addMatchParameter, addPeptideMatchParameter, addProteinMatchParameter, addSpectrumMatch, addSpectrumMatch, addSpectrumMatchParameter, buildPeptidesAndProteins, buildPeptidesAndProteins, close, convert, establishConnection, getDefaultReference, getFileName, getMatchParameter, getMatchType, getMethodUsed, getOrderedSpectrumFileNames, getPeptideIdentification, getPeptideMatch, getPeptideMatch, getPeptideMatchParameter, getPeptideMatchParameter, getProteinIdentification, getProteinMap, getProteinMatch, getProteinMatch, getProteinMatchParameter, getProteinMatchParameter, getSerializationDirectory, getSpectrumFiles, getSpectrumIdentification, getSpectrumIdentification, getSpectrumIdentificationMap, getSpectrumIdentificationSize, getSpectrumMatch, getSpectrumMatch, getSpectrumMatchParameter, getSpectrumMatchParameter, isDB, loadPeptideMatches, loadPeptideMatches, loadPeptideMatchParameters, loadPeptideMatchParameters, loadProteinMatches, loadProteinMatches, loadProteinMatchParameters, loadProteinMatchParameters, loadSpectrumMatches, loadSpectrumMatches, loadSpectrumMatchParameters, loadSpectrumMatchParameters, matchExists, peptideDetailsInCache, proteinDetailsInCache, removeMatch, removePeptideMatch, removeProteinMatch, removeSpectrumMatch, setDirectory, setIsDB, setOrderedListOfSpectrumFileNames, updatePeptideMatch, updatePeptideMatchParameter, updateProteinMatch, updateProteinMatchParameter, updateSpectrumMapping, updateSpectrumMatch, updateSpectrumMatchParameter |