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Bio::DB::ReferenceI(3)User Contributed Perl DocumentatioBio::DB::ReferenceI(3)

NAME
       Bio::DB::ReferenceI - A RandomAccessI-like abstract interface for
       retrieving Reference data from a sequence database and returning
       Bio::Annotation::Reference objects

SYNOPSIS
	 #
	 # get a database object somehow using a concrete class
	 #

	 $ref = $db->get_Reference_by_id('123456');

	 #
	 # $ref is a Bio::Annotation::Reference object
	 #

DESCRIPTION
       This is a pure interface class - in other words, all this does is
       define methods which other (concrete) classes will actually implement.

       The Bio::DB::ReferenceI class defines methods used to retrieve
       reference data from a sequence.	This is returned in the form of
       Bio::Annotation::Reference objects.

       At the moment it is just the ability to make Bio::Annotation::Reference
       objects from a name or unique id (id), an accession number (acc), and
       so on.

CONTACT
       Ewan Birney originally wrote Bio::DB::RandomAccessI, from which this
       class is based.

   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@lists.open-bio.org		    - General discussion
	 http://www.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.

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

AUTHOR
       Email cjfields at bioperl dot org

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

   get_Reference_by_id
	Title	: get_Reference_by_id
	Usage	: $ref = $db->get_Reference_by_id('123456')
	Function: Gets a Bio::Annotation::Reference-implementing object by its name (id)
	Returns : a Bio::Annotation::Reference object or undef if not found
	Args	: the id (as a string) of a sequence

   get_Reference_by_acc
	Title	: get_Reference_by_acc
	Usage	: $ref = $db->get_Reference_by_acc('X77802');
	Function: Gets a Bio::Annotation::Reference object by accession number
	Returns : A Bio::Annotation::Reference object or undef if not found
	Args	: accession number (as a string)
	Throws	: "more than one sequences correspond to this accession"
		   if the accession maps to multiple primary ids and
		   method is called in a scalar context

   get_Reference_by_version
	Title	: get_Reference_by_version
	Usage	: $ref = $db->get_Reference_by_version('X77802.1');
	Function: Gets a Bio::Annotation::Reference object by sequence version
	Returns : A Bio::Annotation::Reference object
	Args	: accession.version (as a string)
	Throws	: "acc.version does not exist" exception

perl v5.14.1			  2011-07-22		Bio::DB::ReferenceI(3)
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