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

- NAME
- SYNOPSIS
- DESCRIPTION
- KNOWN BUGS AND CAVEATS

- Bugs, Caveats, and ToDos

- AUTHOR - David Burdick, Nat Goodman
- COPYRIGHT
- APPENDIX

- Constructors
- Simple attributes
- Retrieving Dots (ie, objects connected by the connector)

# 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 This documentation is out of date.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.
    =cut