Raw content of Bio::EnsEMBL::Analysis::RunnableDB::Funcgen::Nessie
<![CDATA[# Ensembl module for Bio::EnsEMBL::Analysis::RunnableDB::Funcgen::Nessie
#
# Copyright (c) 2007 Ensembl
#
=head1 NAME
Bio::EnsEMBL::Analysis::RunnableDB::Funcgen::Nessie
=head1 SYNOPSIS
my $runnable = Bio::EnsEMBL::Analysis::RunnableDB::Funcgen::Nessie->new
(
-db => $db,
-input_id => 'chromosome::20:1:100000:1',
-analysis => $analysis,
);
$runnable->fetch_input;
$runnable->run;
$runnable->write_output;
=head1 DESCRIPTION
This module provides an interface between the ensembl database and
the Runnable Nessie which wraps the program Nessie
=head1 AUTHOR
Stefan Graf, Ensembl Functional Genomics - /
=head1 CONTACT
Post questions to the Ensembl development list: ensembl-dev@ebi.ac.uk
=cut
package Bio::EnsEMBL::Analysis::RunnableDB::Funcgen::Nessie;
use strict;
use warnings;
use Data::Dumper;
use Bio::EnsEMBL::Analysis::Config::General;
use Bio::EnsEMBL::Analysis::Config::Funcgen::Nessie;
use Bio::EnsEMBL::Analysis::RunnableDB;
use Bio::EnsEMBL::Analysis::RunnableDB::Funcgen;
use Bio::EnsEMBL::Analysis::Runnable::Funcgen::Nessie;
use Bio::EnsEMBL::Utils::Exception qw(throw warning stack_trace_dump);
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::Analysis::RunnableDB::Funcgen);
=head2 new
Arg [1] :
Arg [2] :
Description : Instantiates new Nessie runnabledb
Returntype : Bio::EnsEMBL::Analysis::RunnableDB::Funcgen::Nessie object
Exceptions :
Example :
=cut
sub new {
print "Analysis::RunnableDB::Funcgen::Nessie::new\n";
my ($class,@args) = @_;
my $self = $class->SUPER::new(@args);
$self->read_and_check_config($CONFIG);
# add some runnable/program special params to analysis
$self->PARAMETERS(join('; ',
$self->PARAMETERS.$self->TRAIN_PARAMETERS,
$self->PEAK_PARAMETERS));
#print Dumper $self->PARAMETERS;
# 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 TRAIN_PARAMETERS {
my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{'_CONFIG_TRAIN_PARAMETERS'} = $value;
}
if ( exists( $self->{'_CONFIG_TRAIN_PARAMETERS'} ) ) {
return $self->{'_CONFIG_TRAIN_PARAMETERS'};
} else {
return undef;
}
}
sub PEAK_PARAMETERS {
my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{'_CONFIG_PEAK_PARAMETERS'} = $value;
}
if ( exists( $self->{'_CONFIG_PEAK_PARAMETERS'} ) ) {
return $self->{'_CONFIG_PEAK_PARAMETERS'};
} else {
return undef;
}
}
1;
]]>