X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FAnnotationRenderer.java;h=c6b95e4b9e6fa8c46dc7b035c8be2e8365be6c26;hb=a23cf1abf575cbcdbaf6f6948e8a2ee97f570244;hp=34df24f40ad9b6223883a3a7240fb7f43c711cf7;hpb=a70a2441205ea70ff3e2af71a3006fd85b4813cc;p=jalview.git

diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index 34df24f..c6b95e4 100644
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -876,7 +876,7 @@ public class AnnotationRenderer
 
         int profl[] = getProfileFor(aa, column);
         // just try to draw the logo if profl is not null
-        if (profl != null)
+        if (profl != null && profl[1] != 0)
         {
           float ht = normaliseProfile ? y - aa.graphHeight : y1;
           double htn = normaliseProfile ? aa.graphHeight : (y2 - y1);// aa.graphHeight;
@@ -928,7 +928,7 @@ public class AnnotationRenderer
               // g.drawRect(x*av.charWidth, (int)ht, av.charWidth,
               // (int)(scl));
               // g.setColor(profcolour.findColour(dc[0]).darker());
-              g.setColor(profcolour.findColour(dc[0]));
+              g.setColor(profcolour.findColour(dc[0], column));
 
               hght = (ht + (scl - lm.getDescent() - lm.getBaselineOffsets()[lm
                       .getBaselineIndex()]));