Commit 15940b3a authored by Abel Ureta-Vidal's avatar Abel Ureta-Vidal
Browse files

Clean up a bit the runnable and output subroutines

parent 00cf9984
......@@ -427,10 +427,6 @@ sub parameters {
return $self->analysis->parameters;
}
#FIXME kfb 11.01.2006 added runnable method from Pipeline/RunnableDB. Required by
#PairAligner.
=head2 runnable
Title : runnable
......@@ -445,30 +441,20 @@ sub parameters {
sub runnable {
my ($self,$arg) = @_;
if (!defined($self->{'_runnables'})) {
$self->{'_runnables'} = [];
if (!defined($self->{'runnable'})) {
$self->{'runnable'} = [];
}
if (defined($arg)) {
#FIXME kfb 11.01.2006 use Analysis/Runnable object rather than Pipeline/RunnableI
# if ($arg->isa("Bio::EnsEMBL::Pipeline::RunnableI")) {
# push(@{$self->{'_runnables'}},$arg);
# } else {
# &throw("[$arg] is not a Bio::EnsEMBL::Pipeline::RunnableI");
# }
if ($arg->isa("Bio::EnsEMBL::Analysis::Runnable")) {
push(@{$self->{'_runnables'}},$arg);
} else {
&throw("[$arg] is not a Bio::EnsEMBL::Analysis::Runnable");
}
if ($arg->isa("Bio::EnsEMBL::Analysis::Runnable")) {
push(@{$self->{'runnable'}},$arg);
} else {
&throw("[$arg] is not a Bio::EnsEMBL::Analysis::Runnable");
}
return @{$self->{'_runnables'}};
}
return @{$self->{'runnable'}};
}
#FIXME kfb 11.01.2006 added output method from Pipeline/RunnableDB. Required by
#PairAligner.
=head2 output
Title : output
......@@ -478,32 +464,19 @@ sub runnable {
Args : None
=cut
sub output {
my ($self) = @_;
$self->{'_output'} = [];
my @r = $self->runnable;
if(@r && scalar(@r)){
foreach my $r ($self->runnable){
#FIXME debug
print STDERR "Process output " . scalar(@{$r->output}) . "\n";
sub output {
my ($self) = @_;
#FIXME kfb 12.01.2006
#push(@{$self->{'_output'}}, $r->output);
push(@{$self->{'_output'}}, @{$r->output});
}
unless (defined $self->{'output'}) {
$self->{'output'} = [];
foreach my $r (@{$self->runnable}){
push(@{$self->{'output'}}, @{$r->output});
}
}
#FIXME debug
print STDERR "_output " . scalar(@{$self->{'_output'}}) . "\n";
return @{$self->{'_output'}};
return @{$self->{'output'}};
}
1;
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