[Biojava-l] beginners bug fileToBiojava problem with msf format

[Dan Bolser]

Hello, I am a new user to biojava (and almost new to java).

The following code works fine reading a 'FASTA' format file,
but causes an error reading 'MSF' format...

-----
String file     = args[0];
String format   = args[1];
String alphabet = args[2];
      
BufferedReader br = new BufferedReader(new FileReader(file));
      
SequenceIterator seqi = null;
Alignment align = null;
      
if ( format != "MSF" && format != "msf" ){
  seqi = 
    (SequenceIterator)SeqIOTools.fileToBiojava( format, alphabet, br );
}
else{
  align =
    (Alignment)SeqIOTools.fileToBiojava( format, alphabet, br );
}
---- 

Error...

---
Exception in thread "main" java.lang.IllegalArgumentException: No alphabet
was set in the identifier
        at
org.biojava.bio.seq.io.SeqIOTools.fileToBiojava(SeqIOTools.java:801)
        at
org.biojava.bio.seq.io.SeqIOTools.fileToBiojava(SeqIOTools.java:787)
        at
ReadAlignMakeDistribution.main(ReadAlignMakeDistribution.java:60)
---

Line 60 corresponds to the "align = ..." line above.

Like I said, works fine as...

java prog.java fa.fasta fasta PROTEIN

but

java prog.java msf.msf msf PROTEIN

Gives above error... Just as I thought I was begining to understand :.(

I will look at details for Alignment objects...