X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=ecd9370f6e1151508177fe5a8b9929223334a599;hb=f441357783f32298b738d32d5c87000ac0e33768;hp=232a60c14ab05425c511f8858165c751de84f38c;hpb=8dea1b9fa230ed6570f38a756b38c21af0e874c2;p=jalview.git

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 232a60c..ecd9370 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -51,7 +51,6 @@ public class AnnotationPanel extends JPanel implements MouseListener,
     BufferedImage image;
     Graphics2D gg;
     FontMetrics fm;
-    boolean validCharWidth;
     int imgWidth = 0;
     boolean fastPaint = false;
 
@@ -62,6 +61,8 @@ public class AnnotationPanel extends JPanel implements MouseListener,
     int max; //used by mouseDragged to see if user
     boolean mouseDragging = false;
 
+    boolean MAC = false;
+
     /**
      * Creates a new AnnotationPanel object.
      *
@@ -69,6 +70,10 @@ public class AnnotationPanel extends JPanel implements MouseListener,
      */
     public AnnotationPanel(AlignmentPanel ap)
     {
+
+    if(System.getProperty("os.name").startsWith("Mac"))
+      MAC = true;
+
         ToolTipManager.sharedInstance().registerComponent(this);
         ToolTipManager.sharedInstance().setInitialDelay(0);
         ToolTipManager.sharedInstance().setDismissDelay(10000);
@@ -643,7 +648,6 @@ public class AnnotationPanel extends JPanel implements MouseListener,
       if (fm == null)
         fm = g.getFontMetrics();
 
-      validCharWidth = fm.charWidth('M') <= av.charWidth;
 
         g.setColor(Color.white);
         g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight());
@@ -654,8 +658,8 @@ public class AnnotationPanel extends JPanel implements MouseListener,
             g.setColor(Color.white);
             g.fillRect(0, 0, getWidth(), getHeight());
             g.setColor(Color.black);
-            if(validCharWidth)
-            g.drawString("Alignment has no annotations", 20, 15);
+            if(av.validCharWidth)
+              g.drawString("Alignment has no annotations", 20, 15);
 
             return;
         }
@@ -753,7 +757,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                     }
                 }
 
-                if (validCharWidth && validRes &&
+                if (av.validCharWidth && validRes &&
                         (row.annotations[column].displayCharacter.length() > 0))
                 {
 
@@ -789,36 +793,46 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                         {
                         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) ;
+                             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;
@@ -856,39 +870,49 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                 {
                 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) ;
+                   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,
@@ -903,7 +927,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 
 
                 default:
-                    g.setColor(Color.ORANGE);
+                    g.setColor(Color.gray);
                     if(!av.wrapAlignment || endRes==av.endRes)
                       g.fillRect(lastSSX, y + 6 + iconOffset, x - lastSSX, 2);
 
@@ -974,7 +998,6 @@ public class AnnotationPanel extends JPanel implements MouseListener,
       if(sRes>aa.annotations.length)
         return;
 
-      eRes = Math.min(eRes, aa.annotations.length);
 
       int x = 0;
 
@@ -982,6 +1005,8 @@ public class AnnotationPanel extends JPanel implements MouseListener,
       if(eRes<av.endRes)
         eRes++;
 
+      eRes = Math.min(eRes, aa.annotations.length);
+
       if(sRes==0)
       {
         sRes++;
@@ -993,7 +1018,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 
       ////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+1)*av.charWidth,y2);
@@ -1021,9 +1046,11 @@ public class AnnotationPanel extends JPanel implements MouseListener,
           continue;
         }
 
+
           g.setColor(aa.annotations[column].colour);
           y1 = y - (int) (((aa.annotations[column-1].value-min) / range) * graphHeight);
           y2 = y - (int) (((aa.annotations[column].value-min) / range) * graphHeight);
+
           g.drawLine(x-av.charWidth/2, y1, x+av.charWidth/2, y2);
           x += av.charWidth;
 
@@ -1062,7 +1089,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
       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);