Bio::SeqFeature::PositionProxy(3pm)			User Contributed Perl Documentation		       Bio::SeqFeature::PositionProxy(3pm)

NAME

       Bio::SeqFeature::PositionProxy - handle features when truncation/revcom sequences span a feature

SYNOPSIS

	  $proxy = Bio::SeqFeature::PositionProxy->new( -loc => $loc,
							-parent => $basefeature);

	  $seq->add_SeqFeature($feat);

DESCRIPTION

       PositionProxy is a Proxy Sequence Feature to handle truncation and revcomp without duplicating all the data within the sequence features.
       It holds a new location for a sequence feature and the original feature it came from to provide the additional annotation information.

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 the bugs and their resolution.  Bug reports can be submitted via the
       web:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Ewan Birney
       Ewan Birney <birney@sanger.ac.uk>

DEVELOPERS

       This class has been written with an eye out of inheritence. The fields the actual object hash are:

	  _gsf_tag_hash  = reference to a hash for the tags
	  _gsf_sub_array = reference to an array for sub arrays
	  _gsf_start	 = scalar of the start point
	  _gsf_end	 = scalar of the end point
	  _gsf_strand	 = scalar of the strand

APPENDIX

       The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

   location
	Title	: location
	Usage	: my $location = $seqfeature->location()
	Function: returns a location object suitable for identifying location
		  of feature on sequence or parent feature
	Returns : Bio::LocationI object
	Args	: none

   parent
	Title	: parent
	Usage	: my $sf = $proxy->parent()
	Function: returns the seqfeature parent of this proxy
	Returns : Bio::SeqFeatureI object
	Args	: none

   start
	Title	: start
	Usage	: $start = $feat->start
		  $feat->start(20)
	Function: Get
	Returns : integer
	Args	: none

   end
	Title	: end
	Usage	: $end = $feat->end
		  $feat->end($end)
	Function: get
	Returns : integer
	Args	: none

   length
	Title	: length
	Usage	:
	Function:
	Example :
	Returns :
	Args	:

   strand
	Title	: strand
	Usage	: $strand = $feat->strand()
		  $feat->strand($strand)
	Function: get/set on strand information, being 1,-1 or 0
	Returns : -1,1 or 0
	Args	: none

   attach_seq
	Title	: attach_seq
	Usage	: $sf->attach_seq($seq)
	Function: Attaches a Bio::Seq object to this feature. This
		  Bio::Seq object is for the *entire* sequence: ie
		  from 1 to 10000
	Example :
	Returns : TRUE on success
	Args	:

   seq
	Title	: seq
	Usage	: $tseq = $sf->seq()
	Function: returns the truncated sequence (if there) for this
	Example :
	Returns : sub seq on attached sequence bounded by start & end
	Args	: none

   entire_seq
	Title	: entire_seq
	Usage	: $whole_seq = $sf->entire_seq()
	Function: gives the entire sequence that this seqfeature is attached to
	Example :
	Returns :
	Args	:

   seqname
	Title	: seqname
	Usage	: $obj->seq_id($newval)
	Function: There are many cases when you make a feature that you
		  do know the sequence name, but do not know its actual
		  sequence. This is an attribute such that you can store
		  the seqname.

		  This attribute should *not* be used in GFF dumping, as
		  that should come from the collection in which the seq
		  feature was found.
	Returns : value of seqname
	Args	: newvalue (optional)

   Proxies
       These functions chain back to the parent for all non sequence related stuff.

   primary_tag
	Title	: primary_tag
	Usage	: $tag = $feat->primary_tag()
	Function: Returns the primary tag for a feature,
		  eg 'exon'
	Returns : a string
	Args	: none

   source_tag
	Title	: source_tag
	Usage	: $tag = $feat->source_tag()
	Function: Returns the source tag for a feature,
		  eg, 'genscan'
	Returns : a string
	Args	: none

   has_tag
	Title	: has_tag
	Usage	: $tag_exists = $self->has_tag('some_tag')
	Function:
	Returns : TRUE if the specified tag exists, and FALSE otherwise
	Args	:

   each_tag_value
	Title	: each_tag_value
	Usage	: @values = $self->each_tag_value('some_tag')
	Function:
	Returns : An array comprising the values of the specified tag.
	Args	:

   all_tags
	Title	: all_tags
	Usage	: @tags = $feat->all_tags()
	Function: gives all tags for this feature
	Returns : an array of strings
	Args	: none

perl v5.14.2							    2012-03-02				       Bio::SeqFeature::PositionProxy(3pm)