NAME

       Bio::SeqIO::game::seqHandler -- a class for handling game-XML sequences

SYNOPSIS

       This modules is not used directly

DESCRIPTION

       Bio::SeqIO::game::seqHandler processes all of the sequences associated with a game record
       and, via feature handlers, processes the associated annotations

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 of the bugs and their
       resolution. Bug reports can be submitted via the web:

         https://github.com/bioperl/bioperl-live/issues

AUTHOR - Sheldon McKay

       Email mckays@cshl.edu

APPENDIX

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

   new
        Title   : new
        Usage   : my $seqHandler = Bio::SeqIO::game::seqHandler->new($seq, $ann, $comp, $map, $src )
        Function: constructor method to create a sequence handler
        Returns : a sequence handler object
        Args    : $seq  -- an XML sequence element
                  $ann  -- a ref. to a list of <annotation> elements
                  $comp -- a ref. to a list of <computational_analysis> elements (not used yet)
                  $map  -- a <map_position> element
                  $src  -- a flag to indicate that the sequence already has a source feature

   convert
        Title   : convert
        Usage   : @seqs = $seqHandler->convert
        Function: converts the main XML sequence element and associated annotations to Bio::
        Returns : a ref. to a an array containing the sequence object and a ref. to a list of  features
        Args    : none

        Note    : The features and sequence are kept apart to facilitate downstream filtering of features

   _order_feats
        Title   : _order_feats
        Usage   : $self->_order_feats( $self->{seq_h} )
        Function: an internal method to ensure the source feature comes first
                  and keep gene, mRNA and CDS features together
        Returns : a ref. to an array containing the sequence object and a ref. to a list of  features
        Args    : a ref. to a hash of sequences

   _add_seq
        Title   : _add_seq
        Usage   : $self->_add_seq($seq_element)
        Function: an internal method to process the sequence elements
        Returns : nothing
        Args    : a sequence element

   _map_position
        Title   : _map_position
        Usage   : $self->_map_position($map_posn_element)
        Function: an internal method to process the <map_position> element
        Returns : nothing
        Args    : a map_position element

   _annotation
        Title   : _annotation
        Usage   : $self->_annotation($annotation_element)
        Function: an internal method to process <annotation> elements
        Returns : nothing
        Args    : an annotation element

   _seq
        Title   : _seq
        Usage   : my $seq = $self->_seq
        Function: an internal sequence getter/setter
        Returns : a Bio::RichSeq object
        Args    : a sequence ID

   _feat_handler
        Title   : _feat_handler
        Usage   : my $featHandler = $self->_featHandler
        Function: an internal getter/setter for feature handling objects
        Returns : a Bio::SeqIO::game::featHandler object
        Args    : none