# $Id: consensus.pm,v 1.3 2003/06/05 19:15:18 letondal Exp $
# BioPerl module for Bio::Tools::Run::PiseApplication::consensus
#
# 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::consensus

=head1 SYNOPSIS

  #

=head1 DESCRIPTION

Bio::Tools::Run::PiseApplication::consensus

      Bioperl class for:

	CONSENSUS	Identification of consensus patterns in unaligned DNA and protein sequences (Hertz, Stormo)

	References:

		G.Z. Hertz and G.D. Stormo.  Identification of consensus patterns in unaligned DNA and protein sequences: a large-deviation statistical basis for penalizing gaps. In: Proceedings of the Third International Conference on Bioinformatics and Genome Research (H.A. Lim, and C.R. Cantor, editors). World Scientific Publishing Co., Ltd. Singapore, 1995. pages 201--216.



      Parameters: 

        (see also:
          http://bioweb.pasteur.fr/seqanal/interfaces/consensus.html 
         for available values):


		consensus (Excl)
			Program to run

		sequence (Sequence)
			Sequences file (-f)
			pipe: seqsfile

		width (Integer)
			Width of pattern (consensus only) (-L)

		out (String)

		consensus_matrix (String)

		complement (Excl)
			Complement of nucleic acid sequences (-c)

		ascii_alphabet (InFile)
			Alphabet and normalization information (if not DNA) (-a)

		prior (Switch)
			Use the designated prior probabilities of the letters to override the observed frequencies (-d)

		dna (Switch)
			Alphabet and normalization information for DNA

		protein (Switch)
			Alphabet and normalization information for protein

		queue (Integer)
			Maximum number of matrices to save between cycles of the program -- ie: queue size (-q)

		standard_deviation (Float)
			Number of standard deviations to lower the information content at each position before identifying information peaks (mandatory for wconsensus) (-s)

		progeny (Excl)
			Save the top progeny matrices  (-pr1)

		linearly (Switch)
			Seed with the first sequence and proceed linearly through the list (-l)

		max_cycle_nb (Integer)
			Maximum repeat of the matrix building cycle (-n or -N)

		max_cycle (Excl)
			How many words per matrix for each sequence to contribute (-n or -N)

		distance (Integer)
			Minimum distance between the starting points of words within the same matrix pattern (-m)

		terminate (Integer)
			Terminate the program this number of cycles after the current most significant alignment is identified (-t)

		terminal_gap (Excl)
			Permit terminal gaps (-pg) (wconsensus only)

		top_matrices (Integer)
			Number of top matrices to print (-pt)

		final_matrices (Integer)
			Number of final matrices to print (-pf)

=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/consensus.html

=item *

Bio::Tools::Run::PiseApplication

=item *

Bio::Tools::Run::AnalysisFactory::Pise

=item *

Bio::Tools::Run::PiseJob

=back

=cut

#'
package Bio::Tools::Run::PiseApplication::consensus;

use vars qw(@ISA);
use strict;
use Bio::Tools::Run::PiseApplication;

@ISA = qw(Bio::Tools::Run::PiseApplication);

=head2 new

 Title   : new()
 Usage   : my $consensus = Bio::Tools::Run::PiseApplication::consensus->new($location, $email, @params);
 Function: Creates a Bio::Tools::Run::PiseApplication::consensus 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 $consensus = $factory->program('consensus');
 Example : -
 Returns : An instance of Bio::Tools::Run::PiseApplication::consensus.

=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/consensus.pm

    $self->{COMMAND}   = "consensus";
    $self->{VERSION}   = "5.a";
    $self->{TITLE}   = "CONSENSUS";

    $self->{DESCRIPTION}   = "Identification of consensus patterns in unaligned DNA and protein sequences";

    $self->{OPT_EMAIL}   = 0;

    $self->{AUTHORS}   = "Hertz, Stormo";

    $self->{REFERENCE}   = [

         "G.Z. Hertz and G.D. Stormo.  Identification of consensus patterns in unaligned DNA and protein sequences: a large-deviation statistical basis for penalizing gaps. In: Proceedings of the Third International Conference on Bioinformatics and Genome Research (H.A. Lim, and C.R. Cantor, editors). World Scientific Publishing Co., Ltd. Singapore, 1995. pages 201--216.",
 ];

    $self->{_INTERFACE_STANDOUT} = undef;
    $self->{_STANDOUT_FILE} = undef;

    $self->{TOP_PARAMETERS}  = [ 
	"consensus",
	"sequence",
	"width",
	"out",
	"consensus_matrix",
	"matrices",
	"results_file",
	"sequence_wcons",
	"input_options",
	"dna",
	"protein",
	"algorithm_options",
	"output_options",

    ];

    $self->{PARAMETERS_ORDER}  = [
	"consensus", 	# Program to run
	"sequence", 	# Sequences file (-f)
	"width", 	# Width of pattern (consensus only) (-L)
	"out",
	"consensus_matrix",
	"matrices",
	"results_file",
	"sequence_wcons",
	"input_options", 	# Input options
	"complement", 	# Complement of nucleic acid sequences (-c)
	"alphabet_options", 	# Alphabet options
	"ascii_alphabet", 	# Alphabet and normalization information (if not DNA) (-a)
	"prior", 	# Use the designated prior probabilities of the letters to override the observed frequencies (-d)
	"dna", 	# Alphabet and normalization information for DNA
	"protein", 	# Alphabet and normalization information for protein
	"algorithm_options", 	# Algorithm options
	"queue", 	# Maximum number of matrices to save between cycles of the program -- ie: queue size (-q)
	"standard_deviation", 	# Number of standard deviations to lower the information content at each position before identifying information peaks (mandatory for wconsensus) (-s)
	"progeny", 	# Save the top progeny matrices  (-pr1)
	"linearly", 	# Seed with the first sequence and proceed linearly through the list (-l)
	"max_cycle_nb", 	# Maximum repeat of the matrix building cycle (-n or -N)
	"max_cycle", 	# How many words per matrix for each sequence to contribute (-n or -N)
	"distance", 	# Minimum distance between the starting points of words within the same matrix pattern (-m)
	"terminate", 	# Terminate the program this number of cycles after the current most significant alignment is identified (-t)
	"terminal_gap", 	# Permit terminal gaps (-pg) (wconsensus only)
	"output_options", 	# Output options
	"top_matrices", 	# Number of top matrices to print (-pt)
	"final_matrices", 	# Number of final matrices to print (-pf)

    ];

    $self->{TYPE}  = {
	"consensus" => 'Excl',
	"sequence" => 'Sequence',
	"width" => 'Integer',
	"out" => 'String',
	"consensus_matrix" => 'String',
	"matrices" => 'Results',
	"results_file" => 'Results',
	"sequence_wcons" => 'Results',
	"input_options" => 'Paragraph',
	"complement" => 'Excl',
	"alphabet_options" => 'Paragraph',
	"ascii_alphabet" => 'InFile',
	"prior" => 'Switch',
	"dna" => 'Switch',
	"protein" => 'Switch',
	"algorithm_options" => 'Paragraph',
	"queue" => 'Integer',
	"standard_deviation" => 'Float',
	"progeny" => 'Excl',
	"linearly" => 'Switch',
	"max_cycle_nb" => 'Integer',
	"max_cycle" => 'Excl',
	"distance" => 'Integer',
	"terminate" => 'Integer',
	"terminal_gap" => 'Excl',
	"output_options" => 'Paragraph',
	"top_matrices" => 'Integer',
	"final_matrices" => 'Integer',

    };

    $self->{FORMAT}  = {
	"consensus" => {
		"perl" => '"fasta-consensus < $sequence > $sequence.wcons; $consensus "',
	},
	"sequence" => {
		"perl" => '" -f $sequence.wcons"',
	},
	"width" => {
		"perl" => '(defined $value) ? " -L$value" : ""',
	},
	"out" => {
		"perl" => '" > $consensus.results"',
	},
	"consensus_matrix" => {
		"perl" => '" ;consensus-matrix $consensus.results"',
	},
	"matrices" => {
	},
	"results_file" => {
	},
	"sequence_wcons" => {
	},
	"input_options" => {
	},
	"complement" => {
		"perl" => '($value)? " -c$value" : "" ',
	},
	"alphabet_options" => {
	},
	"ascii_alphabet" => {
		"perl" => '($value)? " -a $value" : "" ',
	},
	"prior" => {
		"perl" => '($value)? " -d" : ""',
	},
	"dna" => {
		"perl" => '($value)? " -A a:t c:g" : ""',
	},
	"protein" => {
		"perl" => '($value)? " -a /local/gensoft/lib/consensus/prot-alphabet" : ""',
	},
	"algorithm_options" => {
	},
	"queue" => {
		"perl" => '(defined $value && $value != $vdef)? " -q$value" : ""',
	},
	"standard_deviation" => {
		"perl" => '" -s$value"',
	},
	"progeny" => {
		"perl" => '($value && $value ne $vdef)? " $value" : ""',
	},
	"linearly" => {
		"perl" => '($value)? " -l" : "" ',
	},
	"max_cycle_nb" => {
		"perl" => ' "" ',
	},
	"max_cycle" => {
		"perl" => '($value)? " $max_cycle$max_cycle_nb" : "" ',
	},
	"distance" => {
		"perl" => '(defined $value) ? " -m$value " : ""',
	},
	"terminate" => {
		"perl" => '(defined $value)? " -t$value " : "" ',
	},
	"terminal_gap" => {
		"perl" => '($value && $value ne $vdef) ? " $value" : ""',
	},
	"output_options" => {
	},
	"top_matrices" => {
		"perl" => '($value && $value != $vdef) ? " -pt$value" : ""',
	},
	"final_matrices" => {
		"perl" => '($value && $value != $vdef) ? " -pf$value" : ""',
	},

    };

    $self->{FILENAMES}  = {
	"matrices" => '$consensus.results.matrix.*',
	"results_file" => '$consensus.results',
	"sequence_wcons" => '*.wcons',

    };

    $self->{SEQFMT}  = {
	"sequence" => [8],

    };

    $self->{GROUP}  = {
	"consensus" => 0,
	"sequence" => 1,
	"width" => 2,
	"out" => 50,
	"consensus_matrix" => 100,
	"input_options" => 2,
	"complement" => 2,
	"alphabet_options" => 2,
	"ascii_alphabet" => 2,
	"prior" => 2,
	"algorithm_options" => 2,
	"queue" => 2,
	"standard_deviation" => 2,
	"progeny" => 2,
	"linearly" => 2,
	"max_cycle_nb" => 2,
	"max_cycle" => 2,
	"distance" => 2,
	"terminate" => 2,
	"terminal_gap" => 2,
	"output_options" => 2,
	"top_matrices" => 2,
	"final_matrices" => 2,

    };

    $self->{BY_GROUP_PARAMETERS}  = [
	"consensus",
	"results_file",
	"sequence_wcons",
	"protein",
	"dna",
	"matrices",
	"sequence",
	"width",
	"top_matrices",
	"final_matrices",
	"input_options",
	"complement",
	"alphabet_options",
	"ascii_alphabet",
	"prior",
	"algorithm_options",
	"queue",
	"standard_deviation",
	"progeny",
	"linearly",
	"max_cycle_nb",
	"max_cycle",
	"distance",
	"terminate",
	"terminal_gap",
	"output_options",
	"out",
	"consensus_matrix",

    ];

    $self->{SIZE}  = {

    };

    $self->{ISHIDDEN}  = {
	"consensus" => 0,
	"sequence" => 0,
	"width" => 0,
	"out" => 1,
	"consensus_matrix" => 1,
	"matrices" => 0,
	"results_file" => 0,
	"sequence_wcons" => 0,
	"input_options" => 0,
	"complement" => 0,
	"alphabet_options" => 0,
	"ascii_alphabet" => 0,
	"prior" => 0,
	"dna" => 0,
	"protein" => 0,
	"algorithm_options" => 0,
	"queue" => 0,
	"standard_deviation" => 0,
	"progeny" => 0,
	"linearly" => 0,
	"max_cycle_nb" => 0,
	"max_cycle" => 0,
	"distance" => 0,
	"terminate" => 0,
	"terminal_gap" => 0,
	"output_options" => 0,
	"top_matrices" => 0,
	"final_matrices" => 0,

    };

    $self->{ISCOMMAND}  = {
	"consensus" => 1,
	"sequence" => 0,
	"width" => 0,
	"out" => 0,
	"consensus_matrix" => 0,
	"matrices" => 0,
	"results_file" => 0,
	"sequence_wcons" => 0,
	"input_options" => 0,
	"complement" => 0,
	"alphabet_options" => 0,
	"ascii_alphabet" => 0,
	"prior" => 0,
	"dna" => 0,
	"protein" => 0,
	"algorithm_options" => 0,
	"queue" => 0,
	"standard_deviation" => 0,
	"progeny" => 0,
	"linearly" => 0,
	"max_cycle_nb" => 0,
	"max_cycle" => 0,
	"distance" => 0,
	"terminate" => 0,
	"terminal_gap" => 0,
	"output_options" => 0,
	"top_matrices" => 0,
	"final_matrices" => 0,

    };

    $self->{ISMANDATORY}  = {
	"consensus" => 1,
	"sequence" => 1,
	"width" => 1,
	"out" => 0,
	"consensus_matrix" => 0,
	"matrices" => 0,
	"results_file" => 0,
	"sequence_wcons" => 0,
	"input_options" => 0,
	"complement" => 0,
	"alphabet_options" => 0,
	"ascii_alphabet" => 0,
	"prior" => 0,
	"dna" => 0,
	"protein" => 0,
	"algorithm_options" => 0,
	"queue" => 0,
	"standard_deviation" => 1,
	"progeny" => 0,
	"linearly" => 0,
	"max_cycle_nb" => 0,
	"max_cycle" => 0,
	"distance" => 0,
	"terminate" => 0,
	"terminal_gap" => 0,
	"output_options" => 0,
	"top_matrices" => 0,
	"final_matrices" => 0,

    };

    $self->{PROMPT}  = {
	"consensus" => "Program to run",
	"sequence" => "Sequences file (-f)",
	"width" => "Width of pattern (consensus only) (-L)",
	"out" => "",
	"consensus_matrix" => "",
	"matrices" => "",
	"results_file" => "",
	"sequence_wcons" => "",
	"input_options" => "Input options",
	"complement" => "Complement of nucleic acid sequences (-c)",
	"alphabet_options" => "Alphabet options",
	"ascii_alphabet" => "Alphabet and normalization information (if not DNA) (-a)",
	"prior" => "Use the designated prior probabilities of the letters to override the observed frequencies (-d)",
	"dna" => "Alphabet and normalization information for DNA",
	"protein" => "Alphabet and normalization information for protein",
	"algorithm_options" => "Algorithm options",
	"queue" => "Maximum number of matrices to save between cycles of the program -- ie: queue size (-q)",
	"standard_deviation" => "Number of standard deviations to lower the information content at each position before identifying information peaks (mandatory for wconsensus) (-s)",
	"progeny" => "Save the top progeny matrices  (-pr1)",
	"linearly" => "Seed with the first sequence and proceed linearly through the list (-l)",
	"max_cycle_nb" => "Maximum repeat of the matrix building cycle (-n or -N)",
	"max_cycle" => "How many words per matrix for each sequence to contribute (-n or -N)",
	"distance" => "Minimum distance between the starting points of words within the same matrix pattern (-m)",
	"terminate" => "Terminate the program this number of cycles after the current most significant alignment is identified (-t)",
	"terminal_gap" => "Permit terminal gaps (-pg) (wconsensus only)",
	"output_options" => "Output options",
	"top_matrices" => "Number of top matrices to print (-pt)",
	"final_matrices" => "Number of final matrices to print (-pf)",

    };

    $self->{ISSTANDOUT}  = {
	"consensus" => 0,
	"sequence" => 0,
	"width" => 0,
	"out" => 0,
	"consensus_matrix" => 0,
	"matrices" => 0,
	"results_file" => 0,
	"sequence_wcons" => 0,
	"input_options" => 0,
	"complement" => 0,
	"alphabet_options" => 0,
	"ascii_alphabet" => 0,
	"prior" => 0,
	"dna" => 0,
	"protein" => 0,
	"algorithm_options" => 0,
	"queue" => 0,
	"standard_deviation" => 0,
	"progeny" => 0,
	"linearly" => 0,
	"max_cycle_nb" => 0,
	"max_cycle" => 0,
	"distance" => 0,
	"terminate" => 0,
	"terminal_gap" => 0,
	"output_options" => 0,
	"top_matrices" => 0,
	"final_matrices" => 0,

    };

    $self->{VLIST}  = {

	"consensus" => ['consensus','consensus: search for fixed width patterns','wconsensus','wconsensus: same as consensus, width not fixed',],
	"input_options" => ['complement','alphabet_options',],
	"complement" => ['0','0: ignore the complement','1','1: include both strands as separate sequences','2','2: include both strands as a single sequence','3','3: Assume that the pattern is symmetrical (consensus)',],
	"alphabet_options" => ['ascii_alphabet','prior',],
	"algorithm_options" => ['queue','standard_deviation','progeny','linearly','max_cycle_nb','max_cycle','distance','terminate','terminal_gap',],
	"progeny" => ['-pr1','-pr1: regardless of parentage','-pr2','-pr2: for each parental matrix',],
	"max_cycle" => ['-n','-n: allow each sequence to contribute zero or more words per matrix','-N','-N: allow each sequence to contribute one or more words per matrix',],
	"terminal_gap" => ['-pg0','-pg0: do NOT permit terminal gaps','-pg1','-pg1: permit penalized terminal gaps',],
	"output_options" => ['top_matrices','final_matrices',],
    };

    $self->{FLIST}  = {

    };

    $self->{SEPARATOR}  = {

    };

    $self->{VDEF}  = {
	"consensus" => 'consensus',
	"complement" => '0',
	"prior" => '0',
	"protein" => '1',
	"queue" => '200',
	"standard_deviation" => '1',
	"progeny" => '-pr2',
	"linearly" => '0',
	"terminal_gap" => '-pg0',
	"top_matrices" => '4',
	"final_matrices" => '4',

    };

    $self->{PRECOND}  = {
	"consensus" => { "perl" => '1' },
	"sequence" => { "perl" => '1' },
	"width" => {
		"perl" => '$consensus eq "consensus"',
	},
	"out" => { "perl" => '1' },
	"consensus_matrix" => { "perl" => '1' },
	"matrices" => { "perl" => '1' },
	"results_file" => { "perl" => '1' },
	"sequence_wcons" => { "perl" => '1' },
	"input_options" => { "perl" => '1' },
	"complement" => { "perl" => '1' },
	"alphabet_options" => { "perl" => '1' },
	"ascii_alphabet" => {
		"perl" => '! $dna',
	},
	"prior" => { "perl" => '1' },
	"dna" => { "perl" => '1' },
	"protein" => {
		"perl" => '! $dna',
	},
	"algorithm_options" => { "perl" => '1' },
	"queue" => { "perl" => '1' },
	"standard_deviation" => {
		"perl" => '$consensus eq "wconsensus"',
	},
	"progeny" => { "perl" => '1' },
	"linearly" => { "perl" => '1' },
	"max_cycle_nb" => { "perl" => '1' },
	"max_cycle" => {
		"perl" => 'defined $max_cycle_nb',
	},
	"distance" => {
		"perl" => '$max_cycle ne ""',
	},
	"terminate" => { "perl" => '1' },
	"terminal_gap" => {
		"perl" => '$consensus eq "wconsensus"',
	},
	"output_options" => { "perl" => '1' },
	"top_matrices" => { "perl" => '1' },
	"final_matrices" => { "perl" => '1' },

    };

    $self->{CTRL}  = {
	"complement" => {
		"perl" => {
			'$value eq "3" && $consensus eq "wconsensus"' => "3: this choice is for the consensus program only",
		},
	},
	"distance" => {
		"perl" => {
			'$value <= 0' => "This number must be positive",
		},
	},

    };

    $self->{PIPEOUT}  = {
	"matrices" => {
		 '1' => "consensus_matrix",
	},
	"results_file" => {
		 '1' => "consensus_results",
	},

    };

    $self->{WITHPIPEOUT}  = {

    };

    $self->{PIPEIN}  = {
	"sequence" => {
		 "seqsfile" => '1',
	},

    };

    $self->{WITHPIPEIN}  = {

    };

    $self->{ISCLEAN}  = {
	"consensus" => 0,
	"sequence" => 0,
	"width" => 0,
	"out" => 0,
	"consensus_matrix" => 0,
	"matrices" => 0,
	"results_file" => 0,
	"sequence_wcons" => 0,
	"input_options" => 0,
	"complement" => 0,
	"alphabet_options" => 0,
	"ascii_alphabet" => 0,
	"prior" => 0,
	"dna" => 0,
	"protein" => 0,
	"algorithm_options" => 0,
	"queue" => 0,
	"standard_deviation" => 0,
	"progeny" => 0,
	"linearly" => 0,
	"max_cycle_nb" => 0,
	"max_cycle" => 0,
	"distance" => 0,
	"terminate" => 0,
	"terminal_gap" => 0,
	"output_options" => 0,
	"top_matrices" => 0,
	"final_matrices" => 0,

    };

    $self->{ISSIMPLE}  = {
	"consensus" => 1,
	"sequence" => 1,
	"width" => 1,
	"out" => 0,
	"consensus_matrix" => 0,
	"matrices" => 0,
	"results_file" => 0,
	"sequence_wcons" => 0,
	"input_options" => 0,
	"complement" => 0,
	"alphabet_options" => 0,
	"ascii_alphabet" => 0,
	"prior" => 0,
	"dna" => 1,
	"protein" => 1,
	"algorithm_options" => 0,
	"queue" => 0,
	"standard_deviation" => 0,
	"progeny" => 0,
	"linearly" => 0,
	"max_cycle_nb" => 0,
	"max_cycle" => 0,
	"distance" => 0,
	"terminate" => 0,
	"terminal_gap" => 0,
	"output_options" => 0,
	"top_matrices" => 0,
	"final_matrices" => 0,

    };

    $self->{PARAMFILE}  = {

    };

    $self->{COMMENT}  = {
	"ascii_alphabet" => [
		"Each line contains a letter (a symbol in the alphabet) followed by an optional normalization number (default: 1.0). The normalization is based on the relative prior probabilities of the letters. For nucleic acids, this might be be the genomic frequency of the bases; however, if the -d option is not used, the frequencies observed in your own sequence data are used. In nucleic acid alphabets, a letter and its complement appear on the same line, separated by a colon (a letter can be its own complement, e.g. when using a dimer alphabet).",
		"Complementary letters may use the same normalization number. Only the standard 26 letters are permissible; however, when the -CS option is used, the alphabet is case sensitive so that a total of 52 different characters are possible.",
		"POSSIBLE LINE FORMATS WITHOUT COMPLEMENTARY LETTERS:",
		"letter",
		"letter normalization",
		"POSSIBLE LINE FORMATS WITH COMPLEMENTARY LETTERS:",
		"letter:complement",
		"letter:complement normalization",
		"letter:complement normalization:complement\'s_normalization",
	],
	"prior" => [
		"By default, the program uses the frequencies observed in your own sequence data for the prior probabilities of the letters. However, if the -d option is set, the prior probabilities designated by the alphabet options. If the -d option is not set, they are still used to determine the sequence alphabet, but any prior probability information is ignored.",
	],
	"progeny" => [
		"-pr2 option prevents a strong pattern found in only a subset of the sequences from overwhelming the algorithm and eliminating other potential patterns. This undesirable situation can occur when a subset of the sequences share an evolutionary relationship not common to the majority of the sequences.",
	],
	"linearly" => [
		"This option results in a significant speed up in the program, but the algorithm becomes dependent on the order of the sequence-file names.",
	],
	"distance" => [
		"For wconsensus, the default value is 1.",
		"For consensus, this number is indicated by the width (-L).",
	],
	"terminate" => [
		"default: terminate only when the maximum number of matrix building cycles is completed.",
	],
	"top_matrices" => [
		"A negative value means print all the top matrices.",
	],
	"final_matrices" => [
		"Default when NOT using -n or -N option: print 4 matrices; default when using -n or -N option: print no matrices.",
	],

    };

    $self->{SCALEMIN}  = {

    };

    $self->{SCALEMAX}  = {

    };

    $self->{SCALEINC}  = {

    };

    $self->{INFO}  = {

    };

# -- end of definitions extracted from /local/gensoft/lib/Pise/5.a/PerlDef/consensus.pm



    $self->_init_params(@params);

    return $self;
}



1; # Needed to keep compiler happy

