OpenMS  3.0.0
MSSpectrum.h
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31 // $Maintainer: Timo Sachsenberg$
32 // $Authors: Marc Sturm $
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34 
35 #pragma once
36 
37 #include <OpenMS/KERNEL/Peak1D.h>
42 
43 #include <numeric>
44 
45 namespace OpenMS
46 {
47  enum class DriftTimeUnit;
66  class OPENMS_DLLAPI MSSpectrum final :
67  private std::vector<Peak1D>,
68  public RangeManagerContainer<RangeMZ, RangeIntensity>,
69  public SpectrumSettings
70  {
71 public:
72 
74  struct OPENMS_DLLAPI RTLess
75  {
76  bool operator()(const MSSpectrum& a, const MSSpectrum& b) const;
77  };
78 
80  struct Chunk {
83  bool is_sorted;
84  Chunk(Size start, Size end, bool sorted) : start(start), end(end), is_sorted(sorted) {}
85  };
86 
87  struct Chunks {
88  public:
89  Chunks(const MSSpectrum& s) : spec_(s) {}
90  void add(bool is_sorted)
91  {
92  chunks_.emplace_back((chunks_.empty() ? 0 : chunks_.back().end), spec_.size(), is_sorted);
93  }
94  std::vector<Chunk>& getChunks()
95  {
96  return chunks_;
97  }
98  private:
99  std::vector<Chunk> chunks_;
101  };
102 
104 
105  typedef OpenMS::Peak1D PeakType;
110  typedef std::vector<PeakType> ContainerType;
116  typedef std::vector<FloatDataArray> FloatDataArrays;
119  typedef std::vector<StringDataArray> StringDataArrays;
122  typedef std::vector<IntegerDataArray> IntegerDataArrays;
124 
126 
127  typedef typename ContainerType::iterator Iterator;
130  typedef typename ContainerType::const_iterator ConstIterator;
132  typedef typename ContainerType::reverse_iterator ReverseIterator;
134  typedef typename ContainerType::const_reverse_iterator ConstReverseIterator;
136 
138 
139  using ContainerType::operator[];
140  using ContainerType::begin;
141  using ContainerType::rbegin;
142  using ContainerType::end;
143  using ContainerType::rend;
144  using ContainerType::cbegin;
145  using ContainerType::cend;
146  using ContainerType::resize;
147  using ContainerType::size;
148  using ContainerType::push_back;
149  using ContainerType::emplace_back;
150  using ContainerType::pop_back;
151  using ContainerType::empty;
152  using ContainerType::front;
153  using ContainerType::back;
154  using ContainerType::reserve;
155  using ContainerType::insert;
156  using ContainerType::erase;
157  using ContainerType::swap;
158 
159  using typename ContainerType::iterator;
160  using typename ContainerType::const_iterator;
161  using typename ContainerType::size_type;
162  using typename ContainerType::value_type;
163  using typename ContainerType::reference;
164  using typename ContainerType::const_reference;
165  using typename ContainerType::pointer;
166  using typename ContainerType::difference_type;
167 
169 
170 
172  MSSpectrum();
173 
175  MSSpectrum(const MSSpectrum& source);
176 
178  MSSpectrum(MSSpectrum&&) = default;
179 
181  ~MSSpectrum() = default;
182 
184  MSSpectrum& operator=(const MSSpectrum& source);
185 
187  MSSpectrum& operator=(MSSpectrum&&) & = default;
188 
190  MSSpectrum& operator=(const SpectrumSettings & source);
191 
193  bool operator==(const MSSpectrum& rhs) const;
194 
196  bool operator!=(const MSSpectrum& rhs) const
197  {
198  return !(operator==(rhs));
199  }
200 
201  // Docu in base class (RangeManager)
202  void updateRanges() override;
203 
207  double getRT() const;
208 
210  void setRT(double rt);
211 
220  double getDriftTime() const;
221 
225  void setDriftTime(double dt);
226 
230  DriftTimeUnit getDriftTimeUnit() const;
231 
233  String getDriftTimeUnitAsString() const;
234 
238  void setDriftTimeUnit(DriftTimeUnit dt);
239 
245  UInt getMSLevel() const;
246 
248  void setMSLevel(UInt ms_level);
249 
251  const String& getName() const;
252 
254  void setName(const String& name);
255 
257 
271  const FloatDataArrays& getFloatDataArrays() const;
273 
276  {
277  return float_data_arrays_;
278  }
279 
281  void setFloatDataArrays(const FloatDataArrays& fda);
282 
284  const StringDataArrays& getStringDataArrays() const;
285 
287  StringDataArrays& getStringDataArrays();
288 
290  void setStringDataArrays(const StringDataArrays& sda);
291 
293  const IntegerDataArrays& getIntegerDataArrays() const;
294 
296  IntegerDataArrays& getIntegerDataArrays();
297 
299  void setIntegerDataArrays(const IntegerDataArrays& ida);
301 
303 
304 
309  void sortByIntensity(bool reverse = false);
310 
316  void sortByPosition();
317 
322  void sortByPositionPresorted(const std::vector<Chunk>& chunks);
323 
325  bool isSorted() const;
326 
331  template<class Predicate>
332  bool isSorted(const Predicate& lambda) const
333  {
334  auto value_2_index_wrapper = [this, &lambda](const value_type& value1, const value_type& value2) {
335  // translate values into indices (this relies on no copies being made!)
336  const Size index1 = (&value1) - (&this->front());
337  const Size index2 = (&value2) - (&this->front());
338  // just make sure the pointers above are actually pointing to a Peak inside our container
339  assert(index1 < this->size());
340  assert(index2 < this->size());
341  return lambda(index1, index2);
342  };
343  return std::is_sorted(this->begin(), this->end(), value_2_index_wrapper);
344  }
345 
350  template<class Predicate>
351  void sort(const Predicate& lambda)
352  {
353  std::vector<Size> indices(this->size());
354  std::iota(indices.begin(), indices.end(), 0);
355  std::stable_sort(indices.begin(), indices.end(), lambda);
356  select(indices);
357  }
358 
360 
363 
373  Size findNearest(CoordinateType mz) const;
374 
386  Int findNearest(CoordinateType mz, CoordinateType tolerance) const;
387 
401  Int findNearest(CoordinateType mz, CoordinateType tolerance_left, CoordinateType tolerance_right) const;
402 
414  Int findHighestInWindow(CoordinateType mz, CoordinateType tolerance_left, CoordinateType tolerance_right) const;
415 
421  Iterator MZBegin(CoordinateType mz);
422 
428  Iterator MZBegin(Iterator begin, CoordinateType mz, Iterator end);
429 
435  Iterator MZEnd(CoordinateType mz);
436 
442  Iterator MZEnd(Iterator begin, CoordinateType mz, Iterator end);
443 
449  ConstIterator MZBegin(CoordinateType mz) const;
450 
456  ConstIterator MZBegin(ConstIterator begin, CoordinateType mz, ConstIterator end) const;
457 
463  ConstIterator MZEnd(CoordinateType mz) const;
464 
470  ConstIterator MZEnd(ConstIterator begin, CoordinateType mz, ConstIterator end) const;
471 
479  Iterator PosBegin(CoordinateType mz);
480 
488  Iterator PosBegin(Iterator begin, CoordinateType mz, Iterator end);
489 
497  ConstIterator PosBegin(CoordinateType mz) const;
498 
506  ConstIterator PosBegin(ConstIterator begin, CoordinateType mz, ConstIterator end) const;
507 
515  Iterator PosEnd(CoordinateType mz);
516 
524  Iterator PosEnd(Iterator begin, CoordinateType mz, Iterator end);
525 
533  ConstIterator PosEnd(CoordinateType mz) const;
534 
542  ConstIterator PosEnd(ConstIterator begin, CoordinateType mz, ConstIterator end) const;
543 
546  bool containsIMData() const;
547 
555  std::pair<Size, DriftTimeUnit> getIMData() const;
556 
558 
559 
571  void clear(bool clear_meta_data);
572 
573  /*
574  @brief Select a (subset of) spectrum and its data_arrays, only retaining the indices given in @p indices
575 
576  @param indices Vector of indices to keep
577  @return Reference to this MSSpectrum
578 
579  */
580  MSSpectrum& select(const std::vector<Size>& indices);
581 
582 
593  SpectrumSettings::SpectrumType getType(const bool query_data) const;
594  using SpectrumSettings::getType; // expose base class function
595 
598  ConstIterator getBasePeak() const;
599 
602  Iterator getBasePeak();
603 
605  PeakType::IntensityType calculateTIC() const;
606 
607 protected:
610 
612  double drift_time_;
613 
616 
619 
622 
625 
628 
631  };
632 
633  inline std::ostream& operator<<(std::ostream& os, const MSSpectrum& spec)
634  {
635  os << "-- MSSPECTRUM BEGIN --" << std::endl;
636 
637  // spectrum settings
638  os << static_cast<const SpectrumSettings&>(spec);
639 
640  // peaklist
641  for (MSSpectrum::ConstIterator it = spec.begin(); it != spec.end(); ++it)
642  {
643  os << *it << std::endl;
644  }
645 
646  os << "-- MSSPECTRUM END --" << std::endl;
647  return os;
648  }
649 
650 } // namespace OpenMS
OpenMS::PeakType
Peak2D PeakType
Definition: MassTrace.h:47
OpenMS::DataArrays::IntegerDataArray
Integer data array class.
Definition: DataArrays.h:52
ConsensusXMLFile.h
OpenMS::MSSpectrum::CoordinateType
PeakType::CoordinateType CoordinateType
Coordinate (m/z) type.
Definition: MSSpectrum.h:108
OpenMS::TOPPBase
Base class for TOPP applications.
Definition: TOPPBase.h:147
DataArrays.h
FileHandler.h
SimTypes.h
Size
MSSim.h
double
OpenMS::ConsensusXMLFile::store
void store(const String &filename, const ConsensusMap &consensus_map)
Stores a consensus map to file.
OpenMS::Param::setValue
void setValue(const std::string &key, const ParamValue &value, const std::string &description="", const std::vector< std::string > &tags=std::vector< std::string >())
Sets a value.
OpenMS::IdXMLFile::store
void store(const String &filename, const std::vector< ProteinIdentification > &protein_ids, const std::vector< PeptideIdentification > &peptide_ids, const String &document_id="")
Stores the data in an idXML file.
OpenMS::MSSpectrum::Chunk::is_sorted
bool is_sorted
are the Peaks in [start, end) sorted yet?
Definition: MSSpectrum.h:83
OpenMS::MSSpectrum::RTLess
Comparator for the retention time.
Definition: MSSpectrum.h:74
OpenMS::MSSim::simulate
void simulate(SimTypes::MutableSimRandomNumberGeneratorPtr rnd_gen, SimTypes::SampleChannels &peptides)
General purpose function to simulate a mass spectrometry run.
OpenMS::Param::insert
void insert(const std::string &prefix, const Param &param)
StopWatch.h
OpenMS::StringUtils::reverse
static String & reverse(String &this_s)
Definition: StringUtilsSimple.h:350
OpenMS::FASTAFile
This class serves for reading in and writing FASTA files If the protein/gene sequence contains unusua...
Definition: FASTAFile.h:60
OpenMS::MzMLFile::store
void store(const String &filename, const PeakMap &map) const
Stores a map in an MzML file.
OpenMS::MSSim
Central class for simulation of mass spectrometry experiments.
Definition: MSSim.h:68
OpenMS::MSSpectrum::drift_time_unit_
DriftTimeUnit drift_time_unit_
Drift time unit.
Definition: MSSpectrum.h:615
OpenMS::MzMLFile
File adapter for MzML files.
Definition: MzMLFile.h:57
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::MSSim::getContaminants
const SimTypes::FeatureMapSim & getContaminants() const
Access the contaminants feature map of simulated features.
Peak1D.h
MzMLFile.h
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
IdXMLFile.h
FeatureXMLFile.h
OpenMS::ListUtils::contains
static bool contains(const std::vector< T > &container, const E &elem)
Checks whether the element elem is contained in the given container.
Definition: ListUtils.h:162
DTA2DFile.h
OpenMS::SimTypes::SampleProteins
std::vector< SimProtein > SampleProteins
Container for FASTAEntry & abundance information.
Definition: SimTypes.h:90
OpenMS::MSSim::getLabelingConsensus
ConsensusMap & getLabelingConsensus()
Access the labeling consensus map of simulated features.
OpenMS::MSSpectrum::IntegerDataArray
OpenMS::DataArrays::IntegerDataArray IntegerDataArray
Integer data array vector type.
Definition: MSSpectrum.h:121
OpenMS::SimTypes::MutableSimRandomNumberGeneratorPtr
boost::shared_ptr< SimRandomNumberGenerator > MutableSimRandomNumberGeneratorPtr
Definition: SimTypes.h:174
OpenMS::MSSpectrum::RangeManagerContainerType
RangeManagerContainer< RangeMZ, RangeIntensity > RangeManagerContainerType
RangeManager.
Definition: MSSpectrum.h:112
OpenMS::MSSpectrum::StringDataArrays
std::vector< StringDataArray > StringDataArrays
Definition: MSSpectrum.h:119
OpenMS::DriftTimeUnit
DriftTimeUnit
Drift time unit for ion mobility.
Definition: IMTypes.h:45
OpenMS::SimTypes::SimRandomNumberGenerator
Wrapper class for random number generators used by the simulation classes.
Definition: SimTypes.h:118
OpenMS::MSSpectrum::RangeManagerType
RangeManager< RangeMZ, RangeIntensity > RangeManagerType
Definition: MSSpectrum.h:113
SpectrumSettings.h
OpenMS::MSSpectrum::operator!=
bool operator!=(const MSSpectrum &rhs) const
Equality operator.
Definition: MSSpectrum.h:196
OpenMS::SimTypes::SampleChannels
std::vector< SampleProteins > SampleChannels
Container for multiple channels of SampleProteins.
Definition: SimTypes.h:93
OpenMS::MSSpectrum::name_
String name_
Name.
Definition: MSSpectrum.h:621
OpenMS::Exception::InvalidParameter
Exception indicating that an invalid parameter was handed over to an algorithm.
Definition: Exception.h:339
OpenMS::MSSpectrum::sort
void sort(const Predicate &lambda)
Definition: MSSpectrum.h:351
OpenMS::Int
int Int
Signed integer type.
Definition: Types.h:102
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::RangeManager
Handles the management of a multidimensional range, e.g. RangeMZ and RangeIntensity for spectra.
Definition: RangeManager.h:588
OpenMS::MSSpectrum::Chunks::getChunks
std::vector< Chunk > & getChunks()
Definition: MSSpectrum.h:94
OpenMS::MSSpectrum::isSorted
bool isSorted(const Predicate &lambda) const
Definition: MSSpectrum.h:332
OpenMS::MetaInfoInterface::setMetaValue
void setMetaValue(const String &name, const DataValue &value)
Sets the DataValue corresponding to a name.
OpenMS::MSSpectrum::integer_data_arrays_
IntegerDataArrays integer_data_arrays_
Integer data arrays.
Definition: MSSpectrum.h:630
OpenMS::SpectrumSettings::SpectrumType
SpectrumType
Spectrum peak type.
Definition: SpectrumSettings.h:70
FASTAFile.h
OpenMS::MSSpectrum::string_data_arrays_
StringDataArrays string_data_arrays_
String data arrays.
Definition: MSSpectrum.h:627
OpenMS::StopWatch::getClockTime
double getClockTime() const
OpenMS::MetaInfoInterface
Interface for classes that can store arbitrary meta information (Type-Name-Value tuples).
Definition: MetaInfoInterface.h:60
MzXMLFile.h
OpenMS::MSSpectrum::Chunks::spec_
const MSSpectrum & spec_
Definition: MSSpectrum.h:100
OpenMS::MSSim::getPeakMap
const SimTypes::MSSimExperiment & getPeakMap() const
Access the picked (centroided) experiment.
OpenMS::Param::setSectionDescription
void setSectionDescription(const std::string &key, const std::string &description)
Sets a description for an existing section.
OpenMS::StopWatch::start
void start()
Start the stop watch.
OpenMS::MSSpectrum::Chunk::start
Size start
inclusive
Definition: MSSpectrum.h:81
OpenMS::MSSpectrum::Chunk
Used to remember what subsets in a spectrum are sorted already to allow faster sorting of the spectru...
Definition: MSSpectrum.h:80
OpenMS::SpectrumSettings::getType
SpectrumType getType() const
returns the spectrum type (centroided (PEAKS) or profile data (RAW))
OpenMS::MSSpectrum::IntegerDataArrays
std::vector< IntegerDataArray > IntegerDataArrays
Definition: MSSpectrum.h:122
OpenMS::StopWatch::stop
void stop()
Stop the stop watch (can be resumed later). If the stop watch was not running an exception is thrown.
OpenMS::DefaultParamHandler::setParameters
void setParameters(const Param &param)
Sets the parameters.
OpenMS::MSSim::getChargeConsensus
ConsensusMap & getChargeConsensus()
Access the charge consensus map of simulated features.
OpenMS::DataArrays::StringDataArray
String data array class.
Definition: DataArrays.h:59
RangeManager.h
OpenMS::String::toUpper
String & toUpper()
Converts the string to uppercase.
OpenMS::Peak1D
A 1-dimensional raw data point or peak.
Definition: Peak1D.h:53
OpenMS::operator<<
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)
OpenMS::Citation
Stores Citations for individual TOPP tools.
Definition: TOPPBase.h:73
OpenMS::ConsensusMap
A container for consensus elements.
Definition: ConsensusMap.h:82
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
OpenMS::FeatureXMLFile::store
void store(const String &filename, const FeatureMap &feature_map)
stores the map feature_map in file with name filename.
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::RangeManagerContainer
Definition: RangeManager.h:919
Iterator
OpenMS::StopWatch
This class is used to determine the current process' CPU (user and/or kernel) and wall time.
Definition: StopWatch.h:65
OpenMS::MSSpectrum::FloatDataArrays
std::vector< FloatDataArray > FloatDataArrays
Definition: MSSpectrum.h:116
OpenMS::MSSpectrum::getFloatDataArrays
FloatDataArrays & getFloatDataArrays()
Returns a mutable reference to the float meta data arrays.
Definition: MSSpectrum.h:275
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:71
OpenMS::SimTypes::SimProtein
Plain data object holding sequence and abundance information on a single protein.
Definition: SimTypes.h:73
OpenMS::MSSpectrum::Chunk::end
Size end
not inclusive
Definition: MSSpectrum.h:82
OpenMS::ConsensusMap::getColumnHeaders
const ColumnHeaders & getColumnHeaders() const
Non-mutable access to the file descriptions.
OpenMS::MSSpectrum::retention_time_
double retention_time_
Retention time.
Definition: MSSpectrum.h:609
OpenMS::MSSpectrum::Chunks::add
void add(bool is_sorted)
Definition: MSSpectrum.h:90
OpenMS::MSSpectrum::drift_time_
double drift_time_
Drift time.
Definition: MSSpectrum.h:612
OpenMS::StringUtils::toDouble
static double toDouble(const String &this_s)
Definition: StringUtils.h:216
OPENMS_LOG_ERROR
#define OPENMS_LOG_ERROR
Macro to be used if non-fatal error are reported (processing continues)
Definition: LogStream.h:455
OpenMS::Internal::operator==
bool operator==(const IDBoostGraph::ProteinGroup &lhs, const IDBoostGraph::ProteinGroup &rhs)
OpenMS::FASTAFile::load
void load(const String &filename, std::vector< FASTAEntry > &data) const
loads a FASTA file given by 'filename' and stores the information in 'data' This uses more RAM than r...
OpenMS::FeatureXMLFile
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLFile.h:62
float
OpenMS::MSSim::getSimulatedFeatures
const SimTypes::FeatureMapSim & getSimulatedFeatures() const
Access the simulated features.
OpenMS::MSSpectrum::ms_level_
UInt ms_level_
MS level.
Definition: MSSpectrum.h:618
OpenMS::MSSpectrum::float_data_arrays_
FloatDataArrays float_data_arrays_
Float data arrays.
Definition: MSSpectrum.h:624
OpenMS::MSSpectrum::Chunk::Chunk
Chunk(Size start, Size end, bool sorted)
Definition: MSSpectrum.h:84
OpenMS::SpectrumSettings
Representation of 1D spectrum settings.
Definition: SpectrumSettings.h:63
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:69
OpenMS::MSSpectrum::ContainerType
std::vector< PeakType > ContainerType
Spectrum base type.
Definition: MSSpectrum.h:110
OpenMS::MSSpectrum::Iterator
ContainerType::iterator Iterator
Mutable iterator.
Definition: MSSpectrum.h:128
OpenMS::MSSpectrum::StringDataArray
OpenMS::DataArrays::StringDataArray StringDataArray
String data array vector type.
Definition: MSSpectrum.h:118
OpenMS::MSSpectrum::ConstIterator
ContainerType::const_iterator ConstIterator
Non-mutable iterator.
Definition: MSSpectrum.h:130
OpenMS::MSSpectrum::ReverseIterator
ContainerType::reverse_iterator ReverseIterator
Mutable reverse iterator.
Definition: MSSpectrum.h:132
OpenMS::MSSpectrum::FloatDataArray
OpenMS::DataArrays::FloatDataArray FloatDataArray
Float data array vector type.
Definition: MSSpectrum.h:115
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
OpenMS::MSSpectrum::ConstReverseIterator
ContainerType::const_reverse_iterator ConstReverseIterator
Non-mutable reverse iterator.
Definition: MSSpectrum.h:134
OpenMS::DataArrays::FloatDataArray
Float data array class.
Definition: DataArrays.h:45
OpenMS::MSSpectrum::Chunks::chunks_
std::vector< Chunk > chunks_
Definition: MSSpectrum.h:99
OpenMS::Param::setValidStrings
void setValidStrings(const std::string &key, const std::vector< std::string > &strings)
Sets the valid strings for the parameter key.
OpenMS::UniqueIdInterface::getUniqueId
UInt64 getUniqueId() const
Non-mutable access to unique id - returns the unique id.
Definition: UniqueIdInterface.h:104
OpenMS::ProgressLogger::setLogType
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!
TOPPBase.h
OpenMS::MSSpectrum::Chunks::Chunks
Chunks(const MSSpectrum &s)
Definition: MSSpectrum.h:89
OpenMS::MSSim::getIdentifications
void getIdentifications(std::vector< ProteinIdentification > &proteins, std::vector< PeptideIdentification > &peptides) const
Access the simulated identifications (proteins and peptides)
OpenMS::ConsensusXMLFile
This class provides Input functionality for ConsensusMaps and Output functionality for alignments and...
Definition: ConsensusXMLFile.h:58
OpenMS::IdXMLFile
Used to load and store idXML files.
Definition: IdXMLFile.h:68
OpenMS::MSSim::getExperiment
const SimTypes::MSSimExperiment & getExperiment() const
Access the simulated experiment.
MetaInfoDescription.h
OpenMS::MSSpectrum::Chunks
Definition: MSSpectrum.h:87