X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationPanel.java;h=aef651161be4e7bf7f6670b520e872735f94e6b4;hb=08598b6cbefd6e268c20f7e5ca9785dd5e243a08;hp=afaf10fb4ce6721028d2a843754bd710160e7c94;hpb=cccf011180e8aab681c0c4617902d99435c6b7b4;p=jalview.git

diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java
index afaf10f..aef6511 100755
--- a/src/jalview/appletgui/AnnotationPanel.java
+++ b/src/jalview/appletgui/AnnotationPanel.java
@@ -1,22 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.appletgui;
 
 import java.util.*;
@@ -26,26 +25,37 @@ import java.awt.event.*;
 
 import jalview.datamodel.*;
 
-public class AnnotationPanel
-    extends Panel
-    implements AdjustmentListener, ActionListener, MouseListener, MouseMotionListener
+public class AnnotationPanel extends Panel implements AdjustmentListener,
+        ActionListener, MouseListener, MouseMotionListener
 {
   AlignViewport av;
+
   AlignmentPanel ap;
+
   int activeRow = -1;
 
   Vector activeRes;
+
   static String HELIX = "Helix";
+
   static String SHEET = "Sheet";
+
   static String LABEL = "Label";
+
   static String REMOVE = "Remove Annotation";
+
   static String COLOUR = "Colour";
+
   static Color HELIX_COLOUR = Color.red.darker();
+
   static Color SHEET_COLOUR = Color.green.darker().darker();
 
   Image image;
+
   Graphics gg;
+
   FontMetrics fm;
+
   int imgWidth = 0;
 
   boolean fastPaint = false;
@@ -56,11 +66,7 @@ public class AnnotationPanel
 
   public AnnotationPanel(AlignmentPanel ap)
   {
-    if (System.getProperty("os.name").startsWith("Mac"))
-    {
-      MAC = true;
-    }
-
+    MAC = new jalview.util.Platform().isAMac();
     this.ap = ap;
     av = ap.av;
     setLayout(null);
@@ -70,7 +76,6 @@ public class AnnotationPanel
 
     addMouseListener(this);
 
-
     // ap.annotationScroller.getVAdjustable().addAdjustmentListener( this );
   }
 
@@ -81,13 +86,14 @@ public class AnnotationPanel
 
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
-    ap.alabels.setScrollOffset( -evt.getValue());
+    ap.alabels.setScrollOffset(-evt.getValue());
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
+   * 
+   * @param evt
+   *                DOCUMENT ME!
    */
   public void actionPerformed(ActionEvent evt)
   {
@@ -104,10 +110,9 @@ public class AnnotationPanel
 
     String label = "";
     if (av.colSel != null && av.colSel.size() > 0
-        && anot[av.colSel.getMin()] != null)
+            && 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++)
@@ -124,7 +129,7 @@ public class AnnotationPanel
         return;
       }
 
-      if ( (label.length() > 0) && !aa[activeRow].hasText)
+      if ((label.length() > 0) && !aa[activeRow].hasText)
       {
         aa[activeRow].hasText = true;
       }
@@ -133,7 +138,7 @@ public class AnnotationPanel
       {
         int index = av.getColumnSelection().columnAt(i);
 
-        if(!av.colSel.isVisible(index))
+        if (!av.colSel.isVisible(index))
           continue;
 
         if (anot[index] == null)
@@ -146,9 +151,8 @@ public class AnnotationPanel
     }
     else if (evt.getActionCommand().equals(COLOUR))
     {
-      UserDefinedColours udc = new UserDefinedColours(
-          this,
-         Color.black, ap.alignFrame);
+      UserDefinedColours udc = new UserDefinedColours(this, Color.black,
+              ap.alignFrame);
 
       Color col = udc.getColor();
 
@@ -156,7 +160,7 @@ public class AnnotationPanel
       {
         int index = av.getColumnSelection().columnAt(i);
 
-        if(!av.colSel.isVisible(index))
+        if (!av.colSel.isVisible(index))
           continue;
 
         if (anot[index] == null)
@@ -167,7 +171,8 @@ public class AnnotationPanel
         anot[index].colour = col;
       }
     }
-    else // HELIX OR SHEET
+    else
+    // HELIX OR SHEET
     {
       char type = 0;
       String symbol = "\u03B1";
@@ -194,7 +199,7 @@ public class AnnotationPanel
         return;
       }
 
-      if ( (label.length() > 0) && !aa[activeRow].hasText)
+      if ((label.length() > 0) && !aa[activeRow].hasText)
       {
         aa[activeRow].hasText = true;
       }
@@ -203,7 +208,7 @@ public class AnnotationPanel
       {
         int index = av.getColumnSelection().columnAt(i);
 
-        if(!av.colSel.isVisible(index))
+        if (!av.colSel.isVisible(index))
           continue;
 
         if (anot[index] == null)
@@ -224,10 +229,10 @@ public class AnnotationPanel
 
   String enterLabel(String text, String label)
   {
-    EditNameDialog dialog = new EditNameDialog(text,null,label,null,
-        ap.alignFrame,"Enter Label", 400,200, true);
+    EditNameDialog dialog = new EditNameDialog(text, null, label, null,
+            ap.alignFrame, "Enter Label", 400, 200, true);
 
-    if(dialog.accept)
+    if (dialog.accept)
       return dialog.getName();
     else
       return null;
@@ -235,70 +240,69 @@ public class AnnotationPanel
 
   public void mousePressed(MouseEvent evt)
   {
-      AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
-      if (aa == null)
-      {
-        return;
-      }
-
-      int height = 0;
-      activeRow = -1;
+    AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+    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++)
+    {
+      if (aa[i].visible)
       {
-        if (aa[i].visible)
-        {
-          height += aa[i].height;
-        }
-
-        if (evt.getY() < height)
-        {
-          if (aa[i].editable)
-          {
-            activeRow = i;
-          }
-
-          break;
-        }
+        height += aa[i].height;
       }
 
-      if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK) ==
-        InputEvent.BUTTON3_MASK  && activeRow != -1)
+      if (evt.getY() < height)
       {
-        if (av.getColumnSelection() == null)
+        if (aa[i].editable)
         {
-          return;
+          activeRow = i;
         }
 
-        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;
+        break;
       }
+    }
 
-      if (aa == null)
+    if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK
+            && activeRow != -1)
+    {
+      if (av.getColumnSelection() == null)
       {
         return;
       }
 
-      ap.scalePanel.mousePressed(evt);
+      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)
@@ -307,7 +311,8 @@ public class AnnotationPanel
   }
 
   public void mouseClicked(MouseEvent evt)
-  {}
+  {
+  }
 
   public void mouseDragged(MouseEvent evt)
   {
@@ -346,7 +351,8 @@ public class AnnotationPanel
       res = av.getColumnSelection().adjustForHiddenColumns(res);
     }
 
-    if (row > -1 && res < aa[row].annotations.length && aa[row].annotations[res] != null)
+    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)
@@ -356,16 +362,17 @@ public class AnnotationPanel
       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
@@ -449,7 +456,6 @@ public class AnnotationPanel
     activeRes.addElement(String.valueOf(i));
   }
 
-
   public void update(Graphics g)
   {
     paint(g);
@@ -459,7 +465,7 @@ public class AnnotationPanel
   {
 
     imgWidth = getSize().width;
-    //(av.endRes - av.startRes + 1) * av.charWidth;
+    // (av.endRes - av.startRes + 1) * av.charWidth;
 
     if (image == null || imgWidth != image.getWidth(this))
     {
@@ -486,16 +492,15 @@ public class AnnotationPanel
 
   public void fastPaint(int horizontal)
   {
-    if (horizontal == 0
-        || av.alignment.getAlignmentAnnotation() == null
-        || av.alignment.getAlignmentAnnotation().length < 1
-        )
+    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);
+    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
@@ -512,7 +517,7 @@ public class AnnotationPanel
 
     drawComponent(gg, sr, er);
 
-    gg.translate( -transX, 0);
+    gg.translate(-transX, 0);
 
     fastPaint = true;
     repaint();
@@ -520,10 +525,13 @@ public class AnnotationPanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param g DOCUMENT ME!
-   * @param startRes DOCUMENT ME!
-   * @param endRes DOCUMENT ME!
+   * 
+   * @param g
+   *                DOCUMENT ME!
+   * @param startRes
+   *                DOCUMENT ME!
+   * @param endRes
+   *                DOCUMENT ME!
    */
   public void drawComponent(Graphics g, int startRes, int endRes)
   {
@@ -537,8 +545,8 @@ public class AnnotationPanel
       fm = g.getFontMetrics();
     }
 
-    if ( (av.alignment.getAlignmentAnnotation() == null) ||
-        (av.alignment.getAlignmentAnnotation().length < 1))
+    if ((av.alignment.getAlignmentAnnotation() == null)
+            || (av.alignment.getAlignmentAnnotation().length < 1))
     {
       g.setColor(Color.white);
       g.fillRect(0, 0, getSize().width, getSize().height);
@@ -560,10 +568,10 @@ public class AnnotationPanel
     int lastSSX;
     int iconOffset = av.charHeight / 2;
     boolean validRes = false;
-
+    boolean validEnd = false;
     boolean[] graphGroupDrawn = new boolean[aa.length];
 
-    //\u03B2 \u03B1
+    // \u03B2 \u03B1
     for (int i = 0; i < aa.length; i++)
     {
       AlignmentAnnotation row = aa[i];
@@ -606,7 +614,8 @@ public class AnnotationPanel
       {
         if (av.hasHiddenColumns)
         {
-          column = av.getColumnSelection().adjustForHiddenColumns(startRes + x);
+          column = av.getColumnSelection().adjustForHiddenColumns(
+                  startRes + x);
           if (column > row.annotations.length - 1)
           {
             break;
@@ -617,8 +626,8 @@ public class AnnotationPanel
           column = startRes + x;
         }
 
-        if ( (row.annotations.length <= column) ||
-            (row.annotations[column] == null))
+        if ((row.annotations.length <= column)
+                || (row.annotations[column] == null))
         {
           validRes = false;
         }
@@ -639,22 +648,26 @@ public class AnnotationPanel
 
               if (v == column)
               {
-                g.fillRect(x * av.charWidth, y,
-                           av.charWidth, av.charHeight);
+                g
+                        .fillRect(x * av.charWidth, y, av.charWidth,
+                                av.charHeight);
               }
             }
           }
         }
 
-
-
-        if (av.validCharWidth && validRes &&
-            (row.annotations[column].displayCharacter.length() > 0))
+        if (av.validCharWidth
+                && validRes
+                && (row.annotations[column].displayCharacter != null && row.annotations[column].displayCharacter
+                        .length() > 0))
         {
-          int charOffset = (av.charWidth -
-                            fm.charWidth(row.annotations[column].
-                                         displayCharacter.charAt(
-                                             0))) / 2;
+          int charOffset = (av.getCentreColumnLabels()) ? ((av.charWidth - fm
+                  .charsWidth(row.annotations[column].displayCharacter
+                          .toCharArray(), 0,
+                          row.annotations[column].displayCharacter.length())) / 2)
+                  : (av.charWidth - fm
+                          .charWidth(row.annotations[column].displayCharacter
+                                  .charAt(0))) / 2;
 
           if (row.annotations[column].colour == null)
             g.setColor(Color.black);
@@ -664,87 +677,78 @@ public class AnnotationPanel
           if (column == 0 || row.graph > 0)
           {
             g.drawString(row.annotations[column].displayCharacter,
-                         (x * av.charWidth) + charOffset,
-                         y + iconOffset + 3);
+                    (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 == ' ')))
+          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);
+                    (x * av.charWidth) + charOffset, y + iconOffset + 3);
           }
         }
 
         if (row.hasIcons)
         {
-          if (!validRes ||
-              (row.annotations[column].secondaryStructure != lastSS))
+          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);
+            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;
+              }
 
-              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);
+              int sCol = (lastSSX / av.charWidth) + startRes;
+              int x1 = lastSSX;
+              int x2 = (x * av.charWidth);
 
-                break;
+              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;
+              }
 
-              default:
-                g.setColor(Color.gray);
-                g.fillRect(lastSSX, y + 6 + iconOffset,
-                           (x * av.charWidth) - lastSSX, 2);
+              g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
+              break;
 
-                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)
@@ -767,84 +771,84 @@ public class AnnotationPanel
       if (column >= row.annotations.length)
       {
         column = row.annotations.length - 1;
+        validEnd = false;
+      }
+      else
+      {
+        validEnd = true;
       }
 
-      //  x ++;
+      // 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;
-            }
+        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);
+          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 (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;
-            }
+          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);
+          g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
 
-            break;
+          break;
 
-          case 'E':
-            g.setColor(SHEET_COLOUR);
+        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;
+          if (!validEnd || row.annotations[endRes] == null
+                  || row.annotations[endRes].secondaryStructure != 'E')
+          {
+            g.fillRect(lastSSX, y + 4 + iconOffset, (x * av.charWidth)
+                    - lastSSX - 4, 7);
+            g.fillPolygon(new int[]
+            { (x * av.charWidth) - 4, (x * av.charWidth) - 4,
+                (x * av.charWidth) }, new int[]
+            { y + iconOffset, y + 14 + iconOffset, y + 7 + iconOffset }, 3);
+          }
+          else
+          {
+            g.fillRect(lastSSX, y + 4 + iconOffset, x * av.charWidth
+                    - lastSSX, 7);
+          }
+          break;
 
-          default:
-            g.setColor(Color.gray);
-            if (!av.wrapAlignment || endRes == av.endRes)
-            {
-              g.fillRect(lastSSX, y + 6 + iconOffset,
-                         (x * av.charWidth) - lastSSX, 2);
-            }
+        default:
+          g.setColor(Color.gray);
+          if (!av.wrapAlignment || endRes == av.endRes)
+          {
+            g.fillRect(lastSSX, y + 6 + iconOffset, (x * av.charWidth)
+                    - lastSSX, 2);
+          }
 
-            break;
+          break;
         }
       }
 
@@ -881,9 +885,8 @@ public class AnnotationPanel
             {
               if (aa[gg].graphGroup == row.graphGroup)
               {
-                drawLineGraph(g, aa[gg], startRes, endRes, y,
-                              groupmin, groupmax,
-                              row.graphHeight);
+                drawLineGraph(g, aa[gg], startRes, endRes, y, groupmin,
+                        groupmax, row.graphHeight);
               }
             }
 
@@ -891,14 +894,14 @@ public class AnnotationPanel
           }
           else
           {
-            drawLineGraph(g, row, startRes, endRes,
-                          y, row.graphMin, row.graphMax, row.graphHeight);
+            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);
+          drawBarGraph(g, row, startRes, endRes, row.graphMin,
+                  row.graphMax, y);
         }
       }
 
@@ -914,11 +917,8 @@ public class AnnotationPanel
     }
   }
 
-  public void drawLineGraph(Graphics g, AlignmentAnnotation aa,
-                            int sRes, int eRes,
-                            int y,
-                            float min, float max,
-                            int graphHeight)
+  public void drawLineGraph(Graphics g, AlignmentAnnotation aa, int sRes,
+          int eRes, int y, float min, float max, int graphHeight)
   {
     if (sRes > aa.annotations.length)
     {
@@ -927,7 +927,7 @@ public class AnnotationPanel
 
     int x = 0;
 
-    //Adjustment for fastpaint to left
+    // Adjustment for fastpaint to left
     if (eRes < av.endRes)
     {
       eRes++;
@@ -938,10 +938,10 @@ public class AnnotationPanel
     int y1 = y, y2 = y;
     float range = max - min;
 
-    ////Draw origin
+    // //Draw origin
     if (min < 0)
     {
-      y2 = y - (int) ( (0 - min / range) * graphHeight);
+      y2 = y - (int) ((0 - min / range) * graphHeight);
     }
 
     g.setColor(Color.gray);
@@ -964,8 +964,9 @@ public class AnnotationPanel
       {
         break;
       }
-      
-      if (aa.annotations[column] == null) //  || coaa.annotations[column - 1] == null)
+
+      if (aa.annotations[column] == null) // || coaa.annotations[column - 1] ==
+                                          // null)
       {
         x++;
         continue;
@@ -975,19 +976,21 @@ public class AnnotationPanel
         g.setColor(Color.black);
       else
         g.setColor(aa.annotations[column].colour);
-      if (column==0 || aa.annotations[column-1]==null)
+      if (column == 0 || aa.annotations[column - 1] == null)
+      {
+        y1 = y
+                - (int) (((aa.annotations[column].value - min) / range) * graphHeight);
+      }
+      else
       {
-        y1 = y -
-        (int) ( ( (aa.annotations[column].value - min) / range) * graphHeight);
-      } else {
-        y1 = y -
-        (int) ( ( (aa.annotations[column-1].value - min) / range) * graphHeight);        
+        y1 = y
+                - (int) (((aa.annotations[column - 1].value - min) / range) * graphHeight);
       }
-      y2 = y -
-          (int) ( ( (aa.annotations[column].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);
+      g.drawLine(x * av.charWidth - av.charWidth / 2, y1, x * av.charWidth
+              + av.charWidth / 2, y2);
       x++;
     }
 
@@ -995,15 +998,13 @@ public class AnnotationPanel
     {
       g.setColor(aa.threshold.colour);
 
-      y2 = (int) (y - ( (aa.threshold.value - min) / range) * graphHeight);
+      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)
+  public void drawBarGraph(Graphics g, AlignmentAnnotation aa, int sRes,
+          int eRes, float min, float max, int y)
   {
     if (sRes > aa.annotations.length)
     {
@@ -1018,7 +1019,7 @@ public class AnnotationPanel
 
     if (min < 0)
     {
-      y2 = y - (int) ( (0 - min / (range)) * aa.graphHeight);
+      y2 = y - (int) ((0 - min / (range)) * aa.graphHeight);
     }
 
     g.setColor(Color.gray);
@@ -1052,8 +1053,8 @@ public class AnnotationPanel
       else
         g.setColor(aa.annotations[column].colour);
 
-      y1 = y -
-          (int) ( ( (aa.annotations[column].value - min) / (range)) * aa.graphHeight);
+      y1 = y
+              - (int) (((aa.annotations[column].value - min) / (range)) * aa.graphHeight);
 
       if (y1 - y2 > 0)
       {
@@ -1070,14 +1071,14 @@ public class AnnotationPanel
     if (aa.threshold != null)
     {
       g.setColor(aa.threshold.colour);
-      y2 = (int) (y - ( (aa.threshold.value - min) / range) * aa.graphHeight);
+      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,
-                        int sRes, int eRes)
+  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);
@@ -1093,7 +1094,7 @@ public class AnnotationPanel
       else
         g.setColor(aa.annotations[j].colour);
 
-      height = (int) ( (aa.annotations[j].value / aa.graphMax) * GRAPH_HEIGHT);
+      height = (int) ((aa.annotations[j].value / aa.graphMax) * GRAPH_HEIGHT);
       if (height > y)
       {
         height = y;