consistent percentage gaps filter for conservation calculation.

[jalview.git] / src / jalview / gui / AnnotationPanel.java

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 48f9c20..420e369 100755 (executable)
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -336,21 +336,22 @@ public class AnnotationPanel extends JPanel implements MouseListener, MouseMotio
                                 ap.annotationPanel.getHeight(),\r
                                 BufferedImage.TYPE_INT_RGB);\r
       gg = (Graphics2D) image.getGraphics();\r
-      gg.setColor(Color.white);\r
-      gg.fillRect(0, 0, imgWidth, getHeight());\r
       gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
                           RenderingHints.VALUE_ANTIALIAS_ON);\r
       fm = gg.getFontMetrics();\r
       gg.setFont(av.getFont());\r
 \r
-\r
     drawComponent( gg, av.startRes, av.endRes+1);\r
     g.drawImage( image, 0, 0, this);\r
+\r
   }\r
 \r
   public void fastPaint(int horizontal)\r
 {\r
-  if(image==null || horizontal ==0)\r
+  if( horizontal == 0\r
+     || av.alignment.getAlignmentAnnotation()==null\r
+     || av.alignment.getAlignmentAnnotation().length<1\r
+    )\r
   {\r
     repaint();\r
     return;\r
@@ -387,6 +388,8 @@ public class AnnotationPanel extends JPanel implements MouseListener, MouseMotio
     g.fillRect(0,0,(endRes-startRes) *av.charWidth, getHeight());\r
     if(av.alignment.getAlignmentAnnotation()==null || av.alignment.getAlignmentAnnotation().length<1)\r
     {\r
+      g.setColor(Color.white);\r
+      g.fillRect(0,0,getWidth(), getHeight());\r
       g.setColor(Color.black);\r
       g.drawString("Alignment has no annotations",20,15);\r
       return;\r
@@ -400,6 +403,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, MouseMotio
     int iconOffset = av.charHeight/2;\r
     boolean validRes = false;\r
     //\u03B2 \u03B1\r
+\r
     for(int i=0; i<aa.length; i++)\r
     {\r
       AlignmentAnnotation row = aa[i];\r
@@ -516,7 +520,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, MouseMotio
            height = (int)( (total / row.graphMax) *GRAPH_HEIGHT);\r
 \r
          }\r
-\r
+         g.setColor(row.annotations[j].colour);\r
          g.fillRect(x, y-height, av.charWidth, height );\r
        }\r
 \r