X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=bc14d6637284dff184512cc7a445598730c71b3c;hb=18b27ea838aeaca9964a46c9b833a47fbb372d3b;hp=b8570a9740ceedbc7827dd1a506edbb5c1d4277e;hpb=9fff97021c2c637e426f6971d54dcf3fd4191985;p=jalview.git

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index b8570a9..bc14d66 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)
             {
@@ -519,29 +527,32 @@ 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 +594,9 @@ public class AnnotationPanel extends JPanel implements MouseListener,
         gg.translate(-transX, 0);
 
         fastPaint = true;
+
         repaint();
+
     }
 
     /**
@@ -595,9 +608,12 @@ public class AnnotationPanel extends JPanel implements MouseListener,
      */
     public void drawComponent(Graphics2D g, int startRes, int endRes)
     {
-      if(fm==null)
+      if (fm == null)
         fm = g.getFontMetrics();
 
+		if(fm==null)
+			fm = g.getFontMetrics();
+
         g.setColor(Color.white);
         g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight());
 
@@ -632,6 +648,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                 continue;
             }
 
+
             if (row.isGraph)
             {
                 // this is so that we draw the characters below the graph
@@ -697,14 +714,14 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                     if (j == 0 || row.isGraph)
                     {
                         g.drawString(row.annotations[j].displayCharacter, x+charOffset,
-                            y + iconOffset + 2);
+                            y + iconOffset + 3);
                     }
                     else if (((row.annotations[j - 1] == null) ||
                             (row.annotations[j].displayCharacter != row.annotations[j -
                             1].displayCharacter)))
                     {
                         g.drawString(row.annotations[j].displayCharacter, x+charOffset,
-                            y + iconOffset + 2);
+                            y + iconOffset + 3);
                     }
                 }
 
@@ -839,19 +856,23 @@ 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;
         }