X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FPhylipFile.java;h=e1d82ee0303c7ee63640af9e87a581e61f6f8c6e;hb=e6798fd04b1d7a35836a2e84deae5a94a35b88b9;hp=e8fe7e94b9a371b5cdb0b4778246585211a065b9;hpb=4a5137b64f7ec23db2a09290bfcd392984a52150;p=jalview.git

diff --git a/src/jalview/io/PhylipFile.java b/src/jalview/io/PhylipFile.java
index e8fe7e9..e1d82ee 100644
--- a/src/jalview/io/PhylipFile.java
+++ b/src/jalview/io/PhylipFile.java
@@ -247,7 +247,7 @@ 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);
 
@@ -279,13 +279,13 @@ 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,