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

[Dan Bolser]

I forgot the (probably) important

import java.io.*;
import java.util.*;

import org.biojava.bio.*;
import org.biojava.bio.dist.*;
import org.biojava.bio.seq.*;
import org.biojava.bio.seq.io.*;
import org.biojava.bio.symbol.*;


On Wed, 4 Feb 2004, Dan Bolser wrote:

> 
> 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...
> 
> 
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