OpenMS  2.4.0
MSChromatogram.h
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34 
35 #pragma once
36 
44 
45 namespace OpenMS
46 {
47  class ChromatogramPeak;
48 
54  class OPENMS_DLLAPI MSChromatogram :
55  private std::vector<ChromatogramPeak>,
56  public RangeManager<1>,
58  {
59 
60 public:
61 
63  struct OPENMS_DLLAPI MZLess :
64  public std::binary_function<MSChromatogram, MSChromatogram, bool>
65  {
66  bool operator()(const MSChromatogram& a, const MSChromatogram& b) const;
67  };
68 
76  typedef std::vector<PeakType> ContainerType;
79  typedef std::vector<FloatDataArray> FloatDataArrays;
82  typedef std::vector<StringDataArray> StringDataArrays;
85  typedef std::vector<IntegerDataArray> IntegerDataArrays;
87 
89 
90  typedef typename ContainerType::iterator Iterator;
93  typedef typename ContainerType::const_iterator ConstIterator;
95  typedef typename ContainerType::reverse_iterator ReverseIterator;
97  typedef typename ContainerType::const_reverse_iterator ConstReverseIterator;
99 
101 
102  using ContainerType::operator[];
103  using ContainerType::begin;
104  using ContainerType::rbegin;
105  using ContainerType::end;
106  using ContainerType::rend;
107  using ContainerType::resize;
108  using ContainerType::size;
109  using ContainerType::push_back;
110  using ContainerType::pop_back;
111  using ContainerType::empty;
112  using ContainerType::front;
113  using ContainerType::back;
114  using ContainerType::reserve;
115  using ContainerType::insert;
116  using ContainerType::erase;
117  using ContainerType::swap;
118 
119  using typename ContainerType::iterator;
120  using typename ContainerType::const_iterator;
121  using typename ContainerType::size_type;
122  using typename ContainerType::value_type;
123  using typename ContainerType::reference;
124  using typename ContainerType::const_reference;
125  using typename ContainerType::pointer;
126  using typename ContainerType::difference_type;
128 
131  ContainerType(),
132  RangeManager<1>(),
134  name_(),
135  float_data_arrays_(),
136  string_data_arrays_(),
137  integer_data_arrays_()
138  {}
139 
142  ContainerType(source),
143  RangeManager<1>(source),
144  ChromatogramSettings(source),
145  name_(source.name_),
146  float_data_arrays_(source.float_data_arrays_),
147  string_data_arrays_(source.string_data_arrays_),
148  integer_data_arrays_(source.integer_data_arrays_)
149  {}
150 
152  ~MSChromatogram() override
153  {}
154 
156  MSChromatogram& operator=(const MSChromatogram& source);
157 
159  bool operator==(const MSChromatogram& rhs) const;
160 
162  bool operator!=(const MSChromatogram& rhs) const
163  {
164  return !(operator==(rhs));
165  }
166 
167  // Docu in base class (RangeManager)
168  void updateRanges() override
169  {
170  this->clearRanges();
171  updateRanges_(ContainerType::begin(), ContainerType::end());
172  }
173 
177  const String& getName() const;
178 
180  void setName(const String& name);
181 
183 
185  double getMZ() const;
186 
199  const FloatDataArrays& getFloatDataArrays() const;
202 
204  FloatDataArrays& getFloatDataArrays();
205 
208  {
209  float_data_arrays_ = fda;
210  }
211 
213  const StringDataArrays& getStringDataArrays() const;
214 
216  StringDataArrays& getStringDataArrays();
217 
220  {
221  string_data_arrays_ = sda;
222  }
223 
225  const IntegerDataArrays& getIntegerDataArrays() const;
226 
228  IntegerDataArrays& getIntegerDataArrays();
229 
232  {
233  integer_data_arrays_ = ida;
234  }
235 
237 
240 
245  void sortByIntensity(bool reverse = false);
246 
253  void sortByPosition();
254 
256  bool isSorted() const;
257 
259 
262 
272  Size findNearest(CoordinateType rt) const;
273 
280  Iterator RTBegin(CoordinateType rt);
281 
288  Iterator RTBegin(Iterator begin, CoordinateType rt, Iterator end);
289 
296  Iterator RTEnd(CoordinateType rt);
297 
304  Iterator RTEnd(Iterator begin, CoordinateType rt, Iterator end);
305 
312  ConstIterator RTBegin(CoordinateType rt) const;
313 
320  ConstIterator RTBegin(ConstIterator begin, CoordinateType rt, ConstIterator end) const;
321 
328  ConstIterator RTEnd(CoordinateType rt) const;
329 
330  ConstIterator MZEnd(CoordinateType rt) const;
331 
338  ConstIterator RTEnd(ConstIterator begin, CoordinateType rt, ConstIterator end) const;
339 
348  Iterator PosBegin(CoordinateType rt);
349 
358  Iterator PosBegin(Iterator begin, CoordinateType rt, Iterator end);
359 
368  ConstIterator PosBegin(CoordinateType rt) const;
369 
378  ConstIterator PosBegin(ConstIterator begin, CoordinateType rt, ConstIterator end) const;
379 
388  Iterator PosEnd(CoordinateType rt);
389 
398  Iterator PosEnd(Iterator begin, CoordinateType rt, Iterator end);
399 
408  ConstIterator PosEnd(CoordinateType rt) const;
409 
418  ConstIterator PosEnd(ConstIterator begin, CoordinateType rt, ConstIterator end) const;
419 
425  void clear(bool clear_meta_data);
426 
428 
429 protected:
430 
433 
436 
439 
442  };
443 
445  std::ostream& operator<<(std::ostream& os, const MSChromatogram& chrom);
446 
447 } // namespace OpenMS
448 
FloatDataArrays float_data_arrays_
Float data arrays.
Definition: MSChromatogram.h:435
bool operator!=(const MSChromatogram &rhs) const
Equality operator.
Definition: MSChromatogram.h:162
A more convenient string class.
Definition: String.h:57
std::vector< IntegerDataArray > IntegerDataArrays
Definition: MSChromatogram.h:85
The representation of a chromatogram.
Definition: MSChromatogram.h:54
ContainerType::iterator Iterator
Mutable iterator.
Definition: MSChromatogram.h:91
std::vector< PeakType > ContainerType
Chromatogram base type.
Definition: MSChromatogram.h:76
~MSChromatogram() override
Destructor.
Definition: MSChromatogram.h:152
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806
PeakType::CoordinateType CoordinateType
Coordinate (RT) type.
Definition: MSChromatogram.h:74
void setIntegerDataArrays(const IntegerDataArrays &ida)
Sets the integer meta data arrays.
Definition: MSChromatogram.h:231
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
ContainerType::const_iterator ConstIterator
Non-mutable iterator.
Definition: MSChromatogram.h:93
OpenMS::DataArrays::IntegerDataArray IntegerDataArray
Integer data array vector type.
Definition: MSChromatogram.h:84
MSChromatogram()
Constructor.
Definition: MSChromatogram.h:130
Float data array class.
Definition: DataArrays.h:45
Integer data array class.
Definition: DataArrays.h:51
MSChromatogram(const MSChromatogram &source)
Copy constructor.
Definition: MSChromatogram.h:141
std::vector< StringDataArray > StringDataArrays
Definition: MSChromatogram.h:82
Comparator for the retention time.
Definition: MSChromatogram.h:63
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)
std::vector< FloatDataArray > FloatDataArrays
Definition: MSChromatogram.h:79
OpenMS::DataArrays::StringDataArray StringDataArray
String data array vector type.
Definition: MSChromatogram.h:81
Representation of chromatogram settings, e.g. SRM/MRM chromatograms.
Definition: ChromatogramSettings.h:58
ChromatogramPeak PeakType
Definition: MSChromatogram.h:72
StringDataArrays string_data_arrays_
String data arrays.
Definition: MSChromatogram.h:438
ContainerType::reverse_iterator ReverseIterator
Mutable reverse iterator.
Definition: MSChromatogram.h:95
void setFloatDataArrays(const FloatDataArrays &fda)
Sets the float meta data arrays.
Definition: MSChromatogram.h:207
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
IntegerDataArrays integer_data_arrays_
Integer data arrays.
Definition: MSChromatogram.h:441
OpenMS::DataArrays::FloatDataArray FloatDataArray
Float data array vector type.
Definition: MSChromatogram.h:78
ContainerType::const_reverse_iterator ConstReverseIterator
Non-mutable reverse iterator.
Definition: MSChromatogram.h:97
String name_
Name.
Definition: MSChromatogram.h:432
A 1-dimensional raw data point or peak for chromatograms.
Definition: ChromatogramPeak.h:54
String data array class.
Definition: DataArrays.h:57
Handles the management of a position and intensity range.
Definition: RangeManager.h:47
void setStringDataArrays(const StringDataArrays &sda)
Sets the string meta data arrays.
Definition: MSChromatogram.h:219
void updateRanges() override
Updates minimum and maximum position/intensity.
Definition: MSChromatogram.h:168