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Bio::SeqIO::game::seqHUsereContributed Perl DocBio::SeqIO::game::seqHandler(3)

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

perl v5.24.1			  2017-07-08   Bio::SeqIO::game::seqHandler(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Sheldon McKay | APPENDIX

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