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# $Id: plotcon.pm,v 1.6 2006/07/04 22:23:35 mauricio Exp $
# BioPerl module for Bio::Tools::Run::PiseApplication::plotcon
#
# Cared for by Catherine Letondal <letondal@pasteur.fr>
#
# For copyright and disclaimer see below.
#
# POD documentation - main docs before the code
HideShow 110 lines of Pod
=head1 NAME
Bio::Tools::Run::PiseApplication::plotcon
=head1 SYNOPSIS
  #
=head1 DESCRIPTION
Bio::Tools::Run::PiseApplication::plotcon
      Bioperl class for:
        PLOTCON Plots the quality of conservation of a sequence alignment (EMBOSS)
      Parameters: 
        (see also:
          http://bioweb.pasteur.fr/seqanal/interfaces/plotcon.html 
         for available values):
                plotcon (String)
                init (String)
                msf (Sequence)
                        Sequences file to be read in (-msf)
                        pipe: seqsfile
                winsize (Integer)
                        Window size (-winsize)
                scorefile (Excl)
                        Comparison matrix file (-scorefile)
                data (Switch)
                        Display as data (-data)
                graph (Excl)
                        graph (-graph)
                outfile (OutFile)
                        Display as data (-outfile)
                auto (String)
                psouput (String)
=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/plotcon.html
=item *
Bio::Tools::Run::PiseApplication
=item *
Bio::Tools::Run::AnalysisFactory::Pise
=item *
Bio::Tools::Run::PiseJob
=back
=cut
#'
package Bio::Tools::Run::PiseApplication::plotcon;
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 $plotcon = Bio::Tools::Run::PiseApplication::plotcon->new($location, $email, @params);
 Function: Creates a Bio::Tools::Run::PiseApplication::plotcon 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 $plotcon = $factory->program('plotcon');
 Example : -
 Returns : An instance of Bio::Tools::Run::PiseApplication::plotcon.
=cut
sub new {
    my ($class, $location, $email, @params) = @_;
    my $self = $class->SUPER::new($location, $email);
# -- begin of definitions extracted from /local/gensoft/lib/Pise/5.a/PerlDef/plotcon.pm
    $self->{COMMAND}   = "plotcon";
    $self->{VERSION}   = "5.a";
    $self->{TITLE}   = "PLOTCON";
    $self->{DESCRIPTION}   = "Plots the quality of conservation of a sequence alignment (EMBOSS)";
    $self->{OPT_EMAIL}   = 0;
    $self->{CATEGORIES}   =  [  
         "alignment:multiple",
  ];
    $self->{DOCLINK}   = "http://www.uk.embnet.org/Software/EMBOSS/Apps/plotcon.html";
    $self->{_INTERFACE_STANDOUT} = undef;
    $self->{_STANDOUT_FILE} = undef;
    $self->{TOP_PARAMETERS}  = [ 
        "plotcon",
        "init",
        "input",
        "required",
        "advanced",
        "output",
        "auto",
        "psouput",
        "psresults",
        "metaresults",
        "dataresults",
        "pngresults",
    ];
    $self->{PARAMETERS_ORDER}  = [
        "plotcon",
        "init",
        "input",        # input Section
        "msf",  # Sequences file to be read in (-msf)
        "required",     # required Section
        "winsize",      # Window size (-winsize)
        "advanced",     # advanced Section
        "scorefile",    # Comparison matrix file (-scorefile)
        "output",       # output Section
        "data",         # Display as data (-data)
        "graph",        # graph (-graph)
        "outfile",      # Display as data (-outfile)
        "auto",
        "psouput",
        "psresults",
        "metaresults",
        "dataresults",
        "pngresults",
    ];
    $self->{TYPE}  = {
        "plotcon" => 'String',
        "init" => 'String',
        "input" => 'Paragraph',
        "msf" => 'Sequence',
        "required" => 'Paragraph',
        "winsize" => 'Integer',
        "advanced" => 'Paragraph',
        "scorefile" => 'Excl',
        "output" => 'Paragraph',
        "data" => 'Switch',
        "graph" => 'Excl',
        "outfile" => 'OutFile',
        "auto" => 'String',
        "psouput" => 'String',
        "psresults" => 'Results',
        "metaresults" => 'Results',
        "dataresults" => 'Results',
        "pngresults" => 'Results',
    };
    $self->{FORMAT}  = {
        "init" => {
                "perl" => ' "" ',
        },
        "input" => {
        },
        "msf" => {
                "perl" => '" -msf=$value -sformat=fasta"',
        },
        "required" => {
        },
        "winsize" => {
                "perl" => '" -winsize=$value"',
        },
        "advanced" => {
        },
        "scorefile" => {
                "perl" => '($value)? " -scorefile=$value" : ""',
        },
        "output" => {
        },
        "data" => {
                "perl" => '($value)? " -data" : ""',
        },
        "graph" => {
                "perl" => '($value)? " -graph=$value" : ""',
        },
        "outfile" => {
                "perl" => '($value)? " -outfile=$value" : ""',
        },
        "auto" => {
                "perl" => '" -auto -stdout"',
        },
        "psouput" => {
                "perl" => '" -goutfile=plotcon"',
        },
        "psresults" => {
        },
        "metaresults" => {
        },
        "dataresults" => {
        },
        "pngresults" => {
        },
        "plotcon" => {
                "perl" => '"plotcon"',
        }
    };
    $self->{FILENAMES}  = {
        "psresults" => '*.ps',
        "metaresults" => '*.meta',
        "dataresults" => '*.dat',
        "pngresults" => '*.png *.2 *.3',
    };
    $self->{SEQFMT}  = {
        "msf" => [8],
    };
    $self->{GROUP}  = {
        "init" => -10,
        "msf" => 1,
        "winsize" => 2,
        "scorefile" => 3,
        "data" => 4,
        "graph" => 5,
        "outfile" => 6,
        "auto" => 7,
        "psouput" => 100,
        "plotcon" => 0
    };
    $self->{BY_GROUP_PARAMETERS}  = [
        "init",
        "input",
        "pngresults",
        "required",
        "plotcon",
        "advanced",
        "output",
        "psresults",
        "metaresults",
        "dataresults",
        "msf",
        "winsize",
        "scorefile",
        "data",
        "graph",
        "outfile",
        "auto",
        "psouput",
    ];
    $self->{SIZE}  = {
    };
    $self->{ISHIDDEN}  = {
        "init" => 1,
        "input" => 0,
        "msf" => 0,
        "required" => 0,
        "winsize" => 0,
        "advanced" => 0,
        "scorefile" => 0,
        "output" => 0,
        "data" => 0,
        "graph" => 0,
        "outfile" => 0,
        "auto" => 1,
        "psouput" => 1,
        "psresults" => 0,
        "metaresults" => 0,
        "dataresults" => 0,
        "pngresults" => 0,
        "plotcon" => 1
    };
    $self->{ISCOMMAND}  = {
        "init" => 0,
        "input" => 0,
        "msf" => 0,
        "required" => 0,
        "winsize" => 0,
        "advanced" => 0,
        "scorefile" => 0,
        "output" => 0,
        "data" => 0,
        "graph" => 0,
        "outfile" => 0,
        "auto" => 0,
        "psouput" => 0,
        "psresults" => 0,
        "metaresults" => 0,
        "dataresults" => 0,
        "pngresults" => 0,
    };
    $self->{ISMANDATORY}  = {
        "init" => 0,
        "input" => 0,
        "msf" => 1,
        "required" => 0,
        "winsize" => 1,
        "advanced" => 0,
        "scorefile" => 0,
        "output" => 0,
        "data" => 0,
        "graph" => 0,
        "outfile" => 0,
        "auto" => 0,
        "psouput" => 0,
        "psresults" => 0,
        "metaresults" => 0,
        "dataresults" => 0,
        "pngresults" => 0,
    };
    $self->{PROMPT}  = {
        "init" => "",
        "input" => "input Section",
        "msf" => "Sequences file to be read in (-msf)",
        "required" => "required Section",
        "winsize" => "Window size (-winsize)",
        "advanced" => "advanced Section",
        "scorefile" => "Comparison matrix file (-scorefile)",
        "output" => "output Section",
        "data" => "Display as data (-data)",
        "graph" => "graph (-graph)",
        "outfile" => "Display as data (-outfile)",
        "auto" => "",
        "psouput" => "",
        "psresults" => "",
        "metaresults" => "",
        "dataresults" => "",
        "pngresults" => "",
    };
    $self->{ISSTANDOUT}  = {
        "init" => 0,
        "input" => 0,
        "msf" => 0,
        "required" => 0,
        "winsize" => 0,
        "advanced" => 0,
        "scorefile" => 0,
        "output" => 0,
        "data" => 0,
        "graph" => 0,
        "outfile" => 0,
        "auto" => 0,
        "psouput" => 0,
        "psresults" => 0,
        "metaresults" => 0,
        "dataresults" => 0,
        "pngresults" => 0,
    };
    $self->{VLIST}  = {
        "input" => ['msf',],
        "required" => ['winsize',],
        "advanced" => ['scorefile',],
        "scorefile" => ['EPAM60','EPAM60','EPAM290','EPAM290','EPAM470','EPAM470','EPAM110','EPAM110','EBLOSUM50','EBLOSUM50','EPAM220','EPAM220','EBLOSUM62-12','EBLOSUM62-12','EPAM400','EPAM400','EPAM150','EPAM150','EPAM330','EPAM330','EBLOSUM55','EBLOSUM55','EPAM30','EPAM30','EPAM260','EPAM260','EBLOSUM90','EBLOSUM90','EPAM440','EPAM440','EPAM190','EPAM190','EPAM370','EPAM370','EPAM70','EPAM70','EPAM480','EPAM480','EPAM120','EPAM120','EDNAMAT','EDNAMAT','EPAM300','EPAM300','EBLOSUM60','EBLOSUM60','EPAM230','EPAM230','EBLOSUM62','EBLOSUM62','EPAM410','EPAM410','EPAM160','EPAM160','EPAM340','EPAM340','EBLOSUM65','EBLOSUM65','EPAM40','EPAM40','EPAM270','EPAM270','EPAM450','EPAM450','EPAM380','EPAM380','EPAM80','EPAM80','EPAM490','EPAM490','EBLOSUM30','EBLOSUM30','EBLOSUMN','EBLOSUMN','EPAM200','EPAM200','EPAM130','EPAM130','EBLOSUM35','EBLOSUM35','EPAM310','EPAM310','EBLOSUM70','EBLOSUM70','EPAM10','EPAM10','EPAM240','EPAM240','EPAM420','EPAM420','EPAM170','EPAM170','EBLOSUM75','EBLOSUM75','EPAM350','EPAM350','EPAM280','EPAM280','EPAM50','EPAM50','EPAM460','EPAM460','EPAM390','EPAM390','EPAM90','EPAM90','EPAM100','EPAM100','EBLOSUM40','EBLOSUM40','EPAM210','EPAM210','EPAM140','EPAM140','EBLOSUM45','EBLOSUM45','EPAM320','EPAM320','EBLOSUM80','EBLOSUM80','EPAM500','EPAM500','EPAM20','EPAM20','EPAM250','EPAM250','EPAM430','EPAM430','EPAM180','EPAM180','EBLOSUM85','EBLOSUM85','EPAM360','EPAM360',],
        "output" => ['data','graph','outfile',],
        "graph" => ['colourps','colourps','tek4107t','tek4107t','tekt','tekt','hpgl','hpgl','x11','x11','cps','cps','none','none','xwindows','xwindows','tek','tek','null','null','text','text','meta','meta','xterm','xterm','ps','ps','png','png','hp7470','hp7470','postscript','postscript','data','data','hp7580','hp7580','tektronics','tektronics',],
    };
    $self->{FLIST}  = {
    };
    $self->{SEPARATOR}  = {
    };
    $self->{VDEF}  = {
        "winsize" => '4',
        "data" => '0',
        "graph" => 'postscript',
    };
    $self->{PRECOND}  = {
        "init" => { "perl" => '1' },
        "input" => { "perl" => '1' },
        "msf" => { "perl" => '1' },
        "required" => { "perl" => '1' },
        "winsize" => { "perl" => '1' },
        "advanced" => { "perl" => '1' },
        "scorefile" => { "perl" => '1' },
        "output" => { "perl" => '1' },
        "data" => { "perl" => '1' },
        "graph" => {
                "acd" => '@(!$(data))',
        },
        "outfile" => {
                "perl" => '$data',
                "acd" => '$data',
        },
        "auto" => { "perl" => '1' },
        "psouput" => {
                "perl" => '$graph eq "postscript" || $graph eq "ps" || $graph eq "colourps"  || $graph eq "cps" || $graph eq "png"',
        },
        "psresults" => {
                "perl" => '$graph eq "postscript" || $graph eq "ps" || $graph eq "colourps" || $graph eq "cps"',
        },
        "metaresults" => {
                "perl" => '$graph eq "meta"',
        },
        "dataresults" => {
                "perl" => '$graph eq "data"',
        },
        "pngresults" => {
                "perl" => '$graph eq "png"',
        },
    };
    $self->{CTRL}  = {
    };
    $self->{PIPEOUT}  = {
    };
    $self->{WITHPIPEOUT}  = {
    };
    $self->{PIPEIN}  = {
        "msf" => {
                 "seqsfile" => '1',
        },
    };
    $self->{WITHPIPEIN}  = {
    };
    $self->{ISCLEAN}  = {
        "init" => 0,
        "input" => 0,
        "msf" => 0,
        "required" => 0,
        "winsize" => 0,
        "advanced" => 0,
        "scorefile" => 0,
        "output" => 0,
        "data" => 0,
        "graph" => 0,
        "outfile" => 0,
        "auto" => 0,
        "psouput" => 0,
        "psresults" => 0,
        "metaresults" => 0,
        "dataresults" => 0,
        "pngresults" => 0,
    };
    $self->{ISSIMPLE}  = {
        "init" => 0,
        "input" => 0,
        "msf" => 1,
        "required" => 0,
        "winsize" => 1,
        "advanced" => 0,
        "scorefile" => 0,
        "output" => 0,
        "data" => 0,
        "graph" => 0,
        "outfile" => 0,
        "auto" => 0,
        "psouput" => 0,
        "psresults" => 0,
        "metaresults" => 0,
        "dataresults" => 0,
        "pngresults" => 0,
    };
    $self->{PARAMFILE}  = {
    };
    $self->{COMMENT}  = {
        "msf" => [
                "File containing a sequence alignment",
        ],
        "winsize" => [
                "Number of columns to average alignment quality over. The larger this value is, the smoother the plot will be.",
        ],
        "scorefile" => [
                "This is the scoring matrix file used when comparing sequences.  By default it is the file \'EBLOSUM62\' (for proteins) or the file \'EDNAFULL\' (for nucleic sequences).  These files are found in the \'data\' directory of the EMBOSS installation.",
        ],
        "data" => [
                "Output the match data to a file instead of plotting it",
        ],
    };
    $self->{SCALEMIN}  = {
    };
    $self->{SCALEMAX}  = {
    };
    $self->{SCALEINC}  = {
    };
    $self->{INFO}  = {
    };
# -- end of definitions extracted from /local/gensoft/lib/Pise/5.a/PerlDef/plotcon.pm
    $self->_init_params(@params);
    return $self;
}
1; # Needed to keep compiler happy