| Package | Description |
|---|---|
| umich.ms.fileio.filetypes.mzidentml.jaxb.standard |
| Modifier and Type | Class and Description |
|---|---|
class |
AbstractContactType
A contact is either a person or an organization.
|
class |
AnalysisSoftwareType
The software used for performing the analyses.
|
class |
BibliographicReferenceType
Represents bibliographic references.
|
class |
DBSequenceType
A database sequence from the specified SearchDatabase (nucleic acid or amino acid).
|
class |
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.
|
class |
ExternalDataType
Data external to the XML instance document.
|
class |
MassTableType
The masses of residues used in the search.
|
class |
MeasureType
References to CV terms defining the measures about product ions to be reported in SpectrumIdentificationItem
|
class |
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 |
OrganizationType
Organizations are entities like companies, universities, government agencies.
|
class |
PeptideEvidenceType
PeptideEvidence links a specific Peptide element to a specific position in a DBSequence.
|
class |
PeptideType
One (poly)peptide (a sequence with modifications).
|
class |
PersonType
A person's name and contact details.
|
class |
ProteinAmbiguityGroupType
A set of logically related results from a protein detection, for example to represent conflicting assignments of peptides to proteins.
|
class |
ProteinDetectionHypothesisType
A single result of the ProteinDetection analysis (i.e.
|
class |
ProteinDetectionListType
The protein list resulting from a protein detection process.
|
class |
ProteinDetectionProtocolType
The parameters and settings of a ProteinDetection process.
|
class |
ProteinDetectionType
An Analysis which assembles a set of peptides (e.g.
|
class |
ProtocolApplicationType
The use of a protocol with the requisite Parameters and ParameterValues.
|
class |
ProviderType
The provider of the document in terms of the Contact and the software the produced the document instance.
|
class |
SampleType
A description of the sample analysed by mass spectrometry using CVParams or UserParams.
|
class |
SearchDatabaseType
A database for searching mass spectra.
|
class |
SourceFileType
A file from which this mzIdentML instance was created.
|
class |
SpectraDataType
A data set containing spectra data (consisting of one or more spectra).
|
class |
SpectrumIdentificationItemType
An identification of a single (poly)peptide, resulting from querying an input spectra, along with the set of confidence values for that identification.
|
class |
SpectrumIdentificationListType
Represents the set of all search results from SpectrumIdentification.
|
class |
SpectrumIdentificationProtocolType
The parameters and settings of a SpectrumIdentification analysis.
|
class |
SpectrumIdentificationResultType
All identifications made from searching one spectrum.
|
class |
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.
|
class |
TranslationTableType
The table used to translate codons into nucleic acids e.g.
|
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