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://bioperl.org/Support.html  - 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

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