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# $Id: pyramids.pm,v 1.6 2006/07/04 22:23:35 mauricio Exp $
# BioPerl module for Bio::Tools::Run::PiseApplication::pyramids
#
# Cared for by Catherine Letondal <letondal@pasteur.fr>
#
# For copyright and disclaimer see below.
#
# POD documentation - main docs before the code
HideShow 102 lines of Pod
=head1 NAME
Bio::Tools::Run::PiseApplication::pyramids
=head1 SYNOPSIS
  #
=head1 DESCRIPTION
Bio::Tools::Run::PiseApplication::pyramids
      Bioperl class for:
        PYRAMIDS        A pyramidal analysis tool for sequence  clustering (JC AUDE)
      Parameters: 
        (see also:
          http://bioweb.pasteur.fr/seqanal/interfaces/pyramids.html 
         for available values):
                pyramids (String)
                infile (InFile)
                        Distances matrix File
                        pipe: phylip_dist
                out_file (OutFile)
                rect (Excl)
                        Matrix format
                pyr_file (OutFile)
                        pipe: pyramid_file
                uti_file (OutFile)
                pyt_file (OutFile)
                        pipe: pyramid_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/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/pyramids.html
=item *
Bio::Tools::Run::PiseApplication
=item *
Bio::Tools::Run::AnalysisFactory::Pise
=item *
Bio::Tools::Run::PiseJob
=back
=cut
#'
package Bio::Tools::Run::PiseApplication::pyramids;
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 $pyramids = Bio::Tools::Run::PiseApplication::pyramids->new($location, $email, @params);
 Function: Creates a Bio::Tools::Run::PiseApplication::pyramids 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 $pyramids = $factory->program('pyramids');
 Example : -
 Returns : An instance of Bio::Tools::Run::PiseApplication::pyramids.
=cut
sub new {
    my ($class, $location, $email, @params) = @_;
    my $self = $class->SUPER::new($location, $email);
# -- begin of definitions extracted from /local/gensoft/lib/Pise/5.a/PerlDef/pyramids.pm
    $self->{COMMAND}   = "pyramids";
    $self->{VERSION}   = "5.a";
    $self->{TITLE}   = "PYRAMIDS";
    $self->{DESCRIPTION}   = "A pyramidal analysis tool for sequence  clustering";
    $self->{OPT_EMAIL}   = 0;
    $self->{AUTHORS}   = "JC AUDE";
    $self->{_INTERFACE_STANDOUT} = undef;
    $self->{_STANDOUT_FILE} = undef;
    $self->{TOP_PARAMETERS}  = [ 
        "pyramids",
        "infile",
        "out_file",
        "rect",
        "pyr_file",
        "uti_file",
        "pyt_file",
    ];
    $self->{PARAMETERS_ORDER}  = [
        "pyramids",
        "infile",       # Distances matrix File
        "out_file",
        "rect",         # Matrix format
        "pyr_file",
        "uti_file",
        "pyt_file",
    ];
    $self->{TYPE}  = {
        "pyramids" => 'String',
        "infile" => 'InFile',
        "out_file" => 'OutFile',
        "rect" => 'Excl',
        "pyr_file" => 'OutFile',
        "uti_file" => 'OutFile',
        "pyt_file" => 'OutFile',
    };
    $self->{FORMAT}  = {
        "pyramids" => {
                "seqlab" => 'pyramids',
                "perl" => '"pyramids"',
        },
        "infile" => {
                "perl" => '" $value"',
        },
        "out_file" => {
                "perl" => '" results"',
        },
        "rect" => {
                "perl" => '" -$value"',
        },
        "pyr_file" => {
                "perl" => '""',
        },
        "uti_file" => {
                "perl" => '""',
        },
        "pyt_file" => {
                "perl" => '""',
        },
    };
    $self->{FILENAMES}  = {
    };
    $self->{SEQFMT}  = {
    };
    $self->{GROUP}  = {
        "pyramids" => 0,
        "infile" => 2,
        "out_file" => 3,
        "rect" => 1,
        "pyr_file" => 10,
        "uti_file" => 10,
        "pyt_file" => 10,
    };
    $self->{BY_GROUP_PARAMETERS}  = [
        "pyramids",
        "rect",
        "infile",
        "out_file",
        "pyr_file",
        "uti_file",
        "pyt_file",
    ];
    $self->{SIZE}  = {
    };
    $self->{ISHIDDEN}  = {
        "pyramids" => 1,
        "infile" => 0,
        "out_file" => 1,
        "rect" => 0,
        "pyr_file" => 1,
        "uti_file" => 1,
        "pyt_file" => 1,
    };
    $self->{ISCOMMAND}  = {
        "pyramids" => 1,
        "infile" => 0,
        "out_file" => 0,
        "rect" => 0,
        "pyr_file" => 0,
        "uti_file" => 0,
        "pyt_file" => 0,
    };
    $self->{ISMANDATORY}  = {
        "pyramids" => 0,
        "infile" => 1,
        "out_file" => 0,
        "rect" => 1,
        "pyr_file" => 0,
        "uti_file" => 0,
        "pyt_file" => 0,
    };
    $self->{PROMPT}  = {
        "pyramids" => "",
        "infile" => "Distances matrix File",
        "out_file" => "",
        "rect" => "Matrix format",
        "pyr_file" => "",
        "uti_file" => "",
        "pyt_file" => "",
    };
    $self->{ISSTANDOUT}  = {
        "pyramids" => 0,
        "infile" => 0,
        "out_file" => 0,
        "rect" => 0,
        "pyr_file" => 0,
        "uti_file" => 0,
        "pyt_file" => 0,
    };
    $self->{VLIST}  = {
        "rect" => ['RE','Rectangular (Phylip)','TS','Triangular superior','TI','Triangular inferior',],
    };
    $self->{FLIST}  = {
    };
    $self->{SEPARATOR}  = {
    };
    $self->{VDEF}  = {
        "out_file" => 'results',
        "rect" => 'RE',
        "pyr_file" => '"$out_file.pyr"',
        "uti_file" => '"$out_file.uti"',
        "pyt_file" => '"$out_file.pyt"',
    };
    $self->{PRECOND}  = {
        "pyramids" => { "perl" => '1' },
        "infile" => { "perl" => '1' },
        "out_file" => { "perl" => '1' },
        "rect" => { "perl" => '1' },
        "pyr_file" => { "perl" => '1' },
        "uti_file" => { "perl" => '1' },
        "pyt_file" => { "perl" => '1' },
    };
    $self->{CTRL}  = {
    };
    $self->{PIPEOUT}  = {
        "pyr_file" => {
                 '1' => "pyramid_file",
        },
        "pyt_file" => {
                 '1' => "pyramid_file",
        },
    };
    $self->{WITHPIPEOUT}  = {
        "pyr_file" => {
                 "pyramid_file" => ["uti_file",]
        },
        "pyt_file" => {
                 "pyramid_file" => ["uti_file",]
        },
    };
    $self->{PIPEIN}  = {
        "infile" => {
                 "phylip_dist" => '1',
        },
    };
    $self->{WITHPIPEIN}  = {
    };
    $self->{ISCLEAN}  = {
        "pyramids" => 0,
        "infile" => 0,
        "out_file" => 0,
        "rect" => 0,
        "pyr_file" => 0,
        "uti_file" => 0,
        "pyt_file" => 0,
    };
    $self->{ISSIMPLE}  = {
        "pyramids" => 1,
        "infile" => 1,
        "out_file" => 0,
        "rect" => 0,
        "pyr_file" => 0,
        "uti_file" => 0,
        "pyt_file" => 0,
    };
    $self->{PARAMFILE}  = {
    };
    $self->{COMMENT}  = {
    };
    $self->{SCALEMIN}  = {
    };
    $self->{SCALEMAX}  = {
    };
    $self->{SCALEINC}  = {
    };
    $self->{INFO}  = {
    };
# -- end of definitions extracted from /local/gensoft/lib/Pise/5.a/PerlDef/pyramids.pm
    $self->_init_params(@params);
    return $self;
}
1; # Needed to keep compiler happy