Matrix Science header

ms_ms1quantitation Member List

This is the complete list of members for ms_ms1quantitation, including all inherited members.
addMatchInferred(const ms_ms1quant_match &siblingMatch, int newCharge)ms_ms1quantitation
addMatchPeptide(matrix_science::ms_protein *hit, matrix_science::ms_peptide *peptide, const matrix_science::ms_quant_component &component)ms_ms1quantitation
addMatchStatus(matrix_science::ms_peptide *peptide, matrix_science::ms_ms1quant_peptide_status::peptideStatus status, matrix_science::ms_protein *hit=0)ms_ms1quantitation
addPeptideQuantKey(const std::string &accession, int dbIdx, const ms_peptide_quant_key &key)ms_customquantitation
addPeptideQuantKeys(const std::string &accession, int dbIdx, const std::vector< ms_peptide_quant_key > &keys)ms_customquantitation
addPeptideQuantKeys(const std::string &accession, int dbIdx, const ms_peptide_quant_key_vector &keys)ms_customquantitation
addPeptideRatio(const ms_peptide_quant_ratio &ratio)ms_customquantitation
appendErrors(const ms_errors &src)ms_errors
calculateGeometricMeanRatio(const std::string &accession, int dbIdx, const std::string &ratioName, const std::vector< double > &sample, const std::vector< double > &logSample, const std::vector< ms_peptide_quant_key > &activeKeys, const std::map< ms_peptide_quant_key, int > &inactiveKeys, double normalityPvalue) const ms_quantitation [protected]
calculateMedianRatio(const std::string &accession, int dbIdx, const std::string &ratioName, const std::vector< double > &sample, const std::vector< double > &logSample, const std::vector< ms_peptide_quant_key > &activeKeys, const std::map< ms_peptide_quant_key, int > &inactiveKeys, double normalityPvalue) const ms_quantitation [protected]
calculateWeightedGeometricMeanRatio(const std::string &accession, int dbIdx, const std::string &ratioName, const std::vector< double > &sample, const std::vector< double > &logSample, const std::vector< double > &weights, const std::vector< ms_peptide_quant_key > &activeKeys, const std::map< ms_peptide_quant_key, int > &inactiveKeys, double normalityPvalue) const ms_quantitation [protected]
clearAllErrors()ms_errors
clearPeptideQuantKeys(const std::string &accession, int dbIdx)ms_customquantitation
clearPeptideRatios()ms_customquantitation
copyFrom(const ms_errors *right)ms_errors
countDistinctPeptides(const std::vector< ms_peptide_quant_key > &activeKeys) const ms_ms1quantitation [protected, virtual]
findMatch(matrix_science::ms_peptide_quant_key matchKey, ms_ms1quant_match *match) const ms_ms1quantitation
findPeptideStatus(int query, int rank, ms_ms1quant_peptide_status *peptideStatus) const ms_ms1quantitation
getAveragePeptideIntensity(const std::string &accession, int dbIdx, double *averageIntensity, int *sampleSize, ms_peptide_quant_key_vector *includeKeys, ms_peptide_quant_key_vector *excludeKeys) const ms_ms1quantitation
getAverageResults() const ms_ms1quantitation
getErrorHandler() const ms_errors
getHit(int index1) const ms_ms1quantitation
getLabelFree(std::string peptideStr, std::string varMods, std::string summedMods, const matrix_science::ms_quant_component &comp) const ms_ms1quantitation
getLastError() const ms_errors
getLastErrorString() const ms_errors
getMatch(int index) const ms_ms1quantitation
getMatch(ms_peptide_quant_key &key) const ms_ms1quantitation
getMatchForHit(int index, int hitId, int memberNumber) const ms_ms1quantitation
getMinNumPeptides() const ms_quantitation [protected]
getNumHits() const ms_ms1quantitation
getNumMatches() const ms_ms1quantitation
getNumMatchesForHit(int hitId, int memberNumber) const ms_ms1quantitation
getNumPeptideStatuses() const ms_ms1quantitation
getPeptideQuantKeys(const std::string &accession, int dbIdx) const ms_quantitation
getPeptideRatio(const ms_peptide_quant_key &key, const std::string &ratioName) const ms_customquantitation [virtual]
getPeptideRatioNormalisationBase(const std::string &ratioName) const ms_quantitation
getPeptideStatus(int index) const ms_ms1quantitation
getProgressInfo()ms_ms1quantitation
getProteinRatio(const std::string &accession, int dbIdx, const std::string &ratioName) const ms_ms1quantitation [virtual]
getProteinRatio(const std::string &accession, int dbIdx, const std::string &ratioName, const ms_peptide_quant_key_vector &includeKeys, const ms_peptide_quant_key_vector &excludeKeys) const ms_ms1quantitation [virtual]
getProteinRatioSample(const std::string &accession, int dbIdx, const std::string &ratioName, const std::vector< ms_peptide_quant_key > &includeKeys, const std::vector< ms_peptide_quant_key > &excludeKeys, std::vector< double > &sample, std::vector< double > &logSample, std::vector< double > &weights, std::vector< ms_peptide_quant_key > &activeKeys, std::map< ms_peptide_quant_key, int > &inactiveKeys, double &normalityPvalue) const ms_quantitation [protected]
getQuantitationDatasources() const ms_ms1quantitation
getQuantitationMethod() const ms_quantitation
getReadableVarMods(std::string varmods)ms_ms1quantitation
getReadableVarModsConcise(std::string varmods)ms_ms1quantitation
getSortedFinitePeptideRatioValues(const std::string &ratioName, const std::set< ms_peptide_quant_key > &keys, const std::set< ms_peptide_quant_key > &includeKeys, const std::set< ms_peptide_quant_key > &excludeKEys, std::vector< double > &values, std::vector< double > &weights, std::vector< ms_peptide_quant_key > &activeKeys, std::map< ms_peptide_quant_key, int > &inactiveKeys) const ms_customquantitation [protected, virtual]
getSummary() const ms_ms1quantitation
getUnnormalisedAveragePeptideRatio(const std::string &ratioName, const std::string &averageType) const ms_customquantitation
getUnnormalisedAveragePeptideRatio(const std::string &ratioName, const std::string &averageType, const ms_peptide_quant_key_vector &keys) const ms_customquantitation
getUnnormalisedAveragePeptideRatio(const std::string &ratioName, const std::string &averageType, const std::string &accession, int dbIdx) const ms_customquantitation
hasPeptideRatio(const ms_peptide_quant_key &key, const std::string &ratioName) const ms_customquantitation [virtual]
initialiseBaseSettings(const ms_quant_method &qmBase, const ms_quant_method &qmConfig)ms_quantitation [protected]
isAverageProtocol() const ms_ms1quantitation
isPeptideRatioExcluded(const ms_peptide_quant_key &key, const std::string &ratioName) const ms_customquantitation [virtual]
isValid() const ms_errors
loadCdbFile(const std::string &cdbFilename, const std::string &cacheFilename, bool revalidateQualityThresholds=true)ms_ms1quantitation
loadXmlFile(const std::string &filename, const std::string &xmlSchemaPath)ms_ms1quantitation
mergeQuantitationResults(const matrix_science::ms_peptidesummary &summary, const matrix_science::ms_quant_method &method, const std::vector< std::string > &cdbFilenames, const std::vector< std::string > &cacheFilenames, const matrix_science::ms_quant_method *originalMethod=0)ms_ms1quantitation [static]
mergeQuantitationResults(const matrix_science::ms_peptidesummary &summary, const matrix_science::ms_quant_method &method, const std::vector< std::string > &xmlFilenames, const std::string &xmlSchemaPath="", const matrix_science::ms_quant_method *originalMethod=0)ms_ms1quantitation [static]
ms_customquantitation(const ms_quant_method &qm)ms_customquantitation [explicit]
ms_customquantitation(const ms_peptidesummary &initFrom)ms_customquantitation [explicit]
ms_customquantitation(const ms_peptidesummary &initFrom, const ms_quant_method &qm)ms_customquantitation
ms_customquantitation(const ms_ms2quantitation &copyFrom)ms_customquantitation [explicit]
ms_errors()ms_errors
ms_ms1quantitation(const ms_peptidesummary &summary, const ms_quant_method &method)ms_ms1quantitation
openQuantitationCdbResults(const matrix_science::ms_peptidesummary &summary, const matrix_science::ms_quant_method &method, const std::string &cdbFilename, const std::string &cacheFilename, const matrix_science::ms_quant_method *originalMethod=0)ms_ms1quantitation [static]
openQuantitationXmlResults(const matrix_science::ms_peptidesummary &summary, const matrix_science::ms_quant_method &method, const std::string &filename, const std::string &xmlSchemaPath="", const matrix_science::ms_quant_method *originalMethod=0)ms_ms1quantitation [static]
proteinKeys_ms_quantitation [protected]
removeMatch(matrix_science::ms_peptide_quant_key matchKey)ms_ms1quantitation
removePeptideQuantKey(const std::string &accession, int dbIdx, const ms_peptide_quant_key &key)ms_customquantitation
removePeptideRatio(const ms_peptide_quant_key &key, const std::string &ratioName)ms_customquantitation
removePeptideRatioNormalisationBase(const std::string &ratioName)ms_quantitation
removePeptideRatioNormalisationBases()ms_quantitation
saveCdbFile(const std::string &cdbFilename, const std::string &cacheFilename)ms_ms1quantitation
saveXmlFile(const std::string &xmlFilename, bool completeReport)ms_ms1quantitation
setAverageNumPeptides(unsigned int num=3)ms_ms1quantitation
setAverageReferenceProtein(const char *accession, int dbIdx, double amount=1.0)ms_ms1quantitation
setAverageSelection(const char *value)ms_ms1quantitation
setMinNumPeptides(int value)ms_quantitation
setPeptideRatioExcluded(const ms_peptide_quant_key &key, const std::string &ratioName)ms_customquantitation [virtual]
setPeptideRatioIncluded(const ms_peptide_quant_key &key, const std::string &ratioName)ms_customquantitation [virtual]
setPeptideRatioNormalisationBase(const std::string &ratioName, double b)ms_quantitation
setProteinRatioType(const char *value)ms_customquantitation [virtual]
setQuantOutliers(const ms_quant_outliers *)ms_customquantitation [virtual]
~ms_customquantitation()ms_customquantitation [virtual]
~ms_errors()ms_errors
~ms_quantitation()=0ms_quantitation [pure virtual]
Copyright © 2016 Matrix Science Ltd.  All Rights Reserved. Generated on Fri Jun 2 2017 01:44:53