X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FPfamFile.java;h=7cb381daa99eb59e8a114b774d5351e87ba285bb;hb=a7bec763a3e4f17a549115f8f9f19ee4c742c26b;hp=bbd441c8378190078a1b23cf352fa079cc3aa5a4;hpb=174230b4233d9ce80f94527768d2cd2f76da11ab;p=jalview.git

diff --git a/src/jalview/io/PfamFile.java b/src/jalview/io/PfamFile.java
index bbd441c..7cb381d 100755
--- a/src/jalview/io/PfamFile.java
+++ b/src/jalview/io/PfamFile.java
@@ -138,9 +138,9 @@ public class PfamFile
     {
       String tmp = printId(s[i]);
 
-      if (s[i].getSequence().length() > max)
+      if (s[i].getSequence().length > max)
       {
-        max = s[i].getSequence().length();
+        max = s[i].getSequence().length;
       }
 
       if (tmp.length() > maxid)
@@ -162,7 +162,7 @@ public class PfamFile
     {
       out.append(new Format("%-" + maxid + "s").form( printId(s[j])+" "));
 
-      out.append(s[j].getSequence() + "\n");
+      out.append(s[j].getSequenceAsString() + "\n");
       j++;
     }