X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=1f437dde913c162bdcc66755f938da6f0b1b8a7c;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=0ea79981081d9f939e35ad4e799ce88ec579f297;hpb=d2642610b86e983bfdde65f7c19c9153206da263;p=jalview.git

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 0ea7998..1f437dd 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -1,604 +1,1017 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 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.gui;
 
-import jalview.datamodel.*;
-import jalview.io.FormatAdapter;
+import java.util.*;
+import java.util.regex.Pattern;
 
 import java.awt.*;
-import java.awt.datatransfer.StringSelection;
+import java.awt.datatransfer.*;
 import java.awt.event.*;
+import java.awt.geom.AffineTransform;
 import java.awt.image.*;
-import java.util.Vector;
-
 import javax.swing.*;
 
+import jalview.datamodel.*;
+import jalview.io.*;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
 public class AnnotationLabels extends JPanel implements MouseListener,
-    MouseMotionListener, ActionListener
+        MouseMotionListener, ActionListener
 {
-    static String ADDNEW = "Add New Row";
-    static String HIDE = "Hide This Row";
-    static String DELETE = "Delete This Row";
-    static String SHOWALL = "Show All Hidden Rows";
-    static String OUTPUT_TEXT = "Export Annotation";
-    static String COPYCONS_SEQ = "Copy Consensus Sequence";
-    boolean resizePanel = false;
-    Image image;
-    AlignmentPanel ap;
-    AlignViewport av;
-    boolean resizing = false;
-    MouseEvent dragEvent;
-    int oldY;
-    int selectedRow;
-    int scrollOffset = 0;
-    Font font = new Font("Arial", Font.PLAIN, 11);
-
-
-    /**
-     * Creates a new AnnotationLabels object.
-     *
-     * @param ap DOCUMENT ME!
-     */
-    public AnnotationLabels(AlignmentPanel ap)
-    {
-        this.ap = ap;
-        av = ap.av;
-        ToolTipManager.sharedInstance().registerComponent(this);
-
-        java.net.URL url = getClass().getResource("/images/idwidth.gif");
-        Image temp = null;
-
-        if (url != null)
-        {
-            temp = java.awt.Toolkit.getDefaultToolkit().createImage(url);
-        }
+  static String TOGGLE_LABELSCALE = "Scale Label to Column";
 
-        try
-        {
-            MediaTracker mt = new MediaTracker(this);
-            mt.addImage(temp, 0);
-            mt.waitForID(0);
-        }
-        catch (Exception ex)
-        {
-        }
+  static String ADDNEW = "Add New Row";
 
-        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;
+  static String EDITNAME = "Edit Label/Description";
 
-        addMouseListener(this);
-        addMouseMotionListener(this);
-    }
+  static String HIDE = "Hide This Row";
 
-    public AnnotationLabels(AlignViewport av)
-    {
-      this.av = av;
-    }
+  static String DELETE = "Delete This Row";
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param y DOCUMENT ME!
-     */
-    public void setScrollOffset(int y)
-    {
-        scrollOffset = y;
-        repaint();
-    }
+  static String SHOWALL = "Show All Hidden Rows";
 
-    void getSelectedRow(int y)
-    {
-      int height = 0;
-      AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+  static String OUTPUT_TEXT = "Export Annotation";
 
-      if(aa!=null)
-      {
-        for (int i = 0; i < aa.length; i++)
-        {
-          if (!aa[i].visible)
-          {
-            continue;
-          }
+  static String COPYCONS_SEQ = "Copy Consensus Sequence";
 
-          height += aa[i].height;
+  boolean resizePanel = false;
 
-          if (y < height)
-          {
-            selectedRow = i;
+  Image image;
 
-            break;
-          }
-        }
-      }
-    }
+  AlignmentPanel ap;
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void actionPerformed(ActionEvent evt)
-    {
-        int dif = 0;
-        AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+  AlignViewport av;
 
-        if (evt.getActionCommand().equals(ADDNEW))
-        {
-            String label = JOptionPane.showInputDialog(this,
-                    "Label for annotation");
+  boolean resizing = false;
 
-            if (label == null)
-            {
-                label = "";
-            }
+  MouseEvent dragEvent;
 
-            AlignmentAnnotation newAnnotation = new AlignmentAnnotation(label,
-                    "New description",
-                    new Annotation[ap.av.alignment.getWidth()]);
+  int oldY;
 
-            ap.av.alignment.addAnnotation(newAnnotation);
-            ap.av.alignment.setAnnotationIndex(newAnnotation, 0);
-            if (aa != null)
-              dif = aa[aa.length - 1].height;
-        }
-        else if (evt.getActionCommand().equals(HIDE))
-        {
-            aa[selectedRow].visible = false;
+  int selectedRow;
 
-            if (aa[selectedRow].label.equals("Quality"))
-            {
-                ap.av.quality = null;
-            }
+  int scrollOffset = 0;
 
-            dif = aa[selectedRow].height * -1;
-        }
-        else if (evt.getActionCommand().equals(DELETE))
-        {
-            ap.av.alignment.deleteAnnotation(aa[selectedRow]);
-            dif = aa[selectedRow].height * -1;
-        }
-        else if (evt.getActionCommand().equals(SHOWALL))
-        {
-            for (int i = 0; i < aa.length; i++)
-            {
-                if (!aa[i].visible)
-                {
-                    dif += aa[i].height;
-                    aa[i].visible = true;
-                }
-            }
-        }
-        else if (evt.getActionCommand().equals(OUTPUT_TEXT))
-        {
-          new AnnotationExporter().exportAnnotations(
-              ap,
-              new AlignmentAnnotation[]
-              {aa[selectedRow]}
-              );
-        }
-        else if (evt.getActionCommand().equals(COPYCONS_SEQ))
-        {
-          SequenceI cons=av.getConsensusSeq();
-          if (cons!=null)
-            copy_annotseqtoclipboard(cons);
+  Font font = new Font("Arial", Font.PLAIN, 11);
 
-        }
+  private boolean hasHiddenRows;
 
-        ap.annotationPanel.adjustPanelHeight();
-        ap.annotationScroller.validate();
-        ap.repaint();
-    }
+  /**
+   * Creates a new AnnotationLabels object.
+   * 
+   * @param ap
+   *          DOCUMENT ME!
+   */
+  public AnnotationLabels(AlignmentPanel ap)
+  {
+    this.ap = ap;
+    av = ap.av;
+    ToolTipManager.sharedInstance().registerComponent(this);
+
+    java.net.URL url = getClass().getResource("/images/idwidth.gif");
+    Image temp = null;
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void mousePressed(MouseEvent evt)
+    if (url != null)
     {
-        getSelectedRow(evt.getY() - scrollOffset);
-        oldY = evt.getY();
+      temp = java.awt.Toolkit.getDefaultToolkit().createImage(url);
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void mouseReleased(MouseEvent evt)
+    try
     {
-        int start = selectedRow;
-        getSelectedRow(evt.getY() - scrollOffset);
-        int end = selectedRow;
+      MediaTracker mt = new MediaTracker(this);
+      mt.addImage(temp, 0);
+      mt.waitForID(0);
+    } catch (Exception ex)
+    {
+    }
 
-        if(start!=end)
+    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);
+    addMouseWheelListener(ap.annotationPanel);
+  }
+
+  public AnnotationLabels(AlignViewport av)
+  {
+    this.av = av;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param y
+   *          DOCUMENT ME!
+   */
+  public void setScrollOffset(int y)
+  {
+    scrollOffset = y;
+    repaint();
+  }
+
+  /**
+   * sets selectedRow to -2 if no annotation preset, -1 if no visible row is at
+   * y
+   * 
+   * @param y
+   *          coordinate position to search for a row
+   */
+  void getSelectedRow(int y)
+  {
+    int height = 0;
+    AlignmentAnnotation[] aa = ap.av.getAlignment()
+            .getAlignmentAnnotation();
+    selectedRow = -2;
+    if (aa != null)
+    {
+      for (int i = 0; i < aa.length; i++)
+      {
+        selectedRow = -1;
+        if (!aa[i].visible)
         {
-          //Swap these annotations
-          AlignmentAnnotation startAA = ap.av.alignment.getAlignmentAnnotation()[start];
-          AlignmentAnnotation endAA = ap.av.alignment.getAlignmentAnnotation()[end];
+          continue;
+        }
 
+        height += aa[i].height;
 
-          ap.av.alignment.getAlignmentAnnotation()[end] = startAA;
-          ap.av.alignment.getAlignmentAnnotation()[start] = endAA;
-        }
+        if (y < height)
+        {
+          selectedRow = i;
 
-        resizePanel = false;
-        dragEvent = null;
-        repaint();
-        ap.annotationPanel.repaint();
+          break;
+        }
+      }
     }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param evt
+   *          DOCUMENT ME!
+   */
+  public void actionPerformed(ActionEvent evt)
+  {
+    AlignmentAnnotation[] aa = ap.av.getAlignment()
+            .getAlignmentAnnotation();
+
+    if (evt.getActionCommand().equals(ADDNEW))
+    {
+      AlignmentAnnotation newAnnotation = new AlignmentAnnotation(null,
+              null, new Annotation[ap.av.getAlignment().getWidth()]);
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void mouseEntered(MouseEvent evt)
+      if (!editLabelDescription(newAnnotation))
+      {
+        return;
+      }
+
+      ap.av.getAlignment().addAnnotation(newAnnotation);
+      ap.av.getAlignment().setAnnotationIndex(newAnnotation, 0);
+    }
+    else if (evt.getActionCommand().equals(EDITNAME))
+    {
+      editLabelDescription(aa[selectedRow]);
+      repaint();
+    }
+    else if (evt.getActionCommand().equals(HIDE))
+    {
+      aa[selectedRow].visible = false;
+    }
+    else if (evt.getActionCommand().equals(DELETE))
+    {
+      ap.av.getAlignment().deleteAnnotation(aa[selectedRow]);
+    }
+    else if (evt.getActionCommand().equals(SHOWALL))
     {
-      if(evt.getY()<10)
+      for (int i = 0; i < aa.length; i++)
       {
-        resizePanel = true;
-        repaint();
+        if (!aa[i].visible && aa[i].annotations != null)
+        {
+          aa[i].visible = true;
+        }
       }
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void mouseExited(MouseEvent evt)
+    else if (evt.getActionCommand().equals(OUTPUT_TEXT))
+    {
+      new AnnotationExporter().exportAnnotations(ap,
+              new AlignmentAnnotation[]
+              { aa[selectedRow] }, null, null);
+    }
+    else if (evt.getActionCommand().equals(COPYCONS_SEQ))
     {
-      if(dragEvent == null)
+      SequenceI cons = null;
+      if (aa[selectedRow].groupRef != null)
       {
-        resizePanel = false;
-        repaint();
+        cons = aa[selectedRow].groupRef.getConsensusSeq();
       }
+      else
+      {
+        cons = av.getConsensusSeq();
+      }
+      if (cons != null)
+      {
+        copy_annotseqtoclipboard(cons);
+      }
+
+    }
+    else if (evt.getActionCommand().equals(TOGGLE_LABELSCALE))
+    {
+      aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void mouseDragged(MouseEvent evt)
+    ap.validateAnnotationDimensions(false);
+    ap.addNotify();
+    ap.repaint();
+    // validate();
+    // ap.paintAlignment(true);
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *          DOCUMENT ME!
+   */
+  boolean editLabelDescription(AlignmentAnnotation annotation)
+  {
+    EditNameDialog dialog = new EditNameDialog(annotation.label,
+            annotation.description, "       Annotation Name ",
+            "Annotation Description ", "Edit Annotation Name/Description",
+            ap.alignFrame);
+
+    if (!dialog.accept)
     {
-      dragEvent = evt;
+      return false;
+    }
+
+    annotation.label = dialog.getName();
 
-      if (resizePanel)
+    String text = dialog.getDescription();
+    if (text != null && text.length() == 0)
+    {
+      text = null;
+    }
+    annotation.description = text;
+
+    return true;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param evt
+   *          DOCUMENT ME!
+   */
+  public void mousePressed(MouseEvent evt)
+  {
+    getSelectedRow(evt.getY() - scrollOffset);
+    oldY = evt.getY();
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param evt
+   *          DOCUMENT ME!
+   */
+  public void mouseReleased(MouseEvent evt)
+  {
+    int start = selectedRow;
+    getSelectedRow(evt.getY() - scrollOffset);
+    int end = selectedRow;
+
+    if (start != end)
+    {
+      // Swap these annotations
+      AlignmentAnnotation startAA = ap.av.getAlignment()
+              .getAlignmentAnnotation()[start];
+      if (end == -1)
       {
-        Dimension d = ap.annotationScroller.getPreferredSize();
-        int dif = evt.getY() - oldY;
+        end = ap.av.getAlignment().getAlignmentAnnotation().length - 1;
+      }
+      AlignmentAnnotation endAA = ap.av.getAlignment()
+              .getAlignmentAnnotation()[end];
 
-        dif /= ap.av.charHeight;
-        dif *= ap.av.charHeight;
+      ap.av.getAlignment().getAlignmentAnnotation()[end] = startAA;
+      ap.av.getAlignment().getAlignmentAnnotation()[start] = endAA;
+    }
 
-        if ( (d.height - dif) > 20)
-        {
-          ap.annotationScroller.setPreferredSize(new Dimension(d.width,
-              d.height - dif));
-          d = ap.annotationSpaceFillerHolder.getPreferredSize();
-          ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension(
-              d.width, d.height - dif));
-          ap.repaint();
-        }
+    resizePanel = false;
+    dragEvent = null;
+    repaint();
+    ap.annotationPanel.repaint();
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param evt
+   *          DOCUMENT ME!
+   */
+  public void mouseEntered(MouseEvent evt)
+  {
+    if (evt.getY() < 10)
+    {
+      resizePanel = true;
+      repaint();
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param evt
+   *          DOCUMENT ME!
+   */
+  public void mouseExited(MouseEvent evt)
+  {
+    if (dragEvent == null)
+    {
+      resizePanel = false;
+      repaint();
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param evt
+   *          DOCUMENT ME!
+   */
+  public void mouseDragged(MouseEvent evt)
+  {
+    dragEvent = evt;
+
+    if (resizePanel)
+    {
+      Dimension d = ap.annotationScroller.getPreferredSize();
+      int dif = evt.getY() - oldY;
 
-        ap.addNotify();
+      dif /= ap.av.charHeight;
+      dif *= ap.av.charHeight;
+
+      if ((d.height - dif) > 20)
+      {
+        ap.annotationScroller.setPreferredSize(new Dimension(d.width,
+                d.height - dif));
+        d = ap.annotationSpaceFillerHolder.getPreferredSize();
+        ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension(
+                d.width, d.height - dif));
+        ap.paintAlignment(true);
       }
-      else
-        repaint();
-    }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void mouseMoved(MouseEvent evt)
+      ap.addNotify();
+    }
+    else
     {
-      resizePanel = evt.getY()<10;
+      repaint();
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param evt
+   *          DOCUMENT ME!
+   */
+  public void mouseMoved(MouseEvent evt)
+  {
+    resizePanel = evt.getY() < 10;
+
+    getSelectedRow(evt.getY() - scrollOffset);
+
+    if (selectedRow > -1
+            && ap.av.getAlignment().getAlignmentAnnotation().length > selectedRow)
+    {
+      AlignmentAnnotation aa = ap.av.getAlignment()
+              .getAlignmentAnnotation()[selectedRow];
 
-      getSelectedRow(evt.getY() - scrollOffset);
+      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(Pattern.compile("<").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(selectedRow>-1)
+      }
+      else
+      {
+        // begin the tooltip's html fragment
+        desc.append("<html>");
+      }
+      if (aa.hasScore())
       {
-        setToolTipText(ap.av.alignment.
-            getAlignmentAnnotation()[selectedRow].description);
+        // 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());
       }
-      repaint();
+      else
+        this.setToolTipText(null);
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void mouseClicked(MouseEvent evt)
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param evt
+   *          DOCUMENT ME!
+   */
+  public void mouseClicked(MouseEvent evt)
+  {
+    AlignmentAnnotation[] aa = ap.av.getAlignment()
+            .getAlignmentAnnotation();
+    if (SwingUtilities.isLeftMouseButton(evt))
     {
-       if(!SwingUtilities.isRightMouseButton(evt))
-         return;
-
-        AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
-
-        if ((aa == null) || (aa.length == 0))
+      if (selectedRow > -1 && selectedRow < aa.length)
+      {
+        if (aa[selectedRow].groupRef != null)
         {
-            JPopupMenu pop = new JPopupMenu("Annotations");
-            JMenuItem item = new JMenuItem(ADDNEW);
-            item.addActionListener(this);
-            pop.add(item);
-            pop.show(this, evt.getX(), evt.getY());
-
-            return;
+          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.paintAlignment(false);
+            PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
+            ap.av.sendSelection();
+          }
+          else
+          {
+            ap.seqPanel.ap.idPanel
+                    .highlightSearchResults(aa[selectedRow].groupRef
+                            .getSequences(null));
+          }
+          return;
         }
+        else if (aa[selectedRow].sequenceRef != null)
+        {
+          Vector sr = new Vector();
+          sr.addElement(aa[selectedRow].sequenceRef);
+          if (evt.getClickCount() == 1)
+          {
+            ap.seqPanel.ap.idPanel.highlightSearchResults(sr);
+          }
+          else if (evt.getClickCount() >= 2)
+          {
+            ap.seqPanel.ap.idPanel.highlightSearchResults(null);
+            SequenceGroup sg = new SequenceGroup();
+            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("Annotations");
-        JMenuItem item = new JMenuItem(ADDNEW);
-        item.addActionListener(this);
-        pop.add(item);
-        item = new JMenuItem(HIDE);
-        item.addActionListener(this);
-        pop.add(item);
-        item = new JMenuItem(DELETE);
-        item.addActionListener(this);
-        pop.add(item);
+    JPopupMenu pop = new JPopupMenu("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);
-        item = new JMenuItem(OUTPUT_TEXT);
-        item.addActionListener(this);
-        pop.add(item);
-        // annotation object should be typed
-        if (aa[selectedRow].label.equals("Consensus"))
+      }
+      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);
+    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)
+    {
+      if (!aa[selectedRow].autoCalculated)
+      {
+        if (aa[selectedRow].graph == AlignmentAnnotation.NO_GRAPH)
         {
+          // display formatting settings for this row.
           pop.addSeparator();
-          final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
-              "Ignore Gaps In Consensus",
-              ap.av.getIgnoreGapsConsensus());
-          cbmi.addActionListener(new ActionListener()
-              {public void actionPerformed(ActionEvent e)
-               {
-                 ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
-               }
-              });
-          pop.add(cbmi);
-          final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ);
-          consclipbrd.addActionListener(this);
-          pop.add(consclipbrd);
+          // av and sequencegroup need to implement same interface for
+          item = new JCheckBoxMenuItem(TOGGLE_LABELSCALE,
+                  aa[selectedRow].scaleColLabel);
+          item.addActionListener(this);
+          pop.add(item);
         }
-
-        pop.show(this, evt.getX(), evt.getY());
-    }
-    /**
-     * do a single sequence copy to jalview and the system clipboard
-     *
-     * @param sq sequence to be copied to clipboard
-     */
-    protected void copy_annotseqtoclipboard(SequenceI sq)
-    {
-      SequenceI [] seqs = new SequenceI[] { sq };
-      String[] omitHidden = null;
-      SequenceI [] dseqs=new SequenceI[] { sq.getDatasetSequence()};
-      if (dseqs[0]==null) {
-        dseqs[0] = new Sequence(sq);
-        dseqs[0].setSequence(
-            jalview.analysis.AlignSeq.extractGaps(
-                jalview.util.Comparison.GapChars,
-                sq.getSequenceAsString()));
-
-        sq.setDatasetSequence(dseqs[0]);
-      }
-      Alignment ds=new Alignment(dseqs);
-      if (av.hasHiddenColumns)
-      {
-        omitHidden = av.getColumnSelection().getVisibleSequenceStrings(0, sq.getLength(), seqs);
       }
-
-      String output = new FormatAdapter().formatSequences(
-          "Fasta",
-          seqs,
-          omitHidden);
-
-
-      Toolkit.getDefaultToolkit().getSystemClipboard()
-          .setContents(new StringSelection(output), Desktop.instance);
-
-      Vector hiddenColumns = null;
-      if(av.hasHiddenColumns)
+      else if (aa[selectedRow].label.indexOf("Consensus") > -1)
       {
-        hiddenColumns =new Vector();
-        for(int i=0; i<av.getColumnSelection().getHiddenColumns().size(); i++)
+        pop.addSeparator();
+        // av and sequencegroup need to implement same interface for
+        final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
+                "Ignore Gaps In Consensus",
+                (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef
+                        .getIgnoreGapsConsensus() : ap.av
+                        .getIgnoreGapsConsensus());
+        final AlignmentAnnotation aaa = aa[selectedRow];
+        cbmi.addActionListener(new ActionListener()
         {
-          int[] region = (int[])
-              av.getColumnSelection().getHiddenColumns().elementAt(i);
+          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.annotationPanel.paint(ap.annotationPanel.getGraphics());
+            }
+            else
+            {
+              ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
+            }
+          }
+        });
+        pop.add(cbmi);
+        // av and sequencegroup need to implement same interface for
+        if (aaa.groupRef != null)
+        {
+          final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
+                  "Show Group Histogram",
+                  aa[selectedRow].groupRef.isShowConsensusHistogram());
+          chist.addActionListener(new ActionListener()
+          {
+            public void actionPerformed(ActionEvent 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());
+            }
+          });
+          pop.add(chist);
+          final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem(
+                  "Show Group Logo",
+                  aa[selectedRow].groupRef.isShowSequenceLogo());
+          cprofl.addActionListener(new ActionListener()
+          {
+            public void actionPerformed(ActionEvent 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());
+            }
+          });
+          pop.add(cprofl);
+          final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem(
+                  "Normalise Group Logo",
+                  aa[selectedRow].groupRef.isNormaliseSequenceLogo());
+          cproflnorm.addActionListener(new ActionListener()
+          {
+            public void actionPerformed(ActionEvent e)
+            {
 
-          hiddenColumns.addElement(new int[]{region[0],
-                            region[1]});
+              // TODO: pass on reference
+              // to ap
+              // so the
+              // view
+              // can be
+              // updated.
+              aaa.groupRef.setNormaliseSequenceLogo(cproflnorm.getState());
+              // automatically enable logo display if we're clicked
+              aaa.groupRef.setshowSequenceLogo(true);
+              ap.repaint();
+              // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+            }
+          });
+          pop.add(cproflnorm);
         }
+        else
+        {
+          final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
+                  "Show Histogram", av.isShowConsensusHistogram());
+          chist.addActionListener(new ActionListener()
+          {
+            public void actionPerformed(ActionEvent e)
+            {
+              // TODO: pass on reference
+              // to ap
+              // so the
+              // view
+              // can be
+              // updated.
+              av.setShowConsensusHistogram(chist.getState());
+              ap.alignFrame.setMenusForViewport();
+              ap.repaint();
+              // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+            }
+          });
+          pop.add(chist);
+          final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
+                  "Show Logo", av.isShowSequenceLogo());
+          cprof.addActionListener(new ActionListener()
+          {
+            public void actionPerformed(ActionEvent e)
+            {
+              // TODO: pass on reference
+              // to ap
+              // so the
+              // view
+              // can be
+              // updated.
+              av.setShowSequenceLogo(cprof.getState());
+              ap.alignFrame.setMenusForViewport();
+              ap.repaint();
+              // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+            }
+          });
+          pop.add(cprof);
+          final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem(
+                  "Normalise Logo", av.isNormaliseSequenceLogo());
+          cprofnorm.addActionListener(new ActionListener()
+          {
+            public void actionPerformed(ActionEvent e)
+            {
+              // TODO: pass on reference
+              // to ap
+              // so the
+              // view
+              // can be
+              // updated.
+              av.setShowSequenceLogo(true);
+              av.setNormaliseSequenceLogo(cprofnorm.getState());
+              ap.alignFrame.setMenusForViewport();
+              ap.repaint();
+              // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+            }
+          });
+          pop.add(cprofnorm);
+        }
+        final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ);
+        consclipbrd.addActionListener(this);
+        pop.add(consclipbrd);
       }
+    }
+    pop.show(this, evt.getX(), evt.getY());
+  }
+
+  /**
+   * do a single sequence copy to jalview and the system clipboard
+   * 
+   * @param sq
+   *          sequence to be copied to clipboard
+   */
+  protected void copy_annotseqtoclipboard(SequenceI sq)
+  {
+    SequenceI[] seqs = new SequenceI[]
+    { sq };
+    String[] omitHidden = null;
+    SequenceI[] dseqs = new SequenceI[]
+    { sq.getDatasetSequence() };
+    if (dseqs[0] == null)
+    {
+      dseqs[0] = new Sequence(sq);
+      dseqs[0].setSequence(jalview.analysis.AlignSeq.extractGaps(
+              jalview.util.Comparison.GapChars, sq.getSequenceAsString()));
 
-      Desktop.jalviewClipboard = new Object[]{ seqs,
-          ds, // what is the dataset of a consensus sequence ? need to flag sequence as special.
-          hiddenColumns};
+      sq.setDatasetSequence(dseqs[0]);
     }
-    /**
-     * DOCUMENT ME!
-     *
-     * @param g1 DOCUMENT ME!
-     */
-    public void paintComponent(Graphics g)
+    Alignment ds = new Alignment(dseqs);
+    if (av.hasHiddenColumns())
     {
+      omitHidden = av.getColumnSelection().getVisibleSequenceStrings(0,
+              sq.getLength(), seqs);
+    }
+
+    String output = new FormatAdapter().formatSequences("Fasta", seqs,
+            omitHidden);
+
+    Toolkit.getDefaultToolkit().getSystemClipboard()
+            .setContents(new StringSelection(output), Desktop.instance);
 
-        int width = getWidth();
-        if(width==0)
-         width = ap.calculateIdWidth().width + 4;
+    Vector hiddenColumns = null;
+    if (av.hasHiddenColumns())
+    {
+      hiddenColumns = new Vector();
+      for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++)
+      {
+        int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
+                .elementAt(i);
 
-       Graphics2D g2 = (Graphics2D) g;
-       if(av.antiAlias)
-        g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
-            RenderingHints.VALUE_ANTIALIAS_ON);
+        hiddenColumns.addElement(new int[]
+        { region[0], region[1] });
+      }
+    }
 
-       drawComponent(g2, width);
+    Desktop.jalviewClipboard = new Object[]
+    { seqs, ds, // what is the dataset of a consensus sequence ? need to flag
+        // sequence as special.
+        hiddenColumns };
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param g1
+   *          DOCUMENT ME!
+   */
+  public void paintComponent(Graphics g)
+  {
+
+    int width = getWidth();
+    if (width == 0)
+    {
+      width = ap.calculateIdWidth().width + 4;
+    }
 
+    Graphics2D g2 = (Graphics2D) g;
+    if (av.antiAlias)
+    {
+      g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+              RenderingHints.VALUE_ANTIALIAS_ON);
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param g DOCUMENT ME!
-     */
-    public void drawComponent(Graphics g, int width)
+    drawComponent(g2, true, width);
+
+  }
+
+  /**
+   * Draw the full set of annotation Labels for the alignment at the given cursor
+   * 
+   * @param g Graphics2D instance (needed for font scaling)
+   * @param width Width for scaling labels
+   *          
+   */
+  public void drawComponent(Graphics g, int width)
+  {
+    drawComponent(g, false, width);
+  }
+
+  private final boolean debugRedraw = false;
+  /**
+   * Draw the full set of annotation Labels for the alignment at the given cursor
+   * 
+   * @param g Graphics2D instance (needed for font scaling)
+   * @param clip - true indicates that only current visible area needs to be rendered
+   * @param width Width for scaling labels         
+   */
+  public void drawComponent(Graphics g, boolean clip, int width)
+  {
+    if (av.getFont().getSize() < 10)
     {
-        if(av.getFont().getSize()<10)
-          g.setFont(font);
-        else
-          g.setFont(av.getFont());
+      g.setFont(font);
+    }
+    else
+    {
+      g.setFont(av.getFont());
+    }
 
-        FontMetrics fm = g.getFontMetrics(g.getFont());
-        g.setColor(Color.white);
-        g.fillRect(0, 0, getWidth(), getHeight());
+    FontMetrics fm = g.getFontMetrics(g.getFont());
+    g.setColor(Color.white);
+    g.fillRect(0, 0, getWidth(), getHeight());
+
+    g.translate(0, scrollOffset);
+    g.setColor(Color.black);
+    
+    AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
+    int fontHeight = g.getFont().getSize();
+    int y = 0;
+    int x = 0;
+    int graphExtras = 0;
+    int offset = 0;
+    Font baseFont = g.getFont();
+    FontMetrics baseMetrics = fm;
+    int ofontH = fontHeight;
+    int sOffset=0;
+    int visHeight = 0;
+    int[] visr = (ap!=null && ap.annotationPanel!=null) ? ap.annotationPanel.getVisibleVRange() : null;
+    if (clip && visr!=null){ 
+      sOffset = visr[0]; 
+      visHeight = visr[1];
+    }
+    boolean visible = true,before=false,after=false;
+    if (aa != null)
+    {
+      hasHiddenRows = false;
+      int olY=0;
+      for (int i = 0; i < aa.length; i++)
+      {
+        visible = true;
+        if (!aa[i].visible)
+        {
+          hasHiddenRows = true;
+          continue;
+        }
+        olY=y;
+        y += aa[i].height;
+        if (clip) {if (y<sOffset)
+        {
+          if (!before)
+          {
+            if (debugRedraw) {
+              System.out.println("before vis: "+i);
+            }
+          before=true;
+          }
+          // don't draw what isn't visible
+          continue;
+        }
+        if (olY>visHeight)
+        {
 
-        g.translate(0, scrollOffset);
+          if (!after)
+          {
+            if (debugRedraw) {
+              System.out.println("Scroll offset: "+sOffset+" after vis: "+i);
+            }
+          after=true;
+          }
+          // don't draw what isn't visible
+          continue;
+        }}
         g.setColor(Color.black);
 
-        AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
-        int fontHeight = g.getFont().getSize();
-        int y = fontHeight;
-        int x = 0;
-        int graphExtras = 0;
+        offset = -aa[i].height / 2;
 
+        if (aa[i].hasText)
+        {
+          offset += fm.getHeight() / 2;
+          offset -= fm.getDescent();
+        }
+        else
+          offset += fm.getDescent();
 
+        x = width - fm.stringWidth(aa[i].label) - 3;
 
-        if (aa != null)
+        if (aa[i].graphGroup > -1)
         {
-            for (int i = 0; i < aa.length; i++)
+          int groupSize = 0;
+          // TODO: JAL-1291 revise rendering model so the graphGroup map is computed efficiently for all visible labels
+          for (int gg = 0; gg < aa.length; gg++)
+          {
+            if (aa[gg].graphGroup == aa[i].graphGroup)
             {
-                if (!aa[i].visible)
-                {
-                    continue;
-                }
-
-                x = width - fm.stringWidth(aa[i].label) - 3;
+              groupSize++;
+            }
+          }
+          if (groupSize * (fontHeight + 8) < aa[i].height)
+          {
+            graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) / 2;
+          }
+          else
+          {
+            // scale font to fit
+            float h = aa[i].height / (float) groupSize, s;
+            if (h < 9)
+            {
+              visible = false;
+            }
+            else
+            {
+              fontHeight = -8 + (int) h;
+              s = ((float) fontHeight) / (float) ofontH;
+              Font f = baseFont.deriveFont(AffineTransform
+                      .getScaleInstance(s, s));
+              g.setFont(f);
+              fm = g.getFontMetrics();
+              graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) / 2;
+            }
+          }
+          if (visible)
+          {
+            for (int gg = 0; gg < aa.length; gg++)
+            {
+              if (aa[gg].graphGroup == aa[i].graphGroup)
+              {
+                x = width - fm.stringWidth(aa[gg].label) - 3;
+                g.drawString(aa[gg].label, x, y - graphExtras);
 
-                if (aa[i].graph>0 && aa[i].graphHeight>0)
+                if (aa[gg]._linecolour != null)
                 {
-                    graphExtras = y;
-
-                    y += (aa[i].height / 3);
-
-                    if(aa[i].graphGroup<0)
-                        graphExtras = y + fontHeight;
-                }
 
-                if(aa[i].graphGroup>-1)
-                {
-                  int groupSize = 0;
-                  for (int gg = 0; gg < aa.length; gg++)
-                  {
-                    if (aa[gg].graphGroup == aa[i].graphGroup)
-                      groupSize++;
-                  }
-
-                  if(groupSize * (fontHeight+8) < aa[i].height)
-                    graphExtras += (aa[i].height -( groupSize * (fontHeight+8)) )/2;
-
-                 for(int gg=0; gg<aa.length; gg++)
-                 {
-                   if(aa[gg].graphGroup==aa[i].graphGroup)
-                   {
-                     x = width - fm.stringWidth(aa[gg].label) - 3;
-                     g.drawString(aa[gg].label, x, graphExtras );
-                     if(aa[gg].annotations[0]!=null)
-                       g.setColor(aa[gg].annotations[0].colour);
-
-                     g.drawLine( x, graphExtras+3,
-                                 x+fm.stringWidth(aa[gg].label),
-                                 graphExtras+3);
-
-                     g.setColor(Color.black);
-                     graphExtras += fontHeight+8;
-                   }
-                 }
+                  g.setColor(aa[gg]._linecolour);
+                  g.drawLine(x, y - graphExtras + 3,
+                          x + fm.stringWidth(aa[gg].label), y - graphExtras
+                                  + 3);
                 }
-                else
-                  g.drawString(aa[i].label, x, y);
 
-                if (aa[i].graph>0)
-                {
-                /*  if (aa[i].graphLines != null)
-                  {
-                    for (int gl = 0; gl < aa[i].graphLines.size(); gl++)
-                    {
-                       x = width - fm.stringWidth(aa[i].getGraphLine(gl).label) - 3;
-                      g.drawString(aa[i].getGraphLine(gl).label, x, graphExtras);
-                      g.setColor(aa[i].getGraphLine(gl).colour);
-                      Graphics2D g2 = (Graphics2D) g;
-                      g2.setStroke(new BasicStroke(1,
-                          BasicStroke.CAP_SQUARE,
-                          BasicStroke.JOIN_ROUND, 3f,
-                          new float[]
-                          {5f, 3f}, 0f));
-
-                      graphExtras += 3;
-
-                      g.drawLine(x, graphExtras,
-                                 x+fm.stringWidth(aa[i].label),
-                                 graphExtras);
-                      g2.setStroke(new BasicStroke());
-                    }
-                  }*/
-                    y += ((2 * aa[i].height) / 3);
-                }
-                else
-                {
-                    y += aa[i].height;
-                }
+                g.setColor(Color.black);
+                graphExtras += fontHeight + 8;
+              }
             }
+          }
+          g.setFont(baseFont);
+          fm = baseMetrics;
+          fontHeight = ofontH;
         }
-
-        if (resizePanel)
-        {
-          g.drawImage(image, 2, 0 - scrollOffset, this);
-        }
-        else if (dragEvent != null && aa!=null)
+        else
         {
-          g.setColor(Color.lightGray);
-          g.drawString(aa[selectedRow].label, dragEvent.getX(), dragEvent.getY() - scrollOffset);
+          g.drawString(aa[i].label, x, y + offset);
         }
+      }
+    }
 
+    if (resizePanel)
+    {
+      g.drawImage(image, 2, 0 - scrollOffset, this);
+    }
+    else if (dragEvent != null && aa != null)
+    {
+      g.setColor(Color.lightGray);
+      g.drawString(aa[selectedRow].label, dragEvent.getX(),
+              dragEvent.getY() - scrollOffset);
+    }
 
-        if ((aa == null) || (aa.length < 1))
-        {
-            g.drawString("Right click", 2, 8);
-            g.drawString("to add annotation", 2, 18);
-        }
+    if (!av.wrapAlignment && ((aa == null) || (aa.length < 1)))
+    {
+      g.drawString("Right click", 2, 8);
+      g.drawString("to add annotation", 2, 18);
     }
+  }
 }