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removed dynamic exception specifications that are deprecated, regarding issue #14

David Rasp authored on 02/04/2019 15:32:12
Showing21 changed files

... ...
@@ -23,7 +23,7 @@ Alphabet::mass_type Alphabet::getMass(size_type index) const {
23 23
 
24 24
 
25 25
 Alphabet::mass_type Alphabet::getMass(const name_type& name) const
26
-										throw (UnknownCharacterException) {
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+										/*throw (UnknownCharacterException)*/ {
27 27
 	return getElement(name).getMass();
28 28
 }
29 29
 
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@@ -36,7 +36,7 @@ bool Alphabet::hasName(const name_type& name) const {
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37 37
 
38 38
 const Alphabet::element_type& Alphabet::getElement(const name_type& name) const
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-											throw (UnknownCharacterException) {
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+											/*throw (UnknownCharacterException)*/ {
40 40
 	const_iterator cit = elements.begin();
41 41
 	for (; cit != elements.end(); ++cit) {
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 		if (cit->getName() == name) {
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@@ -81,13 +81,13 @@ void Alphabet::sortByValues() {
81 81
 }
82 82
 
83 83
 
84
-void Alphabet::load(const std::string& fname) throw (IOException) {
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+void Alphabet::load(const std::string& fname) /*throw (IOException)*/ {
85 85
 	this->load(fname, new AlphabetTextParser);
86 86
 }
87 87
 
88 88
 
89 89
 void Alphabet::load(const std::string& fname, AlphabetParser<>* parser)
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-														throw (IOException) {
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+														/*throw (IOException)*/ {
91 91
 	parser->load(fname);
92 92
 	this->clear();
93 93
 	for (AlphabetParser<>::ContainerType::const_iterator pos =
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@@ -110,7 +110,7 @@ class Alphabet {
110 110
 		 * 			throws @c UnknownCharacterException.
111 111
 		 */
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 		const element_type& getElement(const name_type& name) const
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-									throw (UnknownCharacterException);
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+									/*throw (UnknownCharacterException)*/;
114 114
 
115 115
 		/**
116 116
 		 * Gets the symbol of the element with an index @c index in alphabet.
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@@ -130,7 +130,7 @@ class Alphabet {
130 130
 		 * @see getMass(size_type index)
131 131
 		 */
132 132
 		mass_type getMass(const name_type& name) const
133
-									throw (UnknownCharacterException);
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+									/*throw (UnknownCharacterException)*/;
134 134
 
135 135
 		/**
136 136
 		 * Gets mass of the element with an index @index in alphabet.
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@@ -217,7 +217,7 @@ class Alphabet {
217 217
 		 * @param fname The file name to be loaded.
218 218
 		 * @see load(const std::string& fname, AlphabetParser<>* parser)
219 219
 		 */
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-		virtual void load(const std::string& fname) throw (IOException);
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+		virtual void load(const std::string& fname) /*throw (IOException)*/;
221 221
 
222 222
 
223 223
 		/**
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@@ -231,7 +231,7 @@ class Alphabet {
231 231
 		 * @see AlphabetParser
232 232
 		 */
233 233
 		virtual void load(const std::string& fname, AlphabetParser<>* parser)
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-			throw (IOException);
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+			/*throw (IOException)*/;
235 235
 
236 236
 
237 237
 		/**
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@@ -20,7 +20,7 @@ class AbstractMoleculeSequenceParser {
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 		AbstractMoleculeSequenceParser(): multiplicator(1) {}
21 21
 								
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 		virtual void parse(const sequence_type& sequence) 
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-						throw (UnknownCharacterException) = 0;
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+						/*throw (UnknownCharacterException)*/ = 0;
24 24
 
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 		const container& getElements() const { return elements; }
26 26
 		
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@@ -34,7 +34,7 @@ class AlphabetParser {
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 		 * 
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 		 * @param fname The name of the input source.
36 36
 		 */
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-		void load(const std::string& fname) throw (IOException);
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+		void load(const std::string& fname) /*throw (IOException)*/;
38 38
 		
39 39
 		/**
40 40
 		 * Gets the data that was loaded. 
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@@ -55,7 +55,7 @@ class AlphabetParser {
55 55
 };
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57 57
 template <typename AlphabetElementType, typename Container, typename InputSource>
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-void AlphabetParser<AlphabetElementType, Container, InputSource>::load(const std::string& fname) throw (IOException) {
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+void AlphabetParser<AlphabetElementType, Container, InputSource>::load(const std::string& fname) /*throw (IOException)*/ {
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 	std::ifstream ifs(fname.c_str());
60 60
 	if (!ifs) {
61 61
 		throw IOException("unable to open alphabet resource file: " + fname + "!");
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@@ -12,12 +12,12 @@
12 12
 namespace ims {
13 13
 
14 14
 KeggLigandCompoundsParser::KeggLigandCompoundsParser(const sequence_type& 
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-								sequence) throw (UnknownCharacterException) {
15
+								sequence) /*throw (UnknownCharacterException)*/ {
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 	this->parse(sequence);
17 17
 }
18 18
 
19 19
 void KeggLigandCompoundsParser::parse(const sequence_type& sequence) 
20
-											throw (UnknownCharacterException) {
20
+											/*throw (UnknownCharacterException)*/ {
21 21
 	
22 22
 	const sequence_type delimiters(" \t"), rest_header(".R*+(");
23 23
 	
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@@ -14,10 +14,10 @@ class KeggLigandCompoundsParser : public AbstractMoleculeSequenceParser {
14 14
 		KeggLigandCompoundsParser() : AbstractMoleculeSequenceParser() {}
15 15
 		
16 16
 		KeggLigandCompoundsParser(const sequence_type& sequence) 
17
-									throw (UnknownCharacterException);
17
+									/*throw (UnknownCharacterException)*/;
18 18
 			
19 19
 		virtual void parse(const sequence_type& sequence) 
20
-									throw (UnknownCharacterException);
20
+									/*throw (UnknownCharacterException)*/;
21 21
 		
22 22
 		virtual ~KeggLigandCompoundsParser() {}
23 23
 };
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@@ -21,7 +21,7 @@ class MassesParser {
21 21
 		 * 
22 22
 		 * @param fname The name of the input source.
23 23
 		 */
24
-		void load(const std::string& fname) throw (IOException);
24
+		void load(const std::string& fname) /*throw (IOException)*/;
25 25
 		
26 26
 		/**
27 27
 		 * Gets loaded data.
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@@ -42,7 +42,7 @@ class MassesParser {
42 42
 };
43 43
 
44 44
 template <typename MassesType, typename InputSource>
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-void MassesParser<MassesType, InputSource>::load(const std::string& fname) throw (IOException) {
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+void MassesParser<MassesType, InputSource>::load(const std::string& fname) /*throw (IOException)*/ {
46 46
 	std::ifstream ifs(fname.c_str());
47 47
 	if (!ifs) {
48 48
 		throw IOException("unable to open resource file with masses: " + fname + "!");
... ...
@@ -11,7 +11,7 @@
11 11
 namespace ims {
12 12
 
13 13
 MoleculeIonChargeModificationParser::MoleculeIonChargeModificationParser(
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-					const ion_name_type& sequence) throw (UnknownCharacterException) {
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+					const ion_name_type& sequence) /*throw (UnknownCharacterException)*/ {
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 	parse(sequence);
16 16
 }
17 17
 
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@@ -26,7 +26,8 @@ operator =(const MoleculeIonChargeModificationParser& parser) {
26 26
 }
27 27
 
28 28
 
29
-void MoleculeIonChargeModificationParser::parse(const ion_name_type& sequence) throw (UnknownCharacterException) {
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+void MoleculeIonChargeModificationParser::parse(const ion_name_type& sequence) 
30
+/*throw (UnknownCharacterException)*/ {
30 31
 	
31 32
 	this->clear();
32 33
 	
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@@ -36,7 +36,8 @@ class MoleculeIonChargeModificationParser {
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 			mass_factor(1),		
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 			charge(1) {}
38 38
 		
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-		MoleculeIonChargeModificationParser(const ion_name_type& sequence) throw (UnknownCharacterException);
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+		MoleculeIonChargeModificationParser(const ion_name_type& sequence) 
40
+		    /*throw (UnknownCharacterException)*/;
40 41
 		
41 42
 		MoleculeIonChargeModificationParser(const MoleculeIonChargeModificationParser& parser) :
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 			mass_factor(parser.mass_factor),
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@@ -45,7 +46,7 @@ class MoleculeIonChargeModificationParser {
45 46
 		
46 47
 		MoleculeIonChargeModificationParser& operator =(const MoleculeIonChargeModificationParser& parser);
47 48
 		
48
-		void parse(const ion_name_type& sequence) throw (UnknownCharacterException);
49
+		void parse(const ion_name_type& sequence) /*throw (UnknownCharacterException)*/;
49 50
 
50 51
 		mass_factor_type getMassFactor() const { return mass_factor; }		
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 		charge_type getCharge() const { return charge; }
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@@ -12,12 +12,12 @@
12 12
 namespace ims {
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14 14
 MoleculeSequenceParser::MoleculeSequenceParser(const sequence_type& 
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-								sequence) throw (UnknownCharacterException) {
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+								sequence) /*throw (UnknownCharacterException)*/ {
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 	this->parse(sequence);
17 17
 }
18 18
 
19 19
 void MoleculeSequenceParser::parse(const sequence_type& sequence) 
20
-											throw (UnknownCharacterException) {
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+											/*throw (UnknownCharacterException)*/ {
21 21
 	
22 22
 	const sequence_type delimiters(" \t");
23 23
 	
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@@ -55,7 +55,7 @@ void MoleculeSequenceParser::parse(const sequence_type& sequence)
55 55
 
56 56
 MoleculeSequenceParser::container 
57 57
 MoleculeSequenceParser::parseElements(const sequence_type& sequence)
58
-		 throw (UnknownCharacterException) {
58
+		 /*throw (UnknownCharacterException)*/ {
59 59
 	
60 60
 	container elements;
61 61
 	
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@@ -14,17 +14,17 @@ class MoleculeSequenceParser : public AbstractMoleculeSequenceParser {
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 		MoleculeSequenceParser() : AbstractMoleculeSequenceParser() {}
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 		MoleculeSequenceParser(const sequence_type& sequence) 
17
-									throw (UnknownCharacterException);
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+									/*throw (UnknownCharacterException)*/;
18 18
 			
19 19
 		virtual void parse(const sequence_type& sequence) 
20
-									throw (UnknownCharacterException);
20
+									/*throw (UnknownCharacterException)*/;
21 21
 									
22 22
 		virtual ~MoleculeSequenceParser() {}
23 23
 	
24 24
 	private:
25 25
 		
26 26
 		container parseElements(const sequence_type& sequence)
27
-									throw (UnknownCharacterException);
27
+									/*throw (UnknownCharacterException)*/;
28 28
 		
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 		void addElement(const sequence_type& name, number_type amount, 
30 30
 											container& elements);
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@@ -12,12 +12,12 @@
12 12
 namespace ims {
13 13
 
14 14
 StandardMoleculeSequenceParser::StandardMoleculeSequenceParser(const sequence_type& 
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-								sequence) throw (UnknownCharacterException) {
15
+								sequence) /*throw (UnknownCharacterException)*/ {
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 	this->parse(sequence);
17 17
 }
18 18
 
19 19
 void StandardMoleculeSequenceParser::parse(const sequence_type& sequence) 
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-											throw (UnknownCharacterException) {
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+											/*throw (UnknownCharacterException)*/ {
21 21
 	
22 22
 	const sequence_type delimiters(" \t");
23 23
 	
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@@ -55,7 +55,7 @@ void StandardMoleculeSequenceParser::parse(const sequence_type& sequence)
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56 56
 StandardMoleculeSequenceParser::container 
57 57
 StandardMoleculeSequenceParser::parseElements(const sequence_type& sequence)
58
-		 throw (UnknownCharacterException) {
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+		 /*throw (UnknownCharacterException)*/ {
59 59
 	
60 60
 	container elements;
61 61
 	
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@@ -17,17 +17,17 @@ class StandardMoleculeSequenceParser : public AbstractMoleculeSequenceParser {
17 17
 		StandardMoleculeSequenceParser() : AbstractMoleculeSequenceParser() {}
18 18
 		
19 19
 		StandardMoleculeSequenceParser(const sequence_type& sequence) 
20
-									throw (UnknownCharacterException);
20
+									/*throw (UnknownCharacterException)*/;
21 21
 			
22 22
 		virtual void parse(const sequence_type& sequence) 
23
-									throw (UnknownCharacterException);
23
+									/*throw (UnknownCharacterException)*/;
24 24
 									
25 25
 		virtual ~StandardMoleculeSequenceParser() {}
26 26
 	
27 27
 	private:
28 28
 		
29 29
 		container parseElements(const sequence_type& sequence)
30
-									throw (UnknownCharacterException);
30
+									/*throw (UnknownCharacterException)*/;
31 31
 		
32 32
 		void addElement(const sequence_type& name, number_type amount, 
33 33
 											container& elements);
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@@ -18,7 +18,7 @@ MatchMatrix::~MatchMatrix() {
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 	delete [] matrix;
19 19
 }
20 20
 
21
-void MatchMatrix::set(size_t row, size_t column) throw (IndexOutOfBounds, InvalidMatchMatrix) {
21
+void MatchMatrix::set(size_t row, size_t column) /*throw (IndexOutOfBounds, InvalidMatchMatrix)*/ {
22 22
 	// TODO: This function does not enforce staircase property in all cases
23 23
 	// for example:
24 24
 	// mm.set(6,2);
... ...
@@ -44,7 +44,7 @@ void MatchMatrix::set(size_t row, size_t column) throw (IndexOutOfBounds, Invali
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 	matrix[row].end=std::max(matrix[row].end, (int)column);
45 45
 }
46 46
 
47
-void MatchMatrix::unset(size_t row, size_t column) throw (IndexOutOfBounds, InvalidMatchMatrix) {
47
+void MatchMatrix::unset(size_t row, size_t column) /*throw (IndexOutOfBounds, InvalidMatchMatrix)*/ {
48 48
 	// is given row valid?
49 49
 	if (row>=rows) {
50 50
 		throw IndexOutOfBounds();
... ...
@@ -50,9 +50,9 @@ public:
50 50
 	~MatchMatrix();
51 51
 
52 52
 	/** Set specified entry to 1. */
53
-	void set(std::size_t row, std::size_t column) throw (IndexOutOfBounds, InvalidMatchMatrix);
53
+	void set(std::size_t row, std::size_t column) /*throw (IndexOutOfBounds, InvalidMatchMatrix)*/;
54 54
 	/** Set specified entry to 0. */
55
-	void unset(std::size_t row, std::size_t column) throw (IndexOutOfBounds, InvalidMatchMatrix);
55
+	void unset(std::size_t row, std::size_t column) /*throw (IndexOutOfBounds, InvalidMatchMatrix)*/;
56 56
 
57 57
 	/** Returns number of rows. */
58 58
 	std::size_t getRows();
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@@ -18,7 +18,8 @@ CharacterAlphabet::CharacterAlphabet(const Alphabet& alphabet) : masses(256, -1.
18 18
 	}
19 19
 }
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21
-Alphabet::mass_type CharacterAlphabet::getMass(const char& name) const throw (UnknownCharacterException) {
21
+Alphabet::mass_type CharacterAlphabet::getMass(const char& name) const 
22
+    /*throw (UnknownCharacterException)*/ {
22 23
 	if (name<0) throw UnknownCharacterException();
23 24
 	Alphabet::mass_type result = masses[(size_t)name];
24 25
 	if (result<0.0) throw UnknownCharacterException();
... ...
@@ -15,7 +15,8 @@
15 15
 class CharacterAlphabet {
16 16
 	public:
17 17
 		CharacterAlphabet(const ims::Alphabet& alphabet);
18
-		ims::Alphabet::mass_type getMass(const char& name) const throw (ims::UnknownCharacterException);
18
+		ims::Alphabet::mass_type getMass(const char& name) const 
19
+		    /*throw (ims::UnknownCharacterException)*/;
19 20
 	private:
20 21
 		std::vector<ims::Alphabet::mass_type> masses;
21 22
 };
... ...
@@ -21,7 +21,7 @@ ComposedElement::ComposedElement(const container& elements,
21 21
 
22 22
 
23 23
 ComposedElement::ComposedElement(const name_type& sequence, const Alphabet& alphabet, unsigned sequence_type) 
24
-		throw (UnknownCharacterException) {
24
+		/*throw (UnknownCharacterException)*/ {
25 25
 	this->setSequence(sequence);
26 26
 	std::auto_ptr<sequence_parser_type> parser;
27 27
 	if (sequence_type == TEX_NOTATION_MOLECULE_SEQUENCE_TYPE) {
... ...
@@ -114,7 +114,7 @@ ComposedElement::getElementAbundance(const name_type& name) const {
114 114
 
115 115
 
116 116
 void ComposedElement::initializeElements(const Alphabet& alphabet, std::auto_ptr<sequence_parser_type> parser)
117
-			throw (UnknownCharacterException) {
117
+			/*throw (UnknownCharacterException)*/ {
118 118
 
119 119
 	typedef sequence_parser_type::container parser_container;
120 120
 	// parses sequence
... ...
@@ -92,7 +92,7 @@ class ComposedElement : public Element {
92 92
 		 */
93 93
 		ComposedElement(const name_type& sequence, const Alphabet& alphabet,
94 94
 				unsigned sequence_type = DEFAULT_MOLECULE_SEQUENCE_TYPE)
95
-			throw (UnknownCharacterException);
95
+			/*throw (UnknownCharacterException)*/;
96 96
 		
97 97
 		/**
98 98
 		 * Constructor with a given elemental composition @c decomposition that contains abundances of 
... ...
@@ -202,7 +202,7 @@ class ComposedElement : public Element {
202 202
 		 * @throws UnknownCharacterException if any error happens while parsing	molecule's sequence.
203 203
 		 */
204 204
 		void initializeElements(const Alphabet& alphabet, std::auto_ptr<sequence_parser_type> parser)
205
-			throw (UnknownCharacterException);
205
+			/*throw (UnknownCharacterException)*/;
206 206
 		
207 207
 		void initializeElements(const std::vector<unsigned int>& decomposition, 
208 208
 			const Alphabet& alphabet);
... ...
@@ -54,7 +54,7 @@ void DistributedAlphabet::push_back(const name_type& name, mass_type value,
54 54
 }
55 55
 
56 56
 
57
-void DistributedAlphabet::load(const std::string& name) throw (IOException) {
57
+void DistributedAlphabet::load(const std::string& name) /*throw (IOException)*/ {
58 58
 	// here instead of explicit calling of corresponding parser 
59 59
 	// implemntation constructor
60 60
 	// one should use factory later on, something like this:
... ...
@@ -65,7 +65,7 @@ void DistributedAlphabet::load(const std::string& name) throw (IOException) {
65 65
 
66 66
 
67 67
 void DistributedAlphabet::load(const std::string& name, 
68
-					AlphabetParser<>* parser) throw (IOException) {
68
+					AlphabetParser<>* parser) /*throw (IOException)*/ {
69 69
 	Alphabet::load(name, parser);
70 70
 	DistributedAlphabetParser<> *castedParser = 
71 71
 					dynamic_cast< DistributedAlphabetParser<>* >(parser);
... ...
@@ -100,14 +100,14 @@ class DistributedAlphabet : public Alphabet,
100 100
 		/**
101 101
 		 * @see Alphabet<RealType, ScaledType>::load(const std::string& name)
102 102
 		 */
103
-		virtual void load(const std::string& name) throw (IOException);
103
+		virtual void load(const std::string& name) /*throw (IOException)*/;
104 104
 
105 105
 		/**
106 106
 		 * @see Alphabet<RealType, ScaledType>::load(const std::string& name, 
107 107
 		 * 											AlphabetParser<>* parser)
108 108
 		 */
109 109
 		virtual void load(const std::string& name, AlphabetParser<>* parser) 
110
-														throw (IOException);
110
+														/*throw (IOException)*/;
111 111
 
112 112
 		virtual ~DistributedAlphabet() {}
113 113
 	private: