X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FPfamFile.java;h=57fae00464b5d9895c41445e2376962ed80645ff;hb=cadabddd959db11250cdf19b28606106540b3268;hp=c6c10bdb7b18c193e4d5637c06abc01484280bd7;hpb=4a5137b64f7ec23db2a09290bfcd392984a52150;p=jalview.git

diff --git a/src/jalview/io/PfamFile.java b/src/jalview/io/PfamFile.java
index c6c10bd..57fae00 100755
--- a/src/jalview/io/PfamFile.java
+++ b/src/jalview/io/PfamFile.java
@@ -109,7 +109,7 @@ public class PfamFile extends AlignFile
       }
       if (spces + 1 < line.length())
       {
-        tempseq.append(line.substring(spces + 1));
+        tempseq.append(line.substring(spces + 1).trim());
       }
     }
 
@@ -117,28 +117,27 @@ 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++)
     {
       if (seqhash.get(headers.get(i)) != null)
       {
-        if (maxLength < seqhash.get(headers.get(i)).toString()
-                .length())
+        if (maxLength < seqhash.get(headers.get(i)).toString().length())
         {
           maxLength = seqhash.get(headers.get(i)).toString().length();
         }
 
         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 "
+        jalview.bin.Console.errPrintln("PFAM File reader: Can't find sequence for "
                 + headers.get(i));
       }
     }
@@ -158,10 +157,7 @@ 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)
       {