Some more refactoring, renaming, adding #ifndef guards...

Fixed a warning in SquareSparseMatrix.h regarding a conversion from uint64 to uint

src/exceptions/BaseException.h

@@ -1,5 +1,5 @@
-#ifndef BASEEXCEPTION_H_
+#ifndef MRMC_EXCEPTIONS_BASEEXCEPTION_H_
-#define BASEEXCEPTION_H_
+#define MRMC_EXCEPTIONS_BASEEXCEPTION_H_
 
 #include <exception>
 #include <sstream>
@@ -38,4 +38,4 @@ class BaseException : public std::exception
 } // namespace exceptions
 } // namespace mrmc
 
-#endif // BASEEXCEPTION_H_
+#endif // MRMC_EXCEPTIONS_BASEEXCEPTION_H_

src/exceptions/InvalidSettings.h

@@ -1,16 +0,0 @@
-#ifndef INVALIDSETTINGS_H_
-#define INVALIDSETTINGS_H_
-
-#include "src/exceptions/BaseException.h"
-
-namespace mrmc {
-namespace exceptions {
-
-class InvalidSettings : public BaseException<InvalidSettings>
-{
-};
-
-} // namespace exceptions
-} // namespace mrmc
-
-#endif // INVALIDSETTINGS_H_

src/exceptions/InvalidSettingsException.h

@@ -0,0 +1,16 @@
+#ifndef MRMC_EXCEPTIONS_INVALIDSETTINGSEXCEPTION_H_
+#define MRMC_EXCEPTIONS_INVALIDSETTINGSEXCEPTION_H_
+
+#include "src/exceptions/BaseException.h"
+
+namespace mrmc {
+namespace exceptions {
+
+class InvalidSettingsException : public BaseException<InvalidSettingsException>
+{
+};
+
+} // namespace exceptions
+} // namespace mrmc
+
+#endif // MRMC_EXCEPTIONS_INVALIDSETTINGSEXCEPTION_H_

src/exceptions/NoConvergence.h → src/exceptions/NoConvergenceException.h

@@ -1,5 +1,5 @@
-#ifndef MRMC_EXCEPTIONS_NO_CONVERGENCE_H_
+#ifndef MRMC_EXCEPTIONS_NOCONVERGENCEEXCEPTION_H_
-#define MRMC_EXCEPTIONS_NO_CONVERGENCE_H_
+#define MRMC_EXCEPTIONS_NOCONVERGENCEEXCEPTION_H_
 
 #include <exception>
 
@@ -7,7 +7,7 @@ namespace mrmc {
 namespace exceptions {
 
 //!This exception is thrown when an iterative solver failed to converge with the given maxIterations
-class NoConvergence : public std::exception
+class NoConvergenceException : public std::exception
 {
  public:
 /* The Visual C++-Version of the exception class has constructors accepting
@@ -17,27 +17,27 @@ class NoConvergence : public std::exception
  * constructor is used under linux (which will ignore the parameter)
  */
 #ifdef _WIN32
-   NoConvergence() : exception("::mrmc::NoConvergence"){
+   NoConvergenceException() : exception("::mrmc::exceptions::NoConvergenceException"){
 	   iterations = -1;
 	   maxIterations = -1;
    }
-   NoConvergence(const char * const s, int iterations, int maxIterations): exception(s) {
+   NoConvergenceException(const char * const s, int iterations, int maxIterations): exception(s) {
 	   this->iterations = iterations;
 	   this->maxIterations = maxIterations;
    }
 #else
-   NoConvergence() : exception() {
+   NoConvergenceException() : exception() {
 	   iterations = -1;
 	   maxIterations = -1;
    }
-   NoConvergence(const char * const s, int iterations, int maxIterations): exception() {
+   NoConvergenceException(const char * const s, int iterations, int maxIterations): exception() {
 	   this->iterations = iterations;
 	   this->maxIterations = maxIterations;
    }
 
 #endif
    virtual const char* what() const throw()
-      {  return "mrmc::NoConvergence";  }
+      {  return "mrmc::exceptions::NoConvergenceException";  }
 
    int getIterationCount() const {
 	   return iterations;
@@ -53,4 +53,4 @@ class NoConvergence : public std::exception
 } // namespace exceptions
 } // namespace mrmc
 
-#endif // MRMC_EXCEPTIONS_NO_CONVERGENCE_H_
+#endif // MRMC_EXCEPTIONS_NOCONVERGENCEEXCEPTION_H_

src/modelChecker/EigenDtmcPrctlModelChecker.h

@@ -14,7 +14,7 @@
 #include "src/modelChecker/DtmcPrctlModelChecker.h"
 #include "src/solver/GraphAnalyzer.h"
 #include "src/utility/ConstTemplates.h"
-#include "src/exceptions/NoConvergence.h"
+#include "src/exceptions/NoConvergenceException.h"
 
 #include "Eigen/Sparse"
 #include "Eigen/src/IterativeLinearSolvers/BiCGSTAB.h"
@@ -197,7 +197,7 @@ public:
 				LOG4CPLUS_ERROR(logger, "Solving of Submatrix failed: InvalidInput");
 			} else if(solver.info() == Eigen::ComputationInfo::NoConvergence) {
 				// NoConvergence
-				throw mrmc::exceptions::NoConvergence("Solving of Submatrix with Eigen failed", solver.iterations(), solver.maxIterations());
+				throw mrmc::exceptions::NoConvergenceException("Solving of Submatrix with Eigen failed", solver.iterations(), solver.maxIterations());
 			} else if(solver.info() == Eigen::ComputationInfo::NumericalIssue) {
 				// NumericalIssue
 				LOG4CPLUS_ERROR(logger, "Solving of Submatrix failed: NumericalIssue");

src/modelChecker/GmmxxDtmcPrctlModelChecker.h

@@ -250,7 +250,7 @@ public:
 	 */
 	static void validateLeMethod(const std::string& lemethod) {
 		if (lemethod.compare("bicgstab") != 0 && lemethod.compare("qmr") != 0) {
-			throw exceptions::InvalidSettings() << "Argument " << lemethod << " for option 'lemethod' is invalid.";
+			throw exceptions::InvalidSettingsException() << "Argument " << lemethod << " for option 'lemethod' is invalid.";
 		}
 	}
 
@@ -260,7 +260,7 @@ public:
 	 */
 	static void validatePreconditioner(const std::string& preconditioner) {
 		if (preconditioner.compare("ilu") != 0 && preconditioner.compare("diagonal") != 0 && preconditioner.compare("ildlt") && preconditioner.compare("none") != 0) {
-			throw exceptions::InvalidSettings() << "Argument " << preconditioner << " for option 'precond' is invalid.";
+			throw exceptions::InvalidSettingsException() << "Argument " << preconditioner << " for option 'precond' is invalid.";
 		}
 	}
 };

src/mrmc.cpp

@@ -24,20 +24,19 @@
 #include "src/models/AtomicPropositionsLabeling.h"
 #include "src/modelChecker/EigenDtmcPrctlModelChecker.h"
 #include "src/modelChecker/GmmxxDtmcPrctlModelChecker.h"
-#include "src/parser/readLabFile.h"
+#include "src/parser/LabParser.h"
-#include "src/parser/readTraFile.h"
+#include "src/parser/TraParser.h"
-#include "src/parser/readPrctlFile.h"
+#include "src/parser/PrctlParser.h"
 #include "src/solver/GraphAnalyzer.h"
 #include "src/utility/Settings.h"
 #include "src/formula/Formulas.h"
-#include "src/exceptions/NoConvergence.h"
 
 #include "log4cplus/logger.h"
 #include "log4cplus/loggingmacros.h"
 #include "log4cplus/consoleappender.h"
 #include "log4cplus/fileappender.h"
 
-#include "src/exceptions/InvalidSettings.h"
+#include "src/exceptions/InvalidSettingsException.h"
 
 log4cplus::Logger logger;
 
@@ -76,7 +75,7 @@ int main(const int argc, const char* argv[]) {
 	try {
 		mrmc::settings::Settings::registerModule<mrmc::modelChecker::GmmxxDtmcPrctlModelChecker<double> >();
 		s = mrmc::settings::newInstance(argc, argv, nullptr);
-	} catch (mrmc::exceptions::InvalidSettings& e) {
+	} catch (mrmc::exceptions::InvalidSettingsException& e) {
 		LOG4CPLUS_FATAL(logger, "InvalidSettings error: " << e.what() << ".");
 		LOG4CPLUS_FATAL(logger, "Could not recover from settings error, terminating.");
 		std::cout << "Could not recover from settings error: " << e.what() << "." << std::endl;
@@ -91,7 +90,7 @@ int main(const int argc, const char* argv[]) {
 		return 0;
 	}
 	if (s->isSet("test-prctl")) {
-		mrmc::parser::PRCTLParser parser(s->getString("test-prctl").c_str());
+		mrmc::parser::PrctlParser parser(s->getString("test-prctl").c_str());
 		delete s;
 		return 0;
 	}

src/parser/readLabFile.cpp → src/parser/LabParser.cpp

@@ -1,11 +1,11 @@
 /*!
- * readLabFile.cpp
+ * LabParser.cpp
  *
  *  Created on: 21.11.2012
  *      Author: Gereon Kremer
  */
 
-#include "readLabFile.h"
+#include "src/parser/LabParser.h"
 
 #include "src/exceptions/WrongFileFormatException.h"
 #include "src/exceptions/FileIoException.h"

src/parser/readLabFile.h → src/parser/LabParser.h

@@ -1,5 +1,5 @@
-#ifndef READLABFILE_H_
+#ifndef MRMC_PARSER_LABPARSER_H_
-#define READLABFILE_H_
+#define MRMC_PARSER_LABPARSER_H_
 
 #include "src/models/AtomicPropositionsLabeling.h"
 #include "boost/integer/integer_mask.hpp"
@@ -32,4 +32,4 @@ class LabParser : Parser {
 } // namespace parser
 } // namespace mrmc
 
-#endif /* READLABFILE_H_ */
+#endif /* MRMC_PARSER_LABPARSER_H_ */

src/parser/readPrctlFile.cpp → src/parser/PrctlParser.cpp

@@ -1,4 +1,4 @@
-#include "src/parser/readPrctlFile.h"
+#include "src/parser/PrctlParser.h"
 
 #include <iostream>
 #include <map>
@@ -130,7 +130,7 @@ namespace
 	};
 }
 
-mrmc::parser::PRCTLParser::PRCTLParser(const char* filename)
+mrmc::parser::PrctlParser::PrctlParser(const char* filename)
 {
 	SpiritParser p;
 	mrmc::parser::MappedFile file(filename);

src/parser/readPrctlFile.h → src/parser/PrctlParser.h

@@ -1,5 +1,5 @@
-#ifndef READPRCTLFILE_H_
+#ifndef MRMC_PARSER_PRCTLPARSER_H_
-#define READPRCTLFILE_H_
+#define MRMC_PARSER_PRCTLPARSER_H_
 
 #include "src/formula/PCTLformula.h"
 #include "src/parser/Parser.h"
@@ -10,10 +10,10 @@ namespace parser {
 /*!
  *	@brief Load PRCTL file
  */
-class PRCTLParser : Parser
+class PrctlParser : Parser
 {
 	public:
-		PRCTLParser(const char * filename);
+		PrctlParser(const char * filename);
 		 
 		/*!
 		 *	@brief return formula object parsed from file.
@@ -30,4 +30,4 @@ class PRCTLParser : Parser
 } // namespace parser
 } // namespace mrmc
 
-#endif /* READPRCTLFILE_H_ */
+#endif /* MRMC_PARSER_PRCTLPARSER_H_ */

src/parser/readTraFile.cpp → src/parser/TraParser.cpp

@@ -1,11 +1,11 @@
 /*!
- *	readTraFile.cpp
+ *	TraParser.cpp
  *
  *	Created on: 20.11.2012
  *		Author: Gereon Kremer
  */
 
-#include "src/parser/readTraFile.h"
+#include "src/parser/TraParser.h"
 #include "src/exceptions/FileIoException.h"
 #include "src/exceptions/WrongFileFormatException.h"
 #include "boost/integer/integer_mask.hpp"

src/parser/readTraFile.h → src/parser/TraParser.h

@@ -1,5 +1,5 @@
-#ifndef READTRAFILE_H_
+#ifndef MRMC_PARSER_TRAPARSER_H_
-#define READTRAFILE_H_
+#define MRMC_PARSER_TRAPARSER_H_
 
 #include "src/storage/SquareSparseMatrix.h"
 
@@ -35,4 +35,4 @@ class TraParser : Parser {
 } // namespace parser
 } // namespace mrmc
 
-#endif /* READTRAFILE_H_ */
+#endif /* MRMC_PARSER_TRAPARSER_H_ */

src/storage/SquareSparseMatrix.h

@@ -670,7 +670,7 @@ public:
 			}
 		}
 		// Fill in sentinel element at the end.
-		result->jc[rowCount] = realNonZeros;
+		result->jc[rowCount] = static_cast<unsigned int>(realNonZeros);
 
 		// Now, we can copy the temporary array to the GMMXX format.
 		result->ir.resize(realNonZeros);

src/utility/IoUtility.cpp

@@ -6,8 +6,8 @@
  */
 
 #include "src/utility/IoUtility.h"
-#include "src/parser/readTraFile.h"
+#include "src/parser/TraParser.h"
-#include "src/parser/readLabFile.h"
+#include "src/parser/LabParser.h"
 
 #include <fstream>
 

src/utility/Settings.cpp

@@ -102,16 +102,16 @@ Settings::Settings(const int argc, const char* argv[], const char* filename) {
 		LOG4CPLUS_ERROR(logger, "Could not read config file");
 	}
 	catch (bpo::required_option e) {
-		throw mrmc::exceptions::InvalidSettings() << "Required option missing";
+		throw mrmc::exceptions::InvalidSettingsException() << "Required option missing";
 	}
 	catch (bpo::validation_error e) {
-		throw mrmc::exceptions::InvalidSettings() << "Validation failed: " << e.what();
+		throw mrmc::exceptions::InvalidSettingsException() << "Validation failed: " << e.what();
 	}
 	catch (bpo::invalid_command_line_syntax e) {
-		throw mrmc::exceptions::InvalidSettings() << e.what();
+		throw mrmc::exceptions::InvalidSettingsException() << e.what();
 	}
 	catch (bpo::error e) {
-		throw mrmc::exceptions::InvalidSettings() << e.what();
+		throw mrmc::exceptions::InvalidSettingsException() << e.what();
 	}
 }
 

src/utility/Settings.h

@@ -14,7 +14,7 @@
 #include <utility>
 #include <memory>
 #include <boost/program_options.hpp>
-#include "src/exceptions/InvalidSettings.h"
+#include "src/exceptions/InvalidSettingsException.h"
 
 namespace mrmc {
 
@@ -52,7 +52,7 @@ namespace settings {
 			 */
 			template <typename T>
 			const T& get(const std::string &name) const {
-				if (this->vm.count(name) == 0) throw mrmc::exceptions::InvalidSettings() << "Could not read option " << name << ".";
+				if (this->vm.count(name) == 0) throw mrmc::exceptions::InvalidSettingsException() << "Could not read option " << name << ".";
 				return this->vm[name].as<T>();
 			}
 		

test/parser/ReadLabFileTest.cpp

@@ -8,7 +8,7 @@
 #include "gtest/gtest.h"
 #include "mrmc-config.h"
 #include "src/models/AtomicPropositionsLabeling.h"
-#include "src/parser/readLabFile.h"
+#include "src/parser/LabParser.h"
 #include "src/exceptions/FileIoException.h"
 #include "src/exceptions/WrongFileFormatException.h"
 

test/parser/ReadTraFileTest.cpp

@@ -8,7 +8,7 @@
 #include "gtest/gtest.h"
 #include "mrmc-config.h"
 #include "src/storage/SquareSparseMatrix.h"
-#include "src/parser/readTraFile.h"
+#include "src/parser/TraParser.h"
 #include "src/exceptions/FileIoException.h"
 #include "src/exceptions/WrongFileFormatException.h"