Merge branch 'develop' into features/JAL-2446NCList

[jalview.git] / src / jalview / io / PileUpfile.java

diff --git a/src/jalview/io/PileUpfile.java b/src/jalview/io/PileUpfile.java
index 7b5ce0d..f7f718b 100755 (executable)
--- 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);