X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FConservation.java;h=0aa980534ccd40e78a229de2a828564bf8415469;hb=23d3cb8d0e4c227224587135f41132d436dc1178;hp=b914108dbeb4428eb7eebf2f9d6263feaba02b17;hpb=db8b5a2bbc50c28300729664f5a586b08748bb55;p=jalview.git

diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index b914108..0aa9805 100755
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -165,7 +165,8 @@ public class Conservation
                     {
                         c = sequence.getCharAt(i);
 
-                        if(jalview.util.Comparison.isGap(c))
+                        // No need to check if its a '-'
+                        if(c == '.' || c==' ')
                           c = '-';
 
                         if ('a' <= c && c <= 'z')