print diagnostics when running process

modules/conop/pymod/export_processor.cc

@@ -67,7 +67,8 @@ void export_processor() {
                  &Processor::SetUnkResidueTreatment)
     .add_property("unk_atom_treatment", &Processor::GetUnkAtomTreatment,
                  &Processor::SetUnkAtomTreatment)
-    .def("Process", &Processor::Process)
+    .def("Process", &Processor::Process, 
+         (arg("ent"), arg("log_diags")=true))
   ;
   class_<PyProcessor, boost::noncopyable, 
          boost::shared_ptr<WrappedProcessor>, 

modules/conop/src/processor.cc

@@ -16,6 +16,7 @@
 // along with this library; if not, write to the Free Software Foundation, Inc.,
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
+#include <ost/log.hh>
 #include <ost/mol/xcs_editor.hh>
 #include <ost/mol/bond_handle.hh>
 #include <ost/mol/torsion_handle.hh>
@@ -23,7 +24,8 @@
 
 namespace ost { namespace conop {
 
-DiagnosticsPtr Processor::Process(mol::EntityHandle ent) const
+DiagnosticsPtr Processor::Process(mol::EntityHandle ent, 
+                                  bool log_diags) const
 {
   DiagnosticsPtr diags(new Diagnostics);
   if (!this->BeginProcessing(diags, ent)) {
@@ -32,6 +34,12 @@ DiagnosticsPtr Processor::Process(mol::EntityHandle ent) const
   this->DoProcess(diags, ent);
   
   this->EndProcessing(diags, ent);
+  if (log_diags) {
+    for (Diagnostics::diag_iterator i = diags->diags_begin(),
+         e = diags->diags_end(); i != e; ++i) {
+      LOG_WARNING((*i)->Format(false));
+    }
+  }
   return diags;
 }
 

modules/conop/src/processor.hh

@@ -44,7 +44,7 @@ typedef boost::shared_ptr<Processor> ProcessorPtr;
 // the base class for all options
 class DLLEXPORT_OST_CONOP Processor {
 public:
-  DiagnosticsPtr Process(mol::EntityHandle ent) const;
+  DiagnosticsPtr Process(mol::EntityHandle ent, bool log_diags=true) const;
   virtual ProcessorPtr Copy() const = 0;
 protected:
   virtual void DoProcess(DiagnosticsPtr diags,