, including all inherited members.
| addHeaderField(const std::string &name, const std::string &value) | ms_quantitation | |
| addRawFileField(const unsigned int id, const std::string &name, const std::string &value) | ms_quantitation | |
| 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 | |
| clearHeaderFields() | ms_quantitation | |
| clearRawFileFields() | ms_quantitation | |
| copyFrom(const ms_errors *right) | ms_errors | |
| countDistinctPeptides(const std::vector< ms_peptide_quant_key > &activeKeys) const | ms_ms2quantitation | [virtual] |
| matrix_science::ms_quantitation::countDistinctPeptides(const ms_peptide_quant_key_vector &activeKeys) const | ms_quantitation | [virtual] |
| excludeProteinPeptideRatioKeys(const std::string &accession, int dbIdx, const std::string &ratioName, const ms_peptide_quant_key_vector &excludeKeys) | ms_ms2quantitation | |
| getCombinedReportRatio(const std::string &ratioName) const | ms_ms2quantitation | |
| getCombinedReportRatioNames() const | ms_ms2quantitation | |
| getComponentIntensities(const ms_peptide_quant_key &key, bool raw=false) const | ms_ms2quantitation | |
| getErrorHandler() const | ms_errors | |
| getIntensityNormalisationBase(const std::string &componentName) const | ms_ms2quantitation | |
| getLastError() const | ms_errors | |
| getLastErrorString() const | ms_errors | |
| getMinNumPeptides() const | ms_quantitation | [protected] |
| getPeptideQuantKeys(const std::string &accession, int dbIdx) const | ms_quantitation | |
| getPeptideRatio(const ms_peptide_quant_key &key, const std::string &ratioName) const | ms_ms2quantitation | [virtual] |
| getPeptideRatioNormalisationBase(const std::string &ratioName) const | ms_quantitation | |
| getProgressInfo() | ms_quantitation | |
| getProteinRatio(const std::string &accession, int dbIdx, const std::string &ratioName) const | ms_ms2quantitation | [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_ms2quantitation | [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] |
| getQuantitationMethod() const | ms_quantitation | |
| getReportRatioFromFile(unsigned int fileNum, const std::string &ratioName) const | ms_ms2quantitation | |
| getReportRatioNamesInFile(unsigned int fileNum) const | ms_ms2quantitation | |
| 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_ms2quantitation | [protected, virtual] |
| hasIntensityNormalisation() const | ms_ms2quantitation | |
| hasPeptideRatio(const ms_peptide_quant_key &key, const std::string &ratioName) const | ms_ms2quantitation | [virtual] |
| hasPeptideRatioNormalisation() const | ms_ms2quantitation | |
| includeProteinPeptideRatioKeys(const std::string &accession, int dbIdx, const std::string &ratioName, const ms_peptide_quant_key_vector &includeKeys) | ms_ms2quantitation | |
| initialiseBaseSettings(const ms_quant_method &qmBase, const ms_quant_method &qmConfig) | ms_quantitation | [protected] |
| isPeptideRatioExcluded(const ms_peptide_quant_key &key, const std::string &ratioName) const | ms_ms2quantitation | [virtual] |
| isValid() const | ms_errors | |
| loadCdbFile(const char *path) | ms_ms2quantitation | |
| loadCdbFiles(const std::vector< std::string > &cdbFiles) | ms_ms2quantitation | |
| ms_errors() | ms_errors | |
| ms_ms2quantitation(const ms_peptidesummary &pepsum) | ms_ms2quantitation | [explicit] |
| ms_ms2quantitation(const ms_peptidesummary &pepsum, const ms_quant_method &qm) | ms_ms2quantitation | |
| normaliseIntensities() | ms_ms2quantitation | |
| normalisePeptideRatios() | ms_ms2quantitation | |
| proteinKeys_ | ms_quantitation | [protected] |
| removeCombinedReportRatio(const std::string &ratioName) | ms_ms2quantitation | |
| removeIntensityNormalisationBase(const std::string &componentName) | ms_ms2quantitation | |
| removeIntensityNormalisationBases() | ms_ms2quantitation | |
| removePeptideRatioNormalisationBase(const std::string &ratioName) | ms_quantitation | |
| removePeptideRatioNormalisationBases() | ms_quantitation | |
| removeReportRatioInFile(unsigned int fileNum, const std::string &ratioName) | ms_ms2quantitation | |
| saveCdbFile(const std::string &cdbFilename) | ms_ms2quantitation | |
| saveXmlFile(const std::string &xmlFilename, bool completeReport) | ms_ms2quantitation | |
| setCombinedReportRatio(const std::string &ratioName, const ms_quant_ratio &ratioDef) | ms_ms2quantitation | |
| setIntensityNormalisationBase(const std::string &componentName, double b) | ms_ms2quantitation | |
| setMinNumPeptides(int value) | ms_quantitation | |
| setPeptideRatioExcluded(const ms_peptide_quant_key &key, const std::string &ratioName) | ms_ms2quantitation | [virtual] |
| setPeptideRatioIncluded(const ms_peptide_quant_key &key, const std::string &ratioName) | ms_ms2quantitation | [virtual] |
| setPeptideRatioNormalisationBase(const std::string &ratioName, double b) | ms_quantitation | |
| setProteinRatioType(const char *value) | ms_ms2quantitation | [virtual] |
| setQuantNormalisation(const ms_quant_normalisation *norm) | ms_ms2quantitation | |
| setQuantOutliers(const ms_quant_outliers *) | ms_ms2quantitation | [virtual] |
| setReportRatioInFile(unsigned int fileNum, const std::string &ratioName, const ms_quant_ratio &ratioDef) | ms_ms2quantitation | |
| ~ms_errors() | ms_errors | |
| ~ms_ms2quantitation() | ms_ms2quantitation | [virtual] |
| ~ms_quantitation()=0 | ms_quantitation | [pure virtual] |
