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#doesn't do anything. Used for testing pipeline
package Bio::Pipeline::Runnable::TestRunnable;
use vars qw(@ISA);
use strict;
use Bio::Pipeline::RunnableI;
use Bio::SeqFeature::Generic;
use Bio::SeqIO;
@ISA = qw(Bio::Pipeline::RunnableI);
sub new {
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
$self->{'_output'} = [];
return $self;
}
sub seq {
my ($self,$value) = @_;
if ($value){
$self->{'_seq'} = $value;
}
return $self->{'_seq'};
}
sub datatypes {
my ($self) = @_;
my $dt = Bio::Pipeline::DataType->new(-object_type=>"Bio::PrimarySeqI",
-name=>"sequence",
-reftype=>"SCALAR");
my %dt;
$dt{seq} = $dt;
return %dt;
}
sub run {
my ($self) = @_;
my $seq = $self->seq();
$seq || $self->throw("Input seq not set!");
my $rev = $seq->revcom;
$self->output($rev);
}
sub output {
my ($self,$seq) = @_;
if ($seq){
$self->{'_output'} = $seq;
}
return $self->{'_output'};
}
1;
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