, 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) | 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 value | ms_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) 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 | |
| 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) const | ms_ms1quantitation | [virtual] |
| matrix_science::ms_customquantitation::countDistinctPeptides(const ms_peptide_quant_key_vector &activeKeys) const | ms_quantitation | [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(const ms_peptide_quant_key &key) const | ms_ms1quantitation | |
| getMatchForHit(int index, int hitId, int memberNumber) const | ms_ms1quantitation | |
| getMinNumPeptides() const | ms_quantitation | [protected] |
| getNumGroups() const | ms_ms1quantitation | |
| getNumHits() const | ms_ms1quantitation | |
| getNumMatches() const | ms_ms1quantitation | |
| getNumMatchesForGroup(int groupIndex1) const | ms_ms1quantitation | |
| getNumMatchesForHit(int hitId, int memberNumber) const | ms_ms1quantitation | |
| getNumPeptideStatuses() const | ms_ms1quantitation | |
| getNumProteinFamilies() 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_quantitation | |
| 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] |
| 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_quantitation | [protected] |
| isAverageProtocol() const | ms_ms1quantitation | |
| isDataCached(MS1QUANT_BUGFIX_NUM bugNum) 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 | |
| MERGE_QUANT_APPLY_THRESHOLDS_AFTER_MERGE enum value | ms_ms1quantitation | |
| MERGE_QUANT_DEFAULT_PRECURSOR_METHOD enum value | ms_ms1quantitation | |
| MERGE_QUANT_DEFAULT_REPLICATE_METHOD enum value | ms_ms1quantitation | |
| MERGE_QUANT_MERGE_COMPONENTS_INTO_QUANT_MATCH enum value | ms_ms1quantitation | |
| MERGE_QUANT_QUERY_NUMBERS_ARE_FROM_MERGED_RESULTS enum value | ms_ms1quantitation | |
| MERGE_QUANT_RESULTS_FLAGS enum name | ms_ms1quantitation | |
| MERGE_QUANT_USE_COMPONENT_FILE_INDEX_TO_FIND_XIC enum value | ms_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 name | ms_ms1quantitation | |
| 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 ©From) | 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] |
| readResultCounters(const std::string &cdbFile, int &numMatches, int &numHits, int &numPepGrp, int &numPeptideComponents) | ms_ms1quantitation | [static] |
| 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) | 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_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()=0 | ms_quantitation | [pure virtual] |
