| Package | Description |
|---|---|
| umich.ms.fileio.filetypes.mzidentml | |
| umich.ms.fileio.filetypes.mzidentml.jaxb.standard |
| Class and Description |
|---|
| MzIdentMLType
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 and Description |
|---|
| AbstractContactType
A contact is either a person or an organization.
|
| AbstractParamType
Abstract entity allowing either cvParam or userParam to be referenced in other schemas.
|
| AffiliationType
Java class for AffiliationType complex type.
|
| AmbiguousResidueType
Ambiguous residues e.g.
|
| AnalysisCollectionType
The analyses performed to get the results, which map the input and output data sets.
|
| AnalysisDataType
Data sets generated by the analyses, including peptide and protein lists.
|
| AnalysisProtocolCollectionType
The collection of protocols which include the parameters and settings of the performed analyses.
|
| AnalysisSampleCollectionType
The samples analysed can optionally be recorded using CV terms for descriptions.
|
| AnalysisSoftwareListType
The software packages used to perform the analyses.
|
| AnalysisSoftwareType
The software used for performing the analyses.
|
| AuditCollectionType
The complete set of Contacts (people and organisations) for this file.
|
| BibliographicReferenceType
Represents bibliographic references.
|
| ContactRoleType
The role that a Contact plays in an organization or with respect to the associating class.
|
| CVListType
The list of controlled vocabularies used in the file.
|
| CVParamType
A single entry from an ontology or a controlled
vocabulary.
|
| CvType
A source controlled vocabulary from which cvParams will be obtained.
|
| DatabaseFiltersType
The specification of filters applied to the database searched.
|
| DatabaseTranslationType
A specification of how a nucleic acid sequence database was translated for searching.
|
| DataCollectionType
The collection of input and output data sets of the analyses.
|
| DBSequenceType
A database sequence from the specified SearchDatabase (nucleic acid or amino acid).
|
| EnzymesType
The list of enzymes used in experiment
|
| EnzymeType
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.
|
| ExternalDataType
Data external to the XML instance document.
|
| FileFormatType
The format of the ExternalData file, for example "tiff" for image files.
|
| FilterType
Filters applied to the search database.
|
| FragmentArrayType
An array of values for a given type of measure and for a particular ion type, in parallel to the index of ions identified.
|
| FragmentationTableType
Contains the types of measures that will be reported in generic arrays for each SpectrumIdentificationItem e.g.
|
| FragmentationType
The product ions identified in this result.
|
| IdentifiableType
Other classes in the model can be specified as sub-classes, inheriting from Identifiable.
|
| InputSpectraType
The attribute referencing an identifier within the SpectraData section.
|
| InputSpectrumIdentificationsType
The lists of spectrum identifications that are input to the protein detection process.
|
| InputsType
The inputs to the analyses including the databases searched, the spectral data and the source file converted to mzIdentML.
|
| IonTypeType
IonType defines the index of fragmentation ions being reported, importing a CV term for the type of ion e.g.
|
| MassTableType
The masses of residues used in the search.
|
| MeasureType
References to CV terms defining the measures about product ions to be reported in SpectrumIdentificationItem
|
| ModificationParamsType
The specification of static/variable modifications (e.g.
|
| ModificationType
A molecule modification specification.
|
| MzIdentMLType
The upper-most hierarchy level of mzIdentML with sub-containers for example describing software, protocols and search results (spectrum identifications or protein detection results).
|
| OrganizationType
Organizations are entities like companies, universities, government agencies.
|
| ParamListType
Helper type to allow multiple cvParams or userParams to be given for an element.
|
| ParamType
Helper type to allow either a cvParam or a userParam to be provided for an element.
|
| ParentOrganizationType
The containing organization (the university or business which a lab belongs to, etc.)
|
| PeptideEvidenceRefType
Reference to the PeptideEvidence element identified.
|
| PeptideEvidenceType
PeptideEvidence links a specific Peptide element to a specific position in a DBSequence.
|
| PeptideHypothesisType
Peptide evidence on which this ProteinHypothesis is based by reference to a PeptideEvidence element.
|
| PeptideType
One (poly)peptide (a sequence with modifications).
|
| PersonType
A person's name and contact details.
|
| ProteinAmbiguityGroupType
A set of logically related results from a protein detection, for example to represent conflicting assignments of peptides to proteins.
|
| ProteinDetectionHypothesisType
A single result of the ProteinDetection analysis (i.e.
|
| ProteinDetectionListType
The protein list resulting from a protein detection process.
|
| ProteinDetectionProtocolType
The parameters and settings of a ProteinDetection process.
|
| ProteinDetectionType
An Analysis which assembles a set of peptides (e.g.
|
| ProtocolApplicationType
The use of a protocol with the requisite Parameters and ParameterValues.
|
| ProviderType
The provider of the document in terms of the Contact and the software the produced the document instance.
|
| ResidueType
Java class for ResidueType complex type.
|
| RoleType
The roles (lab equipment sales, contractor, etc.) the Contact fills.
|
| SampleType
A description of the sample analysed by mass spectrometry using CVParams or UserParams.
|
| SearchDatabaseRefType
One of the search databases used.
|
| SearchDatabaseType
A database for searching mass spectra.
|
| SearchModificationType
Specification of a search modification as parameter for a spectra search.
|
| SequenceCollectionType
The collection of sequences (DBSequence or Peptide) identified and their relationship between each other (PeptideEvidence) to be referenced elsewhere in the results.
|
| SourceFileType
A file from which this mzIdentML instance was created.
|
| SpecificityRulesType
The specificity rules of the searched modification including for example the probability of a modification's presence or peptide or protein termini.
|
| SpectraDataType
A data set containing spectra data (consisting of one or more spectra).
|
| SpectrumIdentificationItemRefType
Reference(s) to the SpectrumIdentificationItem element(s) that support the given PeptideEvidence element.
|
| SpectrumIdentificationItemType
An identification of a single (poly)peptide, resulting from querying an input spectra, along with the set of confidence values for that identification.
|
| SpectrumIdentificationListType
Represents the set of all search results from SpectrumIdentification.
|
| SpectrumIdentificationProtocolType
The parameters and settings of a SpectrumIdentification analysis.
|
| SpectrumIdentificationResultType
All identifications made from searching one spectrum.
|
| SpectrumIdentificationType
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.
|
| SpectrumIDFormatType
The format of the spectrum identifier within the source file
|
| SubSampleType
References to the individual component samples within a mixed parent sample.
|
| SubstitutionModificationType
A modification where one residue is substituted by another (amino acid change).
|
| ToleranceType
The tolerance of the search given as a plus and minus value with units.
|
| TranslationTableType
The table used to translate codons into nucleic acids e.g.
|
| UserParamType
A single user-defined parameter.
|
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