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.IX Title "Bio::SeqIO::flybase_chadoxml 3pm"
.TH Bio::SeqIO::flybase_chadoxml 3pm "2018-10-27" "perl v5.26.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.nh
.SH "NAME"
Bio::SeqIO::flybase_chadoxml \- FlyBase variant of chadoxml with sequence output stream
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
It is probably best not to use this object directly, but
rather go through the SeqIO handler system:
.PP
.Vb 2
\&    $writer = Bio::SeqIO\->new(\-file => ">chado.xml",
\&                              \-format => \*(Aqflybase_chadoxml\*(Aq);
\&
\&    # assume you already have Sequence or SeqFeature objects
\&    $writer\->write_seq($seq_obj);
\&
\&    #after writing all seqs
\&    $writer\->close_chadoxml();
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This is a simple subclass of Bio::SeqIO::chadoxml; please see
its documentation for details.
.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 "AUTHOR \- Peili Zhang"
.IX Header "AUTHOR - Peili Zhang"
Email peili@morgan.harvard.edu
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
.SS "return_ftype_hash"
.IX Subsection "return_ftype_hash"
.Vb 8
\& Title    : return_ftype_hash
\& Usage    : $obj\->return_ftype_hash()
\& Function : A simple hash where returning it has be factored out of the main
\&            code to allow subclasses to override it.
\& Returns  : A hash that indicates what the name of the SO term is and what
\&            the name of the Sequence Ontology is in the cv table.
\& Args     : The string that represents the SO term.
\& Status   :
.Ve
.SS "return_reltypename"
.IX Subsection "return_reltypename"
.Vb 7
\& Title    : return_reltypename
\& Usage    : $obj\->return_reltypename
\& Function : Return the appropriate relationship type name depending on the
\&            feature type (typically part_of, but derives_from for polypeptide).
\& Returns  : A relationship type name.
\& Args     : A SO type name.
\& Status   :
.Ve
.SS "write_seq"
.IX Subsection "write_seq"
.Vb 11
\& Title   : write_seq
\& Usage   : $stream\->write_seq(\-seq=>$seq, \-seq_so_type=>$seqSOtype,
\&                  \-src_feature=>$srcfeature,
\&                  \-src_feat_type=>$srcfeattype,
\&                  \-nounflatten=>0 or 1,
\&                  \-is_analysis=>\*(Aqtrue\*(Aq or \*(Aqfalse\*(Aq,
\&                  \-data_source=>$datasource)
\& Function: writes the $seq object (must be seq) into chadoxml.
\& Returns : 1 for success and 0 for error
\& Args     : A Bio::Seq object $seq, optional $seqSOtype, $srcfeature,
\&            $srcfeattype, $nounflatten, $is_analysis and $data_source.
.Ve
.PP
Overrides Bio::SeqIO::chadoxml's write_seq method just to add an internal
close_chadoxml (mimics original use by FlyBase).