X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=c4424655edc22241d5fc2c48aab764569b5101ea;hb=b14411143cbfb4d311f68b3d3b73a645bf8200e8;hp=7f30c2489ada6adc0b43fc1ea0cb955e9877c0b3;hpb=4b65534cd7d7dad17375e16d38848a69f23882b4;p=jalview.git

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 7f30c24..c442465 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -1,355 +1,591 @@
+/*
+ * 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 java.awt.event.*;
-import jalview.datamodel.*;
-import jalview.schemes.*;
-import jalview.analysis.*;
 
+import jalview.analysis.*;
+import jalview.datamodel.*;
 
-public class SeqCanvas extends JPanel
+public class SeqCanvas
+    extends JComponent
 {
-    Image             img;
-    Graphics          gg;
-    int               imgWidth;
-    int               imgHeight;
-
-    AlignViewport     av;
+  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);
+  }
 
-    public boolean paintFlag = false;
+  void drawNorthScale(Graphics g, int startx, int endx, int ypos)
+  {
+    int scalestartx = startx - (startx % 10) + 10;
 
-    boolean showScores = false;
-    boolean displaySearch = false;
-    int [] searchResults = null;
+    g.setColor(Color.black);
 
-    int chunkHeight;
-    int chunkWidth;
+    // 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));
+
+      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;
 
-    public SeqCanvas(AlignViewport av)
+    // EAST SCALE
+    for (int i = 0; i < av.alignment.getHeight(); i++)
     {
-	this.av         = av;
-       setLayout(new BorderLayout());
-       PaintRefresher.Register(this);
+      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)
+      {
+        int x = LABEL_WEST - fm.stringWidth(value + "");
+        g.drawString(value + "", x,
+                     (ypos + (i * av.charHeight)) - (av.charHeight / 5));
+      }
     }
+  }
 
-  public void drawScale(int startx, int endx,int charWidth, int charHeight,int ypos) {
-      int scalestartx = startx - startx%10 + 10;
+  void drawEastScale(Graphics g, int startx, int endx, int ypos)
+  {
+    ypos += av.charHeight;
 
-      gg.setColor(Color.black);
+    // EAST SCALE
+    for (int i = 0; i < av.alignment.getHeight(); i++)
+    {
+      SequenceI seq = av.alignment.getSequenceAt(i);
+      int index = endx;
+      int value = -1;
 
-      for (int i=scalestartx;i < endx;i+= 10) {
-	  String string = String.valueOf(i);
-	  gg.drawString(string,(int)((i-startx-1)*charWidth),ypos+15 - charHeight*(2));
+      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))
+    {
+      return;
+    }
 
-/**
- * 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.
- */
+    gg.copyArea(0, 0, imgWidth, imgHeight, -horizontal * av.charWidth,
+                -vertical * av.charHeight);
 
-  public void paintComponent(Graphics g) {
+    int sr = av.startRes;
+    int er = av.endRes;
+    int ss = av.startSeq;
+    int es = av.endSeq;
+    int transX = 0;
+    int transY = 0;
 
-    AlignmentI da = av.getAlignment();
+    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 (img == null ||
-        imgWidth  !=  getWidth()  ||
-        imgHeight !=  getHeight()
-        || paintFlag)
+      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)
+      {
+        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.
+   */
 
-      imgWidth  = getWidth();
-      imgHeight = getHeight();
 
-      img = createImage(imgWidth,imgHeight);
-      gg  = img.getGraphics();
+  // Set this to false to force a full panel paint
+  public void paintComponent(Graphics g)
+  {
+    if (img!=null
+        && (fastPaint  ||  getWidth() !=  g.getClipBounds().width
+            ||  getHeight() != g.getClipBounds().height))
+    {
+      g.drawImage(img, 0, 0, this);
+      fastPaint = false;
+      return;
+    }
+
+    // this draws the whole of the alignment
+    imgWidth = getWidth();
+    imgHeight = getHeight();
 
-      gg.setFont(av.getFont());
+    imgWidth -= (imgWidth % av.charWidth);
+    imgHeight -= (imgHeight % av.charHeight);
 
-      paintFlag = false;
+    if ( (imgWidth < 1) || (imgHeight < 1))
+    {
+      return;
     }
 
-    chunkWidth  =   getWidth()/av.charWidth;
-    chunkHeight =  (da.getHeight() + 2)*av.charHeight;
+    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 = 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);
+    }
 
+    g.drawImage(img, 0, 0, this);
+  }
 
-    fillBackground(gg,Color.WHITE,0,0,imgWidth,imgHeight);
+  public int getWrappedCanvasWidth(int cwidth)
+  {
+    FontMetrics fm = getFontMetrics(av.getFont());
 
-    /* if (av.getWrapAlignment()) {
-        int offy = av.getStartSeq();
-	  startx = (int)(offy/chunkWidth)*chunkWidth;
-	  endx   = startx + chunkWidth;
-	  starty = offy%chunkHeight;
-	  endy   = starty + da.getHeight();
+    LABEL_EAST = 0;
+    LABEL_WEST = 0;
 
-	  int ypos     = 0;
-	  int rowstart = starty;
+    if (av.scaleRightWrapped)
+    {
+      LABEL_EAST = fm.stringWidth(av.alignment.getWidth() + "000");
+    }
 
-	  if (starty == 0) {
-	      ypos = 2*charHeight;
-	  } else if (starty == 1) {
-	      starty = 0;
-	      ypos = charHeight;
-	  }
+    if (av.scaleLeftWrapped)
+    {
+      LABEL_WEST = fm.stringWidth(av.alignment.getWidth() + "");
+    }
 
-	  if (endy > da.getHeight()) {
-	      endy = da.getHeight();
-	  }
+    return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
+  }
 
-	  if (endx > da.getWidth()) {
-	      endx = da.getWidth();
-	  }
+  public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight,
+                               int startRes)
+  {
+    AlignmentI al = av.getAlignment();
 
-	  if (rowstart < 2) {
-	      drawScale(startx,endx,charWidth,charHeight,ypos);
-	  }
+    FontMetrics fm = getFontMetrics(av.getFont());
 
-	  drawPanel(gg,startx,endx,starty,endy,startx,starty,ypos);
+    int LABEL_EAST = 0;
 
-	  if (rowstart == 0) {
-	      ypos = ypos + chunkHeight;
-	  } else if (rowstart == 1) {
-	      ypos = ypos + chunkHeight;
-	  } else {
-	      ypos   = ypos + chunkHeight - rowstart*charHeight;
-	  }
+    if (av.scaleRightWrapped)
+    {
+      LABEL_EAST = fm.stringWidth(al.getWidth() + "000");
+    }
 
-	  startx += chunkWidth;
-	  endx   = startx + chunkWidth;
-	  starty = 0;
+    int LABEL_WEST = 0;
 
-	  if (endx > da.getWidth()) {
-	      endx = da.getWidth();
-	  }
-	  // Draw the rest of the panels
+    if (av.scaleLeftWrapped)
+    {
+      LABEL_WEST = fm.stringWidth(al.getWidth() + "0");
+    }
 
-	  while (ypos <= getHeight()) {
-	      drawScale(startx,endx,charWidth,charHeight,ypos);
-	      drawPanel(gg,startx,endx,0,da.getHeight(),startx,starty,ypos);
+    int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
+    int cHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;
 
-	      ypos   += chunkHeight;
-	      startx += chunkWidth;
-	      endx   = startx + chunkWidth;
+    av.endRes = av.startRes + cWidth;
 
-	      if (endy > da.getHeight()) {
-		  endy = da.getHeight();
-	      }
+    int endx = (startRes + cWidth) - 1;
+    int ypos = 2 * av.charHeight;
 
-	      if (endx > da.getWidth()) {
-		  endx = da.getWidth();
-	      }
+    while ( (ypos <= canvasHeight) && (startRes < av.alignment.getWidth()))
+    {
+      g.setColor(Color.black);
 
-	  }
+      if (av.scaleLeftWrapped)
+      {
+        drawWestScale(g, startRes, endx, ypos);
       }
-      else*/
+
+      if (av.scaleRightWrapped)
       {
-	  drawPanel(gg,av.startRes,av.endRes,av.startSeq,av.endSeq,av.startRes,av.startSeq,0);
+        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);
 
-  /*  if ((oldendy -oldstarty) > (getWidth() / av.getCharWidth())) {
-      System.out.println("LIMITS ERROR LIMITS ERROR");
-      System.out.println("Corrds " + (oldendy-oldstarty) + " " + (getWidth()/av.getCharWidth()) + " " + getWidth() + " " + av.getCharWidth());
-    }*/
+      if (av.scaleAboveWrapped)
+      {
+        drawNorthScale(g, startRes, endx, ypos);
+      }
 
-    g.drawImage(img,0,0,this);
+      // 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();
+      }
+    }
+  }
 
-  public void drawPanel(Graphics g,int x1,int x2, int y1, int y2,int startx, int starty,int offset) {
+  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;
 
-    g.setFont(av.getFont());
-    int            charWidth  = av.getCharWidth();
-    int            charHeight = av.getCharHeight();
-    RendererI sr = av.getRenderer();
+    /// First draw the sequences
+    /////////////////////////////
+    for (int i = y1; i < y2; i++)
+    {
+      nextSeq = av.alignment.getSequenceAt(i);
 
-    /*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));
+      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 (sr instanceof SequenceRenderer)
-	pid    = AAFrequency.calculate(tmpseq,x1,x2);
+      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);
+      }
+    }
 
-    else if (sr instanceof GraphRenderer)
-	pid = AAFrequency.calculatePID(av.getAlignment().getSequenceAt(0),
-				       av.getAlignment().getSequences(),
-				       av.getPIDWindow(),x1,x2);
+    //
+    /////////////////////////////////////
+    // Now outline any areas if necessary
+    /////////////////////////////////////
+    SequenceGroup group = av.getSelectionGroup();
+    java.util.Vector groups = av.alignment.getGroups();
 
-*/
+    int sx = -1;
+    int sy = -1;
+    int ex = -1;
+    int groupIndex = -1;
 
-   /* if (y2 > starty && y1 < av.getEndSeq())
+    if ( (group == null) && (groups.size() > 0))
     {
-       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()));
-    }*/
+      group = (SequenceGroup) groups.elementAt(0);
+      groupIndex = 0;
+    }
 
-    SequenceI nextSeq;
-    SequenceGroup group=null;
-    SequenceGroup [] groups=null;
-    boolean inGroup=false; // are we in a defined group?
-    boolean inRB=false; //Are we in a rubberband group?
-    int sx=-1, sy=-1, ex=-1, ey=-1;
-    int oldStartX=0,oldEndX=0,oldY=0;
-    int oldRStartX=0,oldREndX=0,oldRY=0;
-    for (int i = y1 ; i < y2 ;i++)
+    if (group != null)
     {
-     nextSeq = av.getAlignment().getSequenceAt(i);
-
-     group = av.alignment.findGroup( nextSeq );
-     groups = av.alignment.findAllGroups( nextSeq );
-
-     sr.drawSequence(g, nextSeq, groups,x1,x2,
-                 (x1 - startx) * charWidth,
-                 offset + AlignmentUtil.getPixelHeight(starty, i, av.getCharHeight()),
-                 charWidth,charHeight,null, i);
-
-
-     if( group!=null )
-     {
+      do
+      {
+        int oldY = -1;
+        int i = 0;
+        boolean inGroup = false;
+        int top = -1;
+        int bottom = -1;
 
-        g.setColor(Color.lightGray);
+        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)))
+          {
+            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, 3f}, 0f));
+                g.setColor(Color.RED);
+              }
+              else
+              {
+                g.setStroke(new BasicStroke());
+                g.setColor(group.getOutlineColour());
+              }
+            }
+          }
+          else
+          {
+            if (inGroup)
+            {
+              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;
+            }
+          }
+        }
 
-        sx = (group.getStartRes()-startx)*charWidth;
-        sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.getCharHeight());
-        ex = (group.getEndRes()+1-startx)*charWidth;
-        ey = offset + AlignmentUtil.getPixelHeight(starty, i+1, av.getCharHeight());
+        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 (!inGroup)
+        if (groupIndex >= groups.size())
         {
-          g.drawLine(sx, sy, ex, sy); // Horizontal, top of new box
-          inGroup=true;
+          break;
         }
 
-        g.drawLine(sx, sy, sx, ey ); // vertical line, left hand side
-        g.drawLine( ex,sy,ex,ey);    // vertical line, right hand side
-        if (i == y2 - 1)// last line of alignment, seal the box
-          g.drawLine(sx, ey, ex, ey); // Horizontal, bottom of old box
-
-        oldStartX = sx;
-        oldEndX = ex;
-        oldY = ey;
-
-     }
-     else if(inGroup)
-     {
-       g.setColor(Color.lightGray);
-       g.drawLine(oldStartX, oldY, oldEndX, oldY); // Horizontal, bottom of old box
-     }
-     else
-       inGroup = false;
-
-     group = av.getRubberbandGroup();
-     if( group != null && group.sequences.contains(nextSeq) )
-     {
-         g.setColor(Color.RED.brighter());
-         sx = (group.getStartRes() - startx) * charWidth;
-         sy = offset +
-             AlignmentUtil.getPixelHeight(starty, i, av.getCharHeight());
-         ex = (group.getEndRes() + 1 - startx) * charWidth;
-         ey = offset +
-             AlignmentUtil.getPixelHeight(starty, i + 1, av.getCharHeight());
-
-         if (!inRB)
-         {
-
-           g.drawLine(sx, sy, ex, sy); // Horizontal, top of new box
-           inRB = true;
-         }
-
-         g.drawLine(sx, sy, sx, ey); // vertical line, left hand side
-         g.drawLine(ex, sy, ex, ey); // vertical line, right hand side
-         if (i == y2 - 1) // last line of alignment, seal the box
-           g.drawLine(sx, ey, ex, ey); // Horizontal, bottom of old box
-
-          oldRStartX = sx;
-          oldREndX = ex;
-          oldRY = ey;
-     }
-     else if(inRB)
-     {
-       g.setColor(Color.RED.brighter());
-       g.drawLine(oldRStartX, oldRY, oldREndX, oldRY); // Horizontal, bottom of old box
-       inRB = false;
-     }
-     else
-       inRB = false;
-
+        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,
-                                  (searchStart - startx) * charWidth,
+
+          if (searchStart < x1)
+          {
+            searchStart = x1;
+          }
+
+          if (searchEnd > x2)
+          {
+            searchEnd = x2;
+          }
+
+          ssr.drawHighlightedText(seq, searchStart, searchEnd,
+                                  (searchStart - startx) * av.charWidth,
                                   offset +
-                                  AlignmentUtil.getPixelHeight(starty, searchSeq,
-              charHeight),
-                                  charWidth,
-                                  charHeight);
+                                  AlignmentUtil.getPixelHeight(starty,
+              searchSeq,
+              av.charHeight), av.charWidth, av.charHeight);
         }
       }
     }
-
-  }
-
-  public void fillBackground(Graphics g,Color c, int x1,int y1,int width,int height) {
-    g.setColor(c);
-    g.fillRect(x1,y1,width,height);
   }
 
-  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();
   }
-
-
 }