| sortByCharge | 0% |
| sortByMassCharge | 0% |
| sortByMass | 0% |
| recordDatabase | 0% |
| initialiseDatabase | 0% |
| setConversionSource | 0% |
| setHeader | 0% |
| sortByIntensity | 0% |
| sortByRank | 0% |
| __construct | 0% |
| isDecoy | 0% |
| reset | 0% |
| sort | 0% |
| validate | 0% |
| sortByScore | 0% |
| setScoreKey | 0% |
| isConversion | 0% |
| __construct | 0% |
| addModification | 0% |
| addParentTolerance | 0% |
| addFragmentTolerance | 0% |
| addEnzyme | 0% |
| addIdentifiedPrecursors | 0% |
| writeCvList | 0% |
| writeMzIdentMl | 0% |
| addDecoyData | 0% |
| addSearchData | 0% |
| flush | 0% |
| close | 0% |
| open | 0% |
| addCv | 0% |
| addScore | 0% |
| addSpectraData | 0% |
| addSoftware | 0% |
| getFdrScore | 0% |
| getFdr | 0% |
| getTranslationTable | 0% |
| getTolerance | 0% |
| getThreshold | 0% |
| getCv | 0% |
| getCvList | 0% |
| isFilterMatch | 0% |
| getProteinEntryType | 0% |
| getSubstitutionModification | 0% |
| getSubSample | 0% |
| parsePeptideEvidenceCv | 0% |
| getSpectrumIdentificationItem | 0% |
| __construct | 0% |
| getSpectrumIdentificationItemRef | 0% |
| getSpectrumIdentificationList | 0% |
| getSpectrumIdentificationResult | 0% |
| getSpectrumIdentificationProtocol | 0% |
| setRankFilter | 0% |
| getReader | 0% |
| setFdrKey | 0% |
| setFdrTableUsage | 0% |
| createModificationFile | 0% |
| getScore | 0% |
| getMatches | 0% |
| getFdrAll | 0% |
| getFalseDiscoryRates | 0% |
| executeCommand | 0% |
| appendArgument | 0% |
| getDatasetFileList | 0% |
| parseInfo | 0% |
| getIdString | 0% |
| setHost | 0% |
| getCommand | 0% |
| search | 0% |
| writeCv | 0% |
| writeDataCollection | 0% |
| __destruct | 0% |
| close | 0% |
| write | 0% |
| writeHeader | 0% |
| writeIdentification | 0% |
| isValid | 0% |
| getModificationString | 0% |
| __construct | 0% |
| writeAttributeNotNull | 0% |
| writePeptide | 0% |
| getId | 0% |
| writeSeq | 0% |
| writePeptideSequence | 0% |
| writeModification | 0% |
| getOboName | 0% |
| writePeptideEvidence | 0% |
| setAverageMassCharge | 0% |
| getAverageMassCharge | 0% |
| hasRetentionTimeWindow | 0% |
| getRetentionTimeWindow | 0% |
| setRetentionTimeWindow | 0% |
| getCvParamName | 0% |
| getCvParam | 0% |
| getAttributeId | 0% |
| getUserParam | 0% |
| getAverageMass | 0% |
| setAverageMass | 0% |
| getCharge | 0% |
| setCharge | 0% |
| getMassCharge | 0% |
| getNeutralMass | 0% |
| getDatabaseEntry | 0% |
| setDatabaseEntry | 0% |
| writeDbSequence | 0% |
| writeSequenceCollection | 0% |
| writeAnalysisSoftwareList | 0% |
| writeDatabaseName | 0% |
| writeFileFormat | 0% |
| writeAnalysisCollection | 0% |
| writeSpectrumIdentification | 0% |
| writeSearchDatabaseRef | 0% |
| writeInputSpectra | 0% |
| writeSearchDatabase | 0% |
| writeSpectrumIdFormat | 0% |
| writeSpectrumIdentificationResult | 0% |
| writeSpectrumIdentificationList | 0% |
| writeAnalysisData | 0% |
| writeSpectrumIdentificationItem | 0% |
| writePeptideEvidenceRef | 0% |
| writeSpectraData | 0% |
| writeInputs | 0% |
| writeAnalysisProtocolCollection | 0% |
| writeSpectrumIdentificationProtocol | 0% |
| writeSpecificityRules | 0% |
| writeSearchModification | 0% |
| writeModificationParams | 0% |
| writeCvParam | 0% |
| writeUserParam | 0% |
| writeSoftwareName | 0% |
| writeAnalysisSoftware | 0% |
| writeSearchType | 0% |
| writeEnzymeName | 0% |
| writeParentTolerance | 0% |
| writeFragmentTolerance | 0% |
| writeTolerance | 0% |
| writeThreshold | 0% |
| writeEnzyme | 0% |
| writeEnzymes | 0% |
| getSpectrumIdFormat | 0% |
| getSpectrumIdentification | 0% |
| getGene | 0% |
| setGene | 0% |
| hasInstance | 0% |
| setTranscript | 0% |
| getTranscript | 0% |
| getOrganism | 0% |
| setOrganism | 0% |
| getInstance | 0% |
| getIdentifier | 0% |
| getType | 0% |
| setType | 0% |
| getName | 0% |
| getInstance | 0% |
| setName | 0% |
| setIdentifier | 0% |
| getName | 0% |
| setType | 0% |
| getType | 0% |
| getAdditionalSearchParams | 0% |
| __construct | 0% |
| parseIdentifier | 0% |
| getAffiliation | 0% |
| getAmigiousResidue | 0% |
| getAnalysisData | 0% |
| getSpectraData | 0% |
| parseModifications | 0% |
| parseAttributes | 0% |
| parseIdentifier | 0% |
| getProtein | 0% |
| parseIdentifier | 0% |
| getProtein | 0% |
| getParser | 0% |
| getProtein | 0% |
| parseIdentifier | 0% |
| setName | 0% |
| getSymbol | 0% |
| setSource | 0% |
| getName | 0% |
| getPrefix | 0% |
| getSource | 0% |
| __construct | 0% |
| __construct | 0% |
| __construct | 0% |
| setName | 0% |
| setPrefix | 0% |
| setSource | 0% |
| getName | 0% |
| getPrefix | 0% |
| getSource | 0% |
| getInstance | 0% |
| __construct | 0% |
| getDatabase | 0% |
| __construct | 0% |
| __construct | 0% |
| setUniqueIdentifier | 0% |
| getEntryVersion | 0% |
| setEntryVersion | 0% |
| getUniqueIdentifier | 0% |
| setName | 0% |
| __construct | 0% |
| getName | 0% |
| getSequenceVersion | 0% |
| setSequenceVersion | 0% |
| __construct | 0% |
| __construct | 0% |
| __construct | 0% |
| getDatabase | 0% |
| getEvidence | 0% |
| setEvidence | 0% |
| getAnalysisParams | 0% |
| getAnalysisCollection | 0% |
| getPeptideHypothesis | 0% |
| getPeptideEvidenceRef | 0% |
| getPeptideEvidence | 0% |
| getPeptideSequence | 0% |
| getPerson | 0% |
| getProteinDetectionHypothesis | 0% |
| getProteinDetection | 0% |
| getProteinAmbiguityGroup | 0% |
| getPeptide | 0% |
| getParentTolerance | 0% |
| getMeasure | 0% |
| getMassTable | 0% |
| getIonType | 0% |
| getModification | 0% |
| getModificationParams | 0% |
| getParent | 0% |
| getOrganization | 0% |
| getProteinDetectionList | 0% |
| getProteinDetectionProtocol | 0% |
| getSequenceCollectionProteins | 0% |
| getSequenceCollectionPeptides | 0% |
| getSequenceCollection | 0% |
| getSiteRegexp | 0% |
| getSoftwareName | 0% |
| getSpecifityRules | 0% |
| getSourceFile | 0% |
| getSeq | 0% |
| getSearchType | 0% |
| getRole | 0% |
| getResidue | 0% |
| getProvider | 0% |
| getSample | 0% |
| getSearchDatabase | 0% |
| getSearchModification | 0% |
| getSearchDatabaseRef | 0% |
| getAnalysisProtocolCollection | 0% |
| getInputs | 0% |
| getDataCollection | 0% |
| parseDbSequenceParam | 0% |
| getDatabaseFilters | 0% |
| getDatabaseName | 0% |
| getEnzyme | 0% |
| getInputSpectrumIdentifications | 0% |
| getDbSequence | 0% |
| getCustomisations | 0% |
| getAnalysisSoftwareList | 0% |
| getAnalysisSampleCollection | 0% |
| getAnalysisSoftware | 0% |
| getAuditCollection | 0% |
| getContactRole | 0% |
| getBibliographicReference | 0% |
| getEnzymeName | 0% |
| getDatabaseTranslation | 0% |
| getFragmentTolerance | 0% |
| getEnzymes | 0% |
| getFilterType | 0% |
| getFragmentation | 0% |
| getFragmentationTable | 0% |
| getInputSpectra | 0% |
| getInclude | 0% |
| getFilter | 0% |
| getFragmentArray | 0% |
| getExclude | 0% |
| getExternalFormatDocumentation | 0% |
| getFileFormat | 0% |
| writeDescription | 44% |
| getRetentionTime | 50% |
| getProtein | 76% |
| parseSequence | 81% |
| writeHeader | 82% |
| next | 85% |
| write | 86% |
| __construct | 87% |
| parseMeta | 88% |