Provided by: libbio-perl-perl_1.7.2-3_all bug


       Bio::SeqIO::flybase_chadoxml - FlyBase variant of chadoxml with sequence output stream


       It is probably best not to use this object directly, but rather go through the SeqIO
       handler system:

           $writer = Bio::SeqIO->new(-file => ">chado.xml",
                                     -format => 'flybase_chadoxml');

           # assume you already have Sequence or SeqFeature objects

           #after writing all seqs


       This is a simple subclass of Bio::SeqIO::chadoxml; please see its documentation for


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AUTHOR - Peili Zhang



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

        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   :

        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   :

        Title   : write_seq
        Usage   : $stream->write_seq(-seq=>$seq, -seq_so_type=>$seqSOtype,
                         -nounflatten=>0 or 1,
                         -is_analysis=>'true' or 'false',
        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.

       Overrides Bio::SeqIO::chadoxml's write_seq method just to add an internal close_chadoxml
       (mimics original use by FlyBase).