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 listsSupport
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://redmine.open-bio.org/projects/bioperl/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 featureconvert
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