X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=1a9541c3794b0a2b44d34ca02bea69145b767270;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=fad9dcd7137d4fd7e1057c950941698da6fb416d;hpb=d7989f319488cc56440f822261bc5014c27e03c6;p=jalview.git

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index fad9dcd..1a9541c 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -20,6 +20,16 @@
  */
 package jalview.gui;
 
+import jalview.analysis.AlignmentUtils;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.io.FormatAdapter;
+import jalview.util.MessageManager;
+
 import java.awt.Color;
 import java.awt.Dimension;
 import java.awt.Font;
@@ -41,6 +51,7 @@ 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;
@@ -50,16 +61,6 @@ import javax.swing.JPopupMenu;
 import javax.swing.SwingUtilities;
 import javax.swing.ToolTipManager;
 
-import jalview.analysis.AlignmentUtils;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.io.FormatAdapter;
-import jalview.util.MessageManager;
-
 /**
  * DOCUMENT ME!
  * 
@@ -69,13 +70,16 @@ import jalview.util.MessageManager;
 public class AnnotationLabels extends JPanel implements MouseListener,
         MouseMotionListener, ActionListener
 {
-  private static final Pattern LEFT_ANGLE_BRACKET_PATTERN = Pattern.compile("<");
+  private static final Pattern LEFT_ANGLE_BRACKET_PATTERN = Pattern
+          .compile("<");
 
-  String TOGGLE_LABELSCALE = MessageManager.getString("label.scale_label_to_column");
+  String TOGGLE_LABELSCALE = MessageManager
+          .getString("label.scale_label_to_column");
 
   String ADDNEW = MessageManager.getString("label.add_new_row");
 
-  String EDITNAME = MessageManager.getString("label.edit_label_description");
+  String EDITNAME = MessageManager
+          .getString("label.edit_label_description");
 
   String HIDE = MessageManager.getString("label.hide_row");
 
@@ -85,7 +89,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
 
   String OUTPUT_TEXT = MessageManager.getString("label.export_annotation");
 
-  String COPYCONS_SEQ = MessageManager.getString("label.copy_consensus_sequence");
+  String COPYCONS_SEQ = MessageManager
+          .getString("label.copy_consensus_sequence");
 
   boolean resizePanel = false;
 
@@ -208,11 +213,13 @@ public class AnnotationLabels extends JPanel implements MouseListener,
    * @param evt
    *          DOCUMENT ME!
    */
+  @Override
   public void actionPerformed(ActionEvent evt)
   {
     AlignmentAnnotation[] aa = ap.av.getAlignment()
             .getAlignmentAnnotation();
 
+    boolean fullRepaint = false;
     if (evt.getActionCommand().equals(ADDNEW))
     {
       AlignmentAnnotation newAnnotation = new AlignmentAnnotation(null,
@@ -225,11 +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))
     {
@@ -238,6 +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))
     {
@@ -248,12 +262,12 @@ public class AnnotationLabels extends JPanel implements MouseListener,
           aa[i].visible = true;
         }
       }
+      fullRepaint = true;
     }
     else if (evt.getActionCommand().equals(OUTPUT_TEXT))
     {
       new AnnotationExporter().exportAnnotations(ap,
-              new AlignmentAnnotation[]
-      { aa[selectedRow] });
+              new AlignmentAnnotation[] { aa[selectedRow] });
     }
     else if (evt.getActionCommand().equals(COPYCONS_SEQ))
     {
@@ -277,18 +291,30 @@ public class AnnotationLabels extends JPanel implements MouseListener,
       aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel;
     }
 
-    refresh();
+    refresh(fullRepaint);
 
   }
 
   /**
    * Redraw sensibly.
+   * 
+   * @adjustHeight if true, try to recalculate panel height for visible
+   *               annotations
    */
-  protected void refresh()
+  protected void refresh(boolean adjustHeight)
   {
-    ap.validateAnnotationDimensions(false);
+    ap.validateAnnotationDimensions(adjustHeight);
     ap.addNotify();
-    ap.repaint();
+    if (adjustHeight)
+    {
+      // sort, repaint, update overview
+      ap.paintAlignment(true);
+    }
+    else
+    {
+      // lightweight repaint
+      ap.repaint();
+    }
   }
 
   /**
@@ -299,6 +325,7 @@ 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",
@@ -321,406 +348,152 @@ 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!
-   */
-  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!
    */
-  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!
-   */
-  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!
-   */
-  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;
+            // }
+            // }
+            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!
-   */
-  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!
-   */
-  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()
-        {
-          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"),
+                  MessageManager.getString("label.show_group_histogram"),
                   aa[selectedRow].groupRef.isShowConsensusHistogram());
           chist.addActionListener(new ActionListener()
           {
+            @Override
             public void actionPerformed(ActionEvent e)
             {
               // TODO: pass on reference
@@ -736,10 +509,11 @@ public class AnnotationLabels extends JPanel implements MouseListener,
           });
           pop.add(chist);
           final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem(
-                          MessageManager.getString("label.show_group_logo"),
+                  MessageManager.getString("label.show_group_logo"),
                   aa[selectedRow].groupRef.isShowSequenceLogo());
           cprofl.addActionListener(new ActionListener()
           {
+            @Override
             public void actionPerformed(ActionEvent e)
             {
               // TODO: pass on reference
@@ -755,10 +529,11 @@ public class AnnotationLabels extends JPanel implements MouseListener,
           });
           pop.add(cprofl);
           final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem(
-                          MessageManager.getString("label.normalise_group_logo"),
+                  MessageManager.getString("label.normalise_group_logo"),
                   aa[selectedRow].groupRef.isNormaliseSequenceLogo());
           cproflnorm.addActionListener(new ActionListener()
           {
+            @Override
             public void actionPerformed(ActionEvent e)
             {
 
@@ -780,9 +555,11 @@ public class AnnotationLabels extends JPanel implements MouseListener,
         else
         {
           final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
-                          MessageManager.getString("label.show_histogram"), av.isShowConsensusHistogram());
+                  MessageManager.getString("label.show_histogram"),
+                  av.isShowConsensusHistogram());
           chist.addActionListener(new ActionListener()
           {
+            @Override
             public void actionPerformed(ActionEvent e)
             {
               // TODO: pass on reference
@@ -799,9 +576,11 @@ public class AnnotationLabels extends JPanel implements MouseListener,
           });
           pop.add(chist);
           final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
-                          MessageManager.getString("label.show_logo"), av.isShowSequenceLogo());
+                  MessageManager.getString("label.show_logo"),
+                  av.isShowSequenceLogo());
           cprof.addActionListener(new ActionListener()
           {
+            @Override
             public void actionPerformed(ActionEvent e)
             {
               // TODO: pass on reference
@@ -818,9 +597,11 @@ public class AnnotationLabels extends JPanel implements MouseListener,
           });
           pop.add(cprof);
           final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem(
-                          MessageManager.getString("label.normalise_logo"), av.isNormaliseSequenceLogo());
+                  MessageManager.getString("label.normalise_logo"),
+                  av.isNormaliseSequenceLogo());
           cprofnorm.addActionListener(new ActionListener()
           {
+            @Override
             public void actionPerformed(ActionEvent e)
             {
               // TODO: pass on reference
@@ -847,6 +628,325 @@ public class AnnotationLabels extends JPanel implements MouseListener,
   }
 
   /**
+   * DOCUMENT ME!
+   * 
+   * @param evt
+   *          DOCUMENT ME!
+   */
+  @Override
+  public void mouseReleased(MouseEvent evt)
+  {
+    if (evt.isPopupTrigger())
+    {
+      showPopupMenu(evt);
+      return;
+    }
+
+    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
@@ -854,11 +954,9 @@ public class AnnotationLabels extends JPanel implements MouseListener,
    */
   protected void copy_annotseqtoclipboard(SequenceI sq)
   {
-    SequenceI[] seqs = new SequenceI[]
-    { sq };
+    SequenceI[] seqs = new SequenceI[] { sq };
     String[] omitHidden = null;
-    SequenceI[] dseqs = new SequenceI[]
-    { sq.getDatasetSequence() };
+    SequenceI[] dseqs = new SequenceI[] { sq.getDatasetSequence() };
     if (dseqs[0] == null)
     {
       dseqs[0] = new Sequence(sq);
@@ -874,8 +972,15 @@ public class AnnotationLabels extends JPanel implements MouseListener,
               sq.getLength(), seqs);
     }
 
+    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, null);
+            omitHidden, alignmentStartEnd);
 
     Toolkit.getDefaultToolkit().getSystemClipboard()
             .setContents(new StringSelection(output), Desktop.instance);
@@ -886,13 +991,14 @@ public class AnnotationLabels extends JPanel implements MouseListener,
       hiddenColumns = new ArrayList<int[]>();
       for (int[] region : av.getColumnSelection().getHiddenColumns())
       {
-        hiddenColumns.add(new int[]
-        { region[0], region[1] });
+        hiddenColumns.add(new int[] { region[0], region[1] });
       }
     }
 
-    Desktop.jalviewClipboard = new Object[]
-    { seqs, ds, // what is the dataset of a consensus sequence ? need to flag
+    Desktop.jalviewClipboard = new Object[] { seqs, ds, // what is the dataset
+                                                        // of a consensus
+                                                        // sequence ? need to
+                                                        // flag
         // sequence as special.
         hiddenColumns };
   }
@@ -903,6 +1009,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
    * @param g1
    *          DOCUMENT ME!
    */
+  @Override
   public void paintComponent(Graphics g)
   {
 
@@ -981,8 +1088,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     int ofontH = fontHeight;
     int sOffset = 0;
     int visHeight = 0;
-    int[] visr = (ap != null && ap.getAnnotationPanel() != null) ? ap.getAnnotationPanel()
-            .getVisibleVRange() : null;
+    int[] visr = (ap != null && ap.getAnnotationPanel() != null) ? ap
+            .getAnnotationPanel().getVisibleVRange() : null;
     if (clip && visr != null)
     {
       sOffset = visr[0];