X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=ccbebd52b44a31b52fadeea629818e494f4db68b;hb=6951479b7dc56bd022ce2c370b7f88b5571004fd;hp=f2603ea3e349eac0f766f836a0fed1b01edd71a4;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index f2603ea..ccbebd5 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -1,255 +1,654 @@
-
-/*
-* 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 javax.swing.*;
-import java.awt.event.*;
-import java.awt.*;
-import java.awt.image.*;
-import jalview.datamodel.*;
-import jalview.io.FormatAdapter;
-
-public class AnnotationLabels extends JPanel implements MouseListener, MouseMotionListener, ActionListener
-{
-  boolean active = false;
-  Image image;
-  AlignmentPanel ap ;
-  boolean resizing = false;
-  int oldY, mouseX;
-  static String ADDNEW = "Add New Row";
-  static String HIDE = "Hide This Row";
-  static String DELETE = "Delete This Row";
-  static String SHOWALL="Show All Hidden Rows";
-  static String OUTPUT_TEXT="Show Values In Textbox";
-  int selectedRow = 0;
-  int scrollOffset = 0;
-
-  public AnnotationLabels(AlignmentPanel ap)
-  {
-    this.ap = ap;
-
-    java.net.URL url = getClass().getResource("/images/idwidth.gif");
-    Image temp = null;
-    if (url != null)
-      temp = java.awt.Toolkit.getDefaultToolkit().createImage(url);
-
-    try
-    {
-      MediaTracker mt = new MediaTracker(this);
-      mt.addImage(temp, 0);
-      mt.waitForID(0);
-    }
-    catch (Exception ex) {}
-
-    BufferedImage bi = new BufferedImage(temp.getHeight(this), temp.getWidth(this),
-                                         BufferedImage.TYPE_INT_RGB);
-    Graphics2D g = (Graphics2D) bi.getGraphics();
-    g.rotate(Math.toRadians(90));
-    g.drawImage(temp, 0, -bi.getWidth(this), this);
-    image = (Image) bi;
-
-    addMouseListener(this);
-    addMouseMotionListener(this);
-  }
-
-  public void setScrollOffset(int y)
-  {
-    scrollOffset = y;
-    repaint();
-  }
-
-  public void actionPerformed(ActionEvent evt)
-  {
-    AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
-
-    if(evt.getActionCommand().equals(ADDNEW))
-    {
-      String label = JOptionPane.showInputDialog(this, "Label for annotation");
-      if(label==null)
-        label = "";
-      ap.av.alignment.addAnnotation(new AlignmentAnnotation
-                                      (label,
-                                       "New description",
-                                       new Annotation[ap.av.alignment.getWidth()]));
-    }
-   else if(evt.getActionCommand().equals(HIDE))
-   {
-     aa[selectedRow].visible = false;
-     if(aa[selectedRow].label.equals("Conservation"))
-       ap.av.showConservation = false;
-     if(aa[selectedRow].label.equals("Quality"))
-       ap.av.showQuality = false;
-     if(aa[selectedRow].label.equals("Consensus"))
-       ap.av.showIdentity = false;
-   }
-   else if(evt.getActionCommand().equals(DELETE))
-   {
-     ap.av.alignment.deleteAnnotation(aa[selectedRow]);
-   }
-   else if(evt.getActionCommand().equals(SHOWALL))
-   {
-       for(int i=0; i<aa.length; i++)
-         aa[i].visible = true;
-   }
-   else if(evt.getActionCommand().equals(OUTPUT_TEXT))
-   {
-     CutAndPasteTransfer cap = new CutAndPasteTransfer();
-     Desktop.addInternalFrame(cap, ap.alignFrame.getTitle()+" - "+ aa[selectedRow].label, 500, 100);
-     cap.setText( aa[selectedRow].toString() );
-   }
-
-   ap.annotationPanel.adjustPanelHeight();
-   ap.repaint();
-
-  }
-
-  public void mousePressed(MouseEvent evt)
-  {
-    int y = evt.getY() - scrollOffset;
-
-      AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
-       if(aa==null || aa.length==0)
-       {
-            JPopupMenu pop = new JPopupMenu("Annotations");
-            JMenuItem item = new JMenuItem(ADDNEW);
-            item.addActionListener(this);
-            pop.add(item);
-            pop.show(this, evt.getX(), evt.getY());
-            return;
-       }
-
-       int height = 0;
-       for (int i = 0; i < aa.length; i++)
-       {
-         if(!aa[i].visible)
-           continue;
-
-         height += aa[i].height;
-         if(y<height)
-         {
-           selectedRow = i;
-           break;
-         }
-       }
-
-      JPopupMenu pop = new JPopupMenu("Annotations");
-      JMenuItem item = new JMenuItem(ADDNEW);
-      item.addActionListener(this);
-      pop.add(item);
-      item = new JMenuItem(HIDE);
-      item.addActionListener(this);
-      pop.add(item);
-      item = new JMenuItem(DELETE);
-      item.addActionListener(this);
-      pop.add(item);
-      item = new JMenuItem(SHOWALL);
-      item.addActionListener(this);
-      pop.add(item);
-      item = new JMenuItem(OUTPUT_TEXT);
-      item.addActionListener(this);
-      pop.add(item);
-      pop.show(this, evt.getX(), evt.getY());
-
-    oldY = evt.getY();
-  }
-
-  public void mouseReleased(MouseEvent evt){ active = false; repaint(); }
-  public void mouseEntered(MouseEvent evt) { active = true;  repaint();}
-  public void mouseExited(MouseEvent evt)  { active = false; repaint();}
-  public void mouseDragged(MouseEvent evt)
-  {
-    active = true;
-    Dimension d = ap.annotationScroller.getPreferredSize();
-    int dif = evt.getY() - oldY;
-
-    dif /= ap.av.charHeight;
-    dif *= ap.av.charHeight;
-
-    if(d.height-dif>20)
-    {
-      ap.annotationScroller.setPreferredSize(new Dimension(d.width,d.height - dif));
-      d = ap.annotationSpaceFillerHolder.getPreferredSize();
-      ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension(d.width,d.height - dif));
-      ap.repaint();
-    }
-    ap.addNotify();
-  }
-
-  public void mouseMoved(MouseEvent evt)   {}
-  public void mouseClicked(MouseEvent evt) {}
-
-  public void paintComponent(Graphics g1)
-  {
-    Graphics2D g = (Graphics2D)g1;
-    g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,RenderingHints.VALUE_ANTIALIAS_ON);
-
-    drawComponent(g);
-  }
-
-  public void drawComponent(Graphics2D g)
-  {
-    FontMetrics fm = g.getFontMetrics(g.getFont());
-    g.setColor(Color.white);
-    g.fillRect(0,0, getWidth(), getHeight());
-
-    g.translate(0, scrollOffset);
-    g.setColor(Color.black);
-
-   AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
-   int y = g.getFont().getSize();
-   int x = 0;
-
-   if(aa!=null)
-   for(int i=0; i<aa.length; i++)
-   {
-     if(!aa[i].visible)
-       continue;
-
-     x = getWidth() - fm.stringWidth(aa[i].label)-3;
-
-     if(aa[i].isGraph)
-       y+=(aa[i].height/3);
-
-     g.drawString(aa[i].label, x, y);
-
-     if(aa[i].isGraph)
-       y+=(2*aa[i].height/3);
-    else
-       y+=aa[i].height;
-   }
-
-   if (active)
-   {
-     if (image != null)
-       g.drawImage(image, 2, 0, this);
-   }
-
-   if (aa == null || aa.length<1)
-   {
-     g.drawString("Right click", 2, 8);
-     g.drawString("to add annotation", 2, 18);
-   }
-
-
-
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * 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
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.gui;
+
+import java.util.*;
+
+import java.awt.*;
+import java.awt.datatransfer.*;
+import java.awt.event.*;
+import java.awt.image.*;
+import javax.swing.*;
+
+import jalview.datamodel.*;
+import jalview.io.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class AnnotationLabels
+    extends JPanel implements MouseListener,
+    MouseMotionListener, ActionListener
+{
+  static String ADDNEW = "Add New Row";
+  static String EDITNAME = "Edit Label/Description";
+  static String HIDE = "Hide This Row";
+  static String DELETE = "Delete This Row";
+  static String SHOWALL = "Show All Hidden Rows";
+  static String OUTPUT_TEXT = "Export Annotation";
+  static String COPYCONS_SEQ = "Copy Consensus Sequence";
+  boolean resizePanel = false;
+  Image image;
+  AlignmentPanel ap;
+  AlignViewport av;
+  boolean resizing = false;
+  MouseEvent dragEvent;
+  int oldY;
+  int selectedRow;
+  int scrollOffset = 0;
+  Font font = new Font("Arial", Font.PLAIN, 11);
+
+  /**
+   * Creates a new AnnotationLabels object.
+   *
+   * @param ap DOCUMENT ME!
+   */
+  public AnnotationLabels(AlignmentPanel ap)
+  {
+    this.ap = ap;
+    av = ap.av;
+    ToolTipManager.sharedInstance().registerComponent(this);
+
+    java.net.URL url = getClass().getResource("/images/idwidth.gif");
+    Image temp = null;
+
+    if (url != null)
+    {
+      temp = java.awt.Toolkit.getDefaultToolkit().createImage(url);
+    }
+
+    try
+    {
+      MediaTracker mt = new MediaTracker(this);
+      mt.addImage(temp, 0);
+      mt.waitForID(0);
+    }
+    catch (Exception ex)
+    {
+    }
+
+    BufferedImage bi = new BufferedImage(temp.getHeight(this),
+                                         temp.getWidth(this),
+                                         BufferedImage.TYPE_INT_RGB);
+    Graphics2D g = (Graphics2D) bi.getGraphics();
+    g.rotate(Math.toRadians(90));
+    g.drawImage(temp, 0, -bi.getWidth(this), this);
+    image = (Image) bi;
+
+    addMouseListener(this);
+    addMouseMotionListener(this);
+  }
+
+  public AnnotationLabels(AlignViewport av)
+  {
+    this.av = av;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param y DOCUMENT ME!
+   */
+  public void setScrollOffset(int y)
+  {
+    scrollOffset = y;
+    repaint();
+  }
+
+  void getSelectedRow(int y)
+  {
+    int height = 0;
+    AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+
+    if (aa != null)
+    {
+      for (int i = 0; i < aa.length; i++)
+      {
+        if (!aa[i].visible)
+        {
+          continue;
+        }
+
+        height += aa[i].height;
+
+        if (y < height)
+        {
+          selectedRow = i;
+
+          break;
+        }
+      }
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void actionPerformed(ActionEvent evt)
+  {
+    int dif = 0;
+    AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+
+    if (evt.getActionCommand().equals(ADDNEW))
+    {
+      AlignmentAnnotation newAnnotation = new AlignmentAnnotation(null,
+          null,
+          new Annotation[ap.av.alignment.getWidth()]);
+
+      if (!editLabelDescription(newAnnotation))
+      {
+        return;
+      }
+
+      ap.av.alignment.addAnnotation(newAnnotation);
+      ap.av.alignment.setAnnotationIndex(newAnnotation, 0);
+      if (aa != null)
+      {
+        dif = aa[aa.length - 1].height;
+      }
+    }
+    else if (evt.getActionCommand().equals(EDITNAME))
+    {
+      editLabelDescription(aa[selectedRow]);
+      repaint();
+    }
+    else if (evt.getActionCommand().equals(HIDE))
+    {
+      aa[selectedRow].visible = false;
+
+      if (aa[selectedRow].label.equals("Quality"))
+      {
+        ap.av.quality = null;
+      }
+
+      dif = aa[selectedRow].height * -1;
+    }
+    else if (evt.getActionCommand().equals(DELETE))
+    {
+      ap.av.alignment.deleteAnnotation(aa[selectedRow]);
+      dif = aa[selectedRow].height * -1;
+    }
+    else if (evt.getActionCommand().equals(SHOWALL))
+    {
+      for (int i = 0; i < aa.length; i++)
+      {
+        if (!aa[i].visible && aa[i].annotations!=null)
+        {
+          dif += aa[i].height;
+          aa[i].visible = true;
+        }
+      }
+    }
+    else if (evt.getActionCommand().equals(OUTPUT_TEXT))
+    {
+      new AnnotationExporter().exportAnnotations(
+          ap,
+          new AlignmentAnnotation[]
+          {aa[selectedRow]},
+          null
+          );
+    }
+    else if (evt.getActionCommand().equals(COPYCONS_SEQ))
+    {
+      SequenceI cons = av.getConsensusSeq();
+      if (cons != null)
+      {
+        copy_annotseqtoclipboard(cons);
+      }
+
+    }
+
+    ap.annotationPanel.adjustPanelHeight();
+    ap.annotationScroller.validate();
+    ap.paintAlignment(true);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  boolean editLabelDescription(AlignmentAnnotation annotation)
+  {
+    EditNameDialog dialog = new EditNameDialog(annotation.label,
+                                               annotation.description,
+                                               "       Annotation Name ",
+                                               "Annotation Description ",
+                                               "Edit Annotation Name/Description");
+
+    if (!dialog.accept)
+    {
+      return false;
+    }
+
+    annotation.label = dialog.getName();
+
+    String text = dialog.getDescription();
+    if (text!=null && text.length() == 0)
+    {
+      text = null;
+    }
+    annotation.description = text;
+
+    return true;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void mousePressed(MouseEvent evt)
+  {
+    getSelectedRow(evt.getY() - scrollOffset);
+    oldY = evt.getY();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void mouseReleased(MouseEvent evt)
+  {
+    int start = selectedRow;
+    getSelectedRow(evt.getY() - scrollOffset);
+    int end = selectedRow;
+
+    if (start != end)
+    {
+      //Swap these annotations
+      AlignmentAnnotation startAA = ap.av.alignment.getAlignmentAnnotation()[
+          start];
+      AlignmentAnnotation endAA = ap.av.alignment.getAlignmentAnnotation()[end];
+
+      ap.av.alignment.getAlignmentAnnotation()[end] = startAA;
+      ap.av.alignment.getAlignmentAnnotation()[start] = endAA;
+    }
+
+    resizePanel = false;
+    dragEvent = null;
+    repaint();
+    ap.annotationPanel.repaint();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void mouseEntered(MouseEvent evt)
+  {
+    if (evt.getY() < 10)
+    {
+      resizePanel = true;
+      repaint();
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void mouseExited(MouseEvent evt)
+  {
+    if (dragEvent == null)
+    {
+      resizePanel = false;
+      repaint();
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void mouseDragged(MouseEvent evt)
+  {
+    dragEvent = evt;
+
+    if (resizePanel)
+    {
+      Dimension d = ap.annotationScroller.getPreferredSize();
+      int dif = evt.getY() - oldY;
+
+      dif /= ap.av.charHeight;
+      dif *= ap.av.charHeight;
+
+      if ( (d.height - dif) > 20)
+      {
+        ap.annotationScroller.setPreferredSize(new Dimension(d.width,
+            d.height - dif));
+        d = ap.annotationSpaceFillerHolder.getPreferredSize();
+        ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension(
+            d.width, d.height - dif));
+        ap.paintAlignment(true);
+      }
+
+      ap.addNotify();
+    }
+    else
+    {
+      repaint();
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void mouseMoved(MouseEvent evt)
+  {
+    resizePanel = evt.getY() < 10;
+
+    getSelectedRow(evt.getY() - scrollOffset);
+
+    if (selectedRow > -1
+        && ap.av.alignment.getAlignmentAnnotation().length > selectedRow)
+    {
+      String desc = ap.av.alignment.
+          getAlignmentAnnotation()[selectedRow].description;
+
+      if (desc != null && !desc.equals("New description"))
+      {
+        setToolTipText(ap.av.alignment.
+                       getAlignmentAnnotation()[selectedRow].description);
+      }
+    }
+
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void mouseClicked(MouseEvent evt)
+  {
+    if (!SwingUtilities.isRightMouseButton(evt))
+    {
+      return;
+    }
+
+    AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+
+    if ( (aa == null) || (aa.length == 0))
+    {
+      JPopupMenu pop = new JPopupMenu("Annotations");
+      JMenuItem item = new JMenuItem(ADDNEW);
+      item.addActionListener(this);
+      pop.add(item);
+      pop.show(this, evt.getX(), evt.getY());
+
+      return;
+    }
+
+    JPopupMenu pop = new JPopupMenu("Annotations");
+    JMenuItem item = new JMenuItem(ADDNEW);
+    item.addActionListener(this);
+    pop.add(item);
+    item = new JMenuItem(EDITNAME);
+    item.addActionListener(this);
+    pop.add(item);
+    item = new JMenuItem(HIDE);
+    item.addActionListener(this);
+    pop.add(item);
+    item = new JMenuItem(DELETE);
+    item.addActionListener(this);
+    pop.add(item);
+    item = new JMenuItem(SHOWALL);
+    item.addActionListener(this);
+    pop.add(item);
+    item = new JMenuItem(OUTPUT_TEXT);
+    item.addActionListener(this);
+    pop.add(item);
+    // annotation object should be typed
+    if (aa[selectedRow] == ap.av.consensus)
+    {
+      pop.addSeparator();
+      final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
+          "Ignore Gaps In Consensus",
+          ap.av.getIgnoreGapsConsensus());
+      cbmi.addActionListener(new ActionListener()
+      {
+        public void actionPerformed(ActionEvent e)
+        {
+          ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
+        }
+      });
+      pop.add(cbmi);
+      final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ);
+      consclipbrd.addActionListener(this);
+      pop.add(consclipbrd);
+    }
+
+    pop.show(this, evt.getX(), evt.getY());
+  }
+
+  /**
+   * do a single sequence copy to jalview and the system clipboard
+   *
+   * @param sq sequence to be copied to clipboard
+   */
+  protected void copy_annotseqtoclipboard(SequenceI sq)
+  {
+    SequenceI[] seqs = new SequenceI[]
+        {
+        sq};
+    String[] omitHidden = null;
+    SequenceI[] dseqs = new SequenceI[]
+        {
+        sq.getDatasetSequence()};
+    if (dseqs[0] == null)
+    {
+      dseqs[0] = new Sequence(sq);
+      dseqs[0].setSequence(
+          jalview.analysis.AlignSeq.extractGaps(
+              jalview.util.Comparison.GapChars,
+              sq.getSequenceAsString()));
+
+      sq.setDatasetSequence(dseqs[0]);
+    }
+    Alignment ds = new Alignment(dseqs);
+    if (av.hasHiddenColumns)
+    {
+      omitHidden = av.getColumnSelection().getVisibleSequenceStrings(0,
+          sq.getLength(), seqs);
+    }
+
+    String output = new FormatAdapter().formatSequences(
+        "Fasta",
+        seqs,
+        omitHidden);
+
+    Toolkit.getDefaultToolkit().getSystemClipboard()
+        .setContents(new StringSelection(output), Desktop.instance);
+
+    Vector hiddenColumns = null;
+    if (av.hasHiddenColumns)
+    {
+      hiddenColumns = new Vector();
+      for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++)
+      {
+        int[] region = (int[])
+            av.getColumnSelection().getHiddenColumns().elementAt(i);
+
+        hiddenColumns.addElement(new int[]
+                                 {region[0],
+                                 region[1]});
+      }
+    }
+
+    Desktop.jalviewClipboard = new Object[]
+        {
+        seqs,
+        ds, // what is the dataset of a consensus sequence ? need to flag sequence as special.
+        hiddenColumns};
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param g1 DOCUMENT ME!
+   */
+  public void paintComponent(Graphics g)
+  {
+
+    int width = getWidth();
+    if (width == 0)
+    {
+      width = ap.calculateIdWidth().width + 4;
+    }
+
+    Graphics2D g2 = (Graphics2D) g;
+    if (av.antiAlias)
+    {
+      g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+                          RenderingHints.VALUE_ANTIALIAS_ON);
+    }
+
+    drawComponent(g2, width);
+
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param g DOCUMENT ME!
+   */
+  public void drawComponent(Graphics g, int width)
+  {
+    if (av.getFont().getSize() < 10)
+    {
+      g.setFont(font);
+    }
+    else
+    {
+      g.setFont(av.getFont());
+    }
+
+    FontMetrics fm = g.getFontMetrics(g.getFont());
+    g.setColor(Color.white);
+    g.fillRect(0, 0, getWidth(), getHeight());
+
+    g.translate(0, scrollOffset);
+    g.setColor(Color.black);
+
+    AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+    int fontHeight = g.getFont().getSize();
+    int y = 0;
+    int x = 0;
+    int graphExtras = 0;
+    int offset =0;
+
+    if (aa != null)
+    {
+      for (int i = 0; i < aa.length; i++)
+      {
+        g.setColor(Color.black);
+
+        if (!aa[i].visible)
+        {
+          continue;
+        }
+
+
+        y += aa[i].height;
+
+        offset = -aa[i].height/2;
+
+        if(aa[i].hasText)
+        {
+          offset += fm.getHeight()/2;
+          offset -= fm.getDescent();
+        }
+        else
+          offset += fm.getDescent();
+
+        x = width - fm.stringWidth(aa[i].label) - 3;
+
+        if (aa[i].graphGroup > -1)
+        {
+          int groupSize = 0;
+          for (int gg = 0; gg < aa.length; gg++)
+          {
+            if (aa[gg].graphGroup == aa[i].graphGroup)
+            {
+              groupSize++;
+            }
+          }
+
+          if (groupSize * (fontHeight + 8) < aa[i].height)
+          {
+            graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) / 2;
+          }
+
+          for (int gg = 0; gg < aa.length; gg++)
+          {
+            if (aa[gg].graphGroup == aa[i].graphGroup)
+            {
+              x = width - fm.stringWidth(aa[gg].label) - 3;
+              g.drawString(aa[gg].label, x,y - graphExtras);
+              if (aa[gg].annotations[0] != null)
+              {
+                g.setColor(aa[gg].annotations[0].colour);
+              }
+
+              g.drawLine(x, y - graphExtras - 3,
+                         x + fm.stringWidth(aa[gg].label),
+                         y - graphExtras - 3);
+
+              g.setColor(Color.black);
+              graphExtras += fontHeight + 8;
+            }
+          }
+        }
+        else
+        {
+          g.drawString(aa[i].label, x, y +offset);
+        }
+      }
+    }
+
+    if (resizePanel)
+    {
+      g.drawImage(image, 2, 0 - scrollOffset, this);
+    }
+    else if (dragEvent != null && aa != null)
+    {
+      g.setColor(Color.lightGray);
+      g.drawString(aa[selectedRow].label, dragEvent.getX(),
+                   dragEvent.getY() - scrollOffset);
+    }
+
+    if ( (aa == null) || (aa.length < 1))
+    {
+      g.drawString("Right click", 2, 8);
+      g.drawString("to add annotation", 2, 18);
+    }
+  }
+}