| Bio::SeqIO::game::seqHandler(3pm) | User Contributed Perl Documentation | Bio::SeqIO::game::seqHandler(3pm) |
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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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
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
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
Title : _add_seq Usage : $self->_add_seq($seq_element) Function: an internal method to process the sequence elements Returns : nothing Args : a sequence element
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
Title : _annotation Usage : $self->_annotation($annotation_element) Function: an internal method to process <annotation> elements Returns : nothing Args : an annotation element
Title : _seq Usage : my $seq = $self->_seq Function: an internal sequence getter/setter Returns : a Bio::RichSeq object Args : a sequence ID
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
| 2021-08-15 | perl v5.32.1 |