X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=789fb3f5b48d74c72947183755a55bf0aaf6e425;hb=6e71f42b0a3713ddbc3054e7ea9d8f5088130ec9;hp=2f02d5793091599b7cd26835c8f6a10925771a32;hpb=f1b17730086767d55e4f5fea54b72e4d30d52e65;p=jalview.git

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 2f02d57..789fb3f 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -1,45 +1,63 @@
+/*
+ * 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 JComponent
+public class SeqCanvas
+    extends JComponent
 {
-     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;
-
-
-    public SeqCanvas(AlignViewport av)
-    {
-	this.av         = av;
-       fr = new FeatureRenderer(av);
-       sr = new SequenceRenderer(av);
-       setLayout(new BorderLayout());
-       PaintRefresher.Register(this);
-
-    }
+  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, av.alignment);
+    setBackground(Color.white);
+  }
 
-  void drawNorthScale(Graphics g, int startx, int endx,int ypos) {
-    int scalestartx = startx - startx % 10 + 10;
+  void drawNorthScale(Graphics g, int startx, int endx, int ypos)
+  {
+    int scalestartx = startx - (startx % 10) + 10;
 
     g.setColor(Color.black);
 
@@ -48,137 +66,161 @@ public class SeqCanvas extends JComponent
     {
       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);
+                   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);
     }
   }
 
   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);
       int index = startx;
       int value = -1;
+
       while (index < endx)
       {
         if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
         {
           index++;
+
           continue;
         }
 
         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(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;
-    // 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)))
-      {
-        index--;
-        continue;
-      }
+    ypos += av.charHeight;
 
-      value = av.alignment.getSequenceAt(i).findPosition(index);
-      break;
-    }
-    if(value!=-1)
-       g.drawString(value + "", 0,  ypos +  i*av.charHeight - av.charHeight/5);
-  }
+    // 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)))
+        {
+          index--;
 
+          continue;
+        }
 
+        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)
+  public void fastPaint(int horizontal, int vertical)
+  {
+    if ( ( (horizontal == 0) && (vertical == 0)) || (gg == null))
+    {
       return;
+    }
 
     gg.copyArea(0, 0, 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;
+    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;
-      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;
+      {
+        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);
+    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 paint(Graphics g)
+  // Set this to false to force a full panel paint
+  public void paintComponent(Graphics g)
   {
-    g.setColor(Color.white);
-    g.fillRect(0, 0, getWidth(), getHeight());
-
-    if (fastPaint)
+    if (fastPaint  ||  getWidth() !=  g.getClipBounds().width
+                   ||  getHeight() != g.getClipBounds().height)
     {
       g.drawImage(img, 0, 0, this);
       fastPaint = false;
@@ -186,39 +228,45 @@ public void fastPaint(int horizontal, int vertical)
     }
 
     // this draws the whole of the alignment
-      imgWidth  = getWidth();
-      imgHeight = getHeight();
-      if(imgWidth<0 || imgHeight<1)
-        return;
+    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 = 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);
+    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);
+    gg.setColor(Color.white);
+    gg.fillRect(0, 0, imgWidth, imgHeight);
 
-    chunkWidth  =   getWrappedCanvasWidth( getWidth() );
-    chunkHeight =  (av.getAlignment().getHeight() + 2)*av.charHeight;
+    chunkWidth = getWrappedCanvasWidth(getWidth());
+    chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;
 
     av.setChunkHeight(chunkHeight);
     av.setChunkWidth(chunkWidth);
 
-
     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);
-
   }
 
-  int LABEL_WEST, LABEL_EAST;
   public int getWrappedCanvasWidth(int cwidth)
   {
     FontMetrics fm = getFontMetrics(av.getFont());
@@ -226,161 +274,199 @@ public void fastPaint(int horizontal, int vertical)
     LABEL_EAST = 0;
     LABEL_WEST = 0;
 
-    if(av.scaleRightWrapped)
-      LABEL_EAST = fm.stringWidth( av.alignment.getWidth()+"000" );
+    if (av.scaleRightWrapped)
+    {
+      LABEL_EAST = fm.stringWidth(av.alignment.getWidth() + "000");
+    }
 
-    if(av.scaleLeftWrapped)
-      LABEL_WEST = fm.stringWidth( av.alignment.getWidth()+"" );
+    if (av.scaleLeftWrapped)
+    {
+      LABEL_WEST = fm.stringWidth(av.alignment.getWidth() + "");
+    }
 
-    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)
+  public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight,
+                               int startRes)
   {
-      AlignmentI al = av.getAlignment();
+    AlignmentI al = av.getAlignment();
+
+    FontMetrics fm = getFontMetrics(av.getFont());
 
-      FontMetrics fm = getFontMetrics(av.getFont());
+    int LABEL_EAST = 0;
 
-      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");
+    if (av.scaleRightWrapped)
+    {
+      LABEL_EAST = fm.stringWidth(al.getWidth() + "000");
+    }
+
+    int LABEL_WEST = 0;
+
+    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;
 
-      int cWidth  =   (canvasWidth - LABEL_EAST -LABEL_WEST)/av.charWidth;
-      int cHeight =  (av.getAlignment().getHeight() + 2)*av.charHeight;
+    av.endRes = av.startRes + cWidth;
 
-      av.endRes = av.startRes + cWidth;
+    int endx = (startRes + cWidth) - 1;
+    int ypos = 2 * av.charHeight;
 
-      int  endx   = startRes+cWidth-1;
-      int  ypos  = 2*av.charHeight;
+    while ( (ypos <= canvasHeight) && (startRes < av.alignment.getWidth()))
+    {
+      g.setColor(Color.black);
 
-      while (ypos <= canvasHeight && startRes<av.alignment.getWidth() )
+      if (av.scaleLeftWrapped)
       {
-        g.setColor(Color.black);
+        drawWestScale(g, startRes, endx, ypos);
+      }
 
-        if(av.scaleLeftWrapped)
-          drawWestScale(g, startRes, endx, ypos);
+      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(av.scaleRightWrapped)
-        {
-          g.translate(canvasWidth - LABEL_EAST +av.charWidth, 0);
-          drawEastScale(g, startRes, endx, ypos);
-          g.translate( - (canvasWidth - LABEL_EAST+av.charWidth), 0);
-        }
+      g.translate(LABEL_WEST, 0);
 
-        g.translate(LABEL_WEST,0);
-        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(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();
+      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 (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);
 
-  synchronized public void drawPanel(Graphics g1,int x1,int x2, int y1, int y2,int startx, int starty,int offset) {
+      ypos += cHeight;
+      startRes += cWidth;
+      endx = (startRes + cWidth) - 1;
+
+      if (endx > al.getWidth())
+      {
+        endx = al.getWidth();
+      }
+    }
+  }
 
-    Graphics2D g = (Graphics2D)g1;
+  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.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);
-     }
+      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, bottom =-1;
+        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 -1;
-
-          if (sx < getWidth()
-              && ex > 0
-              && group.sequences.contains(av.alignment.getSequenceAt(i)))
+          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 ( (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)))
+              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,3f}, 0f ));
+                g.setStroke(new BasicStroke(1,
+                                            BasicStroke.CAP_BUTT,
+                                            BasicStroke.JOIN_ROUND, 3f,
+                                            new float[]
+                                            {5f, 3f}, 0f));
                 g.setColor(Color.RED);
               }
               else
@@ -394,21 +480,21 @@ public void fastPaint(int horizontal, int vertical)
           {
             if (inGroup)
             {
-              g.drawLine(sx, oldY, sx, sy );
-              g.drawLine(sx+ex, oldY, sx+ex, sy );
+              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;
+                top = -1;
               }
+
               if (bottom != -1)
               {
                 g.drawLine(sx, bottom, sx + ex, bottom);
                 bottom = -1;
               }
 
-
               inGroup = false;
             }
           }
@@ -416,79 +502,89 @@ public void fastPaint(int horizontal, int vertical)
 
         if (inGroup)
         {
-
-          if(top!=-1)
+          if (top != -1)
           {
             g.drawLine(sx, top, sx + ex, top);
-            top =-1;
+            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 );
+
+          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;
-          if(searchStart<x1)
+
+          if (searchStart < x1)
+          {
             searchStart = x1;
-          if(searchEnd > x2)
+          }
+
+          if (searchEnd > x2)
+          {
             searchEnd = x2;
-          ssr.drawHighlightedText(av.getAlignment().getSequenceAt(searchSeq),
-                                  searchStart,
-                                  searchEnd,
+          }
+
+          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 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;
 
     repaint();
   }
-
-
 }