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.\" ========================================================================
.\"
.IX Title "Bio::SeqIO::gcg 3pm"
.TH Bio::SeqIO::gcg 3pm "2020-10-28" "perl v5.30.3" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::SeqIO::gcg \- GCG sequence input/output stream
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
Do not use this module directly.  Use it via the Bio::SeqIO class.
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This object can transform Bio::Seq objects to and from \s-1GCG\s0 flat
file databases.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHORS \- Ewan Birney & Lincoln Stein"
.IX Header "AUTHORS - Ewan Birney & Lincoln Stein"
Email: <birney@ebi.ac.uk>
       <lstein@cshl.org>
.SH "CONTRIBUTORS"
.IX Header "CONTRIBUTORS"
Jason Stajich, jason@bioperl.org
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
.SS "next_seq"
.IX Subsection "next_seq"
.Vb 5
\& Title   : next_seq
\& Usage   : $seq = $stream\->next_seq()
\& Function: returns the next sequence in the stream
\& Returns : Bio::Seq object
\& Args    :
.Ve
.SS "write_seq"
.IX Subsection "write_seq"
.Vb 5
\& 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 Bio::PrimarySeqI object
.Ve
.SS "GCG_checksum"
.IX Subsection "GCG_checksum"
.Vb 3
\& 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 Bio::PrimarySeqI implementing object
.Ve
.SS "_validate_checksum"
.IX Subsection "_validate_checksum"
.Vb 9
\& 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 occurred.
\&         :
\& Returns : 1 for success, 0 for failure
\& Args    : string containing parsed seq, value of parsed checksum
.Ve