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OpenMS
2.5.0
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71 void apply(std::vector<PeptideIdentification>& ids,
72 Size number_of_runs = 0);
79 typedef std::map<AASequence, std::pair<Int, std::vector<double> > >
103 virtual void apply_(std::vector<PeptideIdentification>& ids,
107 void updateMembers_()
override;
110 void compareChargeStates_(
Int& recorded_charge,
Int new_charge,
void merge(const Param &toMerge)
Adds missing parameters from the given param toMerge to this param. Existing parameters will not be m...
OpenMS identification format (.idXML)
Definition: FileTypes.h:66
Base class for TOPP applications.
Definition: TOPPBase.h:144
A feature grouping algorithm for unlabeled data.
Definition: FeatureGroupingAlgorithmQT.h:52
void store(const String &filename, const ConsensusMap &consensus_map)
Stores a consensus map to file.
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.
bool count_empty_
Count empty runs in "min_support" calculation? (input parameter)
Definition: ConsensusIDAlgorithm.h:92
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 more convenient string class.
Definition: String.h:58
Iterator begin()
Definition: MSExperiment.h:157
Calculates a consensus from multiple ID runs by averaging the search scores.
Definition: ConsensusIDAlgorithmAverage.h:48
Calculates a consensus from multiple ID runs based on the ranks of the search hits.
Definition: ConsensusIDAlgorithmRanks.h:48
void setRT(double rt)
sets the RT of the MS2 spectrum where the identification occurred
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS consensus map format (.consensusXML)
Definition: FileTypes.h:67
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
std::map< AASequence, std::pair< Int, std::vector< double > > > SequenceGrouping
Mapping: peptide sequence -> (charge, scores)
Definition: ConsensusIDAlgorithm.h:80
const std::vector< PeptideIdentification > & getPeptideIdentifications() const
returns a const reference to the PeptideIdentification vector
const std::vector< ProteinIdentification > & getProteinIdentifications() const
returns a const reference to the protein ProteinIdentification vector
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
const std::vector< PeptideHit > & getHits() const
returns the peptide hits as const
static DateTime now()
Returns the current date and time.
void load(const String &filename, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids)
Loads the identifications of an idXML file without identifier.
#define OPENMS_LOG_FATAL_ERROR
Macro to be used if fatal error are reported (processing stops)
Definition: LogStream.h:450
void setRT(CoordinateType coordinate)
Mutable access to the RT coordinate (index 0)
Definition: Peak2D.h:214
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
std::vector< SpectrumType >::iterator Iterator
Mutable iterator.
Definition: MSExperiment.h:111
std::vector< String > variable_modifications
Allowed variable modifications.
Definition: ProteinIdentification.h:230
OpenMS feature file (.featureXML)
Definition: FileTypes.h:65
double min_support_
Fraction of required support by other ID runs (input parameter)
Definition: ConsensusIDAlgorithm.h:89
Calculates a consensus from multiple ID runs by taking the worst search score (conservative approach)...
Definition: ConsensusIDAlgorithmWorst.h:48
void load(const String &filename, FeatureMap &feature_map)
loads the file with name filename into map and calls updateRanges().
Type
Actual file types enum.
Definition: FileTypes.h:58
static FileTypes::Type getType(const String &filename)
Tries to determine the file type (by name or content)
void setMZ(CoordinateType coordinate)
Mutable access to the m/z coordinate (index 1)
Definition: Peak2D.h:202
void setParameters(const Param ¶m)
Sets the parameters.
const Param & getDefaults() const
Non-mutable access to the default parameters.
static String getVersion()
Return the version number of OpenMS.
Calculates a consensus from multiple ID runs based on PEPs and shared ions.
Definition: ConsensusIDAlgorithmPEPIons.h:48
A container for consensus elements.
Definition: ConsensusMap.h:79
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.
Calculates a consensus from multiple ID runs by taking the best search score.
Definition: ConsensusIDAlgorithmBest.h:48
void load(const String &filename, ConsensusMap &map)
Loads a consensus map from file and calls updateRanges.
std::vector< String > fixed_modifications
Used fixed modifications.
Definition: ProteinIdentification.h:229
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
bool update(const Param &p_outdated, const bool add_unknown=false)
Rescue parameter values from p_outdated to current param.
A container for features.
Definition: FeatureMap.h:95
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 ':')
An LC-MS feature.
Definition: Feature.h:70
Iterator end()
Definition: MSExperiment.h:167
Calculates a consensus from multiple ID runs based on PEPs and sequence similarities.
Definition: ConsensusIDAlgorithmPEPMatrix.h:157
std::vector< ConsensusFeature >::iterator Iterator
Mutable iterator.
Definition: ConsensusMap.h:160
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLFile.h:68
Management and storage of parameters / INI files.
Definition: Param.h:73
void clear(bool clear_meta_data)
Clears all data and meta data.
Representation of a peptide/protein sequence.
Definition: AASequence.h:113
Abstract base class for all ConsensusID algorithms (that calculate a consensus from multiple ID runs)...
Definition: ConsensusIDAlgorithm.h:59
Size number_of_runs_
Number of ID runs.
Definition: ConsensusIDAlgorithm.h:86
void apply(std::vector< PeptideIdentification > &ids, Size number_of_runs=0)
Calculates the consensus ID for a set of peptide identifications of one spectrum or (consensus) featu...
Size considered_hits_
Number of peptide hits considered per ID run (input parameter)
Definition: ConsensusIDAlgorithm.h:83
Search parameters of the DB search.
Definition: ProteinIdentification.h:221
void setMZ(double mz)
sets the MZ of the MS2 spectrum
This class provides Input functionality for ConsensusMaps and Output functionality for alignments and...
Definition: ConsensusXMLFile.h:61
Used to load and store idXML files.
Definition: IdXMLFile.h:63