# $Id: codonw.pm,v 1.3 2003/06/05 19:15:18 letondal Exp $
# BioPerl module for Bio::Tools::Run::PiseApplication::codonw
#
# 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::codonw

=head1 SYNOPSIS

  #

=head1 DESCRIPTION

Bio::Tools::Run::PiseApplication::codonw

      Bioperl class for:

	codonw	Correspondence Analysis of Codon Usage (J. Peden)


      Parameters: 

        (see also:
          http://bioweb.pasteur.fr/seqanal/interfaces/codonw.html 
         for available values):


		codonw (String)

		outfiles (String)

		seqfile (Sequence)
			Sequences File

		gc (Excl)
			Genetic codes

		fop_values (Excl)
			Fop/CBI values

		cai_values (Excl)
			CAI values

		output_type (Switch)
			Output Computer readable

		genes (Switch)
			Concatenate genes (instead of individual genes)

		CAI (Switch)
			Codon Adaptation Index (CAI)

		Fop (Switch)
			Frequency of OPtimal codons (Fop)

		CBI (Switch)
			Codon bias index (CBI)

		cai_file (InFile)
			User input file of CAI values (may be computed by a previous COA)
			pipe: codonw_coa_file

		fop_file (InFile)
			User input file of Fop values (may be computed by a previous COA)

		cbi_file (InFile)
			User input file of CBI values (may be computed by a previous COA)

		ENc (Switch)
			Effective Number of Codons (ENc)

		GC (Switch)
			GC content of gene (G+C)

		GC3s (Switch)
			GC of silent 3rd codon posit. (GC3s)

		silent_bc (Switch)
			Silent base composition

		all_indices (Switch)
			All the above indices

		L_sym (Integer)
			Number of synonymous codons (L_sym)

		L_aa (Switch)
			Total Number of synonymous and non-synonymous codons (L_aa)

		Hydro (Switch)
			Hydrophobicity of protein (Hydro)

		Aromo (Switch)
			Aromaticity of protein (Aromo)

		bulk_output_option (Excl)
			Other output option

		coa_cu (Switch)
			COA on codon usage

		coa_rscu (Switch)
			COA on RSCU

		coa_aa (Switch)
			COA on Amino Acid usage

		coa_expert (Switch)
			Generate detailed(expert) statistics on COA

		coa_axes (Integer)
			Select number of axis to record

		coa_num (Integer)
			Select number of genes to use to identify optimal codons

		cai_coa (OutFile)
			pipe: codonw_coa_file

=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/codonw.html

=item *

Bio::Tools::Run::PiseApplication

=item *

Bio::Tools::Run::AnalysisFactory::Pise

=item *

Bio::Tools::Run::PiseJob

=back

=cut

#'
package Bio::Tools::Run::PiseApplication::codonw;

use vars qw(@ISA);
use strict;
use Bio::Tools::Run::PiseApplication;

@ISA = qw(Bio::Tools::Run::PiseApplication);

=head2 new

 Title   : new()
 Usage   : my $codonw = Bio::Tools::Run::PiseApplication::codonw->new($location, $email, @params);
 Function: Creates a Bio::Tools::Run::PiseApplication::codonw 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 $codonw = $factory->program('codonw');
 Example : -
 Returns : An instance of Bio::Tools::Run::PiseApplication::codonw.

=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/codonw.pm

    $self->{COMMAND}   = "codonw";
    $self->{VERSION}   = "5.a";
    $self->{TITLE}   = "codonw";

    $self->{DESCRIPTION}   = "Correspondence Analysis of Codon Usage";

    $self->{OPT_EMAIL}   = 0;

    $self->{AUTHORS}   = "J. Peden";

    $self->{_INTERFACE_STANDOUT} = undef;
    $self->{_STANDOUT_FILE} = undef;

    $self->{TOP_PARAMETERS}  = [ 
	"codonw",
	"outfiles",
	"results_files",
	"seqfile",
	"defaults",
	"CU_options",
	"COA_options",
	"cai_coa",
	"coa_files",

    ];

    $self->{PARAMETERS_ORDER}  = [
	"codonw",
	"outfiles",
	"results_files",
	"seqfile", 	# Sequences File
	"defaults", 	# Defaults settings
	"gc", 	# Genetic codes
	"fop_values", 	# Fop/CBI values
	"cai_values", 	# CAI values
	"output_type", 	# Output Computer readable
	"genes", 	# Concatenate genes (instead of individual genes)
	"CU_options", 	# Codon usage indices
	"CAI", 	# Codon Adaptation Index (CAI)
	"Fop", 	# Frequency of OPtimal codons (Fop)
	"CBI", 	# Codon bias index (CBI)
	"cai_file", 	# User input file of CAI values (may be computed by a previous COA)
	"fop_file", 	# User input file of Fop values (may be computed by a previous COA)
	"cbi_file", 	# User input file of CBI values (may be computed by a previous COA)
	"ENc", 	# Effective Number of Codons (ENc)
	"GC", 	# GC content of gene (G+C)
	"GC3s", 	# GC of silent 3rd codon posit. (GC3s)
	"silent_bc", 	# Silent base composition
	"all_indices", 	# All the above indices
	"L_sym", 	# Number of synonymous codons (L_sym)
	"L_aa", 	# Total Number of synonymous and non-synonymous codons (L_aa)
	"Hydro", 	# Hydrophobicity of protein (Hydro)
	"Aromo", 	# Aromaticity of protein (Aromo)
	"bulk_output_option", 	# Other output option
	"COA_options", 	# Correspondence analysis options (available for several sequences)
	"coa_cu", 	# COA on codon usage
	"coa_rscu", 	# COA on RSCU
	"coa_aa", 	# COA on Amino Acid usage
	"coa_expert", 	# Generate detailed(expert) statistics on COA
	"coa_axes", 	# Select number of axis to record
	"coa_num", 	# Select number of genes to use to identify optimal codons
	"cai_coa",
	"coa_files",

    ];

    $self->{TYPE}  = {
	"codonw" => 'String',
	"outfiles" => 'String',
	"results_files" => 'Results',
	"seqfile" => 'Sequence',
	"defaults" => 'Paragraph',
	"gc" => 'Excl',
	"fop_values" => 'Excl',
	"cai_values" => 'Excl',
	"output_type" => 'Switch',
	"genes" => 'Switch',
	"CU_options" => 'Paragraph',
	"CAI" => 'Switch',
	"Fop" => 'Switch',
	"CBI" => 'Switch',
	"cai_file" => 'InFile',
	"fop_file" => 'InFile',
	"cbi_file" => 'InFile',
	"ENc" => 'Switch',
	"GC" => 'Switch',
	"GC3s" => 'Switch',
	"silent_bc" => 'Switch',
	"all_indices" => 'Switch',
	"L_sym" => 'Integer',
	"L_aa" => 'Switch',
	"Hydro" => 'Switch',
	"Aromo" => 'Switch',
	"bulk_output_option" => 'Excl',
	"COA_options" => 'Paragraph',
	"coa_cu" => 'Switch',
	"coa_rscu" => 'Switch',
	"coa_aa" => 'Switch',
	"coa_expert" => 'Switch',
	"coa_axes" => 'Integer',
	"coa_num" => 'Integer',
	"cai_coa" => 'OutFile',
	"coa_files" => 'Results',

    };

    $self->{FORMAT}  = {
	"codonw" => {
		"perl" => '"codonw -silent -nomenu -nowarn"',
	},
	"outfiles" => {
		"perl" => '" $seqfile.indices $seqfile.bulk"',
	},
	"results_files" => {
	},
	"seqfile" => {
		"perl" => '  " $value"',
	},
	"defaults" => {
	},
	"gc" => {
		"perl" => '($value && $value ne $vdef)? " -code $value" : "" ',
	},
	"fop_values" => {
		"perl" => '($value)? " -f_type $value" : "" ',
	},
	"cai_values" => {
		"perl" => '($value)? " -c_type $value" : "" ',
	},
	"output_type" => {
		"perl" => '($value)? " -machine" : "" ',
	},
	"genes" => {
		"perl" => '($value)? " -totals" : "" ',
	},
	"CU_options" => {
	},
	"CAI" => {
		"perl" => '($value)? " -cai" : "" ',
	},
	"Fop" => {
		"perl" => '($value)? " -fop" : "" ',
	},
	"CBI" => {
		"perl" => '($value)? " -cbi" : "" ',
	},
	"cai_file" => {
		"perl" => '($value)? " -cai_file $value" : "" ',
	},
	"fop_file" => {
		"perl" => '($value)? " -fop_file $value" : "" ',
	},
	"cbi_file" => {
		"perl" => '($value)? " -cbi_file $value" : "" ',
	},
	"ENc" => {
		"perl" => '($value)? " -enc" : "" ',
	},
	"GC" => {
		"perl" => '($value)? " -gc" : "" ',
	},
	"GC3s" => {
		"perl" => '($value)? " -gc3s" : "" ',
	},
	"silent_bc" => {
		"perl" => '($value)? " -sil_base" : "" ',
	},
	"all_indices" => {
		"perl" => '($value)? " -all_indices" : "" ',
	},
	"L_sym" => {
		"perl" => '(defined $value)? " -L_sym" : "" ',
	},
	"L_aa" => {
		"perl" => '($value)? " -L_aa" : "" ',
	},
	"Hydro" => {
		"perl" => '($value)? " -hyd" : "" ',
	},
	"Aromo" => {
		"perl" => '($value)? " -aro" : "" ',
	},
	"bulk_output_option" => {
		"perl" => '($value && $value ne $vdef)? " $value" : "" ',
	},
	"COA_options" => {
	},
	"coa_cu" => {
		"perl" => '($value)? " -coa_cu" : "" ',
	},
	"coa_rscu" => {
		"perl" => '($value)? " -coa_rscu" : "" ',
	},
	"coa_aa" => {
		"perl" => '($value)? " -coa_aa" : "" ',
	},
	"coa_expert" => {
		"perl" => '($value)? " -coa_expert" : "" ',
	},
	"coa_axes" => {
		"perl" => '(defined $value)? " -coa_axes $value" : "" ',
	},
	"coa_num" => {
		"perl" => '(defined $value)? " -coa_num $value" : "" ',
	},
	"cai_coa" => {
		"perl" => '""',
	},
	"coa_files" => {
	},

    };

    $self->{FILENAMES}  = {
	"results_files" => '*.indices *.bulk',
	"coa_files" => '*.coa coa_raw',

    };

    $self->{SEQFMT}  = {
	"seqfile" => [8],

    };

    $self->{GROUP}  = {
	"codonw" => 0,
	"outfiles" => 2000,
	"seqfile" => 1000,
	"gc" => 2,
	"fop_values" => 2,
	"cai_values" => 2,
	"output_type" => 2,
	"genes" => 3,
	"CAI" => 4,
	"Fop" => 4,
	"CBI" => 4,
	"cai_file" => 2,
	"fop_file" => 2,
	"cbi_file" => 2,
	"ENc" => 4,
	"GC" => 4,
	"GC3s" => 4,
	"silent_bc" => 4,
	"all_indices" => 4,
	"L_sym" => 4,
	"L_aa" => 4,
	"Hydro" => 4,
	"Aromo" => 4,
	"bulk_output_option" => 4,
	"coa_cu" => 3,
	"coa_rscu" => 3,
	"coa_aa" => 3,
	"coa_expert" => 3,
	"coa_axes" => 3,
	"coa_num" => 3,
	"cai_coa" => 1,

    };

    $self->{BY_GROUP_PARAMETERS}  = [
	"codonw",
	"coa_files",
	"results_files",
	"COA_options",
	"defaults",
	"CU_options",
	"cai_coa",
	"fop_values",
	"cai_values",
	"output_type",
	"cai_file",
	"fop_file",
	"cbi_file",
	"gc",
	"coa_rscu",
	"coa_aa",
	"coa_expert",
	"coa_axes",
	"coa_num",
	"coa_cu",
	"genes",
	"all_indices",
	"L_sym",
	"L_aa",
	"Hydro",
	"Aromo",
	"bulk_output_option",
	"CAI",
	"Fop",
	"CBI",
	"ENc",
	"GC",
	"GC3s",
	"silent_bc",
	"seqfile",
	"outfiles",

    ];

    $self->{SIZE}  = {

    };

    $self->{ISHIDDEN}  = {
	"codonw" => 1,
	"outfiles" => 1,
	"results_files" => 0,
	"seqfile" => 0,
	"defaults" => 0,
	"gc" => 0,
	"fop_values" => 0,
	"cai_values" => 0,
	"output_type" => 0,
	"genes" => 0,
	"CU_options" => 0,
	"CAI" => 0,
	"Fop" => 0,
	"CBI" => 0,
	"cai_file" => 0,
	"fop_file" => 0,
	"cbi_file" => 0,
	"ENc" => 0,
	"GC" => 0,
	"GC3s" => 0,
	"silent_bc" => 0,
	"all_indices" => 0,
	"L_sym" => 0,
	"L_aa" => 0,
	"Hydro" => 0,
	"Aromo" => 0,
	"bulk_output_option" => 0,
	"COA_options" => 0,
	"coa_cu" => 0,
	"coa_rscu" => 0,
	"coa_aa" => 0,
	"coa_expert" => 0,
	"coa_axes" => 0,
	"coa_num" => 0,
	"cai_coa" => 1,
	"coa_files" => 0,

    };

    $self->{ISCOMMAND}  = {
	"codonw" => 1,
	"outfiles" => 0,
	"results_files" => 0,
	"seqfile" => 0,
	"defaults" => 0,
	"gc" => 0,
	"fop_values" => 0,
	"cai_values" => 0,
	"output_type" => 0,
	"genes" => 0,
	"CU_options" => 0,
	"CAI" => 0,
	"Fop" => 0,
	"CBI" => 0,
	"cai_file" => 0,
	"fop_file" => 0,
	"cbi_file" => 0,
	"ENc" => 0,
	"GC" => 0,
	"GC3s" => 0,
	"silent_bc" => 0,
	"all_indices" => 0,
	"L_sym" => 0,
	"L_aa" => 0,
	"Hydro" => 0,
	"Aromo" => 0,
	"bulk_output_option" => 0,
	"COA_options" => 0,
	"coa_cu" => 0,
	"coa_rscu" => 0,
	"coa_aa" => 0,
	"coa_expert" => 0,
	"coa_axes" => 0,
	"coa_num" => 0,
	"cai_coa" => 0,
	"coa_files" => 0,

    };

    $self->{ISMANDATORY}  = {
	"codonw" => 0,
	"outfiles" => 0,
	"results_files" => 0,
	"seqfile" => 1,
	"defaults" => 0,
	"gc" => 0,
	"fop_values" => 0,
	"cai_values" => 0,
	"output_type" => 0,
	"genes" => 0,
	"CU_options" => 0,
	"CAI" => 0,
	"Fop" => 0,
	"CBI" => 0,
	"cai_file" => 0,
	"fop_file" => 0,
	"cbi_file" => 0,
	"ENc" => 0,
	"GC" => 0,
	"GC3s" => 0,
	"silent_bc" => 0,
	"all_indices" => 0,
	"L_sym" => 0,
	"L_aa" => 0,
	"Hydro" => 0,
	"Aromo" => 0,
	"bulk_output_option" => 0,
	"COA_options" => 0,
	"coa_cu" => 0,
	"coa_rscu" => 0,
	"coa_aa" => 0,
	"coa_expert" => 0,
	"coa_axes" => 0,
	"coa_num" => 0,
	"cai_coa" => 0,
	"coa_files" => 0,

    };

    $self->{PROMPT}  = {
	"codonw" => "",
	"outfiles" => "",
	"results_files" => "",
	"seqfile" => "Sequences File",
	"defaults" => "Defaults settings",
	"gc" => "Genetic codes",
	"fop_values" => "Fop/CBI values",
	"cai_values" => "CAI values",
	"output_type" => "Output Computer readable",
	"genes" => "Concatenate genes (instead of individual genes)",
	"CU_options" => "Codon usage indices",
	"CAI" => "Codon Adaptation Index (CAI)",
	"Fop" => "Frequency of OPtimal codons (Fop)",
	"CBI" => "Codon bias index (CBI)",
	"cai_file" => "User input file of CAI values (may be computed by a previous COA)",
	"fop_file" => "User input file of Fop values (may be computed by a previous COA)",
	"cbi_file" => "User input file of CBI values (may be computed by a previous COA)",
	"ENc" => "Effective Number of Codons (ENc)",
	"GC" => "GC content of gene (G+C)",
	"GC3s" => "GC of silent 3rd codon posit. (GC3s)",
	"silent_bc" => "Silent base composition",
	"all_indices" => "All the above indices",
	"L_sym" => "Number of synonymous codons (L_sym)",
	"L_aa" => "Total Number of synonymous and non-synonymous codons (L_aa)",
	"Hydro" => "Hydrophobicity of protein (Hydro)",
	"Aromo" => "Aromaticity of protein (Aromo)",
	"bulk_output_option" => "Other output option",
	"COA_options" => "Correspondence analysis options (available for several sequences)",
	"coa_cu" => "COA on codon usage",
	"coa_rscu" => "COA on RSCU",
	"coa_aa" => "COA on Amino Acid usage",
	"coa_expert" => "Generate detailed(expert) statistics on COA",
	"coa_axes" => "Select number of axis to record",
	"coa_num" => "Select number of genes to use to identify optimal codons",
	"cai_coa" => "",
	"coa_files" => "",

    };

    $self->{ISSTANDOUT}  = {
	"codonw" => 0,
	"outfiles" => 0,
	"results_files" => 0,
	"seqfile" => 0,
	"defaults" => 0,
	"gc" => 0,
	"fop_values" => 0,
	"cai_values" => 0,
	"output_type" => 0,
	"genes" => 0,
	"CU_options" => 0,
	"CAI" => 0,
	"Fop" => 0,
	"CBI" => 0,
	"cai_file" => 0,
	"fop_file" => 0,
	"cbi_file" => 0,
	"ENc" => 0,
	"GC" => 0,
	"GC3s" => 0,
	"silent_bc" => 0,
	"all_indices" => 0,
	"L_sym" => 0,
	"L_aa" => 0,
	"Hydro" => 0,
	"Aromo" => 0,
	"bulk_output_option" => 0,
	"COA_options" => 0,
	"coa_cu" => 0,
	"coa_rscu" => 0,
	"coa_aa" => 0,
	"coa_expert" => 0,
	"coa_axes" => 0,
	"coa_num" => 0,
	"cai_coa" => 0,
	"coa_files" => 0,

    };

    $self->{VLIST}  = {

	"defaults" => ['gc','fop_values','cai_values','output_type','genes',],
	"gc" => ['0','(0) Universal Genetic code [TGA=* TAA=* TAG=*]','1','(1) Vertebrate Mitochondrial code [AGR=* ATA=M TGA=W]','2','(2) Yeast Mitochondrial code [CTN=* ATA=M TGA=W]','3','(3) Filamentous fungi Mitochondrial code [TGA=W]','4','(4) Insects and Plathyhelminthes Mitochondrial co [ATA=M TGA=W AGR=S]','5','(5) Nuclear code of Cilitia [UAA=Q=Gln UAG=Q]','6','(6) Nuclear code of Euplotes [UGA=C]','7','(7) Mitochondrial code of Echinoderms UGA=W AGR=S AAA=N',],
	"fop_values" => ['0','(0) Escherichia coli','1','(1) Bacillus subtilis','2','(2) Dictyostelium discoideum','3','(3) Aspergillus nidulans','4','(4) Saccharomyces cerevisiae','5','(5) Drosophila melanogaster','6','(6) Caenorhabditis elegans','7','(7) Neurospora crassa',],
	"cai_values" => ['0','(0) Escherichia coli','1','(1) Bacillus subtilis','2','(2) Saccharomyces cerevisiae',],
	"CU_options" => ['CAI','Fop','CBI','cai_file','fop_file','cbi_file','ENc','GC','GC3s','silent_bc','all_indices','L_sym','L_aa','Hydro','Aromo','bulk_output_option',],
	"bulk_output_option" => ['-cu','Codon Usage (CU)','-aau','Amino Acid Usage (AAU)','-raau','Relative Amino Acid Usage (RAAU)','-cutab','Tabulation of codon usage','-cutot','Tabulation of dataset\'s codon usage','-rscu','Relative Synonymous Codon Usage (RSCU)','-fasta','fasta format','-reader','Reader format (codons are seperated by spaces)','-transl','Conceptual translation of DNA to amino acid','-base','Detailed report of codon G+C composition','-dinuc','Dinucleotide usage of the three codon pos.','-noblk','No bulk output to be written to file',],
	"COA_options" => ['coa_cu','coa_rscu','coa_aa','coa_expert','coa_axes','coa_num',],
    };

    $self->{FLIST}  = {

    };

    $self->{SEPARATOR}  = {

    };

    $self->{VDEF}  = {
	"gc" => '0',
	"fop_values" => '0',
	"cai_values" => '0',
	"output_type" => '0',
	"bulk_output_option" => '-cu',
	"cai_coa" => '"cai.coa"',

    };

    $self->{PRECOND}  = {
	"codonw" => { "perl" => '1' },
	"outfiles" => { "perl" => '1' },
	"results_files" => { "perl" => '1' },
	"seqfile" => { "perl" => '1' },
	"defaults" => { "perl" => '1' },
	"gc" => { "perl" => '1' },
	"fop_values" => { "perl" => '1' },
	"cai_values" => { "perl" => '1' },
	"output_type" => { "perl" => '1' },
	"genes" => { "perl" => '1' },
	"CU_options" => { "perl" => '1' },
	"CAI" => {
		"perl" => '! $all_indices',
	},
	"Fop" => {
		"perl" => '! $all_indices',
	},
	"CBI" => {
		"perl" => '! $all_indices',
	},
	"cai_file" => {
		"perl" => '$CAI',
	},
	"fop_file" => {
		"perl" => '$Fop',
	},
	"cbi_file" => {
		"perl" => '$CBI',
	},
	"ENc" => {
		"perl" => '! $all_indices',
	},
	"GC" => {
		"perl" => '! $all_indices',
	},
	"GC3s" => {
		"perl" => '! $all_indices',
	},
	"silent_bc" => {
		"perl" => '! $all_indices',
	},
	"all_indices" => { "perl" => '1' },
	"L_sym" => { "perl" => '1' },
	"L_aa" => { "perl" => '1' },
	"Hydro" => { "perl" => '1' },
	"Aromo" => { "perl" => '1' },
	"bulk_output_option" => { "perl" => '1' },
	"COA_options" => { "perl" => '1' },
	"coa_cu" => { "perl" => '1' },
	"coa_rscu" => { "perl" => '1' },
	"coa_aa" => { "perl" => '1' },
	"coa_expert" => { "perl" => '1' },
	"coa_axes" => { "perl" => '1' },
	"coa_num" => { "perl" => '1' },
	"cai_coa" => { "perl" => '1' },
	"coa_files" => {
		"perl" => '$coa_cu || $coa_rscu || $coa_aa',
	},

    };

    $self->{CTRL}  = {

    };

    $self->{PIPEOUT}  = {
	"cai_coa" => {
		 '1' => "codonw_coa_file",
	},

    };

    $self->{WITHPIPEOUT}  = {

    };

    $self->{PIPEIN}  = {
	"cai_file" => {
		 "codonw_coa_file" => '1',
	},

    };

    $self->{WITHPIPEIN}  = {

    };

    $self->{ISCLEAN}  = {
	"codonw" => 0,
	"outfiles" => 0,
	"results_files" => 0,
	"seqfile" => 0,
	"defaults" => 0,
	"gc" => 0,
	"fop_values" => 0,
	"cai_values" => 0,
	"output_type" => 0,
	"genes" => 0,
	"CU_options" => 0,
	"CAI" => 0,
	"Fop" => 0,
	"CBI" => 0,
	"cai_file" => 0,
	"fop_file" => 0,
	"cbi_file" => 0,
	"ENc" => 0,
	"GC" => 0,
	"GC3s" => 0,
	"silent_bc" => 0,
	"all_indices" => 0,
	"L_sym" => 0,
	"L_aa" => 0,
	"Hydro" => 0,
	"Aromo" => 0,
	"bulk_output_option" => 0,
	"COA_options" => 0,
	"coa_cu" => 0,
	"coa_rscu" => 0,
	"coa_aa" => 0,
	"coa_expert" => 0,
	"coa_axes" => 0,
	"coa_num" => 0,
	"cai_coa" => 0,
	"coa_files" => 0,

    };

    $self->{ISSIMPLE}  = {
	"codonw" => 0,
	"outfiles" => 0,
	"results_files" => 0,
	"seqfile" => 1,
	"defaults" => 0,
	"gc" => 0,
	"fop_values" => 0,
	"cai_values" => 0,
	"output_type" => 0,
	"genes" => 0,
	"CU_options" => 0,
	"CAI" => 0,
	"Fop" => 0,
	"CBI" => 0,
	"cai_file" => 0,
	"fop_file" => 0,
	"cbi_file" => 0,
	"ENc" => 0,
	"GC" => 0,
	"GC3s" => 0,
	"silent_bc" => 0,
	"all_indices" => 0,
	"L_sym" => 0,
	"L_aa" => 0,
	"Hydro" => 0,
	"Aromo" => 0,
	"bulk_output_option" => 0,
	"COA_options" => 0,
	"coa_cu" => 0,
	"coa_rscu" => 0,
	"coa_aa" => 0,
	"coa_expert" => 0,
	"coa_axes" => 0,
	"coa_num" => 0,
	"cai_coa" => 0,
	"coa_files" => 0,

    };

    $self->{PARAMFILE}  = {

    };

    $self->{COMMENT}  = {
	"coa_num" => [
		"Values can be whole numbers or a percentage (5 or 10%).",
	],

    };

    $self->{SCALEMIN}  = {

    };

    $self->{SCALEMAX}  = {

    };

    $self->{SCALEINC}  = {

    };

    $self->{INFO}  = {

    };

# -- end of definitions extracted from /local/gensoft/lib/Pise/5.a/PerlDef/codonw.pm



    $self->_init_params(@params);

    return $self;
}



1; # Needed to keep compiler happy

