X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=5f0d3c88798bd7d80aa60d6dd0cda7d7cacbe87c;hb=246746e55bd02c66746d5cd872f49890cbae206a;hp=4f984fd1e6a7ea091ceedb36ea5b201f6137a5d3;hpb=6df80899bb3100cd38064c62cda5a2bb85b4528d;p=jalview.git

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 4f984fd..5f0d3c8 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -92,6 +92,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
     public void adjustPanelHeight()
     {
         // setHeight of panels
+        image = null;
         AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
         int height = 0;
 
@@ -147,6 +148,8 @@ public class AnnotationPanel extends JPanel implements MouseListener,
         if (activeRow == -1)
         {
             AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+            if(aa==null)
+              return;
 
             for (int j = 0; j < aa.length; j++)
             {
@@ -177,6 +180,8 @@ public class AnnotationPanel extends JPanel implements MouseListener,
         if (activeRow == -1)
         {
             AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+            if(aa==null)
+              return;
 
             for (int j = 0; j < aa.length; j++)
             {
@@ -332,7 +337,10 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 
         for (int i = 0; i < aa.length; i++)
         {
-            height += aa[i].height;
+            if (aa[i].visible)
+            {
+              height += aa[i].height;
+            }
 
             if (evt.getY() < height)
             {
@@ -531,24 +539,18 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 
       imgWidth = (av.endRes - av.startRes + 1) * av.charWidth;
 
-      if (image != null && imgWidth == image.getWidth())
+      if (image == null || imgWidth != image.getWidth())
       {
-        //This will be called by a mouse over, tool tip etc
-        // no need to redraw whole image
-        g.drawImage(image, 0, 0, this);
-        fastPaint = false;
-        return;
+        image = new BufferedImage(imgWidth, ap.annotationPanel.getHeight(),
+                                  BufferedImage.TYPE_INT_RGB);
+        gg = (Graphics2D) image.getGraphics();
+        gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+                            RenderingHints.VALUE_ANTIALIAS_ON);
+
+        gg.setFont(av.getFont());
+        fm = gg.getFontMetrics();
       }
 
-      image = new BufferedImage(imgWidth, ap.annotationPanel.getHeight(),
-                                BufferedImage.TYPE_INT_RGB);
-      gg = (Graphics2D) image.getGraphics();
-      gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
-                          RenderingHints.VALUE_ANTIALIAS_ON);
-
-      gg.setFont(av.getFont());
-      fm = gg.getFontMetrics();
-
       drawComponent(gg, av.startRes, av.endRes + 1);
       g.drawImage(image, 0, 0, this);
     }
@@ -640,6 +642,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                 continue;
             }
 
+
             if (row.isGraph)
             {
                 // this is so that we draw the characters below the graph
@@ -847,19 +850,23 @@ public class AnnotationPanel extends JPanel implements MouseListener,
     }
 
     // used by overview window
-    public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, int y)
+    public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, int y, int sRes, int eRes)
     {
         g.setColor(Color.white);
         g.fillRect(0, 0, width, y);
         g.setColor(new Color(0, 0, 180));
 
-        int x = 0;
 
-        for (int j = 0; j < aa.annotations.length; j++)
+        int x = 0, height;
+
+        for (int j = sRes; j < eRes; j++)
         {
             g.setColor(new Color(0, 0, 180));
 
-            int height = (int) ((aa.annotations[j].value / aa.graphMax) * GRAPH_HEIGHT);
+            height = (int) ((aa.annotations[j].value / aa.graphMax) * GRAPH_HEIGHT);
+            if(height>y)
+              height = y;
+
             g.fillRect(x, y - height, av.charWidth, height);
             x += av.charWidth;
         }