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OpenMS
2.4.0
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103 std::vector<MultiplexIsotopicPeakPattern> generatePeakPatterns_(
int charge_min,
int charge_max,
int peaks_per_peptide_max,
const std::vector<MultiplexDeltaMasses>& mass_pattern_list);
113 std::vector<double> determinePeptideIntensitiesCentroided_(
const MultiplexIsotopicPeakPattern& pattern,
const std::multimap<size_t, MultiplexSatelliteCentroided >& satellites);
123 std::vector<double> determinePeptideIntensitiesProfile_(
const MultiplexIsotopicPeakPattern& pattern,
const std::multimap<size_t, MultiplexSatelliteProfile >& satellites);
132 void generateMapsCentroided_(
const std::vector<MultiplexIsotopicPeakPattern>& patterns,
const std::vector<MultiplexFilteredMSExperiment>& filter_results, std::vector<std::map<int, GridBasedCluster> >& cluster_results);
141 void generateMapsProfile_(
const std::vector<MultiplexIsotopicPeakPattern>& patterns,
const std::vector<MultiplexFilteredMSExperiment>& filter_results,
const std::vector<std::map<int, GridBasedCluster> >& cluster_results);
Base class for TOPP applications.
Definition: TOPPBase.h:150
ConsensusMap consensus_map_
Definition: FeatureFinderMultiplexAlgorithm.h:91
void run(const PeakMap &, std::vector< MassTrace > &)
Main method of MassTraceDetection. Extracts mass traces of a MSExperiment and gathers them into a vec...
Param copy(const String &prefix, bool remove_prefix=false) const
Returns a new Param object containing all entries that start with prefix.
A mass trace extraction method that gathers peaks similar in m/z and moving along retention time.
Definition: MassTraceDetection.h:72
void run(MSExperiment &exp, bool progress)
main method for feature detection
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
Base::iterator Iterator
Definition: FeatureMap.h:137
Param getParameters(const String &algorithm_name) const
Returns the default parameters for the algorithm with name algorithm_name.
void sortSpectra(bool sort_mz=true)
Sorts the data points by retention time.
void store(const String &filename, const PeakMap &map) const
Stores a map in an MzML file.
void setValue(const String &key, const DataValue &value, const String &description="", const StringList &tags=StringList())
Sets a value.
File adapter for MzML files.
Definition: MzMLFile.h:55
ProgressLogger prog_log_
Definition: FeatureFinderMultiplexAlgorithm.h:75
A more convenient string class.
Definition: String.h:57
Iterator begin()
Definition: MSExperiment.h:157
void setValidStrings(const String &key, const std::vector< String > &strings)
Sets the valid strings for the parameter key.
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
data structure for pattern of isotopic peaks
Definition: MultiplexIsotopicPeakPattern.h:54
#define LOG_ERROR
Macro to be used if non-fatal error are reported (processing continues)
Definition: LogStream.h:446
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
bool progress_
Definition: FeatureFinderMultiplexAlgorithm.h:77
#define LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:454
static const String getProductName()
const DataValue & getValue(const String &key) const
Returns a value of a parameter.
void setPrimaryMSRunPath(const StringList &s)
set the file path to the primary MS run (usually the mzML file obtained after data conversion from ra...
#define OPENMS_PRECONDITION(condition, message)
Precondition macro.
Definition: openms/include/OpenMS/CONCEPT/Macros.h:106
FeatureMap & getFeatureMap()
get methods
@ PROFILE
profile data
Definition: SpectrumSettings.h:74
Size size() const
Definition: MSExperiment.h:127
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
std::map< String, double > label_mass_shift_
Definition: FeatureFinderMultiplexAlgorithm.h:87
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:175
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
bool toBool() const
Conversion to bool.
#define LOG_DEBUG
Macro for general debugging information.
Definition: LogStream.h:458
static const std::string NamesOfPolarity[SIZE_OF_POLARITY]
Names of polarity of the ion source.
Definition: IonSource.h:147
Extracts chromatographic peaks from a mass trace.
Definition: ElutionPeakDetection.h:76
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
#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
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...
SpectrumType
Spectrum peak type.
Definition: SpectrumSettings.h:70
unsigned charge_min_
Definition: FeatureFinderMultiplexAlgorithm.h:79
ConsensusMap & getConsensusMap()
unsigned charge_max_
Definition: FeatureFinderMultiplexAlgorithm.h:80
The main feature finder class.
Definition: FeatureFinder.h:56
Size setUniqueId()
Assigns a new, valid unique id. Always returns 1.
Definition: UniqueIdInterface.h:150
void setParameters(const Param ¶m)
Sets the parameters.
MSExperiment exp_profile_
Definition: FeatureFinderMultiplexAlgorithm.h:72
Size applyMemberFunction(Size(Type::*member_function)())
Applies a member function of Type to the container itself and all features (including subordinates)....
Definition: FeatureMap.h:274
const Param & getDefaults() const
Non-mutable access to the default parameters.
const Param & getParameters() const
Non-mutable access to the parameters.
bool empty() const
Definition: MSExperiment.h:137
void filterByPeakWidth(std::vector< MassTrace > &, std::vector< MassTrace > &)
Filter out mass traces below lower 5 % quartile and above upper 95 % quartile.
static const String getProductName()
A container for consensus elements.
Definition: ConsensusMap.h:75
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:73
void store(const String &filename, const FeatureMap &feature_map)
stores the map feature_map in file with name filename.
unsigned isotopes_per_peptide_max_
Definition: FeatureFinderMultiplexAlgorithm.h:83
void addChromatogram(const MSChromatogram &chromatogram)
adds a chromatogram to the list
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
const ColumnHeaders & getColumnHeaders() const
Non-mutable access to the file descriptions.
MSExperiment exp_centroid_
Definition: FeatureFinderMultiplexAlgorithm.h:73
void setSectionDescription(const String &key, const String &description)
Sets a description for an existing section.
A container for features.
Definition: FeatureMap.h:93
void remove(const String &key)
Remove the entry key or a section key (when suffix is ':')
Iterator end()
Definition: MSExperiment.h:167
FeatureMap feature_map_
Definition: FeatureFinderMultiplexAlgorithm.h:90
const std::vector< MSSpectrum > & getSpectra() const
returns the spectrum list
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLFile.h:68
Options for loading files containing peak data.
Definition: PeakFileOptions.h:47
void getPrimaryMSRunPath(StringList &toFill) const
get the file path to the first MS run
@ QUANTITATION
Quantitation.
Definition: DataProcessing.h:72
Definition: FeatureFinderMultiplexAlgorithm.h:55
void detectPeaks(MassTrace &mt, std::vector< MassTrace > &single_mtraces)
Extracts chromatographic peaks from a single MassTrace and stores the resulting split traces in a vec...
void updateRanges() override
Updates minimum and maximum position/intensity.
Management and storage of parameters / INI files.
Definition: Param.h:74
void setMSLevels(const std::vector< Int > &levels)
sets the desired MS levels for peaks to load
void run(const String &algorithm_name, PeakMap &input_map, FeatureMap &features, const Param ¶m, const FeatureMap &seeds)
Executes the FeatureFinder using the given algorithm.
File is empty.
Definition: Exception.h:594
void insert(const String &prefix, const Param ¶m)
PeakFileOptions & getOptions()
Mutable access to the options for loading/storing.
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!
This class provides Input functionality for ConsensusMaps and Output functionality for alignments and...
Definition: ConsensusXMLFile.h:61
unsigned isotopes_per_peptide_min_
Definition: FeatureFinderMultiplexAlgorithm.h:82