X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FPfamFile.java;h=1e16348a2506db0d6716f04b79b8236f6dec3dd9;hb=a9177efb4097815d9a8031aa22700c61a7d6260a;hp=68aeb6852747dfea3b1ded8ac003427b00b5fece;hpb=3d0101179759ef157b088ea135423cd909512d9f;p=jalview.git

diff --git a/src/jalview/io/PfamFile.java b/src/jalview/io/PfamFile.java
index 68aeb68..1e16348 100755
--- a/src/jalview/io/PfamFile.java
+++ b/src/jalview/io/PfamFile.java
@@ -137,8 +137,9 @@ public class PfamFile extends AlignFile
       }
       else
       {
-        System.err.println("PFAM File reader: Can't find sequence for "
-                + headers.get(i));
+        jalview.bin.Console
+                .errPrintln("PFAM File reader: Can't find sequence for "
+                        + headers.get(i));
       }
     }
   }
@@ -157,10 +158,7 @@ public class PfamFile extends AlignFile
     {
       String tmp = printId(s[i], jvsuffix);
 
-      if (s[i].getSequence().length > max)
-      {
-        max = s[i].getSequence().length;
-      }
+      max = Math.max(max, s[i].getLength());
 
       if (tmp.length() > maxid)
       {