moved autoflow where it belongs - into the AnalysisJob

modules/Bio/EnsEMBL/Hive/AnalysisJob.pm

@@ -139,6 +139,28 @@ sub stderr_file {
   return $self->{'_stderr_file'};
 }
 
+
+=head2 autoflow
+
+    Title   :  autoflow
+    Function:  Gets/sets flag for whether the job should
+               be automatically dataflowed on branch 1 when the job completes.
+               If the subclass manually sends a job along branch 1 with dataflow_output_id,
+               the autoflow will turn itself off.
+    Returns :  boolean (1=default|0)
+
+=cut
+
+sub autoflow {
+  my $self = shift;
+
+  $self->{'_autoflow'} = shift if(@_);
+  $self->{'_autoflow'} = 1 unless(defined($self->{'_autoflow'}));  
+
+  return $self->{'_autoflow'};
+}
+
+
 ##-----------------[indicators to the Worker]--------------------------------
 
 

modules/Bio/EnsEMBL/Hive/Process.pm

@@ -270,24 +270,6 @@ sub input_job {
   return $self->{'_input_job'};
 }
 
-=head2 autoflow_inputjob
-
-    Title   :  autoflow_inputjob
-    Function:  Gets/sets flag for whether the input_job should
-               be automatically dataflowed on branch code 1 when the
-               job completes.  If the subclass manually sends a job along
-               branch 1 with dataflow_output_id, the autoflow will be turned off.
-    Returns :  boolean (1/0/undef)
-
-=cut
-
-sub autoflow_inputjob {
-  my $self = shift;
-  $self->{'_autoflow_inputjob'} = shift if(@_);
-  $self->{'_autoflow_inputjob'}=1 unless(defined($self->{'_autoflow_inputjob'}));  
-  return $self->{'_autoflow_inputjob'};
-}
-
 =head2 dataflow_output_id
 
     Title        :  dataflow_output_id
@@ -323,7 +305,7 @@ sub dataflow_output_id {
     my $semaphored_job_id = $create_job_options->{'-semaphored_job_id'} ||= $self->input_job->semaphored_job_id();
 
         # if branch_code is set to 1 (explicitly or impliticly), turn off automatic dataflow:
-    $self->autoflow_inputjob(0) if($branch_code==1);
+    $self->input_job->autoflow(0) if($branch_code==1);
 
     my @output_job_ids = ();
     my $job_adaptor = $self->db->get_AnalysisJobAdaptor;

modules/Bio/EnsEMBL/Hive/Worker.pm

@@ -656,7 +656,7 @@ sub run_module_with_job {
     $runObj->queen($self->queen);
     $runObj->worker($self);
     $runObj->debug($self->debug);
-    $runObj->autoflow_inputjob(1);
+    $job->autoflow(1);
   } else {
     $runObj->input_id($job->input_id);
     $runObj->db($self->db);
@@ -687,7 +687,7 @@ sub run_module_with_job {
         $runObj->write_output;
         $self->{'writing_stopwatch'}->pause();
 
-        if( $native_hive_process and $runObj->autoflow_inputjob ) {
+        if( $native_hive_process and $job->autoflow ) {
             printf("AUTOFLOW input->output\n") if($self->debug);
             $runObj->dataflow_output_id();
         }