# $Id: comalign.pm,v 1.3 2003/06/05 19:15:18 letondal Exp $
# BioPerl module for Bio::Tools::Run::PiseApplication::comalign
#
# Cared for by Catherine Letondal <letondal@pasteur.fr>
#
# For copyright and disclaimer see below.
#
# POD documentation - main docs before the code

=head1 NAME

Bio::Tools::Run::PiseApplication::comalign

=head1 SYNOPSIS

  #

=head1 DESCRIPTION

Bio::Tools::Run::PiseApplication::comalign

      Bioperl class for:

	ComAlign	Combining many multiple alignments in one improved alignment (O. Caprani, K. Bucka-Lassen)


      Parameters: 

        (see also:
          http://bioweb.pasteur.fr/seqanal/interfaces/comalign.html 
         for available values):


		comalign (String)

		seq (Sequence)
			Sequences File (-f)
			pipe: seqsfile

		seed (Integer)
			Random seed number (-s)

		seqnb (Integer)
			Number of sequences that are to be aligned (-n)

		iterations (Integer)
			Number of iterations (-i)

		score (Integer)
			score: ComAlign records the time it took to  find a solution as good as this score (-l)

		time (Integer)
			ComAlign marks the best solution found after this number of 1/100 seconds (-t)

		last_iterations (Integer)
			Makes ComAlign terminate if the score hasn't changed within the last this number of iterations (-c)

		print_best (Switch)
			Print the best found alignment on termination (-a)

=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/MailList.shtml  - About the mailing lists

=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
email or the web:

  bioperl-bugs@bioperl.org
  http://bioperl.org/bioperl-bugs/

=head1 AUTHOR

Catherine Letondal (letondal@pasteur.fr)

=head1 COPYRIGHT

Copyright (C) 2003 Institut Pasteur & Catherine Letondal.
All Rights Reserved.

This module is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.

=head1 DISCLAIMER

This software is provided "as is" without warranty of any kind.

=head1 SEE ALSO

=over

=item *

http://bioweb.pasteur.fr/seqanal/interfaces/comalign.html

=item *

Bio::Tools::Run::PiseApplication

=item *

Bio::Tools::Run::AnalysisFactory::Pise

=item *

Bio::Tools::Run::PiseJob

=back

=cut

#'
package Bio::Tools::Run::PiseApplication::comalign;

use vars qw(@ISA);
use strict;
use Bio::Tools::Run::PiseApplication;

@ISA = qw(Bio::Tools::Run::PiseApplication);

=head2 new

 Title   : new()
 Usage   : my $comalign = Bio::Tools::Run::PiseApplication::comalign->new($location, $email, @params);
 Function: Creates a Bio::Tools::Run::PiseApplication::comalign object.
           This method should not be used directly, but rather by 
           a Bio::Tools::Run::AnalysisFactory::Pise instance.
           my $factory = Bio::Tools::Run::AnalysisFactory::Pise->new();
           my $comalign = $factory->program('comalign');
 Example : -
 Returns : An instance of Bio::Tools::Run::PiseApplication::comalign.

=cut

sub new {
    my ($class, $location, $email, @params) = @_;
    my $self = $class->SUPER::new($location, $email);

# -- begin of definitions extracted from /local/gensoft/lib/Pise/5.a/PerlDef/comalign.pm

    $self->{COMMAND}   = "comalign";
    $self->{VERSION}   = "5.a";
    $self->{TITLE}   = "ComAlign";

    $self->{DESCRIPTION}   = "Combining many multiple alignments in one improved alignment";

    $self->{OPT_EMAIL}   = 0;

    $self->{CATEGORIES}   =  [  

         "alignment:multiple",
  ];

    $self->{AUTHORS}   = "O. Caprani, K. Bucka-Lassen";

    $self->{_INTERFACE_STANDOUT} = undef;
    $self->{_STANDOUT_FILE} = undef;

    $self->{TOP_PARAMETERS}  = [ 
	"comalign",
	"seq",
	"seed",
	"seqnb",
	"iterations",
	"score",
	"time",
	"last_iterations",
	"print_best",

    ];

    $self->{PARAMETERS_ORDER}  = [
	"comalign",
	"seq", 	# Sequences File (-f)
	"seed", 	# Random seed number (-s)
	"seqnb", 	# Number of sequences that are to be aligned (-n)
	"iterations", 	# Number of iterations (-i)
	"score", 	# score: ComAlign records the time it took to  find a solution as good as this score (-l)
	"time", 	# ComAlign marks the best solution found after this number of 1/100 seconds (-t)
	"last_iterations", 	# Makes ComAlign terminate if the score hasn't changed within the last this number of iterations (-c)
	"print_best", 	# Print the best found alignment on termination (-a)

    ];

    $self->{TYPE}  = {
	"comalign" => 'String',
	"seq" => 'Sequence',
	"seed" => 'Integer',
	"seqnb" => 'Integer',
	"iterations" => 'Integer',
	"score" => 'Integer',
	"time" => 'Integer',
	"last_iterations" => 'Integer',
	"print_best" => 'Switch',

    };

    $self->{FORMAT}  = {
	"comalign" => {
		"perl" => '"ComAlign"',
	},
	"seq" => {
		"perl" => '" -f$value"',
	},
	"seed" => {
		"perl" => '(defined $value && $value != $vdef) ? " -s$value" : ""',
	},
	"seqnb" => {
		"perl" => '(defined $value && $value != $vdef) ? " -n$value" : ""',
	},
	"iterations" => {
		"perl" => '(defined $value && $value != $vdef) ? " -i$value" : ""',
	},
	"score" => {
		"perl" => '(defined $value) ? " -l$value" : ""',
	},
	"time" => {
		"perl" => '(defined $value) ? " -t$value" : ""',
	},
	"last_iterations" => {
		"perl" => '(defined $value && $value != $vdef) ? " -c$value" : ""',
	},
	"print_best" => {
		"perl" => '($value) ? " -a" : ""',
	},

    };

    $self->{FILENAMES}  = {

    };

    $self->{SEQFMT}  = {
	"seq" => [8],

    };

    $self->{GROUP}  = {
	"comalign" => 0,
	"seq" => 1,
	"seed" => 1,
	"seqnb" => 1,
	"iterations" => 1,
	"score" => 1,
	"time" => 1,
	"last_iterations" => 1,
	"print_best" => 1,

    };

    $self->{BY_GROUP_PARAMETERS}  = [
	"comalign",
	"seq",
	"seed",
	"seqnb",
	"iterations",
	"score",
	"time",
	"last_iterations",
	"print_best",

    ];

    $self->{SIZE}  = {

    };

    $self->{ISHIDDEN}  = {
	"comalign" => 1,
	"seq" => 0,
	"seed" => 0,
	"seqnb" => 0,
	"iterations" => 0,
	"score" => 0,
	"time" => 0,
	"last_iterations" => 0,
	"print_best" => 0,

    };

    $self->{ISCOMMAND}  = {
	"comalign" => 1,
	"seq" => 0,
	"seed" => 0,
	"seqnb" => 0,
	"iterations" => 0,
	"score" => 0,
	"time" => 0,
	"last_iterations" => 0,
	"print_best" => 0,

    };

    $self->{ISMANDATORY}  = {
	"comalign" => 0,
	"seq" => 1,
	"seed" => 0,
	"seqnb" => 0,
	"iterations" => 0,
	"score" => 0,
	"time" => 0,
	"last_iterations" => 0,
	"print_best" => 0,

    };

    $self->{PROMPT}  = {
	"comalign" => "",
	"seq" => "Sequences File (-f)",
	"seed" => "Random seed number (-s)",
	"seqnb" => "Number of sequences that are to be aligned (-n)",
	"iterations" => "Number of iterations (-i)",
	"score" => "score: ComAlign records the time it took to  find a solution as good as this score (-l)",
	"time" => "ComAlign marks the best solution found after this number of 1/100 seconds (-t)",
	"last_iterations" => "Makes ComAlign terminate if the score hasn't changed within the last this number of iterations (-c)",
	"print_best" => "Print the best found alignment on termination (-a)",

    };

    $self->{ISSTANDOUT}  = {
	"comalign" => 0,
	"seq" => 0,
	"seed" => 0,
	"seqnb" => 0,
	"iterations" => 0,
	"score" => 0,
	"time" => 0,
	"last_iterations" => 0,
	"print_best" => 0,

    };

    $self->{VLIST}  = {

    };

    $self->{FLIST}  = {

    };

    $self->{SEPARATOR}  = {

    };

    $self->{VDEF}  = {
	"seed" => '1',
	"seqnb" => '2',
	"iterations" => '10',
	"last_iterations" => '20',
	"print_best" => '1',

    };

    $self->{PRECOND}  = {
	"comalign" => { "perl" => '1' },
	"seq" => { "perl" => '1' },
	"seed" => { "perl" => '1' },
	"seqnb" => { "perl" => '1' },
	"iterations" => { "perl" => '1' },
	"score" => { "perl" => '1' },
	"time" => { "perl" => '1' },
	"last_iterations" => { "perl" => '1' },
	"print_best" => { "perl" => '1' },

    };

    $self->{CTRL}  = {

    };

    $self->{PIPEOUT}  = {

    };

    $self->{WITHPIPEOUT}  = {

    };

    $self->{PIPEIN}  = {
	"seq" => {
		 "seqsfile" => '1',
	},

    };

    $self->{WITHPIPEIN}  = {

    };

    $self->{ISCLEAN}  = {
	"comalign" => 0,
	"seq" => 0,
	"seed" => 0,
	"seqnb" => 0,
	"iterations" => 0,
	"score" => 0,
	"time" => 0,
	"last_iterations" => 0,
	"print_best" => 0,

    };

    $self->{ISSIMPLE}  = {
	"comalign" => 0,
	"seq" => 1,
	"seed" => 0,
	"seqnb" => 0,
	"iterations" => 0,
	"score" => 0,
	"time" => 0,
	"last_iterations" => 0,
	"print_best" => 0,

    };

    $self->{PARAMFILE}  = {

    };

    $self->{COMMENT}  = {
	"iterations" => [
		"On each iteration a new alignment is added to the pool of alignments ComAlign is working on",
	],

    };

    $self->{SCALEMIN}  = {

    };

    $self->{SCALEMAX}  = {

    };

    $self->{SCALEINC}  = {

    };

    $self->{INFO}  = {

    };

# -- end of definitions extracted from /local/gensoft/lib/Pise/5.a/PerlDef/comalign.pm



    $self->_init_params(@params);

    return $self;
}



1; # Needed to keep compiler happy

