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