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