X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationPanel.java;h=71f51eaa1c165af833eab70fa4428d47383b1bb2;hb=e30c8f0736f711e2dc7c32680ac57a28c77d567d;hp=d9b8dd3ce3ada5ca36d901a1abaf006658a709a0;hpb=4e37dfef4e89b0f123a60dea64cf088cb80c5d89;p=jalview.git

diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java
index d9b8dd3..71f51ea 100755
--- a/src/jalview/appletgui/AnnotationPanel.java
+++ b/src/jalview/appletgui/AnnotationPanel.java
@@ -51,11 +51,16 @@ public class AnnotationPanel
 
   public static int GRAPH_HEIGHT = 40;
 
+  boolean MAC = false;
+
   public AnnotationPanel(AlignmentPanel ap)
   {
+    if (System.getProperty("os.name").startsWith("Mac"))
+      MAC = true;
+
     this.ap = ap;
     av = ap.av;
-    this.setLayout(null);
+    setLayout(null);
     adjustPanelHeight();
 
     addMouseMotionListener(new MouseMotionAdapter()
@@ -126,9 +131,6 @@ public class AnnotationPanel
     }
 
     this.setSize(getSize().width, height);
-    if(ap!=null)
-       ap.annotationScroller.setSize(getSize().width, height);
-
 
     repaint();
 
@@ -206,6 +208,8 @@ public class AnnotationPanel
 
   public void paint(Graphics g)
   {
+
+
     imgWidth = (av.endRes - av.startRes + 1) * av.charWidth;
 
     if (image == null || imgWidth != image.getWidth(this))
@@ -225,6 +229,8 @@ public class AnnotationPanel
     }
 
     drawComponent(gg, av.startRes, av.endRes + 1);
+    g.setColor(Color.white);
+    g.fillRect(0, 0, getSize().width, getSize().height);
     g.drawImage(image, 0, 0, this);
   }
 
@@ -286,14 +292,14 @@ public class AnnotationPanel
           g.setColor(Color.white);
           g.fillRect(0, 0, getSize().width, getSize().height);
           g.setColor(Color.black);
-          g.drawString("Alignment has no annotations", 20, 15);
+          if(av.validCharWidth)
+            g.drawString("Alignment has no annotations", 20, 15);
 
           return;
       }
 
       AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
 
-      int j;
       int x = 0;
       int y = 0;
       char lastSS;
@@ -356,8 +362,8 @@ public class AnnotationPanel
               x = (column - startRes) * av.charWidth;
 
 
-              if (validRes &&
-                      (row.annotations[column].displayCharacter.length() > 0))
+              if (av.validCharWidth && validRes &&
+                        (row.annotations[column].displayCharacter.length() > 0))
               {
                 int charOffset = (av.charWidth -
                     fm.charWidth(row.annotations[column].displayCharacter.charAt(
@@ -391,11 +397,21 @@ public class AnnotationPanel
                       {
                       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 - lastSSX, 7, 8, 8);
+                          break;
+                        }
+
                         int sCol = (lastSSX / av.charWidth) + startRes;
                         int x1 = lastSSX;
                         int x2 = x;
 
-                       if(row.annotations[sCol-1]==null ||
+                       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) ;
@@ -459,12 +475,22 @@ public class AnnotationPanel
               {
               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 - lastSSX, 7, 8, 8);
+                  break;
+                }
+
 
                 int sCol = (lastSSX / av.charWidth) + startRes;
                 int x1 = lastSSX;
                 int x2 = x;
 
-               if(row.annotations[sCol-1]==null ||
+               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) ;
@@ -577,7 +603,6 @@ public class AnnotationPanel
       return;
 
 
-    eRes = Math.min(eRes, aa.annotations.length);
 
     int x = 0;
 
@@ -585,6 +610,9 @@ public class AnnotationPanel
     if(eRes<av.endRes)
       eRes++;
 
+    eRes = Math.min(eRes, aa.annotations.length);
+
+
     if(sRes==0)
     {
       sRes++;
@@ -596,7 +624,7 @@ public class AnnotationPanel
 
     ////Draw origin
     if(min<0)
-      y2 = (int)(y - (0-min / range)*graphHeight);
+      y2 = y - (int)((0-min / range)*graphHeight);
 
     g.setColor(Color.gray);
     g.drawLine(x-av.charWidth,y2,(eRes-sRes)*av.charWidth,y2);
@@ -644,7 +672,7 @@ public class AnnotationPanel
     y1 = y2 = y;
 
     if(min<0)
-      y2 = (int)(y - (0-min / (range))*aa.graphHeight);
+      y2 = y -(int)( (0-min / (range))*aa.graphHeight);
 
     g.setColor(Color.gray);