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# $Id: gibbs.pm,v 1.6 2006/07/04 22:23:34 mauricio Exp $
# BioPerl module for Bio::Tools::Run::PiseApplication::gibbs
#
# Cared for by Catherine Letondal <letondal@pasteur.fr>
#
# For copyright and disclaimer see below.
#
# POD documentation - main docs before the code
HideShow 172 lines of Pod
=head1 NAME
Bio::Tools::Run::PiseApplication::gibbs
=head1 SYNOPSIS
  #
=head1 DESCRIPTION
Bio::Tools::Run::PiseApplication::gibbs
      Bioperl class for:
        GIBBS   motif sampling (Neuwald & Lawrence)
        References:
                Neuwald, Liu, and Lawrence (1995). Gibbs motif sampling: detection of bacterial outer membrane protein repeats.  Protein Science 4, 1618-1632. (for Gibbs site sampling, Gibbs motif sampling, purge, and scan programs)
                Lawrence, Altschul, Boguski, Liu, Neuwald and Wootton (1993) Detecting Subtle Sequence Signals: A Gibbs Sampling Strategy for Multiple Alignment, Science 262:208-214.  (for Gibbs site sampling program)
      Parameters: 
        (see also:
          http://bioweb.pasteur.fr/seqanal/interfaces/gibbs.html 
         for available values):
                gibbs (String)
                sequence (Sequence)
                        Sequences file
                lengths (String)
                        Lengths of elements for each type (eg: e1,e2)
                expected (String)
                        Expected number of elements for each type (eg: l1,l2) (motif sampler)
                purge (Switch)
                        Run purge to remove closely related sequences
                scan (Switch)
                        Create a scan output file (file.sn) (-f)
                sites_cycles (Integer)
                        Maximum number of cycles in each run (-m)
                element_order (Switch)
                        Use element order in probabilities (-o)
                sites_pseudo_counts (Float)
                        Pseudo counts for ordering model (-q)
                readings (Integer)
                        Number of near-optimum readings taken (-R)
                wilcoxon (Switch)
                        Output wilcoxon rank test information (-w)
                fractional_weight (Float)
                        Fractional weight (0 to 1.0) on priors (-W)
                cycles (Integer)
                        Number of cycles between shifts (sites sampler) or maximum number of cycles per run  (motif sampler) (-c)
                cutoff (Float)
                        Prob. cutoff for near optimum sampling (-C)
                fragmentation (Switch)
                        Use fragmentation (-d)
                convergence (Integer)
                        Rapid convergence limit (higher = longer to converge) (-L)
                nucleic (Switch)
                        Use nucleic acid alphabet (-n)
                pseudo_counts (Float)
                        Number of pseudo counts for product multinomial model (-p)
                shuffle (Switch)
                        Randomly shuffle input sequences (-r)
                seed (Integer)
                        Seed for random number generator (-s)
                sampling_runs (Integer)
                        Maximum number of sampling runs (-t)
                low_complexity (Switch)
                        Remove protein low complexity regions (-x)
                score (Integer)
                        Score threshold
                method (Excl)
                        Heuristic method
                keep (Switch)
                        Keep first sequence in the set (-q)
                mask (Switch)
                        Use xnu to mask low complexity regions (-x)
                purge_sep (String)
                scan_file (OutFile)
                        pipe: gibbs_motif
=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/gibbs.html
=item *
Bio::Tools::Run::PiseApplication
=item *
Bio::Tools::Run::AnalysisFactory::Pise
=item *
Bio::Tools::Run::PiseJob
=back
=cut
#'
package Bio::Tools::Run::PiseApplication::gibbs;
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 $gibbs = Bio::Tools::Run::PiseApplication::gibbs->new($location, $email, @params);
 Function: Creates a Bio::Tools::Run::PiseApplication::gibbs 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 $gibbs = $factory->program('gibbs');
 Example : -
 Returns : An instance of Bio::Tools::Run::PiseApplication::gibbs.
=cut
sub new {
    my ($class, $location, $email, @params) = @_;
    my $self = $class->SUPER::new($location, $email);
# -- begin of definitions extracted from /local/gensoft/lib/Pise/5.a/PerlDef/gibbs.pm
    $self->{COMMAND}   = "gibbs";
    $self->{VERSION}   = "5.a";
    $self->{TITLE}   = "GIBBS";
    $self->{DESCRIPTION}   = "motif sampling";
    $self->{OPT_EMAIL}   = 0;
    $self->{AUTHORS}   = "Neuwald & Lawrence";
    $self->{REFERENCE}   = [
         "Neuwald, Liu, and Lawrence (1995). Gibbs motif sampling: detection of bacterial outer membrane protein repeats.  Protein Science 4, 1618-1632. (for Gibbs site sampling, Gibbs motif sampling, purge, and scan programs)",
         "Lawrence, Altschul, Boguski, Liu, Neuwald and Wootton (1993) Detecting Subtle Sequence Signals: A Gibbs Sampling Strategy for Multiple Alignment, Science 262:208-214.  (for Gibbs site sampling program)",
 ];
    $self->{_INTERFACE_STANDOUT} = undef;
    $self->{_STANDOUT_FILE} = undef;
    $self->{TOP_PARAMETERS}  = [ 
        "gibbs",
        "sequence",
        "lengths",
        "expected",
        "purge",
        "output_options",
        "control_options",
        "cycles",
        "cutoff",
        "fragmentation",
        "convergence",
        "nucleic",
        "pseudo_counts",
        "shuffle",
        "seed",
        "sampling_runs",
        "low_complexity",
        "purge_options",
        "scan_file",
    ];
    $self->{PARAMETERS_ORDER}  = [
        "gibbs",
        "sequence",     # Sequences file
        "lengths",      # Lengths of elements for each type (eg: e1,e2)
        "expected",     # Expected number of elements for each type (eg: l1,l2) (motif sampler)
        "purge",        # Run purge to remove closely related sequences
        "output_options",       # Output options
        "scan",         # Create a scan output file (file.sn) (-f)
        "control_options",      # Control options
        "sites_options",        # Sites sampler options
        "sites_cycles",         # Maximum number of cycles in each run (-m)
        "element_order",        # Use element order in probabilities (-o)
        "sites_pseudo_counts",  # Pseudo counts for ordering model (-q)
        "readings",     # Number of near-optimum readings taken (-R)
        "motif_options",        # Motif sampler options
        "wilcoxon",     # Output wilcoxon rank test information (-w)
        "fractional_weight",    # Fractional weight (0 to 1.0) on priors (-W)
        "cycles",       # Number of cycles between shifts (sites sampler) or maximum number of cycles per run  (motif sampler) (-c)
        "cutoff",       # Prob. cutoff for near optimum sampling (-C)
        "fragmentation",        # Use fragmentation (-d)
        "convergence",  # Rapid convergence limit (higher = longer to converge) (-L)
        "nucleic",      # Use nucleic acid alphabet (-n)
        "pseudo_counts",        # Number of pseudo counts for product multinomial model (-p)
        "shuffle",      # Randomly shuffle input sequences (-r)
        "seed",         # Seed for random number generator (-s)
        "sampling_runs",        # Maximum number of sampling runs (-t)
        "low_complexity",       # Remove protein low complexity regions (-x)
        "purge_options",        # purge options
        "score",        # Score threshold
        "method",       # Heuristic method
        "keep",         # Keep first sequence in the set (-q)
        "mask",         # Use xnu to mask low complexity regions (-x)
        "purge_sep",
        "purged_sequence",
        "scan_file",
    ];
    $self->{TYPE}  = {
        "gibbs" => 'String',
        "sequence" => 'Sequence',
        "lengths" => 'String',
        "expected" => 'String',
        "purge" => 'Switch',
        "output_options" => 'Paragraph',
        "scan" => 'Switch',
        "control_options" => 'Paragraph',
        "sites_options" => 'Paragraph',
        "sites_cycles" => 'Integer',
        "element_order" => 'Switch',
        "sites_pseudo_counts" => 'Float',
        "readings" => 'Integer',
        "motif_options" => 'Paragraph',
        "wilcoxon" => 'Switch',
        "fractional_weight" => 'Float',
        "cycles" => 'Integer',
        "cutoff" => 'Float',
        "fragmentation" => 'Switch',
        "convergence" => 'Integer',
        "nucleic" => 'Switch',
        "pseudo_counts" => 'Float',
        "shuffle" => 'Switch',
        "seed" => 'Integer',
        "sampling_runs" => 'Integer',
        "low_complexity" => 'Switch',
        "purge_options" => 'Paragraph',
        "score" => 'Integer',
        "method" => 'Excl',
        "keep" => 'Switch',
        "mask" => 'Switch',
        "purge_sep" => 'String',
        "purged_sequence" => 'Results',
        "scan_file" => 'OutFile',
    };
    $self->{FORMAT}  = {
        "gibbs" => {
                "perl" => '"gibbs "',
        },
        "sequence" => {
                "perl" => '($purge)? " $sequence.b$score" : " $sequence"',
        },
        "lengths" => {
                "perl" => '" $value"',
        },
        "expected" => {
                "perl" => '" $value"',
        },
        "purge" => {
                "perl" => '($value)? "purge $sequence" : ""',
        },
        "output_options" => {
        },
        "scan" => {
                "perl" => '($value)? " -f" : ""',
        },
        "control_options" => {
        },
        "sites_options" => {
        },
        "sites_cycles" => {
                "perl" => '(defined $value)? " -m$value" : ""',
        },
        "element_order" => {
                "perl" => '($value)? " -o" : ""',
        },
        "sites_pseudo_counts" => {
                "perl" => '(defined $value)? " -q$value" : ""',
        },
        "readings" => {
                "perl" => '(defined $value)? " -R$value" : ""',
        },
        "motif_options" => {
        },
        "wilcoxon" => {
                "perl" => '($value)? " -w" : ""',
        },
        "fractional_weight" => {
                "perl" => '(defined $value)? " -W$value" : ""',
        },
        "cycles" => {
                "perl" => '(defined $value)? " -c$value" : ""',
        },
        "cutoff" => {
                "perl" => '(defined $value)? " -C$value" : ""',
        },
        "fragmentation" => {
                "perl" => '($value)? "" : " -d"',
        },
        "convergence" => {
                "perl" => '(defined $value)? " -L$value" : ""',
        },
        "nucleic" => {
                "perl" => '($value)? " -n" : ""',
        },
        "pseudo_counts" => {
                "perl" => '(defined $value)? " -p$value" : ""',
        },
        "shuffle" => {
                "perl" => '($value)? " -r" : ""',
        },
        "seed" => {
                "perl" => '(defined $value)? " -s$value" : ""',
        },
        "sampling_runs" => {
                "perl" => '(defined $value)? " -t$value" : ""',
        },
        "low_complexity" => {
                "perl" => '($value)? "" : " -x"',
        },
        "purge_options" => {
        },
        "score" => {
                "perl" => '" $value"',
        },
        "method" => {
                "perl" => '($value && $value ne $vdef)? " $value" : ""',
        },
        "keep" => {
                "perl" => '($value)? " -q" : ""',
        },
        "mask" => {
                "perl" => '($value)? "" : " -x"',
        },
        "purge_sep" => {
                "perl" => '";"',
        },
        "purged_sequence" => {
        },
        "scan_file" => {
                "perl" => '""',
        },
    };
    $self->{FILENAMES}  = {
        "purged_sequence" => '$sequence.b$score',
    };
    $self->{SEQFMT}  = {
        "sequence" => [8],
    };
    $self->{GROUP}  = {
        "gibbs" => 0,
        "sequence" => 1,
        "lengths" => 2,
        "expected" => 3,
        "purge" => -10,
        "output_options" => 4,
        "scan" => 4,
        "control_options" => 4,
        "sites_options" => 4,
        "sites_cycles" => 4,
        "element_order" => 4,
        "sites_pseudo_counts" => 4,
        "readings" => 4,
        "motif_options" => 4,
        "wilcoxon" => 4,
        "fractional_weight" => 4,
        "cycles" => 4,
        "cutoff" => 4,
        "fragmentation" => 4,
        "convergence" => 4,
        "nucleic" => 4,
        "pseudo_counts" => 4,
        "shuffle" => 4,
        "seed" => 4,
        "sampling_runs" => 4,
        "low_complexity" => 4,
        "score" => -9,
        "method" => -8,
        "keep" => -8,
        "mask" => -8,
        "purge_sep" => -1,
    };
    $self->{BY_GROUP_PARAMETERS}  = [
        "purge",
        "score",
        "mask",
        "method",
        "keep",
        "purge_sep",
        "gibbs",
        "purge_options",
        "purged_sequence",
        "scan_file",
        "sequence",
        "lengths",
        "expected",
        "motif_options",
        "wilcoxon",
        "fractional_weight",
        "cycles",
        "cutoff",
        "fragmentation",
        "convergence",
        "nucleic",
        "pseudo_counts",
        "shuffle",
        "seed",
        "sampling_runs",
        "low_complexity",
        "output_options",
        "scan",
        "control_options",
        "sites_options",
        "sites_cycles",
        "element_order",
        "sites_pseudo_counts",
        "readings",
    ];
    $self->{SIZE}  = {
    };
    $self->{ISHIDDEN}  = {
        "gibbs" => 1,
        "sequence" => 0,
        "lengths" => 0,
        "expected" => 0,
        "purge" => 0,
        "output_options" => 0,
        "scan" => 0,
        "control_options" => 0,
        "sites_options" => 0,
        "sites_cycles" => 0,
        "element_order" => 0,
        "sites_pseudo_counts" => 0,
        "readings" => 0,
        "motif_options" => 0,
        "wilcoxon" => 0,
        "fractional_weight" => 0,
        "cycles" => 0,
        "cutoff" => 0,
        "fragmentation" => 0,
        "convergence" => 0,
        "nucleic" => 0,
        "pseudo_counts" => 0,
        "shuffle" => 0,
        "seed" => 0,
        "sampling_runs" => 0,
        "low_complexity" => 0,
        "purge_options" => 0,
        "score" => 0,
        "method" => 0,
        "keep" => 0,
        "mask" => 0,
        "purge_sep" => 1,
        "purged_sequence" => 0,
        "scan_file" => 1,
    };
    $self->{ISCOMMAND}  = {
        "gibbs" => 1,
        "sequence" => 0,
        "lengths" => 0,
        "expected" => 0,
        "purge" => 0,
        "output_options" => 0,
        "scan" => 0,
        "control_options" => 0,
        "sites_options" => 0,
        "sites_cycles" => 0,
        "element_order" => 0,
        "sites_pseudo_counts" => 0,
        "readings" => 0,
        "motif_options" => 0,
        "wilcoxon" => 0,
        "fractional_weight" => 0,
        "cycles" => 0,
        "cutoff" => 0,
        "fragmentation" => 0,
        "convergence" => 0,
        "nucleic" => 0,
        "pseudo_counts" => 0,
        "shuffle" => 0,
        "seed" => 0,
        "sampling_runs" => 0,
        "low_complexity" => 0,
        "purge_options" => 0,
        "score" => 0,
        "method" => 0,
        "keep" => 0,
        "mask" => 0,
        "purge_sep" => 0,
        "purged_sequence" => 0,
        "scan_file" => 0,
    };
    $self->{ISMANDATORY}  = {
        "gibbs" => 0,
        "sequence" => 1,
        "lengths" => 1,
        "expected" => 0,
        "purge" => 0,
        "output_options" => 0,
        "scan" => 0,
        "control_options" => 0,
        "sites_options" => 0,
        "sites_cycles" => 0,
        "element_order" => 0,
        "sites_pseudo_counts" => 0,
        "readings" => 0,
        "motif_options" => 0,
        "wilcoxon" => 0,
        "fractional_weight" => 0,
        "cycles" => 0,
        "cutoff" => 0,
        "fragmentation" => 0,
        "convergence" => 0,
        "nucleic" => 0,
        "pseudo_counts" => 0,
        "shuffle" => 0,
        "seed" => 0,
        "sampling_runs" => 0,
        "low_complexity" => 0,
        "purge_options" => 0,
        "score" => 1,
        "method" => 0,
        "keep" => 0,
        "mask" => 0,
        "purge_sep" => 0,
        "purged_sequence" => 0,
        "scan_file" => 0,
    };
    $self->{PROMPT}  = {
        "gibbs" => "",
        "sequence" => "Sequences file",
        "lengths" => "Lengths of elements for each type (eg: e1,e2)",
        "expected" => "Expected number of elements for each type (eg: l1,l2) (motif sampler)",
        "purge" => "Run purge to remove closely related sequences",
        "output_options" => "Output options",
        "scan" => "Create a scan output file (file.sn) (-f)",
        "control_options" => "Control options",
        "sites_options" => "Sites sampler options",
        "sites_cycles" => "Maximum number of cycles in each run (-m)",
        "element_order" => "Use element order in probabilities (-o)",
        "sites_pseudo_counts" => "Pseudo counts for ordering model (-q)",
        "readings" => "Number of near-optimum readings taken (-R)",
        "motif_options" => "Motif sampler options",
        "wilcoxon" => "Output wilcoxon rank test information (-w)",
        "fractional_weight" => "Fractional weight (0 to 1.0) on priors (-W)",
        "cycles" => "Number of cycles between shifts (sites sampler) or maximum number of cycles per run  (motif sampler) (-c)",
        "cutoff" => "Prob. cutoff for near optimum sampling (-C)",
        "fragmentation" => "Use fragmentation (-d)",
        "convergence" => "Rapid convergence limit (higher = longer to converge) (-L)",
        "nucleic" => "Use nucleic acid alphabet (-n)",
        "pseudo_counts" => "Number of pseudo counts for product multinomial model (-p)",
        "shuffle" => "Randomly shuffle input sequences (-r)",
        "seed" => "Seed for random number generator (-s)",
        "sampling_runs" => "Maximum number of sampling runs (-t)",
        "low_complexity" => "Remove protein low complexity regions (-x)",
        "purge_options" => "purge options",
        "score" => "Score threshold",
        "method" => "Heuristic method",
        "keep" => "Keep first sequence in the set (-q)",
        "mask" => "Use xnu to mask low complexity regions (-x)",
        "purge_sep" => "",
        "purged_sequence" => "",
        "scan_file" => "",
    };
    $self->{ISSTANDOUT}  = {
        "gibbs" => 0,
        "sequence" => 0,
        "lengths" => 0,
        "expected" => 0,
        "purge" => 0,
        "output_options" => 0,
        "scan" => 0,
        "control_options" => 0,
        "sites_options" => 0,
        "sites_cycles" => 0,
        "element_order" => 0,
        "sites_pseudo_counts" => 0,
        "readings" => 0,
        "motif_options" => 0,
        "wilcoxon" => 0,
        "fractional_weight" => 0,
        "cycles" => 0,
        "cutoff" => 0,
        "fragmentation" => 0,
        "convergence" => 0,
        "nucleic" => 0,
        "pseudo_counts" => 0,
        "shuffle" => 0,
        "seed" => 0,
        "sampling_runs" => 0,
        "low_complexity" => 0,
        "purge_options" => 0,
        "score" => 0,
        "method" => 0,
        "keep" => 0,
        "mask" => 0,
        "purge_sep" => 0,
        "purged_sequence" => 0,
        "scan_file" => 0,
    };
    $self->{VLIST}  = {
        "output_options" => ['scan',],
        "control_options" => ['sites_options','motif_options',],
        "sites_options" => ['sites_cycles','element_order','sites_pseudo_counts','readings',],
        "motif_options" => ['wilcoxon','fractional_weight',],
        "purge_options" => ['score','method','keep','mask','purge_sep','purged_sequence',],
        "method" => ['-b','-b: blast','-e','-e: exhaustive',],
    };
    $self->{FLIST}  = {
    };
    $self->{SEPARATOR}  = {
    };
    $self->{VDEF}  = {
        "purge" => '0',
        "scan" => '0',
        "element_order" => '0',
        "wilcoxon" => '0',
        "fragmentation" => '1',
        "nucleic" => '0',
        "shuffle" => '0',
        "low_complexity" => '1',
        "method" => '-b',
        "keep" => '0',
        "mask" => '1',
        "scan_file" => '"$sequence.sn"',
    };
    $self->{PRECOND}  = {
        "gibbs" => { "perl" => '1' },
        "sequence" => { "perl" => '1' },
        "lengths" => { "perl" => '1' },
        "expected" => { "perl" => '1' },
        "purge" => { "perl" => '1' },
        "output_options" => { "perl" => '1' },
        "scan" => { "perl" => '1' },
        "control_options" => { "perl" => '1' },
        "sites_options" => { "perl" => '1' },
        "sites_cycles" => { "perl" => '1' },
        "element_order" => { "perl" => '1' },
        "sites_pseudo_counts" => { "perl" => '1' },
        "readings" => { "perl" => '1' },
        "motif_options" => { "perl" => '1' },
        "wilcoxon" => { "perl" => '1' },
        "fractional_weight" => { "perl" => '1' },
        "cycles" => { "perl" => '1' },
        "cutoff" => { "perl" => '1' },
        "fragmentation" => { "perl" => '1' },
        "convergence" => { "perl" => '1' },
        "nucleic" => { "perl" => '1' },
        "pseudo_counts" => { "perl" => '1' },
        "shuffle" => { "perl" => '1' },
        "seed" => { "perl" => '1' },
        "sampling_runs" => { "perl" => '1' },
        "low_complexity" => { "perl" => '1' },
        "purge_options" => {
                "perl" => '$purge',
        },
        "score" => {
                "perl" => '$purge',
        },
        "method" => {
                "perl" => '$purge',
        },
        "keep" => {
                "perl" => '$purge',
        },
        "mask" => {
                "perl" => '$purge',
        },
        "purge_sep" => {
                "perl" => '$purge',
        },
        "purged_sequence" => {
                "perl" => '$purge',
        },
        "scan_file" => { "perl" => '1' },
    };
    $self->{CTRL}  = {
        "fractional_weight" => {
                "perl" => {
                        '$value < 0 || $value > 1.0' => "The value must be between 0 to 1.0",
                },
        },
        "cutoff" => {
                "perl" => {
                        '$value < 0 || $value > 1' => "(0 < Cutoff <= 1)",
                },
        },
    };
    $self->{PIPEOUT}  = {
        "scan_file" => {
                 '$scan' => "gibbs_motif",
        },
    };
    $self->{WITHPIPEOUT}  = {
    };
    $self->{PIPEIN}  = {
    };
    $self->{WITHPIPEIN}  = {
    };
    $self->{ISCLEAN}  = {
        "gibbs" => 0,
        "sequence" => 0,
        "lengths" => 0,
        "expected" => 0,
        "purge" => 0,
        "output_options" => 0,
        "scan" => 0,
        "control_options" => 0,
        "sites_options" => 0,
        "sites_cycles" => 0,
        "element_order" => 0,
        "sites_pseudo_counts" => 0,
        "readings" => 0,
        "motif_options" => 0,
        "wilcoxon" => 0,
        "fractional_weight" => 0,
        "cycles" => 0,
        "cutoff" => 0,
        "fragmentation" => 0,
        "convergence" => 0,
        "nucleic" => 0,
        "pseudo_counts" => 0,
        "shuffle" => 0,
        "seed" => 0,
        "sampling_runs" => 0,
        "low_complexity" => 0,
        "purge_options" => 0,
        "score" => 0,
        "method" => 0,
        "keep" => 0,
        "mask" => 0,
        "purge_sep" => 0,
        "purged_sequence" => 0,
        "scan_file" => 0,
    };
    $self->{ISSIMPLE}  = {
        "gibbs" => 0,
        "sequence" => 1,
        "lengths" => 1,
        "expected" => 1,
        "purge" => 0,
        "output_options" => 0,
        "scan" => 0,
        "control_options" => 0,
        "sites_options" => 0,
        "sites_cycles" => 0,
        "element_order" => 0,
        "sites_pseudo_counts" => 0,
        "readings" => 0,
        "motif_options" => 0,
        "wilcoxon" => 0,
        "fractional_weight" => 0,
        "cycles" => 0,
        "cutoff" => 0,
        "fragmentation" => 0,
        "convergence" => 0,
        "nucleic" => 0,
        "pseudo_counts" => 0,
        "shuffle" => 0,
        "seed" => 0,
        "sampling_runs" => 0,
        "low_complexity" => 0,
        "purge_options" => 0,
        "score" => 0,
        "method" => 0,
        "keep" => 0,
        "mask" => 0,
        "purge_sep" => 0,
        "purged_sequence" => 0,
        "scan_file" => 0,
    };
    $self->{PARAMFILE}  = {
    };
    $self->{COMMENT}  = {
        "lengths" => [
                "format:",
                "long[,long]",
                "example:",
                "18,18,18",
        ],
        "expected" => [
                "format:",
                "long[,long]",
                "example:",
                "18,18,18",
        ],
    };
    $self->{SCALEMIN}  = {
    };
    $self->{SCALEMAX}  = {
    };
    $self->{SCALEINC}  = {
    };
    $self->{INFO}  = {
    };
# -- end of definitions extracted from /local/gensoft/lib/Pise/5.a/PerlDef/gibbs.pm
    $self->_init_params(@params);
    return $self;
}
1; # Needed to keep compiler happy