[gt-users] FASTA stream input implemented?

[David Ellinghaus]

Hi, thanks for the advice!  :-)
>> Alternatively, you can try to implement a sequence stream the way the
>> GtNodeStream for annotations is implemented (look at the *_stream.[ch]
>> files in extended). Such as stream could pass around GtSeq objects
>> instead of GtGenomeNodes. The GtSeqIterator interface looks already
>> quite like that, just without the stream connection capability.
>>     
>
> Yes, that would be the best solution (but the stream returns
> GtSequenceNode objects and not GtSeq objects).
> You can easily implement it yourself (let's call it FastaInStream).
> The FastaInStream would implement the NodeStream interface (you can
> copy the BedInStream for example).
> The constructor gets the Fasta file name(s) and creates an
> GtSeqIterator internally (to process the Fasta file(s)).
> In the _next method, you would just call the GtSeqIterator to retrieve
> the next Fasta sequence, create a GtSequenceNode and return it.
>   

I have copied extended/bed_in_stream.c and changed it to fasta_in_stream.c.
But I am not sure when to call the _next method to retrieve the next 
Fasta sequence,
do you mean in the fasta_in_stream_next() method?
Or do I have to write my own GtFASTAParser struct as well as functions
like gt_fasta_parser_parse() in a new file called extended/fasta_parser.c?
(Sorry, but I am just a little confused how the stream actually works.)

Best regards
David

PS: I attached my new fasta_in_stream.c so far.

-- 
David Ellinghaus
Institute for Clinical Molecular Biology
Christian-Albrechts-University Campus Kiel
House 6, Arnold-Heller-Str.3
D-24105 Kiel, Germany

Email:  d.ellinghaus at ikmb.uni-kiel.de
Phone:  +49-(0)431-597-1963
FAX  :  +49-(0)431-597-1842

-------------- next part --------------
A non-text attachment was scrubbed...
Name: fasta_in_stream.c
Type: text/x-csrc
Size: 3694 bytes
Desc: not available
Url : http://genometools.org/pipermail/gt-users/attachments/20090219/029caa8a/attachment.bin