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Bio::SeqFeature::ToolsUserHContributed PerBio::SeqFeature::Tools::IDHandler(3)

NAME
       Bio::SeqFeature::Tools::IDHandler - maps	$seq_feature->primary_tag

SYNOPSIS
	 use Bio::SeqIO;
	 use Bio::SeqFeature::Tools::IDHandler;

DESCRIPTION
       Class to	map $seq_feature->primary_tag

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 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 - Chris Mungall
       Email:  cjm@fruitfly.org

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

   new
	Title	: new
	Usage	: $unflattener = Bio::SeqFeature::Tools::IDHandler->new();
	Function: constructor
	Example	:
	Returns	: a new	Bio::SeqFeature::Tools::IDHandler
	Args	: see below

   set_ParentIDs_from_hierarchy()
	Title	: set_ParentIDs_from_hierarchy()
	Usage	: $idhandler->set_ParentIDs_from_hierarchy($fholder)
	Function: populates tags Parent	and ID via holder hierarchy
	Example	:
	Returns	:
	Args	: Bio::featureHolderI (either a	SeqFeature or a	Seq)

       This is mainly for GFF3 export

       GFF3 uses the tags ID and Parent	to represent the feature containment
       hierarchy; it does NOT use the feature holder tree

       This method sets	Parent (and ID for any parents not set)	based on
       feature holder/containement hierarchy, ready for	GFF3 output

   create_hierarchy_from_ParentIDs
	Title	: create_hierarchy_from_ParentIDs
	Usage	: $idhandler->set_ParentIDs_from_hierarchy($fholder)
	Function: inverse of set_ParentIDs_from_hierarchy
	Example	:
	Returns	: list of top SeqFeatures
	Args	:

   generate_unique_persistent_id
	Title	: generate_unique_persistent_id
	Usage	:
	Function: generates a unique and persistent identifier for this
	Example	:
	Returns	: value	of primary_id (a scalar)
	Args	:

       Will generate an	ID, and	set primary_id() (see above)

       The ID is a string generated from

	 seq_id
	 primary_tag
	 start
	 end

       There are three underlying assumptions: that all	the above accessors
       are set;	that seq_id is a persistent and	unique identifier for the
       sequence	containing this	feature; and that

	 (seq_id, primary_tag, start, end)

       is a "unique constraint"	over features

       The ID is persistent, so	long as	none of	these values change - if they
       do, it is considered a separate entity

perl v5.24.1			  2017-07-Bio::SeqFeature::Tools::IDHandler(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Chris Mungall | APPENDIX

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