X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=e16867a4c0d9389ee6614cc6ec625068a1a235dd;hb=163ed5b997bbda48e4cdd950e87a8fe01baae7fb;hp=3105ab9e3d49d39959ec09d782af917269d3899b;hpb=3ef0beaad016ac06b8947feb0f36d06b1e956d59;p=jalview.git

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 3105ab9..e16867a 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -27,6 +27,7 @@ import jalview.datamodel.Annotation;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.io.FileFormat;
 import jalview.io.FormatAdapter;
 import jalview.util.MessageManager;
 
@@ -51,7 +52,6 @@ import java.awt.image.BufferedImage;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
-import java.util.List;
 import java.util.regex.Pattern;
 
 import javax.swing.JCheckBoxMenuItem;
@@ -219,6 +219,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     AlignmentAnnotation[] aa = ap.av.getAlignment()
             .getAlignmentAnnotation();
 
+    boolean fullRepaint = false;
     if (evt.getActionCommand().equals(ADDNEW))
     {
       AlignmentAnnotation newAnnotation = new AlignmentAnnotation(null,
@@ -231,11 +232,16 @@ public class AnnotationLabels extends JPanel implements MouseListener,
 
       ap.av.getAlignment().addAnnotation(newAnnotation);
       ap.av.getAlignment().setAnnotationIndex(newAnnotation, 0);
+      fullRepaint = true;
     }
     else if (evt.getActionCommand().equals(EDITNAME))
     {
+      String name = aa[selectedRow].label;
       editLabelDescription(aa[selectedRow]);
-      repaint();
+      if (!name.equalsIgnoreCase(aa[selectedRow].label))
+      {
+        fullRepaint = true;
+      }
     }
     else if (evt.getActionCommand().equals(HIDE))
     {
@@ -244,6 +250,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     else if (evt.getActionCommand().equals(DELETE))
     {
       ap.av.getAlignment().deleteAnnotation(aa[selectedRow]);
+      ap.av.getCalcManager().removeWorkerForAnnotation(aa[selectedRow]);
+      fullRepaint = true;
     }
     else if (evt.getActionCommand().equals(SHOWALL))
     {
@@ -254,6 +262,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
           aa[i].visible = true;
         }
       }
+      fullRepaint = true;
     }
     else if (evt.getActionCommand().equals(OUTPUT_TEXT))
     {
@@ -282,18 +291,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
       aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel;
     }
 
-    refresh();
-
-  }
+    ap.refresh(fullRepaint);
 
-  /**
-   * Redraw sensibly.
-   */
-  protected void refresh()
-  {
-    ap.validateAnnotationDimensions(false);
-    ap.addNotify();
-    ap.repaint();
   }
 
   /**
@@ -304,6 +303,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
    */
   boolean editLabelDescription(AlignmentAnnotation annotation)
   {
+    // TODO i18n
     EditNameDialog dialog = new EditNameDialog(annotation.label,
             annotation.description, "       Annotation Name ",
             "Annotation Description ", "Edit Annotation Name/Description",
@@ -326,418 +326,145 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     return true;
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param evt
-   *          DOCUMENT ME!
-   */
   @Override
   public void mousePressed(MouseEvent evt)
   {
     getSelectedRow(evt.getY() - getScrollOffset());
     oldY = evt.getY();
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param evt
-   *          DOCUMENT ME!
-   */
-  @Override
-  public void mouseReleased(MouseEvent evt)
-  {
-    int start = selectedRow;
-    getSelectedRow(evt.getY() - getScrollOffset());
-    int end = selectedRow;
-
-    if (start != end)
+    if (evt.isPopupTrigger())
     {
-      // Swap these annotations
-      AlignmentAnnotation startAA = ap.av.getAlignment()
-              .getAlignmentAnnotation()[start];
-      if (end == -1)
-      {
-        end = ap.av.getAlignment().getAlignmentAnnotation().length - 1;
-      }
-      AlignmentAnnotation endAA = ap.av.getAlignment()
-              .getAlignmentAnnotation()[end];
-
-      ap.av.getAlignment().getAlignmentAnnotation()[end] = startAA;
-      ap.av.getAlignment().getAlignmentAnnotation()[start] = endAA;
+      showPopupMenu(evt);
     }
-
-    resizePanel = false;
-    dragEvent = null;
-    repaint();
-    ap.getAnnotationPanel().repaint();
   }
 
   /**
-   * DOCUMENT ME!
+   * Build and show the Pop-up menu at the right-click mouse position
    * 
    * @param evt
-   *          DOCUMENT ME!
    */
-  @Override
-  public void mouseEntered(MouseEvent evt)
+  void showPopupMenu(MouseEvent evt)
   {
-    if (evt.getY() < 10)
-    {
-      resizePanel = true;
-      repaint();
-    }
-  }
+    evt.consume();
+    final AlignmentAnnotation[] aa = ap.av.getAlignment()
+            .getAlignmentAnnotation();
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param evt
-   *          DOCUMENT ME!
-   */
-  @Override
-  public void mouseExited(MouseEvent evt)
-  {
-    if (dragEvent == null)
+    JPopupMenu pop = new JPopupMenu(
+            MessageManager.getString("label.annotations"));
+    JMenuItem item = new JMenuItem(ADDNEW);
+    item.addActionListener(this);
+    pop.add(item);
+    if (selectedRow < 0)
     {
-      resizePanel = false;
-      repaint();
+      if (hasHiddenRows)
+      { // let the user make everything visible again
+        item = new JMenuItem(SHOWALL);
+        item.addActionListener(this);
+        pop.add(item);
+      }
+      pop.show(this, evt.getX(), evt.getY());
+      return;
     }
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param evt
-   *          DOCUMENT ME!
-   */
-  @Override
-  public void mouseDragged(MouseEvent evt)
-  {
-    dragEvent = evt;
-
-    if (resizePanel)
+    item = new JMenuItem(EDITNAME);
+    item.addActionListener(this);
+    pop.add(item);
+    item = new JMenuItem(HIDE);
+    item.addActionListener(this);
+    pop.add(item);
+    // JAL-1264 hide all sequence-specific annotations of this type
+    if (selectedRow < aa.length)
     {
-      Dimension d = ap.annotationScroller.getPreferredSize();
-      int dif = evt.getY() - oldY;
-
-      dif /= ap.av.getCharHeight();
-      dif *= ap.av.getCharHeight();
-
-      if ((d.height - dif) > 20)
+      if (aa[selectedRow].sequenceRef != null)
       {
-        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);
+        final String label = aa[selectedRow].label;
+        JMenuItem hideType = new JMenuItem();
+        String text = MessageManager.getString("label.hide_all") + " "
+                + label;
+        hideType.setText(text);
+        hideType.addActionListener(new ActionListener()
+        {
+          @Override
+          public void actionPerformed(ActionEvent e)
+          {
+            AlignmentUtils.showOrHideSequenceAnnotations(
+                    ap.av.getAlignment(), Collections.singleton(label),
+                    null, false, false);
+            // for (AlignmentAnnotation ann : ap.av.getAlignment()
+            // .getAlignmentAnnotation())
+            // {
+            // if (ann.sequenceRef != null && ann.label != null
+            // && ann.label.equals(label))
+            // {
+            // ann.visible = false;
+            // }
+            // }
+            ap.refresh(true);
+          }
+        });
+        pop.add(hideType);
       }
-
-      ap.addNotify();
     }
-    else
+    item = new JMenuItem(DELETE);
+    item.addActionListener(this);
+    pop.add(item);
+    if (hasHiddenRows)
     {
-      repaint();
+      item = new JMenuItem(SHOWALL);
+      item.addActionListener(this);
+      pop.add(item);
     }
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param evt
-   *          DOCUMENT ME!
-   */
-  @Override
-  public void mouseMoved(MouseEvent evt)
-  {
-    resizePanel = evt.getY() < 10;
-
-    getSelectedRow(evt.getY() - getScrollOffset());
-
-    if (selectedRow > -1
-            && ap.av.getAlignment().getAlignmentAnnotation().length > selectedRow)
+    item = new JMenuItem(OUTPUT_TEXT);
+    item.addActionListener(this);
+    pop.add(item);
+    // TODO: annotation object should be typed for autocalculated/derived
+    // property methods
+    if (selectedRow < aa.length)
     {
-      AlignmentAnnotation aa = ap.av.getAlignment()
-              .getAlignmentAnnotation()[selectedRow];
-
-      StringBuffer desc = new StringBuffer();
-      if (aa.description != null
-              && !aa.description.equals("New description"))
+      final String label = aa[selectedRow].label;
+      if (!aa[selectedRow].autoCalculated)
       {
-        // TODO: we could refactor and merge this code with the code in
-        // jalview.gui.SeqPanel.mouseMoved(..) that formats sequence feature
-        // tooltips
-        desc.append(aa.getDescription(true).trim());
-        // check to see if the description is an html fragment.
-        if (desc.length() < 6
-                || (desc.substring(0, 6).toLowerCase().indexOf("<html>") < 0))
+        if (aa[selectedRow].graph == AlignmentAnnotation.NO_GRAPH)
         {
-          // clean the description ready for embedding in html
-          desc = new StringBuffer(LEFT_ANGLE_BRACKET_PATTERN.matcher(desc)
-                  .replaceAll("&lt;"));
-          desc.insert(0, "<html>");
+          // display formatting settings for this row.
+          pop.addSeparator();
+          // av and sequencegroup need to implement same interface for
+          item = new JCheckBoxMenuItem(TOGGLE_LABELSCALE,
+                  aa[selectedRow].scaleColLabel);
+          item.addActionListener(this);
+          pop.add(item);
         }
-        else
+      }
+      else if (label.indexOf("Consensus") > -1)
+      {
+        pop.addSeparator();
+        // av and sequencegroup need to implement same interface for
+        final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
+                MessageManager.getString("label.ignore_gaps_consensus"),
+                (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef
+                        .getIgnoreGapsConsensus() : ap.av
+                        .isIgnoreGapsConsensus());
+        final AlignmentAnnotation aaa = aa[selectedRow];
+        cbmi.addActionListener(new ActionListener()
         {
-          // remove terminating html if any
-          int i = desc.substring(desc.length() - 7).toLowerCase()
-                  .lastIndexOf("</html>");
-          if (i > -1)
+          @Override
+          public void actionPerformed(ActionEvent e)
           {
-            desc.setLength(desc.length() - 7 + i);
+            if (aaa.groupRef != null)
+            {
+              // TODO: pass on reference to ap so the view can be updated.
+              aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState());
+              ap.getAnnotationPanel().paint(
+                      ap.getAnnotationPanel().getGraphics());
+            }
+            else
+            {
+              ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
+            }
+            ap.alignmentChanged();
           }
-        }
-        if (aa.hasScore())
-        {
-          desc.append("<br/>");
-        }
-        // if (aa.hasProperties())
-        // {
-        // desc.append("<table>");
-        // for (String prop : aa.getProperties())
-        // {
-        // desc.append("<tr><td>" + prop + "</td><td>"
-        // + aa.getProperty(prop) + "</td><tr>");
-        // }
-        // desc.append("</table>");
-        // }
-      }
-      else
-      {
-        // begin the tooltip's html fragment
-        desc.append("<html>");
-        if (aa.hasScore())
-        {
-          // TODO: limit precision of score to avoid noise from imprecise
-          // doubles
-          // (64.7 becomes 64.7+/some tiny value).
-          desc.append(" Score: " + aa.score);
-        }
-      }
-      if (desc.length() > 6)
-      {
-        desc.append("</html>");
-        this.setToolTipText(desc.toString());
-      }
-      else
-      {
-        this.setToolTipText(null);
-      }
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param evt
-   *          DOCUMENT ME!
-   */
-  @Override
-  public void mouseClicked(MouseEvent evt)
-  {
-    final AlignmentAnnotation[] aa = ap.av.getAlignment()
-            .getAlignmentAnnotation();
-    if (SwingUtilities.isLeftMouseButton(evt))
-    {
-      if (selectedRow > -1 && selectedRow < aa.length)
-      {
-        if (aa[selectedRow].groupRef != null)
-        {
-          if (evt.getClickCount() >= 2)
-          {
-            // todo: make the ap scroll to the selection - not necessary, first
-            // click highlights/scrolls, second selects
-            ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null);
-            ap.av.setSelectionGroup(// new SequenceGroup(
-            aa[selectedRow].groupRef); // );
-            ap.paintAlignment(false);
-            PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
-            ap.av.sendSelection();
-          }
-          else
-          {
-            ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(
-                    aa[selectedRow].groupRef.getSequences(null));
-          }
-          return;
-        }
-        else if (aa[selectedRow].sequenceRef != null)
-        {
-          if (evt.getClickCount() == 1)
-          {
-            ap.getSeqPanel().ap
-                    .getIdPanel()
-                    .highlightSearchResults(
-                            Arrays.asList(new SequenceI[] { aa[selectedRow].sequenceRef }));
-          }
-          else if (evt.getClickCount() >= 2)
-          {
-            ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null);
-            SequenceGroup sg = ap.av.getSelectionGroup();
-            if (sg != null)
-            {
-              // we make a copy rather than edit the current selection if no
-              // modifiers pressed
-              // see Enhancement JAL-1557
-              if (!(evt.isControlDown() || evt.isShiftDown()))
-              {
-                sg = new SequenceGroup(sg);
-                sg.clear();
-                sg.addSequence(aa[selectedRow].sequenceRef, false);
-              }
-              else
-              {
-                if (evt.isControlDown())
-                {
-                  sg.addOrRemove(aa[selectedRow].sequenceRef, true);
-                }
-                else
-                {
-                  // notionally, we should also add intermediate sequences from
-                  // last added sequence ?
-                  sg.addSequence(aa[selectedRow].sequenceRef, true);
-                }
-              }
-            }
-            else
-            {
-              sg = new SequenceGroup();
-              sg.setStartRes(0);
-              sg.setEndRes(ap.av.getAlignment().getWidth() - 1);
-              sg.addSequence(aa[selectedRow].sequenceRef, false);
-            }
-            ap.av.setSelectionGroup(sg);
-            ap.av.sendSelection();
-            ap.paintAlignment(false);
-            PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
-          }
-
-        }
-      }
-    }
-    if (!SwingUtilities.isRightMouseButton(evt))
-    {
-      return;
-    }
-
-    JPopupMenu pop = new JPopupMenu(
-            MessageManager.getString("label.annotations"));
-    JMenuItem item = new JMenuItem(ADDNEW);
-    item.addActionListener(this);
-    pop.add(item);
-    if (selectedRow < 0)
-    {
-      if (hasHiddenRows)
-      { // let the user make everything visible again
-        item = new JMenuItem(SHOWALL);
-        item.addActionListener(this);
-        pop.add(item);
-      }
-      pop.show(this, evt.getX(), evt.getY());
-      return;
-    }
-    item = new JMenuItem(EDITNAME);
-    item.addActionListener(this);
-    pop.add(item);
-    item = new JMenuItem(HIDE);
-    item.addActionListener(this);
-    pop.add(item);
-    // JAL-1264 hide all sequence-specific annotations of this type
-    if (selectedRow < aa.length)
-    {
-      if (aa[selectedRow].sequenceRef != null)
-      {
-        final String label = aa[selectedRow].label;
-        JMenuItem hideType = new JMenuItem();
-        String text = MessageManager.getString("label.hide_all") + " "
-                + label;
-        hideType.setText(text);
-        hideType.addActionListener(new ActionListener()
-        {
-          @Override
-          public void actionPerformed(ActionEvent e)
-          {
-            AlignmentUtils.showOrHideSequenceAnnotations(
-                    ap.av.getAlignment(), Collections.singleton(label),
-                    null, false, false);
-            // for (AlignmentAnnotation ann : ap.av.getAlignment()
-            // .getAlignmentAnnotation())
-            // {
-            // if (ann.sequenceRef != null && ann.label != null
-            // && ann.label.equals(label))
-            // {
-            // ann.visible = false;
-            // }
-            // }
-            refresh();
-          }
-        });
-        pop.add(hideType);
-      }
-    }
-    item = new JMenuItem(DELETE);
-    item.addActionListener(this);
-    pop.add(item);
-    if (hasHiddenRows)
-    {
-      item = new JMenuItem(SHOWALL);
-      item.addActionListener(this);
-      pop.add(item);
-    }
-    item = new JMenuItem(OUTPUT_TEXT);
-    item.addActionListener(this);
-    pop.add(item);
-    // TODO: annotation object should be typed for autocalculated/derived
-    // property methods
-    if (selectedRow < aa.length)
-    {
-      final String label = aa[selectedRow].label;
-      if (!aa[selectedRow].autoCalculated)
-      {
-        if (aa[selectedRow].graph == AlignmentAnnotation.NO_GRAPH)
-        {
-          // display formatting settings for this row.
-          pop.addSeparator();
-          // av and sequencegroup need to implement same interface for
-          item = new JCheckBoxMenuItem(TOGGLE_LABELSCALE,
-                  aa[selectedRow].scaleColLabel);
-          item.addActionListener(this);
-          pop.add(item);
-        }
-      }
-      else if (label.indexOf("Consensus") > -1)
-      {
-        pop.addSeparator();
-        // av and sequencegroup need to implement same interface for
-        final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
-                MessageManager.getString("label.ignore_gaps_consensus"),
-                (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef
-                        .getIgnoreGapsConsensus() : ap.av
-                        .isIgnoreGapsConsensus());
-        final AlignmentAnnotation aaa = aa[selectedRow];
-        cbmi.addActionListener(new ActionListener()
-        {
-          @Override
-          public void actionPerformed(ActionEvent e)
-          {
-            if (aaa.groupRef != null)
-            {
-              // TODO: pass on reference to ap so the view can be updated.
-              aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState());
-              ap.getAnnotationPanel().paint(
-                      ap.getAnnotationPanel().getGraphics());
-            }
-            else
-            {
-              ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
-            }
-          }
-        });
-        pop.add(cbmi);
-        // av and sequencegroup need to implement same interface for
-        if (aaa.groupRef != null)
+        });
+        pop.add(cbmi);
+        // av and sequencegroup need to implement same interface for
+        if (aaa.groupRef != null)
         {
           final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
                   MessageManager.getString("label.show_group_histogram"),
@@ -879,52 +606,370 @@ public class AnnotationLabels extends JPanel implements MouseListener,
   }
 
   /**
-   * do a single sequence copy to jalview and the system clipboard
+   * DOCUMENT ME!
    * 
-   * @param sq
-   *          sequence to be copied to clipboard
+   * @param evt
+   *          DOCUMENT ME!
    */
-  protected void copy_annotseqtoclipboard(SequenceI sq)
+  @Override
+  public void mouseReleased(MouseEvent evt)
   {
-    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())
+    if (evt.isPopupTrigger())
     {
-      omitHidden = av.getColumnSelection().getVisibleSequenceStrings(0,
-              sq.getLength(), seqs);
+      showPopupMenu(evt);
+      return;
     }
 
-    int[] alignmentStartEnd = new int[] { 0, ds.getWidth() - 1 };
-    List<int[]> hiddenCols = av.getColumnSelection().getHiddenColumns();
-    if (hiddenCols != null)
-    {
-      alignmentStartEnd = av.getAlignment().getVisibleStartAndEndIndex(
-              hiddenCols);
-    }
-    String output = new FormatAdapter().formatSequences("Fasta", seqs,
-            omitHidden, alignmentStartEnd);
+    int start = selectedRow;
+    getSelectedRow(evt.getY() - getScrollOffset());
+    int end = selectedRow;
+
+    if (start != end)
+    {
+      // Swap these annotations
+      AlignmentAnnotation startAA = ap.av.getAlignment()
+              .getAlignmentAnnotation()[start];
+      if (end == -1)
+      {
+        end = ap.av.getAlignment().getAlignmentAnnotation().length - 1;
+      }
+      AlignmentAnnotation endAA = ap.av.getAlignment()
+              .getAlignmentAnnotation()[end];
+
+      ap.av.getAlignment().getAlignmentAnnotation()[end] = startAA;
+      ap.av.getAlignment().getAlignmentAnnotation()[start] = endAA;
+    }
+
+    resizePanel = false;
+    dragEvent = null;
+    repaint();
+    ap.getAnnotationPanel().repaint();
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param evt
+   *          DOCUMENT ME!
+   */
+  @Override
+  public void mouseEntered(MouseEvent evt)
+  {
+    if (evt.getY() < 10)
+    {
+      resizePanel = true;
+      repaint();
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param evt
+   *          DOCUMENT ME!
+   */
+  @Override
+  public void mouseExited(MouseEvent evt)
+  {
+    if (dragEvent == null)
+    {
+      resizePanel = false;
+      repaint();
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param evt
+   *          DOCUMENT ME!
+   */
+  @Override
+  public void mouseDragged(MouseEvent evt)
+  {
+    dragEvent = evt;
+
+    if (resizePanel)
+    {
+      Dimension d = ap.annotationScroller.getPreferredSize();
+      int dif = evt.getY() - oldY;
+
+      dif /= ap.av.getCharHeight();
+      dif *= ap.av.getCharHeight();
+
+      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!
+   */
+  @Override
+  public void mouseMoved(MouseEvent evt)
+  {
+    resizePanel = evt.getY() < 10;
+
+    getSelectedRow(evt.getY() - getScrollOffset());
+
+    if (selectedRow > -1
+            && ap.av.getAlignment().getAlignmentAnnotation().length > selectedRow)
+    {
+      AlignmentAnnotation aa = ap.av.getAlignment()
+              .getAlignmentAnnotation()[selectedRow];
+
+      StringBuffer desc = new StringBuffer();
+      if (aa.description != null
+              && !aa.description.equals("New description"))
+      {
+        // TODO: we could refactor and merge this code with the code in
+        // jalview.gui.SeqPanel.mouseMoved(..) that formats sequence feature
+        // tooltips
+        desc.append(aa.getDescription(true).trim());
+        // check to see if the description is an html fragment.
+        if (desc.length() < 6
+                || (desc.substring(0, 6).toLowerCase().indexOf("<html>") < 0))
+        {
+          // clean the description ready for embedding in html
+          desc = new StringBuffer(LEFT_ANGLE_BRACKET_PATTERN.matcher(desc)
+                  .replaceAll("&lt;"));
+          desc.insert(0, "<html>");
+        }
+        else
+        {
+          // remove terminating html if any
+          int i = desc.substring(desc.length() - 7).toLowerCase()
+                  .lastIndexOf("</html>");
+          if (i > -1)
+          {
+            desc.setLength(desc.length() - 7 + i);
+          }
+        }
+        if (aa.hasScore())
+        {
+          desc.append("<br/>");
+        }
+        // if (aa.hasProperties())
+        // {
+        // desc.append("<table>");
+        // for (String prop : aa.getProperties())
+        // {
+        // desc.append("<tr><td>" + prop + "</td><td>"
+        // + aa.getProperty(prop) + "</td><tr>");
+        // }
+        // desc.append("</table>");
+        // }
+      }
+      else
+      {
+        // begin the tooltip's html fragment
+        desc.append("<html>");
+        if (aa.hasScore())
+        {
+          // TODO: limit precision of score to avoid noise from imprecise
+          // doubles
+          // (64.7 becomes 64.7+/some tiny value).
+          desc.append(" Score: " + aa.score);
+        }
+      }
+      if (desc.length() > 6)
+      {
+        desc.append("</html>");
+        this.setToolTipText(desc.toString());
+      }
+      else
+      {
+        this.setToolTipText(null);
+      }
+    }
+  }
+
+  @Override
+  public void mouseClicked(MouseEvent evt)
+  {
+    final AlignmentAnnotation[] aa = ap.av.getAlignment()
+            .getAlignmentAnnotation();
+    if (!evt.isPopupTrigger() && SwingUtilities.isLeftMouseButton(evt))
+    {
+      if (selectedRow > -1 && selectedRow < aa.length)
+      {
+        if (aa[selectedRow].groupRef != null)
+        {
+          if (evt.getClickCount() >= 2)
+          {
+            // todo: make the ap scroll to the selection - not necessary, first
+            // click highlights/scrolls, second selects
+            ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null);
+            // process modifiers
+            SequenceGroup sg = ap.av.getSelectionGroup();
+            if (sg == null
+                    || sg == aa[selectedRow].groupRef
+                    || !(jalview.util.Platform.isControlDown(evt) || evt
+                            .isShiftDown()))
+            {
+              if (jalview.util.Platform.isControlDown(evt)
+                      || evt.isShiftDown())
+              {
+                // clone a new selection group from the associated group
+                ap.av.setSelectionGroup(new SequenceGroup(
+                        aa[selectedRow].groupRef));
+              }
+              else
+              {
+                // set selection to the associated group so it can be edited
+                ap.av.setSelectionGroup(aa[selectedRow].groupRef);
+              }
+            }
+            else
+            {
+              // modify current selection with associated group
+              int remainToAdd = aa[selectedRow].groupRef.getSize();
+              for (SequenceI sgs : aa[selectedRow].groupRef.getSequences())
+              {
+                if (jalview.util.Platform.isControlDown(evt))
+                {
+                  sg.addOrRemove(sgs, --remainToAdd == 0);
+                }
+                else
+                {
+                  // notionally, we should also add intermediate sequences from
+                  // last added sequence ?
+                  sg.addSequence(sgs, --remainToAdd == 0);
+                }
+              }
+            }
+
+            ap.paintAlignment(false);
+            PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
+            ap.av.sendSelection();
+          }
+          else
+          {
+            ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(
+                    aa[selectedRow].groupRef.getSequences(null));
+          }
+          return;
+        }
+        else if (aa[selectedRow].sequenceRef != null)
+        {
+          if (evt.getClickCount() == 1)
+          {
+            ap.getSeqPanel().ap
+                    .getIdPanel()
+                    .highlightSearchResults(
+                            Arrays.asList(new SequenceI[] { aa[selectedRow].sequenceRef }));
+          }
+          else if (evt.getClickCount() >= 2)
+          {
+            ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null);
+            SequenceGroup sg = ap.av.getSelectionGroup();
+            if (sg != null)
+            {
+              // we make a copy rather than edit the current selection if no
+              // modifiers pressed
+              // see Enhancement JAL-1557
+              if (!(jalview.util.Platform.isControlDown(evt) || evt
+                      .isShiftDown()))
+              {
+                sg = new SequenceGroup(sg);
+                sg.clear();
+                sg.addSequence(aa[selectedRow].sequenceRef, false);
+              }
+              else
+              {
+                if (jalview.util.Platform.isControlDown(evt))
+                {
+                  sg.addOrRemove(aa[selectedRow].sequenceRef, true);
+                }
+                else
+                {
+                  // notionally, we should also add intermediate sequences from
+                  // last added sequence ?
+                  sg.addSequence(aa[selectedRow].sequenceRef, true);
+                }
+              }
+            }
+            else
+            {
+              sg = new SequenceGroup();
+              sg.setStartRes(0);
+              sg.setEndRes(ap.av.getAlignment().getWidth() - 1);
+              sg.addSequence(aa[selectedRow].sequenceRef, false);
+            }
+            ap.av.setSelectionGroup(sg);
+            ap.paintAlignment(false);
+            PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
+            ap.av.sendSelection();
+          }
+
+        }
+      }
+      return;
+    }
+  }
+
+  /**
+   * 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.getAlignment().getHiddenColumns()
+              .getVisibleSequenceStrings(0,
+              sq.getLength(), seqs);
+    }
+
+    int[] alignmentStartEnd = new int[] { 0, ds.getWidth() - 1 };
+    if (av.hasHiddenColumns())
+    {
+      alignmentStartEnd = av.getAlignment().getHiddenColumns()
+            .getVisibleStartAndEndIndex(av.getAlignment().getWidth());
+    }
+
+    String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
+            seqs, omitHidden, alignmentStartEnd);
 
     Toolkit.getDefaultToolkit().getSystemClipboard()
             .setContents(new StringSelection(output), Desktop.instance);
 
     ArrayList<int[]> hiddenColumns = null;
+
     if (av.hasHiddenColumns())
     {
-      hiddenColumns = new ArrayList<int[]>();
-      for (int[] region : av.getColumnSelection().getHiddenColumns())
-      {
-        hiddenColumns.add(new int[] { region[0], region[1] });
-      }
+      hiddenColumns = av.getAlignment().getHiddenColumns()
+              .getHiddenColumnsCopy();
     }
 
     Desktop.jalviewClipboard = new Object[] { seqs, ds, // what is the dataset