Package uk.ac.ebi.jmzidml.model.mzidml

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



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