TOPPMetaProSIP Class Reference

Inheritance diagram for TOPPMetaProSIP:

Public Member Functions
	TOPPMetaProSIP ()
Public Member Functions inherited from TOPPBase
	TOPPBase (const String &name, const String &description, bool official=true, const std::vector< Citation > &citations={})
	Constructor. More...
virtual	~TOPPBase ()
	Destructor. More...
ExitCodes	main (int argc, const char **argv)
	Main routine of all TOPP applications. More...

Protected Member Functions
void	registerOptionsAndFlags_ () override
	Sets the valid command line options (with argument) and flags (without argument). More...
void	filterIsotopicIntensities (vector< double >::const_iterator &pattern_begin, vector< double >::const_iterator &pattern_end, vector< double >::const_iterator &intensities_begin, vector< double >::const_iterator &intensities_end, double TIC_threshold=0.99)
	> filter intensity to remove noise or additional incorporation peaks that otherwise might interfere with correlation calculation More...
void	calculateCorrelation (Size n_element, const vector< double > &isotopic_intensities, IsotopePatterns patterns, MapRateToScoreType &map_rate_to_correlation_score, String labeling_element, double mass, double min_correlation_distance_to_averagine)
	Returns highest scoring rate and score pair in the map. More...
void	getBestRateScorePair (const MapRateToScoreType &map_rate_to_score, double &best_rate, double &best_score)
PeakSpectrum	extractPeakSpectrum (Size element_count, double mass_diff, double rt, double feature_hit_theoretical_mz, Int feature_hit_charge, const PeakMap &peak_map)
vector< double >	extractIsotopicIntensities (Size element_count, double mass_diff, double mz_tolerance_ppm, double seed_rt, double seed_mz, double seed_charge, const PeakMap &peak_map)
void	writePeakIntensities_ (SVOutStream &out_stream, vector< double > isotopic_intensities, bool write_13Cpeaks)
MapRateToScoreType	normalizeToMax (const MapRateToScoreType &map_rate_to_decomposition_weight)
vector< double >	findApexRT (const FeatureMap::iterator feature_it, double hit_rt, const PeakMap &peak_map, Size n_scans)
PeakSpectrum	mergeSpectra (const PeakMap &to_merge)
PeakSpectrum	isotopicIntensitiesToSpectrum (double mz_start, double mass_diff, Int charge, vector< double > isotopic_intensities)
	> converts a vector of isotopic intensities to a peak spectrum starting at mz=mz_start with mass_diff/charge step size More...
void	extractIncorporationsAtCorrelationMaxima (SIPPeptide &sip_peptide, const IsotopePatterns &patterns, double weight_merge_window=5.0, double min_corr_threshold=0.5, double min_decomposition_weight=10.0)
void	extractIncorporationsAtHeighestDecompositionWeights (SIPPeptide &sip_peptide, const IsotopePatterns &patterns, double weight_merge_window=5.0, double min_corr_threshold=0.5, double min_low_RIA_threshold=-1, double min_decomposition_weight=10.0)
	> Collect decomposition coefficients. Starting at the largest decomposition weights merge smaller weights in the merge window. More...
double	calculateGlobalLR (const vector< double > &isotopic_intensities)
	> calculate the global labeling ration based on all but the first 4 peaks More...
ExitCodes	main_ (int, const char **) override
	The actual "main" method. main_() is invoked by main(). More...
Protected Member Functions inherited from TOPPBase
const String &	getIniLocation_ () const
	Returns the location of the ini file where parameters are taken from. E.g. if the command line was TOPPTool -instance 17, then this will be "TOPPTool:17:". Note the ':' at the end. More...
const String &	toolName_ () const
	Returns the tool name. More...
void	printUsage_ ()
	Prints the tool-specific command line options and appends the common options. More...
bool	parseRange_ (const String &text, double &low, double &high) const
	Parses a range string ([a]:[b]) into two variables (doubles) More...
bool	parseRange_ (const String &text, Int &low, Int &high) const
	Parses a range string ([a]:[b]) into two variables (integers) More...
bool	writeCTD_ ()
	Write common tool description (CTD) file. More...
ExitCodes	writeWSDL_ (const String &filename)
	Write WSDL file and validate it. Returns EXECUTION_OK or INTERNAL_ERROR (if validation failed) More...
String	getParamArgument_ (const Param::ParamEntry &entry) const
	Utility function that determines a suitable argument value for the given Param::ParamEntry. More...
std::vector< ParameterInformation >	paramToParameterInformation_ (const Param &param) const
	Translates the given parameter object into a vector of ParameterInformation, that can be utilized for cl parsing. More...
ParameterInformation	paramEntryToParameterInformation_ (const Param::ParamEntry &entry, const String &argument="", const String &full_name="") const
	Transforms a ParamEntry object to command line parameter (ParameterInformation). More...
void	registerParamSubsectionsAsTOPPSubsections_ (const Param &param)
void	registerFullParam_ (const Param &param)
	Register command line parameters for all entries in a Param object. More...
void	registerStringOption_ (const String &name, const String &argument, const String &default_value, const String &description, bool required=true, bool advanced=false)
	Registers a string option. More...
void	setValidStrings_ (const String &name, const std::vector< String > &strings)
	Sets the valid strings for a string option or a whole string list. More...
void	setValidStrings_ (const String &name, const std::string vstrings[], int count)
	Sets the valid strings for a string option or a whole string list. More...
void	registerInputFile_ (const String &name, const String &argument, const String &default_value, const String &description, bool required=true, bool advanced=false, const StringList &tags=StringList())
	Registers an input file option. More...
void	registerOutputFile_ (const String &name, const String &argument, const String &default_value, const String &description, bool required=true, bool advanced=false)
	Registers an output file option. More...
void	setValidFormats_ (const String &name, const std::vector< String > &formats, const bool force_OpenMS_format=true)
	Sets the formats for a input/output file option or for all members of an input/output file lists. More...
void	registerDoubleOption_ (const String &name, const String &argument, double default_value, const String &description, bool required=true, bool advanced=false)
	Registers a double option. More...
void	setMinInt_ (const String &name, Int min)
	Sets the minimum value for the integer parameter(can be a list of integers,too) name. More...
void	setMaxInt_ (const String &name, Int max)
	Sets the maximum value for the integer parameter(can be a list of integers,too) name. More...
void	setMinFloat_ (const String &name, double min)
	Sets the minimum value for the floating point parameter(can be a list of floating points,too) name. More...
void	setMaxFloat_ (const String &name, double max)
	Sets the maximum value for the floating point parameter(can be a list of floating points,too) name. More...
void	registerIntOption_ (const String &name, const String &argument, Int default_value, const String &description, bool required=true, bool advanced=false)
	Registers an integer option. More...
void	registerIntList_ (const String &name, const String &argument, IntList default_value, const String &description, bool required=true, bool advanced=false)
	Registers a list of integers option. More...
void	registerDoubleList_ (const String &name, const String &argument, DoubleList default_value, const String &description, bool required=true, bool advanced=false)
	Registers a list of doubles option. More...
void	registerStringList_ (const String &name, const String &argument, StringList default_value, const String &description, bool required=true, bool advanced=false)
	Registers a list of strings option. More...
void	registerInputFileList_ (const String &name, const String &argument, StringList default_value, const String &description, bool required=true, bool advanced=false, const StringList &tags=StringList())
	Registers a list of input files option. More...
void	registerOutputFileList_ (const String &name, const String &argument, StringList default_value, const String &description, bool required=true, bool advanced=false)
	Registers a list of output files option. More...
void	registerFlag_ (const String &name, const String &description, bool advanced=false)
	Registers a flag. More...
void	registerSubsection_ (const String &name, const String &description)
	Registers an allowed subsection in the INI file (usually from OpenMS algorithms). More...
void	registerTOPPSubsection_ (const String &name, const String &description)
	Registers an allowed subsection in the INI file originating from the TOPP tool itself. More...
void	addEmptyLine_ ()
	Adds an empty line between registered variables in the documentation. More...
String	getStringOption_ (const String &name) const
	Returns the value of a previously registered string option. More...
double	getDoubleOption_ (const String &name) const
	Returns the value of a previously registered double option. More...
Int	getIntOption_ (const String &name) const
	Returns the value of a previously registered integer option. More...
StringList	getStringList_ (const String &name) const
	Returns the value of a previously registered StringList. More...
IntList	getIntList_ (const String &name) const
	Returns the value of a previously registered IntList. More...
DoubleList	getDoubleList_ (const String &name) const
	Returns the value of a previously registered DoubleList. More...
bool	getFlag_ (const String &name) const
	Returns the value of a previously registered flag. More...
const ParameterInformation &	findEntry_ (const String &name) const
	Finds the entry in the parameters_ array that has the name name. More...
Param const &	getParam_ () const
	Return all parameters relevant to this TOPP tool. More...
void	checkParam_ (const Param &param, const String &filename, const String &location) const
	Checks top-level entries of param according to the information during registration. More...
void	checkIfIniParametersAreApplicable_ (const Param &ini_params)
	Checks if the parameters of the provided ini file are applicable to this tool. More...
void	writeLog_ (const String &text) const
	Writes a string to the log file and to std::cout. More...
void	writeDebug_ (const String &text, UInt min_level) const
	Writes a text to the log file and to std::cout if the debug level is at least min_level. More...
void	writeDebug_ (const String &text, const Param &param, UInt min_level) const
	Writes a String followed by a Param to the log file and to std::cout if the debug level is at least min_level. More...
String	makeTempDirectory_ () const
	Creates a unique temporary directory and returns its name (you have to clean it up yourself) More...
String	makeAutoRemoveTempDirectory_ (Int keep_debug=2)
	Creates a unique temporary directory and returns its name (will be cleaned up automatically if debug level is high enough) More...
void	removeTempDirectory_ (const String &dirname, Int keep_debug=2) const
	Removes a (temporary) directory. More...
ExitCodes	runExternalProcess_ (const QString &executable, const QStringList &arguments, const QString &workdir="") const
	Runs an external process via QProcess and reports its status in the logs. More...
void	inputFileReadable_ (const String &filename, const String &param_name) const
	Checks if an input file exists, is readable and is not empty. More...
void	outputFileWritable_ (const String &filename, const String &param_name) const
	Checks if an output file is writable. More...
void	addDataProcessing_ (ConsensusMap &map, const DataProcessing &dp) const
	Data processing setter for consensus maps. More...
void	addDataProcessing_ (FeatureMap &map, const DataProcessing &dp) const
	Data processing setter for feature maps. More...
void	addDataProcessing_ (PeakMap &map, const DataProcessing &dp) const
	Data processing setter for peak maps. More...
DataProcessing	getProcessingInfo_ (DataProcessing::ProcessingAction action) const
	Returns the data processing information. More...
DataProcessing	getProcessingInfo_ (const std::set< DataProcessing::ProcessingAction > &actions) const
	Returns the data processing information. More...

Protected Attributes
Size	ADDITIONAL_ISOTOPES
std::string	FEATURE_STRING
std::string	UNASSIGNED_ID_STRING
std::string	UNIDENTIFIED_STRING
Protected Attributes inherited from TOPPBase
String	version_
	Version string (if empty, the OpenMS/TOPP version is printed) More...
String	verboseVersion_
	Version string including additional revision/date time information. Note: This differs from version_ only if not provided by the user. More...
bool	official_
	Flag indicating if this an official TOPP tool. More...
std::vector< Citation >	citations_
	Papers, specific for this tool (will be shown in '–help') More...
ProgressLogger::LogType	log_type_
	Type of progress logging. More...
bool	test_mode_
	Test mode. More...
Int	debug_level_
	Debug level set by -debug. More...

Additional Inherited Members
Public Types inherited from TOPPBase
enum	ExitCodes {   EXECUTION_OK, INPUT_FILE_NOT_FOUND, INPUT_FILE_NOT_READABLE, INPUT_FILE_CORRUPT,   INPUT_FILE_EMPTY, CANNOT_WRITE_OUTPUT_FILE, ILLEGAL_PARAMETERS, MISSING_PARAMETERS,   UNKNOWN_ERROR, EXTERNAL_PROGRAM_ERROR, PARSE_ERROR, INCOMPATIBLE_INPUT_DATA,   INTERNAL_ERROR, UNEXPECTED_RESULT }
	Exit codes. More...
Static Public Member Functions inherited from TOPPBase
static void	setMaxNumberOfThreads (int num_threads)
	Sets the maximal number of usable threads. More...
Static Protected Attributes inherited from TOPPBase
static String	topp_ini_file_
	.TOPP.ini file for storing system default parameters More...
static const Citation	cite_openms_
	The OpenMS citation. More...

Constructor & Destructor Documentation

TOPPMetaProSIP()

TOPPMetaProSIP ( )

inline

Member Function Documentation

calculateCorrelation()

void calculateCorrelation ( Size  n_element, const vector< double > &  isotopic_intensities, IsotopePatterns  patterns, MapRateToScoreType &  map_rate_to_correlation_score, String  labeling_element, double  mass, double  min_correlation_distance_to_averagine  )

inlineprotected

Returns highest scoring rate and score pair in the map.

References CoarseIsotopePatternGenerator::estimateFromPeptideWeight(), IsotopeDistribution::getContainer(), and OpenMS::Math::pearsonCorrelationCoefficient().

calculateGlobalLR()

double calculateGlobalLR ( const vector< double > &  isotopic_intensities )

inlineprotected

> calculate the global labeling ration based on all but the first 4 peaks

References OpenMS::Math::sum().

extractIncorporationsAtCorrelationMaxima()

void extractIncorporationsAtCorrelationMaxima ( SIPPeptide &  sip_peptide, const IsotopePatterns &  patterns, double  weight_merge_window = 5.0, double  min_corr_threshold = 0.5, double  min_decomposition_weight = 10.0  )

inlineprotected

> Collect decomposition coefficients in the merge window around the correlation maximum. > Final list of RIAs is constructed for the peptide.

References SIPIncorporation::abundance, SIPPeptide::charge, SIPIncorporation::correlation, SIPPeptide::correlation_map, SIPPeptide::correlation_maxima, SIPPeptide::decomposition_map, SIPPeptide::explained_TIC_fraction, SIPPeptide::incorporations, OpenMS::Constants::k, LOG_WARN, SIPPeptide::mass_diff, SIPPeptide::mz_theo, SIPPeptide::non_zero_decomposition_coefficients, and SIPIncorporation::rate.

extractIncorporationsAtHeighestDecompositionWeights()

void extractIncorporationsAtHeighestDecompositionWeights ( SIPPeptide &  sip_peptide, const IsotopePatterns &  patterns, double  weight_merge_window = 5.0, double  min_corr_threshold = 0.5, double  min_low_RIA_threshold = -1, double  min_decomposition_weight = 10.0  )

inlineprotected

> Collect decomposition coefficients. Starting at the largest decomposition weights merge smaller weights in the merge window.

References SIPIncorporation::abundance, SIPPeptide::charge, SIPIncorporation::correlation, SIPPeptide::correlation_map, SIPPeptide::decomposition_map, SIPPeptide::explained_TIC_fraction, SIPPeptide::incorporations, SIPPeptide::mass_diff, SIPPeptide::mz_theo, SIPPeptide::non_zero_decomposition_coefficients, and SIPIncorporation::rate.

extractIsotopicIntensities()

vector<double> extractIsotopicIntensities ( Size  element_count, double  mass_diff, double  mz_tolerance_ppm, double  seed_rt, double  seed_mz, double  seed_charge, const PeakMap &  peak_map  )

inlineprotected

References MSExperiment::areaBeginConst(), MSExperiment::areaEndConst(), and OpenMS::Constants::k.

extractPeakSpectrum()

PeakSpectrum extractPeakSpectrum ( Size  element_count, double  mass_diff, double  rt, double  feature_hit_theoretical_mz, Int  feature_hit_charge, const PeakMap &  peak_map  )

inlineprotected

References MSSpectrum::MZBegin(), MSSpectrum::MZEnd(), and MSExperiment::RTBegin().

filterIsotopicIntensities()

void filterIsotopicIntensities ( vector< double >::const_iterator &  pattern_begin, vector< double >::const_iterator &  pattern_end, vector< double >::const_iterator &  intensities_begin, vector< double >::const_iterator &  intensities_end, double  TIC_threshold = 0.99  )

inlineprotected

> filter intensity to remove noise or additional incorporation peaks that otherwise might interfere with correlation calculation

Calculates the correlation between measured isotopic_intensities and the theoretical isotopic patterns for all incorporation rates

References LOG_ERROR.

findApexRT()

vector<double> findApexRT ( const FeatureMap::iterator  feature_it, double  hit_rt, const PeakMap &  peak_map, Size  n_scans  )

inlineprotected

References MSExperiment::areaBeginConst(), MSExperiment::areaEndConst(), AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT >::getRT(), DIntervalBase< D >::maxPosition(), DIntervalBase< D >::minPosition(), MSExperiment::RTBegin(), Peak2D::setIntensity(), Peak2D::setMZ(), and Peak2D::setRT().

getBestRateScorePair()

void getBestRateScorePair ( const MapRateToScoreType &  map_rate_to_score, double &  best_rate, double &  best_score  )

inlineprotected

isotopicIntensitiesToSpectrum()

PeakSpectrum isotopicIntensitiesToSpectrum ( double  mz_start, double  mass_diff, Int  charge, vector< double >  isotopic_intensities  )

inlineprotected

> converts a vector of isotopic intensities to a peak spectrum starting at mz=mz_start with mass_diff/charge step size

References Peak1D::setIntensity(), and Peak1D::setMZ().

main_()

ExitCodes main_ ( int  argc, const char **  argv  )

inlineoverrideprotectedvirtual

The actual "main" method. main_() is invoked by main().

< number of PSMs. If 0 IDMapper has not been called.

Implements TOPPBase.

References SIPPeptide::accessions, SIPPeptide::accumulated, PeptideIdentification::assignRanks(), MetaProSIPDecomposition::calculateDecompositionWeightsIsotopicPatterns(), MetaProSIPDecomposition::calculateIsotopePatternsFor13CRange(), MetaProSIPDecomposition::calculateIsotopePatternsFor13CRangeOfAveraginePeptide(), MetaProSIPDecomposition::calculateIsotopePatternsFor15NRange(), MetaProSIPDecomposition::calculateIsotopePatternsFor15NRangeOfAveraginePeptide(), MetaProSIPDecomposition::calculateIsotopePatternsFor18ORange(), MetaProSIPDecomposition::calculateIsotopePatternsFor18ORangeOfAveraginePeptide(), MetaProSIPDecomposition::calculateIsotopePatternsFor2HRange(), MetaProSIPDecomposition::calculateIsotopePatternsFor2HRangeOfAveraginePeptide(), SIPPeptide::charge, RIntegration::checkRDependencies(), MSExperiment::clear(), MetaProSIPClustering::clusterSIPPeptides(), SIPPeptide::correlation_map, SIPPeptide::correlation_maxima, MetaProSIPReporting::createCSVReport(), MetaProSIPReporting::createPeptideCentricCSVReport(), MetaProSIPReporting::createQualityReport(), SIPPeptide::decomposition_map, MSExperiment::empty(), PeptideHit::extractProteinAccessionsSet(), MetaProSIPXICExtraction::extractXICsOfIsotopeTraces(), SIPPeptide::feature_mz, SIPPeptide::feature_rt, SIPPeptide::feature_type, ThresholdMower::filterPeakMap(), seqan::find(), AASequence::fromString(), Residue::Full, PeptideHit::getCharge(), AASequence::getFormula(), MetaProSIPInterpolation::getHighPoints(), PeptideIdentification::getHits(), MSExperiment::getMaxRT(), MSExperiment::getMinRT(), AASequence::getMonoWeight(), MetaProSIPDecomposition::getNumberOfLabelingElements(), MzMLFile::getOptions(), MetaProSIPClustering::getRIAClusterCenter(), PeptideHit::getScore(), PeptideHit::getSequence(), File::getTempDirectory(), FeatureMap::getUnassignedPeptideIdentifications(), SIPPeptide::global_LR, SIPPeptide::incorporations, PeptideIdentification::insertHit(), MzMLFile::load(), FeatureXMLFile::load(), FASTAFile::load(), LOG_DEBUG, LOG_ERROR, LOG_INFO, LOG_WARN, SIPPeptide::mass_diff, SIPPeptide::mass_theo, SIPPeptide::mz_theo, SIPPeptide::patterns, OpenMS::Constants::PROTON_MASS_U, String::random(), SIPPeptide::reconstruction_monoistopic, SIPPeptide::RR, MSExperiment::RTBegin(), SIPPeptide::score, SIPPeptide::sequence, PeptideHit::setCharge(), PeptideIdentification::setHigherScoreBetter(), PeptideIdentification::setHits(), MetaInfoInterface::setMetaValue(), MSSpectrum::setMSLevel(), PeakFileOptions::setMSLevels(), Peak2D::setMZ(), DefaultParamHandler::setParameters(), BaseFeature::setPeptideIdentifications(), Peak2D::setRT(), PeptideHit::setSequence(), Param::setValue(), MSExperiment::size(), MSExperiment::sortSpectra(), String::substitute(), String::toQString(), AASequence::toString(), String::toUpper(), String::trim(), SIPPeptide::unique, FeatureMap::updateRanges(), and MSExperiment::updateRanges().

mergeSpectra()

PeakSpectrum mergeSpectra ( const PeakMap &  to_merge )

inlineprotected

References MSExperiment::size(), and MSSpectrum::sortByPosition().

normalizeToMax()

MapRateToScoreType normalizeToMax ( const MapRateToScoreType &  map_rate_to_decomposition_weight )

inlineprotected

References LOG_DEBUG.

registerOptionsAndFlags_()

void registerOptionsAndFlags_ ( )

inlineoverrideprotectedvirtual

Sets the valid command line options (with argument) and flags (without argument).

The options '-ini' '-log' '-instance' '-debug' and the flag '–help' are automatically registered.

Implements TOPPBase.

writePeakIntensities_()

void writePeakIntensities_ ( SVOutStream &  out_stream, vector< double >  isotopic_intensities, bool  write_13Cpeaks  )

inlineprotected

References OpenMS::Constants::k, String::number(), and OpenMS::Internal::ClassTest::ratio.

Member Data Documentation

ADDITIONAL_ISOTOPES

Size ADDITIONAL_ISOTOPES

protected

FEATURE_STRING

std::string FEATURE_STRING

protected

UNASSIGNED_ID_STRING

std::string UNASSIGNED_ID_STRING

protected

UNIDENTIFIED_STRING

std::string UNIDENTIFIED_STRING

protected