X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=e0b36d37a8530646f29a7ebb78d882f6bc8176b3;hb=a2497c9a753e13eeb17d33f73a697b4ad7ebdbc3;hp=41bbb43608eac3a21c2d2807d478f51bc2f7bec0;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 41bbb43..e0b36d3 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -1,607 +1,1275 @@
 /*
-* 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
-*/
-
+ * 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
+ */
 package jalview.gui;
 
 import jalview.datamodel.*;
 
-import javax.swing.*;
 import java.awt.*;
 import java.awt.event.*;
-import java.util.*;
 import java.awt.image.*;
 
-public class AnnotationPanel extends JPanel implements MouseListener, MouseMotionListener, ActionListener, AdjustmentListener
-{
-  AlignViewport av;
-  AlignmentPanel ap;
-  int activeRow =-1;
+import javax.swing.*;
 
-  ArrayList 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();
 
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class AnnotationPanel extends JPanel implements MouseListener,
+    MouseMotionListener, ActionListener, AdjustmentListener
+{
+    final String HELIX = "Helix";
+    final String SHEET = "Sheet";
+    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();
+
+    /** DOCUMENT ME!! */
+    AlignViewport av;
+    AlignmentPanel ap;
+    int activeRow = -1;
+    BufferedImage image;
+    BufferedImage fadedImage;
+    Graphics2D gg;
+    FontMetrics fm;
+    int imgWidth = 0;
+    boolean fastPaint = false;
+
+    //Used For mouse Dragging and resizing graphs
+    int graphStretch = -1;
+    int graphStretchY = -1;
+    int min; //used by mouseDragged to see if user
+    int max; //used by mouseDragged to see if user
+    boolean mouseDragging = false;
+
+    boolean MAC = false;
+
+    /**
+     * Creates a new AnnotationPanel object.
+     *
+     * @param ap DOCUMENT ME!
+     */
+    public AnnotationPanel(AlignmentPanel ap)
+    {
 
-  BufferedImage image;
-  Graphics2D gg;
-  FontMetrics fm;
-  int imgWidth=0;
+    if(System.getProperty("os.name").startsWith("Mac"))
+      MAC = true;
+
+        ToolTipManager.sharedInstance().registerComponent(this);
+        ToolTipManager.sharedInstance().setInitialDelay(0);
+        ToolTipManager.sharedInstance().setDismissDelay(10000);
+        this.ap = ap;
+        av = ap.av;
+        this.setLayout(null);
+        addMouseListener(this);
+        addMouseMotionListener(this);
+        ap.annotationScroller.getVerticalScrollBar().addAdjustmentListener(this);
+    }
+
+    public AnnotationPanel(AlignViewport av)
+    {
+      this.av = av;
+    }
 
-  boolean fastPaint = false;
 
-  public static int GRAPH_HEIGHT = 40;
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void adjustmentValueChanged(AdjustmentEvent evt)
+    {
+        ap.alabels.setScrollOffset(-evt.getValue());
+    }
 
+    /**
+     * DOCUMENT ME!
+     */
+    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;
+                }
+
+                height += aa[i].height;
+            }
+        }
+        else
+        {
+            height = 20;
+        }
 
-  public AnnotationPanel(AlignmentPanel ap)
-  {
-    this.ap = ap;
-    av = ap.av;
-    this.setLayout(null);
-    addMouseListener(this);
-    addMouseMotionListener(this);
-    adjustPanelHeight();
+        this.setPreferredSize(new Dimension(1, height));
 
+        return height;
+    }
 
-    ap.annotationScroller.getVerticalScrollBar().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++)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void actionPerformed(ActionEvent evt)
     {
-      if(!aa[i].visible)
-        continue;
+        AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+        Annotation[] anot = aa[activeRow].annotations;
 
-      aa[i].height = 0;
+        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))
+        {
+            String label = JOptionPane.showInputDialog(this, "Enter Label ",
+                    "Enter label", JOptionPane.QUESTION_MESSAGE);
+
+            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 (anot[index] == null)
+                {
+                    anot[index] = new Annotation(label, "", ' ', 0);
+                }
+
+                anot[index].displayCharacter = label;
+            }
+        }
+        else if (evt.getActionCommand().equals(COLOUR))
+        {
+            Color col = JColorChooser.showDialog(this,
+                    "Choose foreground colour", Color.black);
 
-      if(aa[i].hasText)
-        aa[i].height += av.charHeight;
-      if (aa[i].hasIcons)
-        aa[i].height += 16;
+            for (int i = 0; i < av.getColumnSelection().size(); i++)
+            {
+                int index = av.getColumnSelection().columnAt(i);
 
-      if (aa[i].isGraph)
-        aa[i].height += GRAPH_HEIGHT;
+                if (anot[index] == null)
+                {
+                    anot[index] = new Annotation("", "", ' ', 0);
+                }
 
-      if(aa[i].height==0)
-        aa[i].height = 20;
-      height += aa[i].height;
-    }
-  else height=20;
-    this.setPreferredSize(new Dimension(1, height));
+                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";
+            }
+
+            if (!aa[activeRow].hasIcons)
+            {
+                aa[activeRow].hasIcons = true;
+            }
+
+            String label = JOptionPane.showInputDialog("Enter a label for the structure?",
+                    symbol);
+
+            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 (anot[index] == null)
+                {
+                    anot[index] = new Annotation(label, "", type, 0);
+                }
+
+                anot[index].secondaryStructure = type;
+                anot[index].displayCharacter = label;
+            }
+        }
+
+        adjustPanelHeight();
+        repaint();
 
-  }
+        return;
+    }
 
-  public void addEditableColumn(int i)
-  {
-    if(activeRow==-1)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mousePressed(MouseEvent evt)
     {
-      AlignmentAnnotation [] aa = av.alignment.getAlignmentAnnotation();
-      for(int j=0; j<aa.length; j++)
-        if(aa[j].editable)
+
+        AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+        if(aa==null)
+          return;
+
+
+        int height = 0;
+        activeRow = -1;
+
+
+        for (int i = 0; i < aa.length; i++)
         {
-          activeRow = j;
-          break;
+            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(activeRes==null)
-    {
-      activeRes = new ArrayList();
-      activeRes.add(String.valueOf(i));
-      return;
-    }
 
-    activeRes.add(String.valueOf(i));
+        if (SwingUtilities.isRightMouseButton(evt) && activeRow!=-1)
+        {
+            if (av.getColumnSelection() == null)
+            {
+                return;
+            }
+
+            JPopupMenu pop = new JPopupMenu("Structure type");
+            JMenuItem item = new JMenuItem(HELIX);
+            item.addActionListener(this);
+            pop.add(item);
+            item = new JMenuItem(SHEET);
+            item.addActionListener(this);
+            pop.add(item);
+            item = new JMenuItem(LABEL);
+            item.addActionListener(this);
+            pop.add(item);
+            item = new JMenuItem(COLOUR);
+            item.addActionListener(this);
+            pop.add(item);
+            item = new JMenuItem(REMOVE);
+            item.addActionListener(this);
+            pop.add(item);
+            pop.show(this, evt.getX(), evt.getY());
+
+            return;
+        }
 
-  }
+        if (aa == null)
+        {
+            return;
+        }
 
+        int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
 
-  public void actionPerformed(ActionEvent evt)
-  {
+        if(av.hasHiddenColumns)
+          res = av.getColumnSelection().adjustForHiddenColumns(res);
 
-    AlignmentAnnotation [] aa = av.alignment.getAlignmentAnnotation();
-    Annotation [] anot = aa[activeRow].annotations;
+        min = res;
+        max = res;
 
-    if(evt.getActionCommand().equals(REMOVE))
-    {
-      for(int i=0; i<activeRes.size(); i++)
-      {
-        anot[Integer.parseInt(activeRes.get(i).toString())] = null;
-        anot[Integer.parseInt(activeRes.get(i).toString())] = null;
-      }
-    }
-    else if(evt.getActionCommand().equals(LABEL))
-    {
-      String label = JOptionPane.showInputDialog(this, "Enter Label ", "Enter label", JOptionPane.QUESTION_MESSAGE );
-      if(label==null)
-        label = "";
+        if (av.getColumnSelection().contains(res))
+          av.getColumnSelection().removeElement(res);
+        else
+        {
+            av.getColumnSelection().addElement(res);
+            SequenceGroup sg = new SequenceGroup();
 
-      if(label.length()>0 && !aa[activeRow].hasText)
-       aa[activeRow].hasText = true;
+            for (int i = 0; i < av.alignment.getSequences().size(); i++)
+            {
+                sg.addSequence(av.alignment.getSequenceAt(i), false);
+            }
+
+            sg.setStartRes(res);
+            sg.setEndRes(res);
+            av.setSelectionGroup(sg);
+        }
+
+        ap.repaint();
 
-      for(int i=0; i<activeRes.size(); i++)
-      {
-        int index = Integer.parseInt(activeRes.get(i).toString());
-        if(anot[index]==null)
-          anot[index] = new Annotation(label, "", ' ',0);
-        anot[index].displayCharacter = label;
-      }
     }
-    else if(evt.getActionCommand().equals(COLOUR))
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mouseReleased(MouseEvent evt)
     {
-     Color col = JColorChooser.showDialog(this, "Choose foreground colour", Color.black);
-     for (int i = 0; i < activeRes.size(); i++)
-     {
-       int index = Integer.parseInt(activeRes.get(i).toString());
-       if (anot[index] == null)
-         anot[index] = new Annotation("", "", ' ', 0);
-       anot[index].colour = col;
-     }
+      graphStretch = -1;
+      graphStretchY = -1;
+      mouseDragging = false;
     }
-    else // HELIX OR SHEET
-    {
-    char type = 0;
-    String symbol = "\u03B1";
-    if(evt.getActionCommand().equals(HELIX))
-       type = 'H';
-    else if(evt.getActionCommand().equals(SHEET))
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mouseEntered(MouseEvent evt)
     {
-      type = 'E';
-      symbol = "\u03B2";
+      if(mouseDragging)
+        ap.seqPanel.scrollCanvas(null);
     }
 
-    if(!aa[activeRow].hasIcons)
-      aa[activeRow].hasIcons = true;
-
-
-    String label = JOptionPane.showInputDialog("Enter a label for the structure?", symbol );
-    if(label==null)
-       label="";
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mouseExited(MouseEvent evt)
+    {
+      if(mouseDragging)
+        ap.seqPanel.scrollCanvas(evt);
+    }
 
-    if(label.length()>0 && !aa[activeRow].hasText)
-       aa[activeRow].hasText = true;
 
-    for(int i=0; i<activeRes.size(); i++)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mouseDragged(MouseEvent evt)
     {
-      int index = Integer.parseInt(activeRes.get(i).toString());
-      if (anot[index] == null)
+      if(graphStretch>-1)
       {
-        anot[index] = new Annotation(label, "", type, 0);
+        av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY - evt.getY();
+        if(av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight <0)
+          av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight = 0;
+        graphStretchY = evt.getY();
+        adjustPanelHeight();
+        ap.repaint();
       }
+      else
+      {
+        mouseDragging = true;
 
-        anot[ index ].secondaryStructure = type;
-        anot[ index ].displayCharacter = label;
-    }
-    }
-
-    adjustPanelHeight();
-    activeRes = null;
-    repaint();
-    return;
+        int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
 
+        if(av.hasHiddenColumns)
+          res = av.getColumnSelection().adjustForHiddenColumns(res);
 
-  }
+        SequenceGroup sg = av.getSelectionGroup();
 
-  public void mousePressed(MouseEvent evt)
-  {
-    if (SwingUtilities.isRightMouseButton(evt))
-    {
-      if(activeRes==null)
-        return;
+        if (res < min)
+        {
+            min = res;
+        }
 
-      JPopupMenu pop = new JPopupMenu("Structure type");
-      JMenuItem item = new JMenuItem(HELIX);
-      item.addActionListener(this);
-      pop.add(item);
-      item = new JMenuItem(SHEET);
-      item.addActionListener(this);
-      pop.add(item);
-      item = new JMenuItem(LABEL);
-      item.addActionListener(this);
-      pop.add(item);
-      item = new JMenuItem(COLOUR);
-      item.addActionListener(this);
-      pop.add(item);
-      item = new JMenuItem(REMOVE);
-      item.addActionListener(this);
-      pop.add(item);
-      pop.show(this, evt.getX(), evt.getY());
-      return;
-    }
+        if (res > max)
+        {
+            max = res;
+        }
 
+        if (sg != null)
+        {
+            if (!av.getColumnSelection().contains(res))
+            {
+                av.getColumnSelection().addElement(res);
+            }
+
+            if (res > sg.getStartRes())
+            {
+                sg.setEndRes(res);
+            }
+            else if (res < sg.getStartRes())
+            {
+                sg.setStartRes(res);
+            }
+
+            for (int i = min; i <= max; i++)
+            {
+                if ((i < sg.getStartRes()) || (i > sg.getEndRes()))
+                {
+                    av.getColumnSelection().removeElement(i);
+                }
+                else
+                {
+                    av.getColumnSelection().addElement(i);
+                }
+            }
+
+            ap.repaint();
+        }
 
-    AlignmentAnnotation [] aa = av.alignment.getAlignmentAnnotation();
-    if(aa==null)
-      return;
+      }
+    }
 
-    int height = 0;
-    activeRow = -1;
-    for(int i=0; i<aa.length; i++)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mouseMoved(MouseEvent evt)
     {
-      height+= aa[i].height;
+        AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
 
-      if(evt.getY()<height)
-      {
-        if(!aa[i].editable)
+        if (aa == null)
         {
-          activeRes = null;
-          continue;
+            return;
         }
 
-        activeRow = i;
-        break;
-      }
-    }
+        int row = -1;
+        int height = 0;
 
+        for (int i = 0; i < aa.length; i++)
+        {
+            if (aa[i].visible)
+            {
+                height += aa[i].height;
+            }
 
-    int res = evt.getX() / av.getCharWidth() + av.getStartRes();
+            if (evt.getY() < height)
+            {
+                row = i;
 
-    if(evt.isControlDown() || evt.isAltDown())
-      addEditableColumn(res);
+                break;
+            }
+        }
 
-    else if(evt.isShiftDown())
-    {
+        if(row==-1)
+          return;
 
-      if(activeRes==null)
-        activeRes=new ArrayList();
-      else
-      {
-          int start =  Integer.parseInt( activeRes.get( activeRes.size()-1 ).toString() );
-          int end = res;
-          if(end<start)
-          {
-            int temp = end;
-            end = start;
-            start = temp;
-          }
-          for(int n=start; n<=end; n++)
-            addEditableColumn(n);
+        int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
 
-      }
+        if(av.hasHiddenColumns)
+          res = av.getColumnSelection().adjustForHiddenColumns(res);
+
+        if ( aa[row].annotations!=null
+             && row > -1
+             && res < (int) aa[row].annotations.length)
+        {
+            if(aa[row].graphGroup>-1)
+            {
+              StringBuffer tip = new StringBuffer("<html>");
+              for (int gg = 0; gg < aa.length; gg++)
+              {
+                if (aa[gg].graphGroup == aa[row].graphGroup && aa[gg].annotations[res]!=null)
+                  tip.append(aa[gg].label+" "+aa[gg].annotations[res].description+"<br>" );
+              }
+              if(tip.length()!=6)
+              {
+                tip.setLength(tip.length() - 4);
+                this.setToolTipText(tip.toString() + "</html>");
+              }
+            }
+            else if(aa[row].annotations[res] != null)
+              this.setToolTipText(aa[row].annotations[res].description);
+
+            if(aa[row].annotations[res]!=null)
+            {
+              StringBuffer text = new StringBuffer("Sequence position " +
+                                                   (res + 1) + "  " +
+                                                   aa[row].annotations[res].description);
+
+              ap.alignFrame.statusBar.setText(text.toString());
+            }
+        }
     }
-    else
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mouseClicked(MouseEvent evt)
     {
-        activeRes = new ArrayList();
-        activeRes.add( String.valueOf(res) );
     }
 
-    repaint();
-
-  }
-  public void mouseReleased(MouseEvent evt)
-  {  }
-  public void mouseEntered(MouseEvent evt)
-  {  }
-  public void mouseExited(MouseEvent evt)
-  {  }
-  public void mouseDragged(MouseEvent evt)
-  {  }
-  public void mouseMoved(MouseEvent evt)
-  {
-    ToolTipManager.sharedInstance().registerComponent(this);
-    AlignmentAnnotation [] aa = av.alignment.getAlignmentAnnotation();
-    if(aa==null)
-      return;
-
-    int row = -1;
-    int height=0;
-    for(int i=0; i<aa.length; i++)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param g DOCUMENT ME!
+     */
+    public void paintComponent(Graphics g)
     {
+      g.setColor(Color.white);
+      g.fillRect(0, 0, getWidth(), getHeight());
 
-      if( aa[i].visible )
-        height += aa[i].height;
+      if(image!=null)
+      {if (fastPaint
+            || (getVisibleRect().width != g.getClipBounds().width)
+            || (getVisibleRect().height != g.getClipBounds().height))
+        {
+          g.drawImage(image, 0, 0, this);
+          fastPaint = false;
+          return;
+        }
+      }
+      imgWidth = (av.endRes - av.startRes + 1) * av.charWidth;
 
-      if(evt.getY()<height)
+      if (image == null || imgWidth != image.getWidth()
+          || image.getHeight(this) != getHeight())
       {
-        row = i;
-        break;
+        image = new BufferedImage(imgWidth, ap.annotationPanel.getHeight(),
+                                  BufferedImage.TYPE_INT_RGB);
+        gg = (Graphics2D) image.getGraphics();
+
+        if(av.antiAlias)
+        gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+                            RenderingHints.VALUE_ANTIALIAS_ON);
+
+        gg.setFont(av.getFont());
+        fm = gg.getFontMetrics();
+        gg.setColor(Color.white);
+        gg.fillRect(0, 0, imgWidth, image.getHeight());
       }
+
+
+      drawComponent(gg, av.startRes, av.endRes + 1);
+      g.drawImage(image, 0, 0, this);
     }
 
-    int res = evt.getX() / av.getCharWidth() + av.getStartRes();
-    if(row>-1 && res<aa[row].annotations.length && aa[row].annotations[res]!=null)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param horizontal DOCUMENT ME!
+     */
+    public void fastPaint(int horizontal)
     {
-      this.setToolTipText(aa[row].annotations[res].description);
-      StringBuffer text = new StringBuffer("Sequence position " + (res + 1) +
-                                           "  " +
-                                           aa[row].annotations[res].description);
-      ap.alignFrame.statusBar.setText(text.toString());
-    }
+        if ((horizontal == 0)
+            || gg==null
+            || av.alignment.getAlignmentAnnotation()==null
+            || av.alignment.getAlignmentAnnotation().length < 1
+            || av.updatingConsensus
+            || av.updatingConservation)
+        {
+            repaint();
+            return;
+        }
 
+        gg.copyArea(0, 0, imgWidth, getHeight(), -horizontal * av.charWidth, 0);
 
-  }
-  public void mouseClicked(MouseEvent evt) {}
+        int sr = av.startRes;
+        int er = av.endRes + 1;
+        int 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;
+        }
 
-  public void paintComponent(Graphics g)
-  {
-    g.setColor(Color.white);
-    g.fillRect(0,0,getWidth(), getHeight());
+        gg.translate(transX, 0);
+
+        drawComponent(gg, sr, er);
+
+        gg.translate(-transX, 0);
+
+        fastPaint = true;
+
+        repaint();
 
-    if(fastPaint)
-    {
-      g.drawImage(image, 0, 0, this);
-      fastPaint = false;
-      return;
     }
 
-    imgWidth = (av.endRes-av.startRes+1) *av.charWidth;
+    /**
+     * DOCUMENT ME!
+     *
+     * @param g DOCUMENT ME!
+     * @param startRes DOCUMENT ME!
+     * @param endRes DOCUMENT ME!
+     */
+    public void drawComponent(Graphics g, int startRes, int endRes)
+    {
+      if(av.updatingConsensus || av.updatingConservation)
+      {
+        if(image==null)
+         {
+           return;
+         }
+        //We'll keep a record of the old image,
+        //and draw a faded image until the calculation
+        //has completed
+        if(fadedImage==null
+           || fadedImage.getWidth()!=imgWidth
+        || fadedImage.getHeight()!=image.getHeight())
+        {
+          fadedImage = new BufferedImage(
+              imgWidth, image.getHeight(),
+              BufferedImage.TYPE_INT_RGB);
 
-    image = new BufferedImage(imgWidth,
-                                ap.annotationPanel.getHeight(),
-                                BufferedImage.TYPE_INT_RGB);
-      gg = (Graphics2D) image.getGraphics();
-      gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
-                          RenderingHints.VALUE_ANTIALIAS_ON);
+          Graphics2D fadedG = (Graphics2D) fadedImage.getGraphics();
 
-      gg.setFont(av.getFont());
-      fm = gg.getFontMetrics();
+          fadedG.setColor(Color.white);
+        fadedG.fillRect(0, 0, imgWidth, image.getHeight());
 
-    drawComponent( gg, av.startRes, av.endRes+1);
-    g.drawImage( image, 0, 0, this);
+          fadedG.setComposite(
+              AlphaComposite.getInstance(
+                  AlphaComposite.SRC_OVER, .3f));
+          fadedG.drawImage(image, 0, 0, this);
 
-  }
+        }
 
-  public void fastPaint(int horizontal)
-{
-  if( horizontal == 0
-     || av.alignment.getAlignmentAnnotation()==null
-     || av.alignment.getAlignmentAnnotation().length<1
-    )
-  {
-    repaint();
-    return;
-  }
+      }
+      else
+        fadedImage = null;
 
-  gg.copyArea( 0,0, imgWidth, getHeight(), -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;
-  }
+      g.setColor(Color.white);
+      g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight());
 
+      g.setFont(av.getFont());
+      if (fm == null)
+        fm = g.getFontMetrics();
 
-  gg.translate(transX, 0);
 
-  drawComponent(gg, sr, er);
 
-  gg.translate( -transX, 0 );
 
-  fastPaint = true;
-  repaint();
-}
+        if ( (av.alignment.getAlignmentAnnotation() == null) ||
+                (av.alignment.getAlignmentAnnotation().length < 1))
+        {
+            g.setColor(Color.white);
+            g.fillRect(0, 0, getWidth(), getHeight());
+            g.setColor(Color.black);
+            if(av.validCharWidth)
+              g.drawString("Alignment has no annotations", 20, 15);
 
+            return;
+        }
 
-  public void drawComponent(Graphics2D g, int startRes, int endRes)
-  {
-    g.setColor(Color.white);
-    g.fillRect(0,0,(endRes-startRes) *av.charWidth, getHeight());
-    if(av.alignment.getAlignmentAnnotation()==null || av.alignment.getAlignmentAnnotation().length<1)
-    {
-      g.setColor(Color.white);
-      g.fillRect(0,0,getWidth(), getHeight());
-      g.setColor(Color.black);
-      g.drawString("Alignment has no annotations",20,15);
-      return;
-    }
 
-    AlignmentAnnotation [] aa = av.alignment.getAlignmentAnnotation();
+        AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+
+        int x = 0, y = 0;
+        int column=0;
+        char lastSS;
+        int lastSSX;
+        int iconOffset = av.charHeight / 2;
+        boolean validRes = false;
+
+        boolean [] graphGroupDrawn = new boolean[aa.length];
 
-    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++)
+        //\u03B2 \u03B1
+        for (int i = 0; i < aa.length; i++)
+        {
+            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 (av.updatingConsensus && aa[i]==av.consensus)
+            {
+              y += av.charHeight;
+
+              g.drawImage(fadedImage,
+              0,y-row.height,imgWidth, y,
+              0,y-row.height,imgWidth, y, this);
+              g.setColor(Color.black);
+             // g.drawString("Calculating Consensus....",20, y-row.height/2);
+
+              continue;
+            }
+            else if (av.updatingConservation && aa[i].label.equals("Conservation"))
+            {
+
+              y += av.charHeight;
+              g.drawImage(fadedImage,
+                          0, y - row.height, imgWidth, y,
+                          0, y - row.height, imgWidth, y, this);
+
+              g.setColor(Color.black);
+            //  g.drawString("Calculating Conservation.....",20, y-row.height/2);
+
+              continue;
+            }
+            else if (av.updatingConservation && aa[i].label.equals("Quality"))
+            {
+
+              y += av.charHeight;
+              g.drawImage(fadedImage,
+                          0, y - row.height, imgWidth, y,
+                          0, y - row.height, imgWidth, y, this);
+              g.setColor(Color.black);
+             /// g.drawString("Calculating Quality....",20, y-row.height/2);
+
+              continue;
+            }
+
+
+            if (row.hasText)
+            {
+                iconOffset = av.charHeight / 2 + 4;
+            }
+            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.length() > 0))
+                {
+
+                    int charOffset = (av.charWidth -
+                        fm.charWidth(row.annotations[column].displayCharacter.charAt(
+                                0))) / 2;
+                    g.setColor(row.annotations[column].colour);
+
+                    if (column == 0 || row.graph>0)
+                    {
+                        g.drawString(row.annotations[column].displayCharacter,
+                                     (x*av.charWidth)+charOffset,
+                            y + iconOffset );
+                    }
+                    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 );
+                    }
+                }
+
+                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(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;
+
+          //  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 (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+1) * av.charWidth - lastSSX, 7);
+                   }
+                  break;
+
+                default:
+                  g.setColor(Color.gray);
+                  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;
+            }
+        }
+    }
+
+    public void drawLineGraph(Graphics g, AlignmentAnnotation aa,
+                              int sRes, int eRes,
+                              int y,
+                              float min, float max,
+                              int graphHeight)
     {
-      AlignmentAnnotation row = aa[i];
-      if(!row.visible)
-        continue;
+      if(sRes>aa.annotations.length)
+        return;
+
+
+      int x = 0;
 
-      if(row.isGraph)
+      //Adjustment for fastpaint to left
+      if(eRes<av.endRes)
+        eRes++;
+
+      eRes = Math.min(eRes, aa.annotations.length);
+
+      if(sRes==0)
       {
-        // this is so that we draw the characters below the graph
-        y += row.height;
-        if(row.hasText)
-          y -= av.charHeight;
+        x++;
       }
-      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;
+      int y1=y, y2=y;
+      float range = max - min;
 
-       x = (j-startRes)*av.charWidth;
+      ////Draw origin
+      if(min<0)
+        y2 = y - (int)((0-min / range)*graphHeight);
 
+      g.setColor(Color.gray);
+      g.drawLine(x-av.charWidth,y2,(eRes-sRes+1)*av.charWidth,y2);
 
-       if(activeRow==i)
-       {
+      eRes = Math.min(eRes, aa.annotations.length);
 
-         g.setColor(Color.red);
+      int column;
+      int aaMax = aa.annotations.length-1;
 
-         if(activeRes!=null)
-           for (int n = 0; n < activeRes.size(); n++)
-           {
-             int v = Integer.parseInt(activeRes.get(n).toString()) ;
-             if (v == j)
-               g.fillRect( (j-startRes) * av.charWidth, y, av.charWidth, row.height);
-           }
-       }
+      while( x < eRes - sRes )
+      {
+        column = sRes + x;
+        if(av.hasHiddenColumns)
+        {
+          column = av.getColumnSelection().adjustForHiddenColumns(column);
+        }
 
+        if (column > aaMax)
+        {
+          break;
+        }
 
+        if(aa.annotations[column]==null || aa.annotations[column-1]==null)
+        {
+          x++;
+          continue;
+        }
 
-       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)
-          {
-            if (row.annotations[0].secondaryStructure == 'H'
-                || row.annotations[0].secondaryStructure == 'E')
-              g.drawString(row.annotations[j].displayCharacter, x,
-                           y + iconOffset + 2);
-          }
-         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, y + iconOffset + 2);
+          g.setColor(aa.annotations[column].colour);
+          y1 = y - (int) (((aa.annotations[column-1].value-min) / range) * graphHeight);
+          y2 = y - (int) (((aa.annotations[column].value-min) / range) * graphHeight);
 
-        if(!row.hasIcons)
-            g.drawString(row.annotations[j].displayCharacter, x + charOffset,
-                         y + iconOffset + 2);
+          g.drawLine(x*av.charWidth-av.charWidth/2, y1, x*av.charWidth+av.charWidth/2, y2);
+          x ++;
        }
 
-       if(row.hasIcons)
-       if(!validRes || row.annotations[j].secondaryStructure!=lastSS[i])
+       if(aa.threshold!=null)
        {
-         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;
-       }
+           g.setColor(aa.threshold.colour);
+           Graphics2D g2 = (Graphics2D)g;
+           g2.setStroke(new BasicStroke(1,
+                                         BasicStroke.CAP_SQUARE,
+                                         BasicStroke.JOIN_ROUND, 3f,
+                                         new float[] { 5f, 3f }, 0f));
+
+           y2 = (int)(y - ((aa.threshold.value-min) / range)*graphHeight);
+           g.drawLine(0,y2,(eRes-sRes)*av.charWidth,y2);
+           g2.setStroke(new BasicStroke());
+      }
+    }
 
-       if (validRes && row.isGraph)
-       {
-         g.setColor(new Color(0,0,180));
-         int height = (int)((row.annotations[j].value / row.graphMax)*GRAPH_HEIGHT);
+    public void drawBarGraph(Graphics g, AlignmentAnnotation aa,
+                             int sRes, int eRes,
+                             float min, float max,
+                             int y)
+    {
+      if(sRes>aa.annotations.length)
+        return;
 
-         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;
+      eRes = Math.min(eRes, aa.annotations.length);
 
-             total += row.annotations[i2].value;
-           }
+      int x=0, y1=y, y2=y;
 
-           total/=row.windowLength;
-           height = (int)( (total / row.graphMax) *GRAPH_HEIGHT);
+      float range = max - min;
 
-         }
-         g.setColor(row.annotations[j].colour);
-         g.fillRect(x, y-height, av.charWidth, height );
-       }
+      if(min<0)
+        y2 = y - (int)((0-min / (range))*aa.graphHeight);
 
+      g.setColor(Color.gray);
 
-      }
+      g.drawLine(x,y2,(eRes-sRes)*av.charWidth,y2);
 
-      x+=av.charWidth;
+      int column;
+      int aaMax = aa.annotations.length-1;
 
-      if(row.hasIcons)
-      switch (lastSS[i])
+      while( x < eRes-sRes )
       {
-        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;
+        column = sRes + x;
+        if(av.hasHiddenColumns)
+        {
+          column = av.getColumnSelection().adjustForHiddenColumns(column);
+        }
 
-      }
+        if(column > aaMax)
+        {
+            break;
+        }
+
+        if (aa.annotations[column] == null)
+        {
+          x ++;
+          continue;
+        }
 
-       if(row.isGraph && row.hasText)
-         y+=av.charHeight;
-       if(!row.isGraph)
-          y+=aa[i].height;
+          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);
+          Graphics2D g2 = (Graphics2D)g;
+          g2.setStroke(new BasicStroke(1,
+                                        BasicStroke.CAP_SQUARE,
+                                        BasicStroke.JOIN_ROUND, 3f,
+                                        new float[] { 5f, 3f }, 0f));
+
+          y2 = (int)(y - ((aa.threshold.value-min) / range)*aa.graphHeight);
+          g.drawLine(0,y2,(eRes-sRes)*av.charWidth,y2);
+          g2.setStroke(new BasicStroke());
+      }
     }
-  }
-
-  // used by overview window
-  public void drawGraph(Graphics g, AlignmentAnnotation aa,int width, int y)
-  {
-    g.setColor(Color.white);
-    g.fillRect(0,0,width, y);
-    g.setColor(new Color(0,0,180));
-    int x = 0;
-    for(int j=0; j<aa.annotations.length; j++)
+
+    // used by overview window
+    public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, int y, int sRes, int eRes)
     {
+      eRes = Math.min(eRes, aa.annotations.length);
+      g.setColor(Color.white);
+      g.fillRect(0, 0, width, y);
       g.setColor(new Color(0, 0, 180));
-      int height = (int) ( (aa.annotations[j].value / aa.graphMax) * GRAPH_HEIGHT );
-      g.fillRect(x, y - height, av.charWidth, height);
-      x+=av.charWidth;
+
+      int x = 0, height;
+
+      for (int j = sRes; j < eRes; j++)
+      {
+        if (aa.annotations[j] != null)
+        {
+          g.setColor(aa.annotations[j].colour);
+
+          height = (int) ( (aa.annotations[j].value / aa.graphMax) * y);
+          if (height > y)
+            height = y;
+
+          g.fillRect(x, y - height, av.charWidth, height);
+        }
+          x += av.charWidth;
+      }
     }
-  }
+
 }