/ 
FAST-1.0
River stage zero No dependents
/ FAST::Bio::SeqIO::gcg

NAME

FAST::Bio::SeqIO::gcg - GCG sequence input/output stream

SYNOPSIS

Do not use this module directly. Use it via the FAST::Bio::SeqIO class.

DESCRIPTION

This object can transform FAST::Bio::Seq objects to and from GCG flat file databases.

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:

https://redmine.open-bio.org/projects/bioperl/

AUTHORS - Ewan Birney & Lincoln Stein

Email: <birney@ebi.ac.uk> <lstein@cshl.org>

CONTRIBUTORS

Jason Stajich, jason@bioperl.org

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

next_seq

Title   : next_seq
Usage   : $seq = $stream->next_seq()
Function: returns the next sequence in the stream
Returns : FAST::Bio::Seq object
Args    :

write_seq

Title   : write_seq
Usage   : $stream->write_seq(@seq)
Function: writes the formatted $seq object into the stream
Returns : 1 for success and 0 for error
Args    : array of FAST::Bio::PrimarySeqI object

GCG_checksum

Title     : GCG_checksum
Usage     : $cksum = $gcgio->GCG_checksum($seq);
Function  : returns a gcg checksum for the sequence specified

            This method can also be called as a class method.
Example   :
Returns   : a GCG checksum string
Argument  : a FAST::Bio::PrimarySeqI implementing object

_validate_checksum

Title   : _validate_checksum
Usage   : n/a - internal method
Function: if parsed gcg sequence contains a checksum field
        : we compare it to a value computed here on the parsed
        : sequence. A checksum mismatch would indicate some
        : type of parsing failure occured.
        :
Returns : 1 for success, 0 for failure
Args    : string containing parsed seq, value of parsed cheksum