X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=fc31fdfe8b2139db0627b5b51a33c26320b67ccd;hb=e7ed63f1ea56432246a6ed1553f0fe56d26f56ea;hp=6a0daa8cd940ee49420eee283bcb5e6570ea2550;hpb=170c4f875570a1f17224b6cfea21ac696bfe3c6f;p=jalview.git

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index 6a0daa8..fc31fdf 100755
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -27,6 +27,9 @@ public class FeatureRenderer implements RendererI
     while( e.hasMoreElements() )
     {
       SequenceFeature sf = (SequenceFeature)e.nextElement();
+      if(sf.getStart()>seq.getEnd())
+        continue;
+
       int fstart = seq.findIndex(sf.getStart())-1;
       int fend = seq.findIndex(sf.getEnd())-1;
 
@@ -52,11 +55,15 @@ public class FeatureRenderer implements RendererI
         {
           for (int i = fstart; i <= fend; i++)
           {
+            char s = seq.getSequence().charAt(i);
+            if( jalview.util.Comparison.isGap(s) )
+              continue;
+
             g.setColor(Color.blue);
             g.fillRect( (i-start) * width, y1, width, height);
 
             g.setColor(Color.white);
-            char s = seq.getSequence().charAt(i);
+
             FontMetrics fm = g.getFontMetrics();
             int charOffset = (width - fm.charWidth(s)) / 2;
             int pady = height / 5;