Uses of Class
uk.ac.ebi.jmzidml.model.MzIdentMLObject

Packages that use MzIdentMLObject
uk.ac.ebi.jmzidml   
uk.ac.ebi.jmzidml.model   
uk.ac.ebi.jmzidml.model.mzidml   
uk.ac.ebi.jmzidml.model.mzidml.params   
uk.ac.ebi.jmzidml.xml.io   
uk.ac.ebi.jmzidml.xml.jaxb.resolver   
uk.ac.ebi.jmzidml.xml.jaxb.unmarshaller.cache   
 

Uses of MzIdentMLObject in uk.ac.ebi.jmzidml
 

Methods in uk.ac.ebi.jmzidml with type parameters of type MzIdentMLObject
<T extends MzIdentMLObject>
Class<T>
MzIdentMLElement.getClazz()
           
 

Uses of MzIdentMLObject in uk.ac.ebi.jmzidml.model
 

Subclasses of MzIdentMLObject in uk.ac.ebi.jmzidml.model
 class AbstractIdentifiableParamGroup
           
 

Uses of MzIdentMLObject in uk.ac.ebi.jmzidml.model.mzidml
 

Subclasses of MzIdentMLObject in uk.ac.ebi.jmzidml.model.mzidml
 class AbstractContact
          A contact is either a person or an organization.
 class AbstractParam
          Abstract entity allowing either cvParam or userParam to be referenced in other schemas.
 class Affiliation
          Java class for AffiliationType complex type.
 class AmbiguousResidue
          Ambiguous residues e.g.
 class AnalysisCollection
          The analyses performed to get the results, which map the input and output data sets.
 class AnalysisData
          Data sets generated by the analyses, including peptide and protein lists.
 class AnalysisProtocolCollection
          The collection of protocols which include the parameters and settings of the performed analyses.
 class AnalysisSampleCollection
          The samples analysed can optionally be recorded using CV terms for descriptions.
 class AnalysisSoftware
          The software used for performing the analyses.
 class AnalysisSoftwareList
          The software packages used to perform the analyses.
 class AuditCollection
          The complete set of Contacts (people and organisations) for this file.
 class BibliographicReference
          Represents bibliographic references.
 class ContactRole
          The role that a Contact plays in an organization or with respect to the associating class.
 class Cv
          A source controlled vocabulary from which cvParams will be obtained.
 class CvList
          The list of controlled vocabularies used in the file.
 class CvParam
          A single entry from an ontology or a controlled vocabulary.
 class DatabaseFilters
          The specification of filters applied to the database searched.
 class DatabaseTranslation
          A specification of how a nucleic acid sequence database was translated for searching.
 class DataCollection
          The collection of input and output data sets of the analyses.
 class DBSequence
          A database sequence from the specified SearchDatabase (nucleic acid or amino acid).
 class Enzyme
          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.
 class Enzymes
          The list of enzymes used in experiment
 class ExternalData
          Data external to the XML instance document.
 class FileFormat
          The format of the ExternalData file, for example "tiff" for image files.
 class Filter
          Filters applied to the search database.
 class FragmentArray
          An array of values for a given type of measure and for a particular ion type, in parallel to the index of ions identified.
 class Fragmentation
          The product ions identified in this result.
 class FragmentationTable
          Contains the types of measures that will be reported in generic arrays for each SpectrumIdentificationItem e.g.
 class Identifiable
          Other classes in the model can be specified as sub-classes, inheriting from Identifiable.
 class Inputs
          The inputs to the analyses including the databases searched, the spectral data and the source file converted to mzIdentML.
 class InputSpectra
          The attribute referencing an identifier within the SpectraData section.
 class InputSpectrumIdentifications
          The lists of spectrum identifications that are input to the protein detection process.
 class IonType
          IonType defines the index of fragmentation ions being reported, importing a CV term for the type of ion e.g.
 class MassTable
          The masses of residues used in the search.
 class Measure
          References to CV terms defining the measures about product ions to be reported in SpectrumIdentificationItem
 class Modification
          A molecule modification specification.
 class ModificationParams
          The specification of static/variable modifications (e.g.
 class ModParam
          The modification searched for, sourced from e.g.
 class MzIdentML
          The upper-most hierarchy level of mzIdentML with sub-containers for example describing software, protocols and search results (spectrum identifications or protein detection results).
 class Organization
          Organizations are entities like companies, universities, government agencies.
 class Param
          Helper type to allow either a cvParam or a userParam to be provided for an element.
 class ParamList
          Helper type to allow multiple cvParams or userParams to be given for an element.
 class ParentOrganization
          The containing organization (the university or business which a lab belongs to, etc.)
 class Peptide
          One (poly)peptide (a sequence with modifications).
 class PeptideEvidence
          PeptideEvidence links a specific Peptide element to a specific position in a DBSequence.
 class PeptideEvidenceRef
          Reference to the PeptideEvidence element identified.
 class PeptideHypothesis
          Peptide evidence on which this ProteinHypothesis is based by reference to a PeptideEvidence element.
 class Person
          A person's name and contact details.
 class ProteinAmbiguityGroup
          A set of logically related results from a protein detection, for example to represent conflicting assignments of peptides to proteins.
 class ProteinDetection
          An Analysis which assembles a set of peptides (e.g.
 class ProteinDetectionHypothesis
          A single result of the ProteinDetection analysis (i.e.
 class ProteinDetectionList
          The protein list resulting from a protein detection process.
 class ProteinDetectionProtocol
          The parameters and settings of a ProteinDetection process.
 class ProtocolApplication
          The use of a protocol with the requisite Parameters and ParameterValues.
 class Provider
          The provider of the document in terms of the Contact and the software the produced the document instance.
 class Residue
          Java class for ResidueType complex type.
 class Role
          The roles (lab equipment sales, contractor, etc.) the Contact fills.
 class Sample
          A description of the sample analysed by mass spectrometry using CVParams or UserParams.
 class SearchDatabase
          A database for searching mass spectra.
 class SearchDatabaseRef
          One of the search databases used.
 class SearchModification
          Specification of a search modification as parameter for a spectra search.
 class SequenceCollection
          The collection of sequences (DBSequence or Peptide) identified and their relationship between each other (PeptideEvidence) to be referenced elsewhere in the results.
 class SourceFile
          A file from which this mzIdentML instance was created.
 class SpecificityRules
          The specificity rules of the searched modification including for example the probability of a modification's presence or peptide or protein termini.
 class SpectraData
          A data set containing spectra data (consisting of one or more spectra).
 class SpectrumIdentification
          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.
 class SpectrumIdentificationItem
          An identification of a single (poly)peptide, resulting from querying an input spectra, along with the set of confidence values for that identification.
 class SpectrumIdentificationItemRef
          Reference(s) to the SpectrumIdentificationItem element(s) that support the given PeptideEvidence element.
 class SpectrumIdentificationList
          Represents the set of all search results from SpectrumIdentification.
 class SpectrumIdentificationProtocol
          The parameters and settings of a SpectrumIdentification analysis.
 class SpectrumIdentificationResult
          All identifications made from searching one spectrum.
 class SpectrumIDFormat
          The format of the spectrum identifier within the source file
 class SubSample
          References to the individual component samples within a mixed parent sample.
 class SubstitutionModification
          A modification where one residue is substituted by another (amino acid change).
 class Tolerance
          The tolerance of the search given as a plus and minus value with units.
 class TranslationTable
          The table used to translate codons into nucleic acids e.g.
 class UserParam
          A single user-defined parameter.
 

Uses of MzIdentMLObject in uk.ac.ebi.jmzidml.model.mzidml.params
 

Subclasses of MzIdentMLObject in uk.ac.ebi.jmzidml.model.mzidml.params
 class AdditionalParamsCvParam
          User: gokelly Date: 11/04/11 Time: 14:46
 class AdditionalParamsUserParam
          User: gokelly Date: 11/04/11 Time: 14:47
 class AdditionalSearchParamsCvParam
          User: gokelly Date: 11/04/11 Time: 15:30
 class AdditionalSearchParamsUserParam
          User: gokelly Date: 11/04/11 Time: 15:31
 class AmbiguousResidueCvParam
           
 class AmbiguousResidueUserParam
           
 class AnalysisParamsCvParam
          User: gokelly Date: 11/04/11 Time: 10:25
 class AnalysisParamsUserParam
          User: gokelly Date: 11/04/11 Time: 10:25
 class DatabaseNameCvParam
          User: gokelly Date: 4/14/11 Time: 2:06 PM
 class DatabaseNameUserParam
          User: gokelly Date: 4/14/11 Time: 2:06 PM
 class DBSequenceCvParam
           
 class DBSequenceUserParam
           
 class EnzymeNameCvParam
          User: gokelly Date: 11/04/11 Time: 14:10
 class EnzymeNameUserParam
          User: gokelly Date: 11/04/11 Time: 14:10
 class ExcludeCvParam
          User: gokelly Date: 11/04/11 Time: 16:00
 class ExcludeUserParam
          User: gokelly Date: 11/04/11 Time: 16:00
 class FileFormatCvParam
           
 class FilterTypeCvParam
          User: gokelly Date: 4/14/11 Time: 2:09 PM
 class FilterTypeUserParam
          User: gokelly Date: 4/14/11 Time: 2:09 PM
 class IncludeCvParam
          User: gokelly Date: 11/04/11 Time: 15:58
 class IncludeUserParam
          User: gokelly Date: 11/04/11 Time: 15:59
 class IonTypeCvParam
           
 class MassTableCvParam
           
 class MassTableUserParam
           
 class MeasureCvParam
           
 class ModificationCvParam
           
 class ModificationUserParam
           
 class ModParamCvParam
           
 class OrganizationCvParam
          Created by IntelliJ IDEA.
 class OrganizationUserParam
          Created by IntelliJ IDEA.
 class PeptideCvParam
           
 class PeptideEvidenceCvParam
           
 class PeptideEvidenceListCvParam
          Created by IntelliJ IDEA.
 class PeptideEvidenceListUserParam
          Created by IntelliJ IDEA.
 class PeptideEvidenceUserParam
           
 class PeptideUserParam
           
 class PersonCvParam
          Created by IntelliJ IDEA.
 class PersonUserParam
          Created by IntelliJ IDEA.
 class ProteinAmbiguityGroupCvParam
           
 class ProteinAmbiguityGroupUserParam
           
 class ProteinDetectionHypothesisCvParam
           
 class ProteinDetectionHypothesisUserParam
           
 class ProteinDetectionListCvParam
           
 class ProteinDetectionListUserParam
           
 class RoleCvParam
           
 class SampleCvParam
           
 class SampleUserParam
           
 class SearchDatabaseCvParam
           
 class SearchTypeCvParam
          User: gokelly Date: 4/14/11 Time: 2:10 PM
 class SearchTypeUserParam
          User: gokelly Date: 4/14/11 Time: 2:10 PM
 class SoftwareNameCvParam
          User: gokelly Date: 4/14/11 Time: 2:08 PM
 class SoftwareNameUserParam
          User: gokelly Date: 4/14/11 Time: 2:08 PM
 class SourceFileCvParam
           
 class SourceFileUserParam
           
 class SpecificityRulesCvParam
           
 class SpectrumIdentificationItemCvParam
           
 class SpectrumIdentificationItemUserParam
           
 class SpectrumIdentificationListCvParam
           
 class SpectrumIdentificationListUserParam
           
 class SpectrumIdentificationResultCvParam
           
 class SpectrumIdentificationResultUserParam
           
 class SpectrumIDFormatCvParam
           
 class ThresholdCvParam
          User: gokelly Date: 11/04/11 Time: 10:23
 class ThresholdUserParam
          User: gokelly Date: 11/04/11 Time: 10:24
 class ToleranceCvParam
           
 class TranslationTableCvParam
           
 

Uses of MzIdentMLObject in uk.ac.ebi.jmzidml.xml.io
 

Classes in uk.ac.ebi.jmzidml.xml.io with type parameters of type MzIdentMLObject
 class MzIdentMLObjectIterator<T extends MzIdentMLObject>
           
 

Methods in uk.ac.ebi.jmzidml.xml.io with type parameters of type MzIdentMLObject
<T extends MzIdentMLObject>
T
MzIdentMLObjectCache.getCachedObject(String id, Class<T> cls)
           
<T extends MzIdentMLObject>
List<T>
MzIdentMLObjectCache.getEntries(Class<T> clazz)
           
<T extends MzIdentMLObject>
boolean
MzIdentMLObjectCache.hasEntry(Class<T> clazz)
           
<T extends MzIdentMLObject>
String
MzIdentMLMarshaller.marshal(T object)
           
<T extends MzIdentMLObject>
void
MzIdentMLMarshaller.marshal(T object, OutputStream os)
           
<T extends MzIdentMLObject>
void
MzIdentMLMarshaller.marshal(T object, Writer out)
           
<T extends MzIdentMLObject>
String
MzIdentMLMarshaller.marshall(T object)
          Deprecated. 
<T extends MzIdentMLObject>
void
MzIdentMLMarshaller.marshall(T object, OutputStream os)
          Deprecated. 
<T extends MzIdentMLObject>
void
MzIdentMLMarshaller.marshall(T object, Writer out)
          Deprecated. 
<T extends MzIdentMLObject>
T
MzIdentMLUnmarshaller.unmarshal(Class<T> clazz)
          Unmarshal one object for the specified class.
<T extends MzIdentMLObject>
T
MzIdentMLUnmarshaller.unmarshal(Class<T> clazz, String id)
           
<T extends MzIdentMLObject>
T
MzIdentMLUnmarshaller.unmarshal(MzIdentMLElement element)
          Unmarshals one element of the type defined by the MzIdentMLElement.
<T extends MzIdentMLObject>
T
MzIdentMLUnmarshaller.unmarshal(String xpath)
           
<T extends MzIdentMLObject>
Iterator<T>
MzIdentMLUnmarshaller.unmarshalCollectionFromXpath(MzIdentMLElement element)
           
<T extends MzIdentMLObject>
T
MzIdentMLUnmarshaller.unmarshall(Class<T> clazz, String id)
          Deprecated. 
 

Methods in uk.ac.ebi.jmzidml.xml.io with parameters of type MzIdentMLObject
 void MzIdentMLObjectCache.putInCache(String id, MzIdentMLObject object)
           
 

Uses of MzIdentMLObject in uk.ac.ebi.jmzidml.xml.jaxb.resolver
 

Classes in uk.ac.ebi.jmzidml.xml.jaxb.resolver with type parameters of type MzIdentMLObject
 class AbstractReferenceResolver<T extends MzIdentMLObject>
          Abstract base class for the reference resolver classes.
 

Methods in uk.ac.ebi.jmzidml.xml.jaxb.resolver with type parameters of type MzIdentMLObject
<R extends MzIdentMLObject>
R
AbstractReferenceResolver.unmarshal(String refId, Class<R> cls)
           
 

Uses of MzIdentMLObject in uk.ac.ebi.jmzidml.xml.jaxb.unmarshaller.cache
 

Methods in uk.ac.ebi.jmzidml.xml.jaxb.unmarshaller.cache with type parameters of type MzIdentMLObject
<T extends MzIdentMLObject>
T
AdapterObjectCache.getCachedObject(String id, Class<T> cls)
          Retrieve a MzIdentMLObject from the object cache.
<T extends MzIdentMLObject>
List<T>
AdapterObjectCache.getEntries(Class<T> clazz)
           
<T extends MzIdentMLObject>
boolean
AdapterObjectCache.hasEntry(Class<T> clazz)
           
 

Methods in uk.ac.ebi.jmzidml.xml.jaxb.unmarshaller.cache with parameters of type MzIdentMLObject
 void AdapterObjectCache.putInCache(String id, MzIdentMLObject object)
          Stores the Object in a in-memory Map.
 



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