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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)
{
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++)
}
for (i = 0; i < headers.size(); i++)
@@
-131,13
+131,13
@@
public class PfamFile extends AlignFile
}
Sequence newSeq = parseId(headers.get(i).toString());
}
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
{
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));
}
}
+ headers.get(i));
}
}