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