X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=eedb3eb87d92785c2c77487d4891c4d0ac19d718;hb=ec8b46fcbc994a7c3c0bb6e07235cdb564c3991d;hp=c4424655edc22241d5fc2c48aab764569b5101ea;hpb=5ba8b4a50183f8a799069ba7a4dabd4cc2589a5b;p=jalview.git

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index c442465..eedb3eb 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) 2007 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
@@ -22,39 +22,66 @@ import java.awt.*;
 import java.awt.image.*;
 import javax.swing.*;
 
-import jalview.analysis.*;
 import jalview.datamodel.*;
 
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
 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 showScores = false;
-  boolean displaySearch = false;
-  int[] searchResults = null;
-  int chunkHeight;
-  int chunkWidth;
+  SearchResults searchResults = null;
   boolean fastPaint = false;
   int LABEL_WEST;
   int LABEL_EAST;
 
+  int cursorX = 0;
+  int cursorY = 0;
 
-  public SeqCanvas(AlignViewport av)
+  /**
+   * Creates a new SeqCanvas object.
+   *
+   * @param av DOCUMENT ME!
+   */
+  public SeqCanvas(AlignmentPanel ap)
   {
-    this.av = av;
-    fr = new FeatureRenderer(av);
+    this.av = ap.av;
+    fr = new FeatureRenderer(ap);
     sr = new SequenceRenderer(av);
     setLayout(new BorderLayout());
-    PaintRefresher.Register(this, av.alignment);
+    PaintRefresher.Register(this, av.getSequenceSetId());
     setBackground(Color.white);
   }
 
+  public SequenceRenderer getSequenceRenderer()
+  {
+    return sr;
+  }
+
+  public FeatureRenderer getFeatureRenderer()
+  {
+    return fr;
+  }
+
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param g DOCUMENT ME!
+   * @param startx DOCUMENT ME!
+   * @param endx DOCUMENT ME!
+   * @param ypos DOCUMENT ME!
+   */
   void drawNorthScale(Graphics g, int startx, int endx, int ypos)
   {
     int scalestartx = startx - (startx % 10) + 10;
@@ -64,8 +91,13 @@ public class SeqCanvas
     // 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),
@@ -75,12 +107,32 @@ public class SeqCanvas
     }
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param g DOCUMENT ME!
+   * @param startx DOCUMENT ME!
+   * @param endx DOCUMENT ME!
+   * @param ypos DOCUMENT ME!
+   */
   void drawWestScale(Graphics g, int startx, int endx, int ypos)
   {
     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);
@@ -103,21 +155,36 @@ public class SeqCanvas
 
       if (value != -1)
       {
-        int x = LABEL_WEST - fm.stringWidth(value + "");
+        int x = LABEL_WEST - fm.stringWidth(String.valueOf(value)) -
+            av.charWidth / 2;
         g.drawString(value + "", x,
                      (ypos + (i * av.charHeight)) - (av.charHeight / 5));
       }
     }
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param g DOCUMENT ME!
+   * @param startx DOCUMENT ME!
+   * @param endx DOCUMENT ME!
+   * @param ypos DOCUMENT ME!
+   */
   void drawEastScale(Graphics g, int startx, int endx, int ypos)
   {
     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;
 
@@ -130,27 +197,39 @@ public class SeqCanvas
           continue;
         }
 
-        value = av.alignment.getSequenceAt(i).findPosition(index);
+        value = seq.findPosition(index);
 
         break;
       }
 
       if (value != -1)
       {
-        g.drawString(value + "", 0,
+        g.drawString(String.valueOf(value), 0,
                      (ypos + (i * av.charHeight)) - (av.charHeight / 5));
       }
     }
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param horizontal DOCUMENT ME!
+   * @param vertical DOCUMENT ME!
+   */
   public void fastPaint(int horizontal, int vertical)
   {
-    if ( ( (horizontal == 0) && (vertical == 0)) || (gg == null))
+    if (gg == null)
     {
       return;
     }
 
-    gg.copyArea(0, 0, imgWidth, imgHeight, -horizontal * av.charWidth,
+    fastPaint = true;
+
+    gg.copyArea(horizontal * av.charWidth,
+                vertical * av.charHeight,
+                imgWidth,
+                imgHeight,
+                -horizontal * av.charWidth,
                 -vertical * av.charHeight);
 
     int sr = av.startRes;
@@ -162,12 +241,13 @@ public class SeqCanvas
 
     if (horizontal > 0) // scrollbar pulled right, image to the left
     {
+      er++;
       transX = (er - sr - horizontal) * av.charWidth;
       sr = er - horizontal;
     }
     else if (horizontal < 0)
     {
-      er = sr - horizontal;
+      er = sr - horizontal - 1;
     }
     else if (vertical > 0) // scroll down
     {
@@ -193,14 +273,9 @@ public class SeqCanvas
     }
 
     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);
+    drawPanel(gg, sr, er, ss, es, 0);
     gg.translate( -transX, -transY);
 
-    fastPaint = true;
     repaint();
   }
 
@@ -215,13 +290,14 @@ public class SeqCanvas
    * in the adjustment listener in SeqPanel when the scrollbars move.
    */
 
-
   // 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))
+    super.paintComponent(g);
+
+    if (img != null && (fastPaint
+                        || (getVisibleRect().width != g.getClipBounds().width)
+                        || (getVisibleRect().height != g.getClipBounds().height)))
     {
       g.drawImage(img, 0, 0, this);
       fastPaint = false;
@@ -240,20 +316,45 @@ public class SeqCanvas
       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);
+    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);
+          }
+        });
 
-    gg.setColor(Color.white);
-    gg.fillRect(0, 0, imgWidth, imgHeight);
+        return;
+      }
+    }
 
-    chunkWidth = getWrappedCanvasWidth(getWidth());
-    chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;
+    if (av.antiAlias)
+    {
+      gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+                          RenderingHints.VALUE_ANTIALIAS_ON);
+    }
 
-    av.setChunkHeight(chunkHeight);
-    av.setChunkWidth(chunkWidth);
+    gg.setColor(Color.white);
+    gg.fillRect(0, 0, imgWidth, imgHeight);
 
     if (av.getWrapAlignment())
     {
@@ -261,13 +362,21 @@ public class SeqCanvas
     }
     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);
+
+
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param cwidth DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
   public int getWrappedCanvasWidth(int cwidth)
   {
     FontMetrics fm = getFontMetrics(av.getFont());
@@ -277,17 +386,50 @@ public class SeqCanvas
 
     if (av.scaleRightWrapped)
     {
-      LABEL_EAST = fm.stringWidth(av.alignment.getWidth() + "000");
+      LABEL_EAST = fm.stringWidth(getMask());
     }
 
     if (av.scaleLeftWrapped)
     {
-      LABEL_WEST = fm.stringWidth(av.alignment.getWidth() + "");
+      LABEL_WEST = fm.stringWidth(getMask());
     }
 
     return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
   }
 
+  /**
+   * Generates a string of zeroes.
+   * @return String
+   */
+  String getMask()
+  {
+    String mask = "00";
+    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";
+    }
+    return mask;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param g DOCUMENT ME!
+   * @param canvasWidth DOCUMENT ME!
+   * @param canvasHeight DOCUMENT ME!
+   * @param startRes DOCUMENT ME!
+   */
   public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight,
                                int startRes)
   {
@@ -295,30 +437,48 @@ public class SeqCanvas
 
     FontMetrics fm = getFontMetrics(av.getFont());
 
-    int LABEL_EAST = 0;
-
     if (av.scaleRightWrapped)
     {
-      LABEL_EAST = fm.stringWidth(al.getWidth() + "000");
+      LABEL_EAST = fm.stringWidth(getMask());
     }
 
-    int LABEL_WEST = 0;
-
     if (av.scaleLeftWrapped)
     {
-      LABEL_WEST = fm.stringWidth(al.getWidth() + "0");
+      LABEL_WEST = fm.stringWidth(getMask());
+    }
+
+    int hgap = av.charHeight;
+    if (av.scaleAboveWrapped)
+    {
+      hgap += av.charHeight;
     }
 
     int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
-    int cHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;
+    int cHeight = av.getAlignment().getHeight() * av.charHeight;
+
+    av.setWrappedWidth(cWidth);
 
     av.endRes = av.startRes + cWidth;
 
-    int endx = (startRes + cWidth) - 1;
-    int ypos = 2 * av.charHeight;
+    int endx;
+    int ypos = hgap;
+    int maxwidth = av.alignment.getWidth() - 1;
+
+    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);
 
       if (av.scaleLeftWrapped)
@@ -328,9 +488,9 @@ public class SeqCanvas
 
       if (av.scaleRightWrapped)
       {
-        g.translate(canvasWidth - LABEL_EAST + av.charWidth, 0);
+        g.translate(canvasWidth - LABEL_EAST, 0);
         drawEastScale(g, startRes, endx, ypos);
-        g.translate( - (canvasWidth - LABEL_EAST + av.charWidth), 0);
+        g.translate( - (canvasWidth - LABEL_EAST), 0);
       }
 
       g.translate(LABEL_WEST, 0);
@@ -340,6 +500,35 @@ public class SeqCanvas
         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();
@@ -354,68 +543,197 @@ public class SeqCanvas
                   cWidth * av.charWidth, (int) clip.getBounds().getHeight());
       }
 
-      drawPanel(g, startRes, endx, 0, al.getHeight(), startRes, 0, ypos);
+      drawPanel(g, startRes, endx, 0, al.getHeight(), ypos);
+
+      if (av.showAnnotation)
+      {
+        g.translate(0, cHeight + ypos + 3);
+        if (annotations == null)
+        {
+          annotations = new AnnotationPanel(av);
+        }
+
+        annotations.drawComponent( (Graphics2D) g, startRes, endx + 1);
+        g.translate(0, -cHeight - ypos - 3);
+      }
       g.setClip(clip);
       g.translate( -LABEL_WEST, 0);
 
-      ypos += cHeight;
+      ypos += cHeight + getAnnotationHeight() + hgap;
+
       startRes += cWidth;
-      endx = (startRes + cWidth) - 1;
+    }
+  }
 
-      if (endx > al.getWidth())
+  AnnotationPanel annotations;
+  int getAnnotationHeight()
+  {
+    if (!av.showAnnotation)
+    {
+      return 0;
+    }
+
+    if (annotations == null)
+    {
+      annotations = new AnnotationPanel(av);
+    }
+
+    return annotations.adjustPanelHeight();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param g1 DOCUMENT ME!
+   * @param startRes DOCUMENT ME!
+   * @param endRes DOCUMENT ME!
+   * @param startSeq DOCUMENT ME!
+   * @param endSeq DOCUMENT ME!
+   * @param offset DOCUMENT ME!
+   */
+  void drawPanel(Graphics g1, int startRes, int endRes,
+                 int startSeq, int endSeq, int offset)
+  {
+    if (!av.hasHiddenColumns)
+    {
+      draw(g1, startRes, endRes, startSeq, endSeq, offset);
+    }
+    else
+    {
+      java.util.Vector regions = av.getColumnSelection().getHiddenColumns();
+
+      int screenY = 0;
+      int blockStart = startRes;
+      int blockEnd = endRes;
+
+      for (int i = 0; i < regions.size(); i++)
+      {
+        int[] region = (int[]) regions.elementAt(i);
+        int hideStart = region[0];
+        int hideEnd = region[1];
+
+        if (hideStart <= blockStart)
+        {
+          blockStart += (hideEnd - hideStart) + 1;
+          continue;
+        }
+
+        blockEnd = hideStart - 1;
+
+        g1.translate(screenY * av.charWidth, 0);
+
+        draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
+
+        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))
       {
-        endx = al.getWidth();
+        blockEnd = blockStart + (endRes - startRes) - screenY;
+        g1.translate(screenY * av.charWidth, 0);
+        draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
+
+        g1.translate( -screenY * av.charWidth, 0);
       }
     }
+
   }
 
-  synchronized public void drawPanel(Graphics g1, int x1, int x2, int y1,
-                                     int y2, int startx, int starty, int offset)
+  //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)
   {
-    Graphics2D g = (Graphics2D) g1;
     g.setFont(av.getFont());
-    sr.renderGaps(av.renderGaps);
+    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);
 
-      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);
+      sr.drawSequence(nextSeq, av.alignment.findAllGroups(nextSeq),
+                      startRes, endRes,
+                      offset + ( (i - startSeq) * av.charHeight));
 
       if (av.showSequenceFeatures)
       {
-        fr.drawSequence(g, nextSeq,
-                        av.alignment.findAllGroups(nextSeq), x1, x2,
-                        (x1 - startx) * av.charWidth,
-                        offset +
-                        AlignmentUtil.getPixelHeight(starty, i, av.charHeight),
-                        av.charWidth, av.charHeight);
+        fr.drawSequence(g, nextSeq, startRes, endRes,
+                        offset + ( (i - startSeq) * av.charHeight));
+      }
+
+      /// Highlight search Results once all sequences have been drawn
+      //////////////////////////////////////////////////////////
+      if (searchResults != null)
+      {
+        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.cursorMode && cursorY == i
+          && cursorX >= startRes && cursorX <= endRes)
+      {
+        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
     /////////////////////////////////////
     SequenceGroup group = av.getSelectionGroup();
-    java.util.Vector groups = av.alignment.getGroups();
 
     int sx = -1;
     int sy = -1;
     int ex = -1;
     int groupIndex = -1;
+    int visWidth = (endRes - startRes + 1) * av.charWidth;
 
-    if ( (group == null) && (groups.size() > 0))
+    if ( (group == null) && (av.alignment.getGroups().size() > 0))
     {
-      group = (SequenceGroup) groups.elementAt(0);
+      group = (SequenceGroup) av.alignment.getGroups().elementAt(0);
       groupIndex = 0;
     }
 
@@ -429,21 +747,25 @@ public class SeqCanvas
         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 +
-              AlignmentUtil.getPixelHeight(starty, i, 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 < getWidth()) && (ex > 0) &&
-              group.sequences.contains(av.alignment.getSequenceAt(
-                  i)))
+          if (sx + ex < 0 || sx > visWidth)
+          {
+            continue;
+          }
+
+          if ( (sx <= (endRes - startRes) * av.charWidth) &&
+              group.getSequences(null).
+              contains(av.alignment.getSequenceAt(i)))
           {
             if ( (bottom == -1) &&
-                !group.sequences.contains(
+                !group.getSequences(null).contains(
                     av.alignment.getSequenceAt(i + 1)))
             {
               bottom = sy + av.charHeight;
@@ -452,7 +774,7 @@ public class SeqCanvas
             if (!inGroup)
             {
               if ( ( (top == -1) && (i == 0)) ||
-                  !group.sequences.contains(
+                  !group.getSequences(null).contains(
                       av.alignment.getSequenceAt(i - 1)))
               {
                 top = sy;
@@ -481,8 +803,31 @@ public class SeqCanvas
           {
             if (inGroup)
             {
-              g.drawLine(sx, oldY, sx, sy);
-              g.drawLine(sx + ex, oldY, sx + ex, sy);
+              if (sx >= 0 && sx < visWidth)
+              {
+                g.drawLine(sx, oldY, sx, sy);
+              }
+
+              if (sx + ex < visWidth)
+              {
+                g.drawLine(sx + ex, oldY, sx + ex, sy);
+              }
+
+              if (sx < 0)
+              {
+                ex += sx;
+                sx = 0;
+              }
+
+              if (sx + ex > visWidth)
+              {
+                ex = visWidth;
+              }
+
+              else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)
+              {
+                ex = (endRes - startRes + 1) * av.charWidth;
+              }
 
               if (top != -1)
               {
@@ -503,6 +848,32 @@ public class SeqCanvas
 
         if (inGroup)
         {
+          sy = offset + ( (i - startSeq) * av.charHeight);
+          if (sx >= 0 && sx < visWidth)
+          {
+            g.drawLine(sx, oldY, sx, sy);
+          }
+
+          if (sx + ex < visWidth)
+          {
+            g.drawLine(sx + ex, oldY, sx + ex, sy);
+          }
+
+          if (sx < 0)
+          {
+            ex += sx;
+            sx = 0;
+          }
+
+          if (sx + ex > visWidth)
+          {
+            ex = visWidth;
+          }
+          else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)
+          {
+            ex = (endRes - startRes + 1) * av.charWidth;
+          }
+
           if (top != -1)
           {
             g.drawLine(sx, top, sx + ex, top);
@@ -515,74 +886,35 @@ public class SeqCanvas
             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())
+        g.setStroke(new BasicStroke());
+
+        if (groupIndex >= av.alignment.getGroups().size())
         {
           break;
         }
 
-        group = (SequenceGroup) groups.elementAt(groupIndex);
-      }
-      while (groupIndex < groups.size());
-    }
-
-    /// Highlight search Results once all sequences have been drawn
-    //////////////////////////////////////////////////////////
-    if (displaySearch)
-    {
-      for (int r = 0; r < searchResults.length; r += 3)
-      {
-        int searchSeq = searchResults[r];
-
-        if ( (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;
-          }
+        group = (SequenceGroup) av.alignment.getGroups().elementAt(groupIndex);
 
-          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);
-        }
       }
+      while (groupIndex < av.alignment.getGroups().size());
+
     }
+
   }
 
-  public void highlightSearchResults(int[] results)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param results DOCUMENT ME!
+   */
+  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;