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OpenMS
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128 std::vector<double> & n_term_intensities, std::vector<double> & c_term_intensities, FragmentationType type);
131 void setPeptideProtonDistribution(
const std::vector<double> & bb_charge,
const std::vector<double> & sc_charge);
152 Residue::ResidueType n_term_type, std::vector<double> & n_term_intensities, std::vector<double> & c_term_intensities, FragmentationType type);
155 void calcChargeStateIntensities_(
const AASequence & peptide,
const AASequence & n_term_ion,
const AASequence & c_term_ion,
Int charge,
Residue::ResidueType n_term_type,
double & n_term1,
double & c_term1,
double & n_term2,
double & c_term2, FragmentationType type);
158 void getLeftAndRightGBValues_(
const AASequence & peptide,
double & left_gb,
double & right_gb,
Size position);
Base class for TOPP applications.
Definition: TOPPBase.h:144
Size applyMemberFunction(Size(Type::*member_function)())
Applies a member function of Type to the container itself and all consensus features....
Definition: ConsensusMap.h:335
Representation of an experimental design in OpenMS. Instances can be loaded with the ExperimentalDesi...
Definition: ExperimentalDesign.h:243
static void setRANSACParams(const Math::RANSACParam &p)
Set the global (program wide) parameters for RANSAC.
Param copy(const String &prefix, bool remove_prefix=false) const
Returns a new Param object containing all entries that start with prefix.
static ExperimentalDesign load(const String &tsv_file, bool require_spectra_files)
Loads an experimental design from a tabular separated file.
File adapter for MzTab files.
Definition: MzTabFile.h:58
Resolves shared peptides based on protein scores.
Definition: PeptideProteinResolution.h:86
A feature grouping algorithm for unlabeled data.
Definition: FeatureGroupingAlgorithmQT.h:52
A mass trace extraction method that gathers peaks similar in m/z and moving along retention time.
Definition: MassTraceDetection.h:72
static void keepUniquePeptidesPerProtein(std::vector< PeptideIdentification > &peptides)
Removes all peptides that are not annotated as unique for a protein (by PeptideIndexer)
Definition: PeptideIndexing.h:139
Performs a Bayesian protein inference on Protein/Peptide identifications or ConsensusMap (experimenta...
Definition: BayesianProteinInferenceAlgorithm.h:75
void run(MSExperiment &exp, bool progress)
main method for feature detection
void addTag(const String &key, const String &tag)
Adds the tag tag to the entry key.
void store(const String &filename, const ConsensusMap &consensus_map)
Stores a consensus map to file.
A method or algorithm argument contains illegal values.
Definition: Exception.h:648
static double median(IteratorType begin, IteratorType end, bool sorted=false)
Calculates the median of a range of values.
Definition: StatisticFunctions.h:151
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.
static void convert(UInt64 const input_map_index, PeakMap &input_map, ConsensusMap &output_map, Size n=-1)
Similar to convert for FeatureMaps.
std::vector< double > sc_charge_ion_c_term_
Definition: ProtonDistributionModel.h:166
void sortByPosition()
Lexicographically sorts the peaks by their position (First RT then m/z).
PeakMap & getMSData()
Definition: FeatureFinderIdentificationAlgorithm.h:77
unsigned sample
allows grouping by sample
Definition: ExperimentalDesign.h:261
static String basename(const String &file)
Returns the basename of the file (without the path).
void setIdentifier(const String &id)
sets the identifier
Retention time alignment of different maps.
Definition: DataProcessing.h:68
std::map< unsigned int, std::vector< String > > getFractionToMSFilesMapping() const
return fraction index to file paths (ordered by fraction_group)
static void setCoefficientLimits(double offset, double scale, double power)
Set coefficient boundaries for which the model coefficient must not exceed to be considered a valid m...
A proton distribution model to calculate the proton distribution over charged peptides.
Definition: ProtonDistributionModel.h:70
MODELTYPE
Definition: MZTrafoModel.h:98
void group(const std::vector< FeatureMap > &maps, ConsensusMap &out) override
Applies the algorithm to feature maps.
void setValue(const String &key, const DataValue &value, const String &description="", const StringList &tags=StringList())
Sets a value.
A simple struct to carry all the parameters required for a RANSAC run.
Definition: RANSAC.h:58
ProgressLogger & getProgressLogger()
Definition: FeatureFinderIdentificationAlgorithm.h:83
File adapter for MzML files.
Definition: MzMLFile.h:55
A more convenient string class.
Definition: String.h:59
FragmentationType
the type of fragmentation
Definition: ProtonDistributionModel.h:95
File not found exception.
Definition: Exception.h:523
std::vector< double > DoubleList
Vector of double precision real types.
Definition: ListUtils.h:62
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
static void updateProteinReferences(std::vector< PeptideIdentification > &peptides, const std::vector< ProteinIdentification > &proteins, bool remove_peptides_without_reference=false)
Removes references to missing proteins.
Size size() const
Number of calibration points.
void pickExperiment(const PeakMap &input, PeakMap &output, const bool check_spectrum_type=true) const
Applies the peak-picking algorithm to a map (MSExperiment). This method picks peaks for each scan in ...
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
Data model of MzTab files. Please see the official MzTab specification at https://code....
Definition: MzTab.h:800
static bool updateProteinGroups(std::vector< ProteinIdentification::ProteinGroup > &groups, const std::vector< ProteinHit > &hits)
Update protein groups after protein hits were filtered.
static void resolve(FeatureMap &features, bool keep_matching=false)
Resolves ambiguous annotations of features with peptide identifications. The the filtered identificat...
const DataValue & getValue(const String &key) const
Returns a value of a parameter.
static std::set< Size > correctToHighestIntensityMS1Peak(MSExperiment &exp, double mz_tolerance, bool ppm, std::vector< double > &delta_mzs, std::vector< double > &mzs, std::vector< double > &rts)
Selection of the peak with the highest intensity as corrected precursor mass in a given mass range (e...
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:171
void setPrimaryMSRunPath(const StringList &s)
set the file path to the primary MS run (usually the mzML file obtained after data conversion from ra...
void switchToGeneralScoreType(std::vector< PeptideIdentification > &id, ScoreType type, Size &counter)
Definition: IDScoreSwitcherAlgorithm.h:111
void run(std::vector< PeptideIdentification > peptides, const std::vector< ProteinIdentification > &proteins, std::vector< PeptideIdentification > peptides_ext, std::vector< ProteinIdentification > proteins_ext, FeatureMap &features, const FeatureMap &seeds=FeatureMap())
std::vector< Int > IntList
Vector of signed integers.
Definition: ListUtils.h:55
#define OPENMS_PRECONDITION(condition, message)
Precondition macro.
Definition: openms/include/OpenMS/CONCEPT/Macros.h:136
FeatureMap & getFeatureMap()
get methods
bool clearMetaDataArrays()
Clears the meta data arrays of all contained spectra (float, integer and string arrays)
std::string path
file name, mandatory
Definition: ExperimentalDesign.h:259
#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
A mass recalibration method using linear/quadratic interpolation (robust/weighted) of given reference...
Definition: InternalCalibration.h:61
std::vector< double > bb_charge_
Definition: ProtonDistributionModel.h:161
Definition: PeptideIndexing.h:141
Creates a new Protein ID run into which other runs can be inserted. Creates union of protein hits but...
Definition: IDMergerAlgorithm.h:61
Size size() const
Definition: MSExperiment.h:127
void quantifyPeptides(const std::vector< PeptideIdentification > &peptides=std::vector< PeptideIdentification >())
Compute peptide abundances.
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
Definition: FeatureFinderIdentificationAlgorithm.h:56
void load(const String &filename, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids)
Loads the identifications of an idXML file without identifier.
double E_c_term_
Definition: ProtonDistributionModel.h:169
Exception indicating that an invalid parameter was handed over to an algorithm.
Definition: Exception.h:347
#define OPENMS_LOG_FATAL_ERROR
Macro to be used if fatal error are reported (processing stops)
Definition: LogStream.h:450
static String concatenate(const std::vector< T > &container, const String &glue="")
Concatenates all elements of the container and puts the glue string between elements.
Definition: ListUtils.h:193
static bool validateMatchingFileNames(const StringList &sl1, const StringList &sl2, bool basename=true, bool ignore_extension=true, bool strict=false)
Helper function to test if filenames provided in two StringLists match.
bool calibrate(PeakMap &exp, const IntList &target_mslvl, MZTrafoModel::MODELTYPE model_type, double rt_chunk, bool use_RANSAC, double post_ppm_median, double post_ppm_MAD, const String &file_models="", const String &file_models_plot="", const String &file_residuals="", const String &file_residuals_plot="", const String &rscript_executable="Rscript")
Apply calibration to data.
T getPPMAbs(T mz_obs, T mz_ref)
Compute absolute parts-per-million of two m/z values.
Definition: MathFunctions.h:248
static MzTab exportConsensusMapToMzTab(const ConsensusMap &consensus_map, const String &filename, const bool first_run_inference_only, const bool export_unidentified_features, const bool export_unassigned_ids, const bool export_subfeatures, const bool export_empty_pep_ids=false, const String &title="ConsensusMap export from OpenMS")
export linked peptide features aka consensus map
void sortPeptideIdentificationsByMapIndex()
Sorts PeptideIdentifications of consensus features with respect to their map index.
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
void addSpectrum(const MSSpectrum &spectrum)
adds a spectrum to the list
This class implements a fast peak-picking algorithm best suited for high resolution MS data (FT-ICR-M...
Definition: PeakPickerHiRes.h:73
Algorithm class that implements simple protein inference by aggregation of peptide scores....
Definition: BasicProteinInferenceAlgorithm.h:58
static void removeUnreferencedProteins(ConsensusMap &cmap, bool include_unassigned)
ConsensusMap & appendColumns(const ConsensusMap &rhs)
Add consensus map entries as new columns.
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...
void readQuantData(FeatureMap &features, const ExperimentalDesign &ed)
Read quantitative data from a feature map.
void inferPosteriorProbabilities(std::vector< ProteinIdentification > &proteinIDs, std::vector< PeptideIdentification > &peptideIDs, boost::optional< const ExperimentalDesign > exp_des=boost::optional< const ExperimentalDesign >())
std::vector< double > bb_charge_full_
Definition: ProtonDistributionModel.h:163
const std::vector< ProteinIdentification > & getProteinIdentifications() const
non-mutable access to the protein identifications
unsigned fraction
fraction 1..m, mandatory, 1 if not set
Definition: ExperimentalDesign.h:258
unsigned getNumberOfLabels() const
static void keepBestPeptideHits(std::vector< PeptideIdentification > &peptides, bool strict=false)
Filters peptide identifications keeping only the single best-scoring hit per ID.
std::vector< double > bb_charge_ion_n_term_
Definition: ProtonDistributionModel.h:165
Representation of a peptide evidence.
Definition: PeptideEvidence.h:50
T getPPM(T mz_obs, T mz_ref)
Compute parts-per-million of two m/z values.
Definition: MathFunctions.h:233
std::map< std::pair< String, unsigned >, unsigned > getPathLabelToFractionGroupMapping(bool use_basename_only) const
return <file_path, label> to fraction_group mapping
void align(std::vector< DataType > &data, std::vector< TransformationDescription > &transformations, Int reference_index=-1)
Align feature maps, consensus maps, peak maps, or peptide identifications.
Definition: MapAlignmentAlgorithmIdentification.h:107
std::vector< double > bb_charge_ion_c_term_
Definition: ProtonDistributionModel.h:167
void store(const String &filename, const MzTab &mz_tab) const
Size setUniqueId()
Assigns a new, valid unique id. Always returns 1.
Definition: UniqueIdInterface.h:146
double MAD(IteratorType begin, IteratorType end, double median_of_numbers)
median absolute deviation (MAD)
Definition: StatisticFunctions.h:198
unsigned fraction_group
fraction group id
Definition: ExperimentalDesign.h:257
Definition: IDScoreSwitcherAlgorithm.h:47
const std::vector< PeptideIdentification > & getUnassignedPeptideIdentifications() const
non-mutable access to the unassigned peptide identifications
void setParameters(const Param ¶m)
Sets the parameters.
const Param & getDefaults() const
Non-mutable access to the default parameters.
Definition: ProtonDistributionModel.h:98
const Param & getParameters() const
Non-mutable access to the parameters.
bool empty() const
Definition: MSExperiment.h:137
Definition: ExperimentalDesign.h:253
Feature grouping
Definition: DataProcessing.h:73
ResidueType
Definition: Residue.h:151
ExitCodes
Exit codes.
Definition: PeptideIndexing.h:135
Definition: MZTrafoModel.h:98
A container for consensus elements.
Definition: ConsensusMap.h:80
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
void store(const String &filename, const FeatureMap &feature_map)
stores the map feature_map in file with name filename.
double E_
Definition: ProtonDistributionModel.h:168
A map alignment algorithm based on peptide identifications from MS2 spectra.
Definition: MapAlignmentAlgorithmIdentification.h:71
Calculates false discovery rates (FDR) from identifications.
Definition: FalseDiscoveryRate.h:77
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
std::vector< MSFileSectionEntry > MSFileSection
Definition: ExperimentalDesign.h:313
void buildGraph(ProteinIdentification &protein, const std::vector< PeptideIdentification > &peptides, bool skip_sort=false)
void run(std::vector< PeptideIdentification > &pep_ids, std::vector< ProteinIdentification > &prot_ids) const
const ColumnHeaders & getColumnHeaders() const
Non-mutable access to the file descriptions.
Size fillCalibrants(const PeakMap exp, const std::vector< InternalCalibration::LockMass > &ref_masses, double tol_ppm, bool lock_require_mono, bool lock_require_iso, CalibrationData &failed_lock_masses, bool verbose=true)
Extract calibrants from Raw data (mzML)
std::vector< double > sc_charge_ion_n_term_
Definition: ProtonDistributionModel.h:164
#define OPENMS_LOG_ERROR
Macro to be used if non-fatal error are reported (processing continues)
Definition: LogStream.h:455
static String absolutePath(const String &file)
Replaces the relative path in the argument with the absolute path.
const ProteinQuant & getProteinResults()
Get protein abundance data.
A container for features.
Definition: FeatureMap.h:97
Logger::LogStream OpenMS_Log_debug
Global static instance of a LogStream to capture messages classified as debug output....
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:62
void remove(const String &key)
Remove the entry key or a section key (when suffix is ':')
void filterPeakMap(PeakMap &exp)
void clear(bool clear_meta_data=true)
Clears all data and meta data.
Definition: PeptideIndexing.h:138
Refreshes the protein references for all peptide hits in a vector of PeptideIdentifications and adds ...
Definition: PeptideIndexing.h:126
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLFile.h:68
unsigned getNumberOfFractionGroups() const
ThresholdMower removes all peaks below a threshold.
Definition: ThresholdMower.h:51
Definition: FeatureFinderMultiplexAlgorithm.h:56
static void removeEmptyIdentifications(std::vector< IdentificationType > &ids)
Removes peptide or protein identifications that have no hits in them.
Definition: IDFilter.h:810
std::vector< double > sc_charge_full_
Definition: ProtonDistributionModel.h:162
const char * getMessage() const noexcept
Returns the message.
void run(const PeakMap &, std::vector< MassTrace > &, const Size max_traces=0)
Main method of MassTraceDetection. Extracts mass traces of a MSExperiment and gathers them into a vec...
static String stripExtension(const String &filename)
If filename contains an extension, it will be removed (including the '.'). Special extensions,...
Management and storage of parameters / INI files.
Definition: Param.h:73
void applyBasic(std::vector< PeptideIdentification > &ids)
simpler reimplemetation of the apply function above.
void clear(bool clear_meta_data)
Clears all data and meta data.
Representation of a peptide/protein sequence.
Definition: AASequence.h:111
unsigned label
the label (e.g.,: 1 for label-free, 1..8 for TMT8plex)
Definition: ExperimentalDesign.h:260
void storeLFQ(const String &filename, const ConsensusMap &consensus_map, const ExperimentalDesign &design, const StringList &reannotate_filenames, const bool is_isotope_label_type, const String &bioreplicate, const String &condition, const String &retention_time_summarization_method)
store label free experiment (MSstats)
File adapter for MzTab files.
Definition: MSstatsFile.h:57
static void filterHitsByScore(std::vector< IdentificationType > &ids, double threshold_score)
Filters peptide or protein identifications according to the score of the hits.
Definition: IDFilter.h:822
#define OPENMS_LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:465
MS:1001220 peptide bond up to the C-terminus.
Definition: Residue.h:161
void setMSFileSection(const MSFileSection &msfile_section)
static void removeDecoyHits(std::vector< IdentificationType > &ids)
Removes hits annotated as decoys from peptide or protein identifications.
Definition: IDFilter.h:922
Definition: PeptideIndexing.h:137
std::vector< double > sc_charge_
Definition: ProtonDistributionModel.h:160
Creates and maintains a boost graph based on the OpenMS ID datastructures.
Definition: IDBoostGraph.h:81
void insert(const String &prefix, const Param ¶m)
Size< TNeedle >::Type position(const PatternAuxData< TNeedle > &dh)
Definition: AhoCorasickAmbiguous.h:561
void setExperimentType(const String &experiment_type)
Mutable access to the experiment type.
#define OPENMS_POSTCONDITION(condition, message)
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/Macros.h:48
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!
bool sameNrOfMSFilesPerFraction() const
void quantifyProteins(const ProteinIdentification &proteins=ProteinIdentification())
Compute protein abundances.
const CalibrationData & getCalibrationPoints() const
Get container of calibration points.
double E_n_term_
Definition: ProtonDistributionModel.h:170
This class provides Input functionality for ConsensusMaps and Output functionality for alignments and...
Definition: ConsensusXMLFile.h:62
Used to load and store idXML files.
Definition: IdXMLFile.h:63
static void annotateQuantificationsToProteins(const ProteinQuant &protein_quants, ProteinIdentification &proteins, const UInt n_samples, bool remove_unquantified=true)
Annotate protein quant results as meta data to protein ids.
FASTAContainer<TFI_File> will make FASTA entries available chunk-wise from start to end by loading it...
Definition: FASTAContainer.h:93
void swap(MSExperiment &from)
Swaps the content of this map with the content of from.
Representation of a peptide hit.
Definition: PeptideHit.h:55
Helper class for peptide and protein quantification based on feature data annotated with IDs.
Definition: PeptideAndProteinQuant.h:53