OpenMS  3.0.0
OpenSwathHelper.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 2002-2022.
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: Hannes Roest $
32 // $Authors: Hannes Roest $
33 // --------------------------------------------------------------------------
34 
35 #pragma once
36 
42 
43 namespace OpenMS
44 {
48  class OPENMS_DLLAPI OpenSwathHelper
49  {
50 
51 public:
52 
65  static String computePrecursorId(const String& transition_group_id, int isotope)
66  {
67  return transition_group_id + "_Precursor_i" + String(isotope);
68  }
69 
81  static String computeTransitionGroupId(const String& precursor_id)
82  {
83  std::vector<String> substrings;
84  precursor_id.split("_", substrings);
85 
86  if (substrings.size() == 3) return substrings[0];
87  else if (substrings.size() > 3)
88  {
89  String r;
90  for (Size k = 0; k < substrings.size() - 2; k++) r += substrings[k] + "_";
91  return r.prefix(r.size() - 1);
92  }
93  return "";
94  }
95 
107  static void selectSwathTransitions(const OpenMS::TargetedExperiment& targeted_exp,
108  OpenMS::TargetedExperiment& selected_transitions,
109  double min_upper_edge_dist,
110  double lower, double upper);
111 
123  static void selectSwathTransitions(const OpenSwath::LightTargetedExperiment& targeted_exp,
124  OpenSwath::LightTargetedExperiment& selected_transitions,
125  double min_upper_edge_dist,
126  double lower, double upper);
127 
145  static void checkSwathMap(const OpenMS::PeakMap& swath_map,
146  double& lower, double& upper, double& center);
147 
159  template <class TargetedExperimentT>
161  const TargetedExperimentT& targeted_exp,
162  TargetedExperimentT& selected_transitions,
163  double min_upper_edge_dist)
164  {
165  if (exp.empty() || exp[0].getPrecursors().empty())
166  {
167  std::cerr << "WARNING: File " << exp.getLoadedFilePath()
168  << " does not have any experiments or any precursors. Is it a SWATH map? "
169  << "I will move to the next map."
170  << std::endl;
171  return false;
172  }
173  double upper, lower, center;
174  OpenSwathHelper::checkSwathMap(exp, lower, upper, center);
175  OpenSwathHelper::selectSwathTransitions(targeted_exp, selected_transitions, min_upper_edge_dist, lower, upper);
176  if (selected_transitions.getTransitions().size() == 0)
177  {
178  std::cerr << "WARNING: For File " << exp.getLoadedFilePath()
179  << " no transition were within the precursor window of " << lower << " to " << upper
180  << std::endl;
181  return false;
182  }
183  return true;
184 
185  }
186 
196  static std::pair<double,double> estimateRTRange(const OpenSwath::LightTargetedExperiment & exp);
197 
212  static std::map<std::string, double> simpleFindBestFeature(const OpenMS::MRMFeatureFinderScoring::TransitionGroupMapType & transition_group_map,
213  bool useQualCutoff = false,
214  double qualCutoff = 0.0);
215  };
216 
217 } // namespace OpenMS
218 
LogStream.h
MSDataTransformingConsumer.h
OpenMS::TransitionTSVFile::validateTargetedExperiment
void validateTargetedExperiment(const OpenMS::TargetedExperiment &targeted_exp)
Validate a TargetedExperiment (check that all ids are unique)
OpenMS::TransitionTSVFile
This class supports reading and writing of OpenSWATH transition lists.
Definition: TransitionTSVFile.h:144
OpenMS::TOPPBase
Base class for TOPP applications.
Definition: TOPPBase.h:147
OpenMS::TransitionPQPFile
This class supports reading and writing of PQP files.
Definition: TransitionPQPFile.h:215
TargetedExperiment.h
FileHandler.h
FileTypes.h
OpenMS::TraMLFile::store
void store(const String &filename, const TargetedExperiment &id) const
Stores a map in a TraML file.
OpenMS::TargetedExperiment::getPeptides
const std::vector< Peptide > & getPeptides() const
MapType
PeakMap MapType
Definition: PeakPickerIterative.cpp:84
Size
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::Exception::IllegalArgument
A method or algorithm argument contains illegal values.
Definition: Exception.h:648
OpenMS::DataProcessing::DATA_PROCESSING
General data processing (if no other term applies)
Definition: DataProcessing.h:60
TransitionTSVFile.h
Types.h
OpenMS::Interfaces::IMSDataConsumer
The interface of a consumer of spectra and chromatograms.
Definition: IMSDataConsumer.h:69
OpenMS::TargetedExperimentHelper::Peptide
Represents a peptide (amino acid sequence)
Definition: TargetedExperimentHelper.h:358
OpenMS::MRMDecoy::generateDecoys
void generateDecoys(const OpenMS::TargetedExperiment &exp, OpenMS::TargetedExperiment &dec, const String &method, const double aim_decoy_fraction, const bool switchKR, const String &decoy_tag, const int max_attempts, const double identity_threshold, const double precursor_mz_shift, const double product_mz_shift, const double product_mz_threshold, const std::vector< String > &fragment_types, const std::vector< size_t > &fragment_charges, const bool enable_specific_losses, const bool enable_unspecific_losses, const int round_decPow=-4) const
Generate decoys from a TargetedExperiment.
OpenMS::DocumentIdentifier::getIdentifier
const String & getIdentifier() const
retrieve document identifier (e.g. an LSID)
OpenMS::FileHandler::getTypeByFileName
static FileTypes::Type getTypeByFileName(const String &filename)
Determines the file type from a file name.
OpenMS::MzMLFile::store
void store(const String &filename, const PeakMap &map) const
Stores a map in an MzML file.
OpenMS::ChromatogramExtractorAlgorithm::ExtractionCoordinates
Definition: ChromatogramExtractorAlgorithm.h:64
OpenMS::FileTypes::MRM
SpectraST MRM List.
Definition: FileTypes.h:100
OpenMS::Constants::k
const double k
Definition: Constants.h:153
OpenMS::TargetedExperimentHelper::Peptide::protein_refs
std::vector< String > protein_refs
Definition: TargetedExperimentHelper.h:418
OpenMS::FileTypes::MZML
MzML file (.mzML)
Definition: FileTypes.h:70
OpenMS::FileTypes::MZXML
MzXML file (.mzXML)
Definition: FileTypes.h:62
OpenMS::MetaInfoInterface::getMetaValue
const DataValue & getMetaValue(const String &name, const DataValue &default_value=DataValue::EMPTY) const
Returns the value corresponding to a string, or a default value (default: DataValue::EMPTY) if not fo...
DataFrameWriter.h
OpenMS::ExperimentalSettings
Description of the experimental settings.
Definition: ExperimentalSettings.h:59
OpenMS::MzMLFile
File adapter for MzML files.
Definition: MzMLFile.h:57
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::MRMDecoy
This class generates a TargetedExperiment object with decoys based on a TargetedExperiment object.
Definition: MRMDecoy.h:81
OpenMS::MSDataTransformingConsumer::setSpectraProcessingFunc
virtual void setSpectraProcessingFunc(std::function< void(SpectrumType &)> f_spec)
Sets the lambda function to be called for every spectrum which is passed to this interface.
MzMLFile.h
TransitionExperiment.h
Int
Feature.h
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
SimpleOpenMSSpectraAccessFactory.h
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::DataValue::toString
String toString(bool full_precision=true) const
Conversion to String full_precision Controls number of fractional digits for all double types or list...
OpenMS::OpenSwathHelper::checkSwathMapAndSelectTransitions
static bool checkSwathMapAndSelectTransitions(const OpenMS::PeakMap &exp, const TargetedExperimentT &targeted_exp, TargetedExperimentT &selected_transitions, double min_upper_edge_dist)
Check the map and select transition in one function.
Definition: OpenSwathHelper.h:160
OpenMS::TraMLFile::load
void load(const String &filename, TargetedExperiment &id)
Loads a map from a TraML file.
OpenMS::ChromatogramExtractor::prepare_coordinates
static void prepare_coordinates(std::vector< OpenSwath::ChromatogramPtr > &output_chromatograms, std::vector< ExtractionCoordinates > &coordinates, const OpenMS::TargetedExperiment &transition_exp, const double rt_extraction_window, const bool ms1=false, const int ms1_isotopes=0)
Prepare the extraction coordinates from a TargetedExperiment.
OpenMS::FileTypes::TSV
any TSV file, for example msInspect file or OpenSWATH transition file (see TransitionTSVFile)
Definition: FileTypes.h:86
OpenMS::String::prefix
String prefix(SizeType length) const
returns the prefix of length length
OpenMS::TransitionTSVFile::convertTargetedExperimentToTSV
void convertTargetedExperimentToTSV(const char *filename, OpenMS::TargetedExperiment &targeted_exp)
Write out a targeted experiment (TraML structure) into a tsv file.
OpenMS::Peak2D::getIntensity
IntensityType getIntensity() const
Definition: Peak2D.h:166
ChromatogramExtractor.h
OpenMS::FileTypes::UNKNOWN
Unknown file extension.
Definition: FileTypes.h:58
OPENMS_LOG_WARN
#define OPENMS_LOG_WARN
Macro if a warning, a piece of information which should be read by the user, should be logged.
Definition: LogStream.h:460
OpenSwath::LightTargetedExperiment
Definition: TransitionExperiment.h:218
OpenMS::ReactionMonitoringTransition::DECOY
Decoy transition.
Definition: ReactionMonitoringTransition.h:71
OpenMS::TransformationDescription::invert
void invert()
Computes an (approximate) inverse of the transformation.
ListUtils.h
OpenMS::MRMFeatureFinderScoring::TransitionGroupMapType
std::map< String, MRMTransitionGroupType > TransitionGroupMapType
Definition: MRMFeatureFinderScoring.h:105
OpenSwath::SwathQC
Quality Control function for OpenSwath.
Definition: SwathQC.h:63
OpenMS::TransformationDescription::fitModel
void fitModel(const String &model_type, const Param &params=Param())
Fits a model to the data.
OpenMS::OpenSwathHelper::computePrecursorId
static String computePrecursorId(const String &transition_group_id, int isotope)
Compute unique precursor identifier.
Definition: OpenSwathHelper.h:65
OpenMS::OpenSwathDataAccessHelper::convertTargetedExp
static void convertTargetedExp(const OpenMS::TargetedExperiment &transition_exp_, OpenSwath::LightTargetedExperiment &transition_exp)
convert from the OpenMS TargetedExperiment to the LightTargetedExperiment
SwathWindowLoader.h
OpenMS::OpenSwathHelper::computeTransitionGroupId
static String computeTransitionGroupId(const String &precursor_id)
Compute transition group id.
Definition: OpenSwathHelper.h:81
OpenSwathHelper.h
OpenMS::TargetedExperiment::hasPeptide
bool hasPeptide(const String &ref) const
OpenMS::OpenSwathHelper
A helper class that is used by several OpenSWATH tools.
Definition: OpenSwathHelper.h:48
SwathFile.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::TraMLFile
File adapter for HUPO PSI TraML files.
Definition: TraMLFile.h:63
OpenMS::TargetedExperimentHelper::Peptide::sequence
String sequence
Definition: TargetedExperimentHelper.h:420
Exception.h
OpenMS::DiaPrescore
Scoring of an spectrum given library intensities of a transition group.
Definition: DIAPrescoring.h:59
OpenSwath::LightTargetedExperiment::getTransitions
std::vector< LightTransition > & getTransitions()
Definition: TransitionExperiment.h:230
SwathQC.h
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:52
ProgressLogger.h
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...
MRMFeatureFinderScoring.h
TransformationXMLFile.h
OpenMS::SpectrumSettings::getDataProcessing
std::vector< DataProcessingPtr > & getDataProcessing()
returns a mutable reference to the description of the applied processing
OpenMS::FileHandler
Facilitates file handling by file type recognition.
Definition: FileHandler.h:66
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::FileTypes::Type
Type
Actual file types enum.
Definition: FileTypes.h:56
OpenMS::Exception::UnableToCreateFile
Unable to create file exception.
Definition: Exception.h:636
OpenMS::ReactionMonitoringTransition::getDecoyTransitionType
DecoyTransitionType getDecoyTransitionType() const
Returns the type of transition (target or decoy)
OpenMS::ReactionMonitoringTransition
This class stores a SRM/MRM transition.
Definition: ReactionMonitoringTransition.h:56
OpenMS::MSExperiment::setChromatograms
void setChromatograms(const std::vector< MSChromatogram > &chromatograms)
sets the chromatogram list
OpenMS::ChromatogramExtractor::return_chromatogram
static void return_chromatogram(const std::vector< OpenSwath::ChromatogramPtr > &chromatograms, const std::vector< ChromatogramExtractor::ExtractionCoordinates > &coordinates, TransitionExpT &transition_exp_used, SpectrumSettings settings, std::vector< OpenMS::MSChromatogram > &output_chromatograms, bool ms1, double im_extraction_width=0.0)
This converts the ChromatogramPtr to MSChromatogram and adds meta-information.
Definition: ChromatogramExtractor.h:284
OpenMS::TransformationDescription::getModelType
const String & getModelType() const
Gets the type of the fitted model.
OPENMS_LOG_DEBUG
#define OPENMS_LOG_DEBUG
Macro for general debugging information.
Definition: LogStream.h:470
OpenMS::FileHandler::getType
static FileTypes::Type getType(const String &filename)
Tries to determine the file type (by name or content)
OpenMS::TargetedExperimentHelper::PeptideCompound::hasCharge
bool hasCharge() const
Whether peptide or compound has set charge state.
Definition: TargetedExperimentHelper.h:237
OpenMS::MSDataTransformingConsumer
Transforming consumer of MS data.
Definition: MSDataTransformingConsumer.h:58
OpenMS::String::split
bool split(const char splitter, std::vector< String > &substrings, bool quote_protect=false) const
Splits a string into substrings using splitter as delimiter.
OpenMS::DefaultParamHandler::setParameters
void setParameters(const Param &param)
Sets the parameters.
OpenMS::TransformationDescription::apply
double apply(double value) const
Applies the transformation to value.
ConfidenceScoring.h
OpenMS::DefaultParamHandler::getDefaults
const Param & getDefaults() const
Non-mutable access to the default parameters.
OpenMS::String::toQString
QString toQString() const
Conversion to Qt QString.
OpenMS::ReactionMonitoringTransition::UNKNOWN
Unknown type.
Definition: ReactionMonitoringTransition.h:69
OpenMS::SimpleOpenMSSpectraFactory::getSpectrumAccessOpenMSPtr
static OpenSwath::SpectrumAccessPtr getSpectrumAccessOpenMSPtr(boost::shared_ptr< OpenMS::PeakMap > exp)
Simple Factory method to get a SpectrumAccess Ptr from an MSExperiment.
OpenSwath::CSVWriter
Definition: DataFrameWriter.h:71
OpenMS::MSExperiment::empty
bool empty() const
Definition: MSExperiment.h:130
MRMDecoy.h
OpenMS::DocumentIdentifier::setIdentifier
void setIdentifier(const String &id)
set document identifier (e.g. an LSID)
OpenMS::TransitionPQPFile::convertPQPToTargetedExperiment
void convertPQPToTargetedExperiment(const char *filename, OpenMS::TargetedExperiment &targeted_exp, bool legacy_traml_id=false)
Read in a PQP file and construct a targeted experiment (TraML structure)
OpenSwath::LightTargetedExperiment::transitions
std::vector< LightTransition > transitions
Definition: TransitionExperiment.h:227
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::Peak2D::getRT
CoordinateType getRT() const
Returns the RT coordinate (index 0)
Definition: Peak2D.h:208
OpenMS::TransitionTSVFile::convertTSVToTargetedExperiment
void convertTSVToTargetedExperiment(const char *filename, FileTypes::Type filetype, OpenMS::TargetedExperiment &targeted_exp)
Read in a tsv/mrm file and construct a targeted experiment (TraML structure)
ExperimentalSettings.h
OpenMS::CVTermList::hasCVTerm
bool hasCVTerm(const String &accession) const
checks whether the term has a value
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:71
MSExperiment.h
DataAccessHelper.h
OpenMS::SignedSize
ptrdiff_t SignedSize
Signed Size type e.g. used as pointer difference.
Definition: Types.h:134
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:98
OpenMS::FileTypes::PQP
OpenSWATH Peptide Query Parameter (PQP) SQLite DB, see TransitionPQPFile.
Definition: FileTypes.h:102
OpenMS::TransformationXMLFile
Used to load and store TransformationXML files.
Definition: TransformationXMLFile.h:56
OpenMS::CVTermList::getCVTerms
const std::map< String, std::vector< CVTerm > > & getCVTerms() const
returns the accession string of the term
OpenMS::String::substr
String substr(size_t pos=0, size_t n=npos) const
Wrapper for the STL substr() method. Returns a String object with its contents initialized to a subst...
OpenMS::Feature
An LC-MS feature.
Definition: Feature.h:70
OpenMS::Param::copy
Param copy(const std::string &prefix, bool remove_prefix=false) const
Returns a new Param object containing all entries that start with prefix.
OpenMS::MetaInfoInterface::metaValueExists
bool metaValueExists(const String &name) const
Returns whether an entry with the given name exists.
OpenMS::MetaInfoInterface::getKeys
void getKeys(std::vector< String > &keys) const
Fills the given vector with a list of all keys for which a value is set.
OpenMS::TargetedExperiment::getProteins
const std::vector< Protein > & getProteins() const
OpenSwath::SpectrumAccessPtr
boost::shared_ptr< ISpectrumAccess > SpectrumAccessPtr
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:87
OpenMS::FeatureXMLFile
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLFile.h:62
OpenMS::TargetedExperiment::getPeptideByRef
const Peptide & getPeptideByRef(const String &ref) const
float
OpenMS::SwathFile::loadMzML
std::vector< OpenSwath::SwathMap > loadMzML(const String &file, const String &tmp, boost::shared_ptr< ExperimentalSettings > &exp_meta, const String &readoptions="normal", Interfaces::IMSDataConsumer *plugin_consumer=nullptr)
Loads a Swath run from a single mzML file.
OpenMS::SwathFile
File adapter for Swath files.
Definition: SwathFile.h:67
OpenMS::FileTypes::nameToType
static Type nameToType(const String &name)
OpenMS::TargetedExperiment::getTransitions
const std::vector< ReactionMonitoringTransition > & getTransitions() const
returns the transition list
OpenMS::Internal::OpenMS_locale
const char * OpenMS_locale
OpenMS::TransitionPQPFile::convertTargetedExperimentToPQP
void convertTargetedExperimentToPQP(const char *filename, OpenMS::TargetedExperiment &targeted_exp)
Write out a targeted experiment (TraML structure) into a PQP file.
OpenMS::FileTypes::TRAML
TraML (HUPO PSI format) for transitions (.traML)
Definition: FileTypes.h:80
OpenMS::ConfidenceScoring
Definition: ConfidenceScoring.h:52
OpenMS::SpectrumSettings
Representation of 1D spectrum settings.
Definition: SpectrumSettings.h:63
OpenMS::SwathFile::loadMzXML
std::vector< OpenSwath::SwathMap > loadMzXML(String file, String tmp, boost::shared_ptr< ExperimentalSettings > &exp_meta, String readoptions="normal")
Loads a Swath run from a single mzXML file.
DIAPrescoring.h
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:69
OpenMS::MSExperiment::clear
void clear(bool clear_meta_data)
Clears all data and meta data.
OpenMS::Feature::getSubordinates
const std::vector< Feature > & getSubordinates() const
immutable access to subordinate features
OpenMS::String::ensureLastChar
String & ensureLastChar(char end)
Makes sure the string ends with the character end.
OpenMS::OpenSwathHelper::checkSwathMap
static void checkSwathMap(const OpenMS::PeakMap &swath_map, double &lower, double &upper, double &center)
Get the lower / upper offset for this SWATH map and do some sanity checks.
OpenMS::TargetedExperiment
A description of a targeted experiment containing precursor and production ions.
Definition: TargetedExperiment.h:64
OPENMS_LOG_INFO
#define OPENMS_LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:465
TransitionPQPFile.h
OpenMS::TargetedExperimentHelper::PeptideCompound::getChargeState
int getChargeState() const
Return the peptide or compound charge state.
Definition: TargetedExperimentHelper.h:243
OpenMS::ReactionMonitoringTransition::getPeptideRef
const String & getPeptideRef() const
OpenMS::OpenSwathHelper::selectSwathTransitions
static void selectSwathTransitions(const OpenMS::TargetedExperiment &targeted_exp, OpenMS::TargetedExperiment &selected_transitions, double min_upper_edge_dist, double lower, double upper)
Select transitions between lower and upper and write them into the new TargetedExperiment.
OpenMS::ChromatogramExtractor
The ChromatogramExtractor extracts chromatograms from a spectra file.
Definition: ChromatogramExtractor.h:67
OpenMS::ReactionMonitoringTransition::TARGET
Target transition.
Definition: ReactionMonitoringTransition.h:70
OpenMS::ChromatogramExtractor::extractChromatograms
void extractChromatograms(const ExperimentT &input, ExperimentT &output, OpenMS::TargetedExperiment &transition_exp, double mz_extraction_window, bool ppm, TransformationDescription trafo, double rt_extraction_window, const String &filter)
Extract chromatograms defined by the TargetedExperiment from the input map and write them to the outp...
Definition: ChromatogramExtractor.h:96
TraMLFile.h
OpenMS::TransformationDescription
Generic description of a coordinate transformation.
Definition: TransformationDescription.h:62
OpenMS::MSDataTransformingConsumer::setExperimentalSettingsFunc
virtual void setExperimentalSettingsFunc(std::function< void(const OpenMS::ExperimentalSettings &)> f_exp_settings)
Sets the lambda function to be called when setExperimentalSettings is called via this interface.
OpenMS::DocumentIdentifier::getLoadedFilePath
const String & getLoadedFilePath() const
get the file_name_ which is the absolute path to the file loaded from
StandardTypes.h
OpenMS::UniqueIdInterface::getUniqueId
UInt64 getUniqueId() const
Non-mutable access to unique id - returns the unique id.
Definition: UniqueIdInterface.h:104
File.h
OpenMS::ProgressLogger::setLogType
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!
OpenSwath::IDataFrameWriter
Definition: DataFrameWriter.h:45
TOPPBase.h
OpenMS::FileTypes::typeToName
static String typeToName(Type type)
Returns the name/extension of the type.
OpenMS::ProgressLogger::CMD
Command line progress.
Definition: ProgressLogger.h:70