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# $Id: infoalign.pm,v 1.6 2006/07/04 22:23:34 mauricio Exp $
# BioPerl module for Bio::Tools::Run::PiseApplication::infoalign
#
# Cared for by Catherine Letondal <letondal@pasteur.fr>
#
# For copyright and disclaimer see below.
#
# POD documentation - main docs before the code
HideShow 150 lines of Pod
=head1 NAME
Bio::Tools::Run::PiseApplication::infoalign
=head1 SYNOPSIS
  #
=head1 DESCRIPTION
Bio::Tools::Run::PiseApplication::infoalign
      Bioperl class for:
        INFOALIGN       Information on a multiple sequence alignment (EMBOSS)
      Parameters: 
        (see also:
          http://bioweb.pasteur.fr/seqanal/interfaces/infoalign.html 
         for available values):
                infoalign (String)
                init (String)
                sequence (Sequence)
                        sequence -- gapany [set of sequences] (-sequence)
                        pipe: seqsfile
                refseq (String)
                        The number or the name of the reference sequence (-refseq)
                matrix (Excl)
                        Similarity scoring Matrix file (-matrix)
                plurality (Float)
                        Plurality check % for consensus (-plurality)
                identity (Float)
                        Required % of identities at a position fro consensus (-identity)
                outfile (OutFile)
                        Output sequence details to a file (-outfile)
                html (Switch)
                        Format output as an HTML table (-html)
                only (Switch)
                        Display the specified columns (-only)
                heading (Switch)
                        Display column headings (-heading)
                usa (Switch)
                        Display the USA of the sequence (-usa)
                name (Switch)
                        Display 'name' column (-name)
                seqlength (Switch)
                        Display 'seqlength' column (-seqlength)
                alignlength (Switch)
                        Display 'alignlength' column (-alignlength)
                gaps (Switch)
                        Display number of gaps (-gaps)
                gapcount (Switch)
                        Display number of gap positions (-gapcount)
                idcount (Switch)
                        Display number of identical positions (-idcount)
                simcount (Switch)
                        Display number of similar positions (-simcount)
                diffcount (Switch)
                        Display number of different positions (-diffcount)
                change (Switch)
                        Display % number of changed positions (-change)
                description (Switch)
                        Display 'description' column (-description)
                auto (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/infoalign.html
=item *
Bio::Tools::Run::PiseApplication
=item *
Bio::Tools::Run::AnalysisFactory::Pise
=item *
Bio::Tools::Run::PiseJob
=back
=cut
#'
package Bio::Tools::Run::PiseApplication::infoalign;
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 $infoalign = Bio::Tools::Run::PiseApplication::infoalign->new($location, $email, @params);
 Function: Creates a Bio::Tools::Run::PiseApplication::infoalign 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 $infoalign = $factory->program('infoalign');
 Example : -
 Returns : An instance of Bio::Tools::Run::PiseApplication::infoalign.
=cut
sub new {
    my ($class, $location, $email, @params) = @_;
    my $self = $class->SUPER::new($location, $email);
# -- begin of definitions extracted from /local/gensoft/lib/Pise/5.a/PerlDef/infoalign.pm
    $self->{COMMAND}   = "infoalign";
    $self->{VERSION}   = "5.a";
    $self->{TITLE}   = "INFOALIGN";
    $self->{DESCRIPTION}   = "Information on a multiple sequence alignment (EMBOSS)";
    $self->{OPT_EMAIL}   = 0;
    $self->{CATEGORIES}   =  [  
         "alignment:multiple",
         "information",
  ];
    $self->{DOCLINK}   = "http://www.uk.embnet.org/Software/EMBOSS/Apps/infoalign.html";
    $self->{_INTERFACE_STANDOUT} = undef;
    $self->{_STANDOUT_FILE} = undef;
    $self->{TOP_PARAMETERS}  = [ 
        "infoalign",
        "init",
        "input",
        "advanced",
        "output",
        "auto",
    ];
    $self->{PARAMETERS_ORDER}  = [
        "infoalign",
        "init",
        "input",        # input Section
        "sequence",     # sequence -- gapany [set of sequences] (-sequence)
        "advanced",     # advanced Section
        "refseq",       # The number or the name of the reference sequence (-refseq)
        "matrix",       # Similarity scoring Matrix file (-matrix)
        "plurality",    # Plurality check % for consensus (-plurality)
        "identity",     # Required % of identities at a position fro consensus (-identity)
        "output",       # output Section
        "outfile",      # Output sequence details to a file (-outfile)
        "html",         # Format output as an HTML table (-html)
        "only",         # Display the specified columns (-only)
        "heading",      # Display column headings (-heading)
        "usa",  # Display the USA of the sequence (-usa)
        "name",         # Display 'name' column (-name)
        "seqlength",    # Display 'seqlength' column (-seqlength)
        "alignlength",  # Display 'alignlength' column (-alignlength)
        "gaps",         # Display number of gaps (-gaps)
        "gapcount",     # Display number of gap positions (-gapcount)
        "idcount",      # Display number of identical positions (-idcount)
        "simcount",     # Display number of similar positions (-simcount)
        "diffcount",    # Display number of different positions (-diffcount)
        "change",       # Display % number of changed positions (-change)
        "description",  # Display 'description' column (-description)
        "auto",
    ];
    $self->{TYPE}  = {
        "infoalign" => 'String',
        "init" => 'String',
        "input" => 'Paragraph',
        "sequence" => 'Sequence',
        "advanced" => 'Paragraph',
        "refseq" => 'String',
        "matrix" => 'Excl',
        "plurality" => 'Float',
        "identity" => 'Float',
        "output" => 'Paragraph',
        "outfile" => 'OutFile',
        "html" => 'Switch',
        "only" => 'Switch',
        "heading" => 'Switch',
        "usa" => 'Switch',
        "name" => 'Switch',
        "seqlength" => 'Switch',
        "alignlength" => 'Switch',
        "gaps" => 'Switch',
        "gapcount" => 'Switch',
        "idcount" => 'Switch',
        "simcount" => 'Switch',
        "diffcount" => 'Switch',
        "change" => 'Switch',
        "description" => 'Switch',
        "auto" => 'String',
    };
    $self->{FORMAT}  = {
        "init" => {
                "perl" => ' "" ',
        },
        "input" => {
        },
        "sequence" => {
                "perl" => '" -sequence=$value -sformat=fasta"',
        },
        "advanced" => {
        },
        "refseq" => {
                "perl" => '($value && $value ne $vdef)? " -refseq=$value" : ""',
        },
        "matrix" => {
                "perl" => '($value)? " -matrix=$value" : ""',
        },
        "plurality" => {
                "perl" => '(defined $value && $value != $vdef)? " -plurality=$value" : ""',
        },
        "identity" => {
                "perl" => '(defined $value && $value != $vdef)? " -identity=$value" : ""',
        },
        "output" => {
        },
        "outfile" => {
                "perl" => '" -outfile=$value"',
        },
        "html" => {
                "perl" => '($value)? " -html" : ""',
        },
        "only" => {
                "perl" => '($value)? " -only" : ""',
        },
        "heading" => {
                "perl" => '($value)? " -heading" : ""',
        },
        "usa" => {
                "perl" => '($value)? " -usa" : ""',
        },
        "name" => {
                "perl" => '($value)? " -name" : ""',
        },
        "seqlength" => {
                "perl" => '($value)? " -seqlength" : ""',
        },
        "alignlength" => {
                "perl" => '($value)? " -alignlength" : ""',
        },
        "gaps" => {
                "perl" => '($value)? " -gaps" : ""',
        },
        "gapcount" => {
                "perl" => '($value)? " -gapcount" : ""',
        },
        "idcount" => {
                "perl" => '($value)? " -idcount" : ""',
        },
        "simcount" => {
                "perl" => '($value)? " -simcount" : ""',
        },
        "diffcount" => {
                "perl" => '($value)? " -diffcount" : ""',
        },
        "change" => {
                "perl" => '($value)? " -change" : ""',
        },
        "description" => {
                "perl" => '($value)? " -description" : ""',
        },
        "auto" => {
                "perl" => '" -auto -stdout"',
        },
        "infoalign" => {
                "perl" => '"infoalign"',
        }
    };
    $self->{FILENAMES}  = {
    };
    $self->{SEQFMT}  = {
        "sequence" => [8],
    };
    $self->{GROUP}  = {
        "init" => -10,
        "sequence" => 1,
        "refseq" => 2,
        "matrix" => 3,
        "plurality" => 4,
        "identity" => 5,
        "outfile" => 6,
        "html" => 7,
        "only" => 8,
        "heading" => 9,
        "usa" => 10,
        "name" => 11,
        "seqlength" => 12,
        "alignlength" => 13,
        "gaps" => 14,
        "gapcount" => 15,
        "idcount" => 16,
        "simcount" => 17,
        "diffcount" => 18,
        "change" => 19,
        "description" => 20,
        "auto" => 21,
        "infoalign" => 0
    };
    $self->{BY_GROUP_PARAMETERS}  = [
        "init",
        "input",
        "advanced",
        "output",
        "infoalign",
        "sequence",
        "refseq",
        "matrix",
        "plurality",
        "identity",
        "outfile",
        "html",
        "only",
        "heading",
        "usa",
        "name",
        "seqlength",
        "alignlength",
        "gaps",
        "gapcount",
        "idcount",
        "simcount",
        "diffcount",
        "change",
        "description",
        "auto",
    ];
    $self->{SIZE}  = {
    };
    $self->{ISHIDDEN}  = {
        "init" => 1,
        "input" => 0,
        "sequence" => 0,
        "advanced" => 0,
        "refseq" => 0,
        "matrix" => 0,
        "plurality" => 0,
        "identity" => 0,
        "output" => 0,
        "outfile" => 0,
        "html" => 0,
        "only" => 0,
        "heading" => 0,
        "usa" => 0,
        "name" => 0,
        "seqlength" => 0,
        "alignlength" => 0,
        "gaps" => 0,
        "gapcount" => 0,
        "idcount" => 0,
        "simcount" => 0,
        "diffcount" => 0,
        "change" => 0,
        "description" => 0,
        "auto" => 1,
        "infoalign" => 1
    };
    $self->{ISCOMMAND}  = {
        "init" => 0,
        "input" => 0,
        "sequence" => 0,
        "advanced" => 0,
        "refseq" => 0,
        "matrix" => 0,
        "plurality" => 0,
        "identity" => 0,
        "output" => 0,
        "outfile" => 0,
        "html" => 0,
        "only" => 0,
        "heading" => 0,
        "usa" => 0,
        "name" => 0,
        "seqlength" => 0,
        "alignlength" => 0,
        "gaps" => 0,
        "gapcount" => 0,
        "idcount" => 0,
        "simcount" => 0,
        "diffcount" => 0,
        "change" => 0,
        "description" => 0,
        "auto" => 0,
    };
    $self->{ISMANDATORY}  = {
        "init" => 0,
        "input" => 0,
        "sequence" => 1,
        "advanced" => 0,
        "refseq" => 0,
        "matrix" => 0,
        "plurality" => 0,
        "identity" => 0,
        "output" => 0,
        "outfile" => 1,
        "html" => 0,
        "only" => 0,
        "heading" => 0,
        "usa" => 0,
        "name" => 0,
        "seqlength" => 0,
        "alignlength" => 0,
        "gaps" => 0,
        "gapcount" => 0,
        "idcount" => 0,
        "simcount" => 0,
        "diffcount" => 0,
        "change" => 0,
        "description" => 0,
        "auto" => 0,
    };
    $self->{PROMPT}  = {
        "init" => "",
        "input" => "input Section",
        "sequence" => "sequence -- gapany [set of sequences] (-sequence)",
        "advanced" => "advanced Section",
        "refseq" => "The number or the name of the reference sequence (-refseq)",
        "matrix" => "Similarity scoring Matrix file (-matrix)",
        "plurality" => "Plurality check % for consensus (-plurality)",
        "identity" => "Required % of identities at a position fro consensus (-identity)",
        "output" => "output Section",
        "outfile" => "Output sequence details to a file (-outfile)",
        "html" => "Format output as an HTML table (-html)",
        "only" => "Display the specified columns (-only)",
        "heading" => "Display column headings (-heading)",
        "usa" => "Display the USA of the sequence (-usa)",
        "name" => "Display 'name' column (-name)",
        "seqlength" => "Display 'seqlength' column (-seqlength)",
        "alignlength" => "Display 'alignlength' column (-alignlength)",
        "gaps" => "Display number of gaps (-gaps)",
        "gapcount" => "Display number of gap positions (-gapcount)",
        "idcount" => "Display number of identical positions (-idcount)",
        "simcount" => "Display number of similar positions (-simcount)",
        "diffcount" => "Display number of different positions (-diffcount)",
        "change" => "Display % number of changed positions (-change)",
        "description" => "Display 'description' column (-description)",
        "auto" => "",
    };
    $self->{ISSTANDOUT}  = {
        "init" => 0,
        "input" => 0,
        "sequence" => 0,
        "advanced" => 0,
        "refseq" => 0,
        "matrix" => 0,
        "plurality" => 0,
        "identity" => 0,
        "output" => 0,
        "outfile" => 0,
        "html" => 0,
        "only" => 0,
        "heading" => 0,
        "usa" => 0,
        "name" => 0,
        "seqlength" => 0,
        "alignlength" => 0,
        "gaps" => 0,
        "gapcount" => 0,
        "idcount" => 0,
        "simcount" => 0,
        "diffcount" => 0,
        "change" => 0,
        "description" => 0,
        "auto" => 0,
    };
    $self->{VLIST}  = {
        "input" => ['sequence',],
        "advanced" => ['refseq','matrix','plurality','identity',],
        "matrix" => ['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" => ['outfile','html','only','heading','usa','name','seqlength','alignlength','gaps','gapcount','idcount','simcount','diffcount','change','description',],
    };
    $self->{FLIST}  = {
    };
    $self->{SEPARATOR}  = {
    };
    $self->{VDEF}  = {
        "refseq" => '0',
        "plurality" => '50.0',
        "identity" => '0.0',
        "outfile" => 'outfile.out',
        "html" => '0',
        "only" => '0',
        "heading" => '',
        "usa" => '',
        "name" => '',
        "seqlength" => '',
        "alignlength" => '',
        "gaps" => '',
        "gapcount" => '',
        "idcount" => '',
        "simcount" => '',
        "diffcount" => '',
        "change" => '',
        "description" => '',
    };
    $self->{PRECOND}  = {
        "init" => { "perl" => '1' },
        "input" => { "perl" => '1' },
        "sequence" => { "perl" => '1' },
        "advanced" => { "perl" => '1' },
        "refseq" => { "perl" => '1' },
        "matrix" => { "perl" => '1' },
        "plurality" => { "perl" => '1' },
        "identity" => { "perl" => '1' },
        "output" => { "perl" => '1' },
        "outfile" => { "perl" => '1' },
        "html" => { "perl" => '1' },
        "only" => { "perl" => '1' },
        "heading" => { "perl" => '1' },
        "usa" => { "perl" => '1' },
        "name" => { "perl" => '1' },
        "seqlength" => { "perl" => '1' },
        "alignlength" => { "perl" => '1' },
        "gaps" => { "perl" => '1' },
        "gapcount" => { "perl" => '1' },
        "idcount" => { "perl" => '1' },
        "simcount" => { "perl" => '1' },
        "diffcount" => { "perl" => '1' },
        "change" => { "perl" => '1' },
        "description" => { "perl" => '1' },
        "auto" => { "perl" => '1' },
    };
    $self->{CTRL}  = {
    };
    $self->{PIPEOUT}  = {
    };
    $self->{WITHPIPEOUT}  = {
    };
    $self->{PIPEIN}  = {
        "sequence" => {
                 "seqsfile" => '1',
        },
    };
    $self->{WITHPIPEIN}  = {
    };
    $self->{ISCLEAN}  = {
        "init" => 0,
        "input" => 0,
        "sequence" => 0,
        "advanced" => 0,
        "refseq" => 0,
        "matrix" => 0,
        "plurality" => 0,
        "identity" => 0,
        "output" => 0,
        "outfile" => 0,
        "html" => 0,
        "only" => 0,
        "heading" => 0,
        "usa" => 0,
        "name" => 0,
        "seqlength" => 0,
        "alignlength" => 0,
        "gaps" => 0,
        "gapcount" => 0,
        "idcount" => 0,
        "simcount" => 0,
        "diffcount" => 0,
        "change" => 0,
        "description" => 0,
        "auto" => 0,
    };
    $self->{ISSIMPLE}  = {
        "init" => 0,
        "input" => 0,
        "sequence" => 1,
        "advanced" => 0,
        "refseq" => 0,
        "matrix" => 0,
        "plurality" => 0,
        "identity" => 0,
        "output" => 0,
        "outfile" => 1,
        "html" => 0,
        "only" => 0,
        "heading" => 0,
        "usa" => 0,
        "name" => 0,
        "seqlength" => 0,
        "alignlength" => 0,
        "gaps" => 0,
        "gapcount" => 0,
        "idcount" => 0,
        "simcount" => 0,
        "diffcount" => 0,
        "change" => 0,
        "description" => 0,
        "auto" => 0,
    };
    $self->{PARAMFILE}  = {
    };
    $self->{COMMENT}  = {
        "sequence" => [
                "The sequence alignment to be displayed.",
        ],
        "refseq" => [
                "If you give the number in the alignment or the name of a sequence, it will be taken to be the reference sequence. The reference sequence is the one against which all the other sequences are compared. If this is set to 0 then the consensus sequence will be used as the reference sequence. By default the consensus sequence is used as the reference sequence.",
        ],
        "matrix" => [
                "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.",
        ],
        "plurality" => [
                "Set a cut-off for the % of positive scoring matches below which there is no consensus. The default plurality is taken as 50% of the total weight of all the sequences in the alignment.",
        ],
        "identity" => [
                "Provides the facility of setting the required number of identities at a position for it to give a consensus. Therefore, if this is set to 100% only columns of identities contribute to the consensus.",
        ],
        "outfile" => [
                "If you enter the name of a file here then this program will write the sequence details into that file.",
        ],
        "only" => [
                "This is a way of shortening the command line if you only want a few things to be displayed. Instead of specifying: <BR> \'-nohead -nousa -noname -noalign -nogaps -nogapcount -nosimcount -noidcount -nodiffcount\' <BR> to get only the sequence length output, you can specify <BR> \'-only -seqlength\'",
        ],
    };
    $self->{SCALEMIN}  = {
    };
    $self->{SCALEMAX}  = {
    };
    $self->{SCALEINC}  = {
    };
    $self->{INFO}  = {
    };
# -- end of definitions extracted from /local/gensoft/lib/Pise/5.a/PerlDef/infoalign.pm
    $self->_init_params(@params);
    return $self;
}
1; # Needed to keep compiler happy