/ 
FAST-1.06
River stage zero No dependents
/ FAST::Bio::SeqIO::game::seqHandler

NAME

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

SYNOPSIS

This modules is not used directly

DESCRIPTION

FAST::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://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 $seqHandler = FAST::Bio::SeqIO::game::seqHandler->new($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 FAST::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 FAST::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 FAST::Bio::SeqIO::game::featHandler object
Args    : none