Helix glyphs fixed

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 1b4a230..3b0127d 100755 (executable)
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -51,6 +51,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
     BufferedImage image;\r
     Graphics2D gg;\r
     FontMetrics fm;\r
+    boolean validCharWidth;\r
     int imgWidth = 0;\r
     boolean fastPaint = false;\r
 \r
@@ -635,6 +636,8 @@ public class AnnotationPanel extends JPanel implements MouseListener,
      */\r
     public void drawComponent(Graphics g, int startRes, int endRes)\r
     {\r
+      validCharWidth = fm.charWidth('M') <= av.charWidth;\r
+\r
       g.setFont(av.getFont());\r
 \r
       if (fm == null)\r
@@ -644,12 +647,13 @@ public class AnnotationPanel extends JPanel implements MouseListener,
         g.setColor(Color.white);\r
         g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight());\r
 \r
-        if ((av.alignment.getAlignmentAnnotation() == null) ||\r
+        if ( (av.alignment.getAlignmentAnnotation() == null) ||\r
                 (av.alignment.getAlignmentAnnotation().length < 1))\r
         {\r
             g.setColor(Color.white);\r
             g.fillRect(0, 0, getWidth(), getHeight());\r
             g.setColor(Color.black);\r
+            if(validCharWidth)\r
             g.drawString("Alignment has no annotations", 20, 15);\r
 \r
             return;\r
@@ -705,20 +709,17 @@ public class AnnotationPanel extends JPanel implements MouseListener,
             }\r
 \r
             int column = startRes;\r
-            int yPos = startRes;\r
 \r
-            while (yPos < endRes)\r
+            while (column < endRes)\r
             {\r
               if (av.hasHiddenColumns)\r
               {\r
-                column = av.getColumnSelection().adjustForHiddenColumns(yPos);\r
+                column = av.getColumnSelection().adjustForHiddenColumns(column);\r
                 if (column > row.annotations.length-1)\r
                 {\r
                   break;\r
                 }\r
               }\r
-              else\r
-                column = yPos;\r
 \r
                 if ((row.annotations.length <= column) ||\r
                         (row.annotations[column] == null))\r
@@ -730,7 +731,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                     validRes = true;\r
                 }\r
 \r
-                x = (yPos - startRes) * av.charWidth;\r
+                x = (column - startRes) * av.charWidth;\r
 \r
                 if (activeRow == i)\r
                 {\r
@@ -751,7 +752,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                     }\r
                 }\r
 \r
-                if (validRes &&\r
+                if (validCharWidth && validRes &&\r
                         (row.annotations[column].displayCharacter.length() > 0))\r
                 {\r
 \r
@@ -765,10 +766,13 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                         g.drawString(row.annotations[column].displayCharacter, x+charOffset,\r
                             y + iconOffset + 3);\r
                     }\r
-                    else if (((row.annotations[column - 1] == null)\r
-                              ||\r
-                            (!row.annotations[column].displayCharacter.equals(\r
-                             row.annotations[column - 1].displayCharacter))))\r
+                    else if (\r
+                        row.annotations[column - 1] == null\r
+                        ||(!row.annotations[column].displayCharacter.equals(\r
+                            row.annotations[column - 1].displayCharacter)\r
+                        ||\r
+                  (row.annotations[column].displayCharacter.length() <2 &&\r
+                   row.annotations[column].secondaryStructure==' ')))\r
                     {\r
                         g.drawString(row.annotations[column].displayCharacter, x+charOffset,\r
                             y + iconOffset + 3);\r
@@ -784,9 +788,25 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                         {\r
                         case 'H':\r
                             g.setColor(HELIX_COLOUR);\r
-                            g.fillRoundRect(lastSSX, y + 4 + iconOffset,\r
-                                x - lastSSX, 7, 8, 8);\r
+                            int sCol = (lastSSX / av.charWidth) + startRes;\r
+                            int x1 = lastSSX;\r
+                            int x2 = x;\r
+\r
+                           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
+                             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
+                              x2 -= av.charWidth/2;\r
+                            }\r
 \r
+                            g.fillRect(x1, y+4+iconOffset, x2-x1, 8);\r
                             break;\r
 \r
                         case 'E':\r
@@ -824,7 +844,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                     }\r
                 }\r
 \r
-                yPos++;\r
+                column++;\r
             }\r
 \r
             x += av.charWidth;\r
@@ -834,9 +854,27 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                 switch (lastSS)\r
                 {\r
                 case 'H':\r
-                    g.setColor(HELIX_COLOUR);\r
-                    g.fillRoundRect(lastSSX, y + 4 + iconOffset,\r
-                        x - lastSSX, 7, 8, 8);\r
+                  g.setColor(HELIX_COLOUR);\r
+\r
+                  int sCol = (lastSSX / av.charWidth) + startRes;\r
+                  int x1 = lastSSX;\r
+                  int x2 = x;\r
+\r
+                 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
+                   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
+                    x2 -= av.charWidth/2;\r
+                  }\r
+\r
+                  g.fillRect(x1, y+4+iconOffset, x2-x1, 8);\r
 \r
                     break;\r
 \r
@@ -961,27 +999,23 @@ public class AnnotationPanel extends JPanel implements MouseListener,
       eRes = Math.min(eRes, aa.annotations.length);\r
 \r
       int column = sRes;\r
-      int yPos = sRes;\r
       int aaMax = aa.annotations.length-1;\r
 \r
-      while( yPos < eRes )\r
+      while( column < eRes )\r
       {\r
         if(av.hasHiddenColumns)\r
         {\r
-          column = av.getColumnSelection().adjustForHiddenColumns(yPos);\r
+          column = av.getColumnSelection().adjustForHiddenColumns(column);\r
           if(column > aaMax)\r
           {\r
             break;\r
           }\r
         }\r
-        else\r
-          column = yPos;\r
-\r
-        yPos ++;\r
 \r
         if(aa.annotations[column]==null || aa.annotations[column-1]==null)\r
         {\r
           x+=av.charWidth;\r
+          column ++;\r
           continue;\r
         }\r
 \r
@@ -990,6 +1024,9 @@ public class AnnotationPanel extends JPanel implements MouseListener,
           y2 = y - (int) (((aa.annotations[column].value-min) / range) * graphHeight);\r
           g.drawLine(x-av.charWidth/2, y1, x+av.charWidth/2, y2);\r
           x += av.charWidth;\r
+\r
+          column++;\r
+\r
        }\r
        if(aa.threshold!=null)\r
        {\r
@@ -1031,31 +1068,26 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 \r
 \r
       int column = sRes;\r
-      int yPos = sRes;\r
       int aaMax = aa.annotations.length-1;\r
 \r
-      while( yPos < eRes )\r
+      while( column < eRes )\r
       {\r
         if(av.hasHiddenColumns)\r
         {\r
-          column = av.getColumnSelection().adjustForHiddenColumns(yPos);\r
+          column = av.getColumnSelection().adjustForHiddenColumns(column);\r
           if(column > aaMax)\r
           {\r
             break;\r
           }\r
         }\r
-        else\r
-          column = yPos;\r
-\r
-        yPos ++;\r
 \r
         if (aa.annotations[column] == null)\r
         {\r
           x += av.charWidth;\r
+          column ++;\r
           continue;\r
         }\r
 \r
-\r
           g.setColor(aa.annotations[column].colour);\r
           y1 = y - (int) (((aa.annotations[column].value-min) / (range)) * aa.graphHeight);\r
 \r
@@ -1065,6 +1097,8 @@ public class AnnotationPanel extends JPanel implements MouseListener,
             g.fillRect(x, y1, av.charWidth, y2-y1 );\r
 \r
           x += av.charWidth;\r
+          column ++;\r
+\r
       }\r
       if(aa.threshold!=null)\r
       {\r