X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqCanvas.java;h=618ec8a10a8b2b474e6cf36ed90161afc17755ef;hb=df1c58f9669c477db082016aa919d6c6cc9da071;hp=e0288198d9126b98694e712de7c4a6409a2e60ec;hpb=c80292bb7e300539b0ea8665ed3bee3fa6735dad;p=jalview.git

diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index e028819..618ec8a 100755
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -1,41 +1,80 @@
+/*
+ * 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.awt.*;
-import jalview.datamodel.*;
-import jalview.analysis.*;
 
+import jalview.datamodel.*;
 
-public class SeqCanvas extends Panel
+public class SeqCanvas
+    extends Panel
 {
-    FeatureRenderer fr;
-    SequenceRenderer sr;
-    Image             img;
-    Graphics          gg;
-    int               imgWidth;
-    int               imgHeight;
+  FeatureRenderer fr;
+  SequenceRenderer sr;
+  Image img;
+  Graphics gg;
+  int imgWidth;
+  int imgHeight;
 
-    AlignViewport     av;
+  AlignViewport av;
 
-    boolean showScores = false;
-    boolean displaySearch = false;
-    int [] searchResults = null;
+  SearchResults searchResults = null;
 
-    int chunkHeight;
-    int chunkWidth;
+  int chunkHeight;
+  int chunkWidth;
 
-    boolean fastPaint = false;
+  boolean fastPaint = false;
 
 
-    public SeqCanvas(AlignViewport av)
-    {
-	this.av         = av;
-       fr = new FeatureRenderer(av);
-       sr = new SequenceRenderer(av);
-       PaintRefresher.Register(this);
+  public SeqCanvas(AlignViewport av)
+  {
+    this.av = av;
+    fr = new FeatureRenderer(av);
+    sr = new SequenceRenderer(av);
+    PaintRefresher.Register(this, av.alignment);
+  }
 
-    }
+  public AlignViewport getViewport()
+  {
+    return av;
+  }
+
+  public FeatureRenderer getFeatureRenderer()
+  {
+    return fr;
+  }
+
+  MCview.AppletPDBCanvas pdbCanvas;
+  public SequenceRenderer getSequenceRenderer()
+  {
+    return sr;
+  }
 
-  void drawNorthScale(Graphics g, int startx, int endx,int ypos) {
+  public void setPDBCanvas(MCview.AppletPDBCanvas pc)
+  {
+    pdbCanvas = pc;
+  }
+
+
+  void drawNorthScale(Graphics g, int startx, int endx, int ypos)
+  {
     int scalestartx = startx - startx % 10 + 10;
 
     g.setColor(Color.black);
@@ -57,8 +96,8 @@ public class SeqCanvas extends Panel
   void drawWestScale(Graphics g, int startx, int endx, int ypos)
   {
     FontMetrics fm = getFontMetrics(av.getFont());
-    ypos+= av.charHeight;
-      // EAST SCALE
+    ypos += av.charHeight;
+    // EAST SCALE
     for (int i = 0; i < av.alignment.getHeight(); i++)
     {
       SequenceI seq = av.alignment.getSequenceAt(i);
@@ -75,98 +114,113 @@ public class SeqCanvas extends Panel
         value = av.alignment.getSequenceAt(i).findPosition(index);
         break;
       }
-      if(value!=-1)
+      if (value != -1)
       {
-        int x = LABEL_WEST - fm.stringWidth(value+"");
-        g.drawString(value + "", x,  ypos +  i*av.charHeight - av.charHeight/5);
+        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)
+    ypos += av.charHeight;
+    // EAST 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 = endx;
+      int value = -1;
+      while (index > startx)
       {
-        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)
+      {
+        g.drawString(value + "", av.charWidth/2,
+                     ypos + i * av.charHeight - av.charHeight / 5);
+      }
     }
-    if(value!=-1)
-       g.drawString(value + "", 0,  ypos +  i*av.charHeight - av.charHeight/5);
-  }
-
-}
-
 
+  }
 
-public void fastPaint(int horizontal, int vertical)
-{
-    if (horizontal == 0 && vertical == 0 || gg==null)
+  public void fastPaint(int horizontal, int vertical)
+  {
+    if (fastPaint || gg == null)
+    {
+      repaint();
       return;
+    }
 
-    gg.copyArea(0, 0, imgWidth, imgHeight, -horizontal * av.charWidth,
-                -vertical * av.charHeight);
+    fastPaint = true;
+    gg.copyArea(horizontal * av.charWidth,
+                vertical * av.charHeight,
+                imgWidth,
+                imgHeight,
+                -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;
       sr = er - horizontal;
     }
     else if (horizontal < 0)
+    {
       er = sr - horizontal;
+    }
 
     else if (vertical > 0) // scroll down
     {
       ss = es - vertical;
-      if(ss<av.startSeq) // ie scrolling too fast, more than a page at a time
+      if (ss < av.startSeq) // ie scrolling too fast, more than a page at a time
+      {
         ss = av.startSeq;
+      }
       else
+      {
         transY = imgHeight - vertical * av.charHeight;
+      }
     }
     else if (vertical < 0)
     {
       es = ss - vertical;
-      if(es > av.endSeq)
+      if (es > av.endSeq)
+      {
         es = av.endSeq;
+      }
     }
 
-
     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);
     gg.translate( -transX, -transY);
 
-    fastPaint = true;
     repaint();
 
-}
+  }
 
-/**
- * Definitions of startx and endx (hopefully):
- * SMJS This is what I'm working towards!
- *   startx is the first residue (starting at 0) to display.
- *   endx   is the last residue to display (starting at 0).
- *   starty is the first sequence to display (starting at 0).
- *   endy   is the last sequence to display (starting at 0).
- * NOTE 1: The av limits are set in setFont in this class and
- * in the adjustment listener in SeqPanel when the scrollbars move.
- */
+  /**
+   * Definitions of startx and endx (hopefully):
+   * SMJS This is what I'm working towards!
+   *   startx is the first residue (starting at 0) to display.
+   *   endx   is the last residue to display (starting at 0).
+   *   starty is the first sequence to display (starting at 0).
+   *   endy   is the last sequence to display (starting at 0).
+   * NOTE 1: The av limits are set in setFont in this class and
+   * in the adjustment listener in SeqPanel when the scrollbars move.
+   */
   public void update(Graphics g)
   {
     paint(g);
@@ -174,6 +228,7 @@ public void fastPaint(int horizontal, int vertical)
 
   public void paint(Graphics g)
   {
+
     if (fastPaint)
     {
       g.drawImage(img, 0, 0, this);
@@ -182,154 +237,239 @@ public void fastPaint(int horizontal, int vertical)
     }
 
     // this draws the whole of the alignment
-      imgWidth  = this.getSize().width;
-      imgHeight = this.getSize().height;
-
-      imgWidth -= imgWidth%av.charWidth;
-      imgHeight-= imgHeight%av.charHeight;
-
-      if(imgWidth<1 || imgHeight<1)
-              return;
+    imgWidth = this.getSize().width;
+    imgHeight = this.getSize().height;
 
-      if(img==null || imgWidth!=img.getWidth(this) || imgHeight!=img.getHeight(this))
-      {
-        img = createImage(imgWidth, imgHeight);
-        gg = img.getGraphics();
-        gg.setFont(av.getFont());
-      }
+    imgWidth -= imgWidth % av.charWidth;
+    imgHeight -= imgHeight % av.charHeight;
 
-      gg.setColor(Color.white);
-      gg.fillRect(0,0,imgWidth,imgHeight);
+    if (imgWidth < 1 || imgHeight < 1)
+    {
+      return;
+    }
 
-    chunkWidth  =   getWrappedCanvasWidth( getSize().width );
-    chunkHeight =  (av.getAlignment().getHeight() + 2)*av.charHeight;
+    if (img == null || imgWidth != img.getWidth(this) ||
+        imgHeight != img.getHeight(this))
+    {
+      img = createImage(imgWidth, imgHeight);
+      gg = img.getGraphics();
+      gg.setFont(av.getFont());
+    }
 
-    av.setChunkHeight(chunkHeight);
-    av.setChunkWidth(chunkWidth);
+    gg.setColor(Color.white);
+    gg.fillRect(0, 0, imgWidth, imgHeight);
 
 
     if (av.getWrapAlignment())
-      drawWrappedPanel(gg, getSize().width, getSize().height, av.startRes);
+    {
+      drawWrappedPanel(gg, imgWidth, imgHeight, av.startRes);
+    }
     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, av.startRes,
+                av.startSeq, 0);
+    }
 
     g.drawImage(img, 0, 0, this);
 
+    if (pdbCanvas != null)
+    {
+      pdbCanvas.updateSeqColours();
+    }
   }
 
   int LABEL_WEST, LABEL_EAST;
   public int getWrappedCanvasWidth(int cwidth)
   {
-    FontMetrics fm = getFontMetrics(av.getFont());
+      FontMetrics fm = getFontMetrics(av.getFont());
 
-    LABEL_EAST = 0;
-    LABEL_WEST = 0;
+      LABEL_EAST = 0;
+      LABEL_WEST = 0;
 
-    if(av.scaleRightWrapped)
-      LABEL_EAST = fm.stringWidth( av.alignment.getWidth()+"000" );
+      if (av.scaleRightWrapped)
+      {
+          LABEL_EAST = fm.stringWidth(getMask());
+      }
 
-    if(av.scaleLeftWrapped)
-      LABEL_WEST = fm.stringWidth( av.alignment.getWidth()+"" );
+      if (av.scaleLeftWrapped)
+      {
+          LABEL_WEST = fm.stringWidth(getMask());
+      }
 
-    return  (cwidth - LABEL_EAST -LABEL_WEST)/av.charWidth;
+      return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
   }
 
-  public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight, int startRes)
+
+  /**
+   * Generates a string of zeroes.
+   * @return String
+   */
+  String getMask()
   {
-      AlignmentI al = av.getAlignment();
+    String mask = "00";
+    for (int i = av.alignment.getWidth(); i > 0; i /= 10)
+    {
+      mask += "0";
+    }
+    return mask;
+    }
 
-      FontMetrics fm = getFontMetrics(av.getFont());
+  public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight,
+                               int startRes)
+  {
+    AlignmentI al = av.getAlignment();
 
-      int LABEL_EAST = 0;
-      if(av.scaleRightWrapped)
-        LABEL_EAST = fm.stringWidth( al.getWidth()+"000" );
-      int LABEL_WEST = 0;
-      if(av.scaleLeftWrapped)
-        LABEL_WEST = fm.stringWidth(al.getWidth()+"0");
+    FontMetrics fm = getFontMetrics(av.getFont());
 
+    int LABEL_EAST = 0;
 
-      int cWidth  =   (canvasWidth - LABEL_EAST -LABEL_WEST)/av.charWidth;
-      int cHeight =  (av.getAlignment().getHeight() + 2)*av.charHeight;
+    if (av.scaleRightWrapped)
+    {
+        LABEL_EAST = fm.stringWidth(getMask());
+    }
 
-      av.endRes = av.startRes + cWidth;
+    int LABEL_WEST = 0;
 
-      int  endx   = startRes+cWidth-1;
-      int  ypos  = 2*av.charHeight;
+    if (av.scaleLeftWrapped)
+    {
+        LABEL_WEST = fm.stringWidth(getMask());
+    }
 
-      while (ypos <= canvasHeight && startRes<av.alignment.getWidth() )
-      {
+    int hgap = av.charHeight;
+    if(av.scaleAboveWrapped)
+      hgap += av.charHeight;
+
+    int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
+    int cHeight = av.getAlignment().getHeight() * av.charHeight;
+
+    av.setWrappedWidth(cWidth);
+
+    av.endRes = av.startRes + cWidth;
+
+
+    int endx = (startRes + cWidth) - 1;
+    int ypos = hgap;
+
+
+    while ((ypos <= canvasHeight) && (startRes < av.alignment.getWidth()))
+    {
         g.setColor(Color.black);
 
-        if(av.scaleLeftWrapped)
-          drawWestScale(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);
+        }
+
+        g.translate(LABEL_WEST, 0);
 
-        if(av.scaleRightWrapped)
+        if (av.scaleAboveWrapped)
         {
-          g.translate(canvasWidth - LABEL_EAST +av.charWidth, 0);
-          drawEastScale(g, startRes, endx, ypos);
-          g.translate( - (canvasWidth - LABEL_EAST+av.charWidth), 0);
+            drawNorthScale(g, startRes, endx, ypos);
         }
 
-        g.translate(LABEL_WEST,0);
-        if(av.scaleAboveWrapped)
-          drawNorthScale(g, startRes, endx, ypos);
+
+        if (av.vconsensus!=null && av.alignment.getWidth() >= av.vconsensus.size())
+        {
+          endx = av.vconsensus.size() - 2;
+        }
 
 
-        // When printing we have an extra clipped region,
-        // the Printable page which we need to account for here
-        Shape clip = g.getClip();
-        if(clip==null)
-          g.setClip(0, 0, cWidth*av.charWidth, canvasHeight);
-        else
-          g.setClip(0,
-                    (int)clip.getBounds().y,
-                    cWidth*av.charWidth,
-                    (int)clip.getBounds().height
-                    );
+        if(g.getClip()==null)
+          g.setClip(0, 0, cWidth * av.charWidth, canvasHeight);
 
         drawPanel(g, startRes, endx, 0, al.getHeight(), startRes, 0, ypos);
-        g.setClip(clip);
-        g.translate(-LABEL_WEST,0);
+         g.setClip(null);
+
+
+        if(av.showAnnotation)
+        {
+          g.translate(0, cHeight + ypos+4);
+          if(annotations==null)
+            annotations = new AnnotationPanel(av);
+
+          annotations.drawComponent( g, startRes, endx + 1);
+          g.translate(0, -cHeight - ypos-4);
+        }
+        g.translate(-LABEL_WEST, 0);
+
+        ypos += cHeight+getAnnotationHeight()+hgap;
+
 
-        ypos += cHeight;
         startRes += cWidth;
-        endx = startRes + cWidth - 1;
+        endx = (startRes + cWidth) - 1;
 
         if (endx > al.getWidth())
-          endx = al.getWidth();
-      }
+        {
+            endx = al.getWidth();
+        }
+        }
 
   }
 
+  AnnotationPanel annotations;
+  int getAnnotationHeight()
+  {
+    if(!av.showAnnotation)
+      return 0;
 
-  synchronized public void drawPanel(Graphics g,int x1,int x2, int y1, int y2,int startx, int starty,int offset) {
+    if(annotations==null)
+      annotations = new AnnotationPanel(av);
+
+    return annotations.adjustPanelHeight();
+    }
+
+  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);
 
     SequenceI nextSeq;
-
     /// First draw the sequences
-    /////////////////////////////
-    for (int i = y1 ; i < y2 ;i++)
+  /////////////////////////////
+  for (int i = y1; i < y2; i++)
+  {
+    nextSeq = av.alignment.getSequenceAt(i);
+
+    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)
     {
-     nextSeq = av.alignment.getSequenceAt(i);
-
-     sr.drawSequence(g, nextSeq, av.alignment.findAllGroups( nextSeq ),x1,x2,
-                 (x1 - startx) * av.charWidth,
-                 offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight),
-                 av.charWidth,av.charHeight);
-
-     if(av.showSequenceFeatures)
-     {
-       fr.drawSequence(g, nextSeq, av.alignment.findAllGroups( nextSeq ), x1, x2,
-                       (x1 - startx) * av.charWidth,
-                       offset +
-                       AlignmentUtil.getPixelHeight(starty, i, av.charHeight),
-                       av.charWidth, av.charHeight);
-     }
+      fr.drawSequence(g, nextSeq, x1, x2,
+                      (x1 - startx) * av.charWidth,
+                      offset +
+                      (i - starty) * av.charHeight,
+                      av.charWidth, av.charHeight);
     }
-    //
+    /// Highlight search Results once all sequences have been drawn
+   //////////////////////////////////////////////////////////
+   if (searchResults != null)
+   {
+     int[] visibleResults = searchResults.getResults(nextSeq, x1, x2);
+     if (visibleResults != null)
+       for (int r = 0; r < visibleResults.length; r += 2)
+       {
+         sr.drawHighlightedText(nextSeq, visibleResults[r],
+                                visibleResults[r + 1],
+                                (visibleResults[r] - startx) * av.charWidth,
+                                offset + ( (i - starty) * av.charHeight),
+                                av.charWidth, av.charHeight);
+       }
+   }
+  }
+
     /////////////////////////////////////
 
     // Now outline any areas if necessary
@@ -344,150 +484,156 @@ public void fastPaint(int horizontal, int vertical)
       group = (SequenceGroup) groups.elementAt(0);
       groupIndex = 0;
     }
-
     if (group != null)
-      do
-      {
-        int oldY = -1;
-        int i = 0;
-        boolean inGroup = false;
-        int top=-1, bottom =-1;
-        for (i = y1; i < y2; i++)
+    {
+        do
         {
-          sx = (group.getStartRes() - startx) * av.charWidth;
-          sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight);
-          ex = (group.getEndRes() + 1 - group.getStartRes()) * av.charWidth -1;
-
-          if (sx < getSize().width
-              && ex > 0
-              && group.sequences.contains(av.alignment.getSequenceAt(i)))
-          {
-            if (bottom == -1 && (i==av.alignment.getHeight()-1 ||
-                !group.sequences.contains(av.alignment.getSequenceAt(i + 1))))
-              bottom = sy + av.charHeight ;
-
-            if (!inGroup)
+            int oldY = -1;
+            int i = 0;
+            boolean inGroup = false;
+            int top = -1;
+            int bottom = -1;
+
+            for (i = y1; i < y2; i++)
+            {
+                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)
+                   {
+                     if(i == y2-1 || // Dont check for i+1 if on the bottom row
+                      !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;
+                    }
+                }
+            }
+
+            if (inGroup)
             {
-              if (top == -1 && i==0 ||
-                  !group.sequences.contains(av.alignment.getSequenceAt(i - 1)))
-                top = sy;
+              sy = offset + ( (i - starty) * 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);
 
-              oldY = sy;
-              inGroup = true;
-              if (group == av.getSelectionGroup())
+              if (sx < 0)
               {
-                    g.setColor(new Color(255,0,0));
+                ex += sx;
+                sx = 0;
               }
-              else
-              {
-                    g.setColor(group.getOutlineColour());
-              }
-            }
-          }
-          else
-          {
-            if (inGroup)
-            {
-              g.drawLine(sx, oldY, sx, sy );
-              g.drawLine(sx+ex, oldY, sx+ex, sy );
+
+              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;
+                top = -1;
               }
+
               if (bottom != -1)
               {
-                g.drawLine(sx, bottom, sx + ex, bottom);
+                g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);
                 bottom = -1;
               }
 
-
-              inGroup = false;
+                inGroup = false;
             }
-          }
-        }
-
-        if (inGroup)
-        {
 
-          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;
-
-           }
-          sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight);
-          g.drawLine(sx, oldY, sx, sy );
-          g.drawLine(sx+ex, oldY, sx+ex, sy );
-          inGroup = false;
-        }
-        groupIndex++;
-        if (groupIndex >= groups.size())
-          break;
-
-        group = (SequenceGroup) groups.elementAt(groupIndex);
+            groupIndex++;
 
-      }
-      while (groupIndex < groups.size());
-
-
-    /// 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 (groupIndex >= groups.size())
+            {
+                break;
+            }
 
-        if (searchSeq >= y1 && searchSeq < y2)
-        {
-          SequenceI seq = av.getAlignment().getSequenceAt(searchSeq);
-
-          int searchStart = seq.findIndex( searchResults[r+1] )-1;
-          int searchEnd =  seq.findIndex(  searchResults[r+2] )-1;
-
-          SequenceRenderer ssr = (SequenceRenderer) sr;
-          if(searchStart<x1)
-            searchStart = x1;
-          if(searchEnd > x2)
-            searchEnd = x2;
-
-          ssr.drawHighlightedText(seq,
-                                  searchStart,
-                                  searchEnd,
-                                  (searchStart - startx) * av.charWidth,
-                                  offset +
-                                  AlignmentUtil.getPixelHeight(starty, searchSeq,
-              av.charHeight),
-                                  av.charWidth,
-                                  av.charHeight);
+            group = (SequenceGroup) groups.elementAt(groupIndex);
         }
-      }
+        while (groupIndex < groups.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();
   }
 
-
 }