OpenMS  2.6.0
MapUtilities.h
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31 // $Maintainer: Julianus Pfeuffer$
32 // $Authors: Julianus Pfeuffer $
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34 
35 #pragma once
36 
37 #include <OpenMS/config.h>
39 #include <vector>
40 
41 namespace OpenMS
42 {
48  template <class MapType>
50  {
51  public:
53  template <class T>
54  void applyFunctionOnPeptideHits(T&& f, bool include_unassigned = true)
55  {
56  for (auto& feat : static_cast<MapType&>(*this))
57  {
58  applyFunctionOnPeptideHits_(feat.getPeptideIdentifications(), f);
59  }
60  if (include_unassigned)
61  {
62  applyFunctionOnPeptideHits_(static_cast<MapType&>(*this).getUnassignedPeptideIdentifications(), f);
63  }
64  }
65 
67  template <class T>
68  void applyFunctionOnPeptideIDs(T&& f, bool include_unassigned = true)
69  {
70  for (auto& feat : static_cast<MapType&>(*this))
71  {
72  applyFunctionOnPeptideIDs_(feat.getPeptideIdentifications(), f);
73  }
74  if (include_unassigned)
75  {
76  applyFunctionOnPeptideIDs_(static_cast<MapType&>(*this).getUnassignedPeptideIdentifications(), f);
77  }
78  }
79 
81  template <class T>
82  void applyFunctionOnPeptideHits(T&& f, bool include_unassigned = true) const
83  {
84  for (const auto& feat : static_cast<MapType const&>(*this))
85  {
86  applyFunctionOnPeptideHits_(feat.getPeptideIdentifications(), f);
87  }
88  if (include_unassigned)
89  {
90  applyFunctionOnPeptideHits_(static_cast<MapType const&>(*this).getUnassignedPeptideIdentifications(), f);
91  }
92  }
93 
95  template <class T>
96  void applyFunctionOnPeptideIDs(T&& f, bool include_unassigned = true) const
97  {
98  for (const auto& feat : static_cast<MapType const&>(*this))
99  {
100  applyFunctionOnPeptideIDs_(feat.getPeptideIdentifications(), f);
101  }
102  if (include_unassigned)
103  {
104  applyFunctionOnPeptideIDs_(static_cast<MapType const&>(*this).getUnassignedPeptideIdentifications(), f);
105  }
106  }
107 
108  private:
109  template <class T>
110  void applyFunctionOnPeptideIDs_(std::vector<PeptideIdentification>& idvec, T&& f)
111  {
112  for (auto& id : idvec)
113  {
114  f(id);
115  }
116  }
117 
118  template <class T>
119  void applyFunctionOnPeptideHits_(std::vector<PeptideIdentification>& idvec, T&& f)
120  {
121  for (auto& id : idvec)
122  {
123  for (auto& hit : id.getHits())
124  {
125  f(hit);
126  }
127  }
128  }
129 
130  template <class T>
131  void applyFunctionOnPeptideIDs_(const std::vector<PeptideIdentification>& idvec, T&& f) const
132  {
133  for (const auto& id : idvec)
134  {
135  f(id);
136  }
137  }
138 
139  template <class T>
140  void applyFunctionOnPeptideHits_(const std::vector<PeptideIdentification>& idvec, T&& f) const
141  {
142  for (const auto& id : idvec)
143  {
144  for (const auto& hit : id.getHits())
145  {
146  f(hit);
147  }
148  }
149  }
150  };
151 
152 } // namespace OpenMS
153 
OpenMS::RangeManager::getMax
const PositionType & getMax() const
Returns the maximum position.
Definition: RangeManager.h:117
OpenMS::FileTypes::IDXML
OpenMS identification format (.idXML)
Definition: FileTypes.h:66
ConsensusXMLFile.h
OpenMS::TOPPBase
Base class for TOPP applications.
Definition: TOPPBase.h:144
OpenMS::Param::copy
Param copy(const String &prefix, bool remove_prefix=false) const
Returns a new Param object containing all entries that start with prefix.
FileHandler.h
FileTypes.h
OpenMS::Math::SummaryStatistics::mean
double mean
Definition: StatisticFunctions.h:686
OpenMS::MapAlignmentTransformer::transformRetentionTimes
static void transformRetentionTimes(PeakMap &msexp, const TransformationDescription &trafo, bool store_original_rt=false)
Applies the given transformation to a peak map.
OpenMS::writtenDigits
constexpr Int writtenDigits(const FloatingPointType &=FloatingPointType())
Number of digits commonly used for writing a floating point type (a.k.a. precision)....
Definition: Types.h:294
OpenMS::Math::SummaryStatistics::median
double median
Definition: StatisticFunctions.h:686
double
OpenMS::DataProcessing::NORMALIZATION
Normalization of intensity values.
Definition: DataProcessing.h:70
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::ConsensusMap::updateRanges
void updateRanges() override
Updates minimum and maximum position/intensity.
OpenMS::DocumentIdentifier::getIdentifier
const String & getIdentifier() const
retrieve document identifier (e.g. an LSID)
OpenMS::DataProcessing::ALIGNMENT
Retention time alignment of different maps.
Definition: DataProcessing.h:68
OpenMS::MzMLFile::store
void store(const String &filename, const PeakMap &map) const
Stores a map in an MzML file.
OpenMS::FileTypes::MZML
MzML file (.mzML)
Definition: FileTypes.h:72
OpenMS::MzMLFile
File adapter for MzML files.
Definition: MzMLFile.h:55
OpenMS::String
A more convenient string class.
Definition: String.h:59
OpenMS::MSExperiment::begin
Iterator begin()
Definition: MSExperiment.h:157
MzMLFile.h
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::FileTypes::CONSENSUSXML
OpenMS consensus map format (.consensusXML)
Definition: FileTypes.h:67
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
FeatureXMLFile.h
OpenMS::Math::SummaryStatistics
Helper class to gather (and dump) some statistics from a e.g. vector<double>.
Definition: StatisticFunctions.h:657
StatisticFunctions.h
OpenMS::Param::getValue
const DataValue & getValue(const String &key) const
Returns a value of a parameter.
Map.h
OpenMS::FileTypes::UNKNOWN
Unknown file extension.
Definition: FileTypes.h:60
OpenMS::TransformationDescription::invert
void invert()
Computes an (approximate) inverse of the transformation.
OpenMS::Peak2D::CoordinateType
double CoordinateType
Coordinate type (of the position)
Definition: Peak2D.h:64
OpenMS::DataProcessing::NamesOfProcessingAction
static const std::string NamesOfProcessingAction[SIZE_OF_PROCESSINGACTION]
Names of inlet types.
Definition: DataProcessing.h:83
OpenMS::TransformationDescription::fitModel
void fitModel(const String &model_type, const Param &params=Param())
Fits a model to the data.
OpenMS::IdXMLFile::load
void load(const String &filename, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids)
Loads the identifications of an idXML file without identifier.
OpenMS::Peak2D::MZ
Mass-to-charge dimension id (1 if used as a const int)
Definition: Peak2D.h:76
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::MSExperiment::Iterator
std::vector< SpectrumType >::iterator Iterator
Mutable iterator.
Definition: MSExperiment.h:111
OpenMS::FeatureMap::updateRanges
void updateRanges() override
Updates minimum and maximum position/intensity.
OpenMS::String::number
static String number(double d, UInt n)
returns a string for d with exactly n decimal places
OpenMS::FileTypes::FEATUREXML
OpenMS feature file (.featureXML)
Definition: FileTypes.h:65
OpenMS::Math::SummaryStatistics::variance
double variance
Definition: StatisticFunctions.h:686
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
OpenMS::MzMLFile::load
void load(const String &filename, PeakMap &map)
Loads a map from a MzML file. Spectra and chromatograms are sorted by default (this can be disabled u...
OpenMS::Math::SummaryStatistics::max
T::value_type max
Definition: StatisticFunctions.h:687
OpenMS::Peak2D::IntensityType
float IntensityType
Intensity type.
Definition: Peak2D.h:62
OpenMS::FileHandler
Facilitates file handling by file type recognition.
Definition: FileHandler.h:62
OpenMS::RangeManager::getMaxInt
double getMaxInt() const
Returns the maximum intensity.
Definition: RangeManager.h:129
OpenMS::MapUtilities::applyFunctionOnPeptideHits
void applyFunctionOnPeptideHits(T &&f, bool include_unassigned=true) const
applies a const function on all PeptideHits or only assigned ones
Definition: MapUtilities.h:82
OpenMS::FeatureXMLFile::load
void load(const String &filename, FeatureMap &feature_map)
loads the file with name filename into map and calls updateRanges().
FeatureMap.h
OpenMS::MapUtilities::applyFunctionOnPeptideIDs
void applyFunctionOnPeptideIDs(T &&f, bool include_unassigned=true) const
applies a const function on all PeptideIDs or only assigned ones
Definition: MapUtilities.h:96
OpenMS::FileTypes::Type
Type
Actual file types enum.
Definition: FileTypes.h:58
OpenMS::MapUtilities::applyFunctionOnPeptideIDs
void applyFunctionOnPeptideIDs(T &&f, bool include_unassigned=true)
applies a function on all PeptideIDs or only assigned ones
Definition: MapUtilities.h:68
OpenMS::FileHandler::getType
static FileTypes::Type getType(const String &filename)
Tries to determine the file type (by name or content)
OpenMS::MapUtilities::applyFunctionOnPeptideIDs_
void applyFunctionOnPeptideIDs_(std::vector< PeptideIdentification > &idvec, T &&f)
Definition: MapUtilities.h:110
OpenMS::Math::SummaryStatistics::lowerq
double lowerq
Definition: StatisticFunctions.h:686
OpenMS::operator<<
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)
OpenMS::ConsensusMap
A container for consensus elements.
Definition: ConsensusMap.h:80
OpenMS::ConsensusXMLFile::load
void load(const String &filename, ConsensusMap &map)
Loads a consensus map from file and calls updateRanges.
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
MSExperiment.h
OpenMS::ConsensusMap::getColumnHeaders
const ColumnHeaders & getColumnHeaders() const
Non-mutable access to the file descriptions.
OpenMS::MapUtilities::applyFunctionOnPeptideHits
void applyFunctionOnPeptideHits(T &&f, bool include_unassigned=true)
applies a function on all PeptideHits or only assigned ones
Definition: MapUtilities.h:54
OpenMS::TransformationXMLFile::load
void load(const String &filename, TransformationDescription &transformation, bool fit_model=true)
Loads the transformation from an TransformationXML file.
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:97
OpenMS::TransformationXMLFile
Used to load and store TransformationXML files.
Definition: TransformationXMLFile.h:56
OpenMS::ConsensusMap::getDataProcessing
const std::vector< DataProcessing > & getDataProcessing() const
returns a const reference to the description of the applied data processing
OpenMS::MapUtilities::applyFunctionOnPeptideHits_
void applyFunctionOnPeptideHits_(const std::vector< PeptideIdentification > &idvec, T &&f) const
Definition: MapUtilities.h:140
OpenMS::RangeManager::getMinInt
double getMinInt() const
Returns the minimum intensity.
Definition: RangeManager.h:123
OpenMS::MSExperiment::end
Iterator end()
Definition: MSExperiment.h:167
OpenMS::MapUtilities::applyFunctionOnPeptideHits_
void applyFunctionOnPeptideHits_(std::vector< PeptideIdentification > &idvec, T &&f)
Definition: MapUtilities.h:119
OpenMS::FeatureMap::sortByRT
void sortByRT()
Sort features by RT position.
OpenMS::FeatureXMLFile
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLFile.h:68
OpenMS::FileTypes::nameToType
static Type nameToType(const String &name)
Converts a file type name into a Type.
OpenMS::MSExperiment::updateRanges
void updateRanges() override
Updates minimum and maximum position/intensity.
OpenMS::Peak2D::RT
Retention time dimension id (0 if used as a const int)
Definition: Peak2D.h:75
MapAlignerBase.h
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:73
OpenMS::TransformationXMLFile::store
void store(String filename, const TransformationDescription &transformation)
Stores the data in an TransformationXML file.
OpenMS::Map
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:50
OpenMS::MapUtilities
Utilities for Feature and ConsensusMap.
Definition: MapUtilities.h:49
OpenMS::Math::SummaryStatistics::upperq
double upperq
Definition: StatisticFunctions.h:686
OpenMS::BaseFeature::QualityType
float QualityType
Type of quality values.
Definition: BaseFeature.h:63
PeptideIdentification.h
OpenMS::FeatureMap::getDataProcessing
const std::vector< DataProcessing > & getDataProcessing() const
returns a const reference to the description of the applied data processing
OpenMS::TransformationDescription
Generic description of a coordinate transformation.
Definition: TransformationDescription.h:61
OpenMS::ProgressLogger::setLogType
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!
TOPPBase.h
OpenMS::RangeManager::getMin
const PositionType & getMin() const
Returns the minimum position.
Definition: RangeManager.h:111
OpenMS::Math::SummaryStatistics::min
T::value_type min
Definition: StatisticFunctions.h:687
OpenMS::MapUtilities::applyFunctionOnPeptideIDs_
void applyFunctionOnPeptideIDs_(const std::vector< PeptideIdentification > &idvec, T &&f) const
Definition: MapUtilities.h:131
OpenMS::ConsensusXMLFile
This class provides Input functionality for ConsensusMaps and Output functionality for alignments and...
Definition: ConsensusXMLFile.h:62
OpenMS::IdXMLFile
Used to load and store idXML files.
Definition: IdXMLFile.h:63
OpenMS::FileTypes::typeToName
static String typeToName(Type type)
Returns the name/extension of the type.
OpenMS::ConsensusMap::ColumnHeaders
std::map< UInt64, ColumnHeader > ColumnHeaders
Definition: ConsensusMap.h:168
StringListUtils.h