package Bio::DOOP::DOOP;

use strict;
use warnings;
use Bio::DOOP::DBSQL;
use Bio::DOOP::Cluster;
use Bio::DOOP::ClusterSubset;
use Bio::DOOP::Sequence;
use Bio::DOOP::SequenceFeature;
use Bio::DOOP::Motif;
use Bio::DOOP::Util::Search;
use Bio::DOOP::Util::Sort;
use Bio::DOOP::Util::Filt;
use Bio::DOOP::Util::Run::Mofext;
use Bio::DOOP::Util::Run::Fuzznuc;
use Bio::DOOP::Util::Run::Admin;
use Bio::DOOP::Graphics::Feature;

=head1 NAME

  Bio::DOOP::DOOP - DOOP API main module

=head1 VERSION

Version 1.00

=cut

our $VERSION = '1.00';

=head1 SYNOPSIS

  use Bio::DOOP::DOOP;

  $db = Bio::DOOP::DBSQL->new("doopuser","dooppass","database","localhost");
  $cluster = Bio::DOOP::Cluster->new($db,"8010109","500");
  @seqs = @{$cluster->get_all_seqs};
  foreach $seq (@seqs){
     print $seq->seq,"\n";
  }

=head1 DESCRIPTION

  DoOP is a database containing orthologous clusters of promoters from Homo sapiens, 
  Arabidopsis thaliana and other organisms. Visit the http://doop.abc.hu/ site for
  more information.
  This is a container module for all of the DOOP modules.
  You can simply use this module to access all DOOP objects.
  For more help, please see the documentation of the individual
  objects.

=head1 AUTHORS

  Tibor Nagy, Godollo, Hungary and Endre Sebestyen, Martonvasar, Hungary

=head1 OBJECTS

=head2 Bio::DOOP::DBSQL

  Object for simple SQL queries.

=head2 Bio::DOOP::Cluster

  Object for the clusters.

=head2 Bio::DOOP::ClusterSubset

  Object for the subsets of sequences inside a cluster.

=head2 Bio::DOOP::Sequence

  Object for the cluster (or cluster subset) sequences.

=head2 Bio::DOOP::SequenceFeature

  Object for the different features of the sequences.

=head2 Bio::DOOP::Motif

  Object for the conserved sequence features.

=head2 Bio::DOOP::Util::Search

  Module for different search subrutines.

=head2 Bio::DOOP::Util::Sort

  Sort an array of array by given conditions.

=head2 Bio::DOOP::Util::Filt

  Filter a Cluster array by given conditions.

=head2 Bio::DOOP::Util::Run::Mofext

  Module for Mofext wrapping. Mofext is a motif finder 
  program developed by the author Tibor Nagy.

=head2 Bio::DOOP::Util::Run::Fuzznuc

  Module for controll Emboss program fuzznuc.

=head2 Bio::DOOP::Util::Run::Admin

  Module for controll all the running DOOP wrapper objects

=head2 Bio::DOOP::Graphics::Feature

  Module for generating a picture of the sequences and feature of a cluster.

=cut

=head1 COPYRIGHT & LICENSE

Copyright 2006 Tibor Nagy, all rights reserved.

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

=cut

1;