X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=d97c80f78a0c5f0714f119bf97a9f067932ab88a;hb=783520af519c958e10a2af29f1d4242e1ab890a3;hp=9c2aac0967129359020e0964cbeb5cd74bee03c9;hpb=481f2cbd12ab5527f2d86bf9a08736f3d962cf19;p=jalview.git

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 9c2aac0..d97c80f 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -76,6 +76,12 @@ public class AnnotationPanel extends JPanel implements MouseListener,
         ap.annotationScroller.getVerticalScrollBar().addAdjustmentListener(this);
     }
 
+    public AnnotationPanel(AlignViewport av)
+    {
+      this.av = av;
+    }
+
+
     /**
      * DOCUMENT ME!
      *
@@ -89,7 +95,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
     /**
      * DOCUMENT ME!
      */
-    public void adjustPanelHeight()
+    public int adjustPanelHeight()
     {
         // setHeight of panels
         image = null;
@@ -136,6 +142,8 @@ public class AnnotationPanel extends JPanel implements MouseListener,
         }
 
         this.setPreferredSize(new Dimension(1, height));
+
+        return height;
     }
 
     /**
@@ -148,6 +156,8 @@ 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++)
             {
@@ -178,6 +188,8 @@ 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++)
             {
@@ -526,7 +538,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
       g.setColor(Color.white);
       g.fillRect(0, 0, getWidth(), getHeight());
 
-      if (fastPaint)
+      if (fastPaint && image!=null)
       {
         g.drawImage(image, 0, 0, this);
         fastPaint = false;
@@ -602,8 +614,14 @@ public class AnnotationPanel extends JPanel implements MouseListener,
      * @param startRes DOCUMENT ME!
      * @param endRes DOCUMENT ME!
      */
-    public void drawComponent(Graphics2D g, int startRes, int endRes)
+    public void drawComponent(Graphics g, int startRes, int endRes)
     {
+      g.setFont(av.getFont());
+
+      if (fm == null)
+        fm = g.getFontMetrics();
+
+
         g.setColor(Color.white);
         g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight());
 
@@ -852,13 +870,17 @@ public class AnnotationPanel extends JPanel implements MouseListener,
         g.fillRect(0, 0, width, y);
         g.setColor(new Color(0, 0, 180));
 
-        int x = 0;
+
+        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;
         }