Bio::Root Xref
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Summary
Bio::Root::Xref - A generic cross-reference object.
WARNING: This module is still in the experimental phase and has not been tested.
Package variables
No package variables defined.
Included modules
Bio::Root::Global
Bio::Root::Object ( )
Bio::Root::Vector ( )
Synopsis
 use Bio::Root::Object;

 $myObj->xref($object_ref);
 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.
Methods
_initialize
No description
Code
clear
No description
Code
desc
No description
Code
set_desc
No description
Code
type
No description
Code
Methods description
None available.
Methods code
_initializedescriptionprevnextTop
sub _initialize {
    my( $self, %param ) = @_;

    $self->SUPER::_initialize(%param);
    
    $self->{'_obj'} = ($param{-OBJ} || undef);

    ## By default, all Xrefs are symmetric.
    ## Create symmetric cross-reference in obj.
    if(!$param{-ASYM}) {
	$self->{'_obj'}->xref(-OBJ=>$param{-PARENT});
	$self->{'_type'} = 'sym';
    } else {
	$self->{'_type'} = 'asym';
    }	
}


#####################################################################################
##                                  ACCESSORS                                      ##
#####################################################################################
}
cleardescriptionprevnextTop
sub clear {
## Not implemented. Need to do this carefully.
## Not sure if this method is needed.    
    my ($self) = @_;
}

1;
__END__

#####################################################################################
#                                  END OF CLASS                                     #
#####################################################################################
}
descdescriptionprevnextTop
sub desc {
my ($self) = shift; return $self->{'_desc'};
}
set_descdescriptionprevnextTop
sub set_desc {
my ($self,$desc) = @_; 	     $self->{'_desc'} = $desc;
}
typedescriptionprevnextTop
sub type {
my ($self) = shift; return $self->{'_type'};
}
General documentation
SEE ALSOTop
  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
FEEDBACKTop
Mailing Lists Top
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 BugsTop
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://bugzilla.bioperl.org/
AUTHOR Top
Steve Chervitz <sac@bioperl.org>
See the FEEDBACK section for where to send bug reports and comments.
VERSIONTop
Bio::Root::Xref.pm, 0.01 pre-alpha
COPYRIGHTTop
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.
TODOTop
Update documentation to work with pod2html from Perl 5.004.
DATA MEMBERS Top
 _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.