JAL-629 Change all stdout and stderr output to use Console.outPrintln and Console...

[jalview.git] / src / jalview / io / PfamFile.java

diff --git a/src/jalview/io/PfamFile.java b/src/jalview/io/PfamFile.java
index 9f152cc..57fae00 100755 (executable)
--- 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++)
@@ -131,13 +131,13 @@ 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 "
+        jalview.bin.Console.errPrintln("PFAM File reader: Can't find sequence for "
                 + headers.get(i));
       }
     }