X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=fc31fdfe8b2139db0627b5b51a33c26320b67ccd;hb=6d5aff5f7ace98b6416c7e9dc2a8fdc6ad194902;hp=d21b39e433171a8ba1f6ae05496fe088ec7242d2;hpb=8c6a0091158548409984e31ffbb9d52516b95fa5;p=jalview.git

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index d21b39e..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;
 
@@ -52,20 +55,21 @@ public class FeatureRenderer implements RendererI
         {
           for (int i = fstart; i <= fend; i++)
           {
-           try{
-             g.setColor(Color.blue);
+            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;
             g.drawString(String.valueOf(s),
                          charOffset + x1 + width * (i-start),
                          y1 + height - pady);
-
-           }catch(Exception ex){System.out.println(i+" "+fstart+" "+fend+" " +sf.getDescription()+" "+seq.getName()+" "+seq.getLength()); }
           }
         }
       }