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