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Bio::SeqFeature::PositUserrContributed Perl DBio::SeqFeature::PositionProxy(3)

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://github.com/bioperl/bioperl-live/issues

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	:

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

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

perl v5.24.1			  2017-07-08 Bio::SeqFeature::PositionProxy(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Ewan Birney | DEVELOPERS | APPENDIX

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