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Uses of MzIdentMLObject in uk.ac.ebi.jmzidml |
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Methods in uk.ac.ebi.jmzidml with type parameters of type MzIdentMLObject | ||
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MzIdentMLElement.getClazz()
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Uses of MzIdentMLObject in uk.ac.ebi.jmzidml.model |
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Subclasses of MzIdentMLObject in uk.ac.ebi.jmzidml.model | |
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class |
AbstractIdentifiableParamGroup
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Uses of MzIdentMLObject in uk.ac.ebi.jmzidml.model.mzidml |
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Subclasses of MzIdentMLObject in uk.ac.ebi.jmzidml.model.mzidml | |
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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 |
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Subclasses of MzIdentMLObject in uk.ac.ebi.jmzidml.model.mzidml.params | |
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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
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class |
AmbiguousResidueUserParam
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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
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class |
DBSequenceUserParam
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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
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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
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class |
MassTableCvParam
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class |
MassTableUserParam
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class |
MeasureCvParam
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class |
ModificationCvParam
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class |
ModificationUserParam
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class |
ModParamCvParam
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class |
OrganizationCvParam
Created by IntelliJ IDEA. |
class |
OrganizationUserParam
Created by IntelliJ IDEA. |
class |
PeptideCvParam
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class |
PeptideEvidenceCvParam
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class |
PeptideEvidenceListCvParam
Created by IntelliJ IDEA. |
class |
PeptideEvidenceListUserParam
Created by IntelliJ IDEA. |
class |
PeptideEvidenceUserParam
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class |
PeptideUserParam
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class |
PersonCvParam
Created by IntelliJ IDEA. |
class |
PersonUserParam
Created by IntelliJ IDEA. |
class |
ProteinAmbiguityGroupCvParam
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class |
ProteinAmbiguityGroupUserParam
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class |
ProteinDetectionHypothesisCvParam
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class |
ProteinDetectionHypothesisUserParam
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class |
ProteinDetectionListCvParam
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class |
ProteinDetectionListUserParam
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class |
RoleCvParam
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class |
SampleCvParam
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class |
SampleUserParam
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class |
SearchDatabaseCvParam
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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
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class |
SourceFileUserParam
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class |
SpecificityRulesCvParam
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class |
SpectrumIdentificationItemCvParam
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class |
SpectrumIdentificationItemUserParam
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class |
SpectrumIdentificationListCvParam
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class |
SpectrumIdentificationListUserParam
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class |
SpectrumIdentificationResultCvParam
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class |
SpectrumIdentificationResultUserParam
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class |
SpectrumIDFormatCvParam
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class |
ThresholdCvParam
User: gokelly Date: 11/04/11 Time: 10:23 |
class |
ThresholdUserParam
User: gokelly Date: 11/04/11 Time: 10:24 |
class |
ToleranceCvParam
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class |
TranslationTableCvParam
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Uses of MzIdentMLObject in uk.ac.ebi.jmzidml.xml.io |
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Classes in uk.ac.ebi.jmzidml.xml.io with type parameters of type MzIdentMLObject | |
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class |
MzIdentMLObjectIterator<T extends MzIdentMLObject>
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Methods in uk.ac.ebi.jmzidml.xml.io with type parameters of type MzIdentMLObject | ||
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MzIdentMLObjectCache.getCachedObject(String id,
Class<T> cls)
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MzIdentMLObjectCache.getEntries(Class<T> clazz)
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MzIdentMLObjectCache.hasEntry(Class<T> clazz)
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MzIdentMLMarshaller.marshal(T object)
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MzIdentMLMarshaller.marshal(T object,
OutputStream os)
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MzIdentMLMarshaller.marshal(T object,
Writer out)
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MzIdentMLMarshaller.marshall(T object)
Deprecated. |
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MzIdentMLMarshaller.marshall(T object,
OutputStream os)
Deprecated. |
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MzIdentMLMarshaller.marshall(T object,
Writer out)
Deprecated. |
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MzIdentMLUnmarshaller.unmarshal(Class<T> clazz)
Unmarshal one object for the specified class. |
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MzIdentMLUnmarshaller.unmarshal(Class<T> clazz,
String id)
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MzIdentMLUnmarshaller.unmarshal(MzIdentMLElement element)
Unmarshals one element of the type defined by the MzIdentMLElement. |
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MzIdentMLUnmarshaller.unmarshal(String xpath)
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MzIdentMLUnmarshaller.unmarshalCollectionFromXpath(MzIdentMLElement element)
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MzIdentMLUnmarshaller.unmarshall(Class<T> clazz,
String id)
Deprecated. |
Methods in uk.ac.ebi.jmzidml.xml.io with parameters of type MzIdentMLObject | |
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void |
MzIdentMLObjectCache.putInCache(String id,
MzIdentMLObject object)
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Uses of MzIdentMLObject in uk.ac.ebi.jmzidml.xml.jaxb.resolver |
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Classes in uk.ac.ebi.jmzidml.xml.jaxb.resolver with type parameters of type MzIdentMLObject | |
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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 | ||
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AbstractReferenceResolver.unmarshal(String refId,
Class<R> cls)
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Uses of MzIdentMLObject in uk.ac.ebi.jmzidml.xml.jaxb.unmarshaller.cache |
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Methods in uk.ac.ebi.jmzidml.xml.jaxb.unmarshaller.cache with type parameters of type MzIdentMLObject | ||
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AdapterObjectCache.getCachedObject(String id,
Class<T> cls)
Retrieve a MzIdentMLObject from the object cache. |
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AdapterObjectCache.getEntries(Class<T> clazz)
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AdapterObjectCache.hasEntry(Class<T> clazz)
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Methods in uk.ac.ebi.jmzidml.xml.jaxb.unmarshaller.cache with parameters of type MzIdentMLObject | |
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void |
AdapterObjectCache.putInCache(String id,
MzIdentMLObject object)
Stores the Object in a in-memory Map. |
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