Merge pull request #2678 from RosettaCommons/sergey/f2

Refactoring Rosetta exceptions classes. 

Old repository SHA1: a995eac28418df1f27dd3e6f9ff094c7b6bf2642

.benchmark-signature

@@ -1 +1 @@
-81ed0ca0949fbf6f613a627b76ff8d6320c25377
+dd6176ec1d007b675bcb4cbf88202e3fe5318817

source/external/cxxtest/cxxtestgen.py

@@ -426,7 +426,8 @@ def writePreamble( output ):
         output.write( "#include <cxxtest/%s.h>\n" % gui )
     output.write( "\n" )
     output.write( "//catch unhandled exceptions in unit tests\n" )
-    output.write( "#include <utility/excn/EXCN_Base.hh>\n" )
+    output.write( "#include <utility/excn/Exceptions.hh>\n" )
+    output.write( "#include <cassert>\n" )
     wrotePreamble = 1
 
 def writeMain( output ):
@@ -459,7 +460,7 @@ def writeMain( output ):
             output.write( ' CxxTest::initialize();\n' )
         output.write( ' try{\n' )
         output.write( '  return CxxTest::%s().run();\n' % runner )
-	output.write( ' } catch( utility::excn::EXCN_Base& excn ) {\n' )
+	output.write( ' } catch( utility::excn::Exception& excn ) {\n' )
 	output.write( '  std::cerr\n' )
 	output.write( '   << "ERROR: Unhandled Exception caught by cxxtest: "\n' )
 	output.write( '   << excn << std::endl;\n' )

source/src/apps/benchmark/performance/ScoreEach.bench.hh

@@ -79,7 +79,7 @@ public:
 		core::scoring::methods::EnergyMethodOptions opts;
 		try {
 			enmeth_ = core::scoring::ScoringManager::get_instance()->energy_method( score_type_, opts );
-		} catch (utility::excn::EXCN_Base& excn){
+		} catch (utility::excn::Exception& excn){
 			TR.Error
 				<< "Unable to Test scoring with score type '"
 				<< core::scoring::ScoreTypeManager::name_from_score_type(score_type_)
@@ -100,7 +100,7 @@ public:
 					<< "' gives zero energy with test structure. Timing values may not be informative." << std::endl;
 			}
 			setup_successful_ = true;
-		} catch (utility::excn::EXCN_Base& excn){
+		} catch (utility::excn::Exception& excn){
 			TR.Error
 				<< "Unable to Test scoring with score type '"
 				<< core::scoring::ScoreTypeManager::name_from_score_type(score_type_)
@@ -137,7 +137,7 @@ public:
 					pose_->energies().clear();
 					scorefxn.set_weight(score_type_, 0);
 				}
-			} catch (utility::excn::EXCN_Base& excn){
+			} catch (utility::excn::Exception& excn){
 				TR.Error
 					<< "Unable to Test scoring with score type '"
 					<< core::scoring::ScoreTypeManager::name_from_score_type(score_type_)

source/src/apps/benchmark/performance/performance_benchmark.cc

@@ -438,7 +438,7 @@ int main( int argc, char *argv[])
 
 		// Do not adjust this line without altering the daemon code because it will look for it as signal of normal ending!
 		TR << "Performance Benchmark ended.   --------------------------------" << std::endl;
-	} catch ( utility::excn::EXCN_Base const & e ) {
+	} catch (utility::excn::Exception const & e ) {
 		std::cerr << "caught exception " << e.msg() << std::endl;
 		return -1;
 	}

source/src/apps/benchmark/scientific/ddg_benchmark.cc

@@ -680,7 +680,7 @@ main( int argc, char * argv [] )
 		correlation(ddg_out);
 		exit(0);
 
-	} catch ( utility::excn::EXCN_Base const & e ) {
+	} catch (utility::excn::Exception const & e ) {
 		std::cout << "caught exception " << e.msg() << std::endl;
 		return -1;
 	}

source/src/apps/benchmark/scientific/design_contrast_and_statistic.cc

@@ -339,7 +339,7 @@ int main( int argc, char * argv [] )
 			statistics(sqc_file);
 		}
 
-	} catch ( utility::excn::EXCN_Base const & e ) {
+	} catch (utility::excn::Exception const & e ) {
 		std::cerr << "caught exception " << e.msg() << std::endl;
 		return -1;
 	}

source/src/apps/benchmark/scientific/rotamer_recovery.cc

@@ -32,7 +32,7 @@
 #include <core/scoring/ScoreFunctionFactory.hh>
 
 // Utility Headers
-#include <utility/excn/EXCN_Base.hh>
+#include <utility/excn/Exceptions.hh>
 #include <utility/excn/Exceptions.hh>
 #include <utility/exit.hh>
 #include <utility/vector0.hh>
@@ -59,7 +59,7 @@ using protocols::rotamer_recovery::RotamerRecoveryFactory;
 using protocols::rotamer_recovery::RotamerRecoveryMover;
 using protocols::rotamer_recovery::RotamerRecoveryMoverOP;
 using protocols::jd2::JobDistributor;
-using utility::excn::EXCN_Base;
+using utility::excn::Exception;
 
 static Tracer TR("apps.benchmark.scientific.rotamer_recovery");
 
@@ -136,15 +136,15 @@ main( int argc, char * argv [] )
 				rotamer_recovery_mover->show( fout );
 				fout.close();
 			}
-		} catch (EXCN_Base & excn ) {
+		} catch (Exception & excn ) {
 			TR.Error << "Exception: " << endl;
 			excn.show( TR.Error );
 
 			TR << "Exception: " << endl;
 			excn.show( TR ); //so its also seen in a >LOG file
 		}
 
-	} catch ( utility::excn::EXCN_Base const & e ) {
+	} catch (utility::excn::Exception const & e ) {
 		std::cout << "caught exception " << e.msg() << std::endl;
 		return -1;
 	}

source/src/apps/pilot/amelie/design_tight_clusters.cc

@@ -754,7 +754,7 @@ int main( int argc, char * argv [] )
 		//score_fxn->show(TR, p);
 
 
-	} catch ( utility::excn::EXCN_Base const & e ) {
+	} catch (utility::excn::Exception const & e ) {
 		std::cout << "caught exception " << e.msg() << std::endl;
 		return -1;
 	}

source/src/apps/pilot/amelie/detect_tight_clusters.cc

@@ -1163,7 +1163,7 @@ int main( int argc, char * argv [] )
 		//score_fxn->show(TR, p);
 
 
-	} catch ( utility::excn::EXCN_Base const & e ) {
+	} catch (utility::excn::Exception const & e ) {
 		std::cout << "caught exception " << e.msg() << std::endl;
 		return -1;
 	}

source/src/apps/pilot/andre/SymmDataTest.cc

@@ -181,7 +181,7 @@ main( int argc, char * argv [] )
 		devel::init( argc, argv );
 
 		protocols::viewer::viewer_main( my_main );
-	} catch ( utility::excn::EXCN_Base const & e ) {
+	} catch (utility::excn::Exception const & e ) {
 		std::cout << "caught exception " << e.msg() << std::endl;
 		return -1;
 	}

source/src/apps/pilot/andrew/analyze_rtmin_failures.cc

@@ -190,7 +190,7 @@ int main( int argc, char * argv [] )
 			(*sfxn)(pose);
 			pose.dump_pdb( "rtmin_failure_best_nonnative_rotamer.pdb" );
 		}
-	} catch ( utility::excn::EXCN_Base const & e ) {
+	} catch (utility::excn::Exception const & e ) {
 		std::cout << "caught exception " << e.msg() << std::endl;
 		return -1;
 	}

source/src/apps/pilot/andrew/apl_msd.cc

@@ -164,7 +164,7 @@ int main( int argc, char ** argv )
 			break;
 		}
 
-	} catch ( utility::excn::EXCN_Base const & e ) {
+	} catch (utility::excn::Exception const & e ) {
 		std::cout << "caught exception " << e.msg() << std::endl;
 		return -1;
 	}

source/src/apps/pilot/andrew/domain_assembly_jd2.cc

@@ -35,7 +35,7 @@ int main( int argc, char * argv [] )
 		// GO!
 		protocols::jd2::JobDistributor::get_instance()->go( mover );
 
-	} catch ( utility::excn::EXCN_Base const & e ) {
+	} catch (utility::excn::Exception const & e ) {
 		std::cout << "caught exception " << e.msg() << std::endl;
 		return -1;
 	}

source/src/apps/pilot/andrew/find_buns.cc

@@ -208,7 +208,7 @@ int main( int argc, char * argv [] )
 			std::string outname = inputname.base();
 			write_buns_and_dots_kinemage( outname + "_buried_unsats.kin", outname, pose, rotamer_dots, buns );
 		}
-	} catch ( utility::excn::EXCN_Base const & e ) {
+	} catch (utility::excn::Exception const & e ) {
 		std::cout << "caught exception " << e.msg() << std::endl;
 		return -1;
 	}

source/src/apps/pilot/andrew/fixbb_jd3.cc

@@ -342,7 +342,7 @@ main( int argc, char * argv [] )
 		protocols::jd3::JobQueenOP queen( new FixbbJobQueen );
 		//std::cout << "Fixbb job definition file\n" << queen->job_definition_xsd() << std::endl;
 		jd->go( queen );
-	} catch ( utility::excn::EXCN_Base const & e ) {
+	} catch (utility::excn::Exception const & e ) {
 		std::cout << "caught exception " << e.msg() << std::endl;
 		return -1;
 	}

source/src/apps/pilot/andrew/flex_regions_alc.cc

@@ -82,7 +82,7 @@ int main( int argc, char * argv [] )
 		++ii;
 	}
 
-	} catch ( utility::excn::EXCN_Base const & e ) {
+	} catch (utility::excn::Exception const & e ) {
 		std::cout << "caught exception " << e.msg() << std::endl;
 		return -1;
 	}

source/src/apps/pilot/andrew/interface_ddg_bind.cc

@@ -485,7 +485,7 @@ InterfaceDDGBindJobInputter::fill_jobs( protocols::jd2::JobsContainer & jobs )
 		utility::io::izstream ddg_jobs( jobfname );
 		if ( ! ddg_jobs.good() ) {
 			// could not open jobs file
-			throw utility::excn::EXCN_Msg_Exception( "Could not open interface ddg jobs file: '" + jobfname );
+			throw CREATE_EXCEPTION(utility::excn::Exception,  "Could not open interface ddg jobs file: '" + jobfname );
 		}
 
 		typedef std::pair< std::string, std::string > PDBAndSeqposPair;
@@ -504,34 +504,34 @@ InterfaceDDGBindJobInputter::fill_jobs( protocols::jd2::JobsContainer & jobs )
 				sstream >> pdb;
 				if ( ! sstream.good() ) {
 					// throw an exception
-					throw utility::excn::EXCN_Msg_Exception( "Problem reading '" + jobfname + "' on line " +
+					throw CREATE_EXCEPTION(utility::excn::Exception,  "Problem reading '" + jobfname + "' on line " +
 						utility::to_string( count_line ) + ", which reads:\n" + line );
 				}
 				sstream >> chain;
 				if ( ! sstream.good() ) {
 					// throw an exception
-					throw utility::excn::EXCN_Msg_Exception( "Problem reading '" + jobfname + "' on line " +
+					throw CREATE_EXCEPTION(utility::excn::Exception,  "Problem reading '" + jobfname + "' on line " +
 						utility::to_string( count_line ) + ", which reads:\n" + line );
 				}
 				if ( chain.size() != 1 ) {
-					throw utility::excn::EXCN_Msg_Exception( "Expected to read a chain identifier (or an underscore) "
+					throw CREATE_EXCEPTION(utility::excn::Exception,  "Expected to read a chain identifier (or an underscore) "
 						"after reading the pdb name in file '" + jobfname + "' on line " +
 						utility::to_string( count_line ) + ", which reads:\n" + line );
 				}
 				sstream >> resstring;
 				if ( ! sstream.good() ) {
 					// throw an exception
-					throw utility::excn::EXCN_Msg_Exception( "Problem reading '" + jobfname + "' on line " +
+					throw CREATE_EXCEPTION(utility::excn::Exception,  "Problem reading '" + jobfname + "' on line " +
 						utility::to_string( count_line ) + ", which reads:\n" + line );
 				}
 				sstream >> newaa;
 				if ( ! sstream.good() ) {
 					// throw an exception
-					throw utility::excn::EXCN_Msg_Exception( "Problem reading '" + jobfname + "' on line " +
+					throw CREATE_EXCEPTION(utility::excn::Exception,  "Problem reading '" + jobfname + "' on line " +
 						utility::to_string( count_line ) + ", which reads:\n" + line );
 				}
 				if ( ! core::chemical::oneletter_code_specifies_aa( newaa ) ) {
-					throw utility::excn::EXCN_Msg_Exception( "Could not interpret the input character '" +
+					throw CREATE_EXCEPTION(utility::excn::Exception,  "Could not interpret the input character '" +
 						utility::to_string( newaa ) + "' as an amino acid 1-letter code.\n" + "Problem encountered on line " +
 						utility::to_string( count_line ) + " of file " + jobfname + " which reads " + line );
 				}
@@ -546,8 +546,8 @@ InterfaceDDGBindJobInputter::fill_jobs( protocols::jd2::JobsContainer & jobs )
 				int resid; char insertion_code;
 				try {
 					core::pose::parse_PDBnum_icode( resstring, jobfname, count_line, resid, insertion_code );
-				} catch ( utility::excn::EXCN_Msg_Exception e ) {
-					throw utility::excn::EXCN_Msg_Exception( "Could not interpret the string '" + resstring + "' as a residue identifier\n" + e.msg() );
+				} catch (utility::excn::Exception e ) {
+					throw CREATE_EXCEPTION(utility::excn::Exception,  "Could not interpret the string '" + resstring + "' as a residue identifier\n" + e.msg() );
 				}
 				input_mutation mutation;
 				mutation.resind = core::pose::ResidueIndexDescriptionFromFileOP(
@@ -568,7 +568,7 @@ InterfaceDDGBindJobInputter::fill_jobs( protocols::jd2::JobsContainer & jobs )
 			} else {
 				std::string existing_pdb = base_names[ iibase ];
 				if ( existing_pdb != iipdb ) {
-					throw utility::excn::EXCN_Msg_Exception( "Two different PDBs, '" + existing_pdb + "' and '" +
+					throw CREATE_EXCEPTION(utility::excn::Exception,  "Two different PDBs, '" + existing_pdb + "' and '" +
 						iipdb + " have the same base name, '" + iibase + "' and so the output structure names will collide." +
 						"\nPlease rename one of them." );
 				}
@@ -610,7 +610,7 @@ InterfaceDDGBindJobInputter::fill_jobs( protocols::jd2::JobsContainer & jobs )
 			}
 		}
 	} else {
-		utility::excn::EXCN_Msg_Exception( "InterfaceDDGJobInputter requires the interface_ddg::jobs flag" );
+		throw CREATE_EXCEPTION(utility::excn::Exception,  "InterfaceDDGJobInputter requires the interface_ddg::jobs flag" );
 	}
 
 	for ( std::list< InterfaceDDGBindInnerJobOP >::const_iterator
@@ -752,7 +752,7 @@ int main( int argc, char * argv [] )
 
 		protocols::jd2::JobDistributor::get_instance()->go( iddgm, protocols::jd2::JobInputterOP( new InterfaceDDGBindJobInputter ));
 
-	} catch ( utility::excn::EXCN_Base const & e ) {
+	} catch (utility::excn::Exception const & e ) {
 		std::cout << "caught exception " << e.msg() << std::endl;
 		return -1;
 	}

source/src/apps/pilot/andrew/kellogg_ddg_jd3.cc

@@ -337,7 +337,7 @@ main( int argc, char * argv [] )
 		protocols::jd3::JobQueenOP queen( new FixbbJobQueen );
 		//std::cout << "Fixbb job definition file\n" << queen->job_definition_xsd() << std::endl;
 		jd->go( queen );
-	} catch ( utility::excn::EXCN_Base const & e ) {
+	} catch (utility::excn::Exception const & e ) {
 		std::cout << "caught exception " << e.msg() << std::endl;
 		return -1;
 	}

source/src/apps/pilot/andrew/measure_catalytic_geometry.cc

@@ -173,7 +173,7 @@ int main( int argc, char * argv [] )
 		std::cout << "ANG U1D2 " << numeric::constants::d::radians_to_degrees * numeric::angle_radians( vu1, vd1, vd2 ) << std::endl;
 		std::cout << "DIS U1D1 " <<  vu1.distance( vd1 ) << std::endl;
 
-	} catch ( utility::excn::EXCN_Base const & e ) {
+	} catch (utility::excn::Exception const & e ) {
 		std::cout << "caught exception " << e.msg() << std::endl;
 		return -1;
 	}

source/src/apps/pilot/andrew/measure_lcaa_neighbor_radii.cc

@@ -106,7 +106,7 @@ int main( int argc, char * argv [] )
 			}
 			std::cout << "Max D for " << iirot->name() << " " << std::sqrt(maxd2) << std::endl;
 		}
-	} catch ( utility::excn::EXCN_Base const & e ) {
+	} catch (utility::excn::Exception const & e ) {
 		std::cout << "caught exception " << e.msg() << std::endl;
 		return -1;
 	}

source/src/apps/pilot/andrew/mmt_msd.cc

@@ -424,7 +424,7 @@ int main( int argc, char ** argv )
 			mmt_receiver.main_optimization_loop();
 		}
 
-	} catch ( utility::excn::EXCN_Base const & e ) {
+	} catch (utility::excn::Exception const & e ) {
 		std::cout << "caught exception " << e.msg() << std::endl;
 		return -1;
 	}

source/src/apps/pilot/andrew/mpi_msd.cc

@@ -207,7 +207,7 @@ int main( int argc, char ** argv )
 			utility::io::izstream daf_file( daf_filename );
 			try {
 				daf->initialize_from_input_file( ds, daf_file );
-			} catch ( utility::excn::EXCN_Msg_Exception & e ) {
+			} catch (utility::excn::Exception & e ) {
 				std::cerr << "Caught exception" << std::endl;
 				std::cerr << e.msg() << std::endl;
 				exit(1);
@@ -324,7 +324,7 @@ int main( int argc, char ** argv )
 	MPI_Finalize();
 #endif
 
-	} catch ( utility::excn::EXCN_Base const & e ) {
+	} catch (utility::excn::Exception const & e ) {
 		std::cout << "caught exception " << e.msg() << std::endl;
 		return -1;
 	}

source/src/apps/pilot/andrew/mpi_test.cc

@@ -65,7 +65,7 @@ int main( int argc, char ** argv )
 			TR << "Node " << mpi_rank() << " recieved a single double " << receive_double_from_node( 0 ) << std::endl;
 		}
 
-	} catch ( utility::excn::EXCN_Base const & e ) {
+	} catch (utility::excn::Exception const & e ) {
 		std::cout << "caught exception " << e.msg() << std::endl;
 		return -1;
 	}

source/src/apps/pilot/andrew/relax_jd3.cc

@@ -253,7 +253,7 @@ main( int argc, char * argv [] )
 		protocols::jd3::JobQueenOP queen( new RelaxJobQueen );
 		//std::cout << "Fixbb job definition file\n" << queen->job_definition_xsd() << std::endl;
 		jd->go( queen );
-	} catch ( utility::excn::EXCN_Base const & e ) {
+	} catch ( utility::excn::Exception const & e ) {
 		std::cout << "caught exception " << e.msg() << std::endl;
 		return -1;
 	}

source/src/apps/pilot/andrew/sweep_respair_energies.cc

@@ -1476,7 +1476,7 @@ int main( int argc, char * argv [] )
 			db_session->commit();
 		}
 
-	} catch ( utility::excn::EXCN_Base const & e ) {
+	} catch (utility::excn::Exception const & e ) {
 		std::cerr << "caught exception " << e.msg() << std::endl;
 		return -1;
 	}

source/src/apps/pilot/andrew/version_scorefunction.cc

@@ -248,7 +248,7 @@ int main( int argc, char ** argv )
 			}
 		}
 
-	} catch ( utility::excn::EXCN_Base const & e ) {
+	} catch (utility::excn::Exception const & e ) {
 		std::cout << "caught exception " << e.msg() << std::endl;
 		return -1;
 	}

source/src/apps/pilot/andrew/zn_match_symmdock.cc

@@ -226,7 +226,7 @@ int main( int argc, char * argv [] )
 		// GO!
 		protocols::jd2::JobDistributor::get_instance()->go( seq_mover );
 
-	} catch ( utility::excn::EXCN_Base const & e ) {
+	} catch (utility::excn::Exception const & e ) {
 		std::cout << "caught exception " << e.msg() << std::endl;
 		return -1;
 	}

source/src/apps/pilot/aroop/model_e2c_ubiquitin.cc

@@ -40,7 +40,7 @@ main( int argc, char * argv [] )
 		MoverOP e2ubdock = new ub_e2c::ubi_e2c_modeler();
 		protocols::jobdist::main_plain_mover( *e2ubdock );
 
-	} catch ( utility::excn::EXCN_Base const & e ) {
+	} catch (utility::excn::Exception const & e ) {
 		std::cout << "caught exception " << e.msg() << std::endl;
 		return -1;
 	}

source/src/apps/pilot/arubenstein/sequence_tolerance_mf.cc

@@ -140,7 +140,7 @@ main( int argc, char * argv[] )
 		NEW_OPT(seq_tol::surface, "calculate the the surface score", false);
 		devel::init( argc, argv );
 		protocols::viewer::viewer_main( sequence_tolerance_mf_main );
-	} catch ( utility::excn::EXCN_Base const & e ) {
+	} catch (utility::excn::Exception const & e ) {
 		std::cout << "caught exception " << e.msg() << std::endl;
 	}
 	return 0;