Ewan Birney

NAME

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

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

SYNOPSIS

Object Creation

 use Bio::Root::Object;

 $myObj->xref($object_ref);

Object Manipulation

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

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

DESCRIPTION

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.

SEE ALSO

  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 

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 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:

    bioperl-bugs@bio.perl.org                   
    http://bio.perl.org/bioperl-bugs/           

AUTHOR

Steve Chervitz <sac@bioperl.org>

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

VERSION

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

COPYRIGHT

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.

TODO

Update documentation to work with pod2html from Perl 5.004.

DATA MEMBERS

 _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.