OpenMS  2.4.0
OpenSwathHelper.h
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31 // $Maintainer: Hannes Roest $
32 // $Authors: Hannes Roest $
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34 
35 #pragma once
36 
42 
43 namespace OpenMS
44 {
48  class OPENMS_DLLAPI OpenSwathHelper
49  {
50 
51 public:
52 
56  static String computePrecursorId(const String& transition_group_id, int isotope)
57  {
58  return transition_group_id + "_Precursor_i" + String(isotope);
59  }
60 
72  static void selectSwathTransitions(const OpenMS::TargetedExperiment& targeted_exp,
73  OpenMS::TargetedExperiment& selected_transitions,
74  double min_upper_edge_dist,
75  double lower, double upper);
76 
88  static void selectSwathTransitions(const OpenSwath::LightTargetedExperiment& targeted_exp,
89  OpenSwath::LightTargetedExperiment& selected_transitions,
90  double min_upper_edge_dist,
91  double lower, double upper);
92 
110  static void checkSwathMap(const OpenMS::PeakMap& swath_map,
111  double& lower, double& upper);
112 
124  template <class TargetedExperimentT>
126  const TargetedExperimentT& targeted_exp,
127  TargetedExperimentT& selected_transitions,
128  double min_upper_edge_dist)
129  {
130  if (exp.size() == 0 || exp[0].getPrecursors().size() == 0)
131  {
132  std::cerr << "WARNING: File " << exp.getLoadedFilePath()
133  << " does not have any experiments or any precursors. Is it a SWATH map? "
134  << "I will move to the next map."
135  << std::endl;
136  return false;
137  }
138  double upper, lower;
139  OpenSwathHelper::checkSwathMap(exp, lower, upper);
140  OpenSwathHelper::selectSwathTransitions(targeted_exp, selected_transitions, min_upper_edge_dist, lower, upper);
141  if (selected_transitions.getTransitions().size() == 0)
142  {
143  std::cerr << "WARNING: For File " << exp.getLoadedFilePath()
144  << " no transition were within the precursor window of " << lower << " to " << upper
145  << std::endl;
146  return false;
147  }
148  return true;
149 
150  }
151 
155  static std::pair<double,double> estimateRTRange(const OpenSwath::LightTargetedExperiment & exp);
156 
167  static std::map<std::string, double> simpleFindBestFeature(const OpenMS::MRMFeatureFinderScoring::TransitionGroupMapType & transition_group_map,
168  bool useQualCutoff = false,
169  double qualCutoff = 0.0);
170  };
171 
172 } // namespace OpenMS
173 
TheoreticalSpectrumGeneratorXLMS.h
LogStream.h
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)
This converts the ChromatogramPtr to MSChromatogram and adds meta-information.
Definition: ChromatogramExtractor.h:282
OpenMS::Internal::OpenMSOSInfo
Definition: OpenMSInfo.cpp:68
OpenMS::OPXLDataStructs::CrossLinkSpectrumMatch::percTIC
double percTIC
Definition: OPXLDataStructs.h:130
OpenMS::DataArrays::IntegerDataArray
Integer data array class.
Definition: DataArrays.h:51
OpenMS::TransitionTSVFile::validateTargetedExperiment
void validateTargetedExperiment(const OpenMS::TargetedExperiment &targeted_exp)
Validate a TargetedExperiment (check that all ids are unique)
OpenMS::OPXLDataStructs::CrossLinkSpectrumMatch::total_current
double total_current
Definition: OPXLDataStructs.h:136
OpenMS::ProteinIdentification::SearchParameters::digestion_enzyme
Protease digestion_enzyme
The cleavage site information in details (from ProteaseDB)
Definition: ProteinIdentification.h:118
TOPPOpenPepXLLF::registerOptionsAndFlags_
void registerOptionsAndFlags_() override
Sets the valid command line options (with argument) and flags (without argument).
Definition: OpenPepXLLF.cpp:161
ConsensusXMLFile.h
main
int main(int argc, const char **argv)
Definition: OpenPepXL.cpp:1464
OpenMS::UniqueIdInterface::ensureUniqueId
Size ensureUniqueId()
Assigns a valid unique id, but only if the present one is invalid. Returns 1 if the unique id was cha...
Definition: UniqueIdInterface.h:158
SpectrumHelper.h
OpenMS::TransitionTSVFile
This class supports reading and writing of OpenSWATH transition lists.
Definition: TransitionTSVFile.h:142
OpenMS::TOPPBase
Base class for TOPP applications.
Definition: TOPPBase.h:150
OpenMS::MzIdentMLFile::store
void store(const String &filename, const std::vector< ProteinIdentification > &poid, const std::vector< PeptideIdentification > &peid) const
Stores the identifications in a MzIdentML file.
OpenMS::TransitionPQPFile
This class supports reading and writing of PQP files.
Definition: TransitionPQPFile.h:57
OpenMS::OPXLDataStructs::CrossLinkSpectrumMatch::xcorrx_max
double xcorrx_max
Definition: OPXLDataStructs.h:145
TargetedExperiment.h
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::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
OpenMS::OPXLDataStructs::CrossLinkSpectrumMatch::matched_linear_alpha
Size matched_linear_alpha
Definition: OPXLDataStructs.h:147
OpenMS::OPXLDataStructs::PreprocessedPairSpectra::spectra_xlink_peaks
MSExperiment spectra_xlink_peaks
Definition: OPXLDataStructs.h:298
MapType
PeakMap MapType
Definition: PeakPickerIterative.cpp:84
OpenMS::CVTermList::getCVTerms
const Map< String, std::vector< CVTerm > > & getCVTerms() const
returns the accession string of the term
OpenMS::OPXLDataStructs::CrossLinkSpectrumMatch::cross_link
ProteinProteinCrossLink cross_link
structure of the cross-link
Definition: OPXLDataStructs.h:115
OpenMS::TheoreticalSpectrumGeneratorXLMS::getLinearIonSpectrum
virtual void getLinearIonSpectrum(PeakSpectrum &spectrum, AASequence &peptide, Size link_pos, bool frag_alpha, int charge=1, Size link_pos_2=0) const
Generates fragment ions not containing the cross-linker for one peptide.
OpenMS::OPXLDataStructs::CrossLinkSpectrumMatch::wTIC
double wTIC
Definition: OPXLDataStructs.h:131
ListUtilsIO.h
TOPPOpenPepXL::registerOptionsAndFlags_
void registerOptionsAndFlags_() override
Sets the valid command line options (with argument) and flags (without argument).
Definition: OpenPepXL.cpp:169
OpenMS::Internal::OpenMSOSInfo::getOSAsString
String getOSAsString() const
Definition: OpenMSInfo.cpp:80
XQuestResultXMLFile.h
VersionInfo.h
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
OpenMS::ProteaseDigestion::setEnzyme
void setEnzyme(const String &name)
Sets the enzyme for the digestion (by name)
OpenMS::OPXLDataStructs::CLSMScoreComparator
Comparator to sort CrossLinkSpectrumMatches by the main score.
Definition: OPXLDataStructs.h:179
Types.h
XQuestScores.h
OpenMS::TargetedExperimentHelper::Peptide
Represents a peptide (amino acid sequence)
Definition: TargetedExperimentHelper.h:451
Int
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::FASTAFile
This class serves for reading in and writing FASTA files.
Definition: FASTAFile.h:64
OpenMS::FileHandler::getTypeByFileName
static FileTypes::Type getTypeByFileName(const String &filename)
Determines the file type from a file name.
OpenMS::VersionInfo::getTime
static String getTime()
Return the build time of OpenMS.
OpenMS::MRMFeatureFinderScoring
The MRMFeatureFinder finds and scores peaks of transitions that co-elute.
Definition: MRMFeatureFinderScoring.h:93
OpenMS::MzMLFile::store
void store(const String &filename, const PeakMap &map) const
Stores a map in an MzML file.
OpenMS::Peak1D::setMZ
void setMZ(CoordinateType mz)
Mutable access to m/z.
Definition: Peak1D.h:119
OpenMS::FileTypes::MRM
SpectraST MRM List.
Definition: FileTypes.h:102
OpenMS::Constants::k
const double k
OpenMS::TargetedExperimentHelper::Peptide::protein_refs
std::vector< String > protein_refs
Definition: TargetedExperimentHelper.h:535
OpenMS::FileTypes::MZML
MzML file (.mzML)
Definition: FileTypes.h:72
OpenMS::FileTypes::MZXML
MzXML file (.mzXML)
Definition: FileTypes.h:64
OpenMS::Param::setValue
void setValue(const String &key, const DataValue &value, const String &description="", const StringList &tags=StringList())
Sets a value.
OpenMS::ProteinIdentification::SearchParameters::missed_cleavages
UInt missed_cleavages
The number of allowed missed cleavages.
Definition: ProteinIdentification.h:113
DataFrameWriter.h
OpenMS::ExperimentalSettings
Description of the experimental settings.
Definition: ExperimentalSettings.h:58
OpenMS::MzMLFile
File adapter for MzML files.
Definition: MzMLFile.h:55
OpenMS::String
A more convenient string class.
Definition: String.h:57
OpenMS::OPXLDataStructs::CrossLinkSpectrumMatch::score
double score
final score
Definition: OPXLDataStructs.h:122
OpenMS::MRMDecoy
This class generates a TargetedExperiment object with decoys based on a TargetedExperiment object.
Definition: MRMDecoy.h:88
OpenMS::Exception::Precondition
Precondition failed exception.
Definition: Exception.h:166
OpenMS::ModificationsDB::getInstance
static ModificationsDB * getInstance(OpenMS::String unimod_file="CHEMISTRY/unimod.xml", OpenMS::String psimod_file="CHEMISTRY/PSI-MOD.obo", OpenMS::String xlmod_file="CHEMISTRY/XLMOD.obo")
Returns a pointer to the modifications DB (singleton)
Definition: ModificationsDB.h:77
MzMLFile.h
TransitionExperiment.h
OpenMS::DoubleList
std::vector< double > DoubleList
Vector of double precision real types.
Definition: ListUtils.h:65
OpenMS::Internal::OS_WINDOWS
Definition: OpenMSInfo.cpp:58
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::SpectrumSettings::getPrecursors
const std::vector< Precursor > & getPrecursors() const
returns a const reference to the precursors
SimpleOpenMSSpectraAccessFactory.h
OpenMS::MRMFeatureFinderScoring::pickExperiment
void pickExperiment(PeakMap &chromatograms, FeatureMap &output, TargetedExperiment &transition_exp, TransformationDescription trafo, PeakMap &swath_map)
Picker and prepare functions.
OpenMS::PeakFileOptions::addMSLevel
void addMSLevel(int level)
adds a desired MS level for peaks to load
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::AASequence::getMonoWeight
double getMonoWeight(Residue::ResidueType type=Residue::Full, Int charge=0) const
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:149
OpenMS::File::removeExtension
static String removeExtension(const String &file)
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:125
TOPPOpenPepXL::preprocessPairs_
OPXLDataStructs::PreprocessedPairSpectra preprocessPairs_(const PeakMap &spectra, const vector< pair< Size, Size > > &spectrum_pairs, const double cross_link_mass_iso_shift, double fragment_mass_tolerance, double fragment_mass_tolerance_xlinks, bool fragment_mass_tolerance_unit_ppm, bool deisotope)
Definition: OpenPepXL.cpp:277
LOG_INFO
#define LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:454
OpenMS::MRMAssay::reannotateTransitions
void reannotateTransitions(OpenMS::TargetedExperiment &exp, double precursor_mz_threshold, double product_mz_threshold, const std::vector< String > &fragment_types, const std::vector< size_t > &fragment_charges, bool enable_specific_losses, bool enable_unspecific_losses, int round_decPow=-4)
Annotates and filters transitions in a TargetedExperiment.
OpenMS::TraMLFile::load
void load(const String &filename, TargetedExperiment &id)
Loads a map from a TraML file.
StatisticFunctions.h
OpenMS::FileTypes::TSV
msInspect file (.tsv)
Definition: FileTypes.h:87
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
OpenMS::ModificationsDB
database which holds all residue modifications from UniMod
Definition: ModificationsDB.h:72
OpenMS::AASequence::toString
String toString() const
returns the peptide as string with modifications embedded in brackets
OpenMS::OPXLDataStructs::CrossLinkSpectrumMatch::matched_xlink_beta
Size matched_xlink_beta
Definition: OPXLDataStructs.h:150
OpenMS::ProgressLogger::startProgress
void startProgress(SignedSize begin, SignedSize end, const String &label) const
Initializes the progress display.
OpenMS::PeptideIndexing::run
ExitCodes run(std::vector< FASTAFile::FASTAEntry > &proteins, std::vector< ProteinIdentification > &prot_ids, std::vector< PeptideIdentification > &pep_ids)
forward for old interface and pyOpenMS; use run<T>() for more control
Definition: PeptideIndexing.h:147
TOPPOpenPepXLLF::TOPPOpenPepXLLF
TOPPOpenPepXLLF()
Definition: OpenPepXLLF.cpp:155
OpenMS::Internal::ARCH_32BIT
Definition: OpenMSInfo.cpp:60
OpenMS::IntList
std::vector< Int > IntList
Vector of signed integers.
Definition: ListUtils.h:58
ChromatogramExtractor.h
OpenMS::Internal::OS_MACOS
Definition: OpenMSInfo.cpp:58
OpenMS::OPXLDataStructs::CrossLinkSpectrumMatch::ppm_error_abs_sum_xlinks_alpha
double ppm_error_abs_sum_xlinks_alpha
Definition: OPXLDataStructs.h:160
OpenMS::Internal::OpenMS_OSNames
std::string OpenMS_OSNames[]
Definition: OpenMSInfo.cpp:59
OpenMS::FileTypes::UNKNOWN
Unknown file extension.
Definition: FileTypes.h:60
OpenMS::Constants::PROTON_MASS_U
const double PROTON_MASS_U
OpenSwath::LightTargetedExperiment
Definition: TransitionExperiment.h:206
main
int main(int argc, const char **argv)
Definition: OpenPepXLLF.cpp:1262
OpenMS::MRMAssay::uisTransitions
void uisTransitions(OpenMS::TargetedExperiment &exp, const std::vector< String > &fragment_types, const std::vector< size_t > &fragment_charges, bool enable_specific_losses, bool enable_unspecific_losses, bool enable_ms2_precursors, double mz_threshold, const std::vector< std::pair< double, double > > &swathes, int round_decPow=-4, size_t max_num_alternative_localizations=20, int shuffle_seed=-1, bool disable_decoy_transitions=false)
Annotate UIS / site-specific transitions.
OpenMS::ProgressLogger::endProgress
void endProgress() const
Ends the progress display.
OpenMS::Internal::getOSInfo
static OpenMSOSInfo getOSInfo()
Definition: OpenMSInfo.cpp:92
OpenMS::TheoreticalSpectrumGeneratorXLMS::getXLinkIonSpectrum
virtual void getXLinkIonSpectrum(PeakSpectrum &spectrum, AASequence &peptide, Size link_pos, double precursor_mass, bool frag_alpha, int mincharge, int maxcharge, Size link_pos_2=0) const
Generates fragment ions containing the cross-linker for one peptide.
OpenMS::ReactionMonitoringTransition::DECOY
Decoy transition.
Definition: ReactionMonitoringTransition.h:71
OpenMS::MetaInfoInterface::getMetaValue
const DataValue & getMetaValue(const String &name) const
Returns the value corresponding to a string (or DataValue::EMPTY if not found)
OpenMS::OPXLDataStructs::CrossLinkSpectrumMatch::log_occupancy_beta
double log_occupancy_beta
Definition: OPXLDataStructs.h:144
OpenMS::EnzymaticDigestion::setMissedCleavages
void setMissedCleavages(Size missed_cleavages)
Sets the number of missed cleavages for the digestion (default is 0). This setting is ignored when lo...
OpenMS::TransformationDescription::invert
void invert()
Computes an (approximate) inverse of the transformation.
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)
Prepare the extraction coordinates from a TargetedExperiment.
ListUtils.h
OpenMS::MSExperiment::size
Size size() const
Definition: MSExperiment.h:127
OpenMS::NLargest
NLargest removes all but the n largest peaks.
Definition: NLargest.h:54
OpenMS::MRMFeatureFinderScoring::TransitionGroupMapType
std::map< String, MRMTransitionGroupType > TransitionGroupMapType
Definition: MRMFeatureFinderScoring.h:109
OpenMS::OPXLDataStructs::CrossLinkSpectrumMatch::ppm_error_abs_sum
double ppm_error_abs_sum
Definition: OPXLDataStructs.h:166
OpenMS::TransformationDescription::fitModel
void fitModel(const String &model_type, const Param &params=Param())
Fits a model to the data.
OpenMS::ProteinIdentification::SearchParameters::fragment_mass_tolerance_ppm
bool fragment_mass_tolerance_ppm
Mass tolerance unit of fragment ions (true: ppm, false: Dalton)
Definition: ProteinIdentification.h:115
OpenMS::OpenSwathHelper::computePrecursorId
static String computePrecursorId(const String &transition_group_id, int isotope)
Compute unique precursor identifier.
Definition: OpenSwathHelper.h:56
OpenMS::OpenSwathDataAccessHelper::convertTargetedExp
static void convertTargetedExp(const OpenMS::TargetedExperiment &transition_exp_, OpenSwath::LightTargetedExperiment &transition_exp)
convert from the OpenMS TargetedExperiment to the LightTargetedExperiment
OpenMS::Exception::InvalidParameter
Exception indicating that an invalid parameter was handed over to an algorithm.
Definition: Exception.h:347
TOPPOpenPepXL::TOPPOpenPepXL
TOPPOpenPepXL()
Definition: OpenPepXL.cpp:163
SwathWindowLoader.h
OpenSwathHelper.h
OpenMS::ProteinIdentification::SearchParameters::charges
String charges
The allowed charges for the search.
Definition: ProteinIdentification.h:109
OpenMS::OPXLDataStructs::CrossLinkSpectrumMatch::wTICold
double wTICold
Definition: OPXLDataStructs.h:132
OpenMS::TargetedExperiment::hasPeptide
bool hasPeptide(const String &ref) const
OpenMS::OPXLDataStructs::PreprocessedPairSpectra
The PreprocessedPairSpectra struct represents the result of comparing a light and a heavy labeled spe...
Definition: OPXLDataStructs.h:294
OpenMS::OpenSwathHelper
A helper class that is used by several OpenSWATH tools.
Definition: OpenSwathHelper.h:48
SwathFile.h
OpenMS::ModificationsDB::isInstantiated
static bool isInstantiated()
Check whether ModificationsDB was instantiated before.
OpenMS::MzIdentMLFile
File adapter for MzIdentML files.
Definition: MzIdentMLFile.h:67
OPXLDataStructs.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::OPXLDataStructs::CrossLinkSpectrumMatch::xcorrc_max
double xcorrc_max
Definition: OPXLDataStructs.h:146
LOG_DEBUG
#define LOG_DEBUG
Macro for general debugging information.
Definition: LogStream.h:458
OpenMS::TraMLFile
File adapter for HUPO PSI TraML files.
Definition: TraMLFile.h:63
OpenMS::XQuestResultXMLFile
Used to load and store xQuest result files.
Definition: XQuestResultXMLFile.h:55
MRMAssay.h
OpenMS::TargetedExperimentHelper::Peptide::sequence
String sequence
Definition: TargetedExperimentHelper.h:537
Exception.h
ProteaseDigestion.h
OpenMS::DiaPrescore
Scoring of an spectrum given library intensities of a transition group.
Definition: DIAPrescoring.h:64
OpenMS::OPXLDataStructs::CrossLinkSpectrumMatch::num_iso_peaks_mean_linear_beta
double num_iso_peaks_mean_linear_beta
Definition: OPXLDataStructs.h:154
OpenSwath::LightTargetedExperiment::getTransitions
std::vector< LightTransition > & getTransitions()
Definition: TransitionExperiment.h:218
OpenMS::ProteinIdentification::SearchParameters::variable_modifications
std::vector< String > variable_modifications
Allowed variable modifications.
Definition: ProteinIdentification.h:112
OpenMS::OPXLDataStructs::CrossLinkSpectrumMatch::ppm_error_abs_sum_linear
double ppm_error_abs_sum_linear
Definition: OPXLDataStructs.h:162
OpenMS::ProteinIdentification::SearchParameters::mass_type
PeakMassType mass_type
Mass type of the peaks.
Definition: ProteinIdentification.h:110
OpenMS::OPXLDataStructs::CrossLinkSpectrumMatch::ppm_error_abs_sum_xlinks
double ppm_error_abs_sum_xlinks
Definition: OPXLDataStructs.h:163
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
ProteaseDB.h
LOG_WARN
#define LOG_WARN
Macro if a warning, a piece of information which should be read by the user, should be logged.
Definition: LogStream.h:450
OpenMS::MetaInfoInterface::setMetaValue
void setMetaValue(const String &name, const DataValue &value)
Sets the DataValue corresponding to a name.
OpenMS::DataValue
Class to hold strings, numeric values, lists of strings and lists of numeric values.
Definition: DataValue.h:56
OpenMS::Internal::ARCH_64BIT
Definition: OpenMSInfo.cpp:60
OpenMS::OPXLDataStructs::CrossLinkSpectrumMatch::intsum_beta
double intsum_beta
Definition: OPXLDataStructs.h:135
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...
OpenMS::OPXLDataStructs::CrossLinkSpectrumMatch::num_iso_peaks_mean
double num_iso_peaks_mean
Definition: OPXLDataStructs.h:152
MRMFeatureFinderScoring.h
TransformationXMLFile.h
double
FASTAFile.h
OpenMS::SpectrumSettings::getDataProcessing
std::vector< DataProcessingPtr > & getDataProcessing()
returns a mutable reference to the description of the applied processing
OpenMS::OPXLDataStructs::CrossLinkSpectrumMatch::ppm_error_abs_sum_linear_beta
double ppm_error_abs_sum_linear_beta
Definition: OPXLDataStructs.h:159
OpenMS::TransformationDescription::getModelTypes
static void getModelTypes(StringList &result)
Gets the possible types of models.
OpenMS::OPXLDataStructs::CrossLinkSpectrumMatch::frag_annotations
std::vector< PeptideHit::PeakAnnotation > frag_annotations
Definition: OPXLDataStructs.h:170
OpenMS::ProteinIdentification::SearchParameters::db
String db
The used database.
Definition: ProteinIdentification.h:106
OpenMS::FileHandler
Facilitates file handling by file type recognition.
Definition: FileHandler.h:62
OpenMS::OPXLDataStructs::CrossLinkSpectrumMatch::log_occupancy_alpha
double log_occupancy_alpha
Definition: OPXLDataStructs.h:143
OpenMS::OPXLDataStructs::CrossLinkSpectrumMatch::ppm_error_abs_sum_beta
double ppm_error_abs_sum_beta
Definition: OPXLDataStructs.h:165
OpenMS::FeatureXMLFile::load
void load(const String &filename, FeatureMap &feature_map)
loads the file with name filename into map and calls updateRanges().
OpenMS::Internal::OS_LINUX
Definition: OpenMSInfo.cpp:58
OpenMS::MRMFeatureFinderScoring::setStrictFlag
void setStrictFlag(bool f)
Set the flag for strict mapping.
Definition: MRMFeatureFinderScoring.h:193
OpenMS::FileTypes::Type
Type
Actual file types enum.
Definition: FileTypes.h:58
OpenMS::Exception::UnableToCreateFile
Unable to create file exception.
Definition: Exception.h:636
OpenMS::Internal::ARCH_UNKNOWN
Definition: OpenMSInfo.cpp:60
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
MathFunctions.h
OpenMS::OPXLDataStructs::CrossLinkSpectrumMatch::num_iso_peaks_mean_linear_alpha
double num_iso_peaks_mean_linear_alpha
Definition: OPXLDataStructs.h:153
OpenMS::MSExperiment::setChromatograms
void setChromatograms(const std::vector< MSChromatogram > &chromatograms)
sets the chromatogram list
OpenMS::Peak1D::getMZ
CoordinateType getMZ() const
Non-mutable access to m/z.
Definition: Peak1D.h:113
OpenMS::TransformationDescription::getModelType
const String & getModelType() const
Gets the type of the fitted model.
OpenMS::AASequence::size
Size size() const
returns the number of residues
OpenMS::MRMAssay::detectingTransitions
void detectingTransitions(OpenMS::TargetedExperiment &exp, int min_transitions, int max_transitions)
Select detecting fragment ions.
OpenMS::FileHandler::getType
static FileTypes::Type getType(const String &filename)
Tries to determine the file type (by name or content)
OpenMS::OPXLDataStructs::CrossLinkSpectrumMatch::match_odds
double match_odds
Definition: OPXLDataStructs.h:139
OpenMS::TargetedExperimentHelper::PeptideCompound::hasCharge
bool hasCharge() const
Whether peptide or compound has set charge state.
Definition: TargetedExperimentHelper.h:314
OpenMS::Math::round
T round(T x)
Rounds the value.
Definition: MathFunctions.h:138
OpenMS::OPXLDataStructs::CrossLinkSpectrumMatch::ppm_error_abs_sum_alpha
double ppm_error_abs_sum_alpha
Definition: OPXLDataStructs.h:164
OpenMS::SpectrumSettings::setPrecursors
void setPrecursors(const std::vector< Precursor > &precursors)
sets the precursors
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::OPXLDataStructs::CrossLinkSpectrumMatch::num_iso_peaks_mean_xlinks_alpha
double num_iso_peaks_mean_xlinks_alpha
Definition: OPXLDataStructs.h:155
OpenMS::OPXLDataStructs::CrossLinkSpectrumMatch::xquest_score
double xquest_score
counts, scores and other data for xQuest-like output
Definition: OPXLDataStructs.h:128
OpenMS::TransformationDescription::apply
double apply(double value) const
Applies the transformation to value.
OpenMS::Internal::OS_UNKNOWN
Definition: OpenMSInfo.cpp:58
ConfidenceScoring.h
OpenMS::DefaultParamHandler::getDefaults
const Param & getDefaults() const
Non-mutable access to the default parameters.
OpenMS::OPXLDataStructs::CrossLinkSpectrumMatch::match_odds_beta
double match_odds_beta
Definition: OPXLDataStructs.h:141
OpenMS::ReactionMonitoringTransition::UNKNOWN
Unknown type.
Definition: ReactionMonitoringTransition.h:69
OpenMS::Internal::OpenMSOSInfo::arch
OpenMS_Architecture arch
Definition: OpenMSInfo.cpp:78
OpenMS::Internal::OpenMS_ArchNames
std::string OpenMS_ArchNames[]
Definition: OpenMSInfo.cpp:61
OpenMS::OPXLDataStructs::CrossLinkSpectrumMatch::precursor_correction
int precursor_correction
Definition: OPXLDataStructs.h:168
OpenMS::VersionInfo::getVersion
static String getVersion()
Return the version number of OpenMS.
OpenMS::DefaultParamHandler::getParameters
const Param & getParameters() const
Non-mutable access to the parameters.
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
MRMDecoy.h
OpenMS::OPXLDataStructs::CrossLinkSpectrumMatch::intsum_alpha
double intsum_alpha
Definition: OPXLDataStructs.h:134
OpenMS::DocumentIdentifier::setIdentifier
void setIdentifier(const String &id)
set document identifier (e.g. an LSID)
seqan::find
bool find(TFinder &finder, const Pattern< TNeedle, FuzzyAC > &me, PatternAuxData< TNeedle > &dh)
Definition: AhoCorasickAmbiguous.h:884
OpenMS::OPXLDataStructs::CrossLinkSpectrumMatch::int_sum
double int_sum
Definition: OPXLDataStructs.h:133
OpenMS::ProteinIdentification::SearchParameters::fragment_mass_tolerance
double fragment_mass_tolerance
Mass tolerance of fragment ions (Dalton or ppm)
Definition: ProteinIdentification.h:114
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:215
TOPPOpenPepXLLF::getModifications_
vector< ResidueModification > getModifications_(StringList modNames)
Definition: OpenPepXLLF.cpp:264
OpenMS::Peak1D
A 1-dimensional raw data point or peak.
Definition: Peak1D.h:54
OpenMS::OPXLDataStructs::CrossLinkSpectrumMatch::matched_linear_beta
Size matched_linear_beta
Definition: OPXLDataStructs.h:148
OpenMS::ConsensusMap
A container for consensus elements.
Definition: ConsensusMap.h:75
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:73
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::OPXLDataStructs::PreprocessedPairSpectra::spectra_linear_peaks
MSExperiment spectra_linear_peaks
Definition: OPXLDataStructs.h:297
OpenMS::MSSpectrum::sortByPosition
void sortByPosition()
Lexicographically sorts the peaks by their position.
OpenMS::ConsensusXMLFile::load
void load(const String &filename, ConsensusMap &map)
Loads a consensus map from file and calls updateRanges.
OpenMS::ProteinIdentification::SearchParameters::fixed_modifications
std::vector< String > fixed_modifications
Used fixed modifications.
Definition: ProteinIdentification.h:111
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)
OpenMS::OPXLDataStructs::PreprocessedPairSpectra::spectra_all_peaks
MSExperiment spectra_all_peaks
Definition: OPXLDataStructs.h:299
ModificationsDB.h
OpenMS::MRMAssay::restrictTransitions
void restrictTransitions(OpenMS::TargetedExperiment &exp, double lower_mz_limit, double upper_mz_limit, const std::vector< std::pair< double, double > > &swathes)
Restrict and filter transitions in a TargetedExperiment.
OpenMS::VersionInfo::getRevision
static String getRevision()
Return the revision number from revision control system, e.g. git.
NLargest.h
OpenMS::OpenSwathHelper::checkSwathMap
static void checkSwathMap(const OpenMS::PeakMap &swath_map, double &lower, double &upper)
Get the lower / upper offset for this SWATH map and do some sanity checks.
IDMapper.h
OpenMS::CVTermList::hasCVTerm
bool hasCVTerm(const String &accession) const
checks whether the term has a value
TOPPOpenPepXLLF::main_
ExitCodes main_(int, const char **) override
The actual "main" method. main_() is invoked by main().
Definition: OpenPepXLLF.cpp:278
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
MSExperiment.h
OpenMS::ProteinIdentification::SearchParameters::precursor_mass_tolerance
double precursor_mass_tolerance
Mass tolerance of precursor ions (Dalton or ppm)
Definition: ProteinIdentification.h:116
OpenMS::File::getUserDirectory
static String getUserDirectory()
OpenMS::OPXLDataStructs::CrossLinkSpectrumMatch::scan_index_heavy
Size scan_index_heavy
Definition: OPXLDataStructs.h:119
DataAccessHelper.h
OpenMS::OPXLDataStructs::CrossLinkSpectrumMatch::log_occupancy
double log_occupancy
Definition: OPXLDataStructs.h:142
OpenMS::IdXMLFile::store
void store(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::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:93
OpenMS::FileTypes::PQP
OpenSWATH Peptide Query Parameter (PQP) SQLite DB.
Definition: FileTypes.h:104
TOPPOpenPepXL
Definition: OpenPepXL.cpp:159
OpenMS::PeptideIdentification
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:62
OpenMS::TransformationXMLFile
Used to load and store TransformationXML files.
Definition: TransformationXMLFile.h:56
AASequence.h
OpenMS::OPXLDataStructs::CrossLinkSpectrumMatch::ppm_error_abs_sum_xlinks_beta
double ppm_error_abs_sum_xlinks_beta
Definition: OPXLDataStructs.h:161
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::FASTAFile::load
static void load(const String &filename, std::vector< FASTAEntry > &data)
loads a FASTA file given by 'filename' and stores the information in 'data'
OpenMS::Feature
An LC-MS feature.
Definition: Feature.h:70
OpenMS::Math::mean
static double mean(IteratorType begin, IteratorType end)
Calculates the mean of a range of values.
Definition: StatisticFunctions.h:134
OpenMS::ProteaseDigestion
Class for the enzymatic digestion of proteins.
Definition: ProteaseDigestion.h:60
OpenMS::MetaInfoInterface::metaValueExists
bool metaValueExists(const String &name) const
Returns whether an entry with the given name exists.
OpenMS::getDataArrayByName
DataArrayT::iterator getDataArrayByName(DataArrayT &a, const String &name)
Helper functions for MSSpectrum and MSChromatogram.
Definition: SpectrumHelper.h:49
OPXLHelper.h
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:89
TOPPOpenPepXLLF
Definition: OpenPepXLLF.cpp:151
OpenMS::PeptideIndexing
Refreshes the protein references for all peptide hits in a vector of PeptideIdentifications and adds ...
Definition: PeptideIndexing.h:123
OpenMS::File::getOpenMSDataPath
static String getOpenMSDataPath()
Returns the OpenMS data path (environment variable overwrites the default installation path)
OpenMS::FeatureXMLFile
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLFile.h:68
OpenMS::TargetedExperiment::getPeptideByRef
const Peptide & getPeptideByRef(const String &ref) const
OpenMS::Internal::OpenMSOSInfo::os_version
String os_version
Definition: OpenMSInfo.cpp:77
OpenMS::PeakFileOptions
Options for loading files containing peak data.
Definition: PeakFileOptions.h:47
OpenMS::MSExperiment::getPrimaryMSRunPath
void getPrimaryMSRunPath(StringList &toFill) const
get the file path to the first MS run
OpenMS::DataProcessing::QUANTITATION
Quantitation.
Definition: DataProcessing.h:72
OpenMS::TOPPBase::ExitCodes
ExitCodes
Exit codes.
Definition: TOPPBase.h:155
OpenMS::writtenDigits
Int writtenDigits(const FloatingPointType &=FloatingPointType())
Number of digits commonly used for writing a floating point type (a.k.a. precision)....
Definition: Types.h:294
PeptideIndexing.h
OpenMS::SwathFile
File adapter for Swath files.
Definition: SwathFile.h:62
OpenMS::FileTypes::nameToType
static Type nameToType(const String &name)
Converts a file type name into a Type.
OpenMS::TargetedExperiment::getTransitions
const std::vector< ReactionMonitoringTransition > & getTransitions() const
returns the transition list
String.h
OpenMS::DataValue::toString
String toString() const
Conversion to String.
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:81
OpenMS::ConfidenceScoring
Definition: ConfidenceScoring.h:58
OpenMS::SpectrumSettings
Representation of 1D spectrum settings.
Definition: SpectrumSettings.h:63
OpenMS::PeakFileOptions::clearMSLevels
void clearMSLevels()
clears the MS levels
OpenMS::ProteinIdentification::SearchParameters::precursor_mass_tolerance_ppm
bool precursor_mass_tolerance_ppm
Mass tolerance unit of precursor ions (true: ppm, false: Dalton)
Definition: ProteinIdentification.h:117
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:74
OpenMS::File::getTempDirectory
static String getTempDirectory()
The current OpenMS temporary data path (for temporary files)
OpenMS::SwathFile::loadMzML
std::vector< OpenSwath::SwathMap > loadMzML(String file, String tmp, boost::shared_ptr< ExperimentalSettings > &exp_meta, String readoptions="normal")
Loads a Swath run from a single mzML file.
OpenMS::ModificationsDB::getNumberOfModifications
Size getNumberOfModifications() const
Returns the number of modifications read from the unimod.xml file.
OpenMS::OPXLDataStructs::CrossLinkSpectrumMatch
The CrossLinkSpectrumMatch struct represents a PSM between a ProteinProteinCrossLink and a spectrum i...
Definition: OPXLDataStructs.h:112
OpenMS::MSExperiment::clear
void clear(bool clear_meta_data)
Clears all data and meta data.
OpenMS::OPXLDataStructs::CrossLinkSpectrumMatch::pre_score
double pre_score
Definition: OPXLDataStructs.h:129
OpenMS::VersionInfo::getBranch
static String getBranch()
Return the branch name from revision control system, e.g. git.
ModifiedPeptideGenerator.h
OpenMS::Feature::getSubordinates
const std::vector< Feature > & getSubordinates() const
immutable access to subordinate features
OpenMS::NLargest::filterSpectrum
void filterSpectrum(SpectrumType &spectrum)
Definition: NLargest.h:78
OpenMS::OPXLDataStructs::CrossLinkSpectrumMatch::num_iso_peaks_mean_xlinks_beta
double num_iso_peaks_mean_xlinks_beta
Definition: OPXLDataStructs.h:156
OpenMS::Internal::OpenMS_Architecture
OpenMS_Architecture
Definition: OpenMSInfo.cpp:60
OpenMS::TargetedExperiment
A description of a targeted experiment containing precursor and production ions.
Definition: TargetedExperiment.h:64
TransitionPQPFile.h
OPXLSpectrumProcessingAlgorithms.h
OpenMS::TheoreticalSpectrumGeneratorXLMS
Generates theoretical spectra for cross-linked peptides.
Definition: TheoreticalSpectrumGeneratorXLMS.h:56
OpenMS::MSSpectrum::getIntegerDataArrays
const IntegerDataArrays & getIntegerDataArrays() const
Returns a const reference to the integer meta data arrays.
OpenMS::TargetedExperimentHelper::PeptideCompound::getChargeState
int getChargeState() const
Return the peptide or compound charge state.
Definition: TargetedExperimentHelper.h:320
OpenMS::MRMAssay
Generate assays from a TargetedExperiment.
Definition: MRMAssay.h:66
OpenMS::Internal::OpenMS_OS
OpenMS_OS
Definition: OpenMSInfo.cpp:58
OpenMS::OPXLDataStructs::AASeqWithMassComparator
The AASeqWithMassComparator is a comparator for AASeqWithMass objects.
Definition: OPXLDataStructs.h:272
OpenMS::Internal::OpenMSOSInfo::OpenMSOSInfo
OpenMSOSInfo()
Definition: OpenMSInfo.cpp:70
OpenMS::ReactionMonitoringTransition::getPeptideRef
const String & getPeptideRef() const
OpenMS::Constants::C13C12_MASSDIFF_U
const double C13C12_MASSDIFF_U
OpenMS::OPXLDataStructs::CrossLinkSpectrumMatch::precursor_error_ppm
double precursor_error_ppm
Definition: OPXLDataStructs.h:137
OpenMS::XQuestResultXMLFile::store
void store(const String &filename, const std::vector< ProteinIdentification > &poid, const std::vector< PeptideIdentification > &peid) const
Stores the identifications in a xQuest XML file.
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::OPXLDataStructs::CrossLinkSpectrumMatch::ppm_error_abs_sum_linear_alpha
double ppm_error_abs_sum_linear_alpha
Definition: OPXLDataStructs.h:158
TOPPOpenPepXL::main_
ExitCodes main_(int, const char **) override
The actual "main" method. main_() is invoked by main().
Definition: OpenPepXL.cpp:486
OpenMS::MetaInfoDescription::setName
void setName(const String &name)
sets the name of the peak annotations
OpenMS::IDMapper
Annotates an MSExperiment, FeatureMap or ConsensusMap with peptide identifications.
Definition: IDMapper.h:66
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
OpenMS::ChromatogramExtractor
The ChromatogramExtractor extracts chromatograms from a spectra file.
Definition: ChromatogramExtractor.h:66
OpenMS::ReactionMonitoringTransition::TARGET
Target transition.
Definition: ReactionMonitoringTransition.h:70
OpenMS::ProteinIdentification::SearchParameters
Search parameters of the DB search.
Definition: ProteinIdentification.h:103
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:95
TraMLFile.h
OpenMS::TransformationDescription
Generic description of a coordinate transformation.
Definition: TransformationDescription.h:60
OpenMS::DataArrays::FloatDataArray
Float data array class.
Definition: DataArrays.h:45
OpenMS::Internal::OpenMSOSInfo::getArchAsString
String getArchAsString() const
Definition: OpenMSInfo.cpp:85
OpenMS::OPXLDataStructs::CrossLinkSpectrumMatch::scan_index_light
Size scan_index_light
reference to pair of spectra
Definition: OPXLDataStructs.h:118
OpenMS::DocumentIdentifier::getLoadedFilePath
const String & getLoadedFilePath() const
get the file_name_ which is the absolute path to the file loaded from
OpenMS::TOPPBase::main
ExitCodes main(int argc, const char **argv)
Main routine of all TOPP applications.
StandardTypes.h
OpenMS::UniqueIdInterface::getUniqueId
UInt64 getUniqueId() const
Non-mutable access to unique id - returns the unique id.
Definition: UniqueIdInterface.h:109
File.h
MzIdentMLFile.h
OpenMS::MzMLFile::getOptions
PeakFileOptions & getOptions()
Mutable access to the options for loading/storing.
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
OpenMS::Internal::OpenMSOSInfo::os
OpenMS_OS os
Definition: OpenMSInfo.cpp:76
TOPPBase.h
OpenMS::SwathWindowLoader::readSwathWindows
static void readSwathWindows(const std::string &filename, std::vector< double > &swath_prec_lower_, std::vector< double > &swath_prec_upper_)
Reading a tab delimited file specifying the SWATH windows.
float
OpenMS::FeatureMap::getProteinIdentifications
const std::vector< ProteinIdentification > & getProteinIdentifications() const
non-mutable access to the protein identifications
OpenMS::OPXLDataStructs::CrossLinkSpectrumMatch::match_odds_alpha
double match_odds_alpha
Definition: OPXLDataStructs.h:140
OpenMS::ConsensusXMLFile
This class provides Input functionality for ConsensusMaps and Output functionality for alignments and...
Definition: ConsensusXMLFile.h:61
OpenMS::IdXMLFile
Used to load and store idXML files.
Definition: IdXMLFile.h:63
OpenMS::Internal::getBinaryArchitecture
OpenMS_Architecture getBinaryArchitecture()
Definition: OpenMSInfo.cpp:191
OpenMS::FileTypes::typeToName
static String typeToName(Type type)
Returns the name/extension of the type.
OpenMS::IDMapper::annotate
void annotate(PeakMap &map, const std::vector< PeptideIdentification > &peptide_ids, const std::vector< ProteinIdentification > &protein_ids, const bool clear_ids=false, const bool mapMS1=false)
Mapping method for peak maps.
Definition: IDMapper.h:96
OpenMS::OPXLDataStructs::CrossLinkSpectrumMatch::matched_xlink_alpha
Size matched_xlink_alpha
Definition: OPXLDataStructs.h:149
OpenMS::ProgressLogger::CMD
Command line progress.
Definition: ProgressLogger.h:72