Raw content of Bio::EnsEMBL::Analysis::RunnableDB::Funcgen::TileMap
<![CDATA[# Ensembl module for Bio::EnsEMBL::Analysis::RunnableDB::Funcgen::TileMap
#
# Copyright (c) 2007 Ensembl
#
=head1 NAME
Bio::EnsEMBL::Analysis::RunnableDB::Funcgen::TileMap
=head1 SYNOPSIS
my $runnable = Bio::EnsEMBL::Analysis::RunnableDB::Funcgen::TileMap->new
(
-db => $db,
-input_id => 'chromosome::20:1:100000:1',
-analysis => $analysis,
);
$runnable->fetch_input;
$runnable->run;
$runnable->write_output;
=head1 DESCRIPTION
This module provides an interface between the ensembl database and
the Runnable TileMap which wraps the program TileMap
=head1 LICENCE
This code is distributed under an Apache style licence. Please see
/info/about/code_licence.html for details.
=head1 AUTHOR
Stefan Graf, Ensembl Functional Genomics -
=head1 CONTACT
Post questions to the Ensembl development list: ensembl-dev@ebi.ac.uk
=cut
package Bio::EnsEMBL::Analysis::RunnableDB::Funcgen::TileMap;
use strict;
use warnings;
use Data::Dumper;
use Bio::EnsEMBL::Analysis::RunnableDB;
use Bio::EnsEMBL::Analysis::RunnableDB::Funcgen;
use Bio::EnsEMBL::Analysis::Runnable::Funcgen::TileMap;
use Bio::EnsEMBL::Analysis::Config::General;
use Bio::EnsEMBL::Analysis::Config::Funcgen::TileMap;
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::Analysis::RunnableDB::Funcgen);
=head2 new
Arg [1] :
Arg [2] :
Description : Instantiates new TileMap runnabledb
Returntype : Bio::EnsEMBL::Analysis::RunnableDB::Funcgen::TileMap object
Exceptions :
Example :
=cut
sub new {
print "Analysis::RunnableDB::Funcgen::TileMap::new\n";
my ($class,@args) = @_;
my $self = $class->SUPER::new(@args);
$self->read_and_check_config($CONFIG);
$self->PARAMETERS(join('; ',
'METHOD='.$self->METHOD,
'POSTPROB='.$self->POSTPROB,
'MAXGAP='.$self->MAXGAP,
'HYBLENGTH='.$self->HYBLENGTH,
'TEMPLATE_FILE='.$self->TEMPLATE_FILE));
# make sure we have the correct analysis object
$self->check_Analysis();
# make sure we can store the correct feature_set, data_sets, and result_sets
$self->check_Sets();
return $self;
}
sub TEMPLATE_FILE {
my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{'_CONFIG_TEMPLATE_FILE'} = $value;
}
if ( exists( $self->{'_CONFIG_TEMPLATE_FILE'} ) ) {
return $self->{'_CONFIG_TEMPLATE_FILE'};
} else {
return undef;
}
}
sub POSTPROB {
my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{'_CONFIG_POSTPROB'} = $value;
}
if ( exists( $self->{'_CONFIG_POSTPROB'} ) ) {
return $self->{'_CONFIG_POSTPROB'};
} else {
return undef;
}
}
sub HYBLENGTH {
my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{'_CONFIG_HYBLENGTH'} = $value;
}
if ( exists( $self->{'_CONFIG_HYBLENGTH'} ) ) {
return $self->{'_CONFIG_HYBLENGTH'};
} else {
return undef;
}
}
sub MAXGAP {
my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{'_CONFIG_MAXGAP'} = $value;
}
if ( exists( $self->{'_CONFIG_MAXGAP'} ) ) {
return $self->{'_CONFIG_MAXGAP'};
} else {
return undef;
}
}
sub METHOD {
my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{'_CONFIG_METHOD'} = $value;
}
if ( exists( $self->{'_CONFIG_METHOD'} ) ) {
return $self->{'_CONFIG_METHOD'};
} else {
return undef;
}
}
1;
]]>