From 2a4c7df784897dfaff344adc47dc712bc5eda6c2 Mon Sep 17 00:00:00 2001
From: Abel Ureta-Vidal <abel@ebi.ac.uk>
Date: Mon, 27 Feb 2006 18:23:41 +0000
Subject: [PATCH] Committed Kathryn changes. Added runnable and output
subroutine. These should make the coding of
Bio::EnsEMBL::Analysis::RunnableDB and Bio::EnsEMBL::Hive::Process more
alike.
---
modules/Bio/EnsEMBL/Hive/Process.pm | 75 +++++++++++++++++++++++++++++
1 file changed, 75 insertions(+)
diff --git a/modules/Bio/EnsEMBL/Hive/Process.pm b/modules/Bio/EnsEMBL/Hive/Process.pm
index d59c8aab1..5c28662fe 100755
--- a/modules/Bio/EnsEMBL/Hive/Process.pm
+++ b/modules/Bio/EnsEMBL/Hive/Process.pm
@@ -428,6 +428,81 @@ sub parameters {
}
+#FIXME kfb 11.01.2006 added runnable method from Pipeline/RunnableDB. Required by
+#PairAligner.
+
+=head2 runnable
+
+ Title : runnable
+ Usage : $self->runnable($arg)
+ Function: Sets a runnable for this RunnableDB
+ Returns : Bio::EnsEMBL::Analysis::Runnable
+ Args : Bio::EnsEMBL::Analysis::Runnable
+
+=cut
+
+
+sub runnable {
+ my ($self,$arg) = @_;
+
+ if (!defined($self->{'_runnables'})) {
+ $self->{'_runnables'} = [];
+ }
+
+ if (defined($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");
+ }
+ }
+
+ return @{$self->{'_runnables'}};
+}
+
+#FIXME kfb 11.01.2006 added output method from Pipeline/RunnableDB. Required by
+#PairAligner.
+=head2 output
+
+ Title : output
+ Usage : $self->output()
+ Function:
+ Returns : Array of Bio::EnsEMBL::FeaturePair
+ Args : None
+
+=cut
+sub output {
+ my ($self) = @_;
+
+ $self->{'_output'} = [];
+
+ my @r = $self->runnable;
+
+
+ if(@r && scalar(@r)){
+ foreach my $r ($self->runnable){
+
+ #FIXME debug
+ print STDERR "Process output " . scalar(@{$r->output}) . "\n";
+
+ #FIXME kfb 12.01.2006
+ #push(@{$self->{'_output'}}, $r->output);
+ push(@{$self->{'_output'}}, @{$r->output});
+ }
+ }
+
+
+ #FIXME debug
+ print STDERR "_output " . scalar(@{$self->{'_output'}}) . "\n";
+ return @{$self->{'_output'}};
+}
1;
--
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