X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=ccbebd52b44a31b52fadeea629818e494f4db68b;hb=6951479b7dc56bd022ce2c370b7f88b5571004fd;hp=a454cf936feddc0d03710570bb97d92124671581;hpb=a2497c9a753e13eeb17d33f73a697b4ad7ebdbc3;p=jalview.git

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index a454cf9..ccbebd5 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -18,17 +18,16 @@
  */
 package jalview.gui;
 
-import jalview.datamodel.*;
-import jalview.io.FormatAdapter;
+import java.util.*;
 
 import java.awt.*;
-import java.awt.datatransfer.StringSelection;
+import java.awt.datatransfer.*;
 import java.awt.event.*;
 import java.awt.image.*;
-import java.util.Vector;
-
 import javax.swing.*;
 
+import jalview.datamodel.*;
+import jalview.io.*;
 
 /**
  * DOCUMENT ME!
@@ -36,624 +35,620 @@ import javax.swing.*;
  * @author $author$
  * @version $Revision$
  */
-public class AnnotationLabels extends JPanel implements MouseListener,
+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);
+  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);
     }
 
-    public AnnotationLabels(AlignViewport av)
+    try
     {
-      this.av = av;
+      MediaTracker mt = new MediaTracker(this);
+      mt.addImage(temp, 0);
+      mt.waitForID(0);
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param y DOCUMENT ME!
-     */
-    public void setScrollOffset(int y)
+    catch (Exception ex)
     {
-        scrollOffset = y;
-        repaint();
     }
 
-    void getSelectedRow(int y)
+    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)
     {
-      int height = 0;
-      AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
-
-      if(aa!=null)
+      for (int i = 0; i < aa.length; i++)
       {
-        for (int i = 0; i < aa.length; i++)
+        if (!aa[i].visible)
         {
-          if (!aa[i].visible)
-          {
-            continue;
-          }
+          continue;
+        }
 
-          height += aa[i].height;
+        height += aa[i].height;
 
-          if (y < height)
-          {
-            selectedRow = i;
+        if (y < height)
+        {
+          selectedRow = i;
 
-            break;
-          }
+          break;
         }
       }
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void actionPerformed(ActionEvent evt)
+  }
+
+  /**
+   * 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))
     {
-        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()]);
+      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)
-                {
-                    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);
-
-        }
+      if (!editLabelDescription(newAnnotation))
+      {
+        return;
+      }
 
-        ap.annotationPanel.adjustPanelHeight();
-        ap.annotationScroller.validate();
-        ap.repaint();
+      ap.av.alignment.addAnnotation(newAnnotation);
+      ap.av.alignment.setAnnotationIndex(newAnnotation, 0);
+      if (aa != null)
+      {
+        dif = aa[aa.length - 1].height;
+      }
     }
-
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    boolean editLabelDescription(AlignmentAnnotation annotation)
+    else if (evt.getActionCommand().equals(EDITNAME))
     {
-      JLabel idlabel = new JLabel(  "      Annotation Label ");
-      JLabel desclabel = new JLabel("Annotation Description ");
-      idlabel.setFont(new Font("Courier", Font.PLAIN, 12));
-      desclabel.setFont(new Font("Courier", Font.PLAIN, 12));
-      JTextField id = new JTextField(annotation.label, 40);
-      JTextField description = new JTextField(annotation.description, 40);
-      JPanel panel = new JPanel(new BorderLayout());
-      JPanel panel2 = new JPanel(new BorderLayout());
-      panel2.add(idlabel, BorderLayout.WEST);
-      panel2.add(id, BorderLayout.CENTER);
-      panel.add(panel2, BorderLayout.NORTH);
-      panel2 = new JPanel(new BorderLayout());
-      panel2.add(desclabel, BorderLayout.WEST);
-      panel2.add(description, BorderLayout.CENTER);
-      panel.add(panel2, BorderLayout.SOUTH);
-
-
-       int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
-          panel, "Edit Annotation Name/Description",
-          JOptionPane.OK_CANCEL_OPTION );
-
-
-        if (reply != JOptionPane.OK_OPTION )
-        {
-            return false;
-        }
-
-
-        annotation.label = id.getText().trim();
+      editLabelDescription(aa[selectedRow]);
+      repaint();
+    }
+    else if (evt.getActionCommand().equals(HIDE))
+    {
+      aa[selectedRow].visible = false;
 
-        String text = description.getText().trim();
-        if(text.length()==0)
-          text = null;
-        annotation.description = text;
+      if (aa[selectedRow].label.equals("Quality"))
+      {
+        ap.av.quality = null;
+      }
 
-        return true;
+      dif = aa[selectedRow].height * -1;
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void mousePressed(MouseEvent evt)
+    else if (evt.getActionCommand().equals(DELETE))
     {
-        getSelectedRow(evt.getY() - scrollOffset);
-        oldY = evt.getY();
+      ap.av.alignment.deleteAnnotation(aa[selectedRow]);
+      dif = aa[selectedRow].height * -1;
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void mouseReleased(MouseEvent evt)
+    else if (evt.getActionCommand().equals(SHOWALL))
     {
-        int start = selectedRow;
-        getSelectedRow(evt.getY() - scrollOffset);
-        int end = selectedRow;
-
-        if(start!=end)
+      for (int i = 0; i < aa.length; i++)
+      {
+        if (!aa[i].visible && aa[i].annotations!=null)
         {
-          //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;
+          dif += aa[i].height;
+          aa[i].visible = true;
         }
-
-        resizePanel = false;
-        dragEvent = null;
-        repaint();
-        ap.annotationPanel.repaint();
+      }
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void mouseEntered(MouseEvent evt)
+    else if (evt.getActionCommand().equals(OUTPUT_TEXT))
     {
-      if(evt.getY()<10)
+      new AnnotationExporter().exportAnnotations(
+          ap,
+          new AlignmentAnnotation[]
+          {aa[selectedRow]},
+          null
+          );
+    }
+    else if (evt.getActionCommand().equals(COPYCONS_SEQ))
+    {
+      SequenceI cons = av.getConsensusSeq();
+      if (cons != null)
       {
-        resizePanel = true;
-        repaint();
+        copy_annotseqtoclipboard(cons);
       }
+
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void mouseExited(MouseEvent evt)
+    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)
     {
-      if(dragEvent == null)
-      {
-        resizePanel = false;
-        repaint();
-      }
+      return false;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void mouseDragged(MouseEvent evt)
+    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)
     {
-      dragEvent = evt;
+      //Swap these annotations
+      AlignmentAnnotation startAA = ap.av.alignment.getAlignmentAnnotation()[
+          start];
+      AlignmentAnnotation endAA = ap.av.alignment.getAlignmentAnnotation()[end];
 
-      if (resizePanel)
-      {
-        Dimension d = ap.annotationScroller.getPreferredSize();
-        int dif = evt.getY() - oldY;
+      ap.av.alignment.getAlignmentAnnotation()[end] = startAA;
+      ap.av.alignment.getAlignmentAnnotation()[start] = endAA;
+    }
 
-        dif /= ap.av.charHeight;
-        dif *= ap.av.charHeight;
+    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;
 
-        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();
-        }
+      dif /= ap.av.charHeight;
+      dif *= ap.av.charHeight;
 
-        ap.addNotify();
+      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);
       }
-      else
-        repaint();
-    }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void mouseMoved(MouseEvent evt)
+      ap.addNotify();
+    }
+    else
     {
-      resizePanel = evt.getY()<10;
+      repaint();
+    }
+  }
 
-      getSelectedRow(evt.getY() - scrollOffset);
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void mouseMoved(MouseEvent evt)
+  {
+    resizePanel = evt.getY() < 10;
 
-      if(selectedRow>-1)
-      {
-        String desc = ap.av.alignment.
-            getAlignmentAnnotation()[selectedRow].description;
+    getSelectedRow(evt.getY() - scrollOffset);
 
-        if (desc != null && !desc.equals("New Description"))
-          setToolTipText(ap.av.alignment.
-                         getAlignmentAnnotation()[selectedRow].description);
+    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);
       }
-      repaint();
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void mouseClicked(MouseEvent evt)
-    {
-       if(!SwingUtilities.isRightMouseButton(evt))
-         return;
+  }
 
-        AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void mouseClicked(MouseEvent evt)
+  {
+    if (!SwingUtilities.isRightMouseButton(evt))
+    {
+      return;
+    }
 
-        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());
+    AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
 
-            return;
-        }
+    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)
+    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)
         {
-          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);
+          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);
-      }
+    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()));
 
-      String output = new FormatAdapter().formatSequences(
-          "Fasta",
-          seqs,
-          omitHidden);
+      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);
+    Toolkit.getDefaultToolkit().getSystemClipboard()
+        .setContents(new StringSelection(output), Desktop.instance);
 
-      Vector hiddenColumns = null;
-      if(av.hasHiddenColumns)
+    Vector hiddenColumns = null;
+    if (av.hasHiddenColumns)
+    {
+      hiddenColumns = new Vector();
+      for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++)
       {
-        hiddenColumns =new Vector();
-        for(int i=0; i<av.getColumnSelection().getHiddenColumns().size(); i++)
-        {
-          int[] region = (int[])
-              av.getColumnSelection().getHiddenColumns().elementAt(i);
+        int[] region = (int[])
+            av.getColumnSelection().getHiddenColumns().elementAt(i);
 
-          hiddenColumns.addElement(new int[]{region[0],
-                            region[1]});
-        }
+        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)
+
+    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;
+    }
 
-        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);
+    }
 
-       Graphics2D g2 = (Graphics2D) g;
-       if(av.antiAlias)
-        g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
-            RenderingHints.VALUE_ANTIALIAS_ON);
+    drawComponent(g2, width);
 
-       drawComponent(g2, width);
+  }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param g DOCUMENT ME!
+   */
+  public void drawComponent(Graphics g, int width)
+  {
+    if (av.getFont().getSize() < 10)
+    {
+      g.setFont(font);
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param g DOCUMENT ME!
-     */
-    public void drawComponent(Graphics g, int width)
+    else
     {
-        if(av.getFont().getSize()<10)
-          g.setFont(font);
-        else
-          g.setFont(av.getFont());
+      g.setFont(av.getFont());
+    }
+
+    FontMetrics fm = g.getFontMetrics(g.getFont());
+    g.setColor(Color.white);
+    g.fillRect(0, 0, getWidth(), getHeight());
 
-        FontMetrics fm = g.getFontMetrics(g.getFont());
-        g.setColor(Color.white);
-        g.fillRect(0, 0, getWidth(), getHeight());
+    g.translate(0, scrollOffset);
+    g.setColor(Color.black);
 
-        g.translate(0, scrollOffset);
+    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);
 
-        AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
-        int fontHeight = g.getFont().getSize();
-        int y = fontHeight;
-        int x = 0;
-        int graphExtras = 0;
+        if (!aa[i].visible)
+        {
+          continue;
+        }
 
 
+        y += aa[i].height;
 
-        if (aa != null)
+        offset = -aa[i].height/2;
+
+        if(aa[i].hasText)
         {
-            for (int i = 0; i < aa.length; i++)
-            {
-                if (!aa[i].visible)
-                {
-                    continue;
-                }
-
-                x = width - fm.stringWidth(aa[i].label) - 3;
-
-                if (aa[i].graph>0 && aa[i].graphHeight>0)
-                {
-                    graphExtras = y;
-
-                    y += (aa[i].height / 3);
-
-                    if(aa[i].graphGroup<0)
-                        graphExtras = y + fontHeight;
-                }
-
-                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, graphExtras );
-                     if(aa[gg].annotations[0]!=null)
-                       g.setColor(aa[gg].annotations[0].colour);
-
-                     g.drawLine( x, graphExtras+3,
-                                 x+fm.stringWidth(aa[gg].label),
-                                 graphExtras+3);
-
-                     g.setColor(Color.black);
-                     graphExtras += fontHeight+8;
-                   }
-                 }
-                }
-                else
-                  g.drawString(aa[i].label, x, y);
-
-                if (aa[i].graph>0)
-                {
-                /*  if (aa[i].graphLines != null)
-                  {
-                    for (int gl = 0; gl < aa[i].graphLines.size(); gl++)
-                    {
-                       x = width - fm.stringWidth(aa[i].getGraphLine(gl).label) - 3;
-                      g.drawString(aa[i].getGraphLine(gl).label, x, graphExtras);
-                      g.setColor(aa[i].getGraphLine(gl).colour);
-                      Graphics2D g2 = (Graphics2D) g;
-                      g2.setStroke(new BasicStroke(1,
-                          BasicStroke.CAP_SQUARE,
-                          BasicStroke.JOIN_ROUND, 3f,
-                          new float[]
-                          {5f, 3f}, 0f));
-
-                      graphExtras += 3;
-
-                      g.drawLine(x, graphExtras,
-                                 x+fm.stringWidth(aa[i].label),
-                                 graphExtras);
-                      g2.setStroke(new BasicStroke());
-                    }
-                  }*/
-                    y += ((2 * aa[i].height) / 3);
-                }
-                else
-                {
-                    y += aa[i].height;
-                }
-            }
+          offset += fm.getHeight()/2;
+          offset -= fm.getDescent();
         }
+        else
+          offset += fm.getDescent();
+
+        x = width - fm.stringWidth(aa[i].label) - 3;
 
-        if (resizePanel)
+        if (aa[i].graphGroup > -1)
         {
-          g.drawImage(image, 2, 0 - scrollOffset, this);
+          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 if (dragEvent != null && aa!=null)
+        else
         {
-          g.setColor(Color.lightGray);
-          g.drawString(aa[selectedRow].label, dragEvent.getX(), dragEvent.getY() - scrollOffset);
+          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);
-        }
+    if ( (aa == null) || (aa.length < 1))
+    {
+      g.drawString("Right click", 2, 8);
+      g.drawString("to add annotation", 2, 18);
     }
+  }
 }