X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=d35cbe851af4a23ed6033ae791fb8f87c9968164;hb=44d9bd9b511490baec5302be3b7756be0adebde3;hp=cc5d760532264f639847d70ff24264e640683f83;hpb=28c732f6b0a3a43029bcc529fef8ac1174befa69;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index cc5d760..d35cbe8 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -144,19 +144,18 @@ public class Sequence implements SequenceI
 
     while (i< sequence.length() && j <= end && j <= pos) {
 
-      String s = sequence.substring(i,i+1);
+      char c = sequence.charAt(i);
 
-      if (!(s.equals(".") || s.equals("-") || s.equals(" "))) {
+      if (!jalview.util.Comparison.isGap((c)))
         j++;
-      }
+
       i++;
     }
-    if (j == end && j < pos) {
+    if (j == end && j < pos)
       return end+1;
-    } else {
-
+    else
       return i;
-    }
+
   }
 
   public int findPosition(int i) {
@@ -164,12 +163,13 @@ public class Sequence implements SequenceI
     int j   = 0;
     int pos = start;
 
-    while (j < i) {
-      String s = sequence.substring(j,j+1);
+    while (j < i)
+    {
+      char c = sequence.charAt(j);
 
-      if (!(s.equals(".") || s.equals("-") || s.equals(" "))) {
+      if (!jalview.util.Comparison.isGap((c)))
         pos++;
-      }
+
       j++;
     }
     return pos;