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

Packages that use uk.ac.ebi.jmzidml.model.mzidml
uk.ac.ebi.jmzidml   
uk.ac.ebi.jmzidml.model   
uk.ac.ebi.jmzidml.model.mzidml   
uk.ac.ebi.jmzidml.model.mzidml.params   
uk.ac.ebi.jmzidml.model.utils   
uk.ac.ebi.jmzidml.xml.jaxb.adapters   
uk.ac.ebi.jmzidml.xml.jaxb.resolver   
 

Classes in uk.ac.ebi.jmzidml.model.mzidml used by uk.ac.ebi.jmzidml
CvParam
          A single entry from an ontology or a controlled vocabulary.
UserParam
          A single user-defined parameter.
 

Classes in uk.ac.ebi.jmzidml.model.mzidml used by uk.ac.ebi.jmzidml.model
CvParam
          A single entry from an ontology or a controlled vocabulary.
Identifiable
          Other classes in the model can be specified as sub-classes, inheriting from Identifiable.
UserParam
          A single user-defined parameter.
 

Classes in uk.ac.ebi.jmzidml.model.mzidml used by uk.ac.ebi.jmzidml.model.mzidml
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.
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).
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.
 

Classes in uk.ac.ebi.jmzidml.model.mzidml used by uk.ac.ebi.jmzidml.model.mzidml.params
AbstractParam
          Abstract entity allowing either cvParam or userParam to be referenced in other schemas.
CvParam
          A single entry from an ontology or a controlled vocabulary.
UserParam
          A single user-defined parameter.
 

Classes in uk.ac.ebi.jmzidml.model.mzidml used by uk.ac.ebi.jmzidml.model.utils
CvParam
          A single entry from an ontology or a controlled vocabulary.
UserParam
          A single user-defined parameter.
 

Classes in uk.ac.ebi.jmzidml.model.mzidml used by uk.ac.ebi.jmzidml.xml.jaxb.adapters
AnalysisSoftware
          The software used for performing the analyses.
Cv
          A source controlled vocabulary from which cvParams will be obtained.
DBSequence
          A database sequence from the specified SearchDatabase (nucleic acid or amino acid).
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
Organization
          Organizations are entities like companies, universities, government agencies.
Peptide
          One (poly)peptide (a sequence with modifications).
PeptideEvidence
          PeptideEvidence links a specific Peptide element to a specific position in a DBSequence.
ProteinDetectionList
          The protein list resulting from a protein detection process.
ProteinDetectionProtocol
          The parameters and settings of a ProteinDetection process.
Sample
          A description of the sample analysed by mass spectrometry using CVParams or UserParams.
SearchDatabase
          A database for searching mass spectra.
SpectraData
          A data set containing spectra data (consisting of one or more spectra).
SpectrumIdentificationList
          Represents the set of all search results from SpectrumIdentification.
SpectrumIdentificationProtocol
          The parameters and settings of a SpectrumIdentification analysis.
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
AbstractParam
          Abstract entity allowing either cvParam or userParam to be referenced in other schemas.
Affiliation
          Java class for AffiliationType complex type.
ContactRole
          The role that a Contact plays in an organization or with respect to the associating class.
CvParam
          A single entry from an ontology or a controlled vocabulary.
DBSequence
          A database sequence from the specified SearchDatabase (nucleic acid or amino acid).
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.
InputSpectra
          The attribute referencing an identifier within the SpectraData section.
InputSpectrumIdentifications
          The lists of spectrum identifications that are input to the protein detection process.
ParentOrganization
          The containing organization (the university or business which a lab belongs to, etc.)
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.
ProteinDetection
          An Analysis which assembles a set of peptides (e.g.
ProteinDetectionHypothesis
          A single result of the ProteinDetection analysis (i.e.
ProteinDetectionProtocol
          The parameters and settings of a ProteinDetection process.
Provider
          The provider of the document in terms of the Contact and the software the produced the document instance.
SearchDatabaseRef
          One of the search databases used.
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.
SpectrumIdentificationProtocol
          The parameters and settings of a SpectrumIdentification analysis.
SpectrumIdentificationResult
          All identifications made from searching one spectrum.
SubSample
          References to the individual component samples within a mixed parent sample.
 



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