Bio::SeqIO::game::seqHandler -- a class for handling game-XML sequences This modules is not used directly Bio::SeqIO::game::seqHandler processes all of the sequences associated with a game record and, via feature handlers, processes the associated annotations

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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 email or the web: bioperl-bugs@bioperl.org http://bugzilla.bioperl.org/ Email smckay@bcgsc.bc.ca 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 Returns : a ref. to a 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