X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationLabels.java;h=201cfae894074e61e74bb8bbc25fd43ee79eaa91;hp=bf6d38d47515a95717218c58ea184fd8fb6aa190;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3

diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java
index bf6d38d..201cfae 100755
--- a/src/jalview/appletgui/AnnotationLabels.java
+++ b/src/jalview/appletgui/AnnotationLabels.java
@@ -1,332 +1,872 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-
-package jalview.appletgui;
-
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.datamodel.*;
-
-public class AnnotationLabels
-    extends Panel implements ActionListener, MouseListener, MouseMotionListener
-{
-  Image image;
-  boolean active = false;
-  AlignmentPanel ap;
-  AlignViewport av;
-  boolean resizing = false;
-  int oldY, mouseX;
-  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 = "Show Values In Textbox";
-  static String COPYCONS_SEQ = "Copy Consensus Sequence";
-
-  int selectedRow = 0;
-  int scrollOffset = 0;
-
-  Tooltip tooltip;
-
-  public AnnotationLabels(AlignmentPanel ap)
-  {
-    this.ap = ap;
-    this.av = ap.av;
-    setLayout(null);
-    addMouseListener(this);
-    addMouseMotionListener(this);
-  }
-
-  public AnnotationLabels(AlignViewport av)
-  {
-    this.av = av;
-  }
-
-  public void setScrollOffset(int y)
-  {
-    scrollOffset = y;
-    repaint();
-  }
-
-  void getSelectedRow(int y)
-  {
-    selectedRow = -1;
-    AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
-
-    if (aa == null)
-    {
-      return;
-    }
-
-    int height = 0;
-    for (int i = 0; i < aa.length; i++)
-    {
-      if (!aa[i].visible)
-      {
-        continue;
-      }
-
-      height += aa[i].height;
-      if (y < height)
-      {
-        selectedRow = i;
-        break;
-      }
-    }
-  }
-
-  public void actionPerformed(ActionEvent evt)
-  {
-    AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
-
-    if (evt.getActionCommand().equals(EDITNAME))
-    {
-      EditNameDialog dialog = new EditNameDialog(
-          aa[selectedRow].label,
-          aa[selectedRow].description,
-          "       Annotation Label",
-          "Annotation Description",
-          ap,
-          "Edit Annotation Name / Description");
-
-      if (dialog.accept)
-      {
-        aa[selectedRow].label = dialog.getName();
-        aa[selectedRow].description = dialog.getDescription();
-        repaint();
-      }
-    }
-    if (evt.getActionCommand().equals(HIDE))
-    {
-      aa[selectedRow].visible = false;
-    }
-    else if (evt.getActionCommand().equals(SHOWALL))
-    {
-      for (int i = 0; i < aa.length; i++)
-      {
-        aa[i].visible = true;
-      }
-    }
-    else if (evt.getActionCommand().equals(OUTPUT_TEXT))
-    {
-      CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame);
-      Frame frame = new Frame();
-      frame.add(cap);
-      jalview.bin.JalviewLite.addFrame(frame,
-                                       ap.alignFrame.getTitle() + " - " +
-                                       aa[selectedRow].label, 500, 100);
-      cap.setText(aa[selectedRow].toString());
-    }
-    else if (evt.getActionCommand().equals(COPYCONS_SEQ))
-    {
-      SequenceI cons = av.getConsensusSeq();
-      if (cons != null)
-      {
-        copy_annotseqtoclipboard(cons);
-      }
-
-    }
-    ap.annotationPanel.adjustPanelHeight();
-    setSize(getSize().width, ap.annotationPanel.getSize().height);
-    ap.validate();
-    ap.repaint();
-  }
-
-  public void mouseMoved(MouseEvent evt)
-  {
-    getSelectedRow(evt.getY() - scrollOffset);
-
-    if (selectedRow > -1)
-    {
-      if (tooltip == null)
-      {
-        tooltip = new Tooltip(ap.av.alignment.
-                              getAlignmentAnnotation()[selectedRow].
-                              description,
-                              this);
-      }
-      else
-      {
-        tooltip.setTip(ap.av.alignment.
-                       getAlignmentAnnotation()[selectedRow].description);
-      }
-    }
-    else if (tooltip != null)
-    {
-      tooltip.setTip("");
-    }
-
-  }
-
-  public void mouseDragged(MouseEvent evt)
-  {}
-
-  public void mouseClicked(MouseEvent evt)
-  {}
-
-  public void mouseReleased(MouseEvent evt)
-  {}
-
-  public void mouseEntered(MouseEvent evt)
-  {}
-
-  public void mouseExited(MouseEvent evt)
-  {}
-
-  public void mousePressed(MouseEvent evt)
-  {
-    AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
-
-    PopupMenu pop = new PopupMenu("Annotations");
-
-    MenuItem item = new MenuItem(EDITNAME);
-    item.addActionListener(this);
-    pop.add(item);
-    item = new MenuItem(HIDE);
-    item.addActionListener(this);
-    pop.add(item);
-    item = new MenuItem(SHOWALL);
-    item.addActionListener(this);
-    pop.add(item);
-    this.add(pop);
-    item = new MenuItem(OUTPUT_TEXT);
-    item.addActionListener(this);
-    pop.add(item);
-
-    if (aa[selectedRow] == ap.av.consensus)
-    {
-      pop.addSeparator();
-      final CheckboxMenuItem cbmi = new CheckboxMenuItem(
-          "Ignore Gaps In Consensus",
-          ap.av.getIgnoreGapsConsensus());
-
-      cbmi.addItemListener(new ItemListener()
-      {
-        public void itemStateChanged(ItemEvent e)
-        {
-          ap.av.setIgnoreGapsConsensus(cbmi.getState());
-          ap.repaint();
-        }
-      });
-      pop.add(cbmi);
-      final MenuItem cpcons = new MenuItem(COPYCONS_SEQ);
-      cpcons.addActionListener(this);
-      pop.add(cpcons);
-    }
-
-    pop.show(this, evt.getX(), evt.getY());
-
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  protected void copy_annotseqtoclipboard(SequenceI sq)
-  {
-    if (sq == null || sq.getLength() < 1)
-    {
-      return;
-    }
-    jalview.appletgui.AlignFrame.copiedSequences = new StringBuffer();
-    jalview.appletgui.AlignFrame.copiedSequences.append(sq.getName() + "\t" +
-        sq.getStart() + "\t" +
-        sq.getEnd() + "\t" +
-        sq.getSequenceAsString() + "\n");
-    if (av.hasHiddenColumns)
-    {
-      jalview.appletgui.AlignFrame.copiedHiddenColumns = new Vector();
-      for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++)
-      {
-        int[] region = (int[])
-            av.getColumnSelection().getHiddenColumns().elementAt(i);
-
-        jalview.appletgui.AlignFrame.copiedHiddenColumns.addElement(new int[]
-            {region[0],
-            region[1]});
-      }
-    }
-  }
-
-  public void update(Graphics g)
-  {
-    paint(g);
-  }
-
-  public void paint(Graphics g)
-  {
-    int w = getSize().width;
-    if (image == null || w != image.getWidth(this))
-    {
-      image = createImage(w, ap.annotationPanel.getSize().height);
-    }
-
-    drawComponent(image.getGraphics(), w);
-    g.drawImage(image, 0, 0, this);
-  }
-
-  public void drawComponent(Graphics g, int width)
-  {
-    g.setFont(av.getFont());
-    FontMetrics fm = g.getFontMetrics(av.getFont());
-    g.setColor(Color.white);
-    g.fillRect(0, 0, getSize().width, getSize().height);
-
-    g.translate(0, scrollOffset);
-    g.setColor(Color.black);
-
-    AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
-    int y = g.getFont().getSize();
-    int x = 0;
-
-    if (aa != null)
-    {
-      for (int i = 0; i < aa.length; i++)
-      {
-        if (!aa[i].visible)
-        {
-          continue;
-        }
-
-        x = width - fm.stringWidth(aa[i].label) - 3;
-
-        if (aa[i].graph > 0)
-        {
-          y += (aa[i].height / 3);
-        }
-
-        g.drawString(aa[i].label, x, y);
-
-        if (aa[i].graph > 0)
-        {
-          y += (2 * aa[i].height / 3);
-        }
-        else
-        {
-          y += aa[i].height;
-        }
-      }
-    }
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.appletgui;
+
+import jalview.analysis.AlignmentUtils;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
+import jalview.util.ParseHtmlBodyAndLinks;
+
+import java.awt.Checkbox;
+import java.awt.CheckboxMenuItem;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.FlowLayout;
+import java.awt.FontMetrics;
+import java.awt.Frame;
+import java.awt.Graphics;
+import java.awt.Image;
+import java.awt.MenuItem;
+import java.awt.Panel;
+import java.awt.PopupMenu;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.InputEvent;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.Vector;
+
+public class AnnotationLabels extends Panel implements ActionListener,
+        MouseListener, MouseMotionListener
+{
+  Image image;
+
+  boolean active = false;
+
+  AlignmentPanel ap;
+
+  AlignViewport av;
+
+  boolean resizing = false;
+
+  int oldY, mouseX;
+
+  static String ADDNEW = "Add New Row";
+
+  static String EDITNAME = "Edit Label/Description";
+
+  static String HIDE = "Hide This Row";
+
+  static String SHOWALL = "Show All Hidden Rows";
+
+  static String OUTPUT_TEXT = "Show Values In Textbox";
+
+  static String COPYCONS_SEQ = "Copy Consensus Sequence";
+
+  int scrollOffset = 0;
+
+  int selectedRow = -1;
+
+  Tooltip tooltip;
+
+  private boolean hasHiddenRows;
+
+  public AnnotationLabels(AlignmentPanel ap)
+  {
+    this.ap = ap;
+    this.av = ap.av;
+    setLayout(null);
+
+    /**
+     * this retrieves the adjustable height glyph from resources. we don't use
+     * it at the moment. java.net.URL url =
+     * getClass().getResource("/images/idwidth.gif"); Image temp = null;
+     * 
+     * if (url != null) { temp =
+     * java.awt.Toolkit.getDefaultToolkit().createImage(url); }
+     * 
+     * try { MediaTracker mt = new MediaTracker(this); mt.addImage(temp, 0);
+     * mt.waitForID(0); } catch (Exception ex) { }
+     * 
+     * BufferedImage bi = new BufferedImage(temp.getHeight(this),
+     * temp.getWidth(this), BufferedImage.TYPE_INT_RGB); Graphics2D g =
+     * (Graphics2D) bi.getGraphics(); g.rotate(Math.toRadians(90));
+     * g.drawImage(temp, 0, -bi.getWidth(this), this); image = (Image) bi;
+     */
+    addMouseListener(this);
+    addMouseMotionListener(this);
+  }
+
+  public AnnotationLabels(AlignViewport av)
+  {
+    this.av = av;
+  }
+
+  public void setScrollOffset(int y, boolean repaint)
+  {
+    scrollOffset = y;
+    if (repaint)
+    {
+      repaint();
+    }
+  }
+
+  /**
+   * 
+   * @param y
+   * @return -2 if no rows are visible at all, -1 if no visible rows were
+   *         selected
+   */
+  int getSelectedRow(int y)
+  {
+    int row = -2;
+    AlignmentAnnotation[] aa = ap.av.getAlignment()
+            .getAlignmentAnnotation();
+
+    if (aa == null)
+    {
+      return row;
+    }
+    int height = 0;
+    for (int i = 0; i < aa.length; i++)
+    {
+      row = -1;
+      if (!aa[i].visible)
+      {
+        continue;
+      }
+      height += aa[i].height;
+      if (y < height)
+      {
+        row = i;
+        break;
+      }
+    }
+
+    return row;
+  }
+
+  public void actionPerformed(ActionEvent evt)
+  {
+    AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
+
+    if (evt.getActionCommand().equals(ADDNEW))
+    {
+      AlignmentAnnotation newAnnotation = new AlignmentAnnotation("", null,
+              new Annotation[ap.av.getAlignment().getWidth()]);
+
+      if (!editLabelDescription(newAnnotation))
+      {
+        return;
+      }
+
+      ap.av.getAlignment().addAnnotation(newAnnotation);
+      ap.av.getAlignment().setAnnotationIndex(newAnnotation, 0);
+    }
+    else if (evt.getActionCommand().equals(EDITNAME))
+    {
+      editLabelDescription(aa[selectedRow]);
+    }
+    else if (evt.getActionCommand().equals(HIDE))
+    {
+      aa[selectedRow].visible = false;
+    }
+    else if (evt.getActionCommand().equals(SHOWALL))
+    {
+      for (int i = 0; i < aa.length; i++)
+      {
+        aa[i].visible = (aa[i].annotations == null) ? false : true;
+      }
+    }
+    else if (evt.getActionCommand().equals(OUTPUT_TEXT))
+    {
+      CutAndPasteTransfer cap = new CutAndPasteTransfer(false,
+              ap.alignFrame);
+      Frame frame = new Frame();
+      frame.add(cap);
+      jalview.bin.JalviewLite.addFrame(frame, ap.alignFrame.getTitle()
+              + " - " + aa[selectedRow].label, 500, 100);
+      cap.setText(aa[selectedRow].toString());
+    }
+    else if (evt.getActionCommand().equals(COPYCONS_SEQ))
+    {
+      SequenceI cons = av.getConsensusSeq();
+      if (cons != null)
+      {
+        copy_annotseqtoclipboard(cons);
+      }
+
+    }
+    refresh();
+  }
+
+  /**
+   * Adjust size and repaint
+   */
+  protected void refresh()
+  {
+    ap.annotationPanel.adjustPanelHeight();
+    setSize(getSize().width, ap.annotationPanel.getSize().height);
+    ap.validate();
+    ap.paintAlignment(true);
+  }
+
+  boolean editLabelDescription(AlignmentAnnotation annotation)
+  {
+    Checkbox padGaps = new Checkbox("Fill Empty Gaps With \""
+            + ap.av.getGapCharacter() + "\"", annotation.padGaps);
+
+    EditNameDialog dialog = new EditNameDialog(annotation.label,
+            annotation.description, "      Annotation Label",
+            "Annotation Description", ap.alignFrame,
+            "Edit Annotation Name / Description", 500, 180, false);
+
+    Panel empty = new Panel(new FlowLayout());
+    empty.add(padGaps);
+    dialog.add(empty);
+    dialog.pack();
+
+    dialog.setVisible(true);
+
+    if (dialog.accept)
+    {
+      annotation.label = dialog.getName();
+      annotation.description = dialog.getDescription();
+      annotation.setPadGaps(padGaps.getState(), av.getGapCharacter());
+      repaint();
+      return true;
+    }
+    else
+    {
+      return false;
+    }
+
+  }
+
+  boolean resizePanel = false;
+
+  public void mouseMoved(MouseEvent evt)
+  {
+    resizePanel = evt.getY() < 10 && evt.getX() < 14;
+    int row = getSelectedRow(evt.getY() + scrollOffset);
+
+    if (row > -1)
+    {
+      ParseHtmlBodyAndLinks phb = new ParseHtmlBodyAndLinks(
+              av.getAlignment().getAlignmentAnnotation()[row]
+                      .getDescription(true),
+              true, "\n");
+      if (tooltip == null)
+      {
+        tooltip = new Tooltip(phb.getNonHtmlContent(), this);
+      }
+      else
+      {
+        tooltip.setTip(phb.getNonHtmlContent());
+      }
+    }
+    else if (tooltip != null)
+    {
+      tooltip.setTip("");
+    }
+  }
+
+  /**
+   * curent drag position
+   */
+  MouseEvent dragEvent = null;
+
+  /**
+   * flag to indicate drag events should be ignored
+   */
+  private boolean dragCancelled = false;
+
+  /**
+   * clear any drag events in progress
+   */
+  public void cancelDrag()
+  {
+    dragEvent = null;
+    dragCancelled = true;
+  }
+
+  public void mouseDragged(MouseEvent evt)
+  {
+    if (dragCancelled)
+    {
+      return;
+    }
+    ;
+    dragEvent = evt;
+
+    if (resizePanel)
+    {
+      Dimension d = ap.annotationPanelHolder.getSize(), e = ap.annotationSpaceFillerHolder
+              .getSize(), f = ap.seqPanelHolder.getSize();
+      int dif = evt.getY() - oldY;
+
+      dif /= ap.av.getCharHeight();
+      dif *= ap.av.getCharHeight();
+
+      if ((d.height - dif) > 20 && (f.height + dif) > 20)
+      {
+        ap.annotationPanel.setSize(d.width, d.height - dif);
+        setSize(new Dimension(e.width, d.height - dif));
+        ap.annotationSpaceFillerHolder.setSize(new Dimension(e.width,
+                d.height - dif));
+        ap.annotationPanelHolder.setSize(new Dimension(d.width, d.height
+                - dif));
+        ap.apvscroll.setValues(ap.apvscroll.getValue(), d.height - dif, 0,
+                av.calcPanelHeight());
+        f.height += dif;
+        ap.seqPanelHolder.setPreferredSize(f);
+        ap.setScrollValues(av.getStartRes(), av.getStartSeq());
+        ap.validate();
+        // ap.paintAlignment(true);
+        ap.addNotify();
+      }
+
+    }
+    else
+    {
+      int diff;
+      if ((diff = 6 - evt.getY()) > 0)
+      {
+        // nudge scroll up
+        ap.apvscroll.setValue(ap.apvscroll.getValue() - diff);
+        ap.adjustmentValueChanged(null);
+
+      }
+      else if ((0 < (diff = 6
+              - ap.annotationSpaceFillerHolder.getSize().height
+              + evt.getY())))
+      {
+        // nudge scroll down
+        ap.apvscroll.setValue(ap.apvscroll.getValue() + diff);
+        ap.adjustmentValueChanged(null);
+      }
+      repaint();
+    }
+  }
+
+  public void mouseClicked(MouseEvent evt)
+  {
+  }
+
+  public void mouseReleased(MouseEvent evt)
+  {
+    if (!resizePanel && !dragCancelled)
+    {
+      int start = selectedRow;
+
+      int end = getSelectedRow(evt.getY() + scrollOffset);
+
+      if (start > -1 && 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;
+    dragCancelled = false;
+    repaint();
+    ap.annotationPanel.repaint();
+  }
+
+  public void mouseEntered(MouseEvent evt)
+  {
+    if (evt.getY() < 10 && evt.getX() < 14)
+    {
+      resizePanel = true;
+      repaint();
+    }
+  }
+
+  public void mouseExited(MouseEvent evt)
+  {
+    dragCancelled = false;
+
+    if (dragEvent == null)
+    {
+      resizePanel = false;
+    }
+    else
+    {
+      if (!resizePanel)
+      {
+        dragEvent = null;
+      }
+    }
+    repaint();
+  }
+
+  public void mousePressed(MouseEvent evt)
+  {
+    oldY = evt.getY();
+    if (resizePanel)
+    {
+      return;
+    }
+    dragCancelled = false;
+    // todo: move below to mouseClicked ?
+    selectedRow = getSelectedRow(evt.getY() + scrollOffset);
+
+    AlignmentAnnotation[] aa = ap.av.getAlignment()
+            .getAlignmentAnnotation();
+
+    // DETECT RIGHT MOUSE BUTTON IN AWT
+    if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
+    {
+
+      PopupMenu popup = new PopupMenu(
+              MessageManager.getString("label.annotations"));
+
+      MenuItem item = new MenuItem(ADDNEW);
+      item.addActionListener(this);
+      popup.add(item);
+      if (selectedRow < 0)
+      {
+        // this never happens at moment: - see comment on JAL-563
+        if (hasHiddenRows)
+        {
+          item = new MenuItem(SHOWALL);
+          item.addActionListener(this);
+          popup.add(item);
+        }
+        this.add(popup);
+        popup.show(this, evt.getX(), evt.getY());
+        return;
+      }
+      // add the rest if there are actually rows to show
+      item = new MenuItem(EDITNAME);
+      item.addActionListener(this);
+      popup.add(item);
+      item = new MenuItem(HIDE);
+      item.addActionListener(this);
+      popup.add(item);
+
+      /*
+       * Hide all <label>:
+       */
+      if (selectedRow < aa.length)
+      {
+        if (aa[selectedRow].sequenceRef != null)
+        {
+          final String label = aa[selectedRow].label;
+          MenuItem hideType = new MenuItem(
+                  MessageManager.getString("label.hide_all") + " " + label);
+          hideType.addActionListener(new ActionListener()
+          {
+            @Override
+            public void actionPerformed(ActionEvent e)
+            {
+              AlignmentUtils.showOrHideSequenceAnnotations(
+                      ap.av.getAlignment(), Collections.singleton(label),
+                      null, false, false);
+              refresh();
+            }
+          });
+          popup.add(hideType);
+        }
+      }
+
+      if (hasHiddenRows)
+      {
+        item = new MenuItem(SHOWALL);
+        item.addActionListener(this);
+        popup.add(item);
+      }
+      this.add(popup);
+      item = new MenuItem(OUTPUT_TEXT);
+      item.addActionListener(this);
+      popup.add(item);
+      if (selectedRow < aa.length)
+      {
+        if (aa[selectedRow].autoCalculated)
+        {
+          if (aa[selectedRow].label.indexOf("Consensus") > -1)
+          {
+            popup.addSeparator();
+            final CheckboxMenuItem cbmi = new CheckboxMenuItem(
+                    MessageManager.getString("label.ignore_gaps_consensus"),
+                    (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef
+                            .getIgnoreGapsConsensus() : ap.av
+                            .isIgnoreGapsConsensus());
+            final AlignmentAnnotation aaa = aa[selectedRow];
+            cbmi.addItemListener(new ItemListener()
+            {
+              public void itemStateChanged(ItemEvent e)
+              {
+                if (aaa.groupRef != null)
+                {
+                  // TODO: pass on reference to ap so the view can be updated.
+                  aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState());
+                }
+                else
+                {
+                  ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
+                }
+                ap.paintAlignment(true);
+              }
+            });
+            popup.add(cbmi);
+            if (aaa.groupRef != null)
+            {
+              final CheckboxMenuItem chist = new CheckboxMenuItem(
+                      MessageManager
+                              .getString("label.show_group_histogram"),
+                      aa[selectedRow].groupRef.isShowConsensusHistogram());
+              chist.addItemListener(new ItemListener()
+              {
+                public void itemStateChanged(ItemEvent e)
+                {
+                  // TODO: pass on reference
+                  // to ap
+                  // so the
+                  // view
+                  // can be
+                  // updated.
+                  aaa.groupRef.setShowConsensusHistogram(chist.getState());
+                  ap.repaint();
+                  // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+                }
+              });
+              popup.add(chist);
+              final CheckboxMenuItem cprofl = new CheckboxMenuItem(
+                      MessageManager.getString("label.show_group_logo"),
+                      aa[selectedRow].groupRef.isShowSequenceLogo());
+              cprofl.addItemListener(new ItemListener()
+              {
+                public void itemStateChanged(ItemEvent e)
+                {
+                  // TODO: pass on reference
+                  // to ap
+                  // so the
+                  // view
+                  // can be
+                  // updated.
+                  aaa.groupRef.setshowSequenceLogo(cprofl.getState());
+                  ap.repaint();
+                  // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+                }
+              });
+
+              popup.add(cprofl);
+              final CheckboxMenuItem cprofn = new CheckboxMenuItem(
+                      MessageManager
+                              .getString("label.normalise_group_logo"),
+                      aa[selectedRow].groupRef.isNormaliseSequenceLogo());
+              cprofn.addItemListener(new ItemListener()
+              {
+                public void itemStateChanged(ItemEvent e)
+                {
+                  // TODO: pass on reference
+                  // to ap
+                  // so the
+                  // view
+                  // can be
+                  // updated.
+                  aaa.groupRef.setshowSequenceLogo(true);
+                  aaa.groupRef.setNormaliseSequenceLogo(cprofn.getState());
+                  ap.repaint();
+                  // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+                }
+              });
+              popup.add(cprofn);
+            }
+            else
+            {
+              final CheckboxMenuItem chist = new CheckboxMenuItem(
+                      MessageManager.getString("label.show_histogram"),
+                      av.isShowConsensusHistogram());
+              chist.addItemListener(new ItemListener()
+              {
+                public void itemStateChanged(ItemEvent e)
+                {
+                  // TODO: pass on reference
+                  // to ap
+                  // so the
+                  // view
+                  // can be
+                  // updated.
+                  av.setShowConsensusHistogram(chist.getState());
+                  ap.alignFrame.showConsensusHistogram.setState(chist
+                          .getState()); // TODO: implement
+                                        // ap.updateGUI()/alignFrame.updateGUI
+                                        // for applet
+                  ap.repaint();
+                  // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+                }
+              });
+              popup.add(chist);
+              final CheckboxMenuItem cprof = new CheckboxMenuItem(
+                      MessageManager.getString("label.show_logo"),
+                      av.isShowSequenceLogo());
+              cprof.addItemListener(new ItemListener()
+              {
+                public void itemStateChanged(ItemEvent e)
+                {
+                  // TODO: pass on reference
+                  // to ap
+                  // so the
+                  // view
+                  // can be
+                  // updated.
+                  av.setShowSequenceLogo(cprof.getState());
+                  ap.alignFrame.showSequenceLogo.setState(cprof.getState()); // TODO:
+                                                                             // implement
+                                                                             // ap.updateGUI()/alignFrame.updateGUI
+                                                                             // for
+                                                                             // applet
+                  ap.repaint();
+                  // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+                }
+              });
+              popup.add(cprof);
+              final CheckboxMenuItem cprofn = new CheckboxMenuItem(
+                      MessageManager.getString("label.normalise_logo"),
+                      av.isNormaliseSequenceLogo());
+              cprofn.addItemListener(new ItemListener()
+              {
+                public void itemStateChanged(ItemEvent e)
+                {
+                  // TODO: pass on reference
+                  // to ap
+                  // so the
+                  // view
+                  // can be
+                  // updated.
+                  av.setShowSequenceLogo(true);
+                  ap.alignFrame.normSequenceLogo.setState(cprofn.getState()); // TODO:
+                                                                              // implement
+                                                                              // ap.updateGUI()/alignFrame.updateGUI
+                                                                              // for
+                                                                              // applet
+                  av.setNormaliseSequenceLogo(cprofn.getState());
+                  ap.repaint();
+                  // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+                }
+              });
+              popup.add(cprofn);
+            }
+
+            item = new MenuItem(COPYCONS_SEQ);
+            item.addActionListener(this);
+            popup.add(item);
+          }
+        }
+      }
+      popup.show(this, evt.getX(), evt.getY());
+    }
+    else
+    {
+      // selection action.
+      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.seqPanel.ap.idPanel.highlightSearchResults(null);
+            ap.av.setSelectionGroup(// new SequenceGroup(
+            aa[selectedRow].groupRef); // );
+            ap.av.sendSelection();
+            ap.paintAlignment(false);
+            PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
+          }
+          else
+          {
+            ap.seqPanel.ap.idPanel
+                    .highlightSearchResults(aa[selectedRow].groupRef
+                            .getSequences(null));
+          }
+          return;
+        }
+        else if (aa[selectedRow].sequenceRef != null)
+        {
+          if (evt.getClickCount() == 1)
+          {
+            ap.seqPanel.ap.idPanel
+                    .highlightSearchResults(Arrays
+                            .asList(new SequenceI[] { aa[selectedRow].sequenceRef }));
+          }
+          else if (evt.getClickCount() >= 2)
+          {
+            ap.seqPanel.ap.idPanel.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.paintAlignment(false);
+            PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
+            ap.av.sendSelection();
+          }
+
+        }
+      }
+
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *          DOCUMENT ME!
+   */
+  protected void copy_annotseqtoclipboard(SequenceI sq)
+  {
+    if (sq == null || sq.getLength() < 1)
+    {
+      return;
+    }
+    jalview.appletgui.AlignFrame.copiedSequences = new StringBuffer();
+    jalview.appletgui.AlignFrame.copiedSequences.append(sq.getName() + "\t"
+            + sq.getStart() + "\t" + sq.getEnd() + "\t"
+            + sq.getSequenceAsString() + "\n");
+    if (av.hasHiddenColumns())
+    {
+      jalview.appletgui.AlignFrame.copiedHiddenColumns = new Vector();
+      for (int[] region : av.getColumnSelection().getHiddenColumns())
+      {
+        jalview.appletgui.AlignFrame.copiedHiddenColumns
+                .addElement(new int[] { region[0], region[1] });
+      }
+    }
+  }
+
+  public void update(Graphics g)
+  {
+    paint(g);
+  }
+
+  public void paint(Graphics g)
+  {
+    int w = getSize().width;
+    int h = getSize().height;
+    if (image == null || w != image.getWidth(this)
+            || h != image.getHeight(this))
+    {
+      image = createImage(w, ap.annotationPanel.getSize().height);
+    }
+
+    drawComponent(image.getGraphics(), w);
+    g.drawImage(image, 0, 0, this);
+  }
+
+  public void drawComponent(Graphics g, int width)
+  {
+    g.setFont(av.getFont());
+    FontMetrics fm = g.getFontMetrics(av.getFont());
+    g.setColor(Color.white);
+    g.fillRect(0, 0, getSize().width, getSize().height);
+
+    g.translate(0, -scrollOffset);
+    g.setColor(Color.black);
+
+    AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
+    int y = 0, fy = g.getFont().getSize();
+    int x = 0, offset;
+
+    if (aa != null)
+    {
+      hasHiddenRows = false;
+      for (int i = 0; i < aa.length; i++)
+      {
+        if (!aa[i].visible)
+        {
+          hasHiddenRows = true;
+          continue;
+        }
+
+        x = width - fm.stringWidth(aa[i].label) - 3;
+
+        y += aa[i].height;
+        offset = -(aa[i].height - fy) / 2;
+
+        g.drawString(aa[i].label, x, y + offset);
+      }
+    }
+    g.translate(0, +scrollOffset);
+    if (resizePanel)
+    {
+      g.setColor(Color.red);
+      g.setPaintMode();
+      g.drawLine(2, 8, 5, 2);
+      g.drawLine(5, 2, 8, 8);
+    }
+    else if (!dragCancelled && dragEvent != null && aa != null)
+    {
+      g.setColor(Color.lightGray);
+      g.drawString(aa[selectedRow].label, dragEvent.getX(),
+              dragEvent.getY());
+    }
+
+    if (!av.getWrapAlignment() && ((aa == null) || (aa.length < 1)))
+    {
+      g.setColor(Color.black);
+      g.drawString(MessageManager.getString("label.right_click"), 2, 8);
+      g.drawString(MessageManager.getString("label.to_add_annotation"), 2,
+              18);
+    }
+  }
+}