X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FPileUpfile.java;h=f7f718b0d34b73c8d3d65a4ddb84d1f934fce25b;hb=be762d8d9c71a7aa3121e845c45911c7192b7827;hp=7b5ce0d3cca1e8ee312bcbfc79b4659b633d862b;hpb=e327ac5df98f528afeb347ac9a79085ad0d0975b;p=jalview.git

diff --git a/src/jalview/io/PileUpfile.java b/src/jalview/io/PileUpfile.java
index 7b5ce0d..f7f718b 100755
--- a/src/jalview/io/PileUpfile.java
+++ b/src/jalview/io/PileUpfile.java
@@ -92,7 +92,7 @@ public class PileUpfile extends MSFfile
       i++;
     }
 
-    out.append("   MSF: " + s[0].getSequence().length
+    out.append("   MSF: " + s[0].getLength()
             + "   Type: P    Check:  " + bigChecksum % 10000 + "   ..");
     out.append(newline);
     out.append(newline);
@@ -151,8 +151,8 @@ public class PileUpfile extends MSFfile
           int start = (i * 50) + (k * 10);
           int end = start + 10;
 
-          if ((end < s[j].getSequence().length)
-                  && (start < s[j].getSequence().length))
+          int length = s[j].getLength();
+          if ((end < length) && (start < length))
           {
             out.append(s[j].getSequence(start, end));
 
@@ -167,7 +167,7 @@ public class PileUpfile extends MSFfile
           }
           else
           {
-            if (start < s[j].getSequence().length)
+            if (start < length)
             {
               out.append(s[j].getSequenceAsString().substring(start));
               out.append(newline);