OpenMS  2.5.0
MSSpectrum.h
Go to the documentation of this file.
1 // --------------------------------------------------------------------------
2 // OpenMS -- Open-Source Mass Spectrometry
3 // --------------------------------------------------------------------------
4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
6 //
7 // This software is released under a three-clause BSD license:
8 // * Redistributions of source code must retain the above copyright
9 // notice, this list of conditions and the following disclaimer.
10 // * Redistributions in binary form must reproduce the above copyright
11 // notice, this list of conditions and the following disclaimer in the
12 // documentation and/or other materials provided with the distribution.
13 // * Neither the name of any author or any participating institution
14 // may be used to endorse or promote products derived from this software
15 // without specific prior written permission.
16 // For a full list of authors, refer to the file AUTHORS.
17 // --------------------------------------------------------------------------
18 // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
19 // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
20 // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
21 // ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
22 // INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
23 // EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
24 // PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
25 // OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
26 // WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
27 // OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
28 // ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
29 //
30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg$
32 // $Authors: Marc Sturm $
33 // --------------------------------------------------------------------------
34 
35 #pragma once
36 
37 #include <OpenMS/KERNEL/Peak1D.h>
44 
45 namespace OpenMS
46 {
47  class Peak1D;
48 
67  class OPENMS_DLLAPI MSSpectrum :
68  private std::vector<Peak1D>,
69  public RangeManager<1>,
70  public SpectrumSettings
71  {
72 public:
73 
75  struct OPENMS_DLLAPI RTLess : public std::binary_function<MSSpectrum, MSSpectrum, bool>
76  {
77  bool operator()(const MSSpectrum& a, const MSSpectrum& b) const;
78  };
79 
81 
82  typedef OpenMS::Peak1D PeakType;
87  typedef std::vector<PeakType> ContainerType;
90  typedef std::vector<FloatDataArray> FloatDataArrays;
93  typedef std::vector<StringDataArray> StringDataArrays;
96  typedef std::vector<IntegerDataArray> IntegerDataArrays;
98 
100 
101  typedef typename ContainerType::iterator Iterator;
104  typedef typename ContainerType::const_iterator ConstIterator;
106  typedef typename ContainerType::reverse_iterator ReverseIterator;
108  typedef typename ContainerType::const_reverse_iterator ConstReverseIterator;
110 
112 
113  using ContainerType::operator[];
114  using ContainerType::begin;
115  using ContainerType::rbegin;
116  using ContainerType::end;
117  using ContainerType::rend;
118  using ContainerType::resize;
119  using ContainerType::size;
120  using ContainerType::push_back;
121  using ContainerType::emplace_back;
122  using ContainerType::pop_back;
123  using ContainerType::empty;
124  using ContainerType::front;
125  using ContainerType::back;
126  using ContainerType::reserve;
127  using ContainerType::insert;
128  using ContainerType::erase;
129  using ContainerType::swap;
130 
131  using typename ContainerType::iterator;
132  using typename ContainerType::const_iterator;
133  using typename ContainerType::size_type;
134  using typename ContainerType::value_type;
135  using typename ContainerType::reference;
136  using typename ContainerType::const_reference;
137  using typename ContainerType::pointer;
138  using typename ContainerType::difference_type;
139 
142 
143 
145  MSSpectrum();
146 
148  MSSpectrum(const MSSpectrum& source);
149 
151  MSSpectrum(MSSpectrum&&) = default;
152 
154  ~MSSpectrum() override
155  {}
156 
158  MSSpectrum& operator=(const MSSpectrum& source);
159 
161  MSSpectrum& operator=(MSSpectrum&&) & = default;
162 
164  MSSpectrum& operator=(const SpectrumSettings & source);
165 
167  bool operator==(const MSSpectrum& rhs) const;
168 
170  bool operator!=(const MSSpectrum& rhs) const
171  {
172  return !(operator==(rhs));
173  }
174 
175  // Docu in base class (RangeManager)
176  void updateRanges() override;
177 
181  double getRT() const;
182 
184  void setRT(double rt);
185 
194  double getDriftTime() const;
195 
199  void setDriftTime(double dt);
200 
204  DriftTimeUnit getDriftTimeUnit() const;
205 
209  void setDriftTimeUnit(DriftTimeUnit dt);
210 
216  UInt getMSLevel() const;
217 
219  void setMSLevel(UInt ms_level);
220 
222  const String& getName() const;
223 
225  void setName(const String& name);
226 
228 
242  const FloatDataArrays& getFloatDataArrays() const;
244 
246  FloatDataArrays& getFloatDataArrays()
247  {
248  return float_data_arrays_;
249  }
250 
252  void setFloatDataArrays(const FloatDataArrays& fda);
253 
255  const StringDataArrays& getStringDataArrays() const;
256 
258  StringDataArrays& getStringDataArrays();
259 
261  void setStringDataArrays(const StringDataArrays& sda);
262 
264  const IntegerDataArrays& getIntegerDataArrays() const;
265 
267  IntegerDataArrays& getIntegerDataArrays();
268 
270  void setIntegerDataArrays(const IntegerDataArrays& ida);
272 
274 
275 
280  void sortByIntensity(bool reverse = false);
281 
287  void sortByPosition();
288 
290  bool isSorted() const;
291 
293 
296 
306  Size findNearest(CoordinateType mz) const;
307 
319  Int findNearest(CoordinateType mz, CoordinateType tolerance) const;
320 
334  Int findNearest(CoordinateType mz, CoordinateType tolerance_left, CoordinateType tolerance_right) const;
335 
341  Iterator MZBegin(CoordinateType mz);
342 
348  Iterator MZBegin(Iterator begin, CoordinateType mz, Iterator end);
349 
355  Iterator MZEnd(CoordinateType mz);
356 
362  Iterator MZEnd(Iterator begin, CoordinateType mz, Iterator end);
363 
369  ConstIterator MZBegin(CoordinateType mz) const;
370 
376  ConstIterator MZBegin(ConstIterator begin, CoordinateType mz, ConstIterator end) const;
377 
383  ConstIterator MZEnd(CoordinateType mz) const;
384 
390  ConstIterator MZEnd(ConstIterator begin, CoordinateType mz, ConstIterator end) const;
391 
399  Iterator PosBegin(CoordinateType mz);
400 
408  Iterator PosBegin(Iterator begin, CoordinateType mz, Iterator end);
409 
417  ConstIterator PosBegin(CoordinateType mz) const;
418 
426  ConstIterator PosBegin(ConstIterator begin, CoordinateType mz, ConstIterator end) const;
427 
435  Iterator PosEnd(CoordinateType mz);
436 
444  Iterator PosEnd(Iterator begin, CoordinateType mz, Iterator end);
445 
453  ConstIterator PosEnd(CoordinateType mz) const;
454 
462  ConstIterator PosEnd(ConstIterator begin, CoordinateType mz, ConstIterator end) const;
463 
465 
466 
472  void clear(bool clear_meta_data);
473 
474  /*
475  @brief Select a (subset of) spectrum and its data_arrays, only retaining the indices given in @p indices
476 
477  @param indices Vector of indices to keep
478  @return Reference to this MSSpectrum
479 
480  */
481  MSSpectrum& select(const std::vector<Size>& indices);
482 
483 
494  SpectrumSettings::SpectrumType getType(const bool query_data) const;
495  using SpectrumSettings::getType; // expose base class function
496 
499  ConstIterator getBasePeak() const;
500 
503  Iterator getBasePeak();
504 
506  PeakType::IntensityType getTIC() const;
507 
508 protected:
511 
513  double drift_time_;
514 
516  DriftTimeUnit drift_time_unit_;
517 
520 
523 
525  FloatDataArrays float_data_arrays_;
526 
528  StringDataArrays string_data_arrays_;
529 
531  IntegerDataArrays integer_data_arrays_;
532  };
533 
534  inline std::ostream& operator<<(std::ostream& os, const MSSpectrum& spec)
535  {
536  os << "-- MSSPECTRUM BEGIN --" << std::endl;
537 
538  // spectrum settings
539  os << static_cast<const SpectrumSettings&>(spec);
540 
541  // peaklist
542  for (MSSpectrum::ConstIterator it = spec.begin(); it != spec.end(); ++it)
543  {
544  os << *it << std::endl;
545  }
546 
547  os << "-- MSSPECTRUM END --" << std::endl;
548  return os;
549  }
550 
551 } // namespace OpenMS
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806
ContainerType::const_iterator ConstIterator
Non-mutable iterator.
Definition: MSSpectrum.h:104
PeakType::CoordinateType CoordinateType
Coordinate (m/z) type.
Definition: MSSpectrum.h:85
IntegerDataArrays integer_data_arrays_
Integer data arrays.
Definition: MSSpectrum.h:531
OpenMS::DataArrays::FloatDataArray FloatDataArray
Float data array vector type.
Definition: MSSpectrum.h:89
Peak2D PeakType
Definition: MassTrace.h:47
String name_
Name.
Definition: MSSpectrum.h:522
OpenMS::DataArrays::IntegerDataArray IntegerDataArray
Integer data array vector type.
Definition: MSSpectrum.h:95
UInt ms_level_
MS level.
Definition: MSSpectrum.h:519
StringDataArrays string_data_arrays_
String data arrays.
Definition: MSSpectrum.h:528
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
ContainerType::reverse_iterator ReverseIterator
Mutable reverse iterator.
Definition: MSSpectrum.h:106
std::vector< FloatDataArray > FloatDataArrays
Definition: MSSpectrum.h:90
~MSSpectrum() override
Destructor.
Definition: MSSpectrum.h:154
Float data array class.
Definition: DataArrays.h:45
Handles the management of a position and intensity range.
Definition: RangeManager.h:47
Comparator for the retention time.
Definition: MSSpectrum.h:75
DriftTimeUnit
Drift time unit.
Definition: Precursor.h:84
String data array class.
Definition: DataArrays.h:59
ContainerType::const_reverse_iterator ConstReverseIterator
Non-mutable reverse iterator.
Definition: MSSpectrum.h:108
Precursor::DriftTimeUnit DriftTimeUnit
Definition: MSSpectrum.h:140
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
DriftTimeUnit drift_time_unit_
Drift time unit.
Definition: MSSpectrum.h:516
SpectrumType
Spectrum peak type.
Definition: SpectrumSettings.h:70
A 1-dimensional raw data point or peak.
Definition: Peak1D.h:54
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
double drift_time_
Drift time.
Definition: MSSpectrum.h:513
std::vector< PeakType > ContainerType
Spectrum base type.
Definition: MSSpectrum.h:87
std::vector< IntegerDataArray > IntegerDataArrays
Definition: MSSpectrum.h:96
Integer data array class.
Definition: DataArrays.h:52
bool operator!=(const MSSpectrum &rhs) const
Equality operator.
Definition: MSSpectrum.h:170
OpenMS::DataArrays::StringDataArray StringDataArray
String data array vector type.
Definition: MSSpectrum.h:92
A more convenient string class.
Definition: String.h:58
FloatDataArrays float_data_arrays_
Float data arrays.
Definition: MSSpectrum.h:525
ContainerType::iterator Iterator
Mutable iterator.
Definition: MSSpectrum.h:102
Representation of 1D spectrum settings.
Definition: SpectrumSettings.h:63
std::vector< StringDataArray > StringDataArrays
Definition: MSSpectrum.h:93
FloatDataArrays & getFloatDataArrays()
Returns a mutable reference to the float meta data arrays.
Definition: MSSpectrum.h:246
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)
double retention_time_
Retention time.
Definition: MSSpectrum.h:510
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
SpectrumType getType() const
returns the spectrum type (centroided (PEAKS) or profile data (RAW))