# $Id: primo.pm,v 1.3 2003/06/11 17:05:26 letondal Exp $
# BioPerl module for Bio::Tools::Run::PiseApplication::primo
#
# 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::primo

=head1 SYNOPSIS

  #

=head1 DESCRIPTION

Bio::Tools::Run::PiseApplication::primo

      Bioperl class for:

	PRIMO	A primer design tool (Kupfer, Li)

	References:

		P. Li, K. C. Kupfer, C. J. Davies, D. Burbee, G. A. Evans, and H. R. Garner. PRIMO: A primer design program that applies base quality statistics for automated large-scale DNA sequencing. Genomics 40:476-485 (1997).



      Parameters: 

        (see also:
          http://bioweb.pasteur.fr/seqanal/interfaces/primo.html 
         for available values):


		primo (String)

		input_file_name (InFile)
			Sequence data

		all (String)

		cover (Switch)
			cover template with walking-primers on both strands (-cover)

		print (Switch)
			print formatted/annotated sequence to log file (-print)

		regions_file (InFile)
			Regions file (-read)

		qual_file (InFile)
			Quality datafile file

		repeats_file (InFile)
			Repeats file

		oligo_file (InFile)
			Oligo file

		rf (String)

		qf (String)

=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/primo.html

=item *

Bio::Tools::Run::PiseApplication

=item *

Bio::Tools::Run::AnalysisFactory::Pise

=item *

Bio::Tools::Run::PiseJob

=back

=cut

#'
package Bio::Tools::Run::PiseApplication::primo;

use vars qw(@ISA);
use strict;
use Bio::Tools::Run::PiseApplication;

@ISA = qw(Bio::Tools::Run::PiseApplication);

=head2 new

 Title   : new()
 Usage   : my $primo = Bio::Tools::Run::PiseApplication::primo->new($location, $email, @params);
 Function: Creates a Bio::Tools::Run::PiseApplication::primo 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 $primo = $factory->program('primo');
 Example : -
 Returns : An instance of Bio::Tools::Run::PiseApplication::primo.

=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/primo.pm

    $self->{COMMAND}   = "primo";
    $self->{VERSION}   = "5.a";
    $self->{TITLE}   = "PRIMO";

    $self->{DESCRIPTION}   = "A primer design tool";

    $self->{OPT_EMAIL}   = 0;

    $self->{AUTHORS}   = "Kupfer, Li";

    $self->{REFERENCE}   = [

         "P. Li, K. C. Kupfer, C. J. Davies, D. Burbee, G. A. Evans, and H. R. Garner. PRIMO: A primer design program that applies base quality statistics for automated large-scale DNA sequencing. Genomics 40:476-485 (1997).",
 ];

    $self->{_INTERFACE_STANDOUT} = undef;
    $self->{_STANDOUT_FILE} = undef;

    $self->{TOP_PARAMETERS}  = [ 
	"primo",
	"input_file_name",
	"all",
	"cover",
	"print",
	"regions_file",
	"qual_file",
	"repeats_file",
	"oligo_file",
	"rf",
	"qf",
	"results_files",

    ];

    $self->{PARAMETERS_ORDER}  = [
	"primo",
	"input_file_name", 	# Sequence data
	"all",
	"cover", 	# cover template with walking-primers on both strands (-cover)
	"print", 	# print formatted/annotated sequence to log file (-print)
	"regions_file", 	# Regions file (-read)
	"qual_file", 	# Quality datafile file
	"repeats_file", 	# Repeats file
	"oligo_file", 	# Oligo file
	"rf",
	"qf",
	"results_files",

    ];

    $self->{TYPE}  = {
	"primo" => 'String',
	"input_file_name" => 'InFile',
	"all" => 'String',
	"cover" => 'Switch',
	"print" => 'Switch',
	"regions_file" => 'InFile',
	"qual_file" => 'InFile',
	"repeats_file" => 'InFile',
	"oligo_file" => 'InFile',
	"rf" => 'String',
	"qf" => 'String',
	"results_files" => 'Results',

    };

    $self->{FORMAT}  = {
	"primo" => {
		"perl" => '"primo"',
	},
	"input_file_name" => {
		"perl" => '" $value"',
	},
	"all" => {
		"perl" => '" -all"',
	},
	"cover" => {
		"perl" => '($value)? " -cover" : ""',
	},
	"print" => {
		"perl" => '($value)? " -print" : ""',
	},
	"regions_file" => {
		"perl" => '($value)? " -read $input_file_name" : ""',
	},
	"qual_file" => {
		"perl" => '($value)? "" : " -noqual"',
	},
	"repeats_file" => {
		"perl" => ' ($value)? "ln -s $value human.rep; " : ""',
	},
	"oligo_file" => {
		"perl" => ' ($value)? "ln -s $value oligo.screen; " : ""',
	},
	"rf" => {
		"perl" => '"ln -s $regions_file $input_file_name.regions; "',
	},
	"qf" => {
		"perl" => '"ln -s $qual_file $input_file_name.qual; "',
	},
	"results_files" => {
	},

    };

    $self->{FILENAMES}  = {
	"results_files" => '*.log *.primers oligo.cri',

    };

    $self->{SEQFMT}  = {
	"input_file_name" => [8],

    };

    $self->{GROUP}  = {
	"primo" => 0,
	"input_file_name" => 1,
	"all" => 10,
	"cover" => 10,
	"print" => 10,
	"regions_file" => 10,
	"qual_file" => 10,
	"repeats_file" => -10,
	"oligo_file" => -10,
	"rf" => -10,
	"qf" => -10,

    };

    $self->{BY_GROUP_PARAMETERS}  = [
	"rf",
	"qf",
	"repeats_file",
	"oligo_file",
	"primo",
	"results_files",
	"input_file_name",
	"all",
	"cover",
	"print",
	"regions_file",
	"qual_file",

    ];

    $self->{SIZE}  = {

    };

    $self->{ISHIDDEN}  = {
	"primo" => 1,
	"input_file_name" => 0,
	"all" => 1,
	"cover" => 0,
	"print" => 0,
	"regions_file" => 0,
	"qual_file" => 0,
	"repeats_file" => 0,
	"oligo_file" => 0,
	"rf" => 1,
	"qf" => 1,
	"results_files" => 0,

    };

    $self->{ISCOMMAND}  = {
	"primo" => 1,
	"input_file_name" => 0,
	"all" => 0,
	"cover" => 0,
	"print" => 0,
	"regions_file" => 0,
	"qual_file" => 0,
	"repeats_file" => 0,
	"oligo_file" => 0,
	"rf" => 0,
	"qf" => 0,
	"results_files" => 0,

    };

    $self->{ISMANDATORY}  = {
	"primo" => 0,
	"input_file_name" => 1,
	"all" => 0,
	"cover" => 0,
	"print" => 0,
	"regions_file" => 0,
	"qual_file" => 0,
	"repeats_file" => 0,
	"oligo_file" => 0,
	"rf" => 0,
	"qf" => 0,
	"results_files" => 0,

    };

    $self->{PROMPT}  = {
	"primo" => "",
	"input_file_name" => "Sequence data",
	"all" => "",
	"cover" => "cover template with walking-primers on both strands (-cover)",
	"print" => "print formatted/annotated sequence to log file (-print)",
	"regions_file" => "Regions file (-read)",
	"qual_file" => "Quality datafile file",
	"repeats_file" => "Repeats file",
	"oligo_file" => "Oligo file",
	"rf" => "",
	"qf" => "",
	"results_files" => "",

    };

    $self->{ISSTANDOUT}  = {
	"primo" => 0,
	"input_file_name" => 0,
	"all" => 0,
	"cover" => 0,
	"print" => 0,
	"regions_file" => 0,
	"qual_file" => 0,
	"repeats_file" => 0,
	"oligo_file" => 0,
	"rf" => 0,
	"qf" => 0,
	"results_files" => 0,

    };

    $self->{VLIST}  = {

    };

    $self->{FLIST}  = {

    };

    $self->{SEPARATOR}  = {

    };

    $self->{VDEF}  = {
	"oligo_file" => 'Name    Oligo\noligo1  GAGGCAGGAGAATGGCAC	',

    };

    $self->{PRECOND}  = {
	"primo" => { "perl" => '1' },
	"input_file_name" => { "perl" => '1' },
	"all" => { "perl" => '1' },
	"cover" => { "perl" => '1' },
	"print" => {
		"perl" => '! $cover',
	},
	"regions_file" => { "perl" => '1' },
	"qual_file" => { "perl" => '1' },
	"repeats_file" => { "perl" => '1' },
	"oligo_file" => { "perl" => '1' },
	"rf" => {
		"perl" => '$regions_file',
	},
	"qf" => {
		"perl" => '$qual_file',
	},
	"results_files" => { "perl" => '1' },

    };

    $self->{CTRL}  = {

    };

    $self->{PIPEOUT}  = {

    };

    $self->{WITHPIPEOUT}  = {

    };

    $self->{PIPEIN}  = {

    };

    $self->{WITHPIPEIN}  = {

    };

    $self->{ISCLEAN}  = {
	"primo" => 0,
	"input_file_name" => 0,
	"all" => 0,
	"cover" => 0,
	"print" => 0,
	"regions_file" => 0,
	"qual_file" => 0,
	"repeats_file" => 0,
	"oligo_file" => 0,
	"rf" => 0,
	"qf" => 0,
	"results_files" => 0,

    };

    $self->{ISSIMPLE}  = {
	"primo" => 0,
	"input_file_name" => 1,
	"all" => 0,
	"cover" => 0,
	"print" => 0,
	"regions_file" => 0,
	"qual_file" => 0,
	"repeats_file" => 0,
	"oligo_file" => 0,
	"rf" => 0,
	"qf" => 0,
	"results_files" => 0,

    };

    $self->{PARAMFILE}  = {

    };

    $self->{COMMENT}  = {
	"repeats_file" => [
		"See the file http://bioweb.pasteur.fr/docs/doc-gensoft/primo/example//human.rep.bac for an example.",
	],

    };

    $self->{SCALEMIN}  = {

    };

    $self->{SCALEMAX}  = {

    };

    $self->{SCALEINC}  = {

    };

    $self->{INFO}  = {

    };

# -- end of definitions extracted from /local/gensoft/lib/Pise/5.a/PerlDef/primo.pm



    $self->_init_params(@params);

    return $self;
}



1; # Needed to keep compiler happy

