X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=1194d08afceca7ad43f51caf76d68317ffdd3b40;hb=1d6ae39a6442c455d362b933f1da89b0a481e5f5;hp=de421ed2eb14ff44b12042f87edc8771fa1f9fbb;hpb=4532dfefeac026198bfea1b9dbe84186e870bfc8;p=jalview.git

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index de421ed..1194d08 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -1,277 +1,470 @@
+/*
+ * 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.gui;
 
 import java.awt.*;
+import java.awt.image.*;
 import javax.swing.*;
-import jalview.datamodel.*;
-import jalview.analysis.*;
 
+import jalview.analysis.*;
+import jalview.datamodel.*;
 
-public class SeqCanvas extends JPanel
+public class SeqCanvas
+    extends JComponent
 {
-     FeatureRenderer fr;
-    Image             img;
-    Graphics2D          gg;
-    int               imgWidth;
-    int               imgHeight;
-
-    AlignViewport     av;
-
-    public boolean paintFlag = false;
-
-    boolean showScores = false;
-    boolean displaySearch = false;
-    int [] searchResults = null;
+  FeatureRenderer fr;
+  SequenceRenderer sr;
+  BufferedImage img;
+  Graphics2D gg;
+  int imgWidth;
+  int imgHeight;
+  AlignViewport av;
+  boolean showScores = false;
+  boolean displaySearch = false;
+  int[] searchResults = null;
+  int chunkHeight;
+  int chunkWidth;
+  boolean fastPaint = false;
+  int LABEL_WEST;
+  int LABEL_EAST;
+
+  public SeqCanvas(AlignViewport av)
+  {
+    this.av = av;
+    fr = new FeatureRenderer(av);
+    sr = new SequenceRenderer(av);
+    setLayout(new BorderLayout());
+    PaintRefresher.Register(this);
+  }
 
-    int chunkHeight;
-    int chunkWidth;
+  void drawNorthScale(Graphics g, int startx, int endx, int ypos)
+  {
+    int scalestartx = startx - (startx % 10) + 10;
 
+    g.setColor(Color.black);
 
-    public SeqCanvas(AlignViewport av)
+    // NORTH SCALE
+    for (int i = scalestartx; i < endx; i += 10)
     {
-	this.av         = av;
-       fr = new FeatureRenderer(av);
-       setLayout(new BorderLayout());
-       PaintRefresher.Register(this);
-
+      String string = String.valueOf(i);
+      g.drawString(string, (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);
     }
+  }
 
-  public void drawScale(Graphics g, int startx, int endx,int ypos) {
-      int scalestartx = startx - startx%10 + 10;
+  void drawWestScale(Graphics g, int startx, int endx, int ypos)
+  {
+    FontMetrics fm = getFontMetrics(av.getFont());
+    ypos += av.charHeight;
 
-      g.setColor(Color.black);
+    // EAST SCALE
+    for (int i = 0; i < av.alignment.getHeight(); i++)
+    {
+      SequenceI seq = av.alignment.getSequenceAt(i);
+      int index = startx;
+      int value = -1;
 
-      for (int i=scalestartx;i < endx;i+= 10)
+      while (index < endx)
       {
-          String string = String.valueOf(i);
-          g.drawString(string,(i-startx-1)*av.charWidth,ypos - av.charHeight/2);
+        if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
+        {
+          index++;
+
+          continue;
+        }
 
-          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 );
+        value = av.alignment.getSequenceAt(i).findPosition(index);
 
+        break;
       }
 
+      if (value != -1)
+      {
+        int x = LABEL_WEST - fm.stringWidth(value + "");
+        g.drawString(value + "", x,
+                     (ypos + (i * av.charHeight)) - (av.charHeight / 5));
+      }
+    }
   }
 
+  void drawEastScale(Graphics g, int startx, int endx, int ypos)
+  {
+    ypos += av.charHeight;
 
-public void fastPaint(int horizontal, int vertical)
-{
-    if(horizontal==0 && vertical==0)
-   {
-     return;
-   }
-
+    // EAST SCALE
+    for (int i = 0; i < av.alignment.getHeight(); i++)
+    {
+      SequenceI seq = av.alignment.getSequenceAt(i);
+      int index = endx;
+      int value = -1;
 
-   if (img==null || paintFlag)
-   {
-      repaint();
-      return;
-   }
+      while (index > startx)
+      {
+        if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
+        {
+          index--;
 
-    gg.copyArea( 0,0, imgWidth, imgHeight, -horizontal*av.charWidth, -vertical*av.charHeight );
+          continue;
+        }
 
- int sr=av.startRes, er=av.endRes+1, 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;
- }
+        value = av.alignment.getSequenceAt(i).findPosition(index);
 
+        break;
+      }
 
+      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))
+    {
+      return;
+    }
 
- if(vertical>0)    // scroll down
- {
-   transY = imgHeight - vertical*av.charHeight;
-   ss = es - vertical;
- }
- else if(vertical<0)
- {
+    gg.copyArea(0, 0, imgWidth, imgHeight, -horizontal * av.charWidth,
+                -vertical * av.charHeight);
 
-     es = ss-vertical;
+    int sr = av.startRes;
+    int er = av.endRes;
+    int ss = av.startSeq;
+    int es = av.endSeq;
+    int transX = 0;
+    int 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;
 
-    gg.translate(transX, transY);
+      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;
 
-    drawPanel(gg, sr,er,ss,es,sr,ss,0);
+      if (es > av.endSeq)
+      {
+        es = av.endSeq;
+      }
+    }
 
-    gg.translate( -transX, -transY );
-    getGraphics().drawImage(img,0,0,this);
+    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);
 
-/**
- * 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.
- */
+    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.
+   */
   public void paintComponent(Graphics g)
   {
+    g.setColor(Color.white);
+    g.fillRect(0, 0, getWidth(), getHeight());
+
+    if (fastPaint)
+    {
+      g.drawImage(img, 0, 0, this);
+      fastPaint = false;
+
+      return;
+    }
+
     // this draws the whole of the alignment
+    imgWidth = getWidth();
+    imgHeight = getHeight();
 
-      imgWidth  = getWidth();
-      imgHeight = getHeight();
+    imgWidth -= (imgWidth % av.charWidth);
+    imgHeight -= (imgHeight % av.charHeight);
 
-      imgWidth -= imgWidth%av.charWidth;
-      imgHeight-= imgHeight%av.charHeight;
+    if ( (imgWidth < 1) || (imgHeight < 1))
+    {
+      return;
+    }
 
-      img = createImage(imgWidth,imgHeight);
-      gg  = (Graphics2D)img.getGraphics();
-      gg.setFont(av.getFont());
-      gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,RenderingHints.VALUE_ANTIALIAS_ON);
-      gg.setClip(0,0,imgWidth, imgHeight);
-      paintFlag = false;
+    img = new BufferedImage(imgWidth, imgHeight, BufferedImage.TYPE_INT_RGB);
+    gg = (Graphics2D) img.getGraphics();
+    gg.setFont(av.getFont());
+    gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+                        RenderingHints.VALUE_ANTIALIAS_ON);
 
+    gg.setColor(Color.white);
+    gg.fillRect(0, 0, imgWidth, imgHeight);
 
-    chunkWidth  =   getWidth()/av.charWidth;
-    chunkHeight =  (av.getAlignment().getHeight() + 2)*av.charHeight;
+    chunkWidth = getWrappedCanvasWidth(getWidth());
+    chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;
 
     av.setChunkHeight(chunkHeight);
     av.setChunkWidth(chunkWidth);
 
-    g.setColor(Color.WHITE);
-    g.fillRect(0,0,getWidth(), getHeight());
-
     if (av.getWrapAlignment())
+    {
       drawWrappedPanel(gg, getWidth(), getHeight(), 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);
+  }
 
-    g.drawImage(img,0,0,this);
+  public int getWrappedCanvasWidth(int cwidth)
+  {
+    FontMetrics fm = getFontMetrics(av.getFont());
 
+    LABEL_EAST = 0;
+    LABEL_WEST = 0;
+
+    if (av.scaleRightWrapped)
+    {
+      LABEL_EAST = fm.stringWidth(av.alignment.getWidth() + "000");
+    }
+
+    if (av.scaleLeftWrapped)
+    {
+      LABEL_WEST = fm.stringWidth(av.alignment.getWidth() + "");
+    }
+
+    return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
   }
 
-  public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight, int startRes)
+  public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight,
+                               int startRes)
   {
-      AlignmentI da = av.getAlignment();
+    AlignmentI al = av.getAlignment();
 
-      int cWidth  =   canvasWidth/av.charWidth;
-      int cHeight =  (av.getAlignment().getHeight() + 2)*av.charHeight;
+    FontMetrics fm = getFontMetrics(av.getFont());
 
-      int  endx   = startRes+cWidth-1;
-      int ypos  = 2*av.charHeight;
+    int LABEL_EAST = 0;
 
-      while (ypos <= canvasHeight)
-      {
-        drawScale(g, startRes, endx, ypos);
-        drawPanel(g, startRes, endx, 0, da.getHeight(), startRes, 0, ypos);
+    if (av.scaleRightWrapped)
+    {
+      LABEL_EAST = fm.stringWidth(al.getWidth() + "000");
+    }
 
-        ypos += cHeight;
-        startRes += cWidth;
-        endx = startRes + cWidth - 1;
+    int LABEL_WEST = 0;
 
-        if (endx > da.getWidth())
-          endx = da.getWidth();
-      }
+    if (av.scaleLeftWrapped)
+    {
+      LABEL_WEST = fm.stringWidth(al.getWidth() + "0");
+    }
 
-  }
+    int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
+    int cHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;
 
+    av.endRes = av.startRes + cWidth;
 
-  public void drawPanel(Graphics g1,int x1,int x2, int y1, int y2,int startx, int starty,int offset) {
+    int endx = (startRes + cWidth) - 1;
+    int ypos = 2 * av.charHeight;
 
+    while ( (ypos <= canvasHeight) && (startRes < av.alignment.getWidth()))
+    {
+      g.setColor(Color.black);
 
-   Graphics2D g = (Graphics2D)g1;
-    g.setFont(av.getFont());
-    RendererI sr = av.getRenderer();
+      if (av.scaleLeftWrapped)
+      {
+        drawWestScale(g, startRes, endx, ypos);
+      }
 
-    /*Vector    pid    = av.getConsensus(false);
-    Vector tmpseq = new Vector();
-    for (int i = 0; i < av.getAlignment().getHeight(); i++)
-	if (!av.getSelection().contains(av.getAlignment().getSequenceAt(i)))
-	    tmpseq.addElement(av.getAlignment().getSequenceAt(i));
+      if (av.scaleRightWrapped)
+      {
+        g.translate(canvasWidth - LABEL_EAST + av.charWidth, 0);
+        drawEastScale(g, startRes, endx, ypos);
+        g.translate( - (canvasWidth - LABEL_EAST + av.charWidth), 0);
+      }
 
-    if (sr instanceof SequenceRenderer)
-	pid    = AAFrequency.calculate(tmpseq,x1,x2);
+      g.translate(LABEL_WEST, 0);
 
-    else if (sr instanceof GraphRenderer)
-	pid = AAFrequency.calculatePID(av.getAlignment().getSequenceAt(0),
-				       av.getAlignment().getSequences(),
-				       av.getPIDWindow(),x1,x2);
+      if (av.scaleAboveWrapped)
+      {
+        drawNorthScale(g, startRes, endx, ypos);
+      }
 
-*/
+      // When printing we have an extra clipped region,
+      // the Printable page which we need to account for here
+      Shape clip = g.getClip();
 
-   /* if (y2 > starty && y1 < av.getEndSeq())
-    {
-       fillBackground(g,
-                   Color.red,
-                   (x1-startx)*charWidth,
-                   offset + AlignmentUtil.getPixelHeight(starty,y1,av.getCharHeight()),
-                   (x2-x1+1)*charWidth,
-                   offset + AlignmentUtil.getPixelHeight(y1,y2,av.getCharHeight()));
-    }*/
+      if (clip == null)
+      {
+        g.setClip(0, 0, cWidth * av.charWidth, canvasHeight);
+      }
+      else
+      {
+        g.setClip(0, (int) clip.getBounds().getY(),
+                  cWidth * av.charWidth, (int) clip.getBounds().getHeight());
+      }
+
+      drawPanel(g, startRes, endx, 0, al.getHeight(), startRes, 0, ypos);
+      g.setClip(clip);
+      g.translate( -LABEL_WEST, 0);
+
+      ypos += cHeight;
+      startRes += cWidth;
+      endx = (startRes + cWidth) - 1;
+
+      if (endx > al.getWidth())
+      {
+        endx = al.getWidth();
+      }
+    }
+  }
+
+  synchronized public void drawPanel(Graphics g1, int x1, int x2, int y1,
+                                     int y2, int startx, int starty, int offset)
+  {
+    Graphics2D g = (Graphics2D) g1;
+    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.getAlignment().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,null, i);
-
-     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, null, i);
-     }
+      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);
+      }
     }
+
     //
     /////////////////////////////////////
-
     // 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 sx = -1;
+    int sy = -1;
+    int ex = -1;
     int groupIndex = -1;
-    if (group == null && groups.size() > 0)
+
+    if ( (group == null) && (groups.size() > 0))
     {
       group = (SequenceGroup) groups.elementAt(0);
       groupIndex = 0;
     }
 
     if (group != null)
+    {
       do
       {
         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 + AlignmentUtil.getPixelHeight(starty, i, av.charHeight);
-          ex = (group.getEndRes() + 1 - group.getStartRes()) * av.charWidth;
-
-          if (group.sequences.contains(av.alignment.getSequenceAt(i))
-              && sx < getWidth()
-              && ex > 0)
+          sy = offset +
+              AlignmentUtil.getPixelHeight(starty, i, av.charHeight);
+          ex = ( ( (group.getEndRes() + 1) - group.getStartRes()) *
+                av.charWidth) -
+              1;
+
+          if ( (sx < getWidth()) && (ex > 0) &&
+              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.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND, 3f, new float[]{5f,2f,2f}, 0f ));
+                g.setStroke(new BasicStroke(1,
+                                            BasicStroke.CAP_BUTT,
+                                            BasicStroke.JOIN_ROUND, 3f,
+                                            new float[]
+                                            {5f, 3f}, 0f));
                 g.setColor(Color.RED);
               }
               else
@@ -285,74 +478,111 @@ public void fastPaint(int horizontal, int vertical)
           {
             if (inGroup)
             {
-              g.drawRect(sx, oldY, ex, (sy - oldY));
+              g.drawLine(sx, oldY, sx, sy);
+              g.drawLine(sx + ex, oldY, sx + ex, sy);
+
+              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 + AlignmentUtil.getPixelHeight(starty, i, av.charHeight);
-          g.drawRect(sx, oldY, ex, (sy - oldY));
+          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);
-
       }
       while (groupIndex < groups.size());
-
+    }
 
     /// Highlight search Results once all sequences have been drawn
     //////////////////////////////////////////////////////////
-    if(displaySearch)
+    if (displaySearch)
     {
-      for(int r=0; r<searchResults.length; r+=3)
+      for (int r = 0; r < searchResults.length; r += 3)
       {
         int searchSeq = searchResults[r];
-        int searchStart = searchResults[r+1];
-        int searchEnd = searchResults[r+2];
 
-        if (searchSeq >= y1 && searchSeq < y2)
+        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;
-          ssr.drawHighlightedText(av.getAlignment().getSequenceAt(searchSeq),
-                                  searchStart,
-                                  searchEnd,
+
+          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);
+                                  AlignmentUtil.getPixelHeight(starty,
+              searchSeq,
+              av.charHeight), av.charWidth, av.charHeight);
         }
       }
     }
-
   }
 
-
-  public int getChunkWidth() {
-    return chunkWidth;
-  }
-
-  public void highlightSearchResults(int [] results)
+  public void highlightSearchResults(int[] results)
   {
     // results are in the order sequence, startRes, endRes
-    if(results==null)
+    if (results == null)
+    {
       displaySearch = false;
+    }
     else
+    {
       displaySearch = true;
+    }
 
     searchResults = results;
 
-    paintFlag = true;
     repaint();
   }
-
-
 }