> 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 = ne
I've checked in the changes.
Looking back at my notes I can see why I left out MSF and Clustal from
the auto-guessing method. By adding them we end up treating some
alignment formats differently to others i.e. MSF/Clustal
vs. fasta/raw. As fasta and raw can be either alignments or single
sequence
> "Dan" == Dan Bolser <[EMAIL PROTECTED]> writes:
[...]
Dan> Just for the record, I see two forms of the fileToBiojava
Dan> function...
Dan> fileToBiojava( int fileType, java.io.BufferedReader br );
Dan> fileToBiojava( java.lang.String formatName, java.lang.String
Dan> al
On 4 Feb 2004, Keith James wrote:
> > "Dan" == Dan Bolser <[EMAIL PROTECTED]> writes:
>
> Dan> Hello, I am a new user to biojava (and almost new to java).
>
> Dan> The following code works fine reading a 'FASTA' format file,
> Dan> but causes an error reading 'MSF' format...
>
>
> "Dan" == Dan Bolser <[EMAIL PROTECTED]> writes:
Dan> Hello, I am a new user to biojava (and almost new to java).
Dan> The following code works fine reading a 'FASTA' format file,
Dan> but causes an error reading 'MSF' format...
[...]
Dan> --- Exception in thread "main"
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
