Helix sizes

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