Bio::SeqIO::game::seqHandler.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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:
   http://bugzilla.open-bio.org/
 
 

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