, including all inherited members.
| appendErrors(const ms_errors &src) | ms_errors | |
| calcFragments(const ms_peptide *peptide, const int seriesID, const bool doubleCharged, const double minMass, const double maxMass, const MASS_TYPE massType, ms_fragmentvector *fragments, ms_errs *err, const FRAG_NL fragNlType=FRAG_NL_PRIMARY) const | ms_aahelper | |
| calcFragments(const ms_peptide *peptide, const int seriesID, const bool doubleCharged, const double minMass, const double maxMass, const MASS_TYPE massType, std::vector< ms_fragment > *fragments, ms_errs *err, const FRAG_NL fragNlType=FRAG_NL_PRIMARY) const | ms_aahelper | |
| calcFragmentsEx(const ms_peptide *peptide, const int seriesID, const int fragCharge, const double minMass, const double maxMass, const MASS_TYPE massType, ms_fragmentvector *fragments, ms_errs *err, const FRAG_NL fragNlType=FRAG_NL_PRIMARY) const | ms_aahelper | |
| calcFragmentsEx(const ms_peptide *peptide, const int seriesID, const int fragCharge, const double minMass, const double maxMass, const MASS_TYPE massType, std::vector< ms_fragment > *fragments, ms_errs *err, const FRAG_NL fragNlType=FRAG_NL_PRIMARY) const | ms_aahelper | |
| calcPeptideMZ(const char *proteinStr, const int proteinLen, const int startPos, const int endPos, const std::vector< int > numThatMustBeModded, const int charge, const MASS_TYPE massType, ms_errs *err) const | ms_aahelper | |
| clearAllErrors() | ms_errors | |
| copyFrom(const ms_aahelper *right) | ms_aahelper | |
| matrix_science::ms_errors::copyFrom(const ms_errors *right) | ms_errors | |
| createCrosslinkedPeptide(const ms_peptide &pepAlpha, const ms_peptide &pepBeta, const ms_linker_site_vector &linkedSites, ms_errs *err) const | ms_aahelper | |
| createPeptide(const char *proteinStr, const int proteinLen, const int startPos, const int endPos, const std::vector< int > varMods, const std::vector< int > varModsWhichNl, const int charge, const MASS_TYPE massType, ms_errs *err) const | ms_aahelper | |
| createPeptide(const char *proteinStr, const int proteinLen, const int startPos, const int endPos, const std::vector< int > varMods, const std::vector< int > varModsWhichNl, const std::vector< int > summedMods, const std::vector< int > summedModsWhichNl, const int charge, const MASS_TYPE massType, ms_errs *err) const | ms_aahelper | |
| defaultValues() | ms_aahelper | |
| FRAG_NL enum name | ms_aahelper | |
| FRAG_NL_PRIMARY enum value | ms_aahelper | |
| FRAG_NL_SECONDARY enum value | ms_aahelper | |
| getEnzyme() const | ms_aahelper | |
| getErrorHandler() const | ms_errors | |
| getFixedMods() const | ms_aahelper | |
| getLastError() const | ms_errors | |
| getLastErrorString() const | ms_errors | |
| getMasses() const | ms_aahelper | |
| getMissed() const | ms_aahelper | |
| getNextPeptide() | ms_aahelper | |
| getPepEnd() const | ms_aahelper | |
| getPepStart() const | ms_aahelper | |
| getVarMods() const | ms_aahelper | |
| isValid() const | ms_errors | |
| ms_aahelper() | ms_aahelper | |
| ms_aahelper(const ms_mascotresfile &resfile, const char *enzymeFileName, const char *quantSchemaFilePath="http://www.matrixscience.com/xmlns/schema/quantitation_2 ../html/xmlns/schema/quantitation_2/quantitation_2.xsd http://www.matrixscience.com/xmlns/schema/quantitation_1 ../html/xmlns/schema/quantitation_1/quantitation_1.xsd", const char *unimodSchemaFilePath="http://www.unimod.org/xmlns/schema/unimod_2 ../html/xmlns/schema/unimod_2/unimod_2.xsd") | ms_aahelper | |
| ms_aahelper(const ms_mascotresults &summary, const char *enzymeFileName, const char *quantSchemaFilePath="http://www.matrixscience.com/xmlns/schema/quantitation_2 ../html/xmlns/schema/quantitation_2/quantitation_2.xsd http://www.matrixscience.com/xmlns/schema/quantitation_1 ../html/xmlns/schema/quantitation_1/quantitation_1.xsd", const char *unimodSchemaFilePath="http://www.unimod.org/xmlns/schema/unimod_2 ../html/xmlns/schema/unimod_2/unimod_2.xsd") | ms_aahelper | |
| ms_aahelper(const ms_aahelper &right) | ms_aahelper | |
| ms_errors() | ms_errors | |
| operator=(const ms_aahelper &right) | ms_aahelper | |
| setAvailableModifications(const ms_modvector *fixedModVector, const ms_modvector *varModVector) | ms_aahelper | |
| setEnzyme(const ms_enzyme *enzyme) | ms_aahelper | |
| setMasses(const ms_masses *masses) | ms_aahelper | |
| startIteratePeptides(const char *sequenceProtein, const int sizeProtein, const int pfa) | ms_aahelper | |
| stopIteratePeptides() | ms_aahelper | |
| ~ms_aahelper() | ms_aahelper | |
| ~ms_errors() | ms_errors | |
