom = sy + av.charHeight;
+             }
+
+             if (!inGroup)
+             {
+               if ( ( (top == -1) && (i == 0)) ||
+                   !group.getSequences(false).contains(
+                       av.alignment.getSequenceAt(i - 1)))
+               {
+                 top = sy;
+               }
+
+               oldY = sy;
+               inGroup = true;
+
+               if (group == av.getSelectionGroup())
+               {
+                 g.setColor(Color.red);
+               }
+               else
+               {
+                 g.setColor(group.getOutlineColour());
+               }
+             }
+           }
+           else
+           {
+             if (inGroup)
+             {
+               if (sx >= 0 && sx < imgWidth)
+                 g.drawLine(sx, oldY, sx, sy);
+
+               if (sx + ex < imgWidth)
+                 g.drawLine(sx + ex, oldY, sx + ex, sy);
+
+               if (sx < 0)
+               {
+                 ex += sx;
+                 sx = 0;
+               }
+
+               if (sx + ex > imgWidth)
+                 ex = imgWidth;
+
+               else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)
+                 ex = (endRes - startRes + 1) * av.charWidth;
+
+               if (top != -1)
+               {
+                 g.drawLine(sx, top, sx + ex, top);
+                 top = -1;
+               }
+
+               if (bottom != -1)
+               {
+                 g.drawLine(sx, bottom, sx + ex, bottom);
+                 bottom = -1;
+               }
+
+               inGroup = false;
+             }
+           }
+         }
+
+         if (inGroup)
+         {
+           sy = offset + ( (i - startSeq) * av.charHeight);
+           if (sx >= 0 && sx < imgWidth)
+             g.drawLine(sx, oldY, sx, sy);
+
+           if (sx + ex < imgWidth)
+             g.drawLine(sx + ex, oldY, sx + ex, sy);
+
+           if (sx < 0)
+           {
+             ex += sx;
+             sx = 0;
+           }
+
+           if (sx + ex > imgWidth)
+             ex = imgWidth;
+           else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)
+             ex = (endRes - startRes + 1) * av.charWidth;
+
+           if (top != -1)
+           {
+             g.drawLine(sx, top, sx + ex, top);
+             top = -1;
+           }
+
+           if (bottom != -1)
+           {
+             g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);
+             bottom = -1;
+           }
+
+           inGroup = false;
+         }
+
+         groupIndex++;
+
+         if (groupIndex >= av.alignment.getGroups().size())
+         {
+           break;
+         }
+
+         group = (SequenceGroup) av.alignment.getGroups().elementAt(groupIndex);
+       }
+       while (groupIndex < av.alignment.getGroups().size());
 
-  }
+     }
+   }
 
-  public void highlightSearchResults(int[] results)
+  public void highlightSearchResults(SearchResults results)
   {
-    // results are in the order sequence, startRes, endRes
-    if (results == null)
-    {
-      displaySearch = false;
-    }
-    else
-    {
-      displaySearch = true;
-    }
-
     searchResults = results;
 
     repaint();