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# $Id: pratt.pm,v 1.6 2006/07/04 22:23:35 mauricio 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
HideShow 189 lines of Pod
=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/wiki/Mailing_lists  - 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.open-bio.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);
HideShow 14 lines of Pod
=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