X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=42424d9dc8a4a30b95cd7f93905ec5d9e0385ec5;hb=32ce9ddb7ce1a68add53dd81785ae428ca136a83;hp=c4424655edc22241d5fc2c48aab764569b5101ea;hpb=5ba8b4a50183f8a799069ba7a4dabd4cc2589a5b;p=jalview.git

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index c442465..42424d9 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -18,574 +18,827 @@
  */
 package jalview.gui;
 
+import jalview.datamodel.*;
+
 import java.awt.*;
 import java.awt.image.*;
+
 import javax.swing.*;
+import jalview.schemes.*;
 
-import jalview.analysis.*;
-import jalview.datamodel.*;
 
-public class SeqCanvas
-    extends JComponent
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class SeqCanvas extends JComponent
 {
-  FeatureRenderer fr;
-  SequenceRenderer sr;
-  BufferedImage img;
-  Graphics2D gg;
-  int imgWidth;
-  int imgHeight;
-  AlignViewport av;
-  boolean showScores = false;
-  boolean displaySearch = false;
-  int[] searchResults = null;
-  int chunkHeight;
-  int chunkWidth;
-  boolean fastPaint = false;
-  int LABEL_WEST;
-  int LABEL_EAST;
-
-
-  public SeqCanvas(AlignViewport av)
-  {
-    this.av = av;
-    fr = new FeatureRenderer(av);
-    sr = new SequenceRenderer(av);
-    setLayout(new BorderLayout());
-    PaintRefresher.Register(this, av.alignment);
-    setBackground(Color.white);
-  }
-
-  void drawNorthScale(Graphics g, int startx, int endx, int ypos)
-  {
-    int scalestartx = startx - (startx % 10) + 10;
-
-    g.setColor(Color.black);
-
-    // NORTH SCALE
-    for (int i = scalestartx; i < endx; i += 10)
+    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)
     {
-      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);
+        this.av = av;
+        fr = new FeatureRenderer(av);
+        sr = new SequenceRenderer(av);
+        setLayout(new BorderLayout());
+        PaintRefresher.Register(this, av.alignment);
+        setBackground(Color.white);
     }
-  }
 
-  void drawWestScale(Graphics g, int startx, int endx, int ypos)
-  {
-    FontMetrics fm = getFontMetrics(av.getFont());
-    ypos += av.charHeight;
+    MCview.PDBCanvas pdbCanvas;
+    public SequenceRenderer getSequenceRenderer()
+    {
+      return sr;
+    }
 
-    // EAST SCALE
-    for (int i = 0; i < av.alignment.getHeight(); i++)
+    public FeatureRenderer getFeatureRenderer()
     {
-      SequenceI seq = av.alignment.getSequenceAt(i);
-      int index = startx;
-      int value = -1;
+      return fr;
+    }
 
-      while (index < endx)
-      {
-        if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
-        {
-          index++;
+    public void setPDBCanvas(MCview.PDBCanvas pc)
+    {
+      pdbCanvas = pc;
+    }
 
-          continue;
-        }
+    public AlignViewport getViewport()
+    {
+      return av;
+    }
 
-        value = av.alignment.getSequenceAt(i).findPosition(index);
 
-        break;
-      }
+    /**
+     * 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;
 
-      if (value != -1)
-      {
-        int x = LABEL_WEST - fm.stringWidth(value + "");
-        g.drawString(value + "", x,
-                     (ypos + (i * av.charHeight)) - (av.charHeight / 5));
-      }
-    }
-  }
+        g.setColor(Color.black);
 
-  void drawEastScale(Graphics g, int startx, int endx, int ypos)
-  {
-    ypos += av.charHeight;
+        // 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);
+        }
+    }
 
-    // EAST SCALE
-    for (int i = 0; i < av.alignment.getHeight(); i++)
+    /**
+     * 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)
     {
-      SequenceI seq = av.alignment.getSequenceAt(i);
-      int index = endx;
-      int value = -1;
+        FontMetrics fm = getFontMetrics(av.getFont());
+        ypos += av.charHeight;
 
-      while (index > startx)
-      {
-        if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
+        // EAST SCALE
+        for (int i = 0; i < av.alignment.getHeight(); i++)
         {
-          index--;
+            SequenceI seq = av.alignment.getSequenceAt(i);
+            int index = startx;
+            int value = -1;
 
-          continue;
-        }
+            while (index < endx)
+            {
+                if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
+                {
+                    index++;
 
-        value = av.alignment.getSequenceAt(i).findPosition(index);
+                    continue;
+                }
 
-        break;
-      }
+                value = av.alignment.getSequenceAt(i).findPosition(index);
 
-      if (value != -1)
-      {
-        g.drawString(value + "", 0,
-                     (ypos + (i * av.charHeight)) - (av.charHeight / 5));
-      }
+                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));
+            }
+        }
     }
-  }
 
-  public void fastPaint(int horizontal, int vertical)
-  {
-    if ( ( (horizontal == 0) && (vertical == 0)) || (gg == null))
+    /**
+     * 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)
     {
-      return;
-    }
+        ypos += av.charHeight;
 
-    gg.copyArea(0, 0, imgWidth, imgHeight, -horizontal * av.charWidth,
-                -vertical * av.charHeight);
+        // EAST SCALE
+        for (int i = 0; i < av.alignment.getHeight(); i++)
+        {
+            SequenceI seq = av.alignment.getSequenceAt(i);
+            int index = endx;
+            int value = -1;
 
-    int sr = av.startRes;
-    int er = av.endRes;
-    int ss = av.startSeq;
-    int es = av.endSeq;
-    int transX = 0;
-    int transY = 0;
+            while (index > startx)
+            {
+                if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
+                {
+                    index--;
 
-    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;
+                    continue;
+                }
 
-      if (ss < av.startSeq)
-      { // ie scrolling too fast, more than a page at a time
-        ss = av.startSeq;
-      }
-      else
-      {
-        transY = imgHeight - (vertical * av.charHeight);
-      }
+                value = av.alignment.getSequenceAt(i).findPosition(index);
+
+                break;
+            }
+
+            if (value != -1)
+            {
+                g.drawString(String.valueOf(value), av.charWidth/2,
+                    (ypos + (i * av.charHeight)) - (av.charHeight / 5));
+            }
+        }
     }
-    else if (vertical < 0)
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param horizontal DOCUMENT ME!
+     * @param vertical DOCUMENT ME!
+     */
+    public void fastPaint(int horizontal, int vertical)
     {
-      es = ss - vertical;
+        if (gg == null)
+        {
+            return;
+        }
 
-      if (es > av.endSeq)
-      {
-        es = av.endSeq;
-      }
+        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;
+
+            if (es > av.endSeq)
+            {
+                es = av.endSeq;
+            }
+        }
+
+        gg.translate(transX, transY);
+        drawPanel(gg, sr, er, ss, es, sr, ss, 0);
+        gg.translate(-transX, -transY);
+
+        fastPaint = true;
+        repaint();
     }
 
-    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.
-   */
-
-
-  // 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))
+    /**
+     * 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)
     {
-      g.drawImage(img, 0, 0, this);
-      fastPaint = false;
-      return;
-    }
+        super.paintComponent(g);
 
-    // this draws the whole of the alignment
-    imgWidth = getWidth();
-    imgHeight = getHeight();
+        sr.renderGaps(av.renderGaps);
 
-    imgWidth -= (imgWidth % av.charWidth);
-    imgHeight -= (imgHeight % av.charHeight);
+        if ( img != null && (fastPaint
+             || (getVisibleRect().width != g.getClipBounds().width)
+             || (getVisibleRect().height != g.getClipBounds().height)))
+        {
+            g.drawImage(img, 0, 0, this);
+            fastPaint = false;
+            return;
+        }
 
-    if ( (imgWidth < 1) || (imgHeight < 1))
-    {
-      return;
-    }
 
-    img = new BufferedImage(imgWidth, imgHeight, BufferedImage.TYPE_INT_RGB);
-    gg = (Graphics2D) img.getGraphics();
-    gg.setFont(av.getFont());
-    gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
-                        RenderingHints.VALUE_ANTIALIAS_ON);
+        // this draws the whole of the alignment
+        imgWidth = getWidth();
+        imgHeight = getHeight();
 
-    gg.setColor(Color.white);
-    gg.fillRect(0, 0, imgWidth, imgHeight);
+        imgWidth -= (imgWidth % av.charWidth);
+        imgHeight -= (imgHeight % av.charHeight);
 
-    chunkWidth = getWrappedCanvasWidth(getWidth());
-    chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;
+        if ((imgWidth < 1) || (imgHeight < 1))
+        {
+            return;
+        }
 
-    av.setChunkHeight(chunkHeight);
-    av.setChunkWidth(chunkWidth);
+        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 (av.getWrapAlignment())
-    {
-      drawWrappedPanel(gg, getWidth(), getHeight(), av.startRes);
-    }
-    else
-    {
-      drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq,
+        gg.setColor(Color.white);
+        gg.fillRect(0, 0, imgWidth, imgHeight);
+
+
+        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);
-  }
+        g.drawImage(img, 0, 0, this);
 
-  public int getWrappedCanvasWidth(int cwidth)
-  {
-    FontMetrics fm = getFontMetrics(av.getFont());
+        if (pdbCanvas != null)
+        {
+         pdbCanvas.updateSeqColours();
+        }
 
-    LABEL_EAST = 0;
-    LABEL_WEST = 0;
+    }
 
-    if (av.scaleRightWrapped)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param cwidth DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getWrappedCanvasWidth(int cwidth)
     {
-      LABEL_EAST = fm.stringWidth(av.alignment.getWidth() + "000");
+        FontMetrics fm = getFontMetrics(av.getFont());
+
+        LABEL_EAST = 0;
+        LABEL_WEST = 0;
+
+        if (av.scaleRightWrapped)
+        {
+            LABEL_EAST = fm.stringWidth(getMask()+"0");
+        }
+
+        if (av.scaleLeftWrapped)
+        {
+            LABEL_WEST = fm.stringWidth(getMask());
+        }
+
+        return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
     }
 
-    if (av.scaleLeftWrapped)
+
+    /**
+     * Generates a string of zeroes.
+     * @return String
+     */
+    String getMask()
     {
-      LABEL_WEST = fm.stringWidth(av.alignment.getWidth() + "");
+      String mask = "0";
+      for (int i = av.alignment.getWidth(); i > 0; i /= 10)
+      {
+        mask += "0";
+      }
+      return mask;
     }
 
-    return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
-  }
+    /**
+     * 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)
+    {
 
-  public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight,
-                               int startRes)
-  {
-    AlignmentI al = av.getAlignment();
+        AlignmentI al = av.getAlignment();
 
-    FontMetrics fm = getFontMetrics(av.getFont());
+        FontMetrics fm = getFontMetrics(av.getFont());
 
-    int LABEL_EAST = 0;
+        int LABEL_EAST = 0;
 
-    if (av.scaleRightWrapped)
-    {
-      LABEL_EAST = fm.stringWidth(al.getWidth() + "000");
-    }
+        if (av.scaleRightWrapped)
+        {
+            LABEL_EAST = fm.stringWidth(getMask()+"0");
+        }
 
-    int LABEL_WEST = 0;
+        int LABEL_WEST = 0;
 
-    if (av.scaleLeftWrapped)
-    {
-      LABEL_WEST = fm.stringWidth(al.getWidth() + "0");
-    }
+        if (av.scaleLeftWrapped)
+        {
+            LABEL_WEST = fm.stringWidth(getMask());
+        }
 
-    int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
-    int cHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;
+        int hgap = av.charHeight;
+        if(av.scaleAboveWrapped)
+          hgap += av.charHeight;
 
-    av.endRes = av.startRes + cWidth;
+        int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
+        int cHeight = av.getAlignment().getHeight() * av.charHeight;
 
-    int endx = (startRes + cWidth) - 1;
-    int ypos = 2 * av.charHeight;
+        av.setWrappedWidth(cWidth);
 
-    while ( (ypos <= canvasHeight) && (startRes < av.alignment.getWidth()))
-    {
-      g.setColor(Color.black);
+        av.endRes = av.startRes + cWidth;
 
-      if (av.scaleLeftWrapped)
-      {
-        drawWestScale(g, startRes, endx, ypos);
-      }
 
-      if (av.scaleRightWrapped)
-      {
-        g.translate(canvasWidth - LABEL_EAST + av.charWidth, 0);
-        drawEastScale(g, startRes, endx, ypos);
-        g.translate( - (canvasWidth - LABEL_EAST + av.charWidth), 0);
-      }
+        int endx = (startRes + cWidth) - 1;
+        int ypos = hgap;
 
-      g.translate(LABEL_WEST, 0);
 
-      if (av.scaleAboveWrapped)
-      {
-        drawNorthScale(g, startRes, endx, ypos);
-      }
+        while ((ypos <= canvasHeight) && (startRes < av.alignment.getWidth()))
+        {
+            g.setFont(av.getFont());
+            g.setColor(Color.black);
 
-      // When printing we have an extra clipped region,
-      // the Printable page which we need to account for here
-      Shape clip = g.getClip();
+            if (av.scaleLeftWrapped)
+            {
+                drawWestScale(g, startRes, endx, ypos);
+            }
 
-      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.scaleRightWrapped)
+            {
+                g.translate(canvasWidth - LABEL_EAST, 0);
+                drawEastScale(g, startRes, endx, ypos);
+                g.translate(-(canvasWidth - LABEL_EAST), 0);
+            }
 
-      drawPanel(g, startRes, endx, 0, al.getHeight(), startRes, 0, ypos);
-      g.setClip(clip);
-      g.translate( -LABEL_WEST, 0);
+            g.translate(LABEL_WEST, 0);
 
-      ypos += cHeight;
-      startRes += cWidth;
-      endx = (startRes + cWidth) - 1;
+            if (av.scaleAboveWrapped)
+            {
+                drawNorthScale(g, startRes, endx, ypos);
+            }
 
-      if (endx > al.getWidth())
-      {
-        endx = al.getWidth();
-      }
-    }
-  }
+            // When printing we have an extra clipped region,
+            // the Printable page which we need to account for here
+            Shape clip = g.getClip();
 
-  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);
+            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;
+            }
 
-    SequenceI nextSeq;
 
-    /// First draw the sequences
-    /////////////////////////////
-    for (int i = y1; i < y2; i++)
+            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()
     {
-      nextSeq = av.alignment.getSequenceAt(i);
+      if(!av.showAnnotation)
+        return 0;
 
-      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(annotations==null)
+        annotations = new AnnotationPanel(av);
 
-      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);
-      }
+      return annotations.adjustPanelHeight();
     }
 
-    //
-    /////////////////////////////////////
-    // Now outline any areas if necessary
-    /////////////////////////////////////
-    SequenceGroup group = av.getSelectionGroup();
-    java.util.Vector groups = av.alignment.getGroups();
+    /**
+     * 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;
 
-    int sx = -1;
-    int sy = -1;
-    int ex = -1;
-    int groupIndex = -1;
+      repaint();
+    }
 
-    if ( (group == null) && (groups.size() > 0))
+    public void decreaseAARation()
     {
-      group = (SequenceGroup) groups.elementAt(0);
-      groupIndex = 0;
+      aaRatio -= .025;
+      if(aaRatio<0)
+        aaRatio = 0;
+
+      repaint();
     }
 
-    if (group != null)
+
+    synchronized public void drawPanel(Graphics g1, int x1, int x2, int y1,
+        int y2, int startx, int starty, int offset)
     {
-      do
-      {
-        int oldY = -1;
-        int i = 0;
-        boolean inGroup = false;
-        int top = -1;
-        int bottom = -1;
+      Graphics2D g = (Graphics2D) g1;
+      g.setFont(av.getFont());
 
-        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;
-            }
+      SequenceI nextSeq, dna = null;
+      int aaHeight = av.charHeight, dnaHeight = av.charHeight;
+      Font dnafont = null, aafont = av.getFont();
 
-            if (!inGroup)
-            {
-              if ( ( (top == -1) && (i == 0)) ||
-                  !group.sequences.contains(
-                      av.alignment.getSequenceAt(i - 1)))
-              {
-                top = sy;
-              }
+ /*     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);
+      }
+*/
 
-              oldY = sy;
-              inGroup = true;
+      ColourSchemeI cs = av.getGlobalColourScheme();
 
-              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)
+        /// First draw the sequences
+        /////////////////////////////
+        for (int i = y1; i < y2; i++)
+        {
+            nextSeq = av.alignment.getSequenceAt(i);
+            g.setFont(aafont);
+         /*   if(av.getShowTranslation())
             {
-              g.drawLine(sx, oldY, sx, sy);
-              g.drawLine(sx + ex, oldY, sx + ex, sy);
-
-              if (top != -1)
+              dna = nextSeq;
+              StringBuffer sb = new StringBuffer();
+              for(int r = 0; r<nextSeq.getLength(); r+=3)
               {
-                g.drawLine(sx, top, sx + ex, top);
-                top = -1;
+                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());
+            }*/
 
-              if (bottom != -1)
-              {
-                g.drawLine(sx, bottom, sx + ex, bottom);
-                bottom = -1;
-              }
+            sr.drawSequence(g, nextSeq, av.alignment.findAllGroups(nextSeq),
+                            x1, x2, (x1 - startx) * av.charWidth,
+                            offset + ( (i - starty) * av.charHeight), av.charWidth,
+                            aaHeight);
 
-              inGroup = false;
+         /*   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);
             }
-          }
         }
 
-        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;
-        }
+        //
+        /////////////////////////////////////
+        // Now outline any areas if necessary
+        /////////////////////////////////////
+        SequenceGroup group = av.getSelectionGroup();
 
-        groupIndex++;
+        int sx = -1;
+        int sy = -1;
+        int ex = -1;
+        int groupIndex = -1;
 
-        if (groupIndex >= groups.size())
+        if ((group == null) && (av.alignment.getGroups().size() > 0))
         {
-          break;
+            group = (SequenceGroup) av.alignment.getGroups().elementAt(0);
+            groupIndex = 0;
         }
 
-        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 (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());
+        }
 
-        if ( (searchSeq >= y1) && (searchSeq < y2))
+        /// Highlight search Results once all sequences have been drawn
+        //////////////////////////////////////////////////////////
+        if (displaySearch)
         {
-          SequenceI seq = av.getAlignment().getSequenceAt(searchSeq);
+            for (int r = 0; r < searchResults.length; r += 3)
+            {
+                int searchSeq = searchResults[r];
 
-          int searchStart = seq.findIndex(searchResults[r + 1]) - 1;
-          int searchEnd = seq.findIndex(searchResults[r + 2]) - 1;
+                if ((searchSeq >= y1) && (searchSeq < y2))
+                {
+                    SequenceI seq = av.getAlignment().getSequenceAt(searchSeq);
 
-          SequenceRenderer ssr = (SequenceRenderer) sr;
+                    int searchStart = seq.findIndex(searchResults[r + 1]) - 1;
+                    int searchEnd = seq.findIndex(searchResults[r + 2]) - 1;
 
-          if (searchStart < x1)
-          {
-            searchStart = x1;
-          }
+                    SequenceRenderer ssr = (SequenceRenderer) sr;
 
-          if (searchEnd > x2)
-          {
-            searchEnd = x2;
-          }
+                    if (searchStart < x1)
+                    {
+                        searchStart = x1;
+                    }
 
-          ssr.drawHighlightedText(seq, searchStart, searchEnd,
-                                  (searchStart - startx) * av.charWidth,
-                                  offset +
-                                  AlignmentUtil.getPixelHeight(starty,
-              searchSeq,
-              av.charHeight), av.charWidth, av.charHeight);
+                    if (searchEnd > x2)
+                    {
+                        searchEnd = x2;
+                    }
+
+                    ssr.drawHighlightedText(seq, searchStart, searchEnd,
+                        (searchStart - startx) * av.charWidth,
+                        offset + ((searchSeq - starty) * av.charHeight),
+                        av.charWidth, av.charHeight);
+                }
+            }
         }
-      }
     }
-  }
 
-  public void highlightSearchResults(int[] results)
-  {
-    // results are in the order sequence, startRes, endRes
-    if (results == null)
-    {
-      displaySearch = false;
-    }
-    else
+    /**
+     * DOCUMENT ME!
+     *
+     * @param results DOCUMENT ME!
+     */
+    public void highlightSearchResults(int[] results)
     {
-      displaySearch = true;
-    }
+        // results are in the order sequence, startRes, endRes
+        if (results == null)
+        {
+            displaySearch = false;
+        }
+        else
+        {
+            displaySearch = true;
+        }
 
-    searchResults = results;
+        searchResults = results;
 
-    repaint();
-  }
+        repaint();
+    }
 }