Added adapters folder and GmmxxAdapter that is a friend class of the matrix class and can convert the sparse matrix to the gmm++ format. Removed this conversion from the matrix class.

src/adapters/GmmxxAdapter.h

@@ -0,0 +1,108 @@
+/*
+ * GmmxxAdapter.h
+ *
+ *  Created on: 24.12.2012
+ *      Author: Christian Dehnert
+ */
+
+#ifndef GMMXXADAPTER_H_
+#define GMMXXADAPTER_H_
+
+#include "src/storage/SquareSparseMatrix.h"
+
+#include "log4cplus/logger.h"
+#include "log4cplus/loggingmacros.h"
+
+extern log4cplus::Logger logger;
+
+namespace mrmc {
+
+namespace adapters {
+
+class GmmxxAdapter {
+public:
+	/*!
+	 * Converts a sparse matrix into the sparse matrix in the gmm++ format.
+	 * @return A pointer to a column-major sparse matrix in gmm++ format.
+	 */
+	template<class T>
+	static gmm::csr_matrix<T>* toGmmxxSparseMatrix(mrmc::storage::SquareSparseMatrix<T> const& matrix) {
+		uint_fast64_t realNonZeros = matrix.getNonZeroEntryCount() + matrix.getDiagonalNonZeroEntryCount();
+		LOG4CPLUS_DEBUG(logger, "Converting matrix with " << realNonZeros << " non-zeros to gmm++ format.");
+
+		// Prepare the resulting matrix.
+		gmm::csr_matrix<T>* result = new gmm::csr_matrix<T>(matrix.rowCount, matrix.rowCount);
+
+		// Reserve enough elements for the row indications.
+		result->jc.reserve(matrix.rowCount + 1);
+
+		// For the column indications and the actual values, we have to gather
+		// the values in a temporary array first, as we have to integrate
+		// the values from the diagonal. For the row indications, we can just count the number of
+		// inserted diagonal elements and add it to the previous value.
+		uint_fast64_t* tmpColumnIndicationsArray = new uint_fast64_t[realNonZeros];
+		T* tmpValueArray = new T[realNonZeros];
+		T zero(0);
+		uint_fast64_t currentPosition = 0;
+		uint_fast64_t insertedDiagonalElements = 0;
+		for (uint_fast64_t i = 0; i < matrix.rowCount; ++i) {
+			// Compute correct start index of row.
+			result->jc[i] = matrix.rowIndications[i] + insertedDiagonalElements;
+
+			// If the current row has no non-zero which is not on the diagonal, we have to check the
+			// diagonal element explicitly.
+			if (matrix.rowIndications[i + 1] - matrix.rowIndications[i] == 0) {
+				if (matrix.diagonalStorage[i] != zero) {
+					tmpColumnIndicationsArray[currentPosition] = i;
+					tmpValueArray[currentPosition] = matrix.diagonalStorage[i];
+					++currentPosition; ++insertedDiagonalElements;
+				}
+			} else {
+				// Otherwise, we can just enumerate the non-zeros which are not on the diagonal
+				// and fit in the diagonal element where appropriate.
+				bool includedDiagonal = false;
+				for (uint_fast64_t j = matrix.rowIndications[i]; j < matrix.rowIndications[i + 1]; ++j) {
+					if (matrix.diagonalStorage[i] != zero && !includedDiagonal && matrix.columnIndications[j] > i) {
+						includedDiagonal = true;
+						tmpColumnIndicationsArray[currentPosition] = i;
+						tmpValueArray[currentPosition] = matrix.diagonalStorage[i];
+						++currentPosition; ++insertedDiagonalElements;
+					}
+					tmpColumnIndicationsArray[currentPosition] = matrix.columnIndications[j];
+					tmpValueArray[currentPosition] = matrix.valueStorage[j];
+					++currentPosition;
+				}
+
+				// If the diagonal element is non-zero and was not inserted until now (i.e. all
+				// off-diagonal elements in the row are before the diagonal element.
+				if (!includedDiagonal && matrix.diagonalStorage[i] != zero) {
+					tmpColumnIndicationsArray[currentPosition] = i;
+					tmpValueArray[currentPosition] = matrix.diagonalStorage[i];
+					++currentPosition; ++insertedDiagonalElements;
+				}
+			}
+		}
+		// Fill in sentinel element at the end.
+		result->jc[matrix.rowCount] = static_cast<unsigned int>(realNonZeros);
+
+		// Now, we can copy the temporary array to the GMMXX format.
+		result->ir.resize(realNonZeros);
+		std::copy(tmpColumnIndicationsArray, tmpColumnIndicationsArray + realNonZeros, result->ir.begin());
+		delete[] tmpColumnIndicationsArray;
+
+		// And do the same thing with the actual values.
+		result->pr.resize(realNonZeros);
+		std::copy(tmpValueArray, tmpValueArray + realNonZeros, result->pr.begin());
+		delete[] tmpValueArray;
+
+		LOG4CPLUS_DEBUG(logger, "Done converting matrix to gmm++ format.");
+
+		return result;
+	}
+};
+
+} //namespace adapters
+
+} //namespace mrmc
+
+#endif /* GMMXXADAPTER_H_ */

src/modelChecker/GmmxxDtmcPrctlModelChecker.h

@@ -16,6 +16,7 @@
 #include "src/utility/Vector.h"
 #include "src/utility/ConstTemplates.h"
 #include "src/utility/Settings.h"
+#include "src/adapters/GmmxxAdapter.h"
 
 #include "gmm/gmm_matrix.h"
 #include "gmm/gmm_iter_solvers.h"
@@ -52,7 +53,7 @@ public:
 		tmpMatrix.makeRowsAbsorbing(~(*leftStates | *rightStates) | *rightStates);
 
 		// Transform the transition probability matrix to the gmm++ format to use its arithmetic.
-		gmm::csr_matrix<Type>* gmmxxMatrix = tmpMatrix.toGMMXXSparseMatrix();
+		gmm::csr_matrix<Type>* gmmxxMatrix = mrmc::adapters::GmmxxAdapter::toGmmxxSparseMatrix<Type>(tmpMatrix);
 
 		// Create the vector with which to multiply.
 		std::vector<Type>* result = new std::vector<Type>(this->getModel().getNumberOfStates());
@@ -80,7 +81,7 @@ public:
 		mrmc::storage::BitVector* nextStates = this->checkStateFormula(formula.getChild());
 
 		// Transform the transition probability matrix to the gmm++ format to use its arithmetic.
-		gmm::csr_matrix<Type>* gmmxxMatrix = this->getModel().getTransitionProbabilityMatrix()->toGMMXXSparseMatrix();
+		gmm::csr_matrix<Type>* gmmxxMatrix = mrmc::adapters::GmmxxAdapter::toGmmxxSparseMatrix<Type>(*this->getModel().getTransitionProbabilityMatrix());
 
 		// Create the vector with which to multiply and initialize it correctly.
 		std::vector<Type> x(this->getModel().getNumberOfStates());
@@ -133,7 +134,7 @@ public:
 			submatrix->convertToEquationSystem();
 
 			// Transform the submatrix to the gmm++ format to use its solvers.
-			gmm::csr_matrix<Type>* gmmxxMatrix = submatrix->toGMMXXSparseMatrix();
+			gmm::csr_matrix<Type>* gmmxxMatrix = mrmc::adapters::GmmxxAdapter::toGmmxxSparseMatrix<Type>(*submatrix);
 			delete submatrix;
 
 			// Initialize the x vector with 0.5 for each element. This is the initial guess for

src/parser/AutoTransitionParser.cpp

@@ -76,4 +76,5 @@ std::pair<TransitionType,TransitionType> AutoTransitionParser::analyzeContent(co
 }
 
 } //namespace parser
-} //namespace mrmc
+} //namespace mrmc

src/storage/SquareSparseMatrix.h

@@ -23,6 +23,9 @@
 
 extern log4cplus::Logger logger;
 
+// Forward declaration for adapter classes.
+namespace mrmc { namespace adapters{ class GmmxxAdapter; } }
+
 namespace mrmc {
 
 namespace storage {
@@ -36,6 +39,10 @@ namespace storage {
 template<class T>
 class SquareSparseMatrix {
 public:
+	/*!
+	 * Declare adapter classes as friends to use internal data.
+	 */
+	friend class mrmc::adapters::GmmxxAdapter;
 
 	/*!
 	 * If we only want to iterate over the columns of the non-zero entries of
@@ -613,84 +620,6 @@ public:
 		return nullptr;
 	}
 
-	/*!
-	 * Converts the matrix into a sparse matrix in the GMMXX format.
-	 * @return A pointer to a column-major sparse matrix in GMMXX format.
-	 */
-	gmm::csr_matrix<T>* toGMMXXSparseMatrix() {
-		uint_fast64_t realNonZeros = getNonZeroEntryCount() + getDiagonalNonZeroEntryCount();
-		LOG4CPLUS_DEBUG(logger, "Converting matrix with " << realNonZeros << " non-zeros to gmm++ format.");
-
-		// Prepare the resulting matrix.
-		gmm::csr_matrix<T>* result = new gmm::csr_matrix<T>(rowCount, rowCount);
-
-		// Reserve enough elements for the row indications.
-		result->jc.reserve(rowCount + 1);
-
-		// For the column indications and the actual values, we have to gather
-		// the values in a temporary array first, as we have to integrate
-		// the values from the diagonal. For the row indications, we can just count the number of
-		// inserted diagonal elements and add it to the previous value.
-		uint_fast64_t* tmpColumnIndicationsArray = new uint_fast64_t[realNonZeros];
-		T* tmpValueArray = new T[realNonZeros];
-		T zero(0);
-		uint_fast64_t currentPosition = 0;
-		uint_fast64_t insertedDiagonalElements = 0;
-		for (uint_fast64_t i = 0; i < rowCount; ++i) {
-			// Compute correct start index of row.
-			result->jc[i] = rowIndications[i] + insertedDiagonalElements;
-
-			// If the current row has no non-zero which is not on the diagonal, we have to check the
-			// diagonal element explicitly.
-			if (rowIndications[i + 1] - rowIndications[i] == 0) {
-				if (diagonalStorage[i] != zero) {
-					tmpColumnIndicationsArray[currentPosition] = i;
-					tmpValueArray[currentPosition] = diagonalStorage[i];
-					++currentPosition; ++insertedDiagonalElements;
-				}
-			} else {
-				// Otherwise, we can just enumerate the non-zeros which are not on the diagonal
-				// and fit in the diagonal element where appropriate.
-				bool includedDiagonal = false;
-				for (uint_fast64_t j = rowIndications[i]; j < rowIndications[i + 1]; ++j) {
-					if (diagonalStorage[i] != zero && !includedDiagonal && columnIndications[j] > i) {
-						includedDiagonal = true;
-						tmpColumnIndicationsArray[currentPosition] = i;
-						tmpValueArray[currentPosition] = diagonalStorage[i];
-						++currentPosition; ++insertedDiagonalElements;
-					}
-					tmpColumnIndicationsArray[currentPosition] = columnIndications[j];
-					tmpValueArray[currentPosition] = valueStorage[j];
-					++currentPosition;
-				}
-
-				// If the diagonal element is non-zero and was not inserted until now (i.e. all
-				// off-diagonal elements in the row are before the diagonal element.
-				if (!includedDiagonal && diagonalStorage[i] != zero) {
-					tmpColumnIndicationsArray[currentPosition] = i;
-					tmpValueArray[currentPosition] = diagonalStorage[i];
-					++currentPosition; ++insertedDiagonalElements;
-				}
-			}
-		}
-		// Fill in sentinel element at the end.
-		result->jc[rowCount] = static_cast<unsigned int>(realNonZeros);
-
-		// Now, we can copy the temporary array to the GMMXX format.
-		result->ir.resize(realNonZeros);
-		std::copy(tmpColumnIndicationsArray, tmpColumnIndicationsArray + realNonZeros, result->ir.begin());
-		delete[] tmpColumnIndicationsArray;
-
-		// And do the same thing with the actual values.
-		result->pr.resize(realNonZeros);
-		std::copy(tmpValueArray, tmpValueArray + realNonZeros, result->pr.begin());
-		delete[] tmpValueArray;
-
-		LOG4CPLUS_DEBUG(logger, "Done converting matrix to gmm++ format.");
-
-		return result;
-	}
-
 	/*!
 	 * Returns the number of non-zero entries that are not on the diagonal.
 	 * @returns The number of non-zero entries that are not on the diagonal.