NAME

Bio::ConnectDots::Dot -- one dot entry for 'connect-the-dots'

SYNOPSIS

  use Bio::ConnectDots::Dot;
  my $locuslink = ...;          #??? set to LocusLink dot somehow
  my $Dot = new Bio::ConnectDots::Dot;
  ???$dot->connectors({LocusID,UniGene,...});   
  ???$locuslink->put($connector);       # add to LocusLink connector object

DESCRIPTION

KNOWN BUGS AND CAVEATS

This is still a work in progress. This documentation is out of date. In any case, this class is no longer used in normal processing

Bugs, Caveats, and ToDos

  TBD

AUTHOR - David Burdick, Nat Goodman

Email dburdick@systemsbiology.org, natg@shore.net

COPYRIGHT

Copyright (c) 2005 Institute for Systems Biology (ISB). All Rights Reserved.

This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

APPENDIX

The rest of the documentation describes the methods.

Constructors

 Title   : new
 Usage   : my $dot = new Bio::ConnectDots::Dot;
 Function: Create empty dot object
 Returns : Bio::ConnectDots::Dot object

Simple attributes

These are methods for getting and setting the values of simple attributes. Each of these can be set in the argument list to new, if desired. Some of these should be read-only (more precisely, should only be written by code internal to the obkect), but this is not enforced. We assume, Perl-style, that programmers will behave nicely and not complain too loudly if the software lets them do something stupid.

Methods have the same name as the attribute. To get the value of attribute xxx, just say $xxx=$object->xxx; To set it, say $object->xxx($new_value); To clear it, say $object->xxx(undef);

 Attr    : connectors
 Function: Hash ref of connected objects. The keys are the Connector names
 Access  : read-write

Retrieving Dots (ie, objects connected by the connector)

 Title   : get_connector
 Usage   : ??? my $dot=$locuslink->get_next;
           my $locusid=$dot->get_connector('LocusID');
           my @locusid=$dot->get_connector('LocusID');
 Args    : Name of Connector (ie, connected object) to retrieve
 Returns : In a scalar context: 
             Returns the connected connector, if there's only one of the given type
             If there are multiple connected dots, returns an arbitray one
           In a list context, returns a list of the connected connectors of the 
           given type.

 Title   : get_dots
 Usage   : ????my $dot=$locuslink->get_next;
           my $aliases=$dot->get_connectors('Alias');
           my @aliases=$dot->get_connectors('Alias');
 Args    : Type of Connector (ie, connected object) to retrieve
           These can be names or objects
 Returns : In a scalar context, returns a list ref of the connected connectors
           of the given type.
           In a list context, returns a list of the connected dots of the 
           given type.