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OpenMS
2.6.0
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83 void mergeIDFiles_(std::vector<ProteinIdentification> & proteins, std::vector<PeptideIdentification> & peptides,
const String & experiment,
StringList & file_paths);
85 void findRelevantFilePaths_(std::map<String, StringList> & design2FileBaseName, std::map<String, StringList> & design2FilePath,
StringList & filePaths);
91 void getSeparator_(
String & separator);
94 void mapFiles2Design_(std::map<String, StringList> & experiments,
TextFile & file);
Base class for TOPP applications.
Definition: TOPPBase.h:144
std::vector< PeptideIdentification > compute(const MSExperiment &exp, FeatureMap &features, const QCBase::SpectraMap &map_to_spectrum)
Calculate the ScanEventNumber, find all unidentified MS2-Spectra and add them to unassigned PeptideId...
File adapter for MzTab files.
Definition: MzTabFile.h:58
OPENMS_UINT64_TYPE UInt64
Unsigned integer type (64bit)
Definition: Types.h:77
Take the original retention time before map alignment and use the alignment's trafoXML for calculatio...
Definition: RTAlignment.h:53
void store(const String &filename, const ConsensusMap &consensus_map)
Stores a consensus map to file.
Storing a status of available/needed inputs (i.e. a set of Requires) as UInt64.
Definition: QCBase.h:120
void addMetaDataMetricsToMzTab(MzTabMetaData &meta)
ToleranceUnit
Definition: FragmentMassError.h:48
void compute(FeatureMap &features, const std::vector< FASTAFile::FASTAEntry > &contaminants)
Checks if the peptides are in the contaminant database.
std::map< String, StringList > identifier_to_msrunpath
Definition: ProteinIdentification.h:80
std::vector< FeatureMap > split(SplitMeta mode=SplitMeta::DISCARD) const
splits ConsensusMap into its original FeatureMaps
Definition: FragmentMassError.h:45
File adapter for MzML files.
Definition: MzMLFile.h:55
A more convenient string class.
Definition: String.h:59
Precondition failed exception.
Definition: Exception.h:166
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
This class provides some basic file handling methods for text files.
Definition: TextFile.h:46
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 void resolve(FeatureMap &features, bool keep_matching=false)
Resolves ambiguous annotations of features with peptide identifications. The the filtered identificat...
std::map< StringList, String > runpath_to_identifier
Definition: ProteinIdentification.h:81
Requires
Enum to encode a file type as a bit.
Definition: QCBase.h:60
void setMetaData(const MzTabMetaData &md)
two way mapping from ms-run-path to protID|pepID-identifier
Definition: ProteinIdentification.h:78
Map to find a spectrum via its NativeID.
Definition: QCBase.h:77
void compute(FeatureMap &fmap, const MSExperiment &exp, const QCBase::SpectraMap &map_to_spectrum, ToleranceUnit tolerance_unit=ToleranceUnit::AUTO, double tolerance=20)
computes FragmentMassError in ppm and Dalton (only of the first PeptideHit of each PepID)
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
Exception indicating that an invalid parameter was handed over to an algorithm.
Definition: Exception.h:347
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 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 compute(FeatureMap &fm, const TransformationDescription &trafo) const
Calculates retention time after map alignment and sets meta values "rt_raw" and "rt_align" in all Pep...
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OPENMS_UINT64_TYPE UID
A unique object ID (as unsigned 64bit type).
Definition: Types.h:120
void compute(FeatureMap &fmap)
Counts the number of MissedCleavages per PeptideIdentification.
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 addMetaDataMetricsToMzTab(MzTabMetaData &meta)
append QC data for given metrics to mzTab's MTD section
const std::vector< ProteinIdentification > & getProteinIdentifications() const
non-mutable access to the protein identifications
void compute(FeatureMap &features, const MSExperiment &exp, const QCBase::SpectraMap &map_to_spectrum)
Writes results as meta values to the PeptideIdentification of the given FeatureMap.
void load(const String &filename, FeatureMap &feature_map)
loads the file with name filename into map and calls updateRanges().
Merge files according to experimental design.
Definition: QuantitativeExperimentalDesign.h:56
void applyFunctionOnPeptideIDs(T &&f, bool include_unassigned=true)
applies a function on all PeptideIDs or only assigned ones
Definition: MapUtilities.h:68
void store(const String &filename, const MzTab &mz_tab) const
bool isRunnable(const Status &s) const
const std::vector< PeptideIdentification > & getUnassignedPeptideIdentifications() const
non-mutable access to the unassigned peptide identifications
static const std::string names_of_toleranceUnit[]
strings corresponding to enum ToleranceUnit
Definition: FragmentMassError.h:56
Not implemented exception.
Definition: Exception.h:436
bool find(TFinder &finder, const Pattern< TNeedle, FuzzyAC > &me, PatternAuxData< TNeedle > &dh)
Definition: AhoCorasickAmbiguous.h:884
void compute(const FeatureMap &feature_map, const MSExperiment &exp, bool assume_all_target=false)
computes Ms2 Identification Rate with FeatureMap
A container for consensus elements.
Definition: ConsensusMap.h:80
const std::vector< PeptideIdentification > & getUnassignedPeptideIdentifications() const
non-mutable access to the unassigned peptide identifications
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.
void load(const String &filename, ConsensusMap &map)
Loads a consensus map from file and calls updateRanges.
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
copy all meta values to all feature maps
This class is a metric for the QualityControl TOPP tool.
Definition: Contaminants.h:53
QC metric calculating (un)calibrated m/z error.
Definition: FWHM.h:54
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
void create(const std::vector< ProteinIdentification > &prot_ids)
Definition: ProteinIdentification.h:89
#define OPENMS_LOG_ERROR
Macro to be used if non-fatal error are reported (processing continues)
Definition: LogStream.h:455
A container for features.
Definition: FeatureMap.h:97
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:62
static void load(const String &filename, std::vector< FASTAEntry > &data)
loads a FASTA file given by 'filename' and stores the information in 'data'
An LC-MS feature.
Definition: Feature.h:70
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLFile.h:68
QC metric calculating (un)calibrated m/z error.
Definition: MzCalibration.h:58
#define OPENMS_LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:465
const MzTabMetaData & getMetaData() const
This class is a metric for the QualityControl-ToppTool.
Definition: Ms2IdentificationRate.h:56
void compute(FeatureMap &features)
Sets the 'mass' metavalue to all PeptideHits by computing the theoretical mass.
This class is a metric for the QualityControl TOPP Tool.
Definition: MissedCleavages.h:55
void compute(const MSExperiment &exp, float bin_size=0)
Compute Total Ion Count and applies the resampling algorithm, if a bin size in RT seconds greater tha...
Helper class for peptide and protein quantification based on feature data annotated with IDs.
Definition: ProteinResolver.h:56
static bool isLabeledExperiment(const ConsensusMap &cm)
check if the IsobaricAnalyzer TOPP tool was used to create this ConsensusMap
void calculateMap(const MSExperiment &exp)
calculate a new map, delete the old one
QC metric calculating theoretical mass of a peptide sequence.
Definition: PeptideMass.h:49
void compute(FeatureMap &features)
Moves FWHM metavalues from the feature to all its PeptideIdentifications (since that's were mzTab tak...
const std::vector< ProteinIdentification > & getProteinIdentifications() const
non-mutable access to the protein identifications
This class provides Input functionality for ConsensusMaps and Output functionality for alignments and...
Definition: ConsensusXMLFile.h:62
QC metric to determine the number of MS2 scans per MS1 scan over RT.
Definition: Ms2SpectrumStats.h:67