# $Id: melting.pm,v 1.3 2003/06/10 09:33:20 letondal Exp $
# BioPerl module for Bio::Tools::Run::PiseApplication::melting
#
# 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::melting

=head1 SYNOPSIS

  #

=head1 DESCRIPTION

Bio::Tools::Run::PiseApplication::melting

      Bioperl class for:

	MELTING	enthalpie, entropy and melting temperature (N. Le Novere)

	References:

		Nicolas Le Novere (2001), MELTING, computing the melting temperature of nucleic acid duplex. Bioinformatics 17(12), 1226-1227



      Parameters: 

        (see also:
          http://bioweb.pasteur.fr/seqanal/interfaces/melting.html 
         for available values):


		melting (String)

		hybridation_type (Excl)
			Hybridisation type (-H)

		nnfile (Excl)
			Nearest Neighbor parameters set (-A)

		sequence (String)
			Sequence string (-S)

		complement_string (String)
			Complementary sequence (-C)

		salt_concentratio (Float)
			Salt concentration (0.0 < x < 10.0 M) (-N)

		nucacid_concentration (Float)
			Nucleic acid concentration in excess (0.0 < x < 0.1 M) (-P)

		correction_factor (Float)
			Nucleic acid correction factor (-F)

		salt_correction (Excl)
			Salt correction (-K)

		approx (Switch)
			Force approximative temperature computation (-x)

		dangling ends (Switch)
			parameters for dangling ends: dnadnade.nn

		mismatches (Switch)
			nn parameters for mismatches: dnadnamm.nn

=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/melting.html

=item *

Bio::Tools::Run::PiseApplication

=item *

Bio::Tools::Run::AnalysisFactory::Pise

=item *

Bio::Tools::Run::PiseJob

=back

=cut

#'
package Bio::Tools::Run::PiseApplication::melting;

use vars qw(@ISA);
use strict;
use Bio::Tools::Run::PiseApplication;

@ISA = qw(Bio::Tools::Run::PiseApplication);

=head2 new

 Title   : new()
 Usage   : my $melting = Bio::Tools::Run::PiseApplication::melting->new($location, $email, @params);
 Function: Creates a Bio::Tools::Run::PiseApplication::melting 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 $melting = $factory->program('melting');
 Example : -
 Returns : An instance of Bio::Tools::Run::PiseApplication::melting.

=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/melting.pm

    $self->{COMMAND}   = "melting";
    $self->{VERSION}   = "5.a";
    $self->{TITLE}   = "MELTING";

    $self->{DESCRIPTION}   = "enthalpie, entropy and melting temperature";

    $self->{OPT_EMAIL}   = 0;

    $self->{CATEGORIES}   =  [  

         "nucleic:composition",
  ];

    $self->{AUTHORS}   = "N. Le Novere";

    $self->{REFERENCE}   = [

         "Nicolas Le Novere (2001), MELTING, computing the melting temperature of nucleic acid duplex. Bioinformatics 17(12), 1226-1227",
 ];

    $self->{_INTERFACE_STANDOUT} = undef;
    $self->{_STANDOUT_FILE} = undef;

    $self->{TOP_PARAMETERS}  = [ 
	"melting",
	"hybridation_type",
	"nnfile",
	"sequence",
	"complement_string",
	"salt_concentratio",
	"nucacid_concentration",
	"correction_factor",
	"salt_correction",
	"approx",
	"dangling ends",
	"mismatches",

    ];

    $self->{PARAMETERS_ORDER}  = [
	"melting",
	"hybridation_type", 	# Hybridisation type (-H)
	"nnfile", 	# Nearest Neighbor parameters set (-A)
	"sequence", 	# Sequence string (-S)
	"complement_string", 	# Complementary sequence (-C)
	"salt_concentratio", 	# Salt concentration (0.0 < x < 10.0 M) (-N)
	"nucacid_concentration", 	# Nucleic acid concentration in excess (0.0 < x < 0.1 M) (-P)
	"correction_factor", 	# Nucleic acid correction factor (-F)
	"salt_correction", 	# Salt correction (-K)
	"approx", 	# Force approximative temperature computation (-x)
	"dangling ends",
	"mismatches", 	# nn parameters for mismatches: dnadnamm.nn

    ];

    $self->{TYPE}  = {
	"melting" => 'String',
	"hybridation_type" => 'Excl',
	"nnfile" => 'Excl',
	"sequence" => 'String',
	"complement_string" => 'String',
	"salt_concentratio" => 'Float',
	"nucacid_concentration" => 'Float',
	"correction_factor" => 'Float',
	"salt_correction" => 'Excl',
	"approx" => 'Switch',
	"dangling ends" => 'Switch',
	"mismatches" => 'Switch',

    };

    $self->{FORMAT}  = {
	"melting" => {
		"perl" => '"melting -q -v"',
	},
	"hybridation_type" => {
		"perl" => '" -H$value"',
	},
	"nnfile" => {
		"perl" => '($value && $value ne $vdef) ? " -A$value" : ""',
	},
	"sequence" => {
		"perl" => '" -S$value"',
	},
	"complement_string" => {
		"perl" => '$value ? " -C$value" : ""',
	},
	"salt_concentratio" => {
		"perl" => '" -N$value"',
	},
	"nucacid_concentration" => {
		"perl" => '$value ? " -P$value" : ""',
	},
	"correction_factor" => {
		"perl" => '$value ? " -F$value" : ""',
	},
	"salt_correction" => {
		"perl" => '$value ? " -K$value" : ""',
	},
	"approx" => {
		"perl" => '$value ? " -x" : ""',
	},
	"dangling ends" => {
		"perl" => '($value)? " -Ddnadnade.nn " : ""',
	},
	"mismatches" => {
		"perl" => '($value)? " -Mdnadnamm.nn " : ""',
	},

    };

    $self->{FILENAMES}  = {

    };

    $self->{SEQFMT}  = {

    };

    $self->{GROUP}  = {
	"melting" => 0,
	"hybridation_type" => 1,
	"nnfile" => 1,
	"sequence" => 1,
	"complement_string" => 1,
	"salt_concentratio" => 1,
	"nucacid_concentration" => 1,
	"correction_factor" => 1,
	"salt_correction" => 1,
	"approx" => 1,
	"dangling ends" => 1,
	"mismatches" => 1,

    };

    $self->{BY_GROUP_PARAMETERS}  = [
	"melting",
	"hybridation_type",
	"nnfile",
	"sequence",
	"complement_string",
	"salt_concentratio",
	"nucacid_concentration",
	"correction_factor",
	"salt_correction",
	"approx",
	"dangling ends",
	"mismatches",

    ];

    $self->{SIZE}  = {

    };

    $self->{ISHIDDEN}  = {
	"melting" => 1,
	"hybridation_type" => 0,
	"nnfile" => 0,
	"sequence" => 0,
	"complement_string" => 0,
	"salt_concentratio" => 0,
	"nucacid_concentration" => 0,
	"correction_factor" => 0,
	"salt_correction" => 0,
	"approx" => 0,
	"dangling ends" => 0,
	"mismatches" => 0,

    };

    $self->{ISCOMMAND}  = {
	"melting" => 1,
	"hybridation_type" => 0,
	"nnfile" => 0,
	"sequence" => 0,
	"complement_string" => 0,
	"salt_concentratio" => 0,
	"nucacid_concentration" => 0,
	"correction_factor" => 0,
	"salt_correction" => 0,
	"approx" => 0,
	"dangling ends" => 0,
	"mismatches" => 0,

    };

    $self->{ISMANDATORY}  = {
	"melting" => 1,
	"hybridation_type" => 1,
	"nnfile" => 1,
	"sequence" => 1,
	"complement_string" => 0,
	"salt_concentratio" => 1,
	"nucacid_concentration" => 1,
	"correction_factor" => 0,
	"salt_correction" => 0,
	"approx" => 0,
	"dangling ends" => 0,
	"mismatches" => 0,

    };

    $self->{PROMPT}  = {
	"melting" => "",
	"hybridation_type" => "Hybridisation type (-H)",
	"nnfile" => "Nearest Neighbor parameters set (-A)",
	"sequence" => "Sequence string (-S)",
	"complement_string" => "Complementary sequence (-C)",
	"salt_concentratio" => "Salt concentration (0.0 < x < 10.0 M) (-N)",
	"nucacid_concentration" => "Nucleic acid concentration in excess (0.0 < x < 0.1 M) (-P)",
	"correction_factor" => "Nucleic acid correction factor (-F)",
	"salt_correction" => "Salt correction (-K)",
	"approx" => "Force approximative temperature computation (-x)",
	"dangling ends" => "parameters for dangling ends: dnadnade.nn",
	"mismatches" => "nn parameters for mismatches: dnadnamm.nn",

    };

    $self->{ISSTANDOUT}  = {
	"melting" => 0,
	"hybridation_type" => 0,
	"nnfile" => 0,
	"sequence" => 0,
	"complement_string" => 0,
	"salt_concentratio" => 0,
	"nucacid_concentration" => 0,
	"correction_factor" => 0,
	"salt_correction" => 0,
	"approx" => 0,
	"dangling ends" => 0,
	"mismatches" => 0,

    };

    $self->{VLIST}  = {

	"hybridation_type" => ['dnadna','Dna/Dna','dnarna','Dna/Rna','rnarna','Rna/Rna',],
	"nnfile" => ['default','(default)','all97a.nn','Allawi et al 1997','bre86a.nn','Breslauer et al 1986','fre86a.nn','Freier et al 1986','san96a.nn','SantaLucia et al 1996','sug95a.nn','Sugimoto et al 1995','sug96a.nn','Sugimoto et al 1996','xia98a.nn','Xia et al 1998',],
	"salt_correction" => ['wet91a','Wetmur 1991','san96a','SantaLucia et al. 1996','san98a','SantaLucia 1998',],
    };

    $self->{FLIST}  = {

    };

    $self->{SEPARATOR}  = {

    };

    $self->{VDEF}  = {
	"nnfile" => 'default',

    };

    $self->{PRECOND}  = {
	"melting" => { "perl" => '1' },
	"hybridation_type" => { "perl" => '1' },
	"nnfile" => { "perl" => '1' },
	"sequence" => { "perl" => '1' },
	"complement_string" => { "perl" => '1' },
	"salt_concentratio" => { "perl" => '1' },
	"nucacid_concentration" => { "perl" => '1' },
	"correction_factor" => { "perl" => '1' },
	"salt_correction" => { "perl" => '1' },
	"approx" => { "perl" => '1' },
	"dangling ends" => { "perl" => '1' },
	"mismatches" => { "perl" => '1' },

    };

    $self->{CTRL}  = {

    };

    $self->{PIPEOUT}  = {

    };

    $self->{WITHPIPEOUT}  = {

    };

    $self->{PIPEIN}  = {

    };

    $self->{WITHPIPEIN}  = {

    };

    $self->{ISCLEAN}  = {
	"melting" => 0,
	"hybridation_type" => 0,
	"nnfile" => 0,
	"sequence" => 0,
	"complement_string" => 0,
	"salt_concentratio" => 0,
	"nucacid_concentration" => 0,
	"correction_factor" => 0,
	"salt_correction" => 0,
	"approx" => 0,
	"dangling ends" => 0,
	"mismatches" => 0,

    };

    $self->{ISSIMPLE}  = {
	"melting" => 0,
	"hybridation_type" => 1,
	"nnfile" => 1,
	"sequence" => 1,
	"complement_string" => 0,
	"salt_concentratio" => 1,
	"nucacid_concentration" => 1,
	"correction_factor" => 0,
	"salt_correction" => 0,
	"approx" => 0,
	"dangling ends" => 0,
	"mismatches" => 0,

    };

    $self->{PARAMFILE}  = {

    };

    $self->{COMMENT}  = {

    };

    $self->{SCALEMIN}  = {

    };

    $self->{SCALEMAX}  = {

    };

    $self->{SCALEINC}  = {

    };

    $self->{INFO}  = {

    };

# -- end of definitions extracted from /local/gensoft/lib/Pise/5.a/PerlDef/melting.pm



    $self->_init_params(@params);

    return $self;
}



1; # Needed to keep compiler happy

