X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationPanel.java;h=4b1baffde21b337dd66d8fc1f732a1b510db4723;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=f7ba2fe79beab8c3057252b4d012c5b0e2a260bc;hpb=21930635bd32076820fe0f474bd8f8f89b84dff2;p=jalview.git

diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java
index f7ba2fe..4b1baff 100755
--- a/src/jalview/appletgui/AnnotationPanel.java
+++ b/src/jalview/appletgui/AnnotationPanel.java
@@ -1,504 +1,700 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 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 AnnotationPanel
-    extends Panel implements AdjustmentListener
-{
-  AlignViewport av;
-  AlignmentPanel ap;
-  int activeRow = -1;
-
-  Vector activeRes;
-  static String HELIX = "Helix";
-  static String SHEET = "Sheet";
-  static String LABEL = "Label";
-  static String REMOVE = "Remove Annotation";
-  static String COLOUR = "Colour";
-  static Color HELIX_COLOUR = Color.red.darker();
-  static Color SHEET_COLOUR = Color.green.darker().darker();
-
-  Image image;
-  Graphics gg;
-  FontMetrics fm;
-  int imgWidth = 0;
-
-  boolean fastPaint = false;
-
-  public static int GRAPH_HEIGHT = 40;
-
-  public AnnotationPanel(AlignmentPanel ap)
-  {
-    this.ap = ap;
-    av = ap.av;
-    this.setLayout(null);
-    adjustPanelHeight();
-
-    addMouseMotionListener(new MouseMotionAdapter()
-    {
-      public void mouseMoved(MouseEvent evt)
-      {
-        doMouseMoved(evt);
-      }
-    });
-
-    // ap.annotationScroller.getVAdjustable().addAdjustmentListener( this );
-  }
-
-  public void adjustmentValueChanged(AdjustmentEvent evt)
-  {
-    ap.alabels.setScrollOffset( -evt.getValue());
-  }
-
-  public void adjustPanelHeight()
-  {
-    // setHeight of panels
-    AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
-    int height = 0;
-    if (aa != null)
-    {
-      for (int i = 0; i < aa.length; i++)
-      {
-        if (!aa[i].visible)
-        {
-          continue;
-        }
-
-        aa[i].height = 0;
-
-        if (aa[i].hasText)
-        {
-          aa[i].height += av.charHeight;
-        }
-        if (aa[i].hasIcons)
-        {
-          aa[i].height += 16;
-        }
-
-        if (aa[i].isGraph)
-        {
-          aa[i].height += GRAPH_HEIGHT;
-        }
-
-        if (aa[i].height == 0)
-        {
-          aa[i].height = 20;
-        }
-        height += aa[i].height;
-      }
-    }
-    else
-    {
-      height = 20;
-    }
-
-    this.setSize(getSize().width, height);
-    ap.annotationScroller.setSize(getSize().width, height);
-
-//  ap.annotationSpaceFillerHolder.setSize(d.width,annotationPanel.getSize().height);
-
-    repaint();
-
-  }
-
-  public void addEditableColumn(int i)
-  {
-    if (activeRow == -1)
-    {
-      AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
-      if(aa ==null)
-        return;
-
-      for (int j = 0; j < aa.length; j++)
-      {
-        if (aa[j].editable)
-        {
-          activeRow = j;
-          break;
-        }
-      }
-    }
-
-    if (activeRes == null)
-    {
-      activeRes = new Vector();
-      activeRes.addElement(String.valueOf(i));
-      return;
-    }
-
-    activeRes.addElement(String.valueOf(i));
-  }
-
-  public void doMouseMoved(MouseEvent evt)
-  {
-    AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
-    if (aa == null)
-    {
-      return;
-    }
-
-    int row = -1;
-    int height = 0;
-    for (int i = 0; i < aa.length; i++)
-    {
-
-      if (aa[i].visible)
-      {
-        height += aa[i].height;
-      }
-
-      if (evt.getY() < height)
-      {
-        row = i;
-        break;
-      }
-    }
-
-    int res = evt.getX() / av.getCharWidth() + av.getStartRes();
-    if (row > -1 && res < aa[row].annotations.length && aa[row].annotations[res] != null)
-    {
-      StringBuffer text = new StringBuffer("Sequence position " + (res + 1) +
-                                           "  " +
-                                           aa[row].annotations[res].description);
-      ap.alignFrame.statusBar.setText(text.toString());
-    }
-  }
-
-  public void update(Graphics g)
-  {
-    paint(g);
-  }
-
-  public void paint(Graphics g)
-  {
-    g.setColor(Color.white);
-    g.fillRect(0,0, getSize().width, getSize().height);
-    imgWidth = (av.endRes - av.startRes + 1) * av.charWidth;
-
-    if (image == null || imgWidth != image.getWidth(this))
-    {
-      image = createImage(imgWidth, ap.annotationPanel.getSize().height);
-      gg = image.getGraphics();
-      gg.setFont(av.getFont());
-      fm = gg.getFontMetrics();
-      fastPaint = false;
-    }
-
-    if (fastPaint)
-    {
-      g.drawImage(image, 0, 0, this);
-      fastPaint = false;
-      return;
-    }
-
-    drawComponent(gg, av.startRes, av.endRes + 1);
-    g.drawImage(image, 0, 0, this);
-
-  }
-
-  public void fastPaint(int horizontal)
-  {
-    if (horizontal == 0
-        || av.alignment.getAlignmentAnnotation() == null
-        || av.alignment.getAlignmentAnnotation().length < 1
-        )
-    {
-      repaint();
-      return;
-    }
-
-    gg.copyArea(0, 0, imgWidth, getSize().height, -horizontal * av.charWidth, 0);
-    int sr = av.startRes, er = av.endRes + 1, transX = 0;
-
-    if (horizontal > 0) // scrollbar pulled right, image to the left
-    {
-      transX = (er - sr - horizontal) * av.charWidth;
-      sr = er - horizontal;
-    }
-    else if (horizontal < 0)
-    {
-      er = sr - horizontal;
-    }
-
-    gg.translate(transX, 0);
-
-    drawComponent(gg, sr, er);
-
-    gg.translate( -transX, 0);
-
-    fastPaint = true;
-    repaint();
-  }
-
-  public void drawComponent(Graphics g, int startRes, int endRes)
-  {
-    g.setColor(Color.white);
-    g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getSize().height);
-    if (av.alignment.getAlignmentAnnotation() == null ||
-        av.alignment.getAlignmentAnnotation().length < 1)
-    {
-      g.setColor(Color.white);
-      g.fillRect(0, 0, getSize().width, getSize().height);
-      g.setColor(Color.black);
-      g.drawString("Alignment has no annotations", 20, 15);
-      return;
-    }
-
-    AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
-
-    int j, x = 0, y = 0;
-    char[] lastSS = new char[aa.length];
-    int[] lastSSX = new int[aa.length];
-    int iconOffset = av.charHeight / 2;
-    boolean validRes = false;
-    //\u03B2 \u03B1
-
-    for (int i = 0; i < aa.length; i++)
-    {
-      AlignmentAnnotation row = aa[i];
-      if (!row.visible)
-      {
-        continue;
-      }
-
-      if (row.isGraph)
-      {
-        // this is so that we draw the characters below the graph
-        y += row.height;
-        if (row.hasText)
-        {
-          y -= av.charHeight;
-        }
-      }
-      if (row.hasText)
-      {
-        iconOffset = av.charHeight / 2;
-      }
-      else
-      {
-        iconOffset = 0;
-      }
-
-      for (j = startRes; j < endRes; j++)
-      {
-        if (row.annotations.length <= j || row.annotations[j] == null)
-        {
-          validRes = false;
-        }
-        else
-        {
-          validRes = true;
-        }
-
-        x = (j - startRes) * av.charWidth;
-
-        if (activeRow == i)
-        {
-
-          g.setColor(Color.red);
-
-          if (activeRes != null)
-          {
-            for (int n = 0; n < activeRes.size(); n++)
-            {
-              int v = Integer.parseInt(activeRes.elementAt(n).toString());
-              if (v == j)
-              {
-                g.fillRect( (j - startRes) * av.charWidth, y, av.charWidth,
-                           row.height);
-              }
-            }
-          }
-        }
-
-        if (validRes && row.annotations[j].displayCharacter.length() > 0)
-        {
-          int charOffset = (av.charWidth -
-                            fm.charWidth(row.annotations[j].displayCharacter.
-                                         charAt(0))) / 2;
-          g.setColor(row.annotations[j].colour);
-          if (j == 0 || row.isGraph)
-          {
-            if (row.annotations[0].secondaryStructure == 'H'
-                || row.annotations[0].secondaryStructure == 'E')
-            {
-              g.drawString(row.annotations[j].displayCharacter, x,
-                           y + iconOffset + 3);
-            }
-          }
-          else if ( (row.annotations[j].secondaryStructure == 'H'
-                     || row.annotations[j].secondaryStructure == 'E') &&
-                   (row.annotations[j - 1] == null ||
-                    row.annotations[j].secondaryStructure !=
-                    row.annotations[j - 1].secondaryStructure))
-          {
-
-            g.drawString(row.annotations[j].displayCharacter, x + charOffset,
-                         y + iconOffset + 3);
-          }
-
-          if (!row.hasIcons)
-          {
-            g.drawString(row.annotations[j].displayCharacter, x + charOffset,
-                         y + iconOffset + 3);
-          }
-        }
-
-        if (row.hasIcons)
-        {
-          if (!validRes || row.annotations[j].secondaryStructure != lastSS[i])
-          {
-            switch (lastSS[i])
-            {
-              case 'H':
-                g.setColor(HELIX_COLOUR);
-                g.fillRoundRect(lastSSX[i], y + 4 + iconOffset, x - lastSSX[i],
-                                7, 8, 8);
-                break;
-              case 'E':
-                g.setColor(SHEET_COLOUR);
-                g.fillRect(lastSSX[i], y + 4 + iconOffset, x - lastSSX[i] - 4,
-                           7);
-                g.fillPolygon(new int[]
-                              {x - 4, x - 4, x}
-                              , new int[]
-                              {y + iconOffset, y + 14 + iconOffset,
-                              y + 8 + iconOffset}, 3);
-                break;
-              case 'C':
-                break;
-              default:
-                g.setColor(Color.gray);
-                g.fillRect(lastSSX[i], y + 6 + iconOffset, x - lastSSX[i], 2);
-                break;
-            }
-
-            if (validRes)
-            {
-              lastSS[i] = row.annotations[j].secondaryStructure;
-            }
-            else
-            {
-              lastSS[i] = ' ';
-            }
-            lastSSX[i] = x;
-          }
-        }
-
-        if (validRes && row.isGraph)
-        {
-          g.setColor(new Color(0, 0, 180));
-          int height = (int) ( (row.annotations[j].value / row.graphMax) *
-                              GRAPH_HEIGHT);
-
-          if (row.windowLength > 1)
-          {
-            int total = 0;
-            for (int i2 = j - (row.windowLength / 2);
-                 i2 < j + (row.windowLength / 2); i2++)
-            {
-              if (i2 < 0 || i2 >= av.alignment.getWidth())
-              {
-                continue;
-              }
-
-              total += row.annotations[i2].value;
-            }
-
-            total /= row.windowLength;
-            height = (int) ( (total / row.graphMax) * GRAPH_HEIGHT);
-
-          }
-          g.setColor(row.annotations[j].colour);
-          g.fillRect(x, y - height, av.charWidth, height);
-        }
-
-      }
-
-      x += av.charWidth;
-
-      if (row.hasIcons)
-      {
-        switch (lastSS[i])
-        {
-          case 'H':
-            g.setColor(HELIX_COLOUR);
-            g.fillRoundRect(lastSSX[i], y + 4 + iconOffset, x - lastSSX[i], 7,
-                            8, 8);
-            break;
-          case 'E':
-            g.setColor(SHEET_COLOUR);
-            g.fillRect(lastSSX[i], y + 4 + iconOffset, x - lastSSX[i] - 4, 7);
-            g.fillPolygon(new int[]
-                          {x - 4, x - 4, x}
-                          , new int[]
-                          {y + iconOffset, y + 14 + iconOffset,
-                          y + 7 + iconOffset}
-                          , 3);
-            break;
-          case 'C':
-            break;
-          default:
-            g.setColor(Color.gray);
-            g.fillRect(lastSSX[i], y + 6 + iconOffset, x - lastSSX[i], 2);
-            break;
-
-        }
-      }
-
-      if (row.isGraph && row.hasText)
-      {
-        y += av.charHeight;
-      }
-      if (!row.isGraph)
-      {
-        y += aa[i].height;
-      }
-    }
-  }
-
-  // used by overview window
-  public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, int y, int sRes, int eRes)
-  {
-      g.setColor(Color.white);
-      g.fillRect(0, 0, width, y);
-      g.setColor(new Color(0, 0, 180));
-
-      int x = 0, height;
-
-      for (int j = sRes; j < eRes; j++)
-      {
-          g.setColor(new Color(0, 0, 180));
-
-          height = (int) ((aa.annotations[j].value / aa.graphMax) * GRAPH_HEIGHT);
-          if(height>y)
-              height = y;
-          g.fillRect(x, y - height, av.charWidth, height);
-          x += av.charWidth;
-      }
-    }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * 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.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.renderer.AnnotationRenderer;
+import jalview.renderer.AwtRenderPanelI;
+import jalview.util.MessageManager;
+
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.FontMetrics;
+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.AdjustmentEvent;
+import java.awt.event.AdjustmentListener;
+import java.awt.event.InputEvent;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+
+public class AnnotationPanel extends Panel implements AwtRenderPanelI,
+        AdjustmentListener, ActionListener, MouseListener,
+        MouseMotionListener
+{
+  AlignViewport av;
+
+  AlignmentPanel ap;
+
+  int activeRow = -1;
+
+  final String HELIX = "Helix";
+
+  final String SHEET = "Sheet";
+
+  /**
+   * For RNA secondary structure "stems" aka helices
+   */
+  final String STEM = "RNA Helix";
+
+  final String LABEL = "Label";
+
+  final String REMOVE = "Remove Annotation";
+
+  final String COLOUR = "Colour";
+
+  final Color HELIX_COLOUR = Color.red.darker();
+
+  final Color SHEET_COLOUR = Color.green.darker().darker();
+
+  Image image;
+
+  Graphics gg;
+
+  FontMetrics fm;
+
+  int imgWidth = 0;
+
+  boolean fastPaint = false;
+
+  // Used For mouse Dragging and resizing graphs
+  int graphStretch = -1;
+
+  int graphStretchY = -1;
+
+  boolean mouseDragging = false;
+
+  public static int GRAPH_HEIGHT = 40;
+
+  boolean MAC = false;
+
+  public final AnnotationRenderer renderer;
+
+  public AnnotationPanel(AlignmentPanel ap)
+  {
+    MAC = new jalview.util.Platform().isAMac();
+    this.ap = ap;
+    av = ap.av;
+    setLayout(null);
+    int height = adjustPanelHeight();
+    ap.apvscroll.setValues(0, getSize().height, 0, height);
+
+    addMouseMotionListener(this);
+
+    addMouseListener(this);
+
+    // ap.annotationScroller.getVAdjustable().addAdjustmentListener( this );
+    renderer = new AnnotationRenderer();
+  }
+
+  public AnnotationPanel(AlignViewport av)
+  {
+    this.av = av;
+    renderer = new AnnotationRenderer();
+  }
+
+  @Override
+  public void adjustmentValueChanged(AdjustmentEvent evt)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param evt
+   *          DOCUMENT ME!
+   */
+  @Override
+  public void actionPerformed(ActionEvent evt)
+  {
+    AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
+    if (aa == null)
+    {
+      return;
+    }
+    Annotation[] anot = aa[activeRow].annotations;
+
+    if (anot.length < av.getColumnSelection().getMax())
+    {
+      Annotation[] temp = new Annotation[av.getColumnSelection().getMax() + 2];
+      System.arraycopy(anot, 0, temp, 0, anot.length);
+      anot = temp;
+      aa[activeRow].annotations = anot;
+    }
+
+    String label = "";
+    if (av.getColumnSelection() != null
+            && av.getColumnSelection().size() > 0
+            && anot[av.getColumnSelection().getMin()] != null)
+    {
+      label = anot[av.getColumnSelection().getMin()].displayCharacter;
+    }
+
+    if (evt.getActionCommand().equals(REMOVE))
+    {
+      for (int i = 0; i < av.getColumnSelection().size(); i++)
+      {
+        anot[av.getColumnSelection().columnAt(i)] = null;
+      }
+    }
+    else if (evt.getActionCommand().equals(LABEL))
+    {
+      label = enterLabel(label, "Enter Label");
+
+      if (label == null)
+      {
+        return;
+      }
+
+      if ((label.length() > 0) && !aa[activeRow].hasText)
+      {
+        aa[activeRow].hasText = true;
+      }
+
+      for (int i = 0; i < av.getColumnSelection().size(); i++)
+      {
+        int index = av.getColumnSelection().columnAt(i);
+
+        if (!av.getColumnSelection().isVisible(index))
+        {
+          continue;
+        }
+
+        if (anot[index] == null)
+        {
+          anot[index] = new Annotation(label, "", ' ', 0);
+        }
+
+        anot[index].displayCharacter = label;
+      }
+    }
+    else if (evt.getActionCommand().equals(COLOUR))
+    {
+      UserDefinedColours udc = new UserDefinedColours(this, Color.black,
+              ap.alignFrame);
+
+      Color col = udc.getColor();
+
+      for (int i = 0; i < av.getColumnSelection().size(); i++)
+      {
+        int index = av.getColumnSelection().columnAt(i);
+
+        if (!av.getColumnSelection().isVisible(index))
+        {
+          continue;
+        }
+
+        if (anot[index] == null)
+        {
+          anot[index] = new Annotation("", "", ' ', 0);
+        }
+
+        anot[index].colour = col;
+      }
+    }
+    else
+    // HELIX OR SHEET
+    {
+      char type = 0;
+      String symbol = "\u03B1";
+
+      if (evt.getActionCommand().equals(HELIX))
+      {
+        type = 'H';
+      }
+      else if (evt.getActionCommand().equals(SHEET))
+      {
+        type = 'E';
+        symbol = "\u03B2";
+      }
+
+      // Added by LML to color stems
+      else if (evt.getActionCommand().equals(STEM))
+      {
+        type = 'S';
+        symbol = "\u03C3";
+      }
+
+      if (!aa[activeRow].hasIcons)
+      {
+        aa[activeRow].hasIcons = true;
+      }
+
+      label = enterLabel(symbol, "Enter Label");
+
+      if (label == null)
+      {
+        return;
+      }
+
+      if ((label.length() > 0) && !aa[activeRow].hasText)
+      {
+        aa[activeRow].hasText = true;
+        if (evt.getActionCommand().equals(STEM))
+        {
+          aa[activeRow].showAllColLabels = true;
+        }
+      }
+
+      for (int i = 0; i < av.getColumnSelection().size(); i++)
+      {
+        int index = av.getColumnSelection().columnAt(i);
+
+        if (!av.getColumnSelection().isVisible(index))
+        {
+          continue;
+        }
+
+        if (anot[index] == null)
+        {
+          anot[index] = new Annotation(label, "", type, 0);
+        }
+
+        anot[index].secondaryStructure = type != 'S' ? type : label
+                .length() == 0 ? ' ' : label.charAt(0);
+        anot[index].displayCharacter = label;
+      }
+    }
+
+    av.getAlignment().validateAnnotation(aa[activeRow]);
+
+    ap.alignmentChanged();
+    adjustPanelHeight();
+    repaint();
+
+    return;
+  }
+
+  String enterLabel(String text, String label)
+  {
+    EditNameDialog dialog = new EditNameDialog(text, null, label, null,
+            ap.alignFrame, "Enter Label", 400, 200, true);
+
+    if (dialog.accept)
+    {
+      return dialog.getName();
+    }
+    else
+    {
+      return null;
+    }
+  }
+
+  @Override
+  public void mousePressed(MouseEvent evt)
+  {
+    AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
+    if (aa == null)
+    {
+      return;
+    }
+
+    int height = -scrollOffset;
+    activeRow = -1;
+
+    for (int i = 0; i < aa.length; i++)
+    {
+      if (aa[i].visible)
+      {
+        height += aa[i].height;
+      }
+
+      if (evt.getY() < height)
+      {
+        if (aa[i].editable)
+        {
+          activeRow = i;
+        }
+        else if (aa[i].graph > 0)
+        {
+          // Stretch Graph
+          graphStretch = i;
+          graphStretchY = evt.getY();
+        }
+
+        break;
+      }
+    }
+
+    if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK
+            && activeRow != -1)
+    {
+      if (av.getColumnSelection() == null)
+      {
+        return;
+      }
+
+      PopupMenu pop = new PopupMenu(
+              MessageManager.getString("label.structure_type"));
+      MenuItem item;
+      /*
+       * Just display the needed structure options
+       */
+      if (av.getAlignment().isNucleotide() == true)
+      {
+        item = new MenuItem(STEM);
+        item.addActionListener(this);
+        pop.add(item);
+      }
+      else
+      {
+        item = new MenuItem(HELIX);
+        item.addActionListener(this);
+        pop.add(item);
+        item = new MenuItem(SHEET);
+        item.addActionListener(this);
+        pop.add(item);
+      }
+      item = new MenuItem(LABEL);
+      item.addActionListener(this);
+      pop.add(item);
+      item = new MenuItem(COLOUR);
+      item.addActionListener(this);
+      pop.add(item);
+      item = new MenuItem(REMOVE);
+      item.addActionListener(this);
+      pop.add(item);
+      ap.alignFrame.add(pop);
+      pop.show(this, evt.getX(), evt.getY());
+
+      return;
+    }
+
+    ap.scalePanel.mousePressed(evt);
+  }
+
+  @Override
+  public void mouseReleased(MouseEvent evt)
+  {
+    graphStretch = -1;
+    graphStretchY = -1;
+    mouseDragging = false;
+    if (needValidating)
+    {
+      ap.validate();
+      needValidating = false;
+    }
+    ap.scalePanel.mouseReleased(evt);
+  }
+
+  @Override
+  public void mouseClicked(MouseEvent evt)
+  {
+  }
+
+  boolean needValidating = false;
+
+  @Override
+  public void mouseDragged(MouseEvent evt)
+  {
+    if (graphStretch > -1)
+    {
+      av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY
+              - evt.getY();
+      if (av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight < 0)
+      {
+        av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight = 0;
+      }
+      graphStretchY = evt.getY();
+      av.calcPanelHeight();
+      needValidating = true;
+      ap.paintAlignment(true);
+    }
+    else
+    {
+      ap.scalePanel.mouseDragged(evt);
+    }
+  }
+
+  @Override
+  public void mouseMoved(MouseEvent evt)
+  {
+    AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
+    if (aa == null)
+    {
+      return;
+    }
+
+    int row = -1;
+    int height = -scrollOffset;
+    for (int i = 0; i < aa.length; i++)
+    {
+
+      if (aa[i].visible)
+      {
+        height += aa[i].height;
+      }
+
+      if (evt.getY() < height)
+      {
+        row = i;
+        break;
+      }
+    }
+
+    int res = evt.getX() / av.getCharWidth() + av.getStartRes();
+
+    if (av.hasHiddenColumns())
+    {
+      res = av.getColumnSelection().adjustForHiddenColumns(res);
+    }
+
+    if (row > -1 && res < aa[row].annotations.length
+            && aa[row].annotations[res] != null)
+    {
+      StringBuffer text = new StringBuffer("Sequence position " + (res + 1));
+      if (aa[row].annotations[res].description != null)
+      {
+        text.append("  " + aa[row].annotations[res].description);
+      }
+      ap.alignFrame.statusBar.setText(text.toString());
+    }
+  }
+
+  @Override
+  public void mouseEntered(MouseEvent evt)
+  {
+    ap.scalePanel.mouseEntered(evt);
+  }
+
+  @Override
+  public void mouseExited(MouseEvent evt)
+  {
+    ap.scalePanel.mouseExited(evt);
+  }
+
+  public int adjustPanelHeight()
+  {
+    return adjustPanelHeight(true);
+  }
+
+  public int adjustPanelHeight(boolean repaint)
+  {
+    int height = av.calcPanelHeight();
+    this.setSize(new Dimension(getSize().width, height));
+    if (repaint)
+    {
+      repaint();
+    }
+    return height;
+  }
+
+  /**
+   * calculate the height for visible annotation, revalidating bounds where
+   * necessary ABSTRACT GUI METHOD
+   * 
+   * @return total height of annotation
+   */
+
+  public void addEditableColumn(int i)
+  {
+    if (activeRow == -1)
+    {
+      AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
+      if (aa == null)
+      {
+        return;
+      }
+
+      for (int j = 0; j < aa.length; j++)
+      {
+        if (aa[j].editable)
+        {
+          activeRow = j;
+          break;
+        }
+      }
+    }
+  }
+
+  @Override
+  public void update(Graphics g)
+  {
+    paint(g);
+  }
+
+  @Override
+  public void paint(Graphics g)
+  {
+    Dimension d = getSize();
+    imgWidth = d.width;
+    // (av.endRes - av.startRes + 1) * av.charWidth;
+    if (imgWidth < 1 || d.height < 1)
+    {
+      return;
+    }
+    if (image == null || imgWidth != image.getWidth(this)
+            || d.height != image.getHeight(this))
+    {
+      image = createImage(imgWidth, d.height);
+      gg = image.getGraphics();
+      gg.setFont(av.getFont());
+      fm = gg.getFontMetrics();
+      fastPaint = false;
+    }
+
+    if (fastPaint)
+    {
+      g.drawImage(image, 0, 0, this);
+      fastPaint = false;
+      return;
+    }
+
+    gg.setColor(Color.white);
+    gg.fillRect(0, 0, getSize().width, getSize().height);
+    drawComponent(gg, av.startRes, av.endRes + 1);
+
+    g.drawImage(image, 0, 0, this);
+  }
+
+  public void fastPaint(int horizontal)
+  {
+    if (horizontal == 0
+            || av.getAlignment().getAlignmentAnnotation() == null
+            || av.getAlignment().getAlignmentAnnotation().length < 1)
+    {
+      repaint();
+      return;
+    }
+
+    gg.copyArea(0, 0, imgWidth, getSize().height,
+            -horizontal * av.getCharWidth(), 0);
+    int sr = av.startRes, er = av.endRes + 1, transX = 0;
+
+    if (horizontal > 0) // scrollbar pulled right, image to the left
+    {
+      transX = (er - sr - horizontal) * av.getCharWidth();
+      sr = er - horizontal;
+    }
+    else if (horizontal < 0)
+    {
+      er = sr - horizontal;
+    }
+
+    gg.translate(transX, 0);
+
+    drawComponent(gg, sr, er);
+
+    gg.translate(-transX, 0);
+
+    fastPaint = true;
+    repaint();
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param g
+   *          DOCUMENT ME!
+   * @param startRes
+   *          DOCUMENT ME!
+   * @param endRes
+   *          DOCUMENT ME!
+   */
+  public void drawComponent(Graphics g, int startRes, int endRes)
+  {
+    Font ofont = av.getFont();
+    g.setFont(ofont);
+
+    g.setColor(Color.white);
+    g.fillRect(0, 0, (endRes - startRes) * av.getCharWidth(),
+            getSize().height);
+
+    if (fm == null)
+    {
+      fm = g.getFontMetrics();
+    }
+
+    if ((av.getAlignment().getAlignmentAnnotation() == null)
+            || (av.getAlignment().getAlignmentAnnotation().length < 1))
+    {
+      g.setColor(Color.white);
+      g.fillRect(0, 0, getSize().width, getSize().height);
+      g.setColor(Color.black);
+      if (av.validCharWidth)
+      {
+        g.drawString(MessageManager
+                .getString("label.alignment_has_no_annotations"), 20, 15);
+      }
+
+      return;
+    }
+    g.translate(0, -scrollOffset);
+    renderer.drawComponent(this, av, g, activeRow, startRes, endRes);
+    g.translate(0, +scrollOffset);
+  }
+
+  int scrollOffset = 0;
+
+  public void setScrollOffset(int value, boolean repaint)
+  {
+    scrollOffset = value;
+    if (repaint)
+    {
+      repaint();
+    }
+  }
+
+  @Override
+  public FontMetrics getFontMetrics()
+  {
+    return fm;
+  }
+
+  @Override
+  public Image getFadedImage()
+  {
+    return image;
+  }
+
+  @Override
+  public int getFadedImageWidth()
+  {
+    return imgWidth;
+  }
+
+  private int[] bounds = new int[2];
+
+  @Override
+  public int[] getVisibleVRange()
+  {
+    if (ap != null && ap.alabels != null)
+    {
+      int sOffset = -ap.alabels.scrollOffset;
+      int visHeight = sOffset + ap.annotationPanelHolder.getHeight();
+      bounds[0] = sOffset;
+      bounds[1] = visHeight;
+      return bounds;
+    }
+    else
+    {
+      return null;
+    }
+  }
+}