X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FPfamFile.java;h=1e16348a2506db0d6716f04b79b8236f6dec3dd9;hb=faf491e024f9835435f5dd6c20a033250dd9297d;hp=bc22fae2933693a7dec73c3ed1a5c81b12ad7a92;hpb=7d67fb613ec026dc9a265e351e7fab542e3f1d61;p=jalview.git

diff --git a/src/jalview/io/PfamFile.java b/src/jalview/io/PfamFile.java
index bc22fae..1e16348 100755
--- a/src/jalview/io/PfamFile.java
+++ b/src/jalview/io/PfamFile.java
@@ -117,8 +117,8 @@ public class PfamFile extends AlignFile
 
     if (noSeqs < 1)
     {
-      throw new IOException(
-              MessageManager.getString("exception.pfam_no_sequences_found"));
+      throw new IOException(MessageManager
+              .getString("exception.pfam_no_sequences_found"));
     }
 
     for (i = 0; i < headers.size(); i++)
@@ -131,14 +131,15 @@ public class PfamFile extends AlignFile
         }
 
         Sequence newSeq = parseId(headers.get(i).toString());
-        newSeq.setSequence(seqhash.get(headers.get(i).toString())
-                .toString());
+        newSeq.setSequence(
+                seqhash.get(headers.get(i).toString()).toString());
         seqs.addElement(newSeq);
       }
       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)
       {