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#
# BioPerl module for Bio::Tools::Run::MCS
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# Cared for by Sendu Bala <bix@sendu.me.uk>
#
# Copyright Sendu Bala
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code

=head1 NAME

Bio::Tools::Run::MCS - Wrapper for MCS

=head1 SYNOPSIS

  use Bio::Tools::Run::MCS;

  # Make a MCS factory
  $factory = Bio::Tools::Run::MCS->new();

  # Run MCS on an alignment
  my @results = $factory->run($alignfilename);

  # or with alignment object
  @results = $factory->run($bio_simplalign);

  # look at the results
  foreach my $feat (@results) {
    my $seq_id = $feat->seq_id;
    my $start = $feat->start;
    my $end = $feat->end;
    my $score = $feat->score;
    my ($pvalue) = $feat->get_tag_values('pvalue');
    my ($kind) = $feat->get_tag_values('kind'); # 'all', 'exon' or 'nonexon'
  }

=head1 DESCRIPTION

This is a wrapper for running the MCS (binCons) scripts by Elliott H Margulies.
You can get details here: http://zoo.nhgri.nih.gov/elliott/mcs_doc/. MCS is used
for the prediciton of transcription factor binding sites and other regions of
the genome conserved amongst different species.

Note that this wrapper assumes you already have alignments, so only uses MCS
for the latter stages (the stages involving align2binomial.pl,
generate_phyloMAX_score.pl and generate_mcs_beta.pl).

You can try supplying normal MCS command-line arguments to new(), eg.

  $factory->new(-percentile => 95)

or calling arg-named methods (excluding the initial
hyphens, eg. 

  $factory->percentile(95)

 to set the --percentile arg).


You will need to enable this MCS wrapper to find the MCS scripts.
This can be done in (at least) three ways:

 1. Make sure the MCS scripts are in your path.
 2. Define an environmental variable MCSDIR which is a 
    directory which contains the MCS scripts:
    In bash:

    export MCSDIR=/home/username/mcs/

    In csh/tcsh:

    setenv MCSDIR /home/username/mcs

 3. Include a definition of an environmental variable MCSDIR in
    every script that will use this MCS wrapper module, e.g.:

    BEGIN { $ENV{MCSDIR} = '/home/username/mcs/' }
    use Bio::Tools::Run::MCS;

=head1 FEEDBACK

=head2 Mailing Lists

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list.  Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

=head2 Support 

Please direct usage questions or support issues to the mailing list:

I<bioperl-l@bioperl.org>

rather than to the module maintainer directly. Many experienced and 
reponsive experts will be able look at the problem and quickly 
address it. Please include a thorough description of the problem 
with code and data examples if at all possible.

=head2 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:

  http://redmine.open-bio.org/projects/bioperl/

=head1 AUTHOR - Sendu Bala

Email bix@sendu.me.uk

=head1 APPENDIX

The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _

=cut

package Bio::Tools::Run::MCS;
use strict;

use Cwd;
use File::Spec;
use Bio::AlignIO;
use Bio::FeatureIO;
use Bio::Annotation::SimpleValue;

use base qw(Bio::Tools::Run::Phylo::PhyloBase);

our $PROGRAM_NAME = 'align2binomial.pl';
our $PROGRAM_DIR;

# methods for the mcs args we support
our @PARAMS   = qw(neutral percentile mcs specificity sensitivity name);
our @SWITCHES = qw(neg-score);

# just to be explicit, args we don't support (yet) or we handle ourselves
our @UNSUPPORTED = qw(ucsc gtf neutral-only fourd-align align-only ar);

BEGIN {
    # lets add all the mcs scripts to the path so that when we call
    # align2binomial.pl it can find its siblings
    $PROGRAM_DIR = $ENV{'MCSDIR'};
    $ENV{PATH} = "$PROGRAM_DIR:$ENV{PATH}" if $PROGRAM_DIR;
}

=head2 program_name

 Title   : program_name
 Usage   : $factory>program_name()
 Function: holds the program name
 Returns : string
 Args    : None

=cut

sub program_name {
    return $PROGRAM_NAME;
}

=head2 program_dir

 Title   : program_dir
 Usage   : $factory->program_dir(@params)
 Function: returns the program directory, obtained from ENV variable.
 Returns : string
 Args    : None

=cut

sub program_dir {
    return $PROGRAM_DIR;
}

=head2 new

 Title   : new
 Usage   : $factory = Bio::Tools::Run::MCS->new()
 Function: creates a new MCS factory
 Returns : Bio::Tools::Run::MCS
 Args    : Many options understood by MCS can be supplied as key =>
           value pairs.

           These options can NOT be used with this wrapper:
           ucsc gtf neutral-only fourd-align align-only ar

=cut

sub new {
    my ($class, @args) = @_;
    my $self = $class->SUPER::new(@args);
    
    $self->_set_from_args(\@args, -methods => [@PARAMS, @SWITCHES, 'quiet'],
                                  -create => 1);