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OpenMS
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73 void apply(std::vector<PeptideIdentification>& ids,
74 const std::map<String, String>& se_info,
75 Size number_of_runs = 0);
77 void apply(std::vector<PeptideIdentification>& ids,
78 Size number_of_runs = 0);
102 typedef std::map<AASequence, HitInfo>
130 virtual void apply_(std::vector<PeptideIdentification>& ids,
131 const std::map<String, String>& se_info,
135 void updateMembers_()
override;
138 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...
Protease digestion_enzyme
The cleavage site information in details (from ProteaseDB)
Definition: ProteinIdentification.h:273
OpenMS identification format (.idXML)
Definition: FileTypes.h:66
Base class for TOPP applications.
Definition: TOPPBase.h:144
static const std::string NamesOfSpecificity[SIZE_OF_SPECIFICITY]
Names of the Specificity.
Definition: EnzymaticDigestion.h:77
std::vector< String > types
Definition: ConsensusIDAlgorithm.h:88
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.
static ProteaseDB * getInstance()
this member function serves as a replacement of the constructor
Definition: DigestionEnzymeDB.h:69
std::set< PeptideEvidence > evidence
Definition: ConsensusIDAlgorithm.h:92
static String basename(const String &file)
Returns the basename of the file (without the path).
Invalid value exception.
Definition: Exception.h:335
String & substitute(char from, char to)
Replaces all occurrences of the character from by the character to.
bool count_empty_
Count empty runs in "min_support" calculation? (input parameter)
Definition: ConsensusIDAlgorithm.h:115
const String & getSearchEngine() const
Returns the type of search engine used.
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.
void setSearchEngineVersion(const String &search_engine_version)
Sets the search engine version.
UInt missed_cleavages
The number of allowed missed cleavages.
Definition: ProteinIdentification.h:268
double support
Definition: ConsensusIDAlgorithm.h:94
A more convenient string class.
Definition: String.h:59
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
void getPrimaryMSRunPath(StringList &output, bool raw=false) const
String target_decoy
Definition: ConsensusIDAlgorithm.h:91
#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
Representation of a protein identification run.
Definition: ProteinIdentification.h:70
const std::vector< PeptideIdentification > & getPeptideIdentifications() const
returns a const reference to the PeptideIdentification vector
bool keep_old_scores_
Keep old scores?
Definition: ConsensusIDAlgorithm.h:118
bool hasSubstring(const String &string) const
true if String contains the string, false otherwise
const std::vector< ProteinIdentification > & getProteinIdentifications() const
returns a const reference to the protein ProteinIdentification vector
fully enzyme specific, e.g., tryptic (ends with KR, AA-before is KR), or peptide is at protein termin...
Definition: EnzymaticDigestion.h:70
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
const std::vector< PeptideHit > & getHits() const
returns the peptide hits as const
bool fragment_mass_tolerance_ppm
Mass tolerance unit of fragment ions (true: ppm, false: Dalton)
Definition: ProteinIdentification.h:270
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.
std::map< AASequence, HitInfo > SequenceGrouping
Mapping: peptide sequence -> (charge, scores)
Definition: ConsensusIDAlgorithm.h:103
no requirements on start / end
Definition: EnzymaticDigestion.h:68
#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
const String & getIdentifier() const
Returns the identifier.
String charges
The allowed charges for the search.
Definition: ProteinIdentification.h:264
const DigestionEnzymeType * getEnzyme(const String &name) const
Definition: DigestionEnzymeDB.h:98
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
bool toBool() const
Conversion to bool.
const String getOriginalSearchEngineName() const
Return the type of search engine that was first applied (e.g., before percolator or consensusID) or "...
std::vector< String > variable_modifications
Allowed variable modifications.
Definition: ProteinIdentification.h:267
OpenMS feature file (.featureXML)
Definition: FileTypes.h:65
void setPrimaryMSRunPath(const StringList &s, bool raw=false)
semi specific, i.e., one of the two cleavage sites must fulfill requirements
Definition: EnzymaticDigestion.h:69
double min_support_
Fraction of required support by other ID runs (input parameter)
Definition: ConsensusIDAlgorithm.h:112
const String & getSearchEngineVersion() const
Returns the search engine version.
String db
The used database.
Definition: ProteinIdentification.h:261
const std::vector< ProteinHit > & getHits() const
Returns the protein hits.
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().
double final_score
Definition: ConsensusIDAlgorithm.h:93
Type
Actual file types enum.
Definition: FileTypes.h:58
no requirements on NTerm (currently not supported in the class)
Definition: EnzymaticDigestion.h:73
no requirements on CTerm (currently not supported in the class)
Definition: EnzymaticDigestion.h:72
Representation of a digestion enzyme for proteins (protease)
Definition: DigestionEnzymeProtein.h:48
Definition: ConsensusIDAlgorithm.h:84
static FileTypes::Type getType(const String &filename)
Tries to determine the file type (by name or content)
bool split(const char splitter, std::vector< String > &substrings, bool quote_protect=false) const
Splits a string into substrings using splitter as delimiter.
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.
void setSearchParameters(const SearchParameters &search_parameters)
Sets the search parameters.
Calculates a consensus from multiple ID runs based on PEPs and shared ions.
Definition: ConsensusIDAlgorithmPEPIons.h:48
double fragment_mass_tolerance
Mass tolerance of fragment ions (Dalton or ppm)
Definition: ProteinIdentification.h:269
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.
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.
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
const SearchParameters & getSearchParameters() const
Returns the search parameters.
std::vector< String > fixed_modifications
Used fixed modifications.
Definition: ProteinIdentification.h:266
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
void setSearchEngine(const String &search_engine)
Sets the search engine type.
double precursor_mass_tolerance
Mass tolerance of precursor ions (Dalton or ppm)
Definition: ProteinIdentification.h:271
bool update(const Param &p_outdated, const bool add_unknown=false)
Rescue parameter values from p_outdated to current param.
Int charge
Definition: ConsensusIDAlgorithm.h:86
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 ':')
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...
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:170
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLFile.h:68
static String stripExtension(const String &filename)
If filename contains an extension, it will be removed (including the '.'). Special extensions,...
void setDateTime(const DateTime &date)
Sets the date of the protein identification run.
bool precursor_mass_tolerance_ppm
Mass tolerance unit of precursor ions (true: ppm, false: Dalton)
Definition: ProteinIdentification.h:272
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:111
void apply(std::vector< PeptideIdentification > &ids, const std::map< String, String > &se_info, Size number_of_runs=0)
Calculates the consensus ID for a set of peptide identifications of one spectrum or (consensus) featu...
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:109
Size considered_hits_
Number of peptide hits considered per ID run (input parameter)
Definition: ConsensusIDAlgorithm.h:106
Search parameters of the DB search.
Definition: ProteinIdentification.h:258
void setMZ(double mz)
sets the MZ of the MS2 spectrum
EnzymaticDigestion::Specificity enzyme_term_specificity
The number of required cutting-rule matching termini during search (none=0, semi=1,...
Definition: ProteinIdentification.h:274
std::ifstream infile
Questionable file tested by TEST_FILE_EQUAL.
std::vector< double > scores
Definition: ConsensusIDAlgorithm.h:87
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