[Biojava-l] TMTOWTDI in biojava?

Dan Bolser dmb at mrc-dunn.cam.ac.uk
Wed Feb 4 10:55:44 EST 2004

Hello, I found an alternate solution...

BufferedReader br = new BufferedReader(new FileReader(file));
MSFAlignmentFormat x = new MSFAlignmentFormat();
Alignment align = x.read( br );

(MSFAlignmentFormat.read( br ) didn't work)

Is this just a matter of taste? Are their preferred ways to do things, or
should we just do things any which way? Does functional overlap exists for
specific reasons, or for exactly this kind of flexibility?

As a new java programer, I am natrually insecure about my code, do I just
need confidence?


On 4 Feb 2004, Keith James wrote:

> >>>>> "Dan" == Dan Bolser <dmb at mrc-dunn.cam.ac.uk> 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"
>     Dan> java.lang.IllegalArgumentException: No alphabet was set in
>     Dan> the identifier at
>     Dan> org.biojava.bio.seq.io.SeqIOTools.fileToBiojava(SeqIOTools.java:801)
>     Dan> at
>     Dan> org.biojava.bio.seq.io.SeqIOTools.fileToBiojava(SeqIOTools.java:787)
>     Dan> at
>     Dan> ReadAlignMakeDistribution.main(ReadAlignMakeDistribution.java:60)
> The exception message here is referring to the integer identifier
> which biojava has for every known combination of file-format (fasta,
> genbank, embl) and alphabet-type (dna, rna, protein). The way these
> are created/interpreted is documented in SeqIOConstants (for the
> sequence formats) and AlignIOConstants (for the alignment
> formats). All the common ones exist as static int fields so that you
> can compare using == or use them in switches.
> The format guessing code (in SeqIOTools.identifyFormat) appears to be
> missing "msf" and "clustal". This is a bug - I'll fix it today. The
> result is that it guesses SeqIOConstants.UNKNOWN as the format
> identifier (which has no alphabet set - hence the message).
> The public method fileToBiojava(int fileType, BufferedReader br)
> should work if you pass it the value AlignIOConstants.MSF_AA
> Keith

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