Bio::DB::ReferenceI.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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