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EmpiricalFormula.h
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35 #ifndef OPENMS_CHEMISTRY_EMPIRICALFORMULA_H
36 #define OPENMS_CHEMISTRY_EMPIRICALFORMULA_H
37 
38 #include <iosfwd>
39 #include <vector>
40 #include <map>
41 
42 #include <OpenMS/CONCEPT/Types.h>
43 
44 namespace OpenMS
45 {
46  class String;
47  class Element;
48  class ElementDB;
49  class IsotopeDistribution;
50 
79  class OPENMS_DLLAPI EmpiricalFormula
80  {
81 
82 protected:
84  typedef std::map<const Element*, SignedSize> MapType_;
85 
86 public:
90  typedef MapType_::const_iterator ConstIterator;
92  typedef MapType_::const_iterator const_iterator;
94 
100 
103 
109  explicit EmpiricalFormula(const String& rhs);
110 
112  EmpiricalFormula(SignedSize number, const Element* element, SignedSize charge = 0);
113 
115  virtual ~EmpiricalFormula();
117 
121  double getMonoWeight() const;
123 
125  double getAverageWeight() const;
126 
134  IsotopeDistribution getIsotopeDistribution(UInt max_depth) const;
135 
137  SignedSize getNumberOf(const Element* element) const;
138 
140  SignedSize getNumberOfAtoms() const;
141 
143  SignedSize getCharge() const;
144 
146  void setCharge(SignedSize charge);
147 
149  String toString() const;
151 
155  EmpiricalFormula& operator=(const EmpiricalFormula& rhs);
157 
159  EmpiricalFormula& operator+=(const EmpiricalFormula& rhs);
160 
162  EmpiricalFormula operator*(const SignedSize& times) const;
163 
165  EmpiricalFormula operator+(const EmpiricalFormula& rhs) const;
166 
168  EmpiricalFormula& operator-=(const EmpiricalFormula& rhs);
169 
171  EmpiricalFormula operator-(const EmpiricalFormula& rhs) const;
172 
174 
178  bool isEmpty() const;
180 
182  bool isCharged() const;
183 
185  bool hasElement(const Element* element) const;
186 
188  bool contains(const EmpiricalFormula& ef);
189 
191  bool operator==(const EmpiricalFormula& rhs) const;
192 
194  bool operator!=(const EmpiricalFormula& rhs) const;
195 
197 
199  friend OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const EmpiricalFormula& formula);
200 
204  inline ConstIterator begin() const { return formula_.begin(); }
205 
206  inline ConstIterator end() const { return formula_.end(); }
208 
209 protected:
210 
212  void removeZeroedElements_();
213 
215 
217 
218  SignedSize parseFormula_(std::map<const Element*, SignedSize>& ef, const String& formula) const;
219 
220  };
221 
222  OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const EmpiricalFormula& formula);
223 
224 } // namespace OpenMS
225 #endif
A more convenient string class.
Definition: String.h:57
SignedSize charge_
Definition: EmpiricalFormula.h:216
Isotope distribution class.
Definition: IsotopeDistribution.h:61
ptrdiff_t SignedSize
Signed Size type e.g. used as pointer difference.
Definition: Types.h:128
MapType_::const_iterator ConstIterator
Iterators.
Definition: EmpiricalFormula.h:91
MapType_ formula_
Definition: EmpiricalFormula.h:214
Representation of an empirical formula.
Definition: EmpiricalFormula.h:79
ConstIterator end() const
Definition: EmpiricalFormula.h:206
Representation of an element.
Definition: Element.h:54
MapType_::const_iterator const_iterator
Definition: EmpiricalFormula.h:92
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)
DPosition< D, TCoordinateType > operator*(DPosition< D, TCoordinateType > position, typename DPosition< D, TCoordinateType >::CoordinateType scalar)
Scalar multiplication (a bit inefficient)
Definition: DPosition.h:421
std::map< const Element *, SignedSize > MapType_
Internal typedef for the used map type.
Definition: EmpiricalFormula.h:84
ConstIterator begin() const
Definition: EmpiricalFormula.h:204
String toString(T i)
toString functions (single argument)
Definition: StringUtils.h:68

OpenMS / TOPP release 2.0.0 Documentation generated on Wed Mar 30 2016 16:18:38 using doxygen 1.8.5