X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=42424d9dc8a4a30b95cd7f93905ec5d9e0385ec5;hb=32ce9ddb7ce1a68add53dd81785ae428ca136a83;hp=507b7b04b94c391f789434ce4e589c70f5294a8c;hpb=00386d5511d779b555e93dbf71f33675937e1570;p=jalview.git

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 507b7b0..42424d9 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -1,315 +1,844 @@
+/*
+ * 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 jalview.datamodel.*;
+
 import java.awt.*;
+import java.awt.image.*;
+
 import javax.swing.*;
-import java.awt.event.*;
-import jalview.datamodel.*;
 import jalview.schemes.*;
-import jalview.analysis.*;
 
 
-public class SeqCanvas extends JPanel
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class SeqCanvas extends JComponent
 {
-     FeatureRenderer fr;
-    Image             img;
-    Graphics          gg;
-    int               imgWidth;
-    int               imgHeight;
+    FeatureRenderer fr;
+    SequenceRenderer sr;
+    BufferedImage img;
+    Graphics2D gg;
+    int imgWidth;
+    int imgHeight;
+    AlignViewport av;
+    boolean displaySearch = false;
+    int[] searchResults = null;
+    boolean fastPaint = false;
+    int LABEL_WEST;
+    int LABEL_EAST;
+
+    /**
+     * Creates a new SeqCanvas object.
+     *
+     * @param av DOCUMENT ME!
+     */
+    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);
+    }
 
-    AlignViewport     av;
+    MCview.PDBCanvas pdbCanvas;
+    public SequenceRenderer getSequenceRenderer()
+    {
+      return sr;
+    }
 
-    public boolean paintFlag = false;
+    public FeatureRenderer getFeatureRenderer()
+    {
+      return fr;
+    }
 
-    boolean showScores = false;
-    boolean displaySearch = false;
-    int [] searchResults = null;
+    public void setPDBCanvas(MCview.PDBCanvas pc)
+    {
+      pdbCanvas = pc;
+    }
 
-    int chunkHeight;
-    int chunkWidth;
+    public AlignViewport getViewport()
+    {
+      return av;
+    }
 
 
-    public SeqCanvas(AlignViewport av)
+    /**
+     * 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)
     {
-	this.av         = av;
-       fr = new FeatureRenderer(av);
-       setLayout(new BorderLayout());
-       PaintRefresher.Register(this);
+        int scalestartx = startx - (startx % 10) + 10;
+
+        g.setColor(Color.black);
 
+        // 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);
+        }
     }
 
-  public void drawScale(Graphics g, int startx, int endx,int ypos) {
-      int scalestartx = startx - startx%10 + 10;
+    /**
+     * 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;
 
-      g.setColor(Color.black);
+        // EAST SCALE
+        for (int i = 0; i < av.alignment.getHeight(); i++)
+        {
+            SequenceI seq = av.alignment.getSequenceAt(i);
+            int index = startx;
+            int value = -1;
+
+            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(String.valueOf(value))-av.charWidth/2;
+                g.drawString(value + "", x,
+                    (ypos + (i * av.charHeight)) - (av.charHeight / 5));
+            }
+        }
+    }
 
-      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);
+    /**
+     * 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;
 
-          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 );
+        // 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);
 
-/**
- * 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.
- */
+                break;
+            }
 
-  public void paintComponent(Graphics g)
-  {
+            if (value != -1)
+            {
+                g.drawString(String.valueOf(value), av.charWidth/2,
+                    (ypos + (i * av.charHeight)) - (av.charHeight / 5));
+            }
+        }
+    }
 
-    if (img==null ||  imgWidth!=getWidth() || imgHeight!=getHeight() || paintFlag)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param horizontal DOCUMENT ME!
+     * @param vertical DOCUMENT ME!
+     */
+    public void fastPaint(int horizontal, int vertical)
     {
-      imgWidth  = getWidth();
-      imgHeight = getHeight();
-      img = createImage(imgWidth,imgHeight);
-      gg  = img.getGraphics();
-      gg.setFont(av.getFont());
-      paintFlag = false;
-    }
+        if (gg == null)
+        {
+            return;
+        }
 
+        gg.copyArea(horizontal * av.charWidth,
+                    vertical * av.charHeight,
+                    imgWidth,
+                    imgHeight,
+                    -horizontal * av.charWidth,
+                    -vertical * av.charHeight);
+
+        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
+        {
+            er ++;
+            transX = (er - sr - horizontal) * av.charWidth;
+            sr = er - horizontal;
+        }
+        else if (horizontal < 0)
+        {
+            er = sr - horizontal-1;
+        }
+        else if (vertical > 0) // scroll down
+        {
+            ss = es - vertical;
+
+            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;
 
-    chunkWidth  =   getWidth()/av.charWidth;
-    chunkHeight =  (av.getAlignment().getHeight() + 2)*av.charHeight;
+            if (es > av.endSeq)
+            {
+                es = av.endSeq;
+            }
+        }
 
-    av.setChunkHeight(chunkHeight);
-    av.setChunkWidth(chunkWidth);
+        gg.translate(transX, transY);
+        drawPanel(gg, sr, er, ss, es, sr, ss, 0);
+        gg.translate(-transX, -transY);
 
-    fillBackground(gg,Color.WHITE,0,0,imgWidth,imgHeight);
+        fastPaint = true;
+        repaint();
+    }
 
-    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);
+    /**
+     * 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.
+     */
+
+    // Set this to false to force a full panel paint
+    public void paintComponent(Graphics g)
+    {
+        super.paintComponent(g);
 
+        sr.renderGaps(av.renderGaps);
 
-    g.drawImage(img,0,0,this);
+        if ( img != null && (fastPaint
+             || (getVisibleRect().width != g.getClipBounds().width)
+             || (getVisibleRect().height != g.getClipBounds().height)))
+        {
+            g.drawImage(img, 0, 0, this);
+            fastPaint = false;
+            return;
+        }
 
-  }
 
-  public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight, int startRes)
-  {
-      AlignmentI da = av.getAlignment();
+        // this draws the whole of the alignment
+        imgWidth = getWidth();
+        imgHeight = getHeight();
 
-      int cWidth  =   canvasWidth/av.charWidth;
-      int cHeight =  (av.getAlignment().getHeight() + 2)*av.charHeight;
+        imgWidth -= (imgWidth % av.charWidth);
+        imgHeight -= (imgHeight % av.charHeight);
 
-      int  endx   = startRes+cWidth-1;
-      int ypos  = 2*av.charHeight;
+        if ((imgWidth < 1) || (imgHeight < 1))
+        {
+            return;
+        }
 
-      while (ypos <= canvasHeight)
-      {
-        drawScale(g, startRes, endx, ypos);
-        drawPanel(g, startRes, endx, 0, da.getHeight(), startRes, 0, ypos);
+        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);
 
-        ypos += cHeight;
-        startRes += cWidth;
-        endx = startRes + cWidth - 1;
+        gg.setColor(Color.white);
+        gg.fillRect(0, 0, imgWidth, imgHeight);
 
-        if (endx > da.getWidth())
-          endx = da.getWidth();
-      }
 
-  }
+        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);
 
-  public void drawPanel(Graphics g,int x1,int x2, int y1, int y2,int startx, int starty,int offset) {
+        if (pdbCanvas != null)
+        {
+         pdbCanvas.updateSeqColours();
+        }
 
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param cwidth DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getWrappedCanvasWidth(int cwidth)
+    {
+        FontMetrics fm = getFontMetrics(av.getFont());
 
-    g.setFont(av.getFont());
-    RendererI sr = av.getRenderer();
+        LABEL_EAST = 0;
+        LABEL_WEST = 0;
 
-    /*Vector    pid    = av.getConsensus(false);
-    Vector tmpseq = new Vector();
-    for (int i = 0; i < av.getAlignment().getHeight(); i++)
-	if (!av.getSelection().contains(av.getAlignment().getSequenceAt(i)))
-	    tmpseq.addElement(av.getAlignment().getSequenceAt(i));
+        if (av.scaleRightWrapped)
+        {
+            LABEL_EAST = fm.stringWidth(getMask()+"0");
+        }
 
-    if (sr instanceof SequenceRenderer)
-	pid    = AAFrequency.calculate(tmpseq,x1,x2);
+        if (av.scaleLeftWrapped)
+        {
+            LABEL_WEST = fm.stringWidth(getMask());
+        }
 
-    else if (sr instanceof GraphRenderer)
-	pid = AAFrequency.calculatePID(av.getAlignment().getSequenceAt(0),
-				       av.getAlignment().getSequences(),
-				       av.getPIDWindow(),x1,x2);
+        return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
+    }
 
-*/
 
-   /* if (y2 > starty && y1 < av.getEndSeq())
+    /**
+     * Generates a string of zeroes.
+     * @return String
+     */
+    String getMask()
     {
-       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()));
-    }*/
-
-    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++)
+      String mask = "0";
+      for (int i = av.alignment.getWidth(); 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)
     {
-     nextSeq = av.getAlignment().getSequenceAt(i);
 
-     group = av.alignment.findGroup( nextSeq );
-     groups = av.alignment.findAllGroups( nextSeq );
+        AlignmentI al = av.getAlignment();
+
+        FontMetrics fm = getFontMetrics(av.getFont());
+
+        int LABEL_EAST = 0;
+
+        if (av.scaleRightWrapped)
+        {
+            LABEL_EAST = fm.stringWidth(getMask()+"0");
+        }
 
-     sr.drawSequence(g, nextSeq, groups,x1,x2,
-                 (x1 - startx) * av.charWidth,
-                 offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight),
-                 av.charWidth,av.charHeight,null, i);
+        int LABEL_WEST = 0;
 
-     if(av.showSequenceFeatures)
-     {
-       fr.drawSequence(g, nextSeq, groups, x1, x2,
-                       (x1 - startx) * av.charWidth,
-                       offset +
-                       AlignmentUtil.getPixelHeight(starty, i, av.charHeight),
-                       av.charWidth, av.charHeight, null, i);
-     }
+        if (av.scaleLeftWrapped)
+        {
+            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() * av.charHeight;
 
+        av.setWrappedWidth(cWidth);
 
-     if( group!=null )
-     {
+        av.endRes = av.startRes + cWidth;
 
-        g.setColor(Color.lightGray);
 
-        sx = (group.getStartRes()-startx)*av.charWidth;
-        sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight);
-        ex = (group.getEndRes()+1-startx)*av.charWidth;
-        ey = offset + AlignmentUtil.getPixelHeight(starty, i+1, av.charHeight);
+        int endx = (startRes + cWidth) - 1;
+        int ypos = hgap;
 
 
-        if (!inGroup)
+        while ((ypos <= canvasHeight) && (startRes < av.alignment.getWidth()))
         {
-          g.drawLine(sx, sy, ex, sy); // Horizontal, top of new box
-          inGroup=true;
+            g.setFont(av.getFont());
+            g.setColor(Color.black);
+
+            if (av.scaleLeftWrapped)
+            {
+                drawWestScale(g, startRes, endx, ypos);
+            }
+
+            if (av.scaleRightWrapped)
+            {
+                g.translate(canvasWidth - LABEL_EAST, 0);
+                drawEastScale(g, startRes, endx, ypos);
+                g.translate(-(canvasWidth - LABEL_EAST), 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());
+            }
+
+            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);
+
+            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);
+            }
+            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();
+            }
         }
+    }
+
+    AnnotationPanel annotations;
+    int getAnnotationHeight()
+    {
+      if(!av.showAnnotation)
+        return 0;
+
+      if(annotations==null)
+        annotations = new AnnotationPanel(av);
 
-        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) * av.charWidth;
-         sy = offset +
-             AlignmentUtil.getPixelHeight(starty, i, av.charHeight);
-         ex = (group.getEndRes() + 1 - startx) * av.charWidth;
-         ey = offset +
-             AlignmentUtil.getPixelHeight(starty, i + 1, av.charHeight);
-
-         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;
+      return annotations.adjustPanelHeight();
+    }
+
+    /**
+     * 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 offset DOCUMENT ME!
+     */
+
+    float aaRatio = 2f/3f;
+    public void increaseAARatio()
+    {
+      aaRatio += .025;
+      if(aaRatio>1)
+        aaRatio = 1;
+
+      repaint();
+    }
+
+    public void decreaseAARation()
+    {
+      aaRatio -= .025;
+      if(aaRatio<0)
+        aaRatio = 0;
 
+      repaint();
     }
 
-    /// Highlight search Results once all sequences have been drawn
-    if(displaySearch)
+
+    synchronized public void drawPanel(Graphics g1, int x1, int x2, int y1,
+        int y2, int startx, int starty, int offset)
     {
-      for(int r=0; r<searchResults.length; r+=3)
+      Graphics2D g = (Graphics2D) g1;
+      g.setFont(av.getFont());
+
+      SequenceI nextSeq, dna = null;
+      int aaHeight = av.charHeight, dnaHeight = av.charHeight;
+      Font dnafont = null, aafont = av.getFont();
+
+ /*     if (av.getShowTranslation())
       {
-        int searchSeq = searchResults[r];
-        int searchStart = searchResults[r+1];
-        int searchEnd = searchResults[r+2];
+        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);
+      }
+*/
+
+      ColourSchemeI cs = av.getGlobalColourScheme();
 
-        if (searchSeq >= y1 && searchSeq < y2)
+        /// First draw the sequences
+        /////////////////////////////
+        for (int i = y1; i < y2; i++)
         {
-          SequenceRenderer ssr = (SequenceRenderer) sr;
-          ssr.drawHighlightedText(av.getAlignment().getSequenceAt(searchSeq),
-                                  searchStart,
-                                  searchEnd,
-                                  (searchStart - startx) * av.charWidth,
-                                  offset +
-                                  AlignmentUtil.getPixelHeight(starty, searchSeq,
-              av.charHeight),
-                                  av.charWidth,
-                                  av.charHeight);
+            nextSeq = av.alignment.getSequenceAt(i);
+            g.setFont(aafont);
+         /*   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(g, nextSeq, av.alignment.findAllGroups(nextSeq),
+                            x1, x2, (x1 - startx) * av.charWidth,
+                            offset + ( (i - starty) * av.charHeight), av.charWidth,
+                            aaHeight);
+
+         /*   if(av.getShowTranslation())
+            {
+              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);
+            }*/
+
+            if (av.showSequenceFeatures)
+            {
+                fr.drawSequence(g, nextSeq, x1, x2,
+                    (x1 - startx) * av.charWidth,
+                    offset + ((i - starty) * av.charHeight), av.charWidth,
+                    av.charHeight);
+            }
         }
-      }
-    }
 
-  }
+        //
+        /////////////////////////////////////
+        // Now outline any areas if necessary
+        /////////////////////////////////////
+        SequenceGroup group = av.getSelectionGroup();
 
-  public void fillBackground(Graphics g,Color c, int x1,int y1,int width,int height) {
-    g.setColor(c);
-    g.fillRect(x1,y1,width,height);
-  }
+        int sx = -1;
+        int sy = -1;
+        int ex = -1;
+        int groupIndex = -1;
 
-  public int getChunkWidth() {
-    return chunkWidth;
-  }
+        if ((group == null) && (av.alignment.getGroups().size() > 0))
+        {
+            group = (SequenceGroup) av.alignment.getGroups().elementAt(0);
+            groupIndex = 0;
+        }
 
-  public void highlightSearchResults(int [] results)
-  {
-    // results are in the order sequence, startRes, endRes
-    if(results==null)
-      displaySearch = false;
-    else
-      displaySearch = true;
+        if (group != null)
+        {
+            do
+            {
+                int oldY = -1;
+                int i = 0;
+                boolean inGroup = false;
+                int top = -1;
+                int bottom = -1;
+
+                for (i = y1; i < y2; i++)
+                {
+                    sx = (group.getStartRes() - startx) * av.charWidth;
+                    sy = offset + ((i - starty) * av.charHeight);
+                    ex = (((group.getEndRes() + 1) - group.getStartRes()) * av.charWidth) -
+                        1;
+
+                    if(sx+ex<0 || sx>imgWidth)
+                    {
+                      continue;
+                    }
+
+                    if ( (sx <= (x2-x1)*av.charWidth) &&
+                            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)
+                      {
+                        if (sx >= 0 && sx < imgWidth)
+                          g.drawLine(sx, oldY, sx, sy);
+
+                        if (sx + ex < imgWidth)
+                          g.drawLine(sx + ex, oldY, sx + ex, sy);
+
+                        if (sx < 0)
+                        {
+                          ex += sx;
+                          sx = 0;
+                        }
+
+                        if (sx + ex > imgWidth)
+                          ex = imgWidth;
+
+                        else if (sx + ex >= (x2 - x1 + 1) * av.charWidth)
+                          ex = (x2 - x1 + 1) * av.charWidth;
+
+                        if (top != -1)
+                        {
+                          g.drawLine(sx, top, sx + ex, top);
+                          top = -1;
+                        }
+
+                        if (bottom != -1)
+                        {
+                          g.drawLine(sx, bottom, sx + ex, bottom);
+                          bottom = -1;
+                        }
+
+                        inGroup = false;
+                        }
+                    }
+                }
+
+                if (inGroup)
+                {
+                  sy = offset + ( (i - starty) * av.charHeight);
+                  if (sx >= 0 && sx < imgWidth)
+                    g.drawLine(sx, oldY, sx, sy);
+
+                  if (sx + ex < imgWidth)
+                    g.drawLine(sx + ex, oldY, sx + ex, sy);
+
+                  if (sx < 0)
+                  {
+                    ex += sx;
+                    sx = 0;
+                  }
+
+                  if (sx + ex > imgWidth)
+                    ex = imgWidth;
+                  else if (sx + ex >= (x2 - x1 + 1) * av.charWidth)
+                    ex = (x2 - x1 + 1) * av.charWidth;
+
+                  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;
+                  }
+
+                    inGroup = false;
+                }
+
+                groupIndex++;
+
+                if (groupIndex >= av.alignment.getGroups().size())
+                {
+                    break;
+                }
+
+                group = (SequenceGroup) av.alignment.getGroups().elementAt(groupIndex);
+            }
+            while (groupIndex < av.alignment.getGroups().size());
+        }
 
-    searchResults = results;
+        /// 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);
+                }
+            }
+        }
+    }
 
-    paintFlag = true;
-    repaint();
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param results DOCUMENT ME!
+     */
+    public void highlightSearchResults(int[] results)
+    {
+        // results are in the order sequence, startRes, endRes
+        if (results == null)
+        {
+            displaySearch = false;
+        }
+        else
+        {
+            displaySearch = true;
+        }
 
+        searchResults = results;
 
+        repaint();
+    }
 }