# remap.pm,v 1.3.2.1 2005/10/09 15:19:48 jason Exp
# BioPerl module for Bio::Tools::Run::PiseApplication::remap
#
# 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::remap

=head1 SYNOPSIS

  #

=head1 DESCRIPTION

Bio::Tools::Run::PiseApplication::remap

      Bioperl class for:

	REMAP	Display a sequence with restriction cut sites, translation etc.. (EMBOSS)


      Parameters: 

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


		remap (String)

		init (String)

		sequence (Sequence)
			sequence -- DNA [sequences] (-sequence)
			pipe: seqsfile

		enzymes (String)
			Comma separated enzyme list (-enzymes)

		sitelen (Integer)
			Minimum recognition site length (-sitelen)

		mincuts (Integer)
			Minimum cuts per RE (-mincuts)

		maxcuts (Integer)
			Maximum cuts per RE (-maxcuts)

		single (Switch)
			Force single site only cuts (-single)

		blunt (Switch)
			Allow blunt end cutters (-blunt)

		sticky (Switch)
			Allow sticky end cutters (-sticky)

		ambiguity (Switch)
			Allow ambiguous matches (-ambiguity)

		plasmid (Switch)
			Allow circular DNA (-plasmid)

		commercial (Switch)
			Only enzymes with suppliers (-commercial)

		table (Excl)
			Code to use -- Genetic codes (-table)

		outfile (OutFile)
			Output sequence details to a file (-outfile)

		cutlist (Switch)
			List the enzymes that cut (-cutlist)

		flatreformat (Switch)
			Display RE sites in flat format (-flatreformat)

		limit (Switch)
			Limits reports to one isoschizomer (-limit)

		preferred (Switch)
			Report preferred isoschizomers (-preferred)

		translation (Switch)
			Display translation (-translation)

		reverse (Switch)
			Display cut sites and translation of reverse sense (-reverse)

		orfminsize (Integer)
			Minimum size of ORFs (-orfminsize)

		uppercase (Integer)
			Regions to put in uppercase (eg: 4-57,78-94) (-uppercase)

		highlight (Integer)
			Regions to colour in HTML (eg: 4-57 red 78-94 green) (-highlight)

		threeletter (Switch)
			Display protein sequences in three-letter code (-threeletter)

		number (Switch)
			Number the sequences (-number)

		width (Integer)
			Width of sequence to display (-width)

		length (Integer)
			Line length of page (0 for indefinite) (-length)

		margin (Integer)
			Margin around sequence for numbering (-margin)

		name (Switch)
			Display sequence ID (-name)

		description (Switch)
			Display description (-description)

		offset (Integer)
			Offset to start numbering the sequence from (-offset)

		html (Switch)
			Use HTML formatting (-html)

		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/remap.html

=item *

Bio::Tools::Run::PiseApplication

=item *

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

=item *

Bio::Tools::Run::PiseJob

=back

=cut

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

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

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

=head2 new

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

=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/remap.pm

    $self->{COMMAND}   = "remap";
    $self->{VERSION}   = "5.a";
    $self->{TITLE}   = "REMAP";

    $self->{DESCRIPTION}   = "Display a sequence with restriction cut sites, translation etc.. (EMBOSS)";

    $self->{OPT_EMAIL}   = 0;

    $self->{CATEGORIES}   =  [  

         "display",

         "nucleic:restriction",

         "nucleic:translation",
  ];

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

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

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

    ];

    $self->{PARAMETERS_ORDER}  = [
	"remap",
	"init",
	"input", 	# input Section
	"sequence", 	# sequence -- DNA [sequences] (-sequence)
	"required", 	# required Section
	"enzymes", 	# Comma separated enzyme list (-enzymes)
	"sitelen", 	# Minimum recognition site length (-sitelen)
	"advanced", 	# advanced Section
	"mincuts", 	# Minimum cuts per RE (-mincuts)
	"maxcuts", 	# Maximum cuts per RE (-maxcuts)
	"single", 	# Force single site only cuts (-single)
	"blunt", 	# Allow blunt end cutters (-blunt)
	"sticky", 	# Allow sticky end cutters (-sticky)
	"ambiguity", 	# Allow ambiguous matches (-ambiguity)
	"plasmid", 	# Allow circular DNA (-plasmid)
	"commercial", 	# Only enzymes with suppliers (-commercial)
	"table", 	# Code to use -- Genetic codes (-table)
	"output", 	# output Section
	"outfile", 	# Output sequence details to a file (-outfile)
	"cutlist", 	# List the enzymes that cut (-cutlist)
	"flatreformat", 	# Display RE sites in flat format (-flatreformat)
	"limit", 	# Limits reports to one isoschizomer (-limit)
	"preferred", 	# Report preferred isoschizomers (-preferred)
	"translation", 	# Display translation (-translation)
	"reverse", 	# Display cut sites and translation of reverse sense (-reverse)
	"orfminsize", 	# Minimum size of ORFs (-orfminsize)
	"uppercase", 	# Regions to put in uppercase (eg: 4-57,78-94) (-uppercase)
	"highlight", 	# Regions to colour in HTML (eg: 4-57 red 78-94 green) (-highlight)
	"threeletter", 	# Display protein sequences in three-letter code (-threeletter)
	"number", 	# Number the sequences (-number)
	"width", 	# Width of sequence to display (-width)
	"length", 	# Line length of page (0 for indefinite) (-length)
	"margin", 	# Margin around sequence for numbering (-margin)
	"name", 	# Display sequence ID (-name)
	"description", 	# Display description (-description)
	"offset", 	# Offset to start numbering the sequence from (-offset)
	"html", 	# Use HTML formatting (-html)
	"auto",

    ];

    $self->{TYPE}  = {
	"remap" => 'String',
	"init" => 'String',
	"input" => 'Paragraph',
	"sequence" => 'Sequence',
	"required" => 'Paragraph',
	"enzymes" => 'String',
	"sitelen" => 'Integer',
	"advanced" => 'Paragraph',
	"mincuts" => 'Integer',
	"maxcuts" => 'Integer',
	"single" => 'Switch',
	"blunt" => 'Switch',
	"sticky" => 'Switch',
	"ambiguity" => 'Switch',
	"plasmid" => 'Switch',
	"commercial" => 'Switch',
	"table" => 'Excl',
	"output" => 'Paragraph',
	"outfile" => 'OutFile',
	"cutlist" => 'Switch',
	"flatreformat" => 'Switch',
	"limit" => 'Switch',
	"preferred" => 'Switch',
	"translation" => 'Switch',
	"reverse" => 'Switch',
	"orfminsize" => 'Integer',
	"uppercase" => 'Integer',
	"highlight" => 'Integer',
	"threeletter" => 'Switch',
	"number" => 'Switch',
	"width" => 'Integer',
	"length" => 'Integer',
	"margin" => 'Integer',
	"name" => 'Switch',
	"description" => 'Switch',
	"offset" => 'Integer',
	"html" => 'Switch',
	"auto" => 'String',

    };

    $self->{FORMAT}  = {
	"init" => {
		"perl" => ' "" ',
	},
	"input" => {
	},
	"sequence" => {
		"perl" => '" -sequence=$value -sformat=fasta"',
	},
	"required" => {
	},
	"enzymes" => {
		"perl" => '" -enzymes=$value"',
	},
	"sitelen" => {
		"perl" => '" -sitelen=$value"',
	},
	"advanced" => {
	},
	"mincuts" => {
		"perl" => '(defined $value && $value != $vdef)? " -mincuts=$value" : ""',
	},
	"maxcuts" => {
		"perl" => '(defined $value && $value != $vdef)? " -maxcuts=$value" : ""',
	},
	"single" => {
		"perl" => '($value)? " -single" : ""',
	},
	"blunt" => {
		"perl" => '($value)? "" : " -noblunt"',
	},
	"sticky" => {
		"perl" => '($value)? "" : " -nosticky"',
	},
	"ambiguity" => {
		"perl" => '($value)? "" : " -noambiguity"',
	},
	"plasmid" => {
		"perl" => '($value)? " -plasmid" : ""',
	},
	"commercial" => {
		"perl" => '($value)? "" : " -nocommercial"',
	},
	"table" => {
		"perl" => '" -table=$value"',
	},
	"output" => {
	},
	"outfile" => {
		"perl" => '" -outfile=$value"',
	},
	"cutlist" => {
		"perl" => '($value)? "" : " -nocutlist"',
	},
	"flatreformat" => {
		"perl" => '($value)? " -flatreformat" : ""',
	},
	"limit" => {
		"perl" => '($value)? "" : " -nolimit"',
	},
	"preferred" => {
		"perl" => '($value)? " -preferred" : ""',
	},
	"translation" => {
		"perl" => '($value)? "" : " -notranslation"',
	},
	"reverse" => {
		"perl" => '($value)? "" : " -noreverse"',
	},
	"orfminsize" => {
		"perl" => '(defined $value && $value != $vdef)? " -orfminsize=$value" : ""',
	},
	"uppercase" => {
		"perl" => '($value)? " -uppercase=$value" : ""',
	},
	"highlight" => {
		"perl" => '($value)? " -highlight=$value" : ""',
	},
	"threeletter" => {
		"perl" => '($value)? " -threeletter" : ""',
	},
	"number" => {
		"perl" => '($value)? " -number" : ""',
	},
	"width" => {
		"perl" => '(defined $value && $value != $vdef)? " -width=$value" : ""',
	},
	"length" => {
		"perl" => '(defined $value && $value != $vdef)? " -length=$value" : ""',
	},
	"margin" => {
		"perl" => '(defined $value && $value != $vdef)? " -margin=$value" : ""',
	},
	"name" => {
		"perl" => '($value)? "" : " -noname"',
	},
	"description" => {
		"perl" => '($value)? "" : " -nodescription"',
	},
	"offset" => {
		"perl" => '(defined $value && $value != $vdef)? " -offset=$value" : ""',
	},
	"html" => {
		"perl" => '($value)? " -html" : ""',
	},
	"auto" => {
		"perl" => '" -auto -stdout"',
	},
	"remap" => {
		"perl" => '"remap"',
	}

    };

    $self->{FILENAMES}  = {

    };

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

    };

    $self->{GROUP}  = {
	"init" => -10,
	"sequence" => 1,
	"enzymes" => 2,
	"sitelen" => 3,
	"mincuts" => 4,
	"maxcuts" => 5,
	"single" => 6,
	"blunt" => 7,
	"sticky" => 8,
	"ambiguity" => 9,
	"plasmid" => 10,
	"commercial" => 11,
	"table" => 12,
	"outfile" => 13,
	"cutlist" => 14,
	"flatreformat" => 15,
	"limit" => 16,
	"preferred" => 17,
	"translation" => 18,
	"reverse" => 19,
	"orfminsize" => 20,
	"uppercase" => 21,
	"highlight" => 22,
	"threeletter" => 23,
	"number" => 24,
	"width" => 25,
	"length" => 26,
	"margin" => 27,
	"name" => 28,
	"description" => 29,
	"offset" => 30,
	"html" => 31,
	"auto" => 32,
	"remap" => 0

    };

    $self->{BY_GROUP_PARAMETERS}  = [
	"init",
	"input",
	"required",
	"advanced",
	"output",
	"remap",
	"sequence",
	"enzymes",
	"sitelen",
	"mincuts",
	"maxcuts",
	"single",
	"blunt",
	"sticky",
	"ambiguity",
	"plasmid",
	"commercial",
	"table",
	"outfile",
	"cutlist",
	"flatreformat",
	"limit",
	"preferred",
	"translation",
	"reverse",
	"orfminsize",
	"uppercase",
	"highlight",
	"threeletter",
	"number",
	"width",
	"length",
	"margin",
	"name",
	"description",
	"offset",
	"html",
	"auto",

    ];

    $self->{SIZE}  = {

    };

    $self->{ISHIDDEN}  = {
	"init" => 1,
	"input" => 0,
	"sequence" => 0,
	"required" => 0,
	"enzymes" => 0,
	"sitelen" => 0,
	"advanced" => 0,
	"mincuts" => 0,
	"maxcuts" => 0,
	"single" => 0,
	"blunt" => 0,
	"sticky" => 0,
	"ambiguity" => 0,
	"plasmid" => 0,
	"commercial" => 0,
	"table" => 0,
	"output" => 0,
	"outfile" => 0,
	"cutlist" => 0,
	"flatreformat" => 0,
	"limit" => 0,
	"preferred" => 0,
	"translation" => 0,
	"reverse" => 0,
	"orfminsize" => 0,
	"uppercase" => 0,
	"highlight" => 0,
	"threeletter" => 0,
	"number" => 0,
	"width" => 0,
	"length" => 0,
	"margin" => 0,
	"name" => 0,
	"description" => 0,
	"offset" => 0,
	"html" => 0,
	"auto" => 1,
	"remap" => 1

    };

    $self->{ISCOMMAND}  = {
	"init" => 0,
	"input" => 0,
	"sequence" => 0,
	"required" => 0,
	"enzymes" => 0,
	"sitelen" => 0,
	"advanced" => 0,
	"mincuts" => 0,
	"maxcuts" => 0,
	"single" => 0,
	"blunt" => 0,
	"sticky" => 0,
	"ambiguity" => 0,
	"plasmid" => 0,
	"commercial" => 0,
	"table" => 0,
	"output" => 0,
	"outfile" => 0,
	"cutlist" => 0,
	"flatreformat" => 0,
	"limit" => 0,
	"preferred" => 0,
	"translation" => 0,
	"reverse" => 0,
	"orfminsize" => 0,
	"uppercase" => 0,
	"highlight" => 0,
	"threeletter" => 0,
	"number" => 0,
	"width" => 0,
	"length" => 0,
	"margin" => 0,
	"name" => 0,
	"description" => 0,
	"offset" => 0,
	"html" => 0,
	"auto" => 0,

    };

    $self->{ISMANDATORY}  = {
	"init" => 0,
	"input" => 0,
	"sequence" => 1,
	"required" => 0,
	"enzymes" => 1,
	"sitelen" => 1,
	"advanced" => 0,
	"mincuts" => 0,
	"maxcuts" => 0,
	"single" => 0,
	"blunt" => 0,
	"sticky" => 0,
	"ambiguity" => 0,
	"plasmid" => 0,
	"commercial" => 0,
	"table" => 1,
	"output" => 0,
	"outfile" => 1,
	"cutlist" => 0,
	"flatreformat" => 0,
	"limit" => 0,
	"preferred" => 0,
	"translation" => 0,
	"reverse" => 0,
	"orfminsize" => 0,
	"uppercase" => 0,
	"highlight" => 0,
	"threeletter" => 0,
	"number" => 0,
	"width" => 0,
	"length" => 0,
	"margin" => 0,
	"name" => 0,
	"description" => 0,
	"offset" => 0,
	"html" => 0,
	"auto" => 0,

    };

    $self->{PROMPT}  = {
	"init" => "",
	"input" => "input Section",
	"sequence" => "sequence -- DNA [sequences] (-sequence)",
	"required" => "required Section",
	"enzymes" => "Comma separated enzyme list (-enzymes)",
	"sitelen" => "Minimum recognition site length (-sitelen)",
	"advanced" => "advanced Section",
	"mincuts" => "Minimum cuts per RE (-mincuts)",
	"maxcuts" => "Maximum cuts per RE (-maxcuts)",
	"single" => "Force single site only cuts (-single)",
	"blunt" => "Allow blunt end cutters (-blunt)",
	"sticky" => "Allow sticky end cutters (-sticky)",
	"ambiguity" => "Allow ambiguous matches (-ambiguity)",
	"plasmid" => "Allow circular DNA (-plasmid)",
	"commercial" => "Only enzymes with suppliers (-commercial)",
	"table" => "Code to use -- Genetic codes (-table)",
	"output" => "output Section",
	"outfile" => "Output sequence details to a file (-outfile)",
	"cutlist" => "List the enzymes that cut (-cutlist)",
	"flatreformat" => "Display RE sites in flat format (-flatreformat)",
	"limit" => "Limits reports to one isoschizomer (-limit)",
	"preferred" => "Report preferred isoschizomers (-preferred)",
	"translation" => "Display translation (-translation)",
	"reverse" => "Display cut sites and translation of reverse sense (-reverse)",
	"orfminsize" => "Minimum size of ORFs (-orfminsize)",
	"uppercase" => "Regions to put in uppercase (eg: 4-57,78-94) (-uppercase)",
	"highlight" => "Regions to colour in HTML (eg: 4-57 red 78-94 green) (-highlight)",
	"threeletter" => "Display protein sequences in three-letter code (-threeletter)",
	"number" => "Number the sequences (-number)",
	"width" => "Width of sequence to display (-width)",
	"length" => "Line length of page (0 for indefinite) (-length)",
	"margin" => "Margin around sequence for numbering (-margin)",
	"name" => "Display sequence ID (-name)",
	"description" => "Display description (-description)",
	"offset" => "Offset to start numbering the sequence from (-offset)",
	"html" => "Use HTML formatting (-html)",
	"auto" => "",

    };

    $self->{ISSTANDOUT}  = {
	"init" => 0,
	"input" => 0,
	"sequence" => 0,
	"required" => 0,
	"enzymes" => 0,
	"sitelen" => 0,
	"advanced" => 0,
	"mincuts" => 0,
	"maxcuts" => 0,
	"single" => 0,
	"blunt" => 0,
	"sticky" => 0,
	"ambiguity" => 0,
	"plasmid" => 0,
	"commercial" => 0,
	"table" => 0,
	"output" => 0,
	"outfile" => 0,
	"cutlist" => 0,
	"flatreformat" => 0,
	"limit" => 0,
	"preferred" => 0,
	"translation" => 0,
	"reverse" => 0,
	"orfminsize" => 0,
	"uppercase" => 0,
	"highlight" => 0,
	"threeletter" => 0,
	"number" => 0,
	"width" => 0,
	"length" => 0,
	"margin" => 0,
	"name" => 0,
	"description" => 0,
	"offset" => 0,
	"html" => 0,
	"auto" => 0,

    };

    $self->{VLIST}  = {

	"input" => ['sequence',],
	"required" => ['enzymes','sitelen',],
	"advanced" => ['mincuts','maxcuts','single','blunt','sticky','ambiguity','plasmid','commercial','table',],
	"table" => ['0','Standard','1','Standard (with alternative initiation codons)','2','Vertebrate Mitochondrial','3','Yeast Mitochondrial','4','Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma','5','Invertebrate Mitochondrial','6','Ciliate Macronuclear and Dasycladacean','9','Echinoderm Mitochondrial','10','Euplotid Nuclear','11','Bacterial','12','Alternative Yeast Nuclear','13','Ascidian Mitochondrial','14','Flatworm Mitochondrial','15','Blepharisma Macronuclear','16','Chlorophycean Mitochondrial','21','Trematode Mitochondrial','22','Scenedesmus obliquus','23','Thraustochytrium Mitochondrial',],
	"output" => ['outfile','cutlist','flatreformat','limit','preferred','translation','reverse','orfminsize','uppercase','highlight','threeletter','number','width','length','margin','name','description','offset','html',],
    };

    $self->{FLIST}  = {

    };

    $self->{SEPARATOR}  = {

    };

    $self->{VDEF}  = {
	"enzymes" => 'all',
	"sitelen" => '4',
	"mincuts" => '1',
	"maxcuts" => '2000000000',
	"single" => '0',
	"blunt" => '1',
	"sticky" => '1',
	"ambiguity" => '1',
	"plasmid" => '0',
	"commercial" => '1',
	"table" => '0',
	"outfile" => 'outfile.out',
	"cutlist" => '1',
	"flatreformat" => '0',
	"limit" => '1',
	"preferred" => '0',
	"translation" => '1',
	"reverse" => '1',
	"orfminsize" => '0',
	"threeletter" => '0',
	"number" => '0',
	"width" => '60',
	"length" => '0',
	"margin" => '10',
	"name" => '1',
	"description" => '1',
	"offset" => '1',
	"html" => '0',

    };

    $self->{PRECOND}  = {
	"init" => { "perl" => '1' },
	"input" => { "perl" => '1' },
	"sequence" => { "perl" => '1' },
	"required" => { "perl" => '1' },
	"enzymes" => { "perl" => '1' },
	"sitelen" => { "perl" => '1' },
	"advanced" => { "perl" => '1' },
	"mincuts" => { "perl" => '1' },
	"maxcuts" => { "perl" => '1' },
	"single" => { "perl" => '1' },
	"blunt" => { "perl" => '1' },
	"sticky" => { "perl" => '1' },
	"ambiguity" => { "perl" => '1' },
	"plasmid" => { "perl" => '1' },
	"commercial" => { "perl" => '1' },
	"table" => { "perl" => '1' },
	"output" => { "perl" => '1' },
	"outfile" => { "perl" => '1' },
	"cutlist" => { "perl" => '1' },
	"flatreformat" => { "perl" => '1' },
	"limit" => { "perl" => '1' },
	"preferred" => { "perl" => '1' },
	"translation" => { "perl" => '1' },
	"reverse" => { "perl" => '1' },
	"orfminsize" => { "perl" => '1' },
	"uppercase" => { "perl" => '1' },
	"highlight" => { "perl" => '1' },
	"threeletter" => { "perl" => '1' },
	"number" => { "perl" => '1' },
	"width" => { "perl" => '1' },
	"length" => { "perl" => '1' },
	"margin" => { "perl" => '1' },
	"name" => { "perl" => '1' },
	"description" => { "perl" => '1' },
	"offset" => { "perl" => '1' },
	"html" => { "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,
	"required" => 0,
	"enzymes" => 0,
	"sitelen" => 0,
	"advanced" => 0,
	"mincuts" => 0,
	"maxcuts" => 0,
	"single" => 0,
	"blunt" => 0,
	"sticky" => 0,
	"ambiguity" => 0,
	"plasmid" => 0,
	"commercial" => 0,
	"table" => 0,
	"output" => 0,
	"outfile" => 0,
	"cutlist" => 0,
	"flatreformat" => 0,
	"limit" => 0,
	"preferred" => 0,
	"translation" => 0,
	"reverse" => 0,
	"orfminsize" => 0,
	"uppercase" => 0,
	"highlight" => 0,
	"threeletter" => 0,
	"number" => 0,
	"width" => 0,
	"length" => 0,
	"margin" => 0,
	"name" => 0,
	"description" => 0,
	"offset" => 0,
	"html" => 0,
	"auto" => 0,

    };

    $self->{ISSIMPLE}  = {
	"init" => 0,
	"input" => 0,
	"sequence" => 1,
	"required" => 0,
	"enzymes" => 1,
	"sitelen" => 1,
	"advanced" => 0,
	"mincuts" => 0,
	"maxcuts" => 0,
	"single" => 0,
	"blunt" => 0,
	"sticky" => 0,
	"ambiguity" => 0,
	"plasmid" => 0,
	"commercial" => 0,
	"table" => 1,
	"output" => 0,
	"outfile" => 1,
	"cutlist" => 0,
	"flatreformat" => 0,
	"limit" => 0,
	"preferred" => 0,
	"translation" => 0,
	"reverse" => 0,
	"orfminsize" => 0,
	"uppercase" => 0,
	"highlight" => 0,
	"threeletter" => 0,
	"number" => 0,
	"width" => 0,
	"length" => 0,
	"margin" => 0,
	"name" => 0,
	"description" => 0,
	"offset" => 0,
	"html" => 0,
	"auto" => 0,

    };

    $self->{PARAMFILE}  = {

    };

    $self->{COMMENT}  = {
	"enzymes" => [
		"The name \'all\' reads in all enzyme names from the REBASE database. You can specify enzymes by giving their names with commas between then, such as: \'HincII,hinfI,ppiI,hindiii\'. <BR> The case of the names is not important. You can specify a file of enzyme names to read in by giving the name of the file holding the enzyme names with a \'\@\' character in front of it, for example, \'\@enz.list\'. <BR> Blank lines and lines starting with a hash character or \'!\' are ignored and all other lines are concatenated together with a comma character \',\' and then treated as the list of enzymes to search for. <BR> An example of a file of enzyme names is: <BR> ! my enzymes <BR> HincII, ppiII <BR> ! other enzymes <BR> hindiii <BR> HinfI <BR> PpiI",
	],
	"outfile" => [
		"If you enter the name of a file here then this program will write the sequence details into that file.",
	],
	"orfminsize" => [
		"Minimum size of Open Reading Frames (ORFs) to display in the translations.",
	],
	"uppercase" => [
		"Regions to put in uppercase. <BR> If this is left blank, then the sequence case is left alone. <BR> A set of regions is specified by a set of pairs of positions. <BR> The positions are integers. <BR> They are separated by any non-digit, non-alpha character. <BR> Examples of region specifications are: <BR> 24-45, 56-78 <BR> 1:45, 67=99;765..888 <BR> 1,5,8,10,23,45,57,99",
	],
	"highlight" => [
		"Regions to colour if formatting for HTML. <BR> If this is left blank, then the sequence is left alone. <BR> A set of regions is specified by a set of pairs of positions. <BR> The positions are integers. <BR> They are followed by any valid HTML font colour. <BR> Examples of region specifications are: <BR> 24-45 blue 56-78 orange <BR> 1-100 green 120-156 red <BR> A file of ranges to colour (one range per line) can be specifed as \'\@filename\'.",
	],
	"name" => [
		"Set this to be false if you do not wish to display the ID name of the sequence",
	],
	"description" => [
		"Set this to be false if you do not wish to display the description of the sequence",
	],

    };

    $self->{SCALEMIN}  = {

    };

    $self->{SCALEMAX}  = {

    };

    $self->{SCALEINC}  = {

    };

    $self->{INFO}  = {

    };

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



    $self->_init_params(@params);

    return $self;
}



1; # Needed to keep compiler happy

