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AbstractContact AbstractIdentifiableParamGroup AbstractParam AbstractParamGroup AbstractParamUnitCvRefResolver AbstractReferenceResolver AbstractResolvingAdapter AdapterObjectCache AdditionalParamsCvParam AdditionalParamsUserParam AdditionalSearchParamsCvParam AdditionalSearchParamsUserParam Affiliation AffiliationRefResolver AmbiguousResidue AmbiguousResidueCvParam AmbiguousResidueUserParam AnalysisCollection AnalysisData AnalysisParamsCvParam AnalysisParamsUserParam AnalysisProtocolCollection AnalysisSampleCollection AnalysisSoftware AnalysisSoftwareAdapter AnalysisSoftwareList AuditCollection BibliographicReference CalendarAdapter Constants Constants.ReferencedType ContactRole ContactRoleRefResolver Cv CvAdapter CvList CvParam CvParamCapable CvParamListCapable CvParamRefResolver DatabaseFilters DatabaseNameCvParam DatabaseNameUserParam DatabaseTranslation DataCollection DBSequence DBSequenceAdapter DBSequenceCvParam DBSequenceRefResolver DBSequenceUserParam Enzyme EnzymeNameCvParam EnzymeNameUserParam Enzymes ExcludeCvParam ExcludeUserParam ExternalData FacadeList FileFormat FileFormatCvParam FileUtils Filter FilterTypeCvParam FilterTypeUserParam FragmentArray FragmentArrayRefResolver Fragmentation FragmentationTable Identifiable IdentifiableMzIdentMLObject IncludeCvParam IncludeUserParam Inputs InputSpectra InputSpectraRefResolver InputSpectrumIdentifications InputSpectrumIdentificationsRefResolver IonType IonTypeCvParam JmzIdentMLParser MarshallerFactory MassTable MassTableAdapter MassTableCvParam MassTableUserParam Measure MeasureAdapter MeasureCvParam ModelConstants Modification ModificationCvParam ModificationParams ModificationUserParam ModParam ModParamCvParam MzIdentML MzIdentMLElement MzIdentMLElementConfig MzIdentMLElementProperties MzIdentMLIndexer MzIdentMLIndexerFactory MzIdentMLMarshaller MzIdentMLNamespaceFilter MzIdentMLObject MzIdentMLObjectCache MzIdentMLObjectIterator MzIdentMLUnmarshaller ObjectClassListener ObjectFactory Organization OrganizationAdapter OrganizationCvParam OrganizationUserParam Param ParamCapable ParamGroupCapable ParamList ParamListCapable ParamListMappings ParamMappings ParamUpdater ParentOrganization ParentOrganizationRefResolver Peptide PeptideAdapter PeptideCvParam PeptideEvidence PeptideEvidenceAdapter PeptideEvidenceCvParam PeptideEvidenceListCvParam PeptideEvidenceListUserParam PeptideEvidenceRef PeptideEvidenceRefResolver PeptideEvidenceResolver PeptideEvidenceUserParam PeptideHypothesis PeptideHypothesisRefResolver PeptideUserParam Person PersonCvParam PersonUserParam ProteinAmbiguityGroup ProteinAmbiguityGroupCvParam ProteinAmbiguityGroupUserParam ProteinDetection ProteinDetectionHypothesis ProteinDetectionHypothesisCvParam ProteinDetectionHypothesisRefResolver ProteinDetectionHypothesisUserParam ProteinDetectionList ProteinDetectionListAdapter ProteinDetectionListCvParam ProteinDetectionListUserParam ProteinDetectionProtocol ProteinDetectionProtocolAdapter ProteinDetectionProtocolRefResolver ProteinDetectionRefResolver ProtocolApplication Provider ProviderRefResolver RawXMLListener Residue Role RoleCvParam Sample SampleAdapter SampleCvParam SampleUserParam SearchDatabase SearchDatabaseAdapter SearchDatabaseCvParam SearchDatabaseRef SearchDatabaseRefResolver SearchModification SearchTypeCvParam SearchTypeUserParam SequenceCollection SoftwareNameCvParam SoftwareNameUserParam SourceFile SourceFileCvParam SourceFileUserParam SpecificityRules SpecificityRulesCvParam SpectraData SpectraDataAdapter SpectrumIdentification SpectrumIdentificationItem SpectrumIdentificationItemCvParam SpectrumIdentificationItemRef SpectrumIdentificationItemRefRefResolver SpectrumIdentificationItemRefResolver SpectrumIdentificationItemUserParam SpectrumIdentificationList SpectrumIdentificationListAdapter SpectrumIdentificationListCvParam SpectrumIdentificationListUserParam SpectrumIdentificationProtocol SpectrumIdentificationProtocolAdapter SpectrumIdentificationProtocolRefResolver SpectrumIdentificationRefResolver SpectrumIdentificationResult SpectrumIdentificationResultCvParam SpectrumIdentificationResultRefResolver SpectrumIdentificationResultUserParam SpectrumIDFormat SpectrumIDFormatCvParam SubSample SubSampleRefResolver SubstitutionModification ThresholdCvParam ThresholdUserParam Tolerance ToleranceCvParam TranslationTable TranslationTableAdapter TranslationTableCvParam UnmarshallerFactory UserParam