From 4675978613749be5019b17c34c0a918631502512 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 28 Apr 2006 17:07:13 +0000
Subject: [PATCH] Helix sizes

---
 src/jalview/gui/AnnotationPanel.java |   22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 8ee0729..f64843a 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -794,29 +794,29 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                            if(row.annotations[sCol-1]==null ||
                               row.annotations[sCol-1].secondaryStructure!='H')
                            {
-                             g.fillArc(lastSSX, y+4+iconOffset, av.charWidth, 8, 90,180) ;
+                             g.fillArc(lastSSX, y+4+iconOffset, av.charWidth+1, 7, 90,180) ;
                              x1 += av.charWidth/2;
                            }
 
                             if(row.annotations[column]==null ||
                                row.annotations[column].secondaryStructure!='H')
                             {
-                              g.fillArc(x-av.charWidth, y+4+iconOffset, av.charWidth, 8, 270,180);
+                              g.fillArc(x-av.charWidth, y+4+iconOffset, av.charWidth, 7, 270,180);
                               x2 -= av.charWidth/2;
                             }
 
-                            g.fillRect(x1, y+4+iconOffset, x2-x1, 8);
+                            g.fillRect(x1, y+4+iconOffset, x2-x1+1, 7);
                             break;
 
                         case 'E':
                             g.setColor(SHEET_COLOUR);
                             g.fillRect(lastSSX, y + 4 + iconOffset,
                                 x - lastSSX - 4, 7);
-                            g.fillPolygon(new int[] { x - 4, x - 4, x },
+                            g.fillPolygon(new int[] { x - 5, x - 5, x },
                                 new int[]
                                 {
                                     y + iconOffset, y + 14 + iconOffset,
-                                    y + 8 + iconOffset
+                                    y + 7 + iconOffset
                                 }, 3);
 
                             break;
@@ -862,31 +862,31 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                  if(row.annotations[sCol-1]==null ||
                     row.annotations[sCol-1].secondaryStructure!='H')
                  {
-                   g.fillArc(lastSSX, y+4+iconOffset, av.charWidth, 8, 90,180) ;
+                   g.fillArc(lastSSX, y+4+iconOffset, av.charWidth+1, 7, 90,180) ;
                    x1 += av.charWidth/2;
                  }
 
                   if(row.annotations[column]==null ||
                      row.annotations[column].secondaryStructure!='H')
                   {
-                    g.fillArc(x-av.charWidth, y+4+iconOffset, av.charWidth, 8, 270,180);
+                    g.fillArc(x-av.charWidth, y+4+iconOffset, av.charWidth, 7, 270,180);
                     x2 -= av.charWidth/2;
                   }
 
-                  g.fillRect(x1, y+4+iconOffset, x2-x1, 8);
+                  g.fillRect(x1, y+4+iconOffset, x2-x1+1, 7);
 
                     break;
 
                 case 'E':
                     g.setColor(SHEET_COLOUR);
 
-                    if (row.annotations[endRes] !=null
-                        && row.annotations[endRes].secondaryStructure != 'E')
+                    if (row.annotations[endRes] ==null
+                        || row.annotations[endRes].secondaryStructure != 'E')
                     {
                       g.fillRect(lastSSX, y + 4 + iconOffset,
                                  x - lastSSX - 4, 7);
                       g.fillPolygon(new int[]
-                                    {x - 4, x - 4, x},
+                                    {x - 5, x - 5, x},
                                     new int[]
                                     {
                                     y + iconOffset, y + 14 + iconOffset,
-- 
1.7.10.2