# pratt.pm,v 1.3.2.1 2005/10/09 15:19:45 jason Exp
# BioPerl module for Bio::Tools::Run::PiseApplication::pratt
#
# 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::pratt

=head1 SYNOPSIS

  #

=head1 DESCRIPTION

Bio::Tools::Run::PiseApplication::pratt

      Bioperl class for:

	Pratt	pattern discovery (K. Sturzrehm, I. Jonassen)


      Parameters: 

        (see also:
          http://bioweb.pasteur.fr/seqanal/interfaces/pratt.html 
         for available values):


		pratt (String)

		seq (Sequence)
			Sequence File

		seqformat (Excl)
			Sequence File format

		CM (Integer)
			CM: min Nr of Seqs to Match (between 2 and 4)

		Cpct (Integer)
			C%: min Percentage Seqs to Match

		PP (Excl)
			PP: pos in seq

		PF (InFile)
			PF: Restriction File name (if PP not off)

		PL (Integer)
			PL: max Pattern Length

		PN (Integer)
			PN: max Nr of Pattern Symbols

		PX (Integer)
			PX: max Nr of consecutive x's

		FN (Integer)
			FN: max Nr of flexible spacers

		FL (Integer)
			FL: max Flexibility

		FP (Integer)
			FP: max Flex.Product

		BI (Switch)
			BI: Input Pattern Symbol File?

		BF (InFile)
			BF: Input Pattern Symbol File name (if BI on)

		BN (Integer)
			BN: Nr of Pattern Symbols Initial Search

		S (Excl)
			S: Scoring

		treefile (InFile)
			Tree File (if Scoring = tree)

		distfile (InFile)
			Distances File (if Scoring = dist)

		swissprotdb (String)

		Z0 (Integer)
			Z0

		Z1 (Integer)
			Z1

		Z2 (Integer)
			Z2

		Z3 (Integer)
			Z3

		G (Excl)
			G: Pattern Graph from:

		GF (InFile)
			Alignment or Query Filename (if G set to al or query)

		E (Integer)
			E: Search Greediness

		R (Switch)
			R: Pattern Refinement

		RG (Switch)
			RG: Generalise ambiguous symbols (if Pattern Refinement on)

		OF (OutFile)
			OF: Output Filename

		OP (Switch)
			OP: PROSITE Pattern Format

		ON (Integer)
			ON: max number patterns

		OA (Integer)
			OA: max number Alignments

		M (Switch)
			M: Print Patterns in sequences

		MR (Integer)
			MR: ratio for printing

		MV (Switch)
			MV: print vertically

=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 the
web:

  http://bugzilla.bioperl.org/

=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/pratt.html

=item *

Bio::Tools::Run::PiseApplication

=item *

Bio::Tools::Run::AnalysisFactory::Pise

=item *

Bio::Tools::Run::PiseJob

=back

=cut

#'
package Bio::Tools::Run::PiseApplication::pratt;

use vars qw(@ISA);
use strict;
use Bio::Tools::Run::PiseApplication;

@ISA = qw(Bio::Tools::Run::PiseApplication);

=head2 new

 Title   : new()
 Usage   : my $pratt = Bio::Tools::Run::PiseApplication::pratt->new($location, $email, @params);
 Function: Creates a Bio::Tools::Run::PiseApplication::pratt 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 $pratt = $factory->program('pratt');
 Example : -
 Returns : An instance of Bio::Tools::Run::PiseApplication::pratt.

=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/pratt.pm

    $self->{COMMAND}   = "pratt";
    $self->{VERSION}   = "5.a";
    $self->{TITLE}   = "Pratt";

    $self->{DESCRIPTION}   = "pattern discovery";

    $self->{OPT_EMAIL}   = 0;

    $self->{AUTHORS}   = "K. Sturzrehm, I. Jonassen";

    $self->{_INTERFACE_STANDOUT} = undef;
    $self->{_STANDOUT_FILE} = undef;

    $self->{TOP_PARAMETERS}  = [ 
	"pratt",
	"seq",
	"seqformat",
	"conservation",
	"restrictions",
	"scoring",
	"search",
	"output",
	"report",

    ];

    $self->{PARAMETERS_ORDER}  = [
	"pratt",
	"seq", 	# Sequence File
	"seqformat", 	# Sequence File format
	"conservation", 	# Pattern conservation parameters
	"CM", 	# CM: min Nr of Seqs to Match (between 2 and 4)
	"Cpct", 	# C%: min Percentage Seqs to Match
	"restrictions", 	# Pattern restrictions parameters
	"PP", 	# PP: pos in seq
	"PF", 	# PF: Restriction File name (if PP not off)
	"PL", 	# PL: max Pattern Length
	"PN", 	# PN: max Nr of Pattern Symbols
	"PX", 	# PX: max Nr of consecutive x's
	"FN", 	# FN: max Nr of flexible spacers
	"FL", 	# FL: max Flexibility
	"FP", 	# FP: max Flex.Product
	"BI", 	# BI: Input Pattern Symbol File?
	"BF", 	# BF: Input Pattern Symbol File name (if BI on)
	"BN", 	# BN: Nr of Pattern Symbols Initial Search
	"scoring", 	# Pattern Scoring parameters
	"S", 	# S: Scoring
	"treefile", 	# Tree File (if Scoring = tree)
	"distfile", 	# Distances File (if Scoring = dist)
	"swissprotdb",
	"mdl_param", 	# MDL parameters (Z0-Z3) (if MDL scoring)
	"Z0", 	# Z0
	"Z1", 	# Z1
	"Z2", 	# Z2
	"Z3", 	# Z3
	"search", 	# Search parameters
	"G", 	# G: Pattern Graph from:
	"GF", 	# Alignment or Query Filename (if G set to al or query)
	"E", 	# E: Search Greediness
	"R", 	# R: Pattern Refinement
	"RG", 	# RG: Generalise ambiguous symbols (if Pattern Refinement on)
	"output", 	# Output options
	"OF", 	# OF: Output Filename
	"outfiles",
	"OP", 	# OP: PROSITE Pattern Format
	"ON", 	# ON: max number patterns
	"OA", 	# OA: max number Alignments
	"M", 	# M: Print Patterns in sequences
	"MR", 	# MR: ratio for printing
	"MV", 	# MV: print vertically
	"report",

    ];

    $self->{TYPE}  = {
	"pratt" => 'String',
	"seq" => 'Sequence',
	"seqformat" => 'Excl',
	"conservation" => 'Paragraph',
	"CM" => 'Integer',
	"Cpct" => 'Integer',
	"restrictions" => 'Paragraph',
	"PP" => 'Excl',
	"PF" => 'InFile',
	"PL" => 'Integer',
	"PN" => 'Integer',
	"PX" => 'Integer',
	"FN" => 'Integer',
	"FL" => 'Integer',
	"FP" => 'Integer',
	"BI" => 'Switch',
	"BF" => 'InFile',
	"BN" => 'Integer',
	"scoring" => 'Paragraph',
	"S" => 'Excl',
	"treefile" => 'InFile',
	"distfile" => 'InFile',
	"swissprotdb" => 'String',
	"mdl_param" => 'Paragraph',
	"Z0" => 'Integer',
	"Z1" => 'Integer',
	"Z2" => 'Integer',
	"Z3" => 'Integer',
	"search" => 'Paragraph',
	"G" => 'Excl',
	"GF" => 'InFile',
	"E" => 'Integer',
	"R" => 'Switch',
	"RG" => 'Switch',
	"output" => 'Paragraph',
	"OF" => 'OutFile',
	"outfiles" => 'Results',
	"OP" => 'Switch',
	"ON" => 'Integer',
	"OA" => 'Integer',
	"M" => 'Switch',
	"MR" => 'Integer',
	"MV" => 'Switch',
	"report" => 'Results',

    };

    $self->{FORMAT}  = {
	"pratt" => {
		"perl" => ' "pratt" ',
	},
	"seq" => {
		"perl" => '" $value"',
	},
	"seqformat" => {
		"perl" => '" $value"',
	},
	"conservation" => {
	},
	"CM" => {
		"perl" => '(defined $value)? " -CM $value":""',
	},
	"Cpct" => {
		"perl" => '(defined $value && $value != $vdef)? " -C% $value":""',
	},
	"restrictions" => {
	},
	"PP" => {
		"perl" => '($value && $value ne $vdef)? " -PP $value":""',
	},
	"PF" => {
		"perl" => '" -PF $value"',
	},
	"PL" => {
		"perl" => '(defined $value && $value != $vdef)? " -PL $value":""',
	},
	"PN" => {
		"perl" => '(defined $value && $value != $vdef)? " -PN $value":" -AUTO"',
	},
	"PX" => {
		"perl" => '(defined $value && $value != $vdef)? " -PX $value":""',
	},
	"FN" => {
		"perl" => '(defined $value && $value != $vdef)? " -FN $value":""',
	},
	"FL" => {
		"perl" => '(defined $value && $value != $vdef)? " -FL $value":""',
	},
	"FP" => {
		"perl" => '(defined $value && $value != $vdef)? " -FP $value":""',
	},
	"BI" => {
		"perl" => '($value)? " -BI on":""',
	},
	"BF" => {
		"perl" => '($value) ? " -BI $value" : "/local/gensoft/lib/pratt/Pratt.sets.big" ',
	},
	"BN" => {
		"perl" => '(defined $value && $value != $vdef)? " -BN $value":""',
	},
	"scoring" => {
	},
	"S" => {
		"perl" => '($value && $value != $vdef)? " -S $value":""',
	},
	"treefile" => {
		"perl" => '" -SF $value "',
	},
	"distfile" => {
		"perl" => '" -SF $value; "',
	},
	"swissprotdb" => {
		"perl" => '" -SF /local/gensoft/lib/pratt/sprot.dat"',
	},
	"mdl_param" => {
	},
	"Z0" => {
		"perl" => '($value != $vdef)? " -Z0 $value" : "" ',
	},
	"Z1" => {
		"perl" => '($value != $vdef)? " -Z1 $value" : ""',
	},
	"Z2" => {
		"perl" => '($value != $vdef)? " -Z2 $value" : ""',
	},
	"Z3" => {
		"perl" => '($value != $vdef)? " -Z3 $value" : ""',
	},
	"search" => {
	},
	"G" => {
		"perl" => '($value && $value ne $vdef)? " -G $value":""',
	},
	"GF" => {
		"perl" => '" -GF $value"',
	},
	"E" => {
		"perl" => '(defined $value && $value != $vdef)? " -E $value":""',
	},
	"R" => {
		"perl" => '(! $value)? " -R off" : "" ',
	},
	"RG" => {
		"perl" => '($value)? " -RG on" : "" ',
	},
	"output" => {
	},
	"OF" => {
		"perl" => '($value)? " -OF $value" : "" ',
	},
	"outfiles" => {
	},
	"OP" => {
		"perl" => '(! $value)? " -OP off " : "" ',
	},
	"ON" => {
		"perl" => '(defined $value && $value != $vdef)? " -ON $value":""',
	},
	"OA" => {
		"perl" => '(defined $value && $value != $vdef)? " -OA $value":""',
	},
	"M" => {
		"perl" => '(! $value)? " -M off " : "" ',
	},
	"MR" => {
		"perl" => '(defined $value && $value != $vdef)? " -MR $value":""',
	},
	"MV" => {
		"perl" => '($value)? " -MV on " : "" ',
	},
	"report" => {
	},

    };

    $self->{FILENAMES}  = {
	"outfiles" => '*.pat',
	"report" => 'report',

    };

    $self->{SEQFMT}  = {

    };

    $self->{GROUP}  = {
	"pratt" => 1,
	"seq" => 4,
	"seqformat" => 3,
	"conservation" => 5,
	"CM" => 5,
	"Cpct" => 5,
	"restrictions" => 5,
	"PP" => 5,
	"PF" => 5,
	"PL" => 5,
	"PN" => 5,
	"PX" => 5,
	"FN" => 5,
	"FL" => 5,
	"FP" => 5,
	"BI" => 5,
	"BF" => 5,
	"BN" => 5,
	"scoring" => 5,
	"S" => 5,
	"treefile" => 5,
	"distfile" => 5,
	"swissprotdb" => 5,
	"mdl_param" => 5,
	"Z0" => 5,
	"Z1" => 5,
	"Z2" => 5,
	"Z3" => 5,
	"search" => 5,
	"G" => 5,
	"GF" => 5,
	"E" => 5,
	"R" => 5,
	"RG" => 5,
	"output" => 5,
	"OF" => 5,
	"outfiles" => 5,
	"OP" => 5,
	"ON" => 5,
	"OA" => 5,
	"M" => 5,
	"MR" => 5,
	"MV" => 5,

    };

    $self->{BY_GROUP_PARAMETERS}  = [
	"report",
	"pratt",
	"seqformat",
	"seq",
	"CM",
	"Cpct",
	"restrictions",
	"PP",
	"PF",
	"PL",
	"PN",
	"PX",
	"FN",
	"FL",
	"FP",
	"BI",
	"BF",
	"BN",
	"scoring",
	"S",
	"treefile",
	"distfile",
	"swissprotdb",
	"mdl_param",
	"Z0",
	"Z1",
	"Z2",
	"Z3",
	"search",
	"G",
	"GF",
	"E",
	"R",
	"RG",
	"output",
	"OF",
	"outfiles",
	"OP",
	"ON",
	"OA",
	"M",
	"MR",
	"MV",
	"conservation",

    ];

    $self->{SIZE}  = {

    };

    $self->{ISHIDDEN}  = {
	"pratt" => 1,
	"seq" => 0,
	"seqformat" => 0,
	"conservation" => 0,
	"CM" => 0,
	"Cpct" => 0,
	"restrictions" => 0,
	"PP" => 0,
	"PF" => 0,
	"PL" => 0,
	"PN" => 0,
	"PX" => 0,
	"FN" => 0,
	"FL" => 0,
	"FP" => 0,
	"BI" => 0,
	"BF" => 0,
	"BN" => 0,
	"scoring" => 0,
	"S" => 0,
	"treefile" => 0,
	"distfile" => 0,
	"swissprotdb" => 1,
	"mdl_param" => 0,
	"Z0" => 0,
	"Z1" => 0,
	"Z2" => 0,
	"Z3" => 0,
	"search" => 0,
	"G" => 0,
	"GF" => 0,
	"E" => 0,
	"R" => 0,
	"RG" => 0,
	"output" => 0,
	"OF" => 0,
	"outfiles" => 0,
	"OP" => 0,
	"ON" => 0,
	"OA" => 0,
	"M" => 0,
	"MR" => 0,
	"MV" => 0,
	"report" => 0,

    };

    $self->{ISCOMMAND}  = {
	"pratt" => 1,
	"seq" => 0,
	"seqformat" => 0,
	"conservation" => 0,
	"CM" => 0,
	"Cpct" => 0,
	"restrictions" => 0,
	"PP" => 0,
	"PF" => 0,
	"PL" => 0,
	"PN" => 0,
	"PX" => 0,
	"FN" => 0,
	"FL" => 0,
	"FP" => 0,
	"BI" => 0,
	"BF" => 0,
	"BN" => 0,
	"scoring" => 0,
	"S" => 0,
	"treefile" => 0,
	"distfile" => 0,
	"swissprotdb" => 0,
	"mdl_param" => 0,
	"Z0" => 0,
	"Z1" => 0,
	"Z2" => 0,
	"Z3" => 0,
	"search" => 0,
	"G" => 0,
	"GF" => 0,
	"E" => 0,
	"R" => 0,
	"RG" => 0,
	"output" => 0,
	"OF" => 0,
	"outfiles" => 0,
	"OP" => 0,
	"ON" => 0,
	"OA" => 0,
	"M" => 0,
	"MR" => 0,
	"MV" => 0,
	"report" => 0,

    };

    $self->{ISMANDATORY}  = {
	"pratt" => 0,
	"seq" => 1,
	"seqformat" => 1,
	"conservation" => 0,
	"CM" => 0,
	"Cpct" => 0,
	"restrictions" => 0,
	"PP" => 0,
	"PF" => 0,
	"PL" => 0,
	"PN" => 0,
	"PX" => 0,
	"FN" => 0,
	"FL" => 0,
	"FP" => 0,
	"BI" => 0,
	"BF" => 0,
	"BN" => 0,
	"scoring" => 0,
	"S" => 0,
	"treefile" => 1,
	"distfile" => 1,
	"swissprotdb" => 0,
	"mdl_param" => 0,
	"Z0" => 1,
	"Z1" => 1,
	"Z2" => 1,
	"Z3" => 1,
	"search" => 0,
	"G" => 0,
	"GF" => 1,
	"E" => 0,
	"R" => 0,
	"RG" => 0,
	"output" => 0,
	"OF" => 0,
	"outfiles" => 0,
	"OP" => 0,
	"ON" => 0,
	"OA" => 0,
	"M" => 0,
	"MR" => 0,
	"MV" => 0,
	"report" => 0,

    };

    $self->{PROMPT}  = {
	"pratt" => "",
	"seq" => "Sequence File",
	"seqformat" => "Sequence File format",
	"conservation" => "Pattern conservation parameters",
	"CM" => "CM: min Nr of Seqs to Match (between 2 and 4)",
	"Cpct" => "C%: min Percentage Seqs to Match",
	"restrictions" => "Pattern restrictions parameters",
	"PP" => "PP: pos in seq",
	"PF" => "PF: Restriction File name (if PP not off)",
	"PL" => "PL: max Pattern Length",
	"PN" => "PN: max Nr of Pattern Symbols",
	"PX" => "PX: max Nr of consecutive x's",
	"FN" => "FN: max Nr of flexible spacers",
	"FL" => "FL: max Flexibility",
	"FP" => "FP: max Flex.Product",
	"BI" => "BI: Input Pattern Symbol File?",
	"BF" => "BF: Input Pattern Symbol File name (if BI on)",
	"BN" => "BN: Nr of Pattern Symbols Initial Search",
	"scoring" => "Pattern Scoring parameters",
	"S" => "S: Scoring",
	"treefile" => "Tree File (if Scoring = tree)",
	"distfile" => "Distances File (if Scoring = dist)",
	"swissprotdb" => "",
	"mdl_param" => "MDL parameters (Z0-Z3) (if MDL scoring)",
	"Z0" => "Z0",
	"Z1" => "Z1",
	"Z2" => "Z2",
	"Z3" => "Z3",
	"search" => "Search parameters",
	"G" => "G: Pattern Graph from:",
	"GF" => "Alignment or Query Filename (if G set to al or query)",
	"E" => "E: Search Greediness",
	"R" => "R: Pattern Refinement",
	"RG" => "RG: Generalise ambiguous symbols (if Pattern Refinement on)",
	"output" => "Output options",
	"OF" => "OF: Output Filename",
	"outfiles" => "",
	"OP" => "OP: PROSITE Pattern Format",
	"ON" => "ON: max number patterns",
	"OA" => "OA: max number Alignments",
	"M" => "M: Print Patterns in sequences",
	"MR" => "MR: ratio for printing",
	"MV" => "MV: print vertically",
	"report" => "",

    };

    $self->{ISSTANDOUT}  = {
	"pratt" => 0,
	"seq" => 0,
	"seqformat" => 0,
	"conservation" => 0,
	"CM" => 0,
	"Cpct" => 0,
	"restrictions" => 0,
	"PP" => 0,
	"PF" => 0,
	"PL" => 0,
	"PN" => 0,
	"PX" => 0,
	"FN" => 0,
	"FL" => 0,
	"FP" => 0,
	"BI" => 0,
	"BF" => 0,
	"BN" => 0,
	"scoring" => 0,
	"S" => 0,
	"treefile" => 0,
	"distfile" => 0,
	"swissprotdb" => 0,
	"mdl_param" => 0,
	"Z0" => 0,
	"Z1" => 0,
	"Z2" => 0,
	"Z3" => 0,
	"search" => 0,
	"G" => 0,
	"GF" => 0,
	"E" => 0,
	"R" => 0,
	"RG" => 0,
	"output" => 0,
	"OF" => 0,
	"outfiles" => 0,
	"OP" => 0,
	"ON" => 0,
	"OA" => 0,
	"M" => 0,
	"MR" => 0,
	"MV" => 0,
	"report" => 0,

    };

    $self->{VLIST}  = {

	"seqformat" => ['swissprot','swissprot','fasta','fasta','gcg','gcg',],
	"conservation" => ['CM','Cpct',],
	"restrictions" => ['PP','PF','PL','PN','PX','FN','FL','FP','BI','BF','BN',],
	"PP" => ['off','off','complete','complete pattern match has to be in this area','start','start: pattern match has to start in this area',],
	"scoring" => ['S','treefile','distfile','swissprotdb','mdl_param',],
	"S" => ['info','info (information content)','mdl','mdl (Minimum Description Length)','tree','tree (diversity calculated from a dendrogram)','dist','dist (distances matrix)','ppv','ppv (Positive Predictive Value)',],
	"mdl_param" => ['Z0','Z1','Z2','Z3',],
	"search" => ['G','GF','E','R','RG',],
	"G" => ['seq','seq','al','al (alignment)','query','query',],
	"output" => ['OF','outfiles','OP','ON','OA','M','MR','MV',],
    };

    $self->{FLIST}  = {

    };

    $self->{SEPARATOR}  = {

    };

    $self->{VDEF}  = {
	"seqformat" => 'fasta',
	"Cpct" => '100',
	"PP" => 'off',
	"PL" => '50',
	"PN" => '50',
	"PX" => '5',
	"FN" => '2',
	"FL" => '2',
	"FP" => '10',
	"BI" => '0',
	"BN" => '20',
	"S" => 'info',
	"Z0" => '10.00',
	"Z1" => '10.00',
	"Z2" => '3.00',
	"Z3" => '10.00',
	"G" => 'seq',
	"E" => '3',
	"R" => '1',
	"RG" => '0',
	"OP" => '1',
	"ON" => '50',
	"OA" => '50',
	"M" => '1',
	"MR" => '10',
	"MV" => '0',

    };

    $self->{PRECOND}  = {
	"pratt" => { "perl" => '1' },
	"seq" => { "perl" => '1' },
	"seqformat" => { "perl" => '1' },
	"conservation" => { "perl" => '1' },
	"CM" => { "perl" => '1' },
	"Cpct" => { "perl" => '1' },
	"restrictions" => { "perl" => '1' },
	"PP" => { "perl" => '1' },
	"PF" => {
		"perl" => '$PP && $PP ne "off"',
	},
	"PL" => { "perl" => '1' },
	"PN" => { "perl" => '1' },
	"PX" => { "perl" => '1' },
	"FN" => { "perl" => '1' },
	"FL" => { "perl" => '1' },
	"FP" => { "perl" => '1' },
	"BI" => { "perl" => '1' },
	"BF" => {
		"perl" => '$BI',
	},
	"BN" => { "perl" => '1' },
	"scoring" => { "perl" => '1' },
	"S" => { "perl" => '1' },
	"treefile" => {
		"perl" => '$S eq "tree"',
	},
	"distfile" => {
		"perl" => '$S eq "dist"',
	},
	"swissprotdb" => {
		"perl" => '$S eq "ppv"',
	},
	"mdl_param" => {
		"perl" => '$S eq "mdl"',
	},
	"Z0" => {
		"perl" => '$S eq "mdl"',
	},
	"Z1" => {
		"perl" => '$S eq "mdl"',
	},
	"Z2" => {
		"perl" => '$S eq "mdl"',
	},
	"Z3" => {
		"perl" => '$S eq "mdl"',
	},
	"search" => { "perl" => '1' },
	"G" => { "perl" => '1' },
	"GF" => {
		"perl" => '$G eq "al" or $G eq "query"',
	},
	"E" => { "perl" => '1' },
	"R" => { "perl" => '1' },
	"RG" => {
		"perl" => '$R',
	},
	"output" => { "perl" => '1' },
	"OF" => { "perl" => '1' },
	"outfiles" => { "perl" => '1' },
	"OP" => { "perl" => '1' },
	"ON" => { "perl" => '1' },
	"OA" => { "perl" => '1' },
	"M" => { "perl" => '1' },
	"MR" => { "perl" => '1' },
	"MV" => { "perl" => '1' },
	"report" => { "perl" => '1' },

    };

    $self->{CTRL}  = {
	"CM" => {
		"perl" => {
			'$value && ($value < 2 || $value > 4)' => "value must be between 2 and 4",
			'$value =~ /\\./ ' => "value must be an integer between 2 and 4",
		},
	},
	"PP" => {
		"perl" => {
			'$PP && $PP ne "off" && ! $PF' => "you must give a file to define the regions (PF)",
		},
	},

    };

    $self->{PIPEOUT}  = {

    };

    $self->{WITHPIPEOUT}  = {

    };

    $self->{PIPEIN}  = {

    };

    $self->{WITHPIPEIN}  = {

    };

    $self->{ISCLEAN}  = {
	"pratt" => 0,
	"seq" => 0,
	"seqformat" => 0,
	"conservation" => 0,
	"CM" => 0,
	"Cpct" => 0,
	"restrictions" => 0,
	"PP" => 0,
	"PF" => 0,
	"PL" => 0,
	"PN" => 0,
	"PX" => 0,
	"FN" => 0,
	"FL" => 0,
	"FP" => 0,
	"BI" => 0,
	"BF" => 0,
	"BN" => 0,
	"scoring" => 0,
	"S" => 0,
	"treefile" => 0,
	"distfile" => 0,
	"swissprotdb" => 0,
	"mdl_param" => 0,
	"Z0" => 0,
	"Z1" => 0,
	"Z2" => 0,
	"Z3" => 0,
	"search" => 0,
	"G" => 0,
	"GF" => 0,
	"E" => 0,
	"R" => 0,
	"RG" => 0,
	"output" => 0,
	"OF" => 0,
	"outfiles" => 0,
	"OP" => 0,
	"ON" => 0,
	"OA" => 0,
	"M" => 0,
	"MR" => 0,
	"MV" => 0,
	"report" => 1,

    };

    $self->{ISSIMPLE}  = {
	"pratt" => 0,
	"seq" => 1,
	"seqformat" => 1,
	"conservation" => 0,
	"CM" => 0,
	"Cpct" => 0,
	"restrictions" => 0,
	"PP" => 0,
	"PF" => 0,
	"PL" => 0,
	"PN" => 0,
	"PX" => 0,
	"FN" => 0,
	"FL" => 0,
	"FP" => 0,
	"BI" => 0,
	"BF" => 0,
	"BN" => 0,
	"scoring" => 0,
	"S" => 0,
	"treefile" => 0,
	"distfile" => 0,
	"swissprotdb" => 0,
	"mdl_param" => 0,
	"Z0" => 0,
	"Z1" => 0,
	"Z2" => 0,
	"Z3" => 0,
	"search" => 0,
	"G" => 0,
	"GF" => 0,
	"E" => 0,
	"R" => 0,
	"RG" => 0,
	"output" => 0,
	"OF" => 0,
	"outfiles" => 0,
	"OP" => 0,
	"ON" => 0,
	"OA" => 0,
	"M" => 0,
	"MR" => 0,
	"MV" => 0,
	"report" => 0,

    };

    $self->{PARAMFILE}  = {

    };

    $self->{COMMENT}  = {
	"PF" => [
		"This file contains lines to restrict pattern searches to certain regions in a sequence, say ACE2_YEAST: ",
		">ACE2_YEAST (100,200)",
	],
	"BF" => [
		"default file is: /local/gensoft/lib/pratt/Pratt.sets.big",
	],
	"GF" => [
		"alignment file must be in CLUSTALW format",
		"query file must be in Fasta format",
	],

    };

    $self->{SCALEMIN}  = {

    };

    $self->{SCALEMAX}  = {

    };

    $self->{SCALEINC}  = {

    };

    $self->{INFO}  = {

    };

# -- end of definitions extracted from /local/gensoft/lib/Pise/5.a/PerlDef/pratt.pm



    $self->_init_params(@params);

    return $self;
}



1; # Needed to keep compiler happy

