X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationPanel.java;h=101bddf40c56877c6c1d35588644235f65165944;hb=1f9990748644d3380bc045aad1f694c0252cc35f;hp=afdc6db3b51d4bb80e096c2ffaf78515b01a5c92;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git

diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java
index afdc6db..101bddf 100755
--- a/src/jalview/appletgui/AnnotationPanel.java
+++ b/src/jalview/appletgui/AnnotationPanel.java
@@ -1,127 +1,443 @@
 /*
-* 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) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 
 package jalview.appletgui;
 
-import jalview.datamodel.*;
+import java.util.*;
 
 import java.awt.*;
 import java.awt.event.*;
-import java.util.*;
 
-public class AnnotationPanel extends Panel implements AdjustmentListener
+import jalview.datamodel.*;
+
+public class AnnotationPanel
+    extends Panel
+    implements AdjustmentListener, ActionListener, MouseListener, MouseMotionListener
 {
   AlignViewport av;
   AlignmentPanel ap;
-  int activeRow =-1;
+  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 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;
+  int imgWidth = 0;
 
   boolean fastPaint = false;
 
   public static int GRAPH_HEIGHT = 40;
 
-
+  boolean MAC = false;
 
   public AnnotationPanel(AlignmentPanel ap)
   {
+    if (System.getProperty("os.name").startsWith("Mac"))
+    {
+      MAC = true;
+    }
+
     this.ap = ap;
     av = ap.av;
-    this.setLayout(null);
+    setLayout(null);
     adjustPanelHeight();
 
-    addMouseMotionListener(new MouseMotionAdapter()
-    {public void mouseMoved(MouseEvent evt)
-          { doMouseMoved(evt); }
-    });
+    addMouseMotionListener(this);
+
+    addMouseListener(this);
+
 
-   // ap.annotationScroller.getVAdjustable().addAdjustmentListener( this );
+    // ap.annotationScroller.getVAdjustable().addAdjustmentListener( this );
+  }
+
+  public AnnotationPanel(AlignViewport av)
+  {
+    this.av = av;
   }
 
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
-    ap.alabels.setScrollOffset( -evt.getValue() );
+    ap.alabels.setScrollOffset( -evt.getValue());
   }
 
-  public void adjustPanelHeight()
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void actionPerformed(ActionEvent evt)
+  {
+    AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+    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.colSel != null && av.colSel.size() > 0
+        && anot[av.colSel.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.colSel.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.colSel.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";
+      }
+
+      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;
+      }
+
+      for (int i = 0; i < av.getColumnSelection().size(); i++)
+      {
+        int index = av.getColumnSelection().columnAt(i);
+
+        if(!av.colSel.isVisible(index))
+          continue;
+
+        if (anot[index] == null)
+        {
+          anot[index] = new Annotation(label, "", type, 0);
+        }
+
+        anot[index].secondaryStructure = type;
+        anot[index].displayCharacter = label;
+      }
+    }
+
+    adjustPanelHeight();
+    repaint();
+
+    return;
+  }
+
+  String enterLabel(String text, String label)
+  {
+    EditNameDialog dialog = new EditNameDialog(text,null,label,null,
+        ap.alignFrame,"Enter Label", 400,200);
+
+    if(dialog.accept)
+      return dialog.getName();
+    else
+      return null;
+  }
+
+  public void mousePressed(MouseEvent evt)
+  {
+      AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+      if (aa == null)
+      {
+        return;
+      }
+
+      int height = 0;
+      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;
+          }
+
+          break;
+        }
+      }
+
+      if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK) ==
+        InputEvent.BUTTON3_MASK  && activeRow != -1)
+      {
+        if (av.getColumnSelection() == null)
+        {
+          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);
+        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;
+      }
+
+      if (aa == null)
+      {
+        return;
+      }
+
+      ap.scalePanel.mousePressed(evt);
+  }
+
+  public void mouseReleased(MouseEvent evt)
+  {
+    ap.scalePanel.mouseReleased(evt);
+  }
+
+  public void mouseClicked(MouseEvent evt)
+  {}
+
+  public void mouseDragged(MouseEvent evt)
+  {
+    ap.scalePanel.mouseDragged(evt);
+  }
+
+  public void mouseMoved(MouseEvent evt)
   {
-    // setHeight of panels
     AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+    if (aa == null)
+    {
+      return;
+    }
+
+    int row = -1;
     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].visible)
+      {
+        height += aa[i].height;
+      }
 
-      if(aa[i].hasText)
-        aa[i].height += av.charHeight;
-      if (aa[i].hasIcons)
-        aa[i].height += 16;
+      if (evt.getY() < height)
+      {
+        row = i;
+        break;
+      }
+    }
 
-      if (aa[i].isGraph)
-        aa[i].height += GRAPH_HEIGHT;
+    int res = evt.getX() / av.getCharWidth() + av.getStartRes();
 
-      if(aa[i].height==0)
-        aa[i].height = 20;
-      height += aa[i].height;
+    if (av.hasHiddenColumns)
+    {
+      res = av.getColumnSelection().adjustForHiddenColumns(res);
     }
-  else height=20;
 
-   this.setSize(getSize().width, height);
-   ap.annotationScroller.setSize(getSize().width, height);
+    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());
+    }
+  }
+  public void mouseEntered(MouseEvent evt)
+  {
+    ap.scalePanel.mouseEntered(evt);
+  }
+  public void mouseExited(MouseEvent evt)
+  {
+    ap.scalePanel.mouseExited(evt);
+  }
+
+
+  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 += GRAPH_HEIGHT;
+        }
+
+        if (aa[i].height == 0)
+        {
+          aa[i].height = 20;
+        }
+        height += aa[i].height;
+      }
+    }
+    else
+    {
+      height = 20;
+    }
 
-//  ap.annotationSpaceFillerHolder.setSize(d.width,annotationPanel.getSize().height);
+    this.setSize(getSize().width, height);
 
-   repaint();
+    repaint();
+
+    return height;
 
   }
 
   public void addEditableColumn(int i)
   {
-    if(activeRow==-1)
+    if (activeRow == -1)
     {
-      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;
+      }
+
+      for (int j = 0; j < aa.length; j++)
+      {
+        if (aa[j].editable)
         {
           activeRow = j;
           break;
         }
+      }
     }
 
-    if(activeRes==null)
+    if (activeRes == null)
     {
       activeRes = new Vector();
       activeRes.addElement(String.valueOf(i));
@@ -131,38 +447,6 @@ public class AnnotationPanel extends Panel implements AdjustmentListener
     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)
   {
@@ -171,258 +455,650 @@ public class AnnotationPanel extends Panel implements AdjustmentListener
 
   public void paint(Graphics g)
   {
-    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;
+    imgWidth = getSize().width;
+    //(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)
+    if (fastPaint)
     {
       g.drawImage(image, 0, 0, this);
       fastPaint = false;
       return;
     }
 
-    drawComponent( gg, av.startRes, av.endRes+1);
-    g.drawImage( image, 0, 0, this);
+    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.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;
-  }
+    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;
 
-  gg.translate(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;
+    }
 
-  drawComponent(gg, sr, er);
+    gg.translate(transX, 0);
 
-  gg.translate( -transX, 0 );
+    drawComponent(gg, sr, er);
 
-  fastPaint = true;
-  repaint();
-}
+    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)
   {
+    g.setFont(av.getFont());
+
     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.fillRect(0, 0, (endRes - startRes) * av.charWidth, getSize().height);
+
+    if (fm == null)
+    {
+      fm = g.getFontMetrics();
+    }
+
+    if ( (av.alignment.getAlignmentAnnotation() == null) ||
+        (av.alignment.getAlignmentAnnotation().length < 1))
     {
       g.setColor(Color.white);
-      g.fillRect(0,0,getSize().width, getSize().height);
+      g.fillRect(0, 0, getSize().width, getSize().height);
       g.setColor(Color.black);
-      g.drawString("Alignment has no annotations",20,15);
+      if (av.validCharWidth)
+      {
+        g.drawString("Alignment has no annotations", 20, 15);
+      }
+
       return;
     }
 
-    AlignmentAnnotation [] aa = av.alignment.getAlignmentAnnotation();
+    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;
+    int x = 0;
+    int y = 0;
+    int column = 0;
+    char lastSS;
+    int lastSSX;
+    int iconOffset = av.charHeight / 2;
     boolean validRes = false;
-    //\u03B2 \u03B1
 
-    for(int i=0; i<aa.length; i++)
+    boolean[] graphGroupDrawn = new boolean[aa.length];
+
+    //\u03B2 \u03B1
+    for (int i = 0; i < aa.length; i++)
     {
       AlignmentAnnotation row = aa[i];
-      if(!row.visible)
+
+      if (!row.visible)
+      {
         continue;
+      }
 
-      if(row.isGraph)
+      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)
+
+        if (row.hasText)
+        {
           y -= av.charHeight;
+        }
+      }
+
+      if (row.hasText)
+      {
+        iconOffset = av.charHeight / 2;
       }
-      if(row.hasText)
-        iconOffset = av.charHeight/2;
       else
+      {
         iconOffset = 0;
+      }
 
-      for(j=startRes; j<endRes; j++)
+      x = 0;
+      while (x < endRes - startRes)
       {
-        if(row.annotations.length<=j || row.annotations[j]==null)
-        validRes = false;
-       else
-         validRes = true;
+        if (av.hasHiddenColumns)
+        {
+          column = av.getColumnSelection().adjustForHiddenColumns(startRes + x);
+          if (column > row.annotations.length - 1)
+          {
+            break;
+          }
+        }
+        else
+        {
+          column = startRes + x;
+        }
 
-       x = (j-startRes)*av.charWidth;
+        if ( (row.annotations.length <= column) ||
+            (row.annotations[column] == null))
+        {
+          validRes = false;
+        }
+        else
+        {
+          validRes = true;
+        }
 
+        if (activeRow == i)
+        {
+          g.setColor(Color.red);
 
-       if(activeRow==i)
-       {
+          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);
+              }
+            }
+          }
+        }
 
-         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 (av.validCharWidth && validRes &&
+            (row.annotations[column].displayCharacter.length() > 0))
+        {
+          int charOffset = (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(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.hasIcons)
+        {
+          if (!validRes ||
+              (row.annotations[column].secondaryStructure != lastSS))
           {
-            if (row.annotations[0].secondaryStructure == 'H'
-                || row.annotations[0].secondaryStructure == 'E')
-              g.drawString(row.annotations[j].displayCharacter, x,
-                           y + iconOffset + 2);
+            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 * 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)
+      {
+        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 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);
-
-        if(!row.hasIcons)
-            g.drawString(row.annotations[j].displayCharacter, x + charOffset,
-                         y + iconOffset + 2);
-       }
-
-       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;
-       }
+          {
+            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)
+  {
+    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);
 
-       if (validRes && row.isGraph)
-       {
-         g.setColor(new Color(0,0,180));
-         int height = (int)((row.annotations[j].value / row.graphMax)*GRAPH_HEIGHT);
+    if (sRes == 0)
+    {
+      sRes++;
+      x += av.charWidth;
+    }
 
-         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;
+    int y1 = y, y2 = y;
+    float range = max - min;
 
-             total += row.annotations[i2].value;
-           }
+    ////Draw origin
+    if (min < 0)
+    {
+      y2 = y - (int) ( (0 - min / range) * graphHeight);
+    }
 
-           total/=row.windowLength;
-           height = (int)( (total / row.graphMax) *GRAPH_HEIGHT);
+    g.setColor(Color.gray);
+    g.drawLine(x - av.charWidth, y2, (eRes - sRes) * av.charWidth, y2);
 
-         }
-         g.setColor(row.annotations[j].colour);
-         g.fillRect(x, y-height, av.charWidth, height );
-       }
+    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);
       }
 
-      x+=av.charWidth;
+      if (column > aaMax)
+      {
+        break;
+      }
 
-      if(row.hasIcons)
-      switch (lastSS[i])
+      if (aa.annotations[column] == null || aa.annotations[column - 1] == null)
       {
-        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;
+        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 - 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);
+    }
+  }
+
+  public void drawBarGraph(Graphics g, AlignmentAnnotation aa,
+                           int sRes, int eRes,
+                           float min, float max,
+                           int y)
+  {
+    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(row.isGraph && row.hasText)
-         y+=av.charHeight;
-       if(!row.isGraph)
-          y+=aa[i].height;
+      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);
     }
   }
 
   // used by overview window
-  public void drawGraph(Graphics g, AlignmentAnnotation aa,int width, int y)
+  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 x = 0;
-    for(int j=0; j<aa.annotations.length; j++)
+    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));
-      int height = (int) ( (aa.annotations[j].value / aa.graphMax) * GRAPH_HEIGHT );
+      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;
+      x += av.charWidth;
     }
   }
 }