Ewan Birney


Bio::Root::Xref - A generic cross-reference object.

WARNING: This module is still in the experimental phase and has not been tested.


Object Creation

 use Bio::Root::Object;


Object Manipulation

 obj()         - Get the cross-referenced object.
 desc()        - Description of the nature of the cross-reference.
 set_desc()    - Set description.
 type()        - Symmetric or assymetric.

 clear()       - remove all cross-references within the Xref object (not implemented).


An instance of Bio::Root::Xref.pm manages sets of objects not necessarily related by inheritance or composition, but by an arbitrary criterion defined by the client. Currently, Bio::Root::Xref inherits from both Bio::Root::Object.pm and Bio::Root::Vector.pm. An Xref object is an example of a heterogeneous Vector object since different objects in the vector need not all derive from the same base class.

The two objects involved in the cross-reference typically involve a symmetrical relationship in which each will have a Xref object relating it to the other object. This relationship is not necessarily transitive, however: if A is an xref of B and B is an xref of C, A is not necessarily an xref of C. Assymetric Xrefs are also possible.

The establishment of cross-references is managed by Bio::Root::Object.pm. See the xref() method in that module.

The API for this module is not complete since the module is under development. Caveat emptor.


  Bio::Root::Object.pm       - Core object
  Bio::Root::Global.pm       - Manages global variables/constants

  http://bio.perl.org/Projects/modules.html  - Online module documentation
  http://bio.perl.org/                       - Bioperl Project Homepage 


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/MailList.shtml - About the mailing lists

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 email or the web:



Steve Chervitz <sac@bioperl.org>

See the FEEDBACK section for where to send bug reports and comments.


Bio::Root::Xref.pm, 0.01 pre-alpha


Copyright (c) 1997-8 Steve Chervitz. All Rights Reserved. This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.


Update documentation to work with pod2html from Perl 5.004.


 _obj   : The object being cross-referenced to the parent.
 _type  : Symmetric or asymmetric
 _desc  : Description associated with the cross-reference

 INHERITED DATA MEMBERS (from Bio::Root::Object)

 _parent : The object receiving the cross-reference.
 _name   : Descriptive nature of the cross-reference.