# matcher.pm,v 1.3.2.1 2005/10/09 15:19:45 jason Exp
# BioPerl module for Bio::Tools::Run::PiseApplication::matcher
#
# 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::matcher

=head1 SYNOPSIS

  #

=head1 DESCRIPTION

Bio::Tools::Run::PiseApplication::matcher

      Bioperl class for:

	MATCHER	Finds the best local alignments between two sequences (EMBOSS)


      Parameters: 

        (see also:
          http://bioweb.pasteur.fr/seqanal/interfaces/matcher.html 
         for available values):


		matcher (String)

		init (String)

		sequencea (Sequence)
			sequencea -- any [single sequence] (-sequencea)
			pipe: seqfile

		sequenceb (Sequence)
			sequenceb [single sequence] (-sequenceb)

		datafile (Excl)
			Matrix file (-datafile)

		alternatives (Integer)
			Number of alternative matches (-alternatives)

		gappenalty (Integer)
			Gap penalty (-gappenalty)

		gaplength (Integer)
			Gap length penalty (-gaplength)

		outfile (OutFile)
			outfile (-outfile)
			pipe: readseq_ok_alig

		outfile_aformat (Excl)
			Alignment output format (-aformat)

		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/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 the
web:

  http://bugzilla.bioperl.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/matcher.html

=item *

Bio::Tools::Run::PiseApplication

=item *

Bio::Tools::Run::AnalysisFactory::Pise

=item *

Bio::Tools::Run::PiseJob

=back

=cut

#'
package Bio::Tools::Run::PiseApplication::matcher;

use vars qw(@ISA);
use strict;
use Bio::Tools::Run::PiseApplication;

@ISA = qw(Bio::Tools::Run::PiseApplication);

=head2 new

 Title   : new()
 Usage   : my $matcher = Bio::Tools::Run::PiseApplication::matcher->new($location, $email, @params);
 Function: Creates a Bio::Tools::Run::PiseApplication::matcher 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 $matcher = $factory->program('matcher');
 Example : -
 Returns : An instance of Bio::Tools::Run::PiseApplication::matcher.

=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/matcher.pm

    $self->{COMMAND}   = "matcher";
    $self->{VERSION}   = "5.a";
    $self->{TITLE}   = "MATCHER";

    $self->{DESCRIPTION}   = "Finds the best local alignments between two sequences (EMBOSS)";

    $self->{OPT_EMAIL}   = 0;

    $self->{CATEGORIES}   =  [  

         "alignment:local",
  ];

    $self->{DOCLINK}   = "http://www.uk.embnet.org/Software/EMBOSS/Apps/matcher.html";

    $self->{_INTERFACE_STANDOUT} = undef;
    $self->{_STANDOUT_FILE} = undef;

    $self->{TOP_PARAMETERS}  = [ 
	"matcher",
	"init",
	"input",
	"advanced",
	"output",
	"auto",

    ];

    $self->{PARAMETERS_ORDER}  = [
	"matcher",
	"init",
	"input", 	# input Section
	"sequencea", 	# sequencea -- any [single sequence] (-sequencea)
	"sequenceb", 	# sequenceb [single sequence] (-sequenceb)
	"advanced", 	# advanced Section
	"datafile", 	# Matrix file (-datafile)
	"alternatives", 	# Number of alternative matches (-alternatives)
	"gappenalty", 	# Gap penalty (-gappenalty)
	"gaplength", 	# Gap length penalty (-gaplength)
	"output", 	# output Section
	"outfile", 	# outfile (-outfile)
	"outfile_aformat", 	# Alignment output format (-aformat)
	"auto",

    ];

    $self->{TYPE}  = {
	"matcher" => 'String',
	"init" => 'String',
	"input" => 'Paragraph',
	"sequencea" => 'Sequence',
	"sequenceb" => 'Sequence',
	"advanced" => 'Paragraph',
	"datafile" => 'Excl',
	"alternatives" => 'Integer',
	"gappenalty" => 'Integer',
	"gaplength" => 'Integer',
	"output" => 'Paragraph',
	"outfile" => 'OutFile',
	"outfile_aformat" => 'Excl',
	"auto" => 'String',

    };

    $self->{FORMAT}  = {
	"init" => {
		"perl" => ' "" ',
	},
	"input" => {
	},
	"sequencea" => {
		"perl" => '" -sequencea=$value -sformat=fasta"',
	},
	"sequenceb" => {
		"perl" => '" -sequenceb=$value -sformat=fasta"',
	},
	"advanced" => {
	},
	"datafile" => {
		"perl" => '($value)? " -datafile=$value" : ""',
	},
	"alternatives" => {
		"perl" => '(defined $value && $value != $vdef)? " -alternatives=$value" : ""',
	},
	"gappenalty" => {
		"perl" => '(defined $value && $value != $vdef)? " -gappenalty=$value" : ""',
	},
	"gaplength" => {
		"perl" => '(defined $value && $value != $vdef)? " -gaplength=$value" : ""',
	},
	"output" => {
	},
	"outfile" => {
		"perl" => '" -outfile=$value"',
	},
	"outfile_aformat" => {
		"perl" => '($value)? " -aformat=$value" : "" ',
	},
	"auto" => {
		"perl" => '" -auto -stdout"',
	},
	"matcher" => {
		"perl" => '"matcher"',
	}

    };

    $self->{FILENAMES}  = {

    };

    $self->{SEQFMT}  = {
	"sequencea" => [8],
	"sequenceb" => [8],

    };

    $self->{GROUP}  = {
	"init" => -10,
	"sequencea" => 1,
	"sequenceb" => 2,
	"datafile" => 3,
	"alternatives" => 4,
	"gappenalty" => 5,
	"gaplength" => 6,
	"outfile" => 7,
	"outfile_aformat" => 7,
	"auto" => 8,
	"matcher" => 0

    };

    $self->{BY_GROUP_PARAMETERS}  = [
	"init",
	"input",
	"advanced",
	"output",
	"matcher",
	"sequencea",
	"sequenceb",
	"datafile",
	"alternatives",
	"gappenalty",
	"gaplength",
	"outfile",
	"outfile_aformat",
	"auto",

    ];

    $self->{SIZE}  = {

    };

    $self->{ISHIDDEN}  = {
	"init" => 1,
	"input" => 0,
	"sequencea" => 0,
	"sequenceb" => 0,
	"advanced" => 0,
	"datafile" => 0,
	"alternatives" => 0,
	"gappenalty" => 0,
	"gaplength" => 0,
	"output" => 0,
	"outfile" => 0,
	"outfile_aformat" => 0,
	"auto" => 1,
	"matcher" => 1

    };

    $self->{ISCOMMAND}  = {
	"init" => 0,
	"input" => 0,
	"sequencea" => 0,
	"sequenceb" => 0,
	"advanced" => 0,
	"datafile" => 0,
	"alternatives" => 0,
	"gappenalty" => 0,
	"gaplength" => 0,
	"output" => 0,
	"outfile" => 0,
	"outfile_aformat" => 0,
	"auto" => 0,

    };

    $self->{ISMANDATORY}  = {
	"init" => 0,
	"input" => 0,
	"sequencea" => 1,
	"sequenceb" => 1,
	"advanced" => 0,
	"datafile" => 0,
	"alternatives" => 0,
	"gappenalty" => 0,
	"gaplength" => 0,
	"output" => 0,
	"outfile" => 1,
	"outfile_aformat" => 0,
	"auto" => 0,

    };

    $self->{PROMPT}  = {
	"init" => "",
	"input" => "input Section",
	"sequencea" => "sequencea -- any [single sequence] (-sequencea)",
	"sequenceb" => "sequenceb [single sequence] (-sequenceb)",
	"advanced" => "advanced Section",
	"datafile" => "Matrix file (-datafile)",
	"alternatives" => "Number of alternative matches (-alternatives)",
	"gappenalty" => "Gap penalty (-gappenalty)",
	"gaplength" => "Gap length penalty (-gaplength)",
	"output" => "output Section",
	"outfile" => "outfile (-outfile)",
	"outfile_aformat" => "Alignment output format (-aformat)",
	"auto" => "",

    };

    $self->{ISSTANDOUT}  = {
	"init" => 0,
	"input" => 0,
	"sequencea" => 0,
	"sequenceb" => 0,
	"advanced" => 0,
	"datafile" => 0,
	"alternatives" => 0,
	"gappenalty" => 0,
	"gaplength" => 0,
	"output" => 0,
	"outfile" => 0,
	"outfile_aformat" => 0,
	"auto" => 0,

    };

    $self->{VLIST}  = {

	"input" => ['sequencea','sequenceb',],
	"advanced" => ['datafile','alternatives','gappenalty','gaplength',],
	"datafile" => ['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','outfile_aformat',],
	"outfile_aformat" => ['','default','fasta','fasta','MSF','MSF',],
    };

    $self->{FLIST}  = {

    };

    $self->{SEPARATOR}  = {

    };

    $self->{VDEF}  = {
	"alternatives" => '1',
	"gappenalty" => '',
	"gaplength" => '',
	"outfile" => 'outfile.align',

    };

    $self->{PRECOND}  = {
	"init" => { "perl" => '1' },
	"input" => { "perl" => '1' },
	"sequencea" => { "perl" => '1' },
	"sequenceb" => { "perl" => '1' },
	"advanced" => { "perl" => '1' },
	"datafile" => { "perl" => '1' },
	"alternatives" => { "perl" => '1' },
	"gappenalty" => { "perl" => '1' },
	"gaplength" => { "perl" => '1' },
	"output" => { "perl" => '1' },
	"outfile" => { "perl" => '1' },
	"outfile_aformat" => { "perl" => '1' },
	"auto" => { "perl" => '1' },

    };

    $self->{CTRL}  = {

    };

    $self->{PIPEOUT}  = {
	"outfile" => {
		 '$outfile_aformat ne ""' => "readseq_ok_alig",
	},

    };

    $self->{WITHPIPEOUT}  = {

    };

    $self->{PIPEIN}  = {
	"sequencea" => {
		 "seqfile" => '1',
	},

    };

    $self->{WITHPIPEIN}  = {

    };

    $self->{ISCLEAN}  = {
	"init" => 0,
	"input" => 0,
	"sequencea" => 0,
	"sequenceb" => 0,
	"advanced" => 0,
	"datafile" => 0,
	"alternatives" => 0,
	"gappenalty" => 0,
	"gaplength" => 0,
	"output" => 0,
	"outfile" => 0,
	"outfile_aformat" => 0,
	"auto" => 0,

    };

    $self->{ISSIMPLE}  = {
	"init" => 0,
	"input" => 0,
	"sequencea" => 1,
	"sequenceb" => 1,
	"advanced" => 0,
	"datafile" => 0,
	"alternatives" => 0,
	"gappenalty" => 0,
	"gaplength" => 0,
	"output" => 0,
	"outfile" => 0,
	"outfile_aformat" => 0,
	"auto" => 0,

    };

    $self->{PARAMFILE}  = {

    };

    $self->{COMMENT}  = {
	"datafile" => [
		"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.",
	],
	"alternatives" => [
		"This sets the number of alternative matches output. By default only the highest scoring alignment is shown. A value of 2 gves you other reasonable alignments. In some cases, for example multidomain proteins of cDNA and gemomic DNA comparisons, there may be other interesting and significant alignments.",
	],
	"gappenalty" => [
		"The gap penalty is the score taken away when a gap is created. The best value depends on the choice of comparison matrix. The default value of 14 assumes you are using the EBLOSUM62 matrix for protein sequences, or a value of 16 and the EDNAFULL matrix for nucleotide sequences. Allowed values: Positive integer",
	],
	"gaplength" => [
		"The gap length, or gap extension, penalty is added to the standard gap penalty for each base or residue in the gap. This is how long gaps are penalized. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty. An exception is where one or both sequences are single reads with possible sequencing errors in which case you would expect many single base gaps. You can get this result by setting the gap penalty to zero (or very low) and using the gap extension penalty to control gap scoring. Allowed values: Positive integer",
	],

    };

    $self->{SCALEMIN}  = {

    };

    $self->{SCALEMAX}  = {

    };

    $self->{SCALEINC}  = {

    };

    $self->{INFO}  = {

    };

# -- end of definitions extracted from /local/gensoft/lib/Pise/5.a/PerlDef/matcher.pm



    $self->_init_params(@params);

    return $self;
}



1; # Needed to keep compiler happy

