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=head1 CONFIGURATION AND ENVIRONMENT

  [mysif]
  adaptor                  = sif
  state                    = on
  transport                = sif
  ; the main SIF file:
  filename                 = /data/interactions.sif
  ; zero or more attribute files:
  attributes               = /data/node-attribute.noa ; /data/edge-attributes.eda
  ; coordinates will be used as 'dbCoordSys':
  coordinates              = MyCoordSys -> 001
  ; static parameters:
  interaction.dbSource     = MyInteractionDB
  interaction.dbSourceCvId = MIDB
  interaction.dbVersion    = 12
  interactor.dbSource      = MyProteinDB
  interactor.dbSourceCvId  = MPDB
  interactor.dbVersion     = 23

=head1 DIAGNOSTICS

Run ProServer with the -debug flag.

=head1 SUBROUTINES/METHODS

=head2 build_interaction - Builds the DAS response

See documentation in superclass.

=head2 capabilities - Provides details of the adaptor's capabilities

This adaptor supports the 'interaction' command only.

=head1 SEE ALSO

=over

=item L<Bio::Das::ProServer::SourceAdaptor::Transport::sif|Bio::Das::ProServer::SourceAdaptor::Transport::sif>

=item L<http://www.cytoscape.org/cgi-bin/moin.cgi/Cytoscape_User_Manual/Network_Formats|http://www.cytoscape.org/cgi-bin/moin.cgi/Cytoscape_User_Manual/Network_Formats> Cytoscape - SIF

=item L<http://www.cytoscape.org/cgi-bin/moin.cgi/Cytoscape_User_Manual/Attributes|http://www.cytoscape.org/cgi-bin/moin.cgi/Cytoscape_User_Manual/Attributes> Cytoscape - Attributes

=back

=head1 DEPENDENCIES

=over

=item L<Carp|Carp> 

=item L<Bio::Das::ProServer::SourceAdaptor|Bio::Das::ProServer::SourceAdaptor> 

=item L<Bio::Das::ProServer::SourceAdaptor::Transport::sif|Bio::Das::ProServer::SourceAdaptor::Transport::sif>

=back

=head1 BUGS AND LIMITATIONS

The Simple Interaction Format is very simple, and therefore only supports a
limited range of DAS annotation details. It also only handles binary
interactions (i.e. those with exactly two interactors).

=head1 INCOMPATIBILITIES

None reported.

=head1 AUTHOR

Andy Jenkinson <andy.jenkinson@ebi.ac.uk>

=head1 LICENSE AND COPYRIGHT

Copyright (c) 2008 EMBL-EBI

=cut