X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=d97c80f78a0c5f0714f119bf97a9f067932ab88a;hb=0705a85fe0a3d391e5aba360340a0c342c898366;hp=4d3fc0f98dfa2f9c096139ca496f301360156c87;hpb=50101c6da4cd0c6cd3d0438fa66905aae30b58b7;p=jalview.git

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 4d3fc0f..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!
      *
@@ -89,9 +95,10 @@ public class AnnotationPanel extends JPanel implements MouseListener,
     /**
      * DOCUMENT ME!
      */
-    public void adjustPanelHeight()
+    public int adjustPanelHeight()
     {
         // setHeight of panels
+        image = null;
         AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
         int height = 0;
 
@@ -135,6 +142,8 @@ public class AnnotationPanel extends JPanel implements MouseListener,
         }
 
         this.setPreferredSize(new Dimension(1, height));
+
+        return height;
     }
 
     /**
@@ -147,6 +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++)
             {
@@ -177,6 +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++)
             {
@@ -332,7 +345,10 @@ 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)
             {
@@ -519,29 +535,32 @@ public class AnnotationPanel extends JPanel implements MouseListener,
      */
     public void paintComponent(Graphics g)
     {
-        g.setColor(Color.white);
-        g.fillRect(0, 0, getWidth(), getHeight());
+      g.setColor(Color.white);
+      g.fillRect(0, 0, getWidth(), getHeight());
 
-        if (fastPaint)
-        {
-            g.drawImage(image, 0, 0, this);
-            fastPaint = false;
-
-            return;
-        }
+      if (fastPaint && image!=null)
+      {
+        g.drawImage(image, 0, 0, this);
+        fastPaint = false;
+        return;
+      }
 
-        imgWidth = (av.endRes - av.startRes + 1) * av.charWidth;
+      imgWidth = (av.endRes - av.startRes + 1) * av.charWidth;
 
+      if (image == null || imgWidth != image.getWidth())
+      {
         image = new BufferedImage(imgWidth, ap.annotationPanel.getHeight(),
-                BufferedImage.TYPE_INT_RGB);
+                                  BufferedImage.TYPE_INT_RGB);
         gg = (Graphics2D) image.getGraphics();
         gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
-            RenderingHints.VALUE_ANTIALIAS_ON);
+                            RenderingHints.VALUE_ANTIALIAS_ON);
 
         gg.setFont(av.getFont());
+        fm = gg.getFontMetrics();
+      }
 
-        drawComponent(gg, av.startRes, av.endRes + 1);
-        g.drawImage(image, 0, 0, this);
+      drawComponent(gg, av.startRes, av.endRes + 1);
+      g.drawImage(image, 0, 0, this);
     }
 
     /**
@@ -583,7 +602,9 @@ public class AnnotationPanel extends JPanel implements MouseListener,
         gg.translate(-transX, 0);
 
         fastPaint = true;
+
         repaint();
+
     }
 
     /**
@@ -593,11 +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)
     {
-      if(fm==null)
+      g.setFont(av.getFont());
+
+      if (fm == null)
         fm = g.getFontMetrics();
 
+
         g.setColor(Color.white);
         g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight());
 
@@ -632,6 +656,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                 continue;
             }
 
+
             if (row.isGraph)
             {
                 // this is so that we draw the characters below the graph
@@ -839,19 +864,23 @@ 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;
         }