X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=449c4494561e47f7b9cfbe9395e9c89d5bdb31db;hb=588042b69abf8e60bcc950b24c283933c7dd422f;hp=48f9c20af2fe494099c75f061a96727bffcdb518;hpb=24efbd38f2c3dceaf6d3e305eef41ba0b0c9ebdc;p=jalview.git

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 48f9c20..449c449 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -1,40 +1,55 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.gui;
 
-import jalview.datamodel.*;
+import java.util.*;
 
-import javax.swing.*;
 import java.awt.*;
 import java.awt.event.*;
-import java.util.*;
 import java.awt.image.*;
+import javax.swing.*;
 
-public class AnnotationPanel extends JPanel implements MouseListener, MouseMotionListener, ActionListener, AdjustmentListener
-{
-  AlignViewport av;
-  AlignmentPanel ap;
-  int activeRow =-1;
+import jalview.datamodel.*;
 
-  ArrayList activeRes;
-  static String HELIX ="Helix";
-  static String SHEET ="Sheet";
-  static String LABEL ="Label";
-  static String REMOVE="Remove Annotation";
-  static String COLOUR="Colour";
+public class AnnotationPanel
+    extends JPanel implements MouseListener,
+    MouseMotionListener, ActionListener, AdjustmentListener
+{
+  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();
 
-
+  public static int GRAPH_HEIGHT = 40;
+  AlignViewport av;
+  AlignmentPanel ap;
+  int activeRow = -1;
+  ArrayList activeRes;
   BufferedImage image;
   Graphics2D gg;
   FontMetrics fm;
-  int imgWidth=0;
-
+  int imgWidth = 0;
   boolean fastPaint = false;
 
-  public static int GRAPH_HEIGHT = 40;
-
-
-
   public AnnotationPanel(AlignmentPanel ap)
   {
     this.ap = ap;
@@ -44,13 +59,12 @@ public class AnnotationPanel extends JPanel implements MouseListener, MouseMotio
     addMouseMotionListener(this);
     adjustPanelHeight();
 
-
-    ap.annotationScroller.getVerticalScrollBar().addAdjustmentListener( this );
+    ap.annotationScroller.getVerticalScrollBar().addAdjustmentListener(this);
   }
 
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
-    ap.alabels.setScrollOffset( -evt.getValue() );
+    ap.alabels.setScrollOffset( -evt.getValue());
   }
 
   public void adjustPanelHeight()
@@ -58,148 +72,199 @@ public class AnnotationPanel extends JPanel implements MouseListener, MouseMotio
     // setHeight of panels
     AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
     int height = 0;
-    if(aa!=null)
-    for (int i = 0; i < aa.length; i++)
+
+    if (aa != null)
     {
-      if(!aa[i].visible)
-        continue;
+      for (int i = 0; i < aa.length; i++)
+      {
+        if (!aa[i].visible)
+        {
+          continue;
+        }
 
-      aa[i].height = 0;
+        aa[i].height = 0;
 
-      if(aa[i].hasText)
-        aa[i].height += av.charHeight;
-      if (aa[i].hasIcons)
-        aa[i].height += 16;
+        if (aa[i].hasText)
+        {
+          aa[i].height += av.charHeight;
+        }
 
-      if (aa[i].isGraph)
-        aa[i].height += GRAPH_HEIGHT;
+        if (aa[i].hasIcons)
+        {
+          aa[i].height += 16;
+        }
 
-      if(aa[i].height==0)
-        aa[i].height = 20;
-      height += aa[i].height;
+        if (aa[i].isGraph)
+        {
+          aa[i].height += GRAPH_HEIGHT;
+        }
+
+        if (aa[i].height == 0)
+        {
+          aa[i].height = 20;
+        }
+
+        height += aa[i].height;
+      }
+    }
+    else
+    {
+      height = 20;
     }
-  else height=20;
-    this.setPreferredSize(new Dimension(1, height));
 
+    this.setPreferredSize(new Dimension(1, 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();
+
+      for (int j = 0; j < aa.length; j++)
+      {
+        if (aa[j].editable)
         {
           activeRow = j;
+
           break;
         }
+      }
     }
 
-    if(activeRes==null)
+    if (activeRes == null)
     {
       activeRes = new ArrayList();
       activeRes.add(String.valueOf(i));
+
       return;
     }
 
     activeRes.add(String.valueOf(i));
-
   }
 
-
   public void actionPerformed(ActionEvent evt)
   {
+    AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+    Annotation[] anot = aa[activeRow].annotations;
 
-    AlignmentAnnotation [] aa = av.alignment.getAlignmentAnnotation();
-    Annotation [] anot = aa[activeRow].annotations;
-
-    if(evt.getActionCommand().equals(REMOVE))
+    if (evt.getActionCommand().equals(REMOVE))
     {
-      for(int i=0; i<activeRes.size(); i++)
+      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))
+    else if (evt.getActionCommand().equals(LABEL))
     {
-      String label = JOptionPane.showInputDialog(this, "Enter Label ", "Enter label", JOptionPane.QUESTION_MESSAGE );
-      if(label==null)
+      String label = JOptionPane.showInputDialog(this, "Enter Label ",
+                                                 "Enter label",
+                                                 JOptionPane.QUESTION_MESSAGE);
+
+      if (label == null)
+      {
         label = "";
+      }
 
-      if(label.length()>0 && !aa[activeRow].hasText)
-       aa[activeRow].hasText = true;
+      if ( (label.length() > 0) && !aa[activeRow].hasText)
+      {
+        aa[activeRow].hasText = true;
+      }
 
-      for(int i=0; i<activeRes.size(); i++)
+      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);
+
+        if (anot[index] == null)
+        {
+          anot[index] = new Annotation(label, "", ' ', 0);
+        }
+
         anot[index].displayCharacter = label;
       }
     }
-    else if(evt.getActionCommand().equals(COLOUR))
+    else if (evt.getActionCommand().equals(COLOUR))
     {
-     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;
-     }
+      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;
+      }
     }
     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";
-    }
+      char type = 0;
+      String symbol = "\u03B1";
 
-    if(!aa[activeRow].hasIcons)
-      aa[activeRow].hasIcons = true;
+      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)
-       label="";
+      String label = JOptionPane.showInputDialog(
+          "Enter a label for the structure?",
+          symbol);
 
-    if(label.length()>0 && !aa[activeRow].hasText)
-       aa[activeRow].hasText = true;
+      if (label == null)
+      {
+        label = "";
+      }
 
-    for(int i=0; i<activeRes.size(); i++)
-    {
-      int index = Integer.parseInt(activeRes.get(i).toString());
-      if (anot[index] == null)
+      if ( (label.length() > 0) && !aa[activeRow].hasText)
       {
-        anot[index] = new Annotation(label, "", type, 0);
+        aa[activeRow].hasText = true;
       }
 
-        anot[ index ].secondaryStructure = type;
-        anot[ index ].displayCharacter = label;
-    }
+      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, "", type, 0);
+        }
+
+        anot[index].secondaryStructure = type;
+        anot[index].displayCharacter = label;
+      }
     }
 
     adjustPanelHeight();
     activeRes = null;
     repaint();
-    return;
-
 
+    return;
   }
 
   public void mousePressed(MouseEvent evt)
   {
     if (SwingUtilities.isRightMouseButton(evt))
     {
-      if(activeRes==null)
+      if (activeRes == null)
+      {
         return;
+      }
 
       JPopupMenu pop = new JPopupMenu("Structure type");
       JMenuItem item = new JMenuItem(HELIX);
@@ -218,358 +283,481 @@ public class AnnotationPanel extends JPanel implements MouseListener, MouseMotio
       item.addActionListener(this);
       pop.add(item);
       pop.show(this, evt.getX(), evt.getY());
+
       return;
     }
 
+    AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
 
-    AlignmentAnnotation [] aa = av.alignment.getAlignmentAnnotation();
-    if(aa==null)
+    if (aa == null)
+    {
       return;
+    }
 
     int height = 0;
     activeRow = -1;
-    for(int i=0; i<aa.length; i++)
+
+    for (int i = 0; i < aa.length; i++)
     {
-      height+= aa[i].height;
+      height += aa[i].height;
 
-      if(evt.getY()<height)
+      if (evt.getY() < height)
       {
-        if(!aa[i].editable)
+        if (!aa[i].editable)
         {
           activeRes = null;
+
           continue;
         }
 
         activeRow = i;
+
         break;
       }
     }
 
+    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
 
-    int res = evt.getX() / av.getCharWidth() + av.getStartRes();
-
-    if(evt.isControlDown() || evt.isAltDown())
+    if (evt.isControlDown() || evt.isAltDown())
+    {
       addEditableColumn(res);
-
-    else if(evt.isShiftDown())
+    }
+    else if (evt.isShiftDown())
     {
-
-      if(activeRes==null)
-        activeRes=new ArrayList();
+      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 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);
+        }
       }
     }
     else
     {
-        activeRes = new ArrayList();
-        activeRes.add( String.valueOf(res) );
+      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)
+
+    AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+
+    if (aa == null)
+    {
       return;
+    }
 
     int row = -1;
-    int height=0;
-    for(int i=0; i<aa.length; i++)
-    {
+    int height = 0;
 
-      if( aa[i].visible )
+    for (int i = 0; i < aa.length; i++)
+    {
+      if (aa[i].visible)
+      {
         height += aa[i].height;
+      }
 
-      if(evt.getY()<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)
+    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+
+    if ( (row > -1) && (res < aa[row].annotations.length) &&
+        (aa[row].annotations[res] != null))
+    {
       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());
+    }
   }
-  public void mouseClicked(MouseEvent evt) {}
 
+  public void mouseClicked(MouseEvent evt)
+  {
+  }
 
   public void paintComponent(Graphics g)
   {
     g.setColor(Color.white);
-    g.fillRect(0,0,getWidth(), getHeight());
+    g.fillRect(0, 0, getWidth(), getHeight());
 
-    if(fastPaint)
+    if (fastPaint)
     {
       g.drawImage(image, 0, 0, this);
       fastPaint = false;
+
       return;
     }
 
-    imgWidth = (av.endRes-av.startRes+1) *av.charWidth;
+    imgWidth = (av.endRes - av.startRes + 1) * av.charWidth;
 
-    image = new BufferedImage(imgWidth,
-                                ap.annotationPanel.getHeight(),
-                                BufferedImage.TYPE_INT_RGB);
-      gg = (Graphics2D) image.getGraphics();
-      gg.setColor(Color.white);
-      gg.fillRect(0, 0, imgWidth, getHeight());
-      gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
-                          RenderingHints.VALUE_ANTIALIAS_ON);
-      fm = gg.getFontMetrics();
-      gg.setFont(av.getFont());
+    image = new BufferedImage(imgWidth, ap.annotationPanel.getHeight(),
+                              BufferedImage.TYPE_INT_RGB);
+    gg = (Graphics2D) image.getGraphics();
+    gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+                        RenderingHints.VALUE_ANTIALIAS_ON);
 
+    gg.setFont(av.getFont());
+    fm = gg.getFontMetrics();
 
-    drawComponent( gg, av.startRes, av.endRes+1);
-    g.drawImage( image, 0, 0, this);
+    drawComponent(gg, av.startRes, av.endRes + 1);
+    g.drawImage(image, 0, 0, this);
   }
 
   public void fastPaint(int horizontal)
-{
-  if(image==null || horizontal ==0)
   {
-    repaint();
-    return;
-  }
+    if ( (horizontal == 0) ||
+        (av.alignment.getAlignmentAnnotation() == null) ||
+        (av.alignment.getAlignmentAnnotation().length < 1))
+    {
+      repaint();
 
-  gg.copyArea( 0,0, imgWidth, getHeight(), -horizontal*av.charWidth, 0 );
-  int sr=av.startRes, er=av.endRes+1, transX=0;
+      return;
+    }
 
-  if(horizontal>0) // scrollbar pulled right, image to the left
-  {
-    transX =  (er-sr-horizontal)*av.charWidth;
-    sr = er - horizontal ;
-  }
-  else if(horizontal<0)
-  {
-    er = sr-horizontal;
-  }
+    gg.copyArea(0, 0, imgWidth, getHeight(), -horizontal * av.charWidth, 0);
 
+    int sr = av.startRes;
+    int er = av.endRes + 1;
+    int 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();
+  }
 
   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.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);
+      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 j;
+    int x = 0;
+    int 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++)
+    for (int i = 0; i < aa.length; i++)
     {
       AlignmentAnnotation row = aa[i];
-      if(!row.visible)
+
+      if (!row.visible)
+      {
         continue;
+      }
 
-      if(row.isGraph)
+      if (row.isGraph)
       {
         // 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++)
+      for (j = startRes; j < endRes; j++)
       {
-        validRes = row.annotations[j]==null?false:true;
-
-       x = (j-startRes)*av.charWidth;
+        if ( (row.annotations.length <= j) ||
+            (row.annotations[j] == null))
+        {
+          validRes = false;
+        }
+        else
+        {
+          validRes = true;
+        }
 
+        x = (j - startRes) * av.charWidth;
 
-       if(activeRow==i)
-       {
+        if (activeRow == i)
+        {
+          g.setColor(Color.red);
 
-         g.setColor(Color.red);
+          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);
+              }
+            }
+          }
+        }
 
-         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);
-           }
-       }
+        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);
+          }
 
+          if (!row.hasIcons)
+          {
+            g.drawString(row.annotations[j].displayCharacter,
+                         x + charOffset, y + iconOffset + 2);
+          }
+        }
 
-       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[j].secondaryStructure != lastSS[i]))
           {
-            if (row.annotations[0].secondaryStructure == 'H'
-                || row.annotations[0].secondaryStructure == 'E')
-              g.drawString(row.annotations[j].displayCharacter, x,
-                           y + iconOffset + 2);
+            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;
           }
-         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 (validRes && row.isGraph)
+        {
+          g.setColor(new Color(0, 0, 180));
 
-        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;
-       }
-
-       if (validRes && row.isGraph)
-       {
-         g.setColor(new Color(0,0,180));
-         int height = (int)((row.annotations[j].value / row.graphMax)*GRAPH_HEIGHT);
-
-         if(row.windowLength>1)
-         {
-           int total =0;
-           for(int i2=j- (row.windowLength/2); i2<j+(row.windowLength/2); i2++)
-           {
-             if(i2<0 || i2>=av.alignment.getWidth())
-               continue;
-
-             total += row.annotations[i2].value;
-           }
-
-           total/=row.windowLength;
-           height = (int)( (total / row.graphMax) *GRAPH_HEIGHT);
-
-         }
-
-         g.fillRect(x, y-height, av.charWidth, height );
-       }
+          int height = (int) ( (row.annotations[j].value / row.graphMax) *
+                              GRAPH_HEIGHT);
+
+          if (row.windowLength > 1)
+          {
+            int total = 0;
 
+            for (int i2 = j - (row.windowLength / 2);
+                 i2 < (j + (row.windowLength / 2)); i2++)
+            {
+              if ( (i2 < 0) || (i2 >= av.alignment.getWidth()))
+              {
+                continue;
+              }
+
+              total += row.annotations[i2].value;
+            }
+
+            total /= row.windowLength;
+            height = (int) ( (total / row.graphMax) * GRAPH_HEIGHT);
+          }
 
+          g.setColor(row.annotations[j].colour);
+          g.fillRect(x, y - height, av.charWidth, height);
+        }
       }
 
-      x+=av.charWidth;
+      x += av.charWidth;
 
-      if(row.hasIcons)
-      switch (lastSS[i])
+      if (row.hasIcons)
       {
-        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;
+        switch (lastSS[i])
+        {
+          case 'H':
+            g.setColor(HELIX_COLOUR);
+            g.fillRoundRect(lastSSX[i], y + 4 + iconOffset,
+                            x - lastSSX[i], 7, 8, 8);
+
+            break;
+
+          case 'E':
+            g.setColor(SHEET_COLOUR);
+            g.fillRect(lastSSX[i], y + 4 + iconOffset,
+                       x - lastSSX[i] - 4, 7);
+            g.fillPolygon(new int[]
+                          {x - 4, x - 4, x},
+                          new int[]
+                          {
+                          y + iconOffset, y + 14 + iconOffset,
+                          y + 7 + iconOffset
+            }, 3);
+
+            break;
+
+          case 'C':
+            break;
+
+          default:
+            g.setColor(Color.gray);
+            g.fillRect(lastSSX[i], y + 6 + iconOffset, x - lastSSX[i], 2);
+
+            break;
+        }
+      }
 
+      if (row.isGraph && row.hasText)
+      {
+        y += av.charHeight;
       }
 
-       if(row.isGraph && row.hasText)
-         y+=av.charHeight;
-       if(!row.isGraph)
-          y+=aa[i].height;
+      if (!row.isGraph)
+      {
+        y += aa[i].height;
+      }
     }
   }
 
   // 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)
   {
     g.setColor(Color.white);
-    g.fillRect(0,0,width, y);
-    g.setColor(new Color(0,0,180));
+    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++)
+
+    for (int j = 0; j < aa.annotations.length; j++)
     {
       g.setColor(new Color(0, 0, 180));
-      int height = (int) ( (aa.annotations[j].value / aa.graphMax) * GRAPH_HEIGHT );
+
+      int height = (int) ( (aa.annotations[j].value / aa.graphMax) *
+                          GRAPH_HEIGHT);
       g.fillRect(x, y - height, av.charWidth, height);
-      x+=av.charWidth;
+      x += av.charWidth;
     }
   }
 }