OpenMS  3.0.0
IMSAlphabet.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Anton Pervukhin <Anton.Pervukhin@CeBiTec.Uni-Bielefeld.DE> $
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34 //
35 
36 #pragma once
37 
38 #include <vector>
39 #include <string>
40 #include <iosfwd>
41 
43 
46 
47 namespace OpenMS
48 {
49 
50  namespace ims
51  {
52 
81  class OPENMS_DLLAPI IMSAlphabet
82  {
83 
84 public:
88  typedef std::vector<element_type> container;
89  typedef container::size_type size_type;
90  typedef container::iterator iterator;
91  typedef container::const_iterator const_iterator;
92  typedef std::vector<name_type> name_container;
93  typedef name_container::iterator name_iterator;
94  typedef name_container::const_iterator const_name_iterator;
95  typedef std::vector<mass_type> mass_container;
96  typedef mass_container::iterator mass_iterator;
97  typedef mass_container::const_iterator const_mass_iterator;
98  typedef std::vector<mass_type> masses_type;
99 
104 
105 
111  explicit IMSAlphabet(const container & elements) :
112  elements_(elements)
113  {}
114 
115 
121  IMSAlphabet(const IMSAlphabet & alphabet) :
122  elements_(alphabet.elements_)
123  {}
124 
130  size_type size() const
131  {
132  return elements_.size();
133  }
134 
142  const element_type & getElement(size_type index) const
143  {
144  return elements_[index];
145  }
146 
157  void setElement(const name_type & name, mass_type mass, bool forced = false);
158 
165  bool erase(const name_type & name);
166 
175  const element_type & getElement(const name_type & name) const;
176 
183  const name_type & getName(size_type index) const;
184 
194  mass_type getMass(const name_type & name) const;
195 
203  mass_type getMass(size_type index) const;
204 
211  masses_type getMasses(size_type isotope_index = 0) const;
212 
218  masses_type getAverageMasses() const;
219 
227  bool hasName(const name_type & name) const;
228 
238  void push_back(const name_type & name, mass_type value)
239  {
240  push_back(element_type(name, value));
241  }
242 
248  void push_back(const element_type & element)
249  {
250  elements_.push_back(element);
251  }
252 
256  void clear()
257  {
258  elements_.clear();
259  }
260 
266  virtual void sortByNames();
267 
268 
274  virtual void sortByValues();
275 
276 
286  virtual void load(const std::string & fname);
287 
288 
300  virtual void load(const std::string & fname, IMSAlphabetParser<> & parser);
301 
302 
306  virtual ~IMSAlphabet() {}
307 
308 private:
313 
317  class OPENMS_DLLAPI MassSortingCriteria_
318  {
319 public:
320  bool operator()(const element_type & el1,
321  const element_type & el2) const
322  {
323  return el1.getMass() < el2.getMass();
324  }
325 
326  };
327 
328  };
329 
336  OPENMS_DLLAPI std::ostream & operator<<(std::ostream & os, const IMSAlphabet & alphabet);
337 
338  } // namespace ims
339 
340 } // namespace OpenMS
341 
OpenMS::ims::IMSAlphabet::const_mass_iterator
mass_container::const_iterator const_mass_iterator
Definition: IMSAlphabet.h:97
OpenMS::ims::IMSAlphabet::push_back
void push_back(const name_type &name, mass_type value)
Definition: IMSAlphabet.h:238
OpenMS::ims::IMSAlphabet::element_type
IMSElement element_type
Definition: IMSAlphabet.h:85
double
OpenMS::ims::IMSAlphabet::mass_iterator
mass_container::iterator mass_iterator
Definition: IMSAlphabet.h:96
OpenMS::ims::IMSAlphabet::masses_type
std::vector< mass_type > masses_type
Definition: IMSAlphabet.h:98
OpenMS::ims::IMSAlphabet::mass_container
std::vector< mass_type > mass_container
Definition: IMSAlphabet.h:95
OpenMS::ims::IMSAlphabet::const_name_iterator
name_container::const_iterator const_name_iterator
Definition: IMSAlphabet.h:94
OpenMS::ims::IMSAlphabet::name_iterator
name_container::iterator name_iterator
Definition: IMSAlphabet.h:93
OpenMS::ims::IMSElement::name_type
std::string name_type
Type of element's name.
Definition: IMSElement.h:62
OpenMS::ims::IMSAlphabet::iterator
container::iterator iterator
Definition: IMSAlphabet.h:90
IMSElement.h
OpenMS::ims::IMSAlphabet::IMSAlphabet
IMSAlphabet()
Definition: IMSAlphabet.h:103
OpenMS::ims::IMSAlphabet::mass_type
element_type::mass_type mass_type
Definition: IMSAlphabet.h:86
OpenMS::ims::IMSAlphabet
Holds an indexed list of bio-chemical elements.
Definition: IMSAlphabet.h:81
OpenMS::ims::IMSAlphabet::IMSAlphabet
IMSAlphabet(const IMSAlphabet &alphabet)
Definition: IMSAlphabet.h:121
OpenMS::ims::IMSAlphabet::const_iterator
container::const_iterator const_iterator
Definition: IMSAlphabet.h:91
OpenMS::ims::IMSAlphabet::container
std::vector< element_type > container
Definition: IMSAlphabet.h:88
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
Exception.h
OpenMS::ims::IMSAlphabet::push_back
void push_back(const element_type &element)
Definition: IMSAlphabet.h:248
OpenMS::ims::IMSAlphabet::getElement
const element_type & getElement(size_type index) const
Definition: IMSAlphabet.h:142
IMSAlphabetParser.h
OpenMS::ims::IMSAlphabet::name_container
std::vector< name_type > name_container
Definition: IMSAlphabet.h:92
OpenMS::ims::IMSAlphabet::size
size_type size() const
Definition: IMSAlphabet.h:130
OpenMS::ims::IMSElement
Represents a chemical atom with name and isotope distribution.
Definition: IMSElement.h:58
OpenMS::ims::IMSAlphabet::MassSortingCriteria_::operator()
bool operator()(const element_type &el1, const element_type &el2) const
Definition: IMSAlphabet.h:320
OpenMS::ims::IMSAlphabet::clear
void clear()
Definition: IMSAlphabet.h:256
OpenMS::ims::IMSAlphabet::MassSortingCriteria_
Private class-functor to sort out elements in mass ascending order.
Definition: IMSAlphabet.h:317
OpenMS::ims::operator<<
std::ostream & operator<<(std::ostream &os, const IMSAlphabet &alphabet)
OpenMS::ims::IMSElement::getMass
mass_type getMass(size_type index=0) const
Definition: IMSElement.h:172
OpenMS::ims::IMSAlphabetParser<>
OpenMS::ims::IMSAlphabet::elements_
container elements_
Definition: IMSAlphabet.h:312
OpenMS::ims::IMSAlphabet::size_type
container::size_type size_type
Definition: IMSAlphabet.h:89
OpenMS::ims::IMSAlphabet::IMSAlphabet
IMSAlphabet(const container &elements)
Definition: IMSAlphabet.h:111
OpenMS::ims::IMSAlphabet::name_type
element_type::name_type name_type
Definition: IMSAlphabet.h:87
OpenMS::ims::IMSAlphabet::~IMSAlphabet
virtual ~IMSAlphabet()
Definition: IMSAlphabet.h:306