X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FPhylipFile.java;h=539826ffb31d811c2a6e3e39a7219386ca7524cd;hb=08ea977287323e63781dddf6f461c0011833bcc2;hp=2a961a2a969e0caa8a39b73056245ee16111e407;hpb=3d0101179759ef157b088ea135423cd909512d9f;p=jalview.git

diff --git a/src/jalview/io/PhylipFile.java b/src/jalview/io/PhylipFile.java
index 2a961a2..539826f 100644
--- a/src/jalview/io/PhylipFile.java
+++ b/src/jalview/io/PhylipFile.java
@@ -248,7 +248,7 @@ public class PhylipFile extends AlignFile
     sb.append(" ");
     // if there are no sequences, then define the number of characters as 0
     sb.append(
-            (sqs.length > 0) ? Integer.toString(sqs[0].getSequence().length)
+(sqs.length > 0) ? Integer.toString(sqs[0].getLength())
                     : "0")
             .append(newline);
 
@@ -280,13 +280,13 @@ public class PhylipFile extends AlignFile
       // sequential has the entire sequence following the name
       if (sequential)
       {
-        sb.append(s.getSequence());
+        sb.append(s.getSequenceAsString());
       }
       else
       {
         // Jalview ensures all sequences are of same length so no need
         // to keep track of min/max length
-        sequenceLength = s.getSequence().length;
+        sequenceLength = s.getLength();
         // interleaved breaks the sequence into chunks for
         // interleavedColumns characters
         sb.append(s.getSequence(0,