Hello,
I hit some trouble writing sequence in a Fasta
format.
The following method of FastaFormat class will
never satisfy its conditions:
public void writeSequence(Sequence seq, String
format, PrintStream os)
throws IOException
{
String requestedFormat = new String(format);
boolean found = false;
String [] formats = (String [])
getFormats().toArray(new String[0]);
if (! found)
throw new IOException("Failed to write: an
invalid file format '"
+ format
+ "' was requested");
writeSequence(seq, os);
}
I suppose here it needs to create Iterator of
allowed formats and scan through it.
I am going to rewrite it and send to the list.
Thanks,
Alexander Churbanov
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