X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=fc31fdfe8b2139db0627b5b51a33c26320b67ccd;hb=77dbfda22963c908129cae7947643ad5fce0caad;hp=6e38f1b9eabfb7788d78e4ecba5547283e7b7224;hpb=22be3f466cd70cb03d5eae619ede8589ae69716a;p=jalview.git

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index 6e38f1b..fc31fdf 100755
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -27,11 +27,17 @@ 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;
 
-      if(    (fstart>=start&&fstart<=end) || (fend>=start&&fend<=end))
+      if(   (fstart<=end && fend>=start)  )
       {
+        if(fstart<0) // fix for if the feature we have starts before the sequence start,
+          fstart = 0;// but the feature end is still valid!!
+
         if(fstart==fend)
         {
           g.setColor(Color.red);
@@ -49,18 +55,21 @@ 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;
             g.drawString(String.valueOf(s),
                          charOffset + x1 + width * (i-start),
                          y1 + height - pady);
-
           }
         }
       }