A B C D E F G H I J L M N O P R S T U V X Y

A

AbstractContact - Class in uk.ac.ebi.jmzidml.model.mzidml
A contact is either a person or an organization.
AbstractContact() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.AbstractContact
 
AbstractIdentifiableParamGroup - Class in uk.ac.ebi.jmzidml.model
 
AbstractIdentifiableParamGroup() - Constructor for class uk.ac.ebi.jmzidml.model.AbstractIdentifiableParamGroup
 
AbstractParam - Class in uk.ac.ebi.jmzidml.model.mzidml
Abstract entity allowing either cvParam or userParam to be referenced in other schemas.
AbstractParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.AbstractParam
 
AbstractParamGroup - Class in uk.ac.ebi.jmzidml.model
 
AbstractParamGroup() - Constructor for class uk.ac.ebi.jmzidml.model.AbstractParamGroup
 
AbstractParamUnitCvRefResolver - Class in uk.ac.ebi.jmzidml.xml.jaxb.resolver
This resolver is to map unitCvRef to an Cv object.
AbstractParamUnitCvRefResolver(MzIdentMLIndexer, MzIdentMLObjectCache) - Constructor for class uk.ac.ebi.jmzidml.xml.jaxb.resolver.AbstractParamUnitCvRefResolver
 
AbstractReferenceResolver<T extends MzIdentMLObject> - Class in uk.ac.ebi.jmzidml.xml.jaxb.resolver
Abstract base class for the reference resolver classes.
AbstractReferenceResolver(MzIdentMLIndexer, MzIdentMLObjectCache) - Constructor for class uk.ac.ebi.jmzidml.xml.jaxb.resolver.AbstractReferenceResolver
 
AbstractResolvingAdapter<ValueType,BoundType> - Class in uk.ac.ebi.jmzidml.xml.jaxb.adapters
 
AbstractResolvingAdapter(MzIdentMLIndexer, AdapterObjectCache) - Constructor for class uk.ac.ebi.jmzidml.xml.jaxb.adapters.AbstractResolvingAdapter
the presence of a constructor forces all subclasses to provide a valid indexer for reference resolving.
AbstractResolvingAdapter(MzIdentMLIndexer, AdapterObjectCache, boolean) - Constructor for class uk.ac.ebi.jmzidml.xml.jaxb.adapters.AbstractResolvingAdapter
 
accession - Variable in class uk.ac.ebi.jmzidml.model.mzidml.CvParam
 
accession - Variable in class uk.ac.ebi.jmzidml.model.mzidml.DBSequence
 
activityDate - Variable in class uk.ac.ebi.jmzidml.model.mzidml.ProtocolApplication
 
AdapterObjectCache - Class in uk.ac.ebi.jmzidml.xml.jaxb.unmarshaller.cache
Java in memory HashMap based Object cache implementation of the MzIdentMLObjectCache.
AdapterObjectCache() - Constructor for class uk.ac.ebi.jmzidml.xml.jaxb.unmarshaller.cache.AdapterObjectCache
 
add(T) - Method in class uk.ac.ebi.jmzidml.model.utils.FacadeList
 
add(int, T) - Method in class uk.ac.ebi.jmzidml.model.utils.FacadeList
Add a new element to the sublist This will add the new element to the immediate index after the element at (index -1) in the sublist
addAll(int, Collection<? extends T>) - Method in class uk.ac.ebi.jmzidml.model.utils.FacadeList
 
AdditionalParamsCvParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
User: gokelly Date: 11/04/11 Time: 14:46
AdditionalParamsCvParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.AdditionalParamsCvParam
 
AdditionalParamsUserParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
User: gokelly Date: 11/04/11 Time: 14:47
AdditionalParamsUserParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.AdditionalParamsUserParam
 
additionalSearchParams - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationProtocol
 
AdditionalSearchParamsCvParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
User: gokelly Date: 11/04/11 Time: 15:30
AdditionalSearchParamsCvParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.AdditionalSearchParamsCvParam
 
AdditionalSearchParamsUserParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
User: gokelly Date: 11/04/11 Time: 15:31
AdditionalSearchParamsUserParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.AdditionalSearchParamsUserParam
 
Affiliation - Class in uk.ac.ebi.jmzidml.model.mzidml
Java class for AffiliationType complex type.
Affiliation() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.Affiliation
 
affiliation - Variable in class uk.ac.ebi.jmzidml.model.mzidml.Person
 
AffiliationRefResolver - Class in uk.ac.ebi.jmzidml.xml.jaxb.resolver
 
AffiliationRefResolver(MzIdentMLIndexer, MzIdentMLObjectCache) - Constructor for class uk.ac.ebi.jmzidml.xml.jaxb.resolver.AffiliationRefResolver
 
afterUnmarshal(Object, Object) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.resolver.AbstractParamUnitCvRefResolver
Method to perform the afterUnmarshal operation if the resolver applies to the specified object.
afterUnmarshal(Object, Object) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.resolver.AffiliationRefResolver
Method to perform the afterUnmarshal operation if the resolver applies to the specified object.
afterUnmarshal(Object, Object) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.resolver.ContactRoleRefResolver
Method to perform the afterUnmarshal operation if the resolver applies to the specified object.
afterUnmarshal(Object, Object) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.resolver.CvParamRefResolver
Method to perform the afterUnmarshal operation if the resolver applies to the specified object.
afterUnmarshal(Object, Object) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.resolver.DBSequenceRefResolver
Method to perform the afterUnmarshal operation if the resolver applies to the specified object.
afterUnmarshal(Object, Object) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.resolver.FragmentArrayRefResolver
Method to perform the afterUnmarshal operation if the resolver applies to the specified object.
afterUnmarshal(Object, Object) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.resolver.InputSpectraRefResolver
Method to perform the afterUnmarshal operation if the resolver applies to the specified object.
afterUnmarshal(Object, Object) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.resolver.InputSpectrumIdentificationsRefResolver
Method to perform the afterUnmarshal operation if the resolver applies to the specified object.
afterUnmarshal(Object, Object) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.resolver.ParentOrganizationRefResolver
Method to perform the afterUnmarshal operation if the resolver applies to the specified object.
afterUnmarshal(Object, Object) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.resolver.PeptideEvidenceRefResolver
Method to perform the afterUnmarshal operation if the resolver applies to the specified object.
afterUnmarshal(Object, Object) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.resolver.PeptideEvidenceResolver
Method to perform the afterUnmarshal operation if the resolver applies to the specified object.
afterUnmarshal(Object, Object) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.resolver.PeptideHypothesisRefResolver
Method to perform the afterUnmarshal operation if the resolver applies to the specified object.
afterUnmarshal(Object, Object) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.resolver.ProteinDetectionHypothesisRefResolver
Method to perform the afterUnmarshal operation if the resolver applies to the specified object.
afterUnmarshal(Object, Object) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.resolver.ProteinDetectionProtocolRefResolver
Method to perform the afterUnmarshal operation if the resolver applies to the specified object.
afterUnmarshal(Object, Object) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.resolver.ProteinDetectionRefResolver
Method to perform the afterUnmarshal operation if the resolver applies to the specified object.
afterUnmarshal(Object, Object) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.resolver.ProviderRefResolver
Method to perform the afterUnmarshal operation if the resolver applies to the specified object.
afterUnmarshal(Object, Object) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.resolver.SearchDatabaseRefResolver
Method to perform the afterUnmarshal operation if the resolver applies to the specified object.
afterUnmarshal(Object, Object) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.resolver.SpectrumIdentificationItemRefRefResolver
Method to perform the afterUnmarshal operation if the resolver applies to the specified object.
afterUnmarshal(Object, Object) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.resolver.SpectrumIdentificationItemRefResolver
Method to perform the afterUnmarshal operation if the resolver applies to the specified object.
afterUnmarshal(Object, Object) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.resolver.SpectrumIdentificationProtocolRefResolver
Method to perform the afterUnmarshal operation if the resolver applies to the specified object.
afterUnmarshal(Object, Object) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.resolver.SpectrumIdentificationRefResolver
Method to perform the afterUnmarshal operation if the resolver applies to the specified object.
afterUnmarshal(Object, Object) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.resolver.SpectrumIdentificationResultRefResolver
Method to perform the afterUnmarshal operation if the resolver applies to the specified object.
afterUnmarshal(Object, Object) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.resolver.SubSampleRefResolver
Method to perform the afterUnmarshal operation if the resolver applies to the specified object.
afterUnmarshal(Object, Object) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.unmarshaller.listeners.RawXMLListener
 
AmbiguousResidue - Class in uk.ac.ebi.jmzidml.model.mzidml
Ambiguous residues e.g.
AmbiguousResidue() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.AmbiguousResidue
 
ambiguousResidue - Variable in class uk.ac.ebi.jmzidml.model.mzidml.MassTable
 
AmbiguousResidueCvParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
 
AmbiguousResidueCvParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.AmbiguousResidueCvParam
 
AmbiguousResidueUserParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
 
AmbiguousResidueUserParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.AmbiguousResidueUserParam
 
AnalysisCollection - Class in uk.ac.ebi.jmzidml.model.mzidml
The analyses performed to get the results, which map the input and output data sets.
AnalysisCollection() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.AnalysisCollection
 
analysisCollection - Variable in class uk.ac.ebi.jmzidml.model.mzidml.MzIdentML
 
AnalysisData - Class in uk.ac.ebi.jmzidml.model.mzidml
Data sets generated by the analyses, including peptide and protein lists.
AnalysisData() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.AnalysisData
 
analysisData - Variable in class uk.ac.ebi.jmzidml.model.mzidml.DataCollection
 
analysisParams - Variable in class uk.ac.ebi.jmzidml.model.mzidml.ProteinDetectionProtocol
 
AnalysisParamsCvParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
User: gokelly Date: 11/04/11 Time: 10:25
AnalysisParamsCvParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.AnalysisParamsCvParam
 
AnalysisParamsUserParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
User: gokelly Date: 11/04/11 Time: 10:25
AnalysisParamsUserParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.AnalysisParamsUserParam
 
AnalysisProtocolCollection - Class in uk.ac.ebi.jmzidml.model.mzidml
The collection of protocols which include the parameters and settings of the performed analyses.
AnalysisProtocolCollection() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.AnalysisProtocolCollection
 
analysisProtocolCollection - Variable in class uk.ac.ebi.jmzidml.model.mzidml.MzIdentML
 
AnalysisSampleCollection - Class in uk.ac.ebi.jmzidml.model.mzidml
The samples analysed can optionally be recorded using CV terms for descriptions.
AnalysisSampleCollection() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.AnalysisSampleCollection
 
analysisSampleCollection - Variable in class uk.ac.ebi.jmzidml.model.mzidml.MzIdentML
 
AnalysisSoftware - Class in uk.ac.ebi.jmzidml.model.mzidml
The software used for performing the analyses.
AnalysisSoftware() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.AnalysisSoftware
 
analysisSoftware - Variable in class uk.ac.ebi.jmzidml.model.mzidml.AnalysisSoftwareList
 
analysisSoftware - Variable in class uk.ac.ebi.jmzidml.model.mzidml.ProteinDetectionProtocol
 
analysisSoftware - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationProtocol
 
AnalysisSoftwareAdapter - Class in uk.ac.ebi.jmzidml.xml.jaxb.adapters
 
AnalysisSoftwareAdapter(MzIdentMLIndexer, AdapterObjectCache) - Constructor for class uk.ac.ebi.jmzidml.xml.jaxb.adapters.AnalysisSoftwareAdapter
 
AnalysisSoftwareList - Class in uk.ac.ebi.jmzidml.model.mzidml
The software packages used to perform the analyses.
AnalysisSoftwareList() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.AnalysisSoftwareList
 
analysisSoftwareList - Variable in class uk.ac.ebi.jmzidml.model.mzidml.MzIdentML
 
analysisSoftwareRef - Variable in class uk.ac.ebi.jmzidml.model.mzidml.ProteinDetectionProtocol
 
analysisSoftwareRef - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationProtocol
 
AuditCollection - Class in uk.ac.ebi.jmzidml.model.mzidml
The complete set of Contacts (people and organisations) for this file.
AuditCollection() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.AuditCollection
 
auditCollection - Variable in class uk.ac.ebi.jmzidml.model.mzidml.MzIdentML
 
authors - Variable in class uk.ac.ebi.jmzidml.model.mzidml.BibliographicReference
 
avgMassDelta - Variable in class uk.ac.ebi.jmzidml.model.mzidml.Modification
 
avgMassDelta - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SubstitutionModification
 

B

beforeMarshal(Object) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.marshaller.listeners.ObjectClassListener
 
BibliographicReference - Class in uk.ac.ebi.jmzidml.model.mzidml
Represents bibliographic references.
BibliographicReference() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.BibliographicReference
 
bibliographicReference - Variable in class uk.ac.ebi.jmzidml.model.mzidml.MzIdentML
 
buildIndex(File) - Method in class uk.ac.ebi.jmzidml.xml.xxindex.MzIdentMLIndexerFactory
 
buildIndex(File, Set<String>) - Method in class uk.ac.ebi.jmzidml.xml.xxindex.MzIdentMLIndexerFactory
 

C

cache - Variable in class uk.ac.ebi.jmzidml.xml.jaxb.adapters.AbstractResolvingAdapter
 
calculatedMassToCharge - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItem
 
calculatedPI - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItem
 
CalendarAdapter - Class in uk.ac.ebi.jmzidml.xml.jaxb.adapters
 
CalendarAdapter() - Constructor for class uk.ac.ebi.jmzidml.xml.jaxb.adapters.CalendarAdapter
 
charge - Variable in class uk.ac.ebi.jmzidml.model.mzidml.IonType
 
chargeState - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItem
 
code - Variable in class uk.ac.ebi.jmzidml.model.mzidml.AmbiguousResidue
 
code - Variable in class uk.ac.ebi.jmzidml.model.mzidml.Residue
 
Constants - Class in uk.ac.ebi.jmzidml.xml
ToDo: Should XML_INDEXED_XPATHS be moved to MzIdentMLIndexerFactory?
Constants() - Constructor for class uk.ac.ebi.jmzidml.xml.Constants
 
Constants.ReferencedType - Enum in uk.ac.ebi.jmzidml.xml
 
contact - Variable in class uk.ac.ebi.jmzidml.model.mzidml.ContactRole
 
contactRef - Variable in class uk.ac.ebi.jmzidml.model.mzidml.ContactRole
 
contactRole - Variable in class uk.ac.ebi.jmzidml.model.mzidml.AnalysisSoftware
 
ContactRole - Class in uk.ac.ebi.jmzidml.model.mzidml
The role that a Contact plays in an organization or with respect to the associating class.
ContactRole() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.ContactRole
 
contactRole - Variable in class uk.ac.ebi.jmzidml.model.mzidml.Provider
 
contactRole - Variable in class uk.ac.ebi.jmzidml.model.mzidml.Sample
 
ContactRoleRefResolver - Class in uk.ac.ebi.jmzidml.xml.jaxb.resolver
 
ContactRoleRefResolver(MzIdentMLIndexer, MzIdentMLObjectCache) - Constructor for class uk.ac.ebi.jmzidml.xml.jaxb.resolver.ContactRoleRefResolver
 
contains(Object) - Method in class uk.ac.ebi.jmzidml.model.utils.FacadeList
Check whether the sublist contains the element
createAffiliation() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of Affiliation
createAmbiguousResidue() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of AmbiguousResidue
createAnalysisCollection() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of AnalysisCollection
createAnalysisData() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of AnalysisData
createAnalysisDataClosingTag() - Method in class uk.ac.ebi.jmzidml.xml.io.MzIdentMLMarshaller
 
createAnalysisDataStartTag() - Method in class uk.ac.ebi.jmzidml.xml.io.MzIdentMLMarshaller
 
createAnalysisProtocolCollection() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of AnalysisProtocolCollection
createAnalysisSampleCollection() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of AnalysisSampleCollection
createAnalysisSoftware() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of AnalysisSoftware
createAnalysisSoftwareList() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of AnalysisSoftwareList
createAuditCollection() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of AuditCollection
createBibliographicReference() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of BibliographicReference
createContactRole() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of ContactRole
createCv() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of Cv
createCvList() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of CvList
createCvParam() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of CvParam
createDatabaseFilters() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of DatabaseFilters
createDatabaseTranslation() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of DatabaseTranslation
createDataCollection() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of DataCollection
createDataCollectionClosingTag() - Method in class uk.ac.ebi.jmzidml.xml.io.MzIdentMLMarshaller
 
createDataCollectionStartTag() - Method in class uk.ac.ebi.jmzidml.xml.io.MzIdentMLMarshaller
 
createDBSequence() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of DBSequence
createEnzyme() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of Enzyme
createEnzymes() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of Enzymes
createExternalData() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of ExternalData
createFileFormat() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of FileFormat
createFilter() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of Filter
createFragmentArray() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of FragmentArray
createFragmentation() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of Fragmentation
createFragmentationTable() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of FragmentationTable
createInputs() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of Inputs
createInputSpectra() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of InputSpectra
createInputSpectrumIdentifications() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of InputSpectrumIdentifications
createIonType() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of IonType
createMassTable() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of MassTable
createMeasure() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of Measure
createModification() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of Modification
createModificationParams() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of ModificationParams
createMzIdentML() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of MzIdentML
createMzIdentML(MzIdentML) - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of JAXBElement<MzIdentML>}
createMzIdentMLClosingTag() - Method in class uk.ac.ebi.jmzidml.xml.io.MzIdentMLMarshaller
 
createMzIdentMLStartTag(String) - Method in class uk.ac.ebi.jmzidml.xml.io.MzIdentMLMarshaller
 
createOrganization() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of Organization
createParam() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of Param
createParamList() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of ParamList
createParentOrganization() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of ParentOrganization
createPeptide() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of Peptide
createPeptideEvidence() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of PeptideEvidence
createPeptideEvidenceRef() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of PeptideEvidenceRef
createPeptideHypothesis() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of PeptideHypothesis
createPerson() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of Person
createProteinAmbiguityGroup() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of ProteinAmbiguityGroup
createProteinDetection() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of ProteinDetection
createProteinDetectionHypothesis() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of ProteinDetectionHypothesis
createProteinDetectionList() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of ProteinDetectionList
createProteinDetectionListClosingTag() - Method in class uk.ac.ebi.jmzidml.xml.io.MzIdentMLMarshaller
 
createProteinDetectionListStartTag(String, String) - Method in class uk.ac.ebi.jmzidml.xml.io.MzIdentMLMarshaller
 
createProteinDetectionProtocol() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of ProteinDetectionProtocol
createProvider() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of Provider
createResidue() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of Residue
createRole() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of Role
createSample() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of Sample
createSearchDatabase() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of SearchDatabase
createSearchDatabaseRef() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of SearchDatabaseRef
createSearchModification() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of SearchModification
createSequenceCollection() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of SequenceCollection
createSourceFile() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of SourceFile
createSpecificityRules() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of SpecificityRules
createSpectraData() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of SpectraData
createSpectrumIdentification() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of SpectrumIdentification
createSpectrumIdentificationItem() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of SpectrumIdentificationItem
createSpectrumIdentificationItemRef() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of SpectrumIdentificationItemRef
createSpectrumIdentificationList() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of SpectrumIdentificationList
createSpectrumIdentificationListClosingTag() - Method in class uk.ac.ebi.jmzidml.xml.io.MzIdentMLMarshaller
 
createSpectrumIdentificationListStartTag(String, String, Long) - Method in class uk.ac.ebi.jmzidml.xml.io.MzIdentMLMarshaller
 
createSpectrumIdentificationProtocol() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of SpectrumIdentificationProtocol
createSpectrumIdentificationResult() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of SpectrumIdentificationResult
createSpectrumIDFormat() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of SpectrumIDFormat
createSubSample() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of SubSample
createSubstitutionModification() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of SubstitutionModification
createTolerance() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of Tolerance
createTranslationTable() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of TranslationTable
createUserParam() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create an instance of UserParam
createXmlHeader() - Method in class uk.ac.ebi.jmzidml.xml.io.MzIdentMLMarshaller
 
creationDate - Variable in class uk.ac.ebi.jmzidml.model.mzidml.MzIdentML
 
cTermGain - Variable in class uk.ac.ebi.jmzidml.model.mzidml.Enzyme
 
customizations - Variable in class uk.ac.ebi.jmzidml.model.mzidml.AnalysisSoftware
 
Cv - Class in uk.ac.ebi.jmzidml.model.mzidml
A source controlled vocabulary from which cvParams will be obtained.
Cv() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.Cv
 
cv - Variable in class uk.ac.ebi.jmzidml.model.mzidml.CvList
 
cv - Variable in class uk.ac.ebi.jmzidml.model.mzidml.CvParam
 
CvAdapter - Class in uk.ac.ebi.jmzidml.xml.jaxb.adapters
 
CvAdapter(MzIdentMLIndexer, AdapterObjectCache) - Constructor for class uk.ac.ebi.jmzidml.xml.jaxb.adapters.CvAdapter
 
CvList - Class in uk.ac.ebi.jmzidml.model.mzidml
The list of controlled vocabularies used in the file.
CvList() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.CvList
 
cvList - Variable in class uk.ac.ebi.jmzidml.model.mzidml.MzIdentML
 
CvParam - Class in uk.ac.ebi.jmzidml.model.mzidml
A single entry from an ontology or a controlled vocabulary.
CvParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.CvParam
 
cvParam - Variable in class uk.ac.ebi.jmzidml.model.mzidml.FileFormat
 
cvParam - Variable in class uk.ac.ebi.jmzidml.model.mzidml.IonType
 
cvParam - Variable in class uk.ac.ebi.jmzidml.model.mzidml.Measure
 
cvParam - Variable in class uk.ac.ebi.jmzidml.model.mzidml.Modification
 
cvParam - Variable in class uk.ac.ebi.jmzidml.model.mzidml.ModParam
 
cvParam - Variable in class uk.ac.ebi.jmzidml.model.mzidml.Role
 
cvParam - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SearchDatabase
 
cvParam - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SearchModification
 
cvParam - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SpecificityRules
 
cvParam - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIDFormat
 
cvParam - Variable in class uk.ac.ebi.jmzidml.model.mzidml.Tolerance
 
cvParam - Variable in class uk.ac.ebi.jmzidml.model.mzidml.TranslationTable
 
CvParamCapable - Interface in uk.ac.ebi.jmzidml.model
This interface defines the presence of a Cvparam getCvParam() method.
CvParamListCapable - Interface in uk.ac.ebi.jmzidml.model
This interface defines the presence of a List getCvParam() method.
CvParamRefResolver - Class in uk.ac.ebi.jmzidml.xml.jaxb.resolver
 
CvParamRefResolver(MzIdentMLIndexer, MzIdentMLObjectCache) - Constructor for class uk.ac.ebi.jmzidml.xml.jaxb.resolver.CvParamRefResolver
 
cvRef - Variable in class uk.ac.ebi.jmzidml.model.mzidml.CvParam
 

D

DatabaseFilters - Class in uk.ac.ebi.jmzidml.model.mzidml
The specification of filters applied to the database searched.
DatabaseFilters() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.DatabaseFilters
 
databaseFilters - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationProtocol
 
databaseName - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SearchDatabase
 
DatabaseNameCvParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
User: gokelly Date: 4/14/11 Time: 2:06 PM
DatabaseNameCvParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.DatabaseNameCvParam
 
DatabaseNameUserParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
User: gokelly Date: 4/14/11 Time: 2:06 PM
DatabaseNameUserParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.DatabaseNameUserParam
 
DatabaseTranslation - Class in uk.ac.ebi.jmzidml.model.mzidml
A specification of how a nucleic acid sequence database was translated for searching.
DatabaseTranslation() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.DatabaseTranslation
 
databaseTranslation - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationProtocol
 
DataCollection - Class in uk.ac.ebi.jmzidml.model.mzidml
The collection of input and output data sets of the analyses.
DataCollection() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.DataCollection
 
dataCollection - Variable in class uk.ac.ebi.jmzidml.model.mzidml.MzIdentML
 
DBSequence - Class in uk.ac.ebi.jmzidml.model.mzidml
A database sequence from the specified SearchDatabase (nucleic acid or amino acid).
DBSequence() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.DBSequence
 
dbSequence - Variable in class uk.ac.ebi.jmzidml.model.mzidml.PeptideEvidence
 
dbSequence - Variable in class uk.ac.ebi.jmzidml.model.mzidml.ProteinDetectionHypothesis
 
dbSequence - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SequenceCollection
 
DBSequenceAdapter - Class in uk.ac.ebi.jmzidml.xml.jaxb.adapters
 
DBSequenceAdapter(MzIdentMLIndexer, AdapterObjectCache) - Constructor for class uk.ac.ebi.jmzidml.xml.jaxb.adapters.DBSequenceAdapter
 
DBSequenceCvParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
 
DBSequenceCvParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.DBSequenceCvParam
 
dbSequenceRef - Variable in class uk.ac.ebi.jmzidml.model.mzidml.PeptideEvidence
 
dbSequenceRef - Variable in class uk.ac.ebi.jmzidml.model.mzidml.ProteinDetectionHypothesis
 
DBSequenceRefResolver - Class in uk.ac.ebi.jmzidml.xml.jaxb.resolver
 
DBSequenceRefResolver(MzIdentMLIndexer, MzIdentMLObjectCache) - Constructor for class uk.ac.ebi.jmzidml.xml.jaxb.resolver.DBSequenceRefResolver
 
DBSequenceUserParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
 
DBSequenceUserParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.DBSequenceUserParam
 
doi - Variable in class uk.ac.ebi.jmzidml.model.mzidml.BibliographicReference
 

E

editor - Variable in class uk.ac.ebi.jmzidml.model.mzidml.BibliographicReference
 
end - Variable in class uk.ac.ebi.jmzidml.model.mzidml.PeptideEvidence
 
Enzyme - Class in uk.ac.ebi.jmzidml.model.mzidml
The details of an individual cleavage enzyme should be provided by giving a regular expression or a CV term if a "standard" enzyme cleavage has been performed.
Enzyme() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.Enzyme
 
enzyme - Variable in class uk.ac.ebi.jmzidml.model.mzidml.Enzymes
 
enzymeName - Variable in class uk.ac.ebi.jmzidml.model.mzidml.Enzyme
 
EnzymeNameCvParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
User: gokelly Date: 11/04/11 Time: 14:10
EnzymeNameCvParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.EnzymeNameCvParam
 
EnzymeNameUserParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
User: gokelly Date: 11/04/11 Time: 14:10
EnzymeNameUserParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.EnzymeNameUserParam
 
Enzymes - Class in uk.ac.ebi.jmzidml.model.mzidml
The list of enzymes used in experiment
Enzymes() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.Enzymes
 
enzymes - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationProtocol
 
equals(Object) - Method in class uk.ac.ebi.jmzidml.model.utils.FacadeList
 
exclude - Variable in class uk.ac.ebi.jmzidml.model.mzidml.Filter
 
ExcludeCvParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
User: gokelly Date: 11/04/11 Time: 16:00
ExcludeCvParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.ExcludeCvParam
 
ExcludeUserParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
User: gokelly Date: 11/04/11 Time: 16:00
ExcludeUserParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.ExcludeUserParam
 
experimentalMassToCharge - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItem
 
ExternalData - Class in uk.ac.ebi.jmzidml.model.mzidml
Data external to the XML instance document.
ExternalData() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.ExternalData
 
externalFormatDocumentation - Variable in class uk.ac.ebi.jmzidml.model.mzidml.ExternalData
 

F

FacadeList<T> - Class in uk.ac.ebi.jmzidml.model.utils
Created by IntelliJ IDEA.
FacadeList(List, Class<T>) - Constructor for class uk.ac.ebi.jmzidml.model.utils.FacadeList
 
fileFormat - Variable in class uk.ac.ebi.jmzidml.model.mzidml.ExternalData
 
FileFormat - Class in uk.ac.ebi.jmzidml.model.mzidml
The format of the ExternalData file, for example "tiff" for image files.
FileFormat() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.FileFormat
 
FileFormatCvParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
 
FileFormatCvParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.FileFormatCvParam
 
FileUtils - Class in uk.ac.ebi.jmzidml.xml.xxindex
 
FileUtils() - Constructor for class uk.ac.ebi.jmzidml.xml.xxindex.FileUtils
 
filter - Variable in class uk.ac.ebi.jmzidml.model.mzidml.DatabaseFilters
 
Filter - Class in uk.ac.ebi.jmzidml.model.mzidml
Filters applied to the search database.
Filter() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.Filter
 
filterType - Variable in class uk.ac.ebi.jmzidml.model.mzidml.Filter
 
FilterTypeCvParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
User: gokelly Date: 4/14/11 Time: 2:09 PM
FilterTypeCvParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.FilterTypeCvParam
 
FilterTypeUserParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
User: gokelly Date: 4/14/11 Time: 2:09 PM
FilterTypeUserParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.FilterTypeUserParam
 
firstName - Variable in class uk.ac.ebi.jmzidml.model.mzidml.Person
 
fixedMod - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SearchModification
 
FragmentArray - Class in uk.ac.ebi.jmzidml.model.mzidml
An array of values for a given type of measure and for a particular ion type, in parallel to the index of ions identified.
FragmentArray() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.FragmentArray
 
fragmentArray - Variable in class uk.ac.ebi.jmzidml.model.mzidml.IonType
 
FragmentArrayRefResolver - Class in uk.ac.ebi.jmzidml.xml.jaxb.resolver
 
FragmentArrayRefResolver(MzIdentMLIndexer, MzIdentMLObjectCache) - Constructor for class uk.ac.ebi.jmzidml.xml.jaxb.resolver.FragmentArrayRefResolver
 
Fragmentation - Class in uk.ac.ebi.jmzidml.model.mzidml
The product ions identified in this result.
Fragmentation() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.Fragmentation
 
fragmentation - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItem
 
FragmentationTable - Class in uk.ac.ebi.jmzidml.model.mzidml
Contains the types of measures that will be reported in generic arrays for each SpectrumIdentificationItem e.g.
FragmentationTable() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.FragmentationTable
 
fragmentationTable - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationList
 
fragmentTolerance - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationProtocol
 
frame - Variable in class uk.ac.ebi.jmzidml.model.mzidml.PeptideEvidence
 
frames - Variable in class uk.ac.ebi.jmzidml.model.mzidml.DatabaseTranslation
 
fullName - Variable in class uk.ac.ebi.jmzidml.model.mzidml.Cv
 

G

get(int) - Method in class uk.ac.ebi.jmzidml.model.utils.FacadeList
Get an element from the original list at index.
getAccession() - Method in class uk.ac.ebi.jmzidml.model.mzidml.CvParam
Gets the value of the accession property.
getAccession() - Method in class uk.ac.ebi.jmzidml.model.mzidml.DBSequence
Gets the value of the accession property.
getActivityDate() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ProtocolApplication
Gets the value of the activityDate property.
getAdditionalSearchParams() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationProtocol
Gets the value of the additionalSearchParams property.
getAffiliation() - Method in class uk.ac.ebi.jmzidml.model.mzidml.Person
Gets the value of the affiliation property.
getAmbiguousResidue() - Method in class uk.ac.ebi.jmzidml.model.mzidml.MassTable
Gets the value of the ambiguousResidue property.
getAnalysisCollection() - Method in class uk.ac.ebi.jmzidml.model.mzidml.MzIdentML
Gets the value of the analysisCollection property.
getAnalysisData() - Method in class uk.ac.ebi.jmzidml.model.mzidml.DataCollection
Gets the value of the analysisData property.
getAnalysisParams() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ProteinDetectionProtocol
Gets the value of the analysisParams property.
getAnalysisProtocolCollection() - Method in class uk.ac.ebi.jmzidml.model.mzidml.MzIdentML
Gets the value of the analysisProtocolCollection property.
getAnalysisSampleCollection() - Method in class uk.ac.ebi.jmzidml.model.mzidml.MzIdentML
Gets the value of the analysisSampleCollection property.
getAnalysisSoftware() - Method in class uk.ac.ebi.jmzidml.model.mzidml.AnalysisSoftwareList
Gets the value of the analysisSoftware property.
getAnalysisSoftware() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ProteinDetectionProtocol
 
getAnalysisSoftware() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationProtocol
 
getAnalysisSoftwareList() - Method in class uk.ac.ebi.jmzidml.model.mzidml.MzIdentML
Gets the value of the analysisSoftwareList property.
getAnalysisSoftwareRef() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ProteinDetectionProtocol
Gets the value of the analysisSoftwareRef property.
getAnalysisSoftwareRef() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationProtocol
Gets the value of the analysisSoftwareRef property.
getAuditCollection() - Method in class uk.ac.ebi.jmzidml.model.mzidml.MzIdentML
Gets the value of the auditCollection property.
getAuthors() - Method in class uk.ac.ebi.jmzidml.model.mzidml.BibliographicReference
Gets the value of the authors property.
getAvgMassDelta() - Method in class uk.ac.ebi.jmzidml.model.mzidml.Modification
Gets the value of the avgMassDelta property.
getAvgMassDelta() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SubstitutionModification
Gets the value of the avgMassDelta property.
getBibliographicReference() - Method in class uk.ac.ebi.jmzidml.model.mzidml.MzIdentML
Gets the value of the bibliographicReference property.
getCachedObject(String, Class<T>) - Method in interface uk.ac.ebi.jmzidml.xml.io.MzIdentMLObjectCache
 
getCachedObject(String, Class<T>) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.unmarshaller.cache.AdapterObjectCache
Retrieve a MzIdentMLObject from the object cache.
getCalculatedMassToCharge() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItem
Gets the value of the calculatedMassToCharge property.
getCalculatedPI() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItem
Gets the value of the calculatedPI property.
getCharge() - Method in class uk.ac.ebi.jmzidml.model.mzidml.IonType
Gets the value of the charge property.
getChargeState() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItem
Gets the value of the chargeState property.
getClassForElementName(String) - Static method in class uk.ac.ebi.jmzidml.model.utils.ModelConstants
 
getClassName() - Method in enum uk.ac.ebi.jmzidml.ParamMappings
 
getClassNames() - Method in enum uk.ac.ebi.jmzidml.ParamListMappings
 
getClazz() - Method in class uk.ac.ebi.jmzidml.model.utils.MzIdentMLElementConfig
 
getClazz() - Method in enum uk.ac.ebi.jmzidml.MzIdentMLElement
 
getClazz() - Method in enum uk.ac.ebi.jmzidml.ParamListMappings
 
getClazz() - Method in enum uk.ac.ebi.jmzidml.ParamMappings
 
getCode() - Method in class uk.ac.ebi.jmzidml.model.mzidml.AmbiguousResidue
Gets the value of the code property.
getCode() - Method in class uk.ac.ebi.jmzidml.model.mzidml.Residue
Gets the value of the code property.
getConfigurations() - Method in class uk.ac.ebi.jmzidml.model.utils.MzIdentMLElementProperties
 
getContact() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ContactRole
 
getContactRef() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ContactRole
Gets the value of the contactRef property.
getContactRole() - Method in class uk.ac.ebi.jmzidml.model.mzidml.AnalysisSoftware
Gets the value of the contactRole property.
getContactRole() - Method in class uk.ac.ebi.jmzidml.model.mzidml.Provider
Gets the value of the contactRole property.
getContactRole() - Method in class uk.ac.ebi.jmzidml.model.mzidml.Sample
Gets the value of the contactRole property.
getCount(String) - Method in interface uk.ac.ebi.jmzidml.xml.xxindex.MzIdentMLIndexer
 
getCreationDate() - Method in class uk.ac.ebi.jmzidml.model.mzidml.MzIdentML
Gets the value of the creationDate property.
getCTermGain() - Method in class uk.ac.ebi.jmzidml.model.mzidml.Enzyme
Gets the value of the cTermGain property.
getCustomizations() - Method in class uk.ac.ebi.jmzidml.model.mzidml.AnalysisSoftware
Gets the value of the customizations property.
getCv() - Method in class uk.ac.ebi.jmzidml.model.mzidml.CvList
Gets the value of the cv property.
getCv() - Method in class uk.ac.ebi.jmzidml.model.mzidml.CvParam
 
getCvList() - Method in class uk.ac.ebi.jmzidml.model.mzidml.MzIdentML
Gets the value of the cvList property.
getCvParam() - Method in class uk.ac.ebi.jmzidml.model.AbstractIdentifiableParamGroup
 
getCvParam() - Method in class uk.ac.ebi.jmzidml.model.AbstractParamGroup
 
getCvParam() - Method in interface uk.ac.ebi.jmzidml.model.CvParamCapable
 
getCvParam() - Method in interface uk.ac.ebi.jmzidml.model.CvParamListCapable
 
getCvParam() - Method in class uk.ac.ebi.jmzidml.model.mzidml.AbstractContact
 
getCvParam() - Method in class uk.ac.ebi.jmzidml.model.mzidml.AmbiguousResidue
 
getCvParam() - Method in class uk.ac.ebi.jmzidml.model.mzidml.DBSequence
 
getCvParam() - Method in class uk.ac.ebi.jmzidml.model.mzidml.FileFormat
Gets the value of the cvParam property.
getCvParam() - Method in class uk.ac.ebi.jmzidml.model.mzidml.IonType
Gets the value of the cvParam property.
getCvParam() - Method in class uk.ac.ebi.jmzidml.model.mzidml.MassTable
 
getCvParam() - Method in class uk.ac.ebi.jmzidml.model.mzidml.Measure
Gets the value of the cvParam property.
getCvParam() - Method in class uk.ac.ebi.jmzidml.model.mzidml.Modification
Gets the value of the cvParam property.
getCvParam() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ModParam
Gets the value of the cvParam property.
getCvParam() - Method in class uk.ac.ebi.jmzidml.model.mzidml.Param
 
getCvParam() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ParamList
Gets the enzyme name cvparams
getCvParam() - Method in class uk.ac.ebi.jmzidml.model.mzidml.Peptide
 
getCvParam() - Method in class uk.ac.ebi.jmzidml.model.mzidml.PeptideEvidence
 
getCvParam() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ProteinAmbiguityGroup
 
getCvParam() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ProteinDetectionHypothesis
 
getCvParam() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ProteinDetectionList
 
getCvParam() - Method in class uk.ac.ebi.jmzidml.model.mzidml.Role
Gets the value of the cvParam property.
getCvParam() - Method in class uk.ac.ebi.jmzidml.model.mzidml.Sample
 
getCvParam() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SearchDatabase
Gets the value of the cvParam property.
getCvParam() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SearchModification
Gets the value of the cvParam property.
getCvParam() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SourceFile
 
getCvParam() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpecificityRules
Gets the value of the cvParam property.
getCvParam() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItem
Get the cv params for SpectrumIdentification
getCvParam() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationList
 
getCvParam() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationResult
Get the cvparams for spectrumidentificationresult
getCvParam() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIDFormat
Gets the value of the cvParam property.
getCvParam() - Method in class uk.ac.ebi.jmzidml.model.mzidml.Tolerance
Gets the value of the cvParam property.
getCvParam() - Method in class uk.ac.ebi.jmzidml.model.mzidml.TranslationTable
Gets the value of the cvParam property.
getCvParam() - Method in interface uk.ac.ebi.jmzidml.model.ParamGroupCapable
 
getCvParamClass() - Method in class uk.ac.ebi.jmzidml.model.utils.MzIdentMLElementConfig
 
getCvParamClass() - Method in enum uk.ac.ebi.jmzidml.MzIdentMLElement
 
getCvRef() - Method in class uk.ac.ebi.jmzidml.model.mzidml.CvParam
Gets the value of the cvRef property.
getDatabaseFilters() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationProtocol
Gets the value of the databaseFilters property.
getDatabaseName() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SearchDatabase
Gets the value of the databaseName property.
getDatabaseTranslation() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationProtocol
Gets the value of the databaseTranslation property.
getDataCollection() - Method in class uk.ac.ebi.jmzidml.model.mzidml.MzIdentML
Gets the value of the dataCollection property.
getDBSequence() - Method in class uk.ac.ebi.jmzidml.model.mzidml.PeptideEvidence
 
getDBSequence() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ProteinDetectionHypothesis
 
getDBSequence() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SequenceCollection
Gets the value of the dbSequence property.
getDBSequenceRef() - Method in class uk.ac.ebi.jmzidml.model.mzidml.PeptideEvidence
Gets the value of the dbSequenceRef property.
getDBSequenceRef() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ProteinDetectionHypothesis
Gets the value of the dbSequenceRef property.
getDoi() - Method in class uk.ac.ebi.jmzidml.model.mzidml.BibliographicReference
Gets the value of the doi property.
getEditor() - Method in class uk.ac.ebi.jmzidml.model.mzidml.BibliographicReference
Gets the value of the editor property.
getElementAttributes(String, Class) - Method in class uk.ac.ebi.jmzidml.xml.io.MzIdentMLUnmarshaller
Method to retrieve attribute name-value pairs for a XML element defined by it's id and Class.
getElementNameForClass(Class) - Static method in class uk.ac.ebi.jmzidml.model.utils.ModelConstants
 
getEnd() - Method in class uk.ac.ebi.jmzidml.model.mzidml.PeptideEvidence
Gets the value of the end property.
getEntries(Class<T>) - Method in interface uk.ac.ebi.jmzidml.xml.io.MzIdentMLObjectCache
 
getEntries(Class<T>) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.unmarshaller.cache.AdapterObjectCache
 
getEnzyme() - Method in class uk.ac.ebi.jmzidml.model.mzidml.Enzymes
Gets the value of the enzyme property.
getEnzymeName() - Method in class uk.ac.ebi.jmzidml.model.mzidml.Enzyme
Gets the value of the enzymeName property.
getEnzymes() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationProtocol
Gets the value of the enzymes property.
getExclude() - Method in class uk.ac.ebi.jmzidml.model.mzidml.Filter
Gets the value of the exclude property.
getExperimentalMassToCharge() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItem
Gets the value of the experimentalMassToCharge property.
getExternalFormatDocumentation() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ExternalData
Gets the value of the externalFormatDocumentation property.
getFileFormat() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ExternalData
Gets the value of the fileFormat property.
getFileFromURL(URL) - Static method in class uk.ac.ebi.jmzidml.xml.xxindex.FileUtils
 
getFilter() - Method in class uk.ac.ebi.jmzidml.model.mzidml.DatabaseFilters
Gets the value of the filter property.
getFilterType() - Method in class uk.ac.ebi.jmzidml.model.mzidml.Filter
Gets the value of the filterType property.
getFirstName() - Method in class uk.ac.ebi.jmzidml.model.mzidml.Person
Gets the value of the firstName property.
getFragmentArray() - Method in class uk.ac.ebi.jmzidml.model.mzidml.IonType
Gets the value of the fragmentArray property.
getFragmentation() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItem
Gets the value of the fragmentation property.
getFragmentationTable() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationList
Gets the value of the fragmentationTable property.
getFragmentTolerance() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationProtocol
Gets the value of the fragmentTolerance property.
getFrame() - Method in class uk.ac.ebi.jmzidml.model.mzidml.PeptideEvidence
Gets the value of the frame property.
getFrames() - Method in class uk.ac.ebi.jmzidml.model.mzidml.DatabaseTranslation
Gets the value of the frames property.
getFullName() - Method in class uk.ac.ebi.jmzidml.model.mzidml.Cv
Gets the value of the fullName property.
getHid() - Method in class uk.ac.ebi.jmzidml.model.MzIdentMLObject
 
getId() - Method in interface uk.ac.ebi.jmzidml.model.IdentifiableMzIdentMLObject
 
getId() - Method in class uk.ac.ebi.jmzidml.model.mzidml.Cv
Gets the value of the id property.
getId() - Method in class uk.ac.ebi.jmzidml.model.mzidml.Identifiable
Gets the value of the id property.
getIDsForElement(MzIdentMLElement) - Method in class uk.ac.ebi.jmzidml.xml.io.MzIdentMLUnmarshaller
Depends on the element being indexed and ID mapped.
getIDsForElement(MzIdentMLElement) - Method in interface uk.ac.ebi.jmzidml.xml.xxindex.MzIdentMLIndexer
Is dependent on the element being indexed and ID mapped.
getInclude() - Method in class uk.ac.ebi.jmzidml.model.mzidml.Filter
Gets the value of the include property.
getIndex() - Method in class uk.ac.ebi.jmzidml.model.mzidml.IonType
Gets the value of the index property.
getIndexElements(String) - Method in interface uk.ac.ebi.jmzidml.xml.xxindex.MzIdentMLIndexer
 
getInputs() - Method in class uk.ac.ebi.jmzidml.model.mzidml.DataCollection
Gets the value of the inputs property.
getInputSpectra() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentification
Gets the value of the inputSpectra property.
getInputSpectrumIdentifications() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ProteinDetection
Gets the value of the inputSpectrumIdentifications property.
getInstance() - Static method in class uk.ac.ebi.jmzidml.xml.jaxb.marshaller.MarshallerFactory
 
getInstance() - Static method in class uk.ac.ebi.jmzidml.xml.jaxb.unmarshaller.UnmarshallerFactory
 
getInstance() - Static method in class uk.ac.ebi.jmzidml.xml.xxindex.MzIdentMLIndexerFactory
 
getIonType() - Method in class uk.ac.ebi.jmzidml.model.mzidml.Fragmentation
Gets the value of the ionType property.
getIssue() - Method in class uk.ac.ebi.jmzidml.model.mzidml.BibliographicReference
Gets the value of the issue property.
getLastName() - Method in class uk.ac.ebi.jmzidml.model.mzidml.Person
Gets the value of the lastName property.
getLength() - Method in class uk.ac.ebi.jmzidml.model.mzidml.DBSequence
Gets the value of the length property.
getLocation() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ExternalData
Gets the value of the location property.
getLocation() - Method in class uk.ac.ebi.jmzidml.model.mzidml.Modification
Gets the value of the location property.
getLocation() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SubstitutionModification
Gets the value of the location property.
getMass() - Method in class uk.ac.ebi.jmzidml.model.mzidml.Residue
Gets the value of the mass property.
getMassDelta() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ModParam
Gets the value of the massDelta property.
getMassDelta() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SearchModification
Gets the value of the massDelta property.
getMassTable() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItem
 
getMassTable() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationProtocol
Gets the value of the massTable property.
getMassTableRef() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItem
Gets the value of the massTableRef property.
getMeasure() - Method in class uk.ac.ebi.jmzidml.model.mzidml.FragmentArray
 
getMeasure() - Method in class uk.ac.ebi.jmzidml.model.mzidml.FragmentationTable
Gets the value of the measure property.
getMeasureRef() - Method in class uk.ac.ebi.jmzidml.model.mzidml.FragmentArray
Gets the value of the measureRef property.
getMidInitials() - Method in class uk.ac.ebi.jmzidml.model.mzidml.Person
Gets the value of the midInitials property.
getMinDistance() - Method in class uk.ac.ebi.jmzidml.model.mzidml.Enzyme
Gets the value of the minDistance property.
getMissedCleavages() - Method in class uk.ac.ebi.jmzidml.model.mzidml.Enzyme
Gets the value of the missedCleavages property.
getModification() - Method in class uk.ac.ebi.jmzidml.model.mzidml.Peptide
Gets the value of the modification property.
getModificationParams() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationProtocol
Gets the value of the modificationParams property.
getMonoisotopicMassDelta() - Method in class uk.ac.ebi.jmzidml.model.mzidml.Modification
Gets the value of the monoisotopicMassDelta property.
getMonoisotopicMassDelta() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SubstitutionModification
Gets the value of the monoisotopicMassDelta property.
getMsLevel() - Method in class uk.ac.ebi.jmzidml.model.mzidml.MassTable
Gets the value of the msLevel property.
getMzIdentMLAttributeXMLString() - Method in interface uk.ac.ebi.jmzidml.xml.xxindex.MzIdentMLIndexer
 
getMzIdentMLId() - Method in class uk.ac.ebi.jmzidml.xml.io.MzIdentMLUnmarshaller
 
getMzIdentMLName() - Method in class uk.ac.ebi.jmzidml.xml.io.MzIdentMLUnmarshaller
 
getMzIdentMLVersion() - Method in class uk.ac.ebi.jmzidml.xml.io.MzIdentMLUnmarshaller
 
getName() - Method in class uk.ac.ebi.jmzidml.model.mzidml.AbstractParam
Gets the value of the name property.
getName() - Method in class uk.ac.ebi.jmzidml.model.mzidml.Identifiable
Gets the value of the name property.
getNTermGain() - Method in class uk.ac.ebi.jmzidml.model.mzidml.Enzyme
Gets the value of the nTermGain property.
getNumDatabaseSequences() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SearchDatabase
Gets the value of the numDatabaseSequences property.
getNumResidues() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SearchDatabase
Gets the value of the numResidues property.
getNumSequencesSearched() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationList
Gets the value of the numSequencesSearched property.
getObjectCountForXpath(String) - Method in class uk.ac.ebi.jmzidml.xml.io.MzIdentMLUnmarshaller
 
getOrganization() - Method in class uk.ac.ebi.jmzidml.model.mzidml.Affiliation
Get the Organization for this Affiliation
getOrganization() - Method in class uk.ac.ebi.jmzidml.model.mzidml.AuditCollection
Returns a list of the Organization objects contained in list returned from getPersonOrOrganization.
getOrganization() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ContactRole
 
getOrganization() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ParentOrganization
 
getOrganizationRef() - Method in class uk.ac.ebi.jmzidml.model.mzidml.Affiliation
Gets the value of the organizationRef property.
getOrganizationRef() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ParentOrganization
Gets the value of the organizationRef property.
getOriginalResidue() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SubstitutionModification
Gets the value of the originalResidue property.
getPages() - Method in class uk.ac.ebi.jmzidml.model.mzidml.BibliographicReference
Gets the value of the pages property.
getParamGroup() - Method in class uk.ac.ebi.jmzidml.model.mzidml.AbstractContact
Attributes of this contact such as address, email, telephone etc.Gets the value of the paramGroup property.
getParamGroup() - Method in class uk.ac.ebi.jmzidml.model.mzidml.AmbiguousResidue
Parameters for capturing e.g.
getParamGroup() - Method in class uk.ac.ebi.jmzidml.model.mzidml.DBSequence
Additional descriptors for the sequence, such as taxon, description line etc.Gets the value of the paramGroup property.
getParamGroup() - Method in class uk.ac.ebi.jmzidml.model.mzidml.MassTable
Additional parameters or descriptors for the MassTable.Gets the value of the paramGroup property.
getParamGroup() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ParamList
Gets the value of the paramGroup property.
getParamGroup() - Method in class uk.ac.ebi.jmzidml.model.mzidml.Peptide
Additional descriptors of this peptide sequence Gets the value of the paramGroup property.
getParamGroup() - Method in class uk.ac.ebi.jmzidml.model.mzidml.PeptideEvidence
Additional parameters or descriptors for the PeptideEvidence.Gets the value of the paramGroup property.
getParamGroup() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ProteinAmbiguityGroup
Scores or parameters associated with the ProteinAmbiguityGroup.Gets the value of the paramGroup property.
getParamGroup() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ProteinDetectionHypothesis
Scores or parameters associated with this ProteinDetectionHypothesis e.g.
getParamGroup() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ProteinDetectionList
Scores or output parameters associated with the whole ProteinDetectionList Gets the value of the paramGroup property.
getParamGroup() - Method in class uk.ac.ebi.jmzidml.model.mzidml.Sample
The characteristics of a Material.Gets the value of the paramGroup property.
getParamGroup() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SourceFile
Any additional parameters description the source file.Gets the value of the paramGroup property.
getParamGroup() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItem
Scores or attributes associated with the SpectrumIdentificationItem e.g.
getParamGroup() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationList
Scores or output parameters associated with the SpectrumIdentificationList.Gets the value of the paramGroup property.
getParamGroup() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationResult
Scores or parameters associated with the SpectrumIdentificationResult (i.e the set of SpectrumIdentificationItems derived from one spectrum) e.g.
getParent() - Method in class uk.ac.ebi.jmzidml.model.mzidml.Organization
Gets the value of the parent property.
getParentTolerance() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationProtocol
Gets the value of the parentTolerance property.
getPeptide() - Method in class uk.ac.ebi.jmzidml.model.mzidml.PeptideEvidence
 
getPeptide() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SequenceCollection
Gets the value of the peptide property.
getPeptide() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItem
 
getPeptideEvidence() - Method in class uk.ac.ebi.jmzidml.model.mzidml.PeptideEvidenceRef
 
getPeptideEvidence() - Method in class uk.ac.ebi.jmzidml.model.mzidml.PeptideHypothesis
 
getPeptideEvidence() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SequenceCollection
Gets the value of the peptideEvidence property.
getPeptideEvidenceRef() - Method in class uk.ac.ebi.jmzidml.model.mzidml.PeptideEvidenceRef
Gets the value of the peptideEvidenceRef property.
getPeptideEvidenceRef() - Method in class uk.ac.ebi.jmzidml.model.mzidml.PeptideHypothesis
Gets the value of the peptideEvidenceRef property.
getPeptideEvidenceRef() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItem
Gets the value of the peptideEvidenceRef property.
getPeptideHypothesis() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ProteinDetectionHypothesis
Gets the value of the peptideHypothesis property.
getPeptideRef() - Method in class uk.ac.ebi.jmzidml.model.mzidml.PeptideEvidence
Gets the value of the peptideRef property.
getPeptideRef() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItem
Gets the value of the peptideRef property.
getPeptideSequence() - Method in class uk.ac.ebi.jmzidml.model.mzidml.Peptide
Gets the value of the peptideSequence property.
getPerson() - Method in class uk.ac.ebi.jmzidml.model.mzidml.AuditCollection
Returns a list of the Person objects contained in list returned from getPersonOrOrganization.
getPerson() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ContactRole
 
getPersonOrOrganization() - Method in class uk.ac.ebi.jmzidml.model.mzidml.AuditCollection
Gets the value of the personOrOrganization property.
getPost() - Method in class uk.ac.ebi.jmzidml.model.mzidml.PeptideEvidence
Gets the value of the post property.
getPre() - Method in class uk.ac.ebi.jmzidml.model.mzidml.PeptideEvidence
Gets the value of the pre property.
getProteinAmbiguityGroup() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ProteinDetectionList
Gets the value of the proteinAmbiguityGroup property.
getProteinDetection() - Method in class uk.ac.ebi.jmzidml.model.mzidml.AnalysisCollection
Gets the value of the proteinDetection property.
getProteinDetectionHypothesis() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ProteinAmbiguityGroup
Gets the value of the proteinDetectionHypothesis property.
getProteinDetectionList() - Method in class uk.ac.ebi.jmzidml.model.mzidml.AnalysisData
Gets the value of the proteinDetectionList property.
getProteinDetectionList() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ProteinDetection
 
getProteinDetectionListRef() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ProteinDetection
Gets the value of the proteinDetectionListRef property.
getProteinDetectionProtocol() - Method in class uk.ac.ebi.jmzidml.model.mzidml.AnalysisProtocolCollection
Gets the value of the proteinDetectionProtocol property.
getProteinDetectionProtocol() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ProteinDetection
 
getProteinDetectionProtocolRef() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ProteinDetection
Gets the value of the proteinDetectionProtocolRef property.
getProvider() - Method in class uk.ac.ebi.jmzidml.model.mzidml.MzIdentML
Gets the value of the provider property.
getPublication() - Method in class uk.ac.ebi.jmzidml.model.mzidml.BibliographicReference
Gets the value of the publication property.
getPublisher() - Method in class uk.ac.ebi.jmzidml.model.mzidml.BibliographicReference
Gets the value of the publisher property.
getQNameForClass(Class) - Static method in class uk.ac.ebi.jmzidml.model.utils.ModelConstants
 
getRank() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItem
Gets the value of the rank property.
getRefResolverClass() - Method in class uk.ac.ebi.jmzidml.model.utils.MzIdentMLElementConfig
 
getRefResolverClass() - Method in enum uk.ac.ebi.jmzidml.MzIdentMLElement
 
getReleaseDate() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SearchDatabase
Gets the value of the releaseDate property.
getReplacementResidue() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SubstitutionModification
Gets the value of the replacementResidue property.
getResidue() - Method in class uk.ac.ebi.jmzidml.model.mzidml.MassTable
Gets the value of the residue property.
getResidues() - Method in class uk.ac.ebi.jmzidml.model.mzidml.Modification
Gets the value of the residues property.
getResidues() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ModParam
Gets the value of the residues property.
getResidues() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SearchModification
Gets the value of the residues property.
getRole() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ContactRole
Gets the value of the role property.
getSample() - Method in class uk.ac.ebi.jmzidml.model.mzidml.AnalysisSampleCollection
Gets the value of the sample property.
getSample() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItem
 
getSample() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SubSample
 
getSampleRef() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItem
Gets the value of the sampleRef property.
getSampleRef() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SubSample
Gets the value of the sampleRef property.
getSearchDatabase() - Method in class uk.ac.ebi.jmzidml.model.mzidml.DBSequence
 
getSearchDatabase() - Method in class uk.ac.ebi.jmzidml.model.mzidml.Inputs
Gets the value of the searchDatabase property.
getSearchDatabase() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SearchDatabaseRef
 
getSearchDatabaseRef() - Method in class uk.ac.ebi.jmzidml.model.mzidml.DBSequence
Gets the value of the searchDatabaseRef property.
getSearchDatabaseRef() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SearchDatabaseRef
Gets the value of the searchDatabaseRef property.
getSearchDatabaseRef() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentification
Gets the value of the searchDatabaseRef property.
getSearchModification() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ModificationParams
Gets the value of the searchModification property.
getSearchType() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationProtocol
Gets the value of the searchType property.
getSeq() - Method in class uk.ac.ebi.jmzidml.model.mzidml.DBSequence
Gets the value of the seq property.
getSequenceCollection() - Method in class uk.ac.ebi.jmzidml.model.mzidml.MzIdentML
Gets the value of the sequenceCollection property.
getSiteRegexp() - Method in class uk.ac.ebi.jmzidml.model.mzidml.Enzyme
Gets the value of the siteRegexp property.
getSoftware() - Method in class uk.ac.ebi.jmzidml.model.mzidml.Provider
 
getSoftwareName() - Method in class uk.ac.ebi.jmzidml.model.mzidml.AnalysisSoftware
Gets the value of the softwareName property.
getSoftwareRef() - Method in class uk.ac.ebi.jmzidml.model.mzidml.Provider
Gets the value of the analysisSoftwareRef property.
getSourceFile() - Method in class uk.ac.ebi.jmzidml.model.mzidml.Inputs
Gets the value of the sourceFile property.
getSpecificityRules() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SearchModification
Gets the value of the specificityRules property.
getSpectraData() - Method in class uk.ac.ebi.jmzidml.model.mzidml.Inputs
Gets the value of the spectraData property.
getSpectraData() - Method in class uk.ac.ebi.jmzidml.model.mzidml.InputSpectra
 
getSpectraData() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationResult
 
getSpectraDataRef() - Method in class uk.ac.ebi.jmzidml.model.mzidml.InputSpectra
Gets the value of the spectraDataRef property.
getSpectraDataRef() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationResult
Gets the value of the spectraDataRef property.
getSpectrumID() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationResult
Gets the value of the spectrumID property.
getSpectrumIdentification() - Method in class uk.ac.ebi.jmzidml.model.mzidml.AnalysisCollection
Gets the value of the spectrumIdentification property.
getSpectrumIdentificationItem() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItemRef
 
getSpectrumIdentificationItem() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationResult
Gets the value of the spectrumIdentificationItem property.
getSpectrumIdentificationItemRef() - Method in class uk.ac.ebi.jmzidml.model.mzidml.PeptideHypothesis
Gets the value of the spectrumIdentificationItemRef property.
getSpectrumIdentificationItemRef() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItemRef
Gets the value of the spectrumIdentificationItemRef property.
getSpectrumIdentificationList() - Method in class uk.ac.ebi.jmzidml.model.mzidml.AnalysisData
Gets the value of the spectrumIdentificationList property.
getSpectrumIdentificationList() - Method in class uk.ac.ebi.jmzidml.model.mzidml.InputSpectrumIdentifications
 
getSpectrumIdentificationList() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentification
 
getSpectrumIdentificationListRef() - Method in class uk.ac.ebi.jmzidml.model.mzidml.InputSpectrumIdentifications
Gets the value of the spectrumIdentificationListRef property.
getSpectrumIdentificationListRef() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentification
Gets the value of the spectrumIdentificationListRef property.
getSpectrumIdentificationProtocol() - Method in class uk.ac.ebi.jmzidml.model.mzidml.AnalysisProtocolCollection
Gets the value of the spectrumIdentificationProtocol property.
getSpectrumIdentificationProtocol() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentification
 
getSpectrumIdentificationProtocolRef() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentification
Gets the value of the spectrumIdentificationProtocolRef property.
getSpectrumIdentificationResult() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationList
Gets the value of the spectrumIdentificationResult property.
getSpectrumIDFormat() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectraData
Gets the value of the spectrumIDFormat property.
getStart() - Method in class uk.ac.ebi.jmzidml.model.mzidml.PeptideEvidence
Gets the value of the start property.
getStartTag(String, Class) - Method in interface uk.ac.ebi.jmzidml.xml.xxindex.MzIdentMLIndexer
 
getSubSample() - Method in class uk.ac.ebi.jmzidml.model.mzidml.Sample
Gets the value of the subSample property.
getSubstitutionModification() - Method in class uk.ac.ebi.jmzidml.model.mzidml.Peptide
Gets the value of the substitutionModification property.
getTagName() - Method in class uk.ac.ebi.jmzidml.model.utils.MzIdentMLElementConfig
 
getTagName() - Method in enum uk.ac.ebi.jmzidml.MzIdentMLElement
 
getThreshold() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ProteinDetectionProtocol
Gets the value of the threshold property.
getThreshold() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationProtocol
Gets the value of the threshold property.
getTitle() - Method in class uk.ac.ebi.jmzidml.model.mzidml.BibliographicReference
Gets the value of the title property.
getTranslationTable() - Method in class uk.ac.ebi.jmzidml.model.mzidml.DatabaseTranslation
Gets the value of the translationTable property.
getTranslationTable() - Method in class uk.ac.ebi.jmzidml.model.mzidml.PeptideEvidence
 
getTranslationTableRef() - Method in class uk.ac.ebi.jmzidml.model.mzidml.PeptideEvidence
Gets the value of the translationTableRef property.
getType() - Method in class uk.ac.ebi.jmzidml.model.mzidml.UserParam
Gets the value of the type property.
getType(Class) - Static method in enum uk.ac.ebi.jmzidml.MzIdentMLElement
 
getType(String) - Static method in enum uk.ac.ebi.jmzidml.MzIdentMLElement
 
getType(Class) - Static method in enum uk.ac.ebi.jmzidml.ParamListMappings
 
getType(Class) - Static method in enum uk.ac.ebi.jmzidml.ParamMappings
 
getUnitAccession() - Method in class uk.ac.ebi.jmzidml.model.mzidml.AbstractParam
Gets the value of the unitAccession property.
getUnitCv() - Method in class uk.ac.ebi.jmzidml.model.mzidml.AbstractParam
 
getUnitCvRef() - Method in class uk.ac.ebi.jmzidml.model.mzidml.AbstractParam
Gets the value of the unitCvRef property.
getUnitName() - Method in class uk.ac.ebi.jmzidml.model.mzidml.AbstractParam
Gets the value of the unitName property.
getUri() - Method in class uk.ac.ebi.jmzidml.model.mzidml.AnalysisSoftware
Gets the value of the uri property.
getUri() - Method in class uk.ac.ebi.jmzidml.model.mzidml.Cv
Gets the value of the uri property.
getUserParam() - Method in class uk.ac.ebi.jmzidml.model.AbstractIdentifiableParamGroup
 
getUserParam() - Method in class uk.ac.ebi.jmzidml.model.AbstractParamGroup
 
getUserParam() - Method in class uk.ac.ebi.jmzidml.model.mzidml.AbstractContact
 
getUserParam() - Method in class uk.ac.ebi.jmzidml.model.mzidml.AmbiguousResidue
 
getUserParam() - Method in class uk.ac.ebi.jmzidml.model.mzidml.DBSequence
 
getUserParam() - Method in class uk.ac.ebi.jmzidml.model.mzidml.MassTable
 
getUserParam() - Method in class uk.ac.ebi.jmzidml.model.mzidml.Param
 
getUserParam() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ParamList
Gets the enzymename userparams
getUserParam() - Method in class uk.ac.ebi.jmzidml.model.mzidml.Peptide
 
getUserParam() - Method in class uk.ac.ebi.jmzidml.model.mzidml.PeptideEvidence
 
getUserParam() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ProteinAmbiguityGroup
 
getUserParam() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ProteinDetectionHypothesis
 
getUserParam() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ProteinDetectionList
 
getUserParam() - Method in class uk.ac.ebi.jmzidml.model.mzidml.Sample
 
getUserParam() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SourceFile
 
getUserParam() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItem
Get the user params for SpectrumIdentification
getUserParam() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationList
 
getUserParam() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationResult
Get the userparams for spectrumidentificationresult
getUserParam() - Method in interface uk.ac.ebi.jmzidml.model.ParamGroupCapable
 
getUserParamClass() - Method in class uk.ac.ebi.jmzidml.model.utils.MzIdentMLElementConfig
 
getUserParamClass() - Method in enum uk.ac.ebi.jmzidml.MzIdentMLElement
 
getValue() - Method in class uk.ac.ebi.jmzidml.model.mzidml.AbstractParam
Gets the value of the value property.
getValues() - Method in class uk.ac.ebi.jmzidml.model.mzidml.FragmentArray
Gets the value of the values property.
getVersion() - Method in class uk.ac.ebi.jmzidml.model.mzidml.AnalysisSoftware
Gets the value of the version property.
getVersion() - Method in class uk.ac.ebi.jmzidml.model.mzidml.Cv
Gets the value of the version property.
getVersion() - Method in class uk.ac.ebi.jmzidml.model.mzidml.MzIdentML
Gets the value of the version property.
getVersion() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SearchDatabase
Gets the value of the version property.
getVolume() - Method in class uk.ac.ebi.jmzidml.model.mzidml.BibliographicReference
Gets the value of the volume property.
getXmlString(String, Class) - Method in interface uk.ac.ebi.jmzidml.xml.xxindex.MzIdentMLIndexer
A method to retrieve the XML String of a specific XML element, providing the unique ID of the element and the Java mapped Class.
getXmlStringIterator(String) - Method in interface uk.ac.ebi.jmzidml.xml.xxindex.MzIdentMLIndexer
 
getXpath() - Method in class uk.ac.ebi.jmzidml.model.utils.MzIdentMLElementConfig
 
getXpath() - Method in enum uk.ac.ebi.jmzidml.MzIdentMLElement
 
getXpath() - Method in interface uk.ac.ebi.jmzidml.xml.xxindex.MzIdentMLIndexer
Retrieves all xpath for which an XML element has been recorded.
getYear() - Method in class uk.ac.ebi.jmzidml.model.mzidml.BibliographicReference
Gets the value of the year property.

H

hasEntry(Class<T>) - Method in interface uk.ac.ebi.jmzidml.xml.io.MzIdentMLObjectCache
 
hasEntry(Class<T>) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.unmarshaller.cache.AdapterObjectCache
 
hashCode() - Method in class uk.ac.ebi.jmzidml.model.utils.FacadeList
 
hasNext() - Method in class uk.ac.ebi.jmzidml.xml.io.MzIdentMLObjectIterator
 

I

id - Variable in class uk.ac.ebi.jmzidml.model.mzidml.Cv
 
id - Variable in class uk.ac.ebi.jmzidml.model.mzidml.Identifiable
 
Identifiable - Class in uk.ac.ebi.jmzidml.model.mzidml
Other classes in the model can be specified as sub-classes, inheriting from Identifiable.
Identifiable() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.Identifiable
 
IdentifiableMzIdentMLObject - Interface in uk.ac.ebi.jmzidml.model
Interface defining the presence of the getId() method.
include - Variable in class uk.ac.ebi.jmzidml.model.mzidml.Filter
 
IncludeCvParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
User: gokelly Date: 11/04/11 Time: 15:58
IncludeCvParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.IncludeCvParam
 
IncludeUserParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
User: gokelly Date: 11/04/11 Time: 15:59
IncludeUserParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.IncludeUserParam
 
independent - Variable in class uk.ac.ebi.jmzidml.model.mzidml.Enzymes
 
index - Variable in class uk.ac.ebi.jmzidml.model.mzidml.IonType
 
index - Variable in class uk.ac.ebi.jmzidml.xml.jaxb.adapters.AbstractResolvingAdapter
 
indexOf(Object) - Method in class uk.ac.ebi.jmzidml.model.utils.FacadeList
Get the index of sublist using a given object
initializeMarshaller() - Method in class uk.ac.ebi.jmzidml.xml.jaxb.marshaller.MarshallerFactory
 
initializeUnmarshaller(MzIdentMLIndexer, MzIdentMLObjectCache, MzIdentMLNamespaceFilter) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.unmarshaller.UnmarshallerFactory
 
inputs - Variable in class uk.ac.ebi.jmzidml.model.mzidml.DataCollection
 
Inputs - Class in uk.ac.ebi.jmzidml.model.mzidml
The inputs to the analyses including the databases searched, the spectral data and the source file converted to mzIdentML.
Inputs() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.Inputs
 
InputSpectra - Class in uk.ac.ebi.jmzidml.model.mzidml
The attribute referencing an identifier within the SpectraData section.
InputSpectra() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.InputSpectra
 
inputSpectra - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentification
 
InputSpectraRefResolver - Class in uk.ac.ebi.jmzidml.xml.jaxb.resolver
 
InputSpectraRefResolver(MzIdentMLIndexer, MzIdentMLObjectCache) - Constructor for class uk.ac.ebi.jmzidml.xml.jaxb.resolver.InputSpectraRefResolver
 
InputSpectrumIdentifications - Class in uk.ac.ebi.jmzidml.model.mzidml
The lists of spectrum identifications that are input to the protein detection process.
InputSpectrumIdentifications() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.InputSpectrumIdentifications
 
inputSpectrumIdentifications - Variable in class uk.ac.ebi.jmzidml.model.mzidml.ProteinDetection
 
InputSpectrumIdentificationsRefResolver - Class in uk.ac.ebi.jmzidml.xml.jaxb.resolver
 
InputSpectrumIdentificationsRefResolver(MzIdentMLIndexer, MzIdentMLObjectCache) - Constructor for class uk.ac.ebi.jmzidml.xml.jaxb.resolver.InputSpectrumIdentificationsRefResolver
 
ionType - Variable in class uk.ac.ebi.jmzidml.model.mzidml.Fragmentation
 
IonType - Class in uk.ac.ebi.jmzidml.model.mzidml
IonType defines the index of fragmentation ions being reported, importing a CV term for the type of ion e.g.
IonType() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.IonType
 
IonTypeCvParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
 
IonTypeCvParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.IonTypeCvParam
 
isAutoRefResolving() - Method in class uk.ac.ebi.jmzidml.model.utils.MzIdentMLElementConfig
 
isAutoRefResolving() - Method in enum uk.ac.ebi.jmzidml.MzIdentMLElement
 
isCached() - Method in class uk.ac.ebi.jmzidml.model.utils.MzIdentMLElementConfig
 
isCached() - Method in enum uk.ac.ebi.jmzidml.MzIdentMLElement
 
isDecoy - Variable in class uk.ac.ebi.jmzidml.model.mzidml.PeptideEvidence
 
isEmpty() - Method in class uk.ac.ebi.jmzidml.model.utils.FacadeList
Check whether the sublist is empty
isFixedMod() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SearchModification
Gets the value of the fixedMod property.
isIdMapped() - Method in class uk.ac.ebi.jmzidml.model.utils.MzIdentMLElementConfig
 
isIdMapped() - Method in enum uk.ac.ebi.jmzidml.MzIdentMLElement
 
isIDmapped(String, Class) - Method in interface uk.ac.ebi.jmzidml.xml.xxindex.MzIdentMLIndexer
 
isIndependent() - Method in class uk.ac.ebi.jmzidml.model.mzidml.Enzymes
Gets the value of the independent property.
isIndexed() - Method in class uk.ac.ebi.jmzidml.model.utils.MzIdentMLElementConfig
 
isIndexed() - Method in enum uk.ac.ebi.jmzidml.MzIdentMLElement
 
isIsDecoy() - Method in class uk.ac.ebi.jmzidml.model.mzidml.PeptideEvidence
Gets the value of the isDecoy property.
isPassThreshold() - Method in class uk.ac.ebi.jmzidml.model.mzidml.ProteinDetectionHypothesis
Gets the value of the passThreshold property.
isPassThreshold() - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItem
Gets the value of the passThreshold property.
isRegisteredClass(Class) - Static method in class uk.ac.ebi.jmzidml.model.utils.ModelConstants
 
isSemiSpecific() - Method in class uk.ac.ebi.jmzidml.model.mzidml.Enzyme
Gets the value of the semiSpecific property.
issue - Variable in class uk.ac.ebi.jmzidml.model.mzidml.BibliographicReference
 
iterator() - Method in class uk.ac.ebi.jmzidml.model.utils.FacadeList
Get an iterator of the sublist

J

JAXB_ENCODING_PROPERTY - Static variable in class uk.ac.ebi.jmzidml.xml.Constants
 
JAXB_FORMATTING_PROPERTY - Static variable in class uk.ac.ebi.jmzidml.xml.Constants
 
JAXB_FRAGMENT_PROPERTY - Static variable in class uk.ac.ebi.jmzidml.xml.Constants
 
JAXB_SCHEMALOCATION_PROPERTY - Static variable in class uk.ac.ebi.jmzidml.xml.Constants
 
JmzIdentMLParser - Class in uk.ac.ebi
 
JmzIdentMLParser() - Constructor for class uk.ac.ebi.JmzIdentMLParser
 

L

lastIndexOf(Object) - Method in class uk.ac.ebi.jmzidml.model.utils.FacadeList
Get the last index of sublist using a given object
lastName - Variable in class uk.ac.ebi.jmzidml.model.mzidml.Person
 
length - Variable in class uk.ac.ebi.jmzidml.model.mzidml.DBSequence
 
listIterator() - Method in class uk.ac.ebi.jmzidml.model.utils.FacadeList
 
listIterator(int) - Method in class uk.ac.ebi.jmzidml.model.utils.FacadeList
 
loadProperties() - Static method in enum uk.ac.ebi.jmzidml.MzIdentMLElement
Read the configuration info from the properties file.
location - Variable in class uk.ac.ebi.jmzidml.model.mzidml.ExternalData
 
location - Variable in class uk.ac.ebi.jmzidml.model.mzidml.Modification
 
location - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SubstitutionModification
 
logger - Static variable in class uk.ac.ebi.jmzidml.xml.jaxb.adapters.AbstractResolvingAdapter
 

M

main(String[]) - Static method in class uk.ac.ebi.JmzIdentMLParser
 
marshal(T) - Method in class uk.ac.ebi.jmzidml.xml.io.MzIdentMLMarshaller
 
marshal(T, OutputStream) - Method in class uk.ac.ebi.jmzidml.xml.io.MzIdentMLMarshaller
 
marshal(T, Writer) - Method in class uk.ac.ebi.jmzidml.xml.io.MzIdentMLMarshaller
 
marshal(AnalysisSoftware) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.adapters.AnalysisSoftwareAdapter
 
marshal(Calendar) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.adapters.CalendarAdapter
 
marshal(Cv) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.adapters.CvAdapter
 
marshal(DBSequence) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.adapters.DBSequenceAdapter
 
marshal(MassTable) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.adapters.MassTableAdapter
 
marshal(Measure) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.adapters.MeasureAdapter
 
marshal(Organization) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.adapters.OrganizationAdapter
 
marshal(Peptide) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.adapters.PeptideAdapter
 
marshal(PeptideEvidence) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.adapters.PeptideEvidenceAdapter
 
marshal(ProteinDetectionList) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.adapters.ProteinDetectionListAdapter
 
marshal(ProteinDetectionProtocol) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.adapters.ProteinDetectionProtocolAdapter
 
marshal(Sample) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.adapters.SampleAdapter
 
marshal(SearchDatabase) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.adapters.SearchDatabaseAdapter
 
marshal(SpectraData) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.adapters.SpectraDataAdapter
 
marshal(SpectrumIdentificationList) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.adapters.SpectrumIdentificationListAdapter
 
marshal(SpectrumIdentificationProtocol) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.adapters.SpectrumIdentificationProtocolAdapter
 
marshal(TranslationTable) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.adapters.TranslationTableAdapter
 
marshall(T) - Method in class uk.ac.ebi.jmzidml.xml.io.MzIdentMLMarshaller
Deprecated. 
marshall(T, OutputStream) - Method in class uk.ac.ebi.jmzidml.xml.io.MzIdentMLMarshaller
Deprecated. 
marshall(T, Writer) - Method in class uk.ac.ebi.jmzidml.xml.io.MzIdentMLMarshaller
Deprecated. 
MarshallerFactory - Class in uk.ac.ebi.jmzidml.xml.jaxb.marshaller
 
mass - Variable in class uk.ac.ebi.jmzidml.model.mzidml.Residue
 
massDelta - Variable in class uk.ac.ebi.jmzidml.model.mzidml.ModParam
 
massDelta - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SearchModification
 
MassTable - Class in uk.ac.ebi.jmzidml.model.mzidml
The masses of residues used in the search.
MassTable() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.MassTable
 
massTable - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItem
 
massTable - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationProtocol
 
MassTableAdapter - Class in uk.ac.ebi.jmzidml.xml.jaxb.adapters
 
MassTableAdapter(MzIdentMLIndexer, AdapterObjectCache) - Constructor for class uk.ac.ebi.jmzidml.xml.jaxb.adapters.MassTableAdapter
 
MassTableCvParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
 
MassTableCvParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.MassTableCvParam
 
massTableRef - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItem
 
MassTableUserParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
 
MassTableUserParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.MassTableUserParam
 
measure - Variable in class uk.ac.ebi.jmzidml.model.mzidml.FragmentArray
 
measure - Variable in class uk.ac.ebi.jmzidml.model.mzidml.FragmentationTable
 
Measure - Class in uk.ac.ebi.jmzidml.model.mzidml
References to CV terms defining the measures about product ions to be reported in SpectrumIdentificationItem
Measure() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.Measure
 
MeasureAdapter - Class in uk.ac.ebi.jmzidml.xml.jaxb.adapters
 
MeasureAdapter(MzIdentMLIndexer, AdapterObjectCache) - Constructor for class uk.ac.ebi.jmzidml.xml.jaxb.adapters.MeasureAdapter
 
MeasureCvParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
 
MeasureCvParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.MeasureCvParam
 
measureRef - Variable in class uk.ac.ebi.jmzidml.model.mzidml.FragmentArray
 
midInitials - Variable in class uk.ac.ebi.jmzidml.model.mzidml.Person
 
minDistance - Variable in class uk.ac.ebi.jmzidml.model.mzidml.Enzyme
 
missedCleavages - Variable in class uk.ac.ebi.jmzidml.model.mzidml.Enzyme
 
ModelConstants - Class in uk.ac.ebi.jmzidml.model.utils
 
ModelConstants() - Constructor for class uk.ac.ebi.jmzidml.model.utils.ModelConstants
 
Modification - Class in uk.ac.ebi.jmzidml.model.mzidml
A molecule modification specification.
Modification() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.Modification
 
modification - Variable in class uk.ac.ebi.jmzidml.model.mzidml.Peptide
 
ModificationCvParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
 
ModificationCvParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.ModificationCvParam
 
ModificationParams - Class in uk.ac.ebi.jmzidml.model.mzidml
The specification of static/variable modifications (e.g.
ModificationParams() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.ModificationParams
 
modificationParams - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationProtocol
 
ModificationUserParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
 
ModificationUserParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.ModificationUserParam
 
ModParam - Class in uk.ac.ebi.jmzidml.model.mzidml
The modification searched for, sourced from e.g.
ModParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.ModParam
 
ModParamCvParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
 
ModParamCvParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.ModParamCvParam
 
monoisotopicMassDelta - Variable in class uk.ac.ebi.jmzidml.model.mzidml.Modification
 
monoisotopicMassDelta - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SubstitutionModification
 
msLevel - Variable in class uk.ac.ebi.jmzidml.model.mzidml.MassTable
 
MzIdentML - Class in uk.ac.ebi.jmzidml.model.mzidml
The upper-most hierarchy level of mzIdentML with sub-containers for example describing software, protocols and search results (spectrum identifications or protein detection results).
MzIdentML() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.MzIdentML
 
MzIdentMLElement - Enum in uk.ac.ebi.jmzidml
For performance reasons (Memory Overflow), all the reference auto-resolving have been switched off.
MzIdentMLElementConfig - Class in uk.ac.ebi.jmzidml.model.utils
User: gokelly Date: 6/9/11 Time: 10:50 AM
MzIdentMLElementConfig() - Constructor for class uk.ac.ebi.jmzidml.model.utils.MzIdentMLElementConfig
 
MzIdentMLElementProperties - Class in uk.ac.ebi.jmzidml.model.utils
User: gokelly Date: 6/9/11 Time: 11:21 AM
MzIdentMLElementProperties() - Constructor for class uk.ac.ebi.jmzidml.model.utils.MzIdentMLElementProperties
 
MzIdentMLIndexer - Interface in uk.ac.ebi.jmzidml.xml.xxindex
 
MzIdentMLIndexerFactory - Class in uk.ac.ebi.jmzidml.xml.xxindex
 
MzIdentMLMarshaller - Class in uk.ac.ebi.jmzidml.xml.io
 
MzIdentMLMarshaller() - Constructor for class uk.ac.ebi.jmzidml.xml.io.MzIdentMLMarshaller
 
MzIdentMLNamespaceFilter - Class in uk.ac.ebi.jmzidml.xml.jaxb.unmarshaller.filters
 
MzIdentMLNamespaceFilter() - Constructor for class uk.ac.ebi.jmzidml.xml.jaxb.unmarshaller.filters.MzIdentMLNamespaceFilter
 
MzIdentMLNamespaceFilter(XMLReader) - Constructor for class uk.ac.ebi.jmzidml.xml.jaxb.unmarshaller.filters.MzIdentMLNamespaceFilter
 
MzIdentMLObject - Class in uk.ac.ebi.jmzidml.model
 
MzIdentMLObject() - Constructor for class uk.ac.ebi.jmzidml.model.MzIdentMLObject
 
MzIdentMLObjectCache - Interface in uk.ac.ebi.jmzidml.xml.io
 
MzIdentMLObjectIterator<T extends MzIdentMLObject> - Class in uk.ac.ebi.jmzidml.xml.io
 
MzIdentMLUnmarshaller - Class in uk.ac.ebi.jmzidml.xml.io
 
MzIdentMLUnmarshaller(URL) - Constructor for class uk.ac.ebi.jmzidml.xml.io.MzIdentMLUnmarshaller
 
MzIdentMLUnmarshaller(File) - Constructor for class uk.ac.ebi.jmzidml.xml.io.MzIdentMLUnmarshaller
 
MzIdentMLUnmarshaller(MzIdentMLIndexer) - Constructor for class uk.ac.ebi.jmzidml.xml.io.MzIdentMLUnmarshaller
 
MzIdentMLUnmarshaller(URL, MzIdentMLObjectCache) - Constructor for class uk.ac.ebi.jmzidml.xml.io.MzIdentMLUnmarshaller
Deprecated. 
MzIdentMLUnmarshaller(File, MzIdentMLObjectCache) - Constructor for class uk.ac.ebi.jmzidml.xml.io.MzIdentMLUnmarshaller
Deprecated. 
MZIDML_NS - Static variable in class uk.ac.ebi.jmzidml.model.utils.ModelConstants
 
MZIDML_SCHEMA - Static variable in class uk.ac.ebi.jmzidml.model.utils.ModelConstants
 
MZIDML_VERSION - Static variable in class uk.ac.ebi.jmzidml.model.utils.ModelConstants
 

N

name - Variable in class uk.ac.ebi.jmzidml.model.mzidml.AbstractParam
 
name - Variable in class uk.ac.ebi.jmzidml.model.mzidml.Identifiable
 
next() - Method in class uk.ac.ebi.jmzidml.xml.io.MzIdentMLObjectIterator
 
nTermGain - Variable in class uk.ac.ebi.jmzidml.model.mzidml.Enzyme
 
numDatabaseSequences - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SearchDatabase
 
numResidues - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SearchDatabase
 
numSequencesSearched - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationList
 

O

ObjectClassListener - Class in uk.ac.ebi.jmzidml.xml.jaxb.marshaller.listeners
Listener to handle class specific pre/post processing steps during marshalling.
ObjectClassListener() - Constructor for class uk.ac.ebi.jmzidml.xml.jaxb.marshaller.listeners.ObjectClassListener
 
ObjectFactory - Class in uk.ac.ebi.jmzidml.model.mzidml
This object contains factory methods for each Java content interface and Java element interface generated in the uk.ac.ebi.jmzidml.model.mzidml package.
ObjectFactory() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.ObjectFactory
Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: uk.ac.ebi.jmzidml.model.mzidml
organization - Variable in class uk.ac.ebi.jmzidml.model.mzidml.Affiliation
 
Organization - Class in uk.ac.ebi.jmzidml.model.mzidml
Organizations are entities like companies, universities, government agencies.
Organization() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.Organization
 
organization - Variable in class uk.ac.ebi.jmzidml.model.mzidml.ParentOrganization
 
OrganizationAdapter - Class in uk.ac.ebi.jmzidml.xml.jaxb.adapters
 
OrganizationAdapter(MzIdentMLIndexer, AdapterObjectCache) - Constructor for class uk.ac.ebi.jmzidml.xml.jaxb.adapters.OrganizationAdapter
 
OrganizationCvParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
Created by IntelliJ IDEA.
OrganizationCvParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.OrganizationCvParam
 
organizationRef - Variable in class uk.ac.ebi.jmzidml.model.mzidml.Affiliation
 
organizationRef - Variable in class uk.ac.ebi.jmzidml.model.mzidml.ParentOrganization
 
OrganizationUserParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
Created by IntelliJ IDEA.
OrganizationUserParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.OrganizationUserParam
 
originalResidue - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SubstitutionModification
 

P

PACKAGE - Static variable in class uk.ac.ebi.jmzidml.model.utils.ModelConstants
 
pages - Variable in class uk.ac.ebi.jmzidml.model.mzidml.BibliographicReference
 
Param - Class in uk.ac.ebi.jmzidml.model.mzidml
Helper type to allow either a cvParam or a userParam to be provided for an element.
Param() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.Param
 
ParamCapable - Interface in uk.ac.ebi.jmzidml.model
User: gokelly Date: 4/14/11 Time: 1:52 PM
paramGroup - Variable in class uk.ac.ebi.jmzidml.model.mzidml.AbstractContact
 
paramGroup - Variable in class uk.ac.ebi.jmzidml.model.mzidml.AmbiguousResidue
 
paramGroup - Variable in class uk.ac.ebi.jmzidml.model.mzidml.DBSequence
 
paramGroup - Variable in class uk.ac.ebi.jmzidml.model.mzidml.MassTable
 
paramGroup - Variable in class uk.ac.ebi.jmzidml.model.mzidml.Param
 
paramGroup - Variable in class uk.ac.ebi.jmzidml.model.mzidml.ParamList
 
paramGroup - Variable in class uk.ac.ebi.jmzidml.model.mzidml.Peptide
 
paramGroup - Variable in class uk.ac.ebi.jmzidml.model.mzidml.PeptideEvidence
 
paramGroup - Variable in class uk.ac.ebi.jmzidml.model.mzidml.ProteinAmbiguityGroup
 
paramGroup - Variable in class uk.ac.ebi.jmzidml.model.mzidml.ProteinDetectionHypothesis
 
paramGroup - Variable in class uk.ac.ebi.jmzidml.model.mzidml.ProteinDetectionList
 
paramGroup - Variable in class uk.ac.ebi.jmzidml.model.mzidml.Sample
 
paramGroup - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SourceFile
 
paramGroup - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItem
 
paramGroup - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationList
 
paramGroup - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationResult
 
ParamGroupCapable - Interface in uk.ac.ebi.jmzidml.model
Defines the methods needed by the Marshal/Unmarshal listeners to split a List into respective List and List and methods used to replace the CvParam/UserParam classes with their respective subclasses.
ParamList - Class in uk.ac.ebi.jmzidml.model.mzidml
Helper type to allow multiple cvParams or userParams to be given for an element.
ParamList() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.ParamList
 
ParamListCapable - Interface in uk.ac.ebi.jmzidml.model
 
ParamListMappings - Enum in uk.ac.ebi.jmzidml
Some classes contain one or more properties of type ParamList.
ParamMappings - Enum in uk.ac.ebi.jmzidml
User: gokelly Date: 4/14/11 Time: 1:56 PM
ParamUpdater - Class in uk.ac.ebi.jmzidml.model.utils
 
ParamUpdater() - Constructor for class uk.ac.ebi.jmzidml.model.utils.ParamUpdater
 
parent - Variable in class uk.ac.ebi.jmzidml.model.mzidml.Organization
 
ParentOrganization - Class in uk.ac.ebi.jmzidml.model.mzidml
The containing organization (the university or business which a lab belongs to, etc.)
ParentOrganization() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.ParentOrganization
 
ParentOrganizationRefResolver - Class in uk.ac.ebi.jmzidml.xml.jaxb.resolver
 
ParentOrganizationRefResolver(MzIdentMLIndexer, MzIdentMLObjectCache) - Constructor for class uk.ac.ebi.jmzidml.xml.jaxb.resolver.ParentOrganizationRefResolver
 
parentTolerance - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationProtocol
 
passThreshold - Variable in class uk.ac.ebi.jmzidml.model.mzidml.ProteinDetectionHypothesis
 
passThreshold - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItem
 
Peptide - Class in uk.ac.ebi.jmzidml.model.mzidml
One (poly)peptide (a sequence with modifications).
Peptide() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.Peptide
 
peptide - Variable in class uk.ac.ebi.jmzidml.model.mzidml.PeptideEvidence
 
peptide - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SequenceCollection
 
peptide - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItem
 
PeptideAdapter - Class in uk.ac.ebi.jmzidml.xml.jaxb.adapters
 
PeptideAdapter(MzIdentMLIndexer, AdapterObjectCache) - Constructor for class uk.ac.ebi.jmzidml.xml.jaxb.adapters.PeptideAdapter
 
PeptideCvParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
 
PeptideCvParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.PeptideCvParam
 
PeptideEvidence - Class in uk.ac.ebi.jmzidml.model.mzidml
PeptideEvidence links a specific Peptide element to a specific position in a DBSequence.
PeptideEvidence() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.PeptideEvidence
 
peptideEvidence - Variable in class uk.ac.ebi.jmzidml.model.mzidml.PeptideEvidenceRef
 
peptideEvidence - Variable in class uk.ac.ebi.jmzidml.model.mzidml.PeptideHypothesis
 
peptideEvidence - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SequenceCollection
 
PeptideEvidenceAdapter - Class in uk.ac.ebi.jmzidml.xml.jaxb.adapters
 
PeptideEvidenceAdapter(MzIdentMLIndexer, AdapterObjectCache) - Constructor for class uk.ac.ebi.jmzidml.xml.jaxb.adapters.PeptideEvidenceAdapter
 
PeptideEvidenceCvParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
 
PeptideEvidenceCvParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.PeptideEvidenceCvParam
 
PeptideEvidenceListCvParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
Created by IntelliJ IDEA.
PeptideEvidenceListCvParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.PeptideEvidenceListCvParam
 
PeptideEvidenceListUserParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
Created by IntelliJ IDEA.
PeptideEvidenceListUserParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.PeptideEvidenceListUserParam
 
PeptideEvidenceRef - Class in uk.ac.ebi.jmzidml.model.mzidml
Reference to the PeptideEvidence element identified.
PeptideEvidenceRef() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.PeptideEvidenceRef
 
peptideEvidenceRef - Variable in class uk.ac.ebi.jmzidml.model.mzidml.PeptideEvidenceRef
 
peptideEvidenceRef - Variable in class uk.ac.ebi.jmzidml.model.mzidml.PeptideHypothesis
 
peptideEvidenceRef - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItem
 
PeptideEvidenceRefResolver - Class in uk.ac.ebi.jmzidml.xml.jaxb.resolver
 
PeptideEvidenceRefResolver(MzIdentMLIndexer, MzIdentMLObjectCache) - Constructor for class uk.ac.ebi.jmzidml.xml.jaxb.resolver.PeptideEvidenceRefResolver
 
PeptideEvidenceResolver - Class in uk.ac.ebi.jmzidml.xml.jaxb.resolver
 
PeptideEvidenceResolver(MzIdentMLIndexer, MzIdentMLObjectCache) - Constructor for class uk.ac.ebi.jmzidml.xml.jaxb.resolver.PeptideEvidenceResolver
 
PeptideEvidenceUserParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
 
PeptideEvidenceUserParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.PeptideEvidenceUserParam
 
PeptideHypothesis - Class in uk.ac.ebi.jmzidml.model.mzidml
Peptide evidence on which this ProteinHypothesis is based by reference to a PeptideEvidence element.
PeptideHypothesis() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.PeptideHypothesis
 
peptideHypothesis - Variable in class uk.ac.ebi.jmzidml.model.mzidml.ProteinDetectionHypothesis
 
PeptideHypothesisRefResolver - Class in uk.ac.ebi.jmzidml.xml.jaxb.resolver
 
PeptideHypothesisRefResolver(MzIdentMLIndexer, MzIdentMLObjectCache) - Constructor for class uk.ac.ebi.jmzidml.xml.jaxb.resolver.PeptideHypothesisRefResolver
 
peptideRef - Variable in class uk.ac.ebi.jmzidml.model.mzidml.PeptideEvidence
 
peptideRef - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItem
 
peptideSequence - Variable in class uk.ac.ebi.jmzidml.model.mzidml.Peptide
 
PeptideUserParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
 
PeptideUserParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.PeptideUserParam
 
Person - Class in uk.ac.ebi.jmzidml.model.mzidml
A person's name and contact details.
Person() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.Person
 
PersonCvParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
Created by IntelliJ IDEA.
PersonCvParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.PersonCvParam
 
personOrOrganization - Variable in class uk.ac.ebi.jmzidml.model.mzidml.AuditCollection
 
PersonUserParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
Created by IntelliJ IDEA.
PersonUserParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.PersonUserParam
 
post - Variable in class uk.ac.ebi.jmzidml.model.mzidml.PeptideEvidence
 
pre - Variable in class uk.ac.ebi.jmzidml.model.mzidml.PeptideEvidence
 
ProteinAmbiguityGroup - Class in uk.ac.ebi.jmzidml.model.mzidml
A set of logically related results from a protein detection, for example to represent conflicting assignments of peptides to proteins.
ProteinAmbiguityGroup() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.ProteinAmbiguityGroup
 
proteinAmbiguityGroup - Variable in class uk.ac.ebi.jmzidml.model.mzidml.ProteinDetectionList
 
ProteinAmbiguityGroupCvParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
 
ProteinAmbiguityGroupCvParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.ProteinAmbiguityGroupCvParam
 
ProteinAmbiguityGroupUserParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
 
ProteinAmbiguityGroupUserParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.ProteinAmbiguityGroupUserParam
 
proteinDetection - Variable in class uk.ac.ebi.jmzidml.model.mzidml.AnalysisCollection
 
ProteinDetection - Class in uk.ac.ebi.jmzidml.model.mzidml
An Analysis which assembles a set of peptides (e.g.
ProteinDetection() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.ProteinDetection
 
proteinDetectionHypothesis - Variable in class uk.ac.ebi.jmzidml.model.mzidml.ProteinAmbiguityGroup
 
ProteinDetectionHypothesis - Class in uk.ac.ebi.jmzidml.model.mzidml
A single result of the ProteinDetection analysis (i.e.
ProteinDetectionHypothesis() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.ProteinDetectionHypothesis
 
ProteinDetectionHypothesisCvParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
 
ProteinDetectionHypothesisCvParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.ProteinDetectionHypothesisCvParam
 
ProteinDetectionHypothesisRefResolver - Class in uk.ac.ebi.jmzidml.xml.jaxb.resolver
 
ProteinDetectionHypothesisRefResolver(MzIdentMLIndexer, MzIdentMLObjectCache) - Constructor for class uk.ac.ebi.jmzidml.xml.jaxb.resolver.ProteinDetectionHypothesisRefResolver
 
ProteinDetectionHypothesisUserParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
 
ProteinDetectionHypothesisUserParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.ProteinDetectionHypothesisUserParam
 
proteinDetectionList - Variable in class uk.ac.ebi.jmzidml.model.mzidml.AnalysisData
 
proteinDetectionList - Variable in class uk.ac.ebi.jmzidml.model.mzidml.ProteinDetection
 
ProteinDetectionList - Class in uk.ac.ebi.jmzidml.model.mzidml
The protein list resulting from a protein detection process.
ProteinDetectionList() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.ProteinDetectionList
 
ProteinDetectionListAdapter - Class in uk.ac.ebi.jmzidml.xml.jaxb.adapters
 
ProteinDetectionListAdapter(MzIdentMLIndexer, AdapterObjectCache) - Constructor for class uk.ac.ebi.jmzidml.xml.jaxb.adapters.ProteinDetectionListAdapter
 
ProteinDetectionListCvParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
 
ProteinDetectionListCvParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.ProteinDetectionListCvParam
 
proteinDetectionListRef - Variable in class uk.ac.ebi.jmzidml.model.mzidml.ProteinDetection
 
ProteinDetectionListUserParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
 
ProteinDetectionListUserParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.ProteinDetectionListUserParam
 
proteinDetectionProtocol - Variable in class uk.ac.ebi.jmzidml.model.mzidml.AnalysisProtocolCollection
 
proteinDetectionProtocol - Variable in class uk.ac.ebi.jmzidml.model.mzidml.ProteinDetection
 
ProteinDetectionProtocol - Class in uk.ac.ebi.jmzidml.model.mzidml
The parameters and settings of a ProteinDetection process.
ProteinDetectionProtocol() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.ProteinDetectionProtocol
 
ProteinDetectionProtocolAdapter - Class in uk.ac.ebi.jmzidml.xml.jaxb.adapters
 
ProteinDetectionProtocolAdapter(MzIdentMLIndexer, AdapterObjectCache) - Constructor for class uk.ac.ebi.jmzidml.xml.jaxb.adapters.ProteinDetectionProtocolAdapter
 
proteinDetectionProtocolRef - Variable in class uk.ac.ebi.jmzidml.model.mzidml.ProteinDetection
 
ProteinDetectionProtocolRefResolver - Class in uk.ac.ebi.jmzidml.xml.jaxb.resolver
 
ProteinDetectionProtocolRefResolver(MzIdentMLIndexer, MzIdentMLObjectCache) - Constructor for class uk.ac.ebi.jmzidml.xml.jaxb.resolver.ProteinDetectionProtocolRefResolver
 
ProteinDetectionRefResolver - Class in uk.ac.ebi.jmzidml.xml.jaxb.resolver
 
ProteinDetectionRefResolver(MzIdentMLIndexer, MzIdentMLObjectCache) - Constructor for class uk.ac.ebi.jmzidml.xml.jaxb.resolver.ProteinDetectionRefResolver
 
ProtocolApplication - Class in uk.ac.ebi.jmzidml.model.mzidml
The use of a protocol with the requisite Parameters and ParameterValues.
ProtocolApplication() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.ProtocolApplication
 
provider - Variable in class uk.ac.ebi.jmzidml.model.mzidml.MzIdentML
 
Provider - Class in uk.ac.ebi.jmzidml.model.mzidml
The provider of the document in terms of the Contact and the software the produced the document instance.
Provider() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.Provider
 
ProviderRefResolver - Class in uk.ac.ebi.jmzidml.xml.jaxb.resolver
 
ProviderRefResolver(MzIdentMLIndexer, MzIdentMLObjectCache) - Constructor for class uk.ac.ebi.jmzidml.xml.jaxb.resolver.ProviderRefResolver
 
publication - Variable in class uk.ac.ebi.jmzidml.model.mzidml.BibliographicReference
 
publisher - Variable in class uk.ac.ebi.jmzidml.model.mzidml.BibliographicReference
 
putInCache(String, MzIdentMLObject) - Method in interface uk.ac.ebi.jmzidml.xml.io.MzIdentMLObjectCache
 
putInCache(IdentifiableMzIdentMLObject) - Method in interface uk.ac.ebi.jmzidml.xml.io.MzIdentMLObjectCache
 
putInCache(String, MzIdentMLObject) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.unmarshaller.cache.AdapterObjectCache
Stores the Object in a in-memory Map.
putInCache(IdentifiableMzIdentMLObject) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.unmarshaller.cache.AdapterObjectCache
Convenience method to store Objects that implement the Identifiable interface.

R

rank - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItem
 
RawXMLListener - Class in uk.ac.ebi.jmzidml.xml.jaxb.unmarshaller.listeners
Listener to handle class specific post processing steps during unmarshalling.
RawXMLListener(MzIdentMLIndexer, MzIdentMLObjectCache) - Constructor for class uk.ac.ebi.jmzidml.xml.jaxb.unmarshaller.listeners.RawXMLListener
 
releaseDate - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SearchDatabase
 
remove(int) - Method in class uk.ac.ebi.jmzidml.model.utils.FacadeList
Remove a element from the original list The index here is the index of the specified element int the original list
remove(Object) - Method in class uk.ac.ebi.jmzidml.model.utils.FacadeList
Remove an object from the sublist
remove() - Method in class uk.ac.ebi.jmzidml.xml.io.MzIdentMLObjectIterator
 
removeAll(Collection<?>) - Method in class uk.ac.ebi.jmzidml.model.utils.FacadeList
 
replacementResidue - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SubstitutionModification
 
residue - Variable in class uk.ac.ebi.jmzidml.model.mzidml.MassTable
 
Residue - Class in uk.ac.ebi.jmzidml.model.mzidml
Java class for ResidueType complex type.
Residue() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.Residue
 
residues - Variable in class uk.ac.ebi.jmzidml.model.mzidml.Modification
 
residues - Variable in class uk.ac.ebi.jmzidml.model.mzidml.ModParam
 
residues - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SearchModification
 
retainAll(Collection<?>) - Method in class uk.ac.ebi.jmzidml.model.utils.FacadeList
 
role - Variable in class uk.ac.ebi.jmzidml.model.mzidml.ContactRole
 
Role - Class in uk.ac.ebi.jmzidml.model.mzidml
The roles (lab equipment sales, contractor, etc.) the Contact fills.
Role() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.Role
 
RoleCvParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
 
RoleCvParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.RoleCvParam
 

S

sample - Variable in class uk.ac.ebi.jmzidml.model.mzidml.AnalysisSampleCollection
 
Sample - Class in uk.ac.ebi.jmzidml.model.mzidml
A description of the sample analysed by mass spectrometry using CVParams or UserParams.
Sample() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.Sample
 
sample - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItem
 
sample - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SubSample
 
SampleAdapter - Class in uk.ac.ebi.jmzidml.xml.jaxb.adapters
 
SampleAdapter(MzIdentMLIndexer, AdapterObjectCache) - Constructor for class uk.ac.ebi.jmzidml.xml.jaxb.adapters.SampleAdapter
 
SampleCvParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
 
SampleCvParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.SampleCvParam
 
sampleRef - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItem
 
sampleRef - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SubSample
 
SampleUserParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
 
SampleUserParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.SampleUserParam
 
searchDatabase - Variable in class uk.ac.ebi.jmzidml.model.mzidml.DBSequence
 
searchDatabase - Variable in class uk.ac.ebi.jmzidml.model.mzidml.Inputs
 
SearchDatabase - Class in uk.ac.ebi.jmzidml.model.mzidml
A database for searching mass spectra.
SearchDatabase() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.SearchDatabase
 
searchDatabase - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SearchDatabaseRef
 
SearchDatabaseAdapter - Class in uk.ac.ebi.jmzidml.xml.jaxb.adapters
 
SearchDatabaseAdapter(MzIdentMLIndexer, AdapterObjectCache) - Constructor for class uk.ac.ebi.jmzidml.xml.jaxb.adapters.SearchDatabaseAdapter
 
SearchDatabaseCvParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
 
SearchDatabaseCvParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.SearchDatabaseCvParam
 
searchDatabaseRef - Variable in class uk.ac.ebi.jmzidml.model.mzidml.DBSequence
 
SearchDatabaseRef - Class in uk.ac.ebi.jmzidml.model.mzidml
One of the search databases used.
SearchDatabaseRef() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.SearchDatabaseRef
 
searchDatabaseRef - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SearchDatabaseRef
 
searchDatabaseRef - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentification
 
SearchDatabaseRefResolver - Class in uk.ac.ebi.jmzidml.xml.jaxb.resolver
 
SearchDatabaseRefResolver(MzIdentMLIndexer, MzIdentMLObjectCache) - Constructor for class uk.ac.ebi.jmzidml.xml.jaxb.resolver.SearchDatabaseRefResolver
 
searchModification - Variable in class uk.ac.ebi.jmzidml.model.mzidml.ModificationParams
 
SearchModification - Class in uk.ac.ebi.jmzidml.model.mzidml
Specification of a search modification as parameter for a spectra search.
SearchModification() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.SearchModification
 
searchType - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationProtocol
 
SearchTypeCvParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
User: gokelly Date: 4/14/11 Time: 2:10 PM
SearchTypeCvParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.SearchTypeCvParam
 
SearchTypeUserParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
User: gokelly Date: 4/14/11 Time: 2:10 PM
SearchTypeUserParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.SearchTypeUserParam
 
semiSpecific - Variable in class uk.ac.ebi.jmzidml.model.mzidml.Enzyme
 
seq - Variable in class uk.ac.ebi.jmzidml.model.mzidml.DBSequence
 
sequenceCollection - Variable in class uk.ac.ebi.jmzidml.model.mzidml.MzIdentML
 
SequenceCollection - Class in uk.ac.ebi.jmzidml.model.mzidml
The collection of sequences (DBSequence or Peptide) identified and their relationship between each other (PeptideEvidence) to be referenced elsewhere in the results.
SequenceCollection() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.SequenceCollection
 
set(int, T) - Method in class uk.ac.ebi.jmzidml.model.utils.FacadeList
Set an new element based on the index of the sublist
setAccession(String) - Method in class uk.ac.ebi.jmzidml.model.mzidml.CvParam
Sets the value of the accession property.
setAccession(String) - Method in class uk.ac.ebi.jmzidml.model.mzidml.DBSequence
Sets the value of the accession property.
setActivityDate(Calendar) - Method in class uk.ac.ebi.jmzidml.model.mzidml.ProtocolApplication
Sets the value of the activityDate property.
setAdditionalSearchParams(ParamList) - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationProtocol
Sets the value of the additionalSearchParams property.
setAnalysisCollection(AnalysisCollection) - Method in class uk.ac.ebi.jmzidml.model.mzidml.MzIdentML
Sets the value of the analysisCollection property.
setAnalysisData(AnalysisData) - Method in class uk.ac.ebi.jmzidml.model.mzidml.DataCollection
Sets the value of the analysisData property.
setAnalysisParams(ParamList) - Method in class uk.ac.ebi.jmzidml.model.mzidml.ProteinDetectionProtocol
Sets the value of the analysisParams property.
setAnalysisProtocolCollection(AnalysisProtocolCollection) - Method in class uk.ac.ebi.jmzidml.model.mzidml.MzIdentML
Sets the value of the analysisProtocolCollection property.
setAnalysisSampleCollection(AnalysisSampleCollection) - Method in class uk.ac.ebi.jmzidml.model.mzidml.MzIdentML
Sets the value of the analysisSampleCollection property.
setAnalysisSoftware(AnalysisSoftware) - Method in class uk.ac.ebi.jmzidml.model.mzidml.ProteinDetectionProtocol
 
setAnalysisSoftware(AnalysisSoftware) - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationProtocol
 
setAnalysisSoftwareList(AnalysisSoftwareList) - Method in class uk.ac.ebi.jmzidml.model.mzidml.MzIdentML
Sets the value of the analysisSoftwareList property.
setAuditCollection(AuditCollection) - Method in class uk.ac.ebi.jmzidml.model.mzidml.MzIdentML
Sets the value of the auditCollection property.
setAuthors(String) - Method in class uk.ac.ebi.jmzidml.model.mzidml.BibliographicReference
Sets the value of the authors property.
setAutoRefResolving(boolean) - Method in class uk.ac.ebi.jmzidml.model.utils.MzIdentMLElementConfig
 
setAvgMassDelta(Double) - Method in class uk.ac.ebi.jmzidml.model.mzidml.Modification
Sets the value of the avgMassDelta property.
setAvgMassDelta(Double) - Method in class uk.ac.ebi.jmzidml.model.mzidml.SubstitutionModification
Sets the value of the avgMassDelta property.
setCached(boolean) - Method in class uk.ac.ebi.jmzidml.model.utils.MzIdentMLElementConfig
 
setCalculatedMassToCharge(Double) - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItem
Sets the value of the calculatedMassToCharge property.
setCalculatedPI(Float) - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItem
Sets the value of the calculatedPI property.
setCharge(int) - Method in class uk.ac.ebi.jmzidml.model.mzidml.IonType
Sets the value of the charge property.
setChargeState(int) - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItem
Sets the value of the chargeState property.
setClazz(Class) - Method in class uk.ac.ebi.jmzidml.model.utils.MzIdentMLElementConfig
 
setCode(String) - Method in class uk.ac.ebi.jmzidml.model.mzidml.AmbiguousResidue
Sets the value of the code property.
setCode(String) - Method in class uk.ac.ebi.jmzidml.model.mzidml.Residue
Sets the value of the code property.
setConfigurations(List<MzIdentMLElementConfig>) - Method in class uk.ac.ebi.jmzidml.model.utils.MzIdentMLElementProperties
 
setContact(AbstractContact) - Method in class uk.ac.ebi.jmzidml.model.mzidml.ContactRole
Set contact.
setContactRole(ContactRole) - Method in class uk.ac.ebi.jmzidml.model.mzidml.AnalysisSoftware
Sets the value of the contactRole property.
setContactRole(ContactRole) - Method in class uk.ac.ebi.jmzidml.model.mzidml.Provider
Sets the value of the contactRole property.
setCreationDate(Calendar) - Method in class uk.ac.ebi.jmzidml.model.mzidml.MzIdentML
Sets the value of the creationDate property.
setCTermGain(String) - Method in class uk.ac.ebi.jmzidml.model.mzidml.Enzyme
Sets the value of the cTermGain property.
setCustomizations(String) - Method in class uk.ac.ebi.jmzidml.model.mzidml.AnalysisSoftware
Sets the value of the customizations property.
setCv(Cv) - Method in class uk.ac.ebi.jmzidml.model.mzidml.CvParam
 
setCvList(CvList) - Method in class uk.ac.ebi.jmzidml.model.mzidml.MzIdentML
Sets the value of the cvList property.
setCvParam(CvParam) - Method in interface uk.ac.ebi.jmzidml.model.CvParamCapable
 
setCvParam(CvParam) - Method in class uk.ac.ebi.jmzidml.model.mzidml.FileFormat
Sets the value of the cvParam property.
setCvParam(CvParam) - Method in class uk.ac.ebi.jmzidml.model.mzidml.IonType
Sets the value of the cvParam property.
setCvParam(CvParam) - Method in class uk.ac.ebi.jmzidml.model.mzidml.ModParam
Sets the value of the cvParam property.
setCvParam(CvParam) - Method in class uk.ac.ebi.jmzidml.model.mzidml.Role
Sets the value of the cvParam property.
setCvParam(CvParam) - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIDFormat
Sets the value of the cvParam property.
setCvParamClass(Class) - Method in class uk.ac.ebi.jmzidml.model.utils.MzIdentMLElementConfig
 
setDatabaseFilters(DatabaseFilters) - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationProtocol
Sets the value of the databaseFilters property.
setDatabaseName(Param) - Method in class uk.ac.ebi.jmzidml.model.mzidml.SearchDatabase
Sets the value of the databaseName property.
setDatabaseTranslation(DatabaseTranslation) - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationProtocol
Sets the value of the databaseTranslation property.
setDataCollection(DataCollection) - Method in class uk.ac.ebi.jmzidml.model.mzidml.MzIdentML
Sets the value of the dataCollection property.
setDBSequence(DBSequence) - Method in class uk.ac.ebi.jmzidml.model.mzidml.PeptideEvidence
 
setDBSequence(DBSequence) - Method in class uk.ac.ebi.jmzidml.model.mzidml.ProteinDetectionHypothesis
 
setDoi(String) - Method in class uk.ac.ebi.jmzidml.model.mzidml.BibliographicReference
Sets the value of the doi property.
setEditor(String) - Method in class uk.ac.ebi.jmzidml.model.mzidml.BibliographicReference
Sets the value of the editor property.
setEnd(Integer) - Method in class uk.ac.ebi.jmzidml.model.mzidml.PeptideEvidence
Sets the value of the end property.
setEnzymeName(ParamList) - Method in class uk.ac.ebi.jmzidml.model.mzidml.Enzyme
Sets the value of the enzymeName property.
setEnzymes(Enzymes) - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationProtocol
Sets the value of the enzymes property.
setExclude(ParamList) - Method in class uk.ac.ebi.jmzidml.model.mzidml.Filter
Sets the value of the exclude property.
setExperimentalMassToCharge(double) - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItem
Sets the value of the experimentalMassToCharge property.
setExternalFormatDocumentation(String) - Method in class uk.ac.ebi.jmzidml.model.mzidml.ExternalData
Sets the value of the externalFormatDocumentation property.
setFileFormat(FileFormat) - Method in class uk.ac.ebi.jmzidml.model.mzidml.ExternalData
Sets the value of the fileFormat property.
setFilterType(Param) - Method in class uk.ac.ebi.jmzidml.model.mzidml.Filter
Sets the value of the filterType property.
setFirstName(String) - Method in class uk.ac.ebi.jmzidml.model.mzidml.Person
Sets the value of the firstName property.
setFixedMod(boolean) - Method in class uk.ac.ebi.jmzidml.model.mzidml.SearchModification
Sets the value of the fixedMod property.
setFragmentation(Fragmentation) - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItem
Sets the value of the fragmentation property.
setFragmentationTable(FragmentationTable) - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationList
Sets the value of the fragmentationTable property.
setFragmentTolerance(Tolerance) - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationProtocol
Sets the value of the fragmentTolerance property.
setFrame(Integer) - Method in class uk.ac.ebi.jmzidml.model.mzidml.PeptideEvidence
Sets the value of the frame property.
setFullName(String) - Method in class uk.ac.ebi.jmzidml.model.mzidml.Cv
Sets the value of the fullName property.
setId(String) - Method in class uk.ac.ebi.jmzidml.model.mzidml.Cv
Sets the value of the id property.
setId(String) - Method in class uk.ac.ebi.jmzidml.model.mzidml.Identifiable
Sets the value of the id property.
setIdMapped(boolean) - Method in class uk.ac.ebi.jmzidml.model.utils.MzIdentMLElementConfig
 
setInclude(ParamList) - Method in class uk.ac.ebi.jmzidml.model.mzidml.Filter
Sets the value of the include property.
setIndependent(Boolean) - Method in class uk.ac.ebi.jmzidml.model.mzidml.Enzymes
Sets the value of the independent property.
setIndexed(boolean) - Method in class uk.ac.ebi.jmzidml.model.utils.MzIdentMLElementConfig
 
setInputs(Inputs) - Method in class uk.ac.ebi.jmzidml.model.mzidml.DataCollection
Sets the value of the inputs property.
setIsDecoy(Boolean) - Method in class uk.ac.ebi.jmzidml.model.mzidml.PeptideEvidence
Sets the value of the isDecoy property.
setIssue(String) - Method in class uk.ac.ebi.jmzidml.model.mzidml.BibliographicReference
Sets the value of the issue property.
setLastName(String) - Method in class uk.ac.ebi.jmzidml.model.mzidml.Person
Sets the value of the lastName property.
setLength(Integer) - Method in class uk.ac.ebi.jmzidml.model.mzidml.DBSequence
Sets the value of the length property.
setLocation(String) - Method in class uk.ac.ebi.jmzidml.model.mzidml.ExternalData
Sets the value of the location property.
setLocation(Integer) - Method in class uk.ac.ebi.jmzidml.model.mzidml.Modification
Sets the value of the location property.
setLocation(Integer) - Method in class uk.ac.ebi.jmzidml.model.mzidml.SubstitutionModification
Sets the value of the location property.
setMass(float) - Method in class uk.ac.ebi.jmzidml.model.mzidml.Residue
Sets the value of the mass property.
setMassDelta(float) - Method in class uk.ac.ebi.jmzidml.model.mzidml.ModParam
Sets the value of the massDelta property.
setMassDelta(float) - Method in class uk.ac.ebi.jmzidml.model.mzidml.SearchModification
Sets the value of the massDelta property.
setMassTable(MassTable) - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItem
 
setMeasure(Measure) - Method in class uk.ac.ebi.jmzidml.model.mzidml.FragmentArray
 
setMidInitials(String) - Method in class uk.ac.ebi.jmzidml.model.mzidml.Person
Sets the value of the midInitials property.
setMinDistance(Integer) - Method in class uk.ac.ebi.jmzidml.model.mzidml.Enzyme
Sets the value of the minDistance property.
setMissedCleavages(Integer) - Method in class uk.ac.ebi.jmzidml.model.mzidml.Enzyme
Sets the value of the missedCleavages property.
setModificationParams(ModificationParams) - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationProtocol
Sets the value of the modificationParams property.
setMonoisotopicMassDelta(Double) - Method in class uk.ac.ebi.jmzidml.model.mzidml.Modification
Sets the value of the monoisotopicMassDelta property.
setMonoisotopicMassDelta(Double) - Method in class uk.ac.ebi.jmzidml.model.mzidml.SubstitutionModification
Sets the value of the monoisotopicMassDelta property.
setName(String) - Method in class uk.ac.ebi.jmzidml.model.mzidml.AbstractParam
Sets the value of the name property.
setName(String) - Method in class uk.ac.ebi.jmzidml.model.mzidml.Identifiable
Sets the value of the name property.
setNTermGain(String) - Method in class uk.ac.ebi.jmzidml.model.mzidml.Enzyme
Sets the value of the nTermGain property.
setNumDatabaseSequences(Long) - Method in class uk.ac.ebi.jmzidml.model.mzidml.SearchDatabase
Sets the value of the numDatabaseSequences property.
setNumResidues(Long) - Method in class uk.ac.ebi.jmzidml.model.mzidml.SearchDatabase
Sets the value of the numResidues property.
setNumSequencesSearched(Long) - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationList
Sets the value of the numSequencesSearched property.
setOrganization(Organization) - Method in class uk.ac.ebi.jmzidml.model.mzidml.Affiliation
Set the Organization for this Affiliation.
setOrganization(Organization) - Method in class uk.ac.ebi.jmzidml.model.mzidml.ParentOrganization
 
setOriginalResidue(String) - Method in class uk.ac.ebi.jmzidml.model.mzidml.SubstitutionModification
Sets the value of the originalResidue property.
setPages(String) - Method in class uk.ac.ebi.jmzidml.model.mzidml.BibliographicReference
Sets the value of the pages property.
setParam(AbstractParam) - Method in class uk.ac.ebi.jmzidml.model.mzidml.Param
Sets the value of the paramGroup property.
setParent(ParentOrganization) - Method in class uk.ac.ebi.jmzidml.model.mzidml.Organization
Sets the value of the parent property.
setParentTolerance(Tolerance) - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationProtocol
Sets the value of the parentTolerance property.
setPassThreshold(boolean) - Method in class uk.ac.ebi.jmzidml.model.mzidml.ProteinDetectionHypothesis
Sets the value of the passThreshold property.
setPassThreshold(boolean) - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItem
Sets the value of the passThreshold property.
setPeptide(Peptide) - Method in class uk.ac.ebi.jmzidml.model.mzidml.PeptideEvidence
 
setPeptide(Peptide) - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItem
 
setPeptideEvidence(PeptideEvidence) - Method in class uk.ac.ebi.jmzidml.model.mzidml.PeptideEvidenceRef
 
setPeptideEvidence(PeptideEvidence) - Method in class uk.ac.ebi.jmzidml.model.mzidml.PeptideHypothesis
 
setPeptideSequence(String) - Method in class uk.ac.ebi.jmzidml.model.mzidml.Peptide
Sets the value of the peptideSequence property.
setPost(String) - Method in class uk.ac.ebi.jmzidml.model.mzidml.PeptideEvidence
Sets the value of the post property.
setPre(String) - Method in class uk.ac.ebi.jmzidml.model.mzidml.PeptideEvidence
Sets the value of the pre property.
setProteinDetection(ProteinDetection) - Method in class uk.ac.ebi.jmzidml.model.mzidml.AnalysisCollection
Sets the value of the proteinDetection property.
setProteinDetectionList(ProteinDetectionList) - Method in class uk.ac.ebi.jmzidml.model.mzidml.AnalysisData
Sets the value of the proteinDetectionList property.
setProteinDetectionList(ProteinDetectionList) - Method in class uk.ac.ebi.jmzidml.model.mzidml.ProteinDetection
 
setProteinDetectionProtocol(ProteinDetectionProtocol) - Method in class uk.ac.ebi.jmzidml.model.mzidml.AnalysisProtocolCollection
Sets the value of the proteinDetectionProtocol property.
setProteinDetectionProtocol(ProteinDetectionProtocol) - Method in class uk.ac.ebi.jmzidml.model.mzidml.ProteinDetection
 
setProvider(Provider) - Method in class uk.ac.ebi.jmzidml.model.mzidml.MzIdentML
Sets the value of the provider property.
setPublication(String) - Method in class uk.ac.ebi.jmzidml.model.mzidml.BibliographicReference
Sets the value of the publication property.
setPublisher(String) - Method in class uk.ac.ebi.jmzidml.model.mzidml.BibliographicReference
Sets the value of the publisher property.
setRank(int) - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItem
Sets the value of the rank property.
setRefResolverClass(Class) - Method in class uk.ac.ebi.jmzidml.model.utils.MzIdentMLElementConfig
 
setReleaseDate(Calendar) - Method in class uk.ac.ebi.jmzidml.model.mzidml.SearchDatabase
Sets the value of the releaseDate property.
setReplacementResidue(String) - Method in class uk.ac.ebi.jmzidml.model.mzidml.SubstitutionModification
Sets the value of the replacementResidue property.
setRole(Role) - Method in class uk.ac.ebi.jmzidml.model.mzidml.ContactRole
Sets the value of the role property.
setSample(Sample) - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItem
 
setSample(Sample) - Method in class uk.ac.ebi.jmzidml.model.mzidml.SubSample
 
setSearchDatabase(SearchDatabase) - Method in class uk.ac.ebi.jmzidml.model.mzidml.DBSequence
 
setSearchDatabase(SearchDatabase) - Method in class uk.ac.ebi.jmzidml.model.mzidml.SearchDatabaseRef
 
setSearchType(Param) - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationProtocol
Sets the value of the searchType property.
setSemiSpecific(Boolean) - Method in class uk.ac.ebi.jmzidml.model.mzidml.Enzyme
Sets the value of the semiSpecific property.
setSeq(String) - Method in class uk.ac.ebi.jmzidml.model.mzidml.DBSequence
Sets the value of the seq property.
setSequenceCollection(SequenceCollection) - Method in class uk.ac.ebi.jmzidml.model.mzidml.MzIdentML
Sets the value of the sequenceCollection property.
setSiteRegexp(String) - Method in class uk.ac.ebi.jmzidml.model.mzidml.Enzyme
Sets the value of the siteRegexp property.
setSoftware(AnalysisSoftware) - Method in class uk.ac.ebi.jmzidml.model.mzidml.Provider
 
setSoftwareName(Param) - Method in class uk.ac.ebi.jmzidml.model.mzidml.AnalysisSoftware
Sets the value of the softwareName property.
setSpectraData(SpectraData) - Method in class uk.ac.ebi.jmzidml.model.mzidml.InputSpectra
 
setSpectraData(SpectraData) - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationResult
 
setSpectrumID(String) - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationResult
Sets the value of the spectrumID property.
setSpectrumIdentificationItem(SpectrumIdentificationItem) - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItemRef
 
setSpectrumIdentificationItemRef(String) - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItemRef
Sets the value of the spectrumIdentificationItemRef property.
setSpectrumIdentificationList(SpectrumIdentificationList) - Method in class uk.ac.ebi.jmzidml.model.mzidml.InputSpectrumIdentifications
 
setSpectrumIdentificationList(SpectrumIdentificationList) - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentification
 
setSpectrumIdentificationProtocol(SpectrumIdentificationProtocol) - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentification
 
setSpectrumIDFormat(SpectrumIDFormat) - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectraData
Sets the value of the spectrumIDFormat property.
setStart(Integer) - Method in class uk.ac.ebi.jmzidml.model.mzidml.PeptideEvidence
Sets the value of the start property.
setTagName(String) - Method in class uk.ac.ebi.jmzidml.model.utils.MzIdentMLElementConfig
 
setThreshold(ParamList) - Method in class uk.ac.ebi.jmzidml.model.mzidml.ProteinDetectionProtocol
Sets the value of the threshold property.
setThreshold(ParamList) - Method in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationProtocol
Sets the value of the threshold property.
setTitle(String) - Method in class uk.ac.ebi.jmzidml.model.mzidml.BibliographicReference
Sets the value of the title property.
setTranslationTable(TranslationTable) - Method in class uk.ac.ebi.jmzidml.model.mzidml.PeptideEvidence
 
setType(String) - Method in class uk.ac.ebi.jmzidml.model.mzidml.UserParam
Sets the value of the type property.
setUnitAccession(String) - Method in class uk.ac.ebi.jmzidml.model.mzidml.AbstractParam
Sets the value of the unitAccession property.
setUnitCv(Cv) - Method in class uk.ac.ebi.jmzidml.model.mzidml.AbstractParam
 
setUnitName(String) - Method in class uk.ac.ebi.jmzidml.model.mzidml.AbstractParam
Sets the value of the unitName property.
setUri(String) - Method in class uk.ac.ebi.jmzidml.model.mzidml.AnalysisSoftware
Sets the value of the uri property.
setUri(String) - Method in class uk.ac.ebi.jmzidml.model.mzidml.Cv
Sets the value of the uri property.
setUserParamClass(Class) - Method in class uk.ac.ebi.jmzidml.model.utils.MzIdentMLElementConfig
 
setValue(String) - Method in class uk.ac.ebi.jmzidml.model.mzidml.AbstractParam
Sets the value of the value property.
setVersion(String) - Method in class uk.ac.ebi.jmzidml.model.mzidml.AnalysisSoftware
Sets the value of the version property.
setVersion(String) - Method in class uk.ac.ebi.jmzidml.model.mzidml.Cv
Sets the value of the version property.
setVersion(String) - Method in class uk.ac.ebi.jmzidml.model.mzidml.MzIdentML
Sets the value of the version property.
setVersion(String) - Method in class uk.ac.ebi.jmzidml.model.mzidml.SearchDatabase
Sets the value of the version property.
setVolume(String) - Method in class uk.ac.ebi.jmzidml.model.mzidml.BibliographicReference
Sets the value of the volume property.
setXpath(String) - Method in class uk.ac.ebi.jmzidml.model.utils.MzIdentMLElementConfig
 
setYear(Integer) - Method in class uk.ac.ebi.jmzidml.model.mzidml.BibliographicReference
Sets the value of the year property.
siteRegexp - Variable in class uk.ac.ebi.jmzidml.model.mzidml.Enzyme
 
size() - Method in class uk.ac.ebi.jmzidml.model.utils.FacadeList
Get the size of the sublist
software - Variable in class uk.ac.ebi.jmzidml.model.mzidml.Provider
 
softwareName - Variable in class uk.ac.ebi.jmzidml.model.mzidml.AnalysisSoftware
 
SoftwareNameCvParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
User: gokelly Date: 4/14/11 Time: 2:08 PM
SoftwareNameCvParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.SoftwareNameCvParam
 
SoftwareNameUserParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
User: gokelly Date: 4/14/11 Time: 2:08 PM
SoftwareNameUserParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.SoftwareNameUserParam
 
softwareRef - Variable in class uk.ac.ebi.jmzidml.model.mzidml.Provider
 
sourceFile - Variable in class uk.ac.ebi.jmzidml.model.mzidml.Inputs
 
SourceFile - Class in uk.ac.ebi.jmzidml.model.mzidml
A file from which this mzIdentML instance was created.
SourceFile() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.SourceFile
 
SourceFileCvParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
 
SourceFileCvParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.SourceFileCvParam
 
SourceFileUserParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
 
SourceFileUserParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.SourceFileUserParam
 
specificityRules - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SearchModification
 
SpecificityRules - Class in uk.ac.ebi.jmzidml.model.mzidml
The specificity rules of the searched modification including for example the probability of a modification's presence or peptide or protein termini.
SpecificityRules() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.SpecificityRules
 
SpecificityRulesCvParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
 
SpecificityRulesCvParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.SpecificityRulesCvParam
 
spectraData - Variable in class uk.ac.ebi.jmzidml.model.mzidml.Inputs
 
spectraData - Variable in class uk.ac.ebi.jmzidml.model.mzidml.InputSpectra
 
SpectraData - Class in uk.ac.ebi.jmzidml.model.mzidml
A data set containing spectra data (consisting of one or more spectra).
SpectraData() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.SpectraData
 
spectraData - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationResult
 
SpectraDataAdapter - Class in uk.ac.ebi.jmzidml.xml.jaxb.adapters
 
SpectraDataAdapter(MzIdentMLIndexer, AdapterObjectCache) - Constructor for class uk.ac.ebi.jmzidml.xml.jaxb.adapters.SpectraDataAdapter
 
spectraDataRef - Variable in class uk.ac.ebi.jmzidml.model.mzidml.InputSpectra
 
spectraDataRef - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationResult
 
spectrumID - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationResult
 
spectrumIdentification - Variable in class uk.ac.ebi.jmzidml.model.mzidml.AnalysisCollection
 
SpectrumIdentification - Class in uk.ac.ebi.jmzidml.model.mzidml
An Analysis which tries to identify peptides in input spectra, referencing the database searched, the input spectra, the output results and the protocol that is run.
SpectrumIdentification() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentification
 
SpectrumIdentificationItem - Class in uk.ac.ebi.jmzidml.model.mzidml
An identification of a single (poly)peptide, resulting from querying an input spectra, along with the set of confidence values for that identification.
SpectrumIdentificationItem() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItem
 
spectrumIdentificationItem - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItemRef
 
spectrumIdentificationItem - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationResult
 
SpectrumIdentificationItemCvParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
 
SpectrumIdentificationItemCvParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.SpectrumIdentificationItemCvParam
 
spectrumIdentificationItemRef - Variable in class uk.ac.ebi.jmzidml.model.mzidml.PeptideHypothesis
 
SpectrumIdentificationItemRef - Class in uk.ac.ebi.jmzidml.model.mzidml
Reference(s) to the SpectrumIdentificationItem element(s) that support the given PeptideEvidence element.
SpectrumIdentificationItemRef() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItemRef
 
spectrumIdentificationItemRef - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItemRef
 
SpectrumIdentificationItemRefRefResolver - Class in uk.ac.ebi.jmzidml.xml.jaxb.resolver
 
SpectrumIdentificationItemRefRefResolver(MzIdentMLIndexer, MzIdentMLObjectCache) - Constructor for class uk.ac.ebi.jmzidml.xml.jaxb.resolver.SpectrumIdentificationItemRefRefResolver
 
SpectrumIdentificationItemRefResolver - Class in uk.ac.ebi.jmzidml.xml.jaxb.resolver
 
SpectrumIdentificationItemRefResolver(MzIdentMLIndexer, MzIdentMLObjectCache) - Constructor for class uk.ac.ebi.jmzidml.xml.jaxb.resolver.SpectrumIdentificationItemRefResolver
 
SpectrumIdentificationItemUserParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
 
SpectrumIdentificationItemUserParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.SpectrumIdentificationItemUserParam
 
spectrumIdentificationList - Variable in class uk.ac.ebi.jmzidml.model.mzidml.AnalysisData
 
spectrumIdentificationList - Variable in class uk.ac.ebi.jmzidml.model.mzidml.InputSpectrumIdentifications
 
spectrumIdentificationList - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentification
 
SpectrumIdentificationList - Class in uk.ac.ebi.jmzidml.model.mzidml
Represents the set of all search results from SpectrumIdentification.
SpectrumIdentificationList() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationList
 
SpectrumIdentificationListAdapter - Class in uk.ac.ebi.jmzidml.xml.jaxb.adapters
 
SpectrumIdentificationListAdapter(MzIdentMLIndexer, AdapterObjectCache) - Constructor for class uk.ac.ebi.jmzidml.xml.jaxb.adapters.SpectrumIdentificationListAdapter
 
SpectrumIdentificationListCvParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
 
SpectrumIdentificationListCvParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.SpectrumIdentificationListCvParam
 
spectrumIdentificationListRef - Variable in class uk.ac.ebi.jmzidml.model.mzidml.InputSpectrumIdentifications
 
spectrumIdentificationListRef - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentification
 
SpectrumIdentificationListUserParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
 
SpectrumIdentificationListUserParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.SpectrumIdentificationListUserParam
 
spectrumIdentificationProtocol - Variable in class uk.ac.ebi.jmzidml.model.mzidml.AnalysisProtocolCollection
 
spectrumIdentificationProtocol - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentification
 
SpectrumIdentificationProtocol - Class in uk.ac.ebi.jmzidml.model.mzidml
The parameters and settings of a SpectrumIdentification analysis.
SpectrumIdentificationProtocol() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationProtocol
 
SpectrumIdentificationProtocolAdapter - Class in uk.ac.ebi.jmzidml.xml.jaxb.adapters
 
SpectrumIdentificationProtocolAdapter(MzIdentMLIndexer, AdapterObjectCache) - Constructor for class uk.ac.ebi.jmzidml.xml.jaxb.adapters.SpectrumIdentificationProtocolAdapter
 
spectrumIdentificationProtocolRef - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentification
 
SpectrumIdentificationProtocolRefResolver - Class in uk.ac.ebi.jmzidml.xml.jaxb.resolver
 
SpectrumIdentificationProtocolRefResolver(MzIdentMLIndexer, MzIdentMLObjectCache) - Constructor for class uk.ac.ebi.jmzidml.xml.jaxb.resolver.SpectrumIdentificationProtocolRefResolver
 
SpectrumIdentificationRefResolver - Class in uk.ac.ebi.jmzidml.xml.jaxb.resolver
 
SpectrumIdentificationRefResolver(MzIdentMLIndexer, MzIdentMLObjectCache) - Constructor for class uk.ac.ebi.jmzidml.xml.jaxb.resolver.SpectrumIdentificationRefResolver
 
spectrumIdentificationResult - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationList
 
SpectrumIdentificationResult - Class in uk.ac.ebi.jmzidml.model.mzidml
All identifications made from searching one spectrum.
SpectrumIdentificationResult() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationResult
 
SpectrumIdentificationResultCvParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
 
SpectrumIdentificationResultCvParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.SpectrumIdentificationResultCvParam
 
SpectrumIdentificationResultRefResolver - Class in uk.ac.ebi.jmzidml.xml.jaxb.resolver
 
SpectrumIdentificationResultRefResolver(MzIdentMLIndexer, MzIdentMLObjectCache) - Constructor for class uk.ac.ebi.jmzidml.xml.jaxb.resolver.SpectrumIdentificationResultRefResolver
 
SpectrumIdentificationResultUserParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
 
SpectrumIdentificationResultUserParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.SpectrumIdentificationResultUserParam
 
spectrumIDFormat - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SpectraData
 
SpectrumIDFormat - Class in uk.ac.ebi.jmzidml.model.mzidml
The format of the spectrum identifier within the source file
SpectrumIDFormat() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIDFormat
 
SpectrumIDFormatCvParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
 
SpectrumIDFormatCvParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.SpectrumIDFormatCvParam
 
splitParamList() - Method in class uk.ac.ebi.jmzidml.model.AbstractParamGroup
 
start - Variable in class uk.ac.ebi.jmzidml.model.mzidml.PeptideEvidence
 
startElement(String, String, String, Attributes) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.unmarshaller.filters.MzIdentMLNamespaceFilter
 
subList(int, int) - Method in class uk.ac.ebi.jmzidml.model.utils.FacadeList
sublist returned is an unmodifiable list, structural change to the sublist is not allowed.
subSample - Variable in class uk.ac.ebi.jmzidml.model.mzidml.Sample
 
SubSample - Class in uk.ac.ebi.jmzidml.model.mzidml
References to the individual component samples within a mixed parent sample.
SubSample() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.SubSample
 
SubSampleRefResolver - Class in uk.ac.ebi.jmzidml.xml.jaxb.resolver
 
SubSampleRefResolver(MzIdentMLIndexer, MzIdentMLObjectCache) - Constructor for class uk.ac.ebi.jmzidml.xml.jaxb.resolver.SubSampleRefResolver
 
substitutionModification - Variable in class uk.ac.ebi.jmzidml.model.mzidml.Peptide
 
SubstitutionModification - Class in uk.ac.ebi.jmzidml.model.mzidml
A modification where one residue is substituted by another (amino acid change).
SubstitutionModification() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.SubstitutionModification
 

T

threshold - Variable in class uk.ac.ebi.jmzidml.model.mzidml.ProteinDetectionProtocol
 
threshold - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationProtocol
 
ThresholdCvParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
User: gokelly Date: 11/04/11 Time: 10:23
ThresholdCvParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.ThresholdCvParam
 
ThresholdUserParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
User: gokelly Date: 11/04/11 Time: 10:24
ThresholdUserParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.ThresholdUserParam
 
title - Variable in class uk.ac.ebi.jmzidml.model.mzidml.BibliographicReference
 
toArray() - Method in class uk.ac.ebi.jmzidml.model.utils.FacadeList
 
toArray(T[]) - Method in class uk.ac.ebi.jmzidml.model.utils.FacadeList
 
Tolerance - Class in uk.ac.ebi.jmzidml.model.mzidml
The tolerance of the search given as a plus and minus value with units.
Tolerance() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.Tolerance
 
ToleranceCvParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
 
ToleranceCvParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.ToleranceCvParam
 
toString() - Method in class uk.ac.ebi.jmzidml.model.utils.FacadeList
This method is overridden to print out the list in concatenated string format
toString() - Method in enum uk.ac.ebi.jmzidml.MzIdentMLElement
 
translationTable - Variable in class uk.ac.ebi.jmzidml.model.mzidml.DatabaseTranslation
 
translationTable - Variable in class uk.ac.ebi.jmzidml.model.mzidml.PeptideEvidence
 
TranslationTable - Class in uk.ac.ebi.jmzidml.model.mzidml
The table used to translate codons into nucleic acids e.g.
TranslationTable() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.TranslationTable
 
TranslationTableAdapter - Class in uk.ac.ebi.jmzidml.xml.jaxb.adapters
 
TranslationTableAdapter(MzIdentMLIndexer, AdapterObjectCache) - Constructor for class uk.ac.ebi.jmzidml.xml.jaxb.adapters.TranslationTableAdapter
 
TranslationTableCvParam - Class in uk.ac.ebi.jmzidml.model.mzidml.params
 
TranslationTableCvParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.params.TranslationTableCvParam
 
translationTableRef - Variable in class uk.ac.ebi.jmzidml.model.mzidml.PeptideEvidence
 
type - Variable in class uk.ac.ebi.jmzidml.model.mzidml.UserParam
 

U

uk.ac.ebi - package uk.ac.ebi
 
uk.ac.ebi.jmzidml - package uk.ac.ebi.jmzidml
 
uk.ac.ebi.jmzidml.model - package uk.ac.ebi.jmzidml.model
 
uk.ac.ebi.jmzidml.model.mzidml - package uk.ac.ebi.jmzidml.model.mzidml
 
uk.ac.ebi.jmzidml.model.mzidml.params - package uk.ac.ebi.jmzidml.model.mzidml.params
 
uk.ac.ebi.jmzidml.model.utils - package uk.ac.ebi.jmzidml.model.utils
 
uk.ac.ebi.jmzidml.xml - package uk.ac.ebi.jmzidml.xml
 
uk.ac.ebi.jmzidml.xml.io - package uk.ac.ebi.jmzidml.xml.io
 
uk.ac.ebi.jmzidml.xml.jaxb.adapters - package uk.ac.ebi.jmzidml.xml.jaxb.adapters
 
uk.ac.ebi.jmzidml.xml.jaxb.marshaller - package uk.ac.ebi.jmzidml.xml.jaxb.marshaller
 
uk.ac.ebi.jmzidml.xml.jaxb.marshaller.listeners - package uk.ac.ebi.jmzidml.xml.jaxb.marshaller.listeners
 
uk.ac.ebi.jmzidml.xml.jaxb.resolver - package uk.ac.ebi.jmzidml.xml.jaxb.resolver
 
uk.ac.ebi.jmzidml.xml.jaxb.unmarshaller - package uk.ac.ebi.jmzidml.xml.jaxb.unmarshaller
 
uk.ac.ebi.jmzidml.xml.jaxb.unmarshaller.cache - package uk.ac.ebi.jmzidml.xml.jaxb.unmarshaller.cache
 
uk.ac.ebi.jmzidml.xml.jaxb.unmarshaller.filters - package uk.ac.ebi.jmzidml.xml.jaxb.unmarshaller.filters
 
uk.ac.ebi.jmzidml.xml.jaxb.unmarshaller.listeners - package uk.ac.ebi.jmzidml.xml.jaxb.unmarshaller.listeners
 
uk.ac.ebi.jmzidml.xml.xxindex - package uk.ac.ebi.jmzidml.xml.xxindex
 
unitAccession - Variable in class uk.ac.ebi.jmzidml.model.mzidml.AbstractParam
 
unitCv - Variable in class uk.ac.ebi.jmzidml.model.mzidml.AbstractParam
 
unitCvRef - Variable in class uk.ac.ebi.jmzidml.model.mzidml.AbstractParam
 
unitName - Variable in class uk.ac.ebi.jmzidml.model.mzidml.AbstractParam
 
unmarshal(Class<T>) - Method in class uk.ac.ebi.jmzidml.xml.io.MzIdentMLUnmarshaller
Unmarshal one object for the specified class.
unmarshal(String) - Method in class uk.ac.ebi.jmzidml.xml.io.MzIdentMLUnmarshaller
 
unmarshal(MzIdentMLElement) - Method in class uk.ac.ebi.jmzidml.xml.io.MzIdentMLUnmarshaller
Unmarshals one element of the type defined by the MzIdentMLElement.
unmarshal(Class<T>, String) - Method in class uk.ac.ebi.jmzidml.xml.io.MzIdentMLUnmarshaller
 
unmarshal(String, Constants.ReferencedType) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.adapters.AbstractResolvingAdapter
 
unmarshal(String) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.adapters.AnalysisSoftwareAdapter
 
unmarshal(String) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.adapters.CalendarAdapter
 
unmarshal(String) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.adapters.CvAdapter
 
unmarshal(String) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.adapters.DBSequenceAdapter
 
unmarshal(String) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.adapters.MassTableAdapter
 
unmarshal(String) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.adapters.MeasureAdapter
 
unmarshal(String) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.adapters.OrganizationAdapter
 
unmarshal(String) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.adapters.PeptideAdapter
 
unmarshal(String) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.adapters.PeptideEvidenceAdapter
 
unmarshal(String) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.adapters.ProteinDetectionListAdapter
 
unmarshal(String) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.adapters.ProteinDetectionProtocolAdapter
 
unmarshal(String) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.adapters.SampleAdapter
 
unmarshal(String) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.adapters.SearchDatabaseAdapter
 
unmarshal(String) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.adapters.SpectraDataAdapter
 
unmarshal(String) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.adapters.SpectrumIdentificationListAdapter
 
unmarshal(String) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.adapters.SpectrumIdentificationProtocolAdapter
 
unmarshal(String) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.adapters.TranslationTableAdapter
 
unmarshal(String, Class<R>) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.resolver.AbstractReferenceResolver
 
unmarshalCollectionFromXpath(MzIdentMLElement) - Method in class uk.ac.ebi.jmzidml.xml.io.MzIdentMLUnmarshaller
 
unmarshall(Class<T>, String) - Method in class uk.ac.ebi.jmzidml.xml.io.MzIdentMLUnmarshaller
Deprecated. 
UnmarshallerFactory - Class in uk.ac.ebi.jmzidml.xml.jaxb.unmarshaller
 
updateCvParamSubclass(CvParam, Class<T>) - Static method in class uk.ac.ebi.jmzidml.model.utils.ParamUpdater
 
updateCvParamSubclassesList(List<CvParam>, Class<T>) - Static method in class uk.ac.ebi.jmzidml.model.utils.ParamUpdater
 
updateObject(AbstractParam) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.resolver.AbstractParamUnitCvRefResolver
 
updateObject(T) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.resolver.AbstractReferenceResolver
 
updateObject(Affiliation) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.resolver.AffiliationRefResolver
 
updateObject(ContactRole) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.resolver.ContactRoleRefResolver
 
updateObject(CvParam) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.resolver.CvParamRefResolver
 
updateObject(DBSequence) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.resolver.DBSequenceRefResolver
 
updateObject(FragmentArray) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.resolver.FragmentArrayRefResolver
 
updateObject(InputSpectra) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.resolver.InputSpectraRefResolver
 
updateObject(InputSpectrumIdentifications) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.resolver.InputSpectrumIdentificationsRefResolver
 
updateObject(ParentOrganization) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.resolver.ParentOrganizationRefResolver
 
updateObject(PeptideEvidenceRef) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.resolver.PeptideEvidenceRefResolver
 
updateObject(PeptideEvidence) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.resolver.PeptideEvidenceResolver
 
updateObject(PeptideHypothesis) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.resolver.PeptideHypothesisRefResolver
 
updateObject(ProteinDetectionHypothesis) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.resolver.ProteinDetectionHypothesisRefResolver
 
updateObject(ProteinDetectionProtocol) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.resolver.ProteinDetectionProtocolRefResolver
 
updateObject(ProteinDetection) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.resolver.ProteinDetectionRefResolver
 
updateObject(Provider) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.resolver.ProviderRefResolver
 
updateObject(SearchDatabaseRef) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.resolver.SearchDatabaseRefResolver
 
updateObject(SpectrumIdentificationItemRef) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.resolver.SpectrumIdentificationItemRefRefResolver
 
updateObject(SpectrumIdentificationItem) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.resolver.SpectrumIdentificationItemRefResolver
 
updateObject(SpectrumIdentificationProtocol) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.resolver.SpectrumIdentificationProtocolRefResolver
 
updateObject(SpectrumIdentification) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.resolver.SpectrumIdentificationRefResolver
 
updateObject(SpectrumIdentificationResult) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.resolver.SpectrumIdentificationResultRefResolver
 
updateObject(SubSample) - Method in class uk.ac.ebi.jmzidml.xml.jaxb.resolver.SubSampleRefResolver
 
updateParamList() - Method in class uk.ac.ebi.jmzidml.model.AbstractParamGroup
 
updateUserParamSubclass(UserParam, Class<T>) - Static method in class uk.ac.ebi.jmzidml.model.utils.ParamUpdater
 
updateUserParamSubclassesList(List<UserParam>, Class<T>) - Static method in class uk.ac.ebi.jmzidml.model.utils.ParamUpdater
 
uri - Variable in class uk.ac.ebi.jmzidml.model.mzidml.AnalysisSoftware
 
uri - Variable in class uk.ac.ebi.jmzidml.model.mzidml.Cv
 
UserParam - Class in uk.ac.ebi.jmzidml.model.mzidml
A single user-defined parameter.
UserParam() - Constructor for class uk.ac.ebi.jmzidml.model.mzidml.UserParam
 
useSpectrumCache - Variable in class uk.ac.ebi.jmzidml.xml.jaxb.adapters.AbstractResolvingAdapter
 

V

value - Variable in class uk.ac.ebi.jmzidml.model.mzidml.AbstractParam
 
valueOf(String) - Static method in enum uk.ac.ebi.jmzidml.MzIdentMLElement
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum uk.ac.ebi.jmzidml.ParamListMappings
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum uk.ac.ebi.jmzidml.ParamMappings
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum uk.ac.ebi.jmzidml.xml.Constants.ReferencedType
Returns the enum constant of this type with the specified name.
values - Variable in class uk.ac.ebi.jmzidml.model.mzidml.FragmentArray
 
values() - Static method in enum uk.ac.ebi.jmzidml.MzIdentMLElement
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum uk.ac.ebi.jmzidml.ParamListMappings
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum uk.ac.ebi.jmzidml.ParamMappings
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum uk.ac.ebi.jmzidml.xml.Constants.ReferencedType
Returns an array containing the constants of this enum type, in the order they are declared.
version - Variable in class uk.ac.ebi.jmzidml.model.mzidml.AnalysisSoftware
 
version - Variable in class uk.ac.ebi.jmzidml.model.mzidml.Cv
 
version - Variable in class uk.ac.ebi.jmzidml.model.mzidml.MzIdentML
 
version - Variable in class uk.ac.ebi.jmzidml.model.mzidml.SearchDatabase
 
volume - Variable in class uk.ac.ebi.jmzidml.model.mzidml.BibliographicReference
 

X

XML_INDEXED_XPATHS - Static variable in class uk.ac.ebi.jmzidml.xml.Constants
 

Y

year - Variable in class uk.ac.ebi.jmzidml.model.mzidml.BibliographicReference
 

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