@@ -38,7 +38,7 @@ imslib/src/ims/decomp/realmassdecomposer.o: imslib/src/ims/decomp/realmassdecomp

 imslib/src/ims/utils/distribution.o: imslib/src/ims/utils/distribution.cpp

 imslib/src/ims/distributionprobabilityscorer.o: imslib/src/ims/distributionprobabilityscorer.cpp

 imslib/src/ims/characteralphabet.o: imslib/src/ims/characteralphabet.cpp

-imslib/src/ims/nitrogenrulefiltero: imslib/src/ims/nitrogenrulefilter.cp

+imslib/src/ims/nitrogenrulefilter.o: imslib/src/ims/nitrogenrulefilter.cpp

 clean:

 	$(MAKE) -C imslib clean

@@ -37,7 +37,7 @@ imslib/src/ims/decomp/realmassdecomposer.o: imslib/src/ims/decomp/realmassdecomp

 imslib/src/ims/utils/distribution.o: imslib/src/ims/utils/distribution.cpp

 imslib/src/ims/distributionprobabilityscorer.o: imslib/src/ims/distributionprobabilityscorer.cpp

 imslib/src/ims/characteralphabet.o: imslib/src/ims/characteralphabet.cpp

-imslib/src/ims/nitrogenrulefiltero: imslib/src/ims/nitrogenrulefilter.cp

+imslib/src/ims/nitrogenrulefilter.o: imslib/src/ims/nitrogenrulefilter.cpp

 clean:

 	$(MAKE) -C imslib clean

@@ -776,7 +776,7 @@ void initializeCHNOPS(alphabet_t& chnops, const int maxisotopes) {

 /* get the list element named str, or return NULL */

 /* http://cran.r-project.org/doc/manuals/R-exts.html#Handling-lists */

-SEXP getListElement(SEXP list, char *str)

+SEXP getListElement(SEXP list, char const *str)

   // {{{ 

 {

@@ -809,7 +809,7 @@ void initializeAlphabet(const SEXP l_alphabet,

   for (int i=0; i < Rf_length(l_alphabet); i++) {

     SEXP l = VECTOR_ELT(l_alphabet,i);

-    const char *symbol = CHAR(Rf_asChar(getListElement(l, "name")));

+    char const *symbol = CHAR(Rf_asChar(getListElement(l, "name")));

     nominal_mass_type nominalmass = (nominal_mass_type) REAL(getListElement(l, "mass"))[0];

@@ -23,7 +23,7 @@ Alphabet::mass_type Alphabet::getMass(size_type index) const {

 Alphabet::mass_type Alphabet::getMass(const name_type& name) const

-										throw (UnknownCharacterException) {

+										/*throw (UnknownCharacterException)*/ {

 	return getElement(name).getMass();

 }

@@ -36,7 +36,7 @@ bool Alphabet::hasName(const name_type& name) const {

 const Alphabet::element_type& Alphabet::getElement(const name_type& name) const

-											throw (UnknownCharacterException) {

+											/*throw (UnknownCharacterException)*/ {

 	const_iterator cit = elements.begin();

 	for (; cit != elements.end(); ++cit) {

 		if (cit->getName() == name) {

@@ -81,13 +81,13 @@ void Alphabet::sortByValues() {

 }

-void Alphabet::load(const std::string& fname) throw (IOException) {

+void Alphabet::load(const std::string& fname) /*throw (IOException)*/ {

 	this->load(fname, new AlphabetTextParser);

 }

 void Alphabet::load(const std::string& fname, AlphabetParser<>* parser)

-														throw (IOException) {

+														/*throw (IOException)*/ {

 	parser->load(fname);

 	this->clear();

 	for (AlphabetParser<>::ContainerType::const_iterator pos =

@@ -110,7 +110,7 @@ class Alphabet {

 		 * 			throws @c UnknownCharacterException.

 		 */

 		const element_type& getElement(const name_type& name) const

-									throw (UnknownCharacterException);

+									/*throw (UnknownCharacterException)*/;

 		/**

 		 * Gets the symbol of the element with an index @c index in alphabet.

@@ -130,7 +130,7 @@ class Alphabet {

 		 * @see getMass(size_type index)

 		 */

 		mass_type getMass(const name_type& name) const

-									throw (UnknownCharacterException);

+									/*throw (UnknownCharacterException)*/;

 		/**

 		 * Gets mass of the element with an index @index in alphabet.

@@ -217,7 +217,7 @@ class Alphabet {

 		 * @param fname The file name to be loaded.

 		 * @see load(const std::string& fname, AlphabetParser<>* parser)

 		 */

-		virtual void load(const std::string& fname) throw (IOException);

+		virtual void load(const std::string& fname) /*throw (IOException)*/;

 		/**

@@ -231,7 +231,7 @@ class Alphabet {

 		 * @see AlphabetParser

 		 */

 		virtual void load(const std::string& fname, AlphabetParser<>* parser)

-			throw (IOException);

+			/*throw (IOException)*/;

 		/**

@@ -20,7 +20,7 @@ class AbstractMoleculeSequenceParser {

 		AbstractMoleculeSequenceParser(): multiplicator(1) {}

 		virtual void parse(const sequence_type& sequence) 

-						throw (UnknownCharacterException) = 0;

+						/*throw (UnknownCharacterException)*/ = 0;

 		const container& getElements() const { return elements; }

@@ -34,7 +34,7 @@ class AlphabetParser {

 		 * 

 		 * @param fname The name of the input source.

 		 */

-		void load(const std::string& fname) throw (IOException);

+		void load(const std::string& fname) /*throw (IOException)*/;

 		/**

 		 * Gets the data that was loaded. 

@@ -55,7 +55,7 @@ class AlphabetParser {

 };

 template <typename AlphabetElementType, typename Container, typename InputSource>

-void AlphabetParser<AlphabetElementType, Container, InputSource>::load(const std::string& fname) throw (IOException) {

+void AlphabetParser<AlphabetElementType, Container, InputSource>::load(const std::string& fname) /*throw (IOException)*/ {

 	std::ifstream ifs(fname.c_str());

 	if (!ifs) {

 		throw IOException("unable to open alphabet resource file: " + fname + "!");

@@ -12,12 +12,12 @@

 namespace ims {

 KeggLigandCompoundsParser::KeggLigandCompoundsParser(const sequence_type& 

-								sequence) throw (UnknownCharacterException) {

+								sequence) /*throw (UnknownCharacterException)*/ {

 	this->parse(sequence);

 }

 void KeggLigandCompoundsParser::parse(const sequence_type& sequence) 

-											throw (UnknownCharacterException) {

+											/*throw (UnknownCharacterException)*/ {

 	const sequence_type delimiters(" \t"), rest_header(".R*+(");

@@ -14,10 +14,10 @@ class KeggLigandCompoundsParser : public AbstractMoleculeSequenceParser {

 		KeggLigandCompoundsParser() : AbstractMoleculeSequenceParser() {}

 		KeggLigandCompoundsParser(const sequence_type& sequence) 

-									throw (UnknownCharacterException);

+									/*throw (UnknownCharacterException)*/;

 		virtual void parse(const sequence_type& sequence) 

-									throw (UnknownCharacterException);

+									/*throw (UnknownCharacterException)*/;

 		virtual ~KeggLigandCompoundsParser() {}

 };

@@ -21,7 +21,7 @@ class MassesParser {

 		 * 

 		 * @param fname The name of the input source.

 		 */

-		void load(const std::string& fname) throw (IOException);

+		void load(const std::string& fname) /*throw (IOException)*/;

 		/**

 		 * Gets loaded data.

@@ -42,7 +42,7 @@ class MassesParser {

 };

 template <typename MassesType, typename InputSource>

-void MassesParser<MassesType, InputSource>::load(const std::string& fname) throw (IOException) {

+void MassesParser<MassesType, InputSource>::load(const std::string& fname) /*throw (IOException)*/ {

 	std::ifstream ifs(fname.c_str());

 	if (!ifs) {

 		throw IOException("unable to open resource file with masses: " + fname + "!");

@@ -11,7 +11,7 @@

 namespace ims {

 MoleculeIonChargeModificationParser::MoleculeIonChargeModificationParser(

-					const ion_name_type& sequence) throw (UnknownCharacterException) {

+					const ion_name_type& sequence) /*throw (UnknownCharacterException)*/ {

 	parse(sequence);

 }

@@ -26,7 +26,8 @@ operator =(const MoleculeIonChargeModificationParser& parser) {

 }

-void MoleculeIonChargeModificationParser::parse(const ion_name_type& sequence) throw (UnknownCharacterException) {

+void MoleculeIonChargeModificationParser::parse(const ion_name_type& sequence) 

+/*throw (UnknownCharacterException)*/ {

 	this->clear();

@@ -36,7 +36,8 @@ class MoleculeIonChargeModificationParser {

 			mass_factor(1),		

 			charge(1) {}

-		MoleculeIonChargeModificationParser(const ion_name_type& sequence) throw (UnknownCharacterException);

+		MoleculeIonChargeModificationParser(const ion_name_type& sequence) 

+		    /*throw (UnknownCharacterException)*/;

 		MoleculeIonChargeModificationParser(const MoleculeIonChargeModificationParser& parser) :

 			mass_factor(parser.mass_factor),

@@ -45,7 +46,7 @@ class MoleculeIonChargeModificationParser {

 		MoleculeIonChargeModificationParser& operator =(const MoleculeIonChargeModificationParser& parser);

-		void parse(const ion_name_type& sequence) throw (UnknownCharacterException);

+		void parse(const ion_name_type& sequence) /*throw (UnknownCharacterException)*/;

 		mass_factor_type getMassFactor() const { return mass_factor; }		

 		charge_type getCharge() const { return charge; }

@@ -12,12 +12,12 @@

 namespace ims {

 MoleculeSequenceParser::MoleculeSequenceParser(const sequence_type& 

-								sequence) throw (UnknownCharacterException) {

+								sequence) /*throw (UnknownCharacterException)*/ {

 	this->parse(sequence);

 }

 void MoleculeSequenceParser::parse(const sequence_type& sequence) 

-											throw (UnknownCharacterException) {

+											/*throw (UnknownCharacterException)*/ {

 	const sequence_type delimiters(" \t");

@@ -55,7 +55,7 @@ void MoleculeSequenceParser::parse(const sequence_type& sequence)

 MoleculeSequenceParser::container 

 MoleculeSequenceParser::parseElements(const sequence_type& sequence)

-		 throw (UnknownCharacterException) {

+		 /*throw (UnknownCharacterException)*/ {

 	container elements;

@@ -14,17 +14,17 @@ class MoleculeSequenceParser : public AbstractMoleculeSequenceParser {

 		MoleculeSequenceParser() : AbstractMoleculeSequenceParser() {}

 		MoleculeSequenceParser(const sequence_type& sequence) 

-									throw (UnknownCharacterException);

+									/*throw (UnknownCharacterException)*/;

 		virtual void parse(const sequence_type& sequence) 

-									throw (UnknownCharacterException);

+									/*throw (UnknownCharacterException)*/;

 		virtual ~MoleculeSequenceParser() {}

 	private:

 		container parseElements(const sequence_type& sequence)

-									throw (UnknownCharacterException);

+									/*throw (UnknownCharacterException)*/;

 		void addElement(const sequence_type& name, number_type amount, 

 											container& elements);

@@ -12,12 +12,12 @@

 namespace ims {

 StandardMoleculeSequenceParser::StandardMoleculeSequenceParser(const sequence_type& 

-								sequence) throw (UnknownCharacterException) {

+								sequence) /*throw (UnknownCharacterException)*/ {

 	this->parse(sequence);

 }

 void StandardMoleculeSequenceParser::parse(const sequence_type& sequence) 

-											throw (UnknownCharacterException) {

+											/*throw (UnknownCharacterException)*/ {

 	const sequence_type delimiters(" \t");

@@ -55,7 +55,7 @@ void StandardMoleculeSequenceParser::parse(const sequence_type& sequence)

 StandardMoleculeSequenceParser::container 

 StandardMoleculeSequenceParser::parseElements(const sequence_type& sequence)

-		 throw (UnknownCharacterException) {

+		 /*throw (UnknownCharacterException)*/ {

 	container elements;

@@ -17,17 +17,17 @@ class StandardMoleculeSequenceParser : public AbstractMoleculeSequenceParser {

 		StandardMoleculeSequenceParser() : AbstractMoleculeSequenceParser() {}

 		StandardMoleculeSequenceParser(const sequence_type& sequence) 

-									throw (UnknownCharacterException);

+									/*throw (UnknownCharacterException)*/;

 		virtual void parse(const sequence_type& sequence) 

-									throw (UnknownCharacterException);

+									/*throw (UnknownCharacterException)*/;

 		virtual ~StandardMoleculeSequenceParser() {}

 	private:

 		container parseElements(const sequence_type& sequence)

-									throw (UnknownCharacterException);

+									/*throw (UnknownCharacterException)*/;

 		void addElement(const sequence_type& name, number_type amount, 

 											container& elements);

@@ -18,7 +18,7 @@ MatchMatrix::~MatchMatrix() {

 	delete [] matrix;

 }

-void MatchMatrix::set(size_t row, size_t column) throw (IndexOutOfBounds, InvalidMatchMatrix) {

+void MatchMatrix::set(size_t row, size_t column) /*throw (IndexOutOfBounds, InvalidMatchMatrix)*/ {

 	// TODO: This function does not enforce staircase property in all cases

 	// for example:

 	// mm.set(6,2);

@@ -44,7 +44,7 @@ void MatchMatrix::set(size_t row, size_t column) throw (IndexOutOfBounds, Invali

 	matrix[row].end=std::max(matrix[row].end, (int)column);

 }

-void MatchMatrix::unset(size_t row, size_t column) throw (IndexOutOfBounds, InvalidMatchMatrix) {

+void MatchMatrix::unset(size_t row, size_t column) /*throw (IndexOutOfBounds, InvalidMatchMatrix)*/ {

 	// is given row valid?

 	if (row>=rows) {

 		throw IndexOutOfBounds();

@@ -50,9 +50,9 @@ public:

 	~MatchMatrix();

 	/** Set specified entry to 1. */

-	void set(std::size_t row, std::size_t column) throw (IndexOutOfBounds, InvalidMatchMatrix);

+	void set(std::size_t row, std::size_t column) /*throw (IndexOutOfBounds, InvalidMatchMatrix)*/;

 	/** Set specified entry to 0. */

-	void unset(std::size_t row, std::size_t column) throw (IndexOutOfBounds, InvalidMatchMatrix);

+	void unset(std::size_t row, std::size_t column) /*throw (IndexOutOfBounds, InvalidMatchMatrix)*/;

 	/** Returns number of rows. */

 	std::size_t getRows();

@@ -18,7 +18,8 @@ CharacterAlphabet::CharacterAlphabet(const Alphabet& alphabet) : masses(256, -1.

 	}

 }

-Alphabet::mass_type CharacterAlphabet::getMass(const char& name) const throw (UnknownCharacterException) {

+Alphabet::mass_type CharacterAlphabet::getMass(const char& name) const 

+    /*throw (UnknownCharacterException)*/ {

 	if (name<0) throw UnknownCharacterException();

 	Alphabet::mass_type result = masses[(size_t)name];

 	if (result<0.0) throw UnknownCharacterException();

@@ -15,7 +15,8 @@

 class CharacterAlphabet {

 	public:

 		CharacterAlphabet(const ims::Alphabet& alphabet);

-		ims::Alphabet::mass_type getMass(const char& name) const throw (ims::UnknownCharacterException);

+		ims::Alphabet::mass_type getMass(const char& name) const 

+		    /*throw (ims::UnknownCharacterException)*/;

 	private:

 		std::vector<ims::Alphabet::mass_type> masses;

 };

@@ -21,7 +21,7 @@ ComposedElement::ComposedElement(const container& elements,

 ComposedElement::ComposedElement(const name_type& sequence, const Alphabet& alphabet, unsigned sequence_type) 

-		throw (UnknownCharacterException) {

+		/*throw (UnknownCharacterException)*/ {

 	this->setSequence(sequence);

 	std::auto_ptr<sequence_parser_type> parser;

 	if (sequence_type == TEX_NOTATION_MOLECULE_SEQUENCE_TYPE) {

@@ -114,7 +114,7 @@ ComposedElement::getElementAbundance(const name_type& name) const {

 void ComposedElement::initializeElements(const Alphabet& alphabet, std::auto_ptr<sequence_parser_type> parser)

-			throw (UnknownCharacterException) {

+			/*throw (UnknownCharacterException)*/ {

 	typedef sequence_parser_type::container parser_container;

 	// parses sequence

@@ -92,7 +92,7 @@ class ComposedElement : public Element {

 		 */

 		ComposedElement(const name_type& sequence, const Alphabet& alphabet,

 				unsigned sequence_type = DEFAULT_MOLECULE_SEQUENCE_TYPE)

-			throw (UnknownCharacterException);

+			/*throw (UnknownCharacterException)*/;

 		/**

 		 * Constructor with a given elemental composition @c decomposition that contains abundances of 

@@ -202,7 +202,7 @@ class ComposedElement : public Element {

 		 * @throws UnknownCharacterException if any error happens while parsing	molecule's sequence.

 		 */

 		void initializeElements(const Alphabet& alphabet, std::auto_ptr<sequence_parser_type> parser)

-			throw (UnknownCharacterException);

+			/*throw (UnknownCharacterException)*/;

 		void initializeElements(const std::vector<unsigned int>& decomposition, 

 			const Alphabet& alphabet);

@@ -54,7 +54,7 @@ void DistributedAlphabet::push_back(const name_type& name, mass_type value,

 }

-void DistributedAlphabet::load(const std::string& name) throw (IOException) {

+void DistributedAlphabet::load(const std::string& name) /*throw (IOException)*/ {

 	// here instead of explicit calling of corresponding parser 

 	// implemntation constructor

 	// one should use factory later on, something like this:

@@ -65,7 +65,7 @@ void DistributedAlphabet::load(const std::string& name) throw (IOException) {

 void DistributedAlphabet::load(const std::string& name, 

-					AlphabetParser<>* parser) throw (IOException) {

+					AlphabetParser<>* parser) /*throw (IOException)*/ {

 	Alphabet::load(name, parser);

 	DistributedAlphabetParser<> *castedParser = 

 					dynamic_cast< DistributedAlphabetParser<>* >(parser);

@@ -100,14 +100,14 @@ class DistributedAlphabet : public Alphabet,

 		/**

 		 * @see Alphabet<RealType, ScaledType>::load(const std::string& name)

 		 */

-		virtual void load(const std::string& name) throw (IOException);

+		virtual void load(const std::string& name) /*throw (IOException)*/;

 		/**

 		 * @see Alphabet<RealType, ScaledType>::load(const std::string& name, 

 		 * 											AlphabetParser<>* parser)

 		 */

 		virtual void load(const std::string& name, AlphabetParser<>* parser) 

-														throw (IOException);

+														/*throw (IOException)*/;

 		virtual ~DistributedAlphabet() {}

 	private: