Matrix Science Mascot Parser toolkit
 
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ms_ms1quantitation Member List

This is the complete list of members for ms_ms1quantitation, including all inherited members.

addHeaderField(const std::string &name, const std::string &value)ms_quantitation
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, const std::string &matchBelongsToComponent, const int thisSubProjectId=matrix_science::ms_quant_file_index::file_index_value_not_set)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
addRawFileField(const unsigned int id, const std::string &name, const std::string &value)ms_quantitation
appendErrors(const ms_errors &src)ms_errors
BUGFIX_12409 enum valuems_ms1quantitation
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) constms_quantitationprotected
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) constms_quantitationprotected
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) constms_quantitationprotected
clearAllErrors()ms_errors
clearHeaderFields()ms_quantitation
clearPeptideQuantKeys(const std::string &accession, int dbIdx)ms_customquantitation
clearPeptideRatios()ms_customquantitation
clearRawFileFields()ms_quantitation
copyFrom(const ms_errors *right)ms_errors
countDistinctPeptides(const std::vector< ms_peptide_quant_key > &activeKeys) constms_ms1quantitationvirtual
countDistinctPeptides(const std::vector< ms_peptide_quant_key > &activeKeys) constms_ms1quantitationvirtual
countDistinctPeptides(const ms_peptide_quant_key_vector &activeKeys) constms_ms1quantitationvirtual
findMatch(matrix_science::ms_peptide_quant_key matchKey, ms_ms1quant_match *match) constms_ms1quantitation
findPeptideStatus(int query, int rank, ms_ms1quant_peptide_status *peptideStatus) constms_ms1quantitation
getAveragePeptideIntensity(const std::string &accession, int dbIdx, double *averageIntensity, int *sampleSize, ms_peptide_quant_key_vector *includeKeys, ms_peptide_quant_key_vector *excludeKeys) constms_ms1quantitation
getAverageResults() constms_ms1quantitation
getErrorHandler() constms_errors
getHit(int index1) constms_ms1quantitation
getLabelFree(std::string peptideStr, std::string varMods, std::string summedMods, const matrix_science::ms_quant_component &comp) constms_ms1quantitation
getLastError() constms_errors
getLastErrorString() constms_errors
getMatch(int index) constms_ms1quantitation
getMatch(const ms_peptide_quant_key &key) constms_ms1quantitation
getMatchForHit(int index, int hitId, int memberNumber) constms_ms1quantitation
getMinNumPeptides() constms_quantitationprotected
getNumGroups() constms_ms1quantitation
getNumHits() constms_ms1quantitation
getNumMatches() constms_ms1quantitation
getNumMatchesForGroup(int groupIndex1) constms_ms1quantitation
getNumMatchesForHit(int hitId, int memberNumber) constms_ms1quantitation
getNumPeptideStatuses() constms_ms1quantitation
getNumProteinFamilies() constms_ms1quantitation
getPeptideQuantKeys(const std::string &accession, int dbIdx) constms_quantitation
getPeptideRatio(const ms_peptide_quant_key &key, const std::string &ratioName) constms_customquantitationvirtual
getPeptideRatioNormalisationBase(const std::string &ratioName) constms_quantitation
getPeptideStatus(int index) constms_ms1quantitation
getPeptideSummary() constms_ms1quantitation
getProgressInfo()ms_quantitation
getProteinRatio(const std::string &accession, int dbIdx, const std::string &ratioName) constms_ms1quantitationvirtual
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) constms_ms1quantitationvirtual
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) constms_quantitationprotected
getQuantitationDatasources() constms_ms1quantitation
getQuantitationMethod() constms_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) constms_customquantitationprotectedvirtual
getSummary() constms_ms1quantitation
getTimeAlignmentData() constms_ms1quantitation
getTimeAlignmentData()ms_ms1quantitation
getUnnormalisedAveragePeptideRatio(const std::string &ratioName, const std::string &averageType) constms_customquantitation
getUnnormalisedAveragePeptideRatio(const std::string &ratioName, const std::string &averageType, const ms_peptide_quant_key_vector &keys) constms_customquantitation
getUnnormalisedAveragePeptideRatio(const std::string &ratioName, const std::string &averageType, const std::string &accession, int dbIdx) constms_customquantitation
hasPeptideRatio(const ms_peptide_quant_key &key, const std::string &ratioName) constms_customquantitationvirtual
initGroupChargeStates(std::set< int > *calc_chargestates, int iGroup1, int minCharge, int maxCharge)ms_ms1quantitation
initialiseBaseSettings(const ms_quant_method &qmBase, const ms_quant_method &qmConfig)ms_quantitationprotected
isAverageProtocol() constms_ms1quantitation
isDataCached(MS1QUANT_BUGFIX_NUM bugNum) constms_ms1quantitation
isPeptideRatioExcluded(const ms_peptide_quant_key &key, const std::string &ratioName) constms_customquantitationvirtual
isValid() constms_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
MERGE_QUANT_APPLY_THRESHOLDS_AFTER_MERGE enum valuems_ms1quantitation
MERGE_QUANT_DEFAULT_PRECURSOR_METHOD enum valuems_ms1quantitation
MERGE_QUANT_DEFAULT_REPLICATE_METHOD enum valuems_ms1quantitation
MERGE_QUANT_MERGE_COMPONENTS_INTO_QUANT_MATCH enum valuems_ms1quantitation
MERGE_QUANT_QUERY_NUMBERS_ARE_FROM_MERGED_RESULTS enum valuems_ms1quantitation
MERGE_QUANT_RESULTS_FLAGS enum namems_ms1quantitation
MERGE_QUANT_USE_COMPONENT_FILE_INDEX_TO_FIND_XIC enum valuems_ms1quantitation
mergeQuantitationResults(const std::vector< std::string > &cdbFilenames, const std::vector< std::string > &cacheFilenames, const MERGE_QUANT_RESULTS_FLAGS flags, const matrix_science::ms_quant_method *originalMethod=0)ms_ms1quantitation
mergeQuantitationResults(const std::vector< std::string > &xmlFilenames, const MERGE_QUANT_RESULTS_FLAGS flags, const std::string &xmlSchemaPath="", const matrix_science::ms_quant_method *originalMethod=0)ms_ms1quantitation
MS1QUANT_BUGFIX_NUM enum namems_ms1quantitation
ms_customquantitation(const ms_quant_method &qm)ms_customquantitationexplicit
ms_customquantitation(const ms_peptidesummary &initFrom)ms_customquantitationexplicit
ms_customquantitation(const ms_peptidesummary &initFrom, const ms_quant_method &qm)ms_customquantitation
ms_customquantitation(const ms_ms2quantitation &copyFrom)ms_customquantitationexplicit
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_ms1quantitationstatic
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_ms1quantitationstatic
proteinKeys_ms_quantitationprotected
readResultCounters(const std::string &cdbFile, int &numMatches, int &numHits, int &numPepGrp, int &numPeptideComponents)ms_ms1quantitationstatic
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, bool createEmptyMissingComponents=false)ms_ms1quantitation
saveXmlFile(const std::string &xmlFilename, bool completeReport, bool saveTimeAlignmentData=false)ms_ms1quantitation
setAverageNumPeptides(unsigned int num=3)ms_ms1quantitation
setAverageReferenceProtein(const char *accession, int dbIdx, bool isReferenceUserSelected)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_customquantitationvirtual
setPeptideRatioIncluded(const ms_peptide_quant_key &key, const std::string &ratioName)ms_customquantitationvirtual
setPeptideRatioNormalisationBase(const std::string &ratioName, double b)ms_quantitation
setProteinRatioType(const char *value)ms_customquantitationvirtual
setQuantOutliers(const ms_quant_outliers *)ms_customquantitationvirtual
setTimeAlignmentData(matrix_science::ms_ms1quant_time_align &alignmentData)ms_ms1quantitation
~ms_customquantitation()ms_customquantitationvirtual
~ms_errors()ms_errors
~ms_quantitation()=0ms_quantitationpure virtual