X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=8a873a22607c4854a2ebb52d3f7241a2186c6e48;hb=bc77e2f0f477053147a4e56b681131c710eb3ec8;hp=7dbb8d3c63c44393165768770cff0e387f043522;hpb=9c2efb07ecb9e429c4adeff76e388c12f0062a8b;p=jalview.git

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 7dbb8d3..8a873a2 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -34,19 +34,23 @@ import javax.swing.*;
  */
 public class SeqCanvas extends JComponent
 {
-    FeatureRenderer fr;
-    SequenceRenderer sr;
+    final FeatureRenderer fr;
+    final SequenceRenderer sr;
     BufferedImage img;
     Graphics2D gg;
     int imgWidth;
     int imgHeight;
     AlignViewport av;
-    boolean displaySearch = false;
-    int[] searchResults = null;
+    SearchResults searchResults = null;
     boolean fastPaint = false;
     int LABEL_WEST;
     int LABEL_EAST;
 
+
+    int cursorX = 0;
+    int cursorY = 0;
+
+
     /**
      * Creates a new SeqCanvas object.
      *
@@ -58,7 +62,7 @@ public class SeqCanvas extends JComponent
         fr = new FeatureRenderer(av);
         sr = new SequenceRenderer(av);
         setLayout(new BorderLayout());
-        PaintRefresher.Register(this, av.alignment);
+        PaintRefresher.Register(this, av.getSequenceSetId());
         setBackground(Color.white);
     }
 
@@ -101,8 +105,11 @@ public class SeqCanvas extends JComponent
         // NORTH SCALE
         for (int i = scalestartx; i < endx; i += 10)
         {
-            String string = String.valueOf(i);
-            g.drawString(string, (i - startx - 1) * av.charWidth,
+            int value = i;
+            if(av.hasHiddenColumns)
+                value = av.getColumnSelection().adjustForHiddenColumns(value);
+
+            g.drawString( String.valueOf(value), (i - startx - 1) * av.charWidth,
                 ypos - (av.charHeight / 2));
 
             g.drawLine(((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
@@ -125,7 +132,17 @@ public class SeqCanvas extends JComponent
         FontMetrics fm = getFontMetrics(av.getFont());
         ypos += av.charHeight;
 
-        // EAST SCALE
+        if(av.hasHiddenColumns)
+        {
+          startx = av.getColumnSelection().adjustForHiddenColumns(startx);
+          endx = av.getColumnSelection().adjustForHiddenColumns(endx);
+        }
+
+        int maxwidth = av.alignment.getWidth();
+        if (av.hasHiddenColumns)
+            maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+
+        // WEST SCALE
         for (int i = 0; i < av.alignment.getHeight(); i++)
         {
             SequenceI seq = av.alignment.getSequenceAt(i);
@@ -167,10 +184,14 @@ public class SeqCanvas extends JComponent
     {
         ypos += av.charHeight;
 
+        if(av.hasHiddenColumns)
+                endx = av.getColumnSelection().adjustForHiddenColumns(endx);
+
+        SequenceI seq;
         // EAST SCALE
         for (int i = 0; i < av.alignment.getHeight(); i++)
         {
-            SequenceI seq = av.alignment.getSequenceAt(i);
+            seq = av.alignment.getSequenceAt(i);
             int index = endx;
             int value = -1;
 
@@ -183,7 +204,7 @@ public class SeqCanvas extends JComponent
                     continue;
                 }
 
-                value = av.alignment.getSequenceAt(i).findPosition(index);
+                value = seq.findPosition(index);
 
                 break;
             }
@@ -204,11 +225,12 @@ public class SeqCanvas extends JComponent
      */
     public void fastPaint(int horizontal, int vertical)
     {
-        if (fastPaint  || gg == null)
+        if (gg == null)
         {
             return;
         }
 
+
         fastPaint = true;
 
         gg.copyArea(horizontal * av.charWidth,
@@ -225,6 +247,7 @@ public class SeqCanvas extends JComponent
         int transX = 0;
         int transY = 0;
 
+
         if (horizontal > 0) // scrollbar pulled right, image to the left
         {
             er ++;
@@ -259,7 +282,7 @@ public class SeqCanvas extends JComponent
         }
 
         gg.translate(transX, transY);
-        drawPanel(gg, sr, er, ss, es, sr, ss, 0);
+        drawPanel(gg, sr, er, ss, es, 0);
         gg.translate(-transX, -transY);
 
         repaint();
@@ -281,7 +304,7 @@ public class SeqCanvas extends JComponent
     {
         super.paintComponent(g);
 
-        sr.renderGaps(av.renderGaps);
+
 
         if ( img != null && (fastPaint
              || (getVisibleRect().width != g.getClipBounds().width)
@@ -305,9 +328,34 @@ public class SeqCanvas extends JComponent
             return;
         }
 
-        img = new BufferedImage(imgWidth, imgHeight, BufferedImage.TYPE_INT_RGB);
-        gg = (Graphics2D) img.getGraphics();
-        gg.setFont(av.getFont());
+        if (img == null || imgWidth != img.getWidth() || imgHeight != img.getHeight())
+        {
+          try{
+            img = new BufferedImage(imgWidth, imgHeight,
+                                    BufferedImage.TYPE_INT_RGB);
+            gg = (Graphics2D) img.getGraphics();
+            gg.setFont(av.getFont());
+          }catch(OutOfMemoryError er)
+          {
+            System.gc();
+            System.out.println(er +" making image, SeqCanvas");
+            javax.swing.SwingUtilities.invokeLater(new Runnable()
+            {
+              public void run()
+              {
+                javax.swing.JOptionPane.showInternalMessageDialog(Desktop.
+                    desktop,
+                    "Out of memory creating alignment image!!"
+                    +
+                    "\nSee help files for increasing Java Virtual Machine memory."
+                    , "Out of memory",
+                    javax.swing.JOptionPane.WARNING_MESSAGE);
+              }
+            });
+
+            return;
+          }
+        }
 
         if (av.antiAlias)
           gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
@@ -323,15 +371,14 @@ public class SeqCanvas extends JComponent
         }
         else
         {
-            drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq,
-                av.startRes, av.startSeq, 0);
+            drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0);
         }
 
         g.drawImage(img, 0, 0, this);
 
         if (pdbCanvas != null)
         {
-         pdbCanvas.updateSeqColours();
+           pdbCanvas.updateSeqColours();
         }
 
     }
@@ -371,7 +418,16 @@ public class SeqCanvas extends JComponent
     String getMask()
     {
       String mask = "00";
-      for (int i = av.alignment.getWidth(); i > 0; i /= 10)
+      int maxWidth = 0;
+      int tmp;
+      for(int i=0; i<av.alignment.getHeight(); i++)
+      {
+        tmp = av.alignment.getSequenceAt(i).getEnd();
+        if(tmp>maxWidth)
+          maxWidth = tmp;
+      }
+
+      for (int i = maxWidth; i > 0; i /= 10)
       {
         mask += "0";
       }
@@ -389,19 +445,16 @@ public class SeqCanvas extends JComponent
     public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight,
         int startRes)
     {
-
         AlignmentI al = av.getAlignment();
 
         FontMetrics fm = getFontMetrics(av.getFont());
 
-        int LABEL_EAST = 0;
 
         if (av.scaleRightWrapped)
         {
             LABEL_EAST = fm.stringWidth(getMask());
         }
 
-        int LABEL_WEST = 0;
 
         if (av.scaleLeftWrapped)
         {
@@ -420,12 +473,22 @@ public class SeqCanvas extends JComponent
         av.endRes = av.startRes + cWidth;
 
 
-        int endx = (startRes + cWidth) - 1;
+        int endx;
         int ypos = hgap;
+        int maxwidth = av.alignment.getWidth();
 
+        if(av.hasHiddenColumns)
+          maxwidth = av.getColumnSelection().findColumnPosition(maxwidth)-1;
 
-        while ((ypos <= canvasHeight) && (startRes < av.alignment.getWidth()))
+        while ((ypos <= canvasHeight) && (startRes < maxwidth))
         {
+          endx = startRes + cWidth -1;
+
+          if (endx > maxwidth)
+          {
+            endx = maxwidth;
+          }
+
             g.setFont(av.getFont());
             g.setColor(Color.black);
 
@@ -448,6 +511,35 @@ public class SeqCanvas extends JComponent
                 drawNorthScale(g, startRes, endx, ypos);
             }
 
+            if (av.hasHiddenColumns && av.showHiddenMarkers)
+            {
+              g.setColor(Color.blue);
+              int res;
+              for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size();
+                   i++)
+              {
+                res = av.getColumnSelection().findHiddenRegionPosition(i) -
+                    startRes;
+
+                if (res < 0 || res > endx - startRes)
+                  continue;
+
+                gg.fillPolygon(new int[]
+                               {res * av.charWidth - av.charHeight / 4,
+                               res * av.charWidth + av.charHeight / 4,
+                               res * av.charWidth},
+                               new int[]
+                               {
+                               ypos - (av.charHeight / 2),
+                               ypos - (av.charHeight / 2),
+                               ypos - (av.charHeight / 2) + 8
+                }, 3);
+
+              }
+            }
+
+
+
             // When printing we have an extra clipped region,
             // the Printable page which we need to account for here
             Shape clip = g.getClip();
@@ -462,13 +554,7 @@ public class SeqCanvas extends JComponent
                     cWidth * av.charWidth, (int) clip.getBounds().getHeight());
             }
 
-            if (av.vconsensus!=null && av.alignment.getWidth() >= av.vconsensus.size())
-            {
-              endx = av.vconsensus.size() - 2;
-            }
-
-
-            drawPanel(g, startRes, endx, 0, al.getHeight(), startRes, 0, ypos);
+            drawPanel(g, startRes, endx, 0, al.getHeight(), ypos);
 
             if(av.showAnnotation)
             {
@@ -476,23 +562,15 @@ public class SeqCanvas extends JComponent
               if(annotations==null)
                 annotations = new AnnotationPanel(av);
 
-              annotations.drawComponent( (Graphics2D) g, startRes, endx + 1);
-              g.translate(0, -cHeight - ypos);
+              annotations.drawComponent( (Graphics2D) g, startRes, endx+1);
+              g.translate(0, -cHeight - ypos -3);
             }
             g.setClip(clip);
             g.translate(-LABEL_WEST, 0);
 
             ypos += cHeight+getAnnotationHeight()+hgap;
-            if(av.showAnnotation)
-              ypos -= 3;
 
             startRes += cWidth;
-            endx = (startRes + cWidth) - 1;
-
-            if (endx > al.getWidth())
-            {
-                endx = al.getWidth();
-            }
         }
     }
 
@@ -512,116 +590,137 @@ public class SeqCanvas extends JComponent
      * DOCUMENT ME!
      *
      * @param g1 DOCUMENT ME!
-     * @param x1 DOCUMENT ME!
-     * @param x2 DOCUMENT ME!
-     * @param y1 DOCUMENT ME!
-     * @param y2 DOCUMENT ME!
-     * @param startx DOCUMENT ME!
-     * @param starty DOCUMENT ME!
+     * @param startRes DOCUMENT ME!
+     * @param endRes DOCUMENT ME!
+     * @param startSeq DOCUMENT ME!
+     * @param endSeq DOCUMENT ME!
      * @param offset DOCUMENT ME!
      */
-
-    float aaRatio = 2f/3f;
-    public void increaseAARatio()
+    void drawPanel(Graphics g1, int startRes, int endRes,
+                    int startSeq, int endSeq, int offset)
     {
-      aaRatio += .025;
-      if(aaRatio>1)
-        aaRatio = 1;
+      if(!av.hasHiddenColumns)
+      {
+        draw(g1, startRes, endRes, startSeq, endSeq, offset);
+      }
+      else
+      {
+        java.util.Vector regions = av.getColumnSelection().getHiddenColumns();
 
-      repaint();
-    }
+        int screenY = 0;
+        int blockStart = startRes;
+        int blockEnd = endRes;
 
-    public void decreaseAARation()
-    {
-      aaRatio -= .025;
-      if(aaRatio<0)
-        aaRatio = 0;
+        for (int i = 0; i < regions.size(); i++)
+        {
+          int[] region = (int[]) regions.elementAt(i);
+          int hideStart = region[0];
+          int hideEnd = region[1];
 
-      repaint();
-    }
+          if (hideStart <= blockStart)
+          {
+            blockStart += (hideEnd - hideStart) + 1;
+            continue;
+          }
 
+          blockEnd = hideStart - 1;
 
-    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());
+          g1.translate(screenY * av.charWidth, 0);
 
-      SequenceI nextSeq;
-     // int aaHeight = av.charHeight;
-     // Font  aafont = av.getFont();
+          draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
 
- /*   dnafont = null, , dna = null, dnaHeight = av.charHeight
-   if (av.getShowTranslation())
-      {
-        aaHeight = (int) (av.getCharHeight() * aaRatio);
-        dnaHeight = (int) (av.getCharHeight() * (1 - aaRatio));
-        java.awt.geom.AffineTransform transform = new java.awt.geom.AffineTransform();
-        transform.scale(1f / 3f, 1);
-        dnafont = new Font(av.getFont().getName(), av.getFont().getStyle(),
-                                dnaHeight);
-        dnafont = dnafont.deriveFont(transform);
-
-        aafont = new Font(av.getFont().getName(), av.getFont().getStyle(),
-                               aaHeight);
-        transform = new java.awt.geom.AffineTransform();
-        transform.scale(1 / aaRatio, 1);
-        aafont = aafont.deriveFont(transform);
+          if(av.getShowHiddenMarkers())
+          {
+            g1.setColor(Color.blue);
+
+            g1.drawLine( (blockEnd - blockStart + 1) * av.charWidth - 1,
+                        0 + offset,
+                        (blockEnd - blockStart + 1) * av.charWidth - 1,
+                        (endSeq - startSeq) * av.charHeight + offset);
+          }
+
+          g1.translate( -screenY * av.charWidth, 0);
+          screenY += blockEnd - blockStart + 1;
+          blockStart = hideEnd + 1;
+        }
+
+        if (screenY <= (endRes - startRes))
+        {
+          blockEnd = blockStart + (endRes - startRes) - screenY;
+          g1.translate(screenY * av.charWidth, 0);
+          draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
+
+          g1.translate( -screenY * av.charWidth, 0);
+        }
       }
-*/
+
+    }
+
+
 
 
+    //int startRes, int endRes, int startSeq, int endSeq, int x, int y,
+    // int x1, int x2, int y1, int y2, int startx, int starty,
+    void draw(Graphics g,
+                   int startRes, int endRes,
+                   int startSeq, int endSeq,
+                   int offset)
+   {
+      g.setFont(av.getFont());
+      sr.prepare(g, av.renderGaps);
+
+      SequenceI nextSeq;
+
         /// First draw the sequences
         /////////////////////////////
-        for (int i = y1; i < y2; i++)
+        for (int i = startSeq; i < endSeq; i++)
         {
             nextSeq = av.alignment.getSequenceAt(i);
 
-         /*   if(av.getShowTranslation())
-            {
-              dna = nextSeq;
-              StringBuffer sb = new StringBuffer();
-              for(int r = 0; r<nextSeq.getLength(); r+=3)
-              {
-                String codon = nextSeq.getSequence(r, r+3);
-                codon = codon.replace('U', 'T');
-                String res = ResidueProperties.codonTranslate(codon);
-                if(res !=null )
-                {
-                  if (res.equals("STOP"))
-                    sb.append("X");
-                  else
-                    sb.append(res);
-                }
-              }
-              nextSeq = new Sequence("d", sb.toString());
-            }*/
+            sr.drawSequence(nextSeq, av.alignment.findAllGroups(nextSeq),
+                            startRes, endRes,
+                            offset + ( (i - startSeq) * av.charHeight));
 
-            sr.drawSequence(g, nextSeq, av.alignment.findAllGroups(nextSeq),
-                            x1, x2, (x1 - startx) * av.charWidth,
-                            offset + ( (i - starty) * av.charHeight), av.charWidth,
-                            av.charHeight);
+            if (av.showSequenceFeatures)
+            {
+                fr.drawSequence(g, nextSeq, startRes, endRes,
+                    offset + ((i - startSeq) * av.charHeight));
+            }
 
-         /*   if(av.getShowTranslation())
+            /// Highlight search Results once all sequences have been drawn
+            //////////////////////////////////////////////////////////
+            if (searchResults != null)
             {
-              av.setGlobalColourScheme(new NucleotideColourScheme());
-              g.setFont(dnafont);
-              sr.drawSequence(g, dna, null,
-                              x1*3, (x2+2) * 3, ( (x1 - startx) * av.charWidth) / 3,
-                              offset + ( (i - starty) * av.charHeight) + aaHeight,
-                              av.charWidth / 3,
-                              dnaHeight);
-              av.setGlobalColourScheme(cs);
-            }*/
+              int[] visibleResults = searchResults.getResults(nextSeq, startRes, endRes);
+              if (visibleResults != null)
+                for (int r = 0; r < visibleResults.length; r += 2)
+                {
+                  sr.drawHighlightedText(nextSeq, visibleResults[r],
+                                         visibleResults[r + 1],
+                                         (visibleResults[r] - startRes) * av.charWidth,
+                                         offset + ( (i - startSeq) * av.charHeight));
+                }
+            }
 
-            if (av.showSequenceFeatures)
+            if(av.cursorMode && cursorY==i
+               && cursorX>=startRes && cursorX<=endRes)
             {
-                fr.drawSequence(g, nextSeq, x1, x2,
-                    (x1 - startx) * av.charWidth,
-                    offset + ((i - starty) * av.charHeight), av.charWidth,
-                    av.charHeight);
+              sr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * av.charWidth,
+                            offset + ( (i - startSeq) * av.charHeight));
             }
-        }
+          }
 
+          if(av.getSelectionGroup()!=null || av.alignment.getGroups().size()>0)
+            drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset);
+
+   }
+
+   void drawGroupsBoundaries(Graphics g1,
+                   int startRes, int endRes,
+                   int startSeq, int endSeq,
+                   int offset)
+   {
+       Graphics2D g = (Graphics2D)g1;
         //
         /////////////////////////////////////
         // Now outline any areas if necessary
@@ -632,6 +731,7 @@ public class SeqCanvas extends JComponent
         int sy = -1;
         int ex = -1;
         int groupIndex = -1;
+        int visWidth = (endRes - startRes +1) * av.charWidth;
 
         if ((group == null) && (av.alignment.getGroups().size() > 0))
         {
@@ -639,6 +739,7 @@ public class SeqCanvas extends JComponent
             groupIndex = 0;
         }
 
+
         if (group != null)
         {
             do
@@ -649,24 +750,24 @@ public class SeqCanvas extends JComponent
                 int top = -1;
                 int bottom = -1;
 
-                for (i = y1; i < y2; i++)
+                for (i = startSeq; i < endSeq; i++)
                 {
-                    sx = (group.getStartRes() - startx) * av.charWidth;
-                    sy = offset + ((i - starty) * av.charHeight);
+                    sx = (group.getStartRes() - startRes) * av.charWidth;
+                    sy = offset + ((i - startSeq) * av.charHeight);
                     ex = (((group.getEndRes() + 1) - group.getStartRes()) * av.charWidth) -
                         1;
 
-                    if(sx+ex<0 || sx>imgWidth)
+                    if(sx+ex<0 || sx>visWidth)
                     {
                       continue;
                     }
 
-                    if ( (sx <= (x2-x1)*av.charWidth) &&
-                            group.sequences.contains(av.alignment.getSequenceAt(
-                                    i)))
+                    if ( (sx <= (endRes-startRes)*av.charWidth) &&
+                            group.getSequences(false).
+                            contains(av.alignment.getSequenceAt(i)))
                     {
                         if ((bottom == -1) &&
-                                !group.sequences.contains(
+                                !group.getSequences(false).contains(
                                     av.alignment.getSequenceAt(i + 1)))
                         {
                             bottom = sy + av.charHeight;
@@ -675,7 +776,7 @@ public class SeqCanvas extends JComponent
                         if (!inGroup)
                         {
                             if (((top == -1) && (i == 0)) ||
-                                    !group.sequences.contains(
+                                    !group.getSequences(false).contains(
                                         av.alignment.getSequenceAt(i - 1)))
                             {
                                 top = sy;
@@ -703,10 +804,10 @@ public class SeqCanvas extends JComponent
                     {
                       if (inGroup)
                       {
-                        if (sx >= 0 && sx < imgWidth)
+                        if (sx >= 0 && sx < visWidth)
                           g.drawLine(sx, oldY, sx, sy);
 
-                        if (sx + ex < imgWidth)
+                        if (sx + ex < visWidth)
                           g.drawLine(sx + ex, oldY, sx + ex, sy);
 
                         if (sx < 0)
@@ -715,11 +816,11 @@ public class SeqCanvas extends JComponent
                           sx = 0;
                         }
 
-                        if (sx + ex > imgWidth)
-                          ex = imgWidth;
+                        if (sx + ex > visWidth)
+                          ex = visWidth;
 
-                        else if (sx + ex >= (x2 - x1 + 1) * av.charWidth)
-                          ex = (x2 - x1 + 1) * av.charWidth;
+                        else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)
+                          ex = (endRes - startRes + 1) * av.charWidth;
 
                         if (top != -1)
                         {
@@ -740,11 +841,11 @@ public class SeqCanvas extends JComponent
 
                 if (inGroup)
                 {
-                  sy = offset + ( (i - starty) * av.charHeight);
-                  if (sx >= 0 && sx < imgWidth)
+                  sy = offset + ( (i - startSeq) * av.charHeight);
+                  if (sx >= 0 && sx < visWidth)
                     g.drawLine(sx, oldY, sx, sy);
 
-                  if (sx + ex < imgWidth)
+                  if (sx + ex < visWidth)
                     g.drawLine(sx + ex, oldY, sx + ex, sy);
 
                   if (sx < 0)
@@ -753,10 +854,10 @@ public class SeqCanvas extends JComponent
                     sx = 0;
                   }
 
-                  if (sx + ex > imgWidth)
-                    ex = imgWidth;
-                  else if (sx + ex >= (x2 - x1 + 1) * av.charWidth)
-                    ex = (x2 - x1 + 1) * av.charWidth;
+                  if (sx + ex > visWidth)
+                    ex = visWidth;
+                  else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)
+                    ex = (endRes - startRes + 1) * av.charWidth;
 
                   if (top != -1)
                   {
@@ -775,50 +876,21 @@ public class SeqCanvas extends JComponent
 
                 groupIndex++;
 
+                g.setStroke(new BasicStroke());
+
                 if (groupIndex >= av.alignment.getGroups().size())
                 {
                     break;
                 }
 
                 group = (SequenceGroup) av.alignment.getGroups().elementAt(groupIndex);
-            }
-            while (groupIndex < av.alignment.getGroups().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 ((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 + ((searchSeq - starty) * av.charHeight),
-                        av.charWidth, av.charHeight);
-                }
             }
+            while (groupIndex < av.alignment.getGroups().size());
+
         }
+
     }
 
     /**
@@ -826,17 +898,9 @@ public class SeqCanvas extends JComponent
      *
      * @param results DOCUMENT ME!
      */
-    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;
-        }
+        img = null;
 
         searchResults = results;