X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationPanel.java;h=e17ce2088f415d45d0c09758cbe0a0061db3238b;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=38e033185f04ce180ded9682b20ac1bfefc751d7;hpb=77ee0174127cb2fd3d817b010b5a36278dd37c45;p=jalview.git

diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java
index 38e0331..e17ce20 100755
--- a/src/jalview/appletgui/AnnotationPanel.java
+++ b/src/jalview/appletgui/AnnotationPanel.java
@@ -1,20 +1,22 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
- * 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 file is part of Jalview.
  * 
- * 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.
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.appletgui;
 
@@ -24,9 +26,13 @@ import java.awt.*;
 import java.awt.event.*;
 
 import jalview.datamodel.*;
+import jalview.renderer.AnnotationRenderer;
+import jalview.renderer.AwtRenderPanelI;
+import jalview.util.MessageManager;
 
-public class AnnotationPanel extends Panel implements AdjustmentListener,
-        ActionListener, MouseListener, MouseMotionListener
+public class AnnotationPanel extends Panel implements AwtRenderPanelI,
+        AdjustmentListener, ActionListener, MouseListener,
+        MouseMotionListener
 {
   AlignViewport av;
 
@@ -36,19 +42,24 @@ public class AnnotationPanel extends Panel implements AdjustmentListener,
 
   Vector activeRes;
 
-  static String HELIX = "Helix";
+  final String HELIX = "Helix";
 
-  static String SHEET = "Sheet";
+  final String SHEET = "Sheet";
+
+  /**
+   * For RNA secondary structure "stems" aka helices
+   */
+  final String STEM = "RNA Helix";
 
-  static String LABEL = "Label";
+  final String LABEL = "Label";
 
-  static String REMOVE = "Remove Annotation";
+  final String REMOVE = "Remove Annotation";
 
-  static String COLOUR = "Colour";
+  final String COLOUR = "Colour";
 
-  static Color HELIX_COLOUR = Color.red.darker();
+  final Color HELIX_COLOUR = Color.red.darker();
 
-  static Color SHEET_COLOUR = Color.green.darker().darker();
+  final Color SHEET_COLOUR = Color.green.darker().darker();
 
   Image image;
 
@@ -59,51 +70,62 @@ public class AnnotationPanel extends Panel implements AdjustmentListener,
   int imgWidth = 0;
 
   boolean fastPaint = false;
-  //Used For mouse Dragging and resizing graphs
+
+  // Used For mouse Dragging and resizing graphs
   int graphStretch = -1;
 
   int graphStretchY = -1;
-  
-  boolean mouseDragging=false;
-  
+
+  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);
-    adjustPanelHeight();
+    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)
   {
-    ap.alabels.setScrollOffset(-evt.getValue());
   }
 
   /**
    * DOCUMENT ME!
    * 
    * @param evt
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
+  @Override
   public void actionPerformed(ActionEvent evt)
   {
-    AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+    AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
+    if (aa == null)
+    {
+      return;
+    }
     Annotation[] anot = aa[activeRow].annotations;
 
     if (anot.length < av.getColumnSelection().getMax())
@@ -115,8 +137,9 @@ public class AnnotationPanel extends Panel implements AdjustmentListener,
     }
 
     String label = "";
-    if (av.colSel != null && av.colSel.size() > 0
-            && anot[av.colSel.getMin()] != null)
+    if (av.getColumnSelection() != null
+            && av.getColumnSelection().size() > 0
+            && anot[av.getColumnSelection().getMin()] != null)
       label = anot[av.getColumnSelection().getMin()].displayCharacter;
 
     if (evt.getActionCommand().equals(REMOVE))
@@ -144,7 +167,7 @@ public class AnnotationPanel extends Panel implements AdjustmentListener,
       {
         int index = av.getColumnSelection().columnAt(i);
 
-        if (!av.colSel.isVisible(index))
+        if (!av.getColumnSelection().isVisible(index))
           continue;
 
         if (anot[index] == null)
@@ -166,7 +189,7 @@ public class AnnotationPanel extends Panel implements AdjustmentListener,
       {
         int index = av.getColumnSelection().columnAt(i);
 
-        if (!av.colSel.isVisible(index))
+        if (!av.getColumnSelection().isVisible(index))
           continue;
 
         if (anot[index] == null)
@@ -193,6 +216,13 @@ public class AnnotationPanel extends Panel implements AdjustmentListener,
         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;
@@ -208,13 +238,17 @@ public class AnnotationPanel extends Panel implements AdjustmentListener,
       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.colSel.isVisible(index))
+        if (!av.getColumnSelection().isVisible(index))
           continue;
 
         if (anot[index] == null)
@@ -222,11 +256,16 @@ public class AnnotationPanel extends Panel implements AdjustmentListener,
           anot[index] = new Annotation(label, "", type, 0);
         }
 
-        anot[index].secondaryStructure = type;
+        
+        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();
 
@@ -244,15 +283,16 @@ public class AnnotationPanel extends Panel implements AdjustmentListener,
       return null;
   }
 
+  @Override
   public void mousePressed(MouseEvent evt)
   {
-    AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+    AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
     if (aa == null)
     {
       return;
     }
 
-    int height = 0;
+    int height = -scrollOffset;
     activeRow = -1;
 
     for (int i = 0; i < aa.length; i++)
@@ -268,13 +308,12 @@ public class AnnotationPanel extends Panel implements AdjustmentListener,
         {
           activeRow = i;
         }
-                else if (aa[i].graph > 0)
+        else if (aa[i].graph > 0)
         {
           // Stretch Graph
           graphStretch = i;
           graphStretchY = evt.getY();
         }
-        
 
         break;
       }
@@ -288,13 +327,27 @@ public class AnnotationPanel extends Panel implements AdjustmentListener,
         return;
       }
 
-      PopupMenu pop = new PopupMenu("Structure type");
-      MenuItem item = new MenuItem(HELIX);
-      item.addActionListener(this);
-      pop.add(item);
-      item = new MenuItem(SHEET);
-      item.addActionListener(this);
-      pop.add(item);
+      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);
@@ -318,30 +371,41 @@ public class AnnotationPanel extends Panel implements AdjustmentListener,
     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.alignment.getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY
+      av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY
               - evt.getY();
-      if (av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight < 0)
+      if (av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight < 0)
       {
-        av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight = 0;
+        av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight = 0;
       }
       graphStretchY = evt.getY();
-      adjustPanelHeight();
+      av.calcPanelHeight();
+      needValidating = true;
       ap.paintAlignment(true);
     }
     else
@@ -350,16 +414,17 @@ public class AnnotationPanel extends Panel implements AdjustmentListener,
     }
   }
 
+  @Override
   public void mouseMoved(MouseEvent evt)
   {
-    AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+    AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
     if (aa == null)
     {
       return;
     }
 
     int row = -1;
-    int height = 0;
+    int height = -scrollOffset;
     for (int i = 0; i < aa.length; i++)
     {
 
@@ -377,7 +442,7 @@ public class AnnotationPanel extends Panel implements AdjustmentListener,
 
     int res = evt.getX() / av.getCharWidth() + av.getStartRes();
 
-    if (av.hasHiddenColumns)
+    if (av.hasHiddenColumns())
     {
       res = av.getColumnSelection().adjustForHiddenColumns(res);
     }
@@ -394,11 +459,13 @@ public class AnnotationPanel extends Panel implements AdjustmentListener,
     }
   }
 
+  @Override
   public void mouseEntered(MouseEvent evt)
   {
     ap.scalePanel.mouseEntered(evt);
   }
 
+  @Override
   public void mouseExited(MouseEvent evt)
   {
     ap.scalePanel.mouseExited(evt);
@@ -406,62 +473,32 @@ public class AnnotationPanel extends Panel implements AdjustmentListener,
 
   public int 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].graph > 0)
-        {
-          aa[i].height += aa[i].graphHeight;
-        }
-
-        if (aa[i].height == 0)
-        {
-          aa[i].height = 20;
-        }
+    return adjustPanelHeight(true);
+  }
 
-        height += aa[i].height;
-      }
-    }
-    else
+  public int adjustPanelHeight(boolean repaint)
+  {
+    int height = av.calcPanelHeight();
+    this.setSize(new Dimension(getSize().width, height));
+    if (repaint)
     {
-      height = 20;
+      repaint();
     }
-
-    this.setSize(getSize().width, height);
-
-    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.alignment.getAlignmentAnnotation();
+      AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
       if (aa == null)
       {
         return;
@@ -487,20 +524,26 @@ public class AnnotationPanel extends Panel implements AdjustmentListener,
     activeRes.addElement(String.valueOf(i));
   }
 
+  @Override
   public void update(Graphics g)
   {
     paint(g);
   }
 
+  @Override
   public void paint(Graphics g)
   {
-
-    imgWidth = getSize().width;
+    Dimension d = getSize();
+    imgWidth = d.width;
     // (av.endRes - av.startRes + 1) * av.charWidth;
-
-    if (image == null || imgWidth != image.getWidth(this))
+    if (imgWidth < 1 || d.height < 1)
     {
-      image = createImage(imgWidth, ap.annotationPanel.getSize().height);
+      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();
@@ -523,8 +566,9 @@ public class AnnotationPanel extends Panel implements AdjustmentListener,
 
   public void fastPaint(int horizontal)
   {
-    if (horizontal == 0 || av.alignment.getAlignmentAnnotation() == null
-            || av.alignment.getAlignmentAnnotation().length < 1)
+    if (horizontal == 0
+            || av.getAlignment().getAlignmentAnnotation() == null
+            || av.getAlignment().getAlignmentAnnotation().length < 1)
     {
       repaint();
       return;
@@ -558,15 +602,16 @@ public class AnnotationPanel extends Panel implements AdjustmentListener,
    * DOCUMENT ME!
    * 
    * @param g
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param startRes
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param endRes
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void drawComponent(Graphics g, int startRes, int endRes)
   {
-    g.setFont(av.getFont());
+    Font ofont = av.getFont();
+    g.setFont(ofont);
 
     g.setColor(Color.white);
     g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getSize().height);
@@ -576,562 +621,68 @@ public class AnnotationPanel extends Panel implements AdjustmentListener,
       fm = g.getFontMetrics();
     }
 
-    if ((av.alignment.getAlignmentAnnotation() == null)
-            || (av.alignment.getAlignmentAnnotation().length < 1))
+    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("Alignment has no annotations", 20, 15);
+        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);
+  }
 
-    AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
-
-    int x = 0;
-    int y = 0;
-    int column = 0;
-    char lastSS;
-    int lastSSX;
-    int iconOffset = av.charHeight / 2;
-    boolean validRes = false;
-    boolean validEnd = false;
-    boolean[] graphGroupDrawn = new boolean[aa.length];
+  int scrollOffset = 0;
 
-    // \u03B2 \u03B1
-    for (int i = 0; i < aa.length; i++)
+  public void setScrollOffset(int value, boolean repaint)
+  {
+    scrollOffset = value;
+    if (repaint)
     {
-      AlignmentAnnotation row = aa[i];
-
-      if (!row.visible)
-      {
-        continue;
-      }
-
-      lastSS = ' ';
-      lastSSX = 0;
-
-      if (row.graph > 0)
-      {
-        if (row.graphGroup > -1 && graphGroupDrawn[row.graphGroup])
-        {
-          continue;
-        }
-
-        // 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;
-      }
-
-      x = 0;
-      while (x < endRes - startRes)
-      {
-        if (av.hasHiddenColumns)
-        {
-          column = av.getColumnSelection().adjustForHiddenColumns(
-                  startRes + x);
-          if (column > row.annotations.length - 1)
-          {
-            break;
-          }
-        }
-        else
-        {
-          column = startRes + x;
-        }
-
-        if ((row.annotations.length <= column)
-                || (row.annotations[column] == null))
-        {
-          validRes = false;
-        }
-        else
-        {
-          validRes = true;
-        }
-
-        if (activeRow == i)
-        {
-          g.setColor(Color.red);
-
-          if (av.getColumnSelection() != null)
-          {
-            for (int n = 0; n < av.getColumnSelection().size(); n++)
-            {
-              int v = av.getColumnSelection().columnAt(n);
-
-              if (v == column)
-              {
-                g
-                        .fillRect(x * av.charWidth, y, av.charWidth,
-                                av.charHeight);
-              }
-            }
-          }
-        }
-
-        if (av.validCharWidth
-                && validRes
-                && (row.annotations[column].displayCharacter != null && row.annotations[column].displayCharacter
-                        .length() > 0))
-        {
-          int charOffset = (av.getCentreColumnLabels()) ? ((av.charWidth - fm
-                  .charsWidth(row.annotations[column].displayCharacter
-                          .toCharArray(), 0,
-                          row.annotations[column].displayCharacter.length())) / 2)
-                  : (av.charWidth - fm
-                          .charWidth(row.annotations[column].displayCharacter
-                                  .charAt(0))) / 2;
-
-          if (row.annotations[column].colour == null)
-            g.setColor(Color.black);
-          else
-            g.setColor(row.annotations[column].colour);
-
-          if (column == 0 || row.graph > 0)
-          {
-            g.drawString(row.annotations[column].displayCharacter,
-                    (x * av.charWidth) + charOffset, y + iconOffset + 3);
-          }
-          else if (row.annotations[column - 1] == null
-                  || (!row.annotations[column].displayCharacter
-                          .equals(row.annotations[column - 1].displayCharacter) || (row.annotations[column].displayCharacter
-                          .length() < 2 && row.annotations[column].secondaryStructure == ' ')))
-          {
-            g.drawString(row.annotations[column].displayCharacter,
-                    (x * av.charWidth) + charOffset, y + iconOffset + 3);
-          }
-        }
-
-        if (row.hasIcons)
-        {
-          if (!validRes
-                  || (row.annotations[column].secondaryStructure != lastSS))
-          {
-            switch (lastSS)
-            {
-            case 'H':
-              g.setColor(HELIX_COLOUR);
-              if (MAC)
-              {
-                // Off by 1 offset when drawing rects and ovals
-                // to offscreen image on the MAC
-                g.fillRoundRect(lastSSX, y + 4 + iconOffset,
-                        (x * av.charWidth) - lastSSX, 7, 8, 8);
-                break;
-              }
-
-              int sCol = (lastSSX / av.charWidth) + startRes;
-              int x1 = lastSSX;
-              int x2 = (x * av.charWidth);
-
-              if (sCol == 0
-                      || row.annotations[sCol - 1] == null
-                      || row.annotations[sCol - 1].secondaryStructure != 'H')
-              {
-                g.fillArc(lastSSX, y + 4 + iconOffset, av.charWidth, 8, 90,
-                        180);
-                x1 += av.charWidth / 2;
-              }
-
-              if (!validRes || row.annotations[column] == null
-                      || row.annotations[column].secondaryStructure != 'H')
-              {
-                g.fillArc((x * av.charWidth) - av.charWidth, y + 4
-                        + iconOffset, av.charWidth, 8, 270, 180);
-                x2 -= av.charWidth / 2;
-              }
-
-              g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
-              break;
-
-            case 'E':
-              g.setColor(SHEET_COLOUR);
-              g.fillRect(lastSSX, y + 4 + iconOffset, (x * av.charWidth)
-                      - lastSSX - 4, 7);
-              g.fillPolygon(new int[]
-              { (x * av.charWidth) - 4, (x * av.charWidth) - 4,
-                  (x * av.charWidth) }, new int[]
-              { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset },
-                      3);
-
-              break;
-
-            default:
-              g.setColor(Color.gray);
-              g.fillRect(lastSSX, y + 6 + iconOffset, (x * av.charWidth)
-                      - lastSSX, 2);
-
-              break;
-            }
-
-            if (validRes)
-            {
-              lastSS = row.annotations[column].secondaryStructure;
-            }
-            else
-            {
-              lastSS = ' ';
-            }
-
-            lastSSX = (x * av.charWidth);
-          }
-        }
-
-        column++;
-        x++;
-      }
-
-      if (column >= row.annotations.length)
-      {
-        column = row.annotations.length - 1;
-        validEnd = false;
-      }
-      else
-      {
-        validEnd = true;
-      }
-
-      // x ++;
-
-      if (row.hasIcons)
-      {
-        switch (lastSS)
-        {
-        case 'H':
-          g.setColor(HELIX_COLOUR);
-          if (MAC)
-          {
-            // Off by 1 offset when drawing rects and ovals
-            // to offscreen image on the MAC
-            g.fillRoundRect(lastSSX, y + 4 + iconOffset, (x * av.charWidth)
-                    - lastSSX, 7, 8, 8);
-            break;
-          }
-
-          int sCol = (lastSSX / av.charWidth) + startRes;
-          int x1 = lastSSX;
-          int x2 = (x * av.charWidth);
-
-          if (sCol == 0 || row.annotations[sCol - 1] == null
-                  || row.annotations[sCol - 1].secondaryStructure != 'H')
-          {
-            g
-                    .fillArc(lastSSX, y + 4 + iconOffset, av.charWidth, 8,
-                            90, 180);
-            x1 += av.charWidth / 2;
-          }
-
-          if (row.annotations[column] == null
-                  || row.annotations[column].secondaryStructure != 'H')
-          {
-            g.fillArc((x * av.charWidth) - av.charWidth,
-                    y + 4 + iconOffset, av.charWidth, 8, 270, 180);
-            x2 -= av.charWidth / 2;
-          }
-
-          g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
-
-          break;
-
-        case 'E':
-          g.setColor(SHEET_COLOUR);
-
-          if (!validEnd || row.annotations[endRes] == null
-                  || row.annotations[endRes].secondaryStructure != 'E')
-          {
-            g.fillRect(lastSSX, y + 4 + iconOffset, (x * av.charWidth)
-                    - lastSSX - 4, 7);
-            g.fillPolygon(new int[]
-            { (x * av.charWidth) - 4, (x * av.charWidth) - 4,
-                (x * av.charWidth) }, new int[]
-            { y + iconOffset, y + 14 + iconOffset, y + 7 + iconOffset }, 3);
-          }
-          else
-          {
-            g.fillRect(lastSSX, y + 4 + iconOffset, x * av.charWidth
-                    - lastSSX, 7);
-          }
-          break;
-
-        default:
-          g.setColor(Color.gray);
-          if (!av.wrapAlignment || endRes == av.endRes)
-          {
-            g.fillRect(lastSSX, y + 6 + iconOffset, (x * av.charWidth)
-                    - lastSSX, 2);
-          }
-
-          break;
-        }
-      }
-
-      if (row.graph > 0 && row.graphHeight> 0)
-      {
-        if (row.graph == AlignmentAnnotation.LINE_GRAPH)
-        {
-          if (row.graphGroup > -1 && !graphGroupDrawn[row.graphGroup])
-          {
-            float groupmax = -999999, groupmin = 9999999;
-            for (int gg = 0; gg < aa.length; gg++)
-            {
-              if (aa[gg].graphGroup != row.graphGroup)
-              {
-                continue;
-              }
-
-              if (aa[gg] != row)
-              {
-                aa[gg].visible = false;
-              }
-
-              if (aa[gg].graphMax > groupmax)
-              {
-                groupmax = aa[gg].graphMax;
-              }
-              if (aa[gg].graphMin < groupmin)
-              {
-                groupmin = aa[gg].graphMin;
-              }
-            }
-
-            for (int gg = 0; gg < aa.length; gg++)
-            {
-              if (aa[gg].graphGroup == row.graphGroup)
-              {
-                drawLineGraph(g, aa[gg], startRes, endRes, y, groupmin,
-                        groupmax, row.graphHeight);
-              }
-            }
-
-            graphGroupDrawn[row.graphGroup] = true;
-          }
-          else
-          {
-            drawLineGraph(g, row, startRes, endRes, y, row.graphMin,
-                    row.graphMax, row.graphHeight);
-          }
-        }
-        else if (row.graph == AlignmentAnnotation.BAR_GRAPH)
-        {
-          drawBarGraph(g, row, startRes, endRes, row.graphMin,
-                  row.graphMax, y);
-        }
-      }
-
-      if (row.graph > 0 && row.hasText)
-      {
-        y += av.charHeight;
-      }
-
-      if (row.graph == 0)
-      {
-        y += aa[i].height;
-      }
+      repaint();
     }
   }
 
-  public void drawLineGraph(Graphics g, AlignmentAnnotation aa, int sRes,
-          int eRes, int y, float min, float max, int graphHeight)
+  @Override
+  public FontMetrics getFontMetrics()
   {
-    if (sRes > aa.annotations.length)
-    {
-      return;
-    }
-
-    int x = 0;
-
-    // Adjustment for fastpaint to left
-    if (eRes < av.endRes)
-    {
-      eRes++;
-    }
-
-    eRes = Math.min(eRes, aa.annotations.length);
-
-    int y1 = y, y2 = y;
-    float range = max - min;
-
-    // //Draw origin
-    if (min < 0)
-    {
-      y2 = y - (int) ((0 - min / range) * graphHeight);
-    }
-
-    g.setColor(Color.gray);
-    g.drawLine(x - av.charWidth, y2, (eRes - sRes) * av.charWidth, y2);
-
-    eRes = Math.min(eRes, aa.annotations.length);
-
-    int column;
-    int aaMax = aa.annotations.length - 1;
-
-    while (x < eRes - sRes)
-    {
-      column = sRes + x;
-      if (av.hasHiddenColumns)
-      {
-        column = av.getColumnSelection().adjustForHiddenColumns(column);
-      }
-
-      if (column > aaMax)
-      {
-        break;
-      }
-
-      if (aa.annotations[column] == null) // || coaa.annotations[column - 1] ==
-                                          // null)
-      {
-        x++;
-        continue;
-      }
-
-      if (aa.annotations[column].colour == null)
-        g.setColor(Color.black);
-      else
-        g.setColor(aa.annotations[column].colour);
-      if (column == 0 || aa.annotations[column - 1] == null)
-      {
-        y1 = y
-                - (int) (((aa.annotations[column].value - min) / range) * graphHeight);
-      }
-      else
-      {
-        y1 = y
-                - (int) (((aa.annotations[column - 1].value - min) / range) * graphHeight);
-      }
-      y2 = y
-              - (int) (((aa.annotations[column].value - min) / range) * graphHeight);
-
-      g.drawLine(x * av.charWidth - av.charWidth / 2, y1, x * av.charWidth
-              + av.charWidth / 2, y2);
-      x++;
-    }
-
-    if (aa.threshold != null)
-    {
-      g.setColor(aa.threshold.colour);
-
-      y2 = (int) (y - ((aa.threshold.value - min) / range) * graphHeight);
-      g.drawLine(0, y2, (eRes - sRes) * av.charWidth, y2);
-    }
+    return fm;
   }
 
-  public void drawBarGraph(Graphics g, AlignmentAnnotation aa, int sRes,
-          int eRes, float min, float max, int y)
+  @Override
+  public Image getFadedImage()
   {
-    if (sRes > aa.annotations.length)
-    {
-      return;
-    }
-
-    eRes = Math.min(eRes, aa.annotations.length);
-
-    int x = 0, y1 = y, y2 = y;
-
-    float range = max - min;
-
-    if (min < 0)
-    {
-      y2 = y - (int) ((0 - min / (range)) * aa.graphHeight);
-    }
-
-    g.setColor(Color.gray);
-
-    g.drawLine(x, y2, (eRes - sRes) * av.charWidth, y2);
-
-    int column;
-    int aaMax = aa.annotations.length - 1;
-
-    while (x < eRes - sRes)
-    {
-      column = sRes + x;
-      if (av.hasHiddenColumns)
-      {
-        column = av.getColumnSelection().adjustForHiddenColumns(column);
-      }
-
-      if (column > aaMax)
-      {
-        break;
-      }
-
-      if (aa.annotations[column] == null)
-      {
-        x++;
-        continue;
-      }
-
-      if (aa.annotations[column].colour == null)
-        g.setColor(Color.black);
-      else
-        g.setColor(aa.annotations[column].colour);
-
-      y1 = y
-              - (int) (((aa.annotations[column].value - min) / (range)) * aa.graphHeight);
-
-      if (y1 - y2 > 0)
-      {
-        g.fillRect(x * av.charWidth, y2, av.charWidth, y1 - y2);
-      }
-      else
-      {
-        g.fillRect(x * av.charWidth, y1, av.charWidth, y2 - y1);
-      }
-
-      x++;
-
-    }
-    if (aa.threshold != null)
-    {
-      g.setColor(aa.threshold.colour);
-      y2 = (int) (y - ((aa.threshold.value - min) / range) * aa.graphHeight);
-      g.drawLine(0, y2, (eRes - sRes) * av.charWidth, y2);
-    }
+    return image;
   }
 
-  // used by overview window
-  public void drawGraph(Graphics g, AlignmentAnnotation aa, int width,
-          int y, int sRes, int eRes)
+  @Override
+  public int getFadedImageWidth()
   {
-    eRes = Math.min(eRes, aa.annotations.length);
-    g.setColor(Color.white);
-    g.fillRect(0, 0, width, y);
-    g.setColor(new Color(0, 0, 180));
+    return imgWidth;
+  }
 
-    int x = 0, height;
+  private int[] bounds = new int[2];
 
-    for (int j = sRes; j < eRes; j++)
+  @Override
+  public int[] getVisibleVRange()
+  {
+    if (ap != null && ap.alabels != null)
     {
-      if (aa.annotations[j].colour == null)
-        g.setColor(Color.black);
-      else
-        g.setColor(aa.annotations[j].colour);
-
-      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;
+      int sOffset = -ap.alabels.scrollOffset;
+      int visHeight = sOffset + ap.annotationPanelHolder.getHeight();
+      bounds[0] = sOffset;
+      bounds[1] = visHeight;
+      return bounds;
     }
+    else
+      return null;
   }
 }