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. |