Uses of Interface
uk.ac.ebi.pride.utilities.data.core.MassSpecObject

Packages that use MassSpecObject

Package	Description
uk.ac.ebi.pride.utilities.data.core

Uses of MassSpecObject in uk.ac.ebi.pride.utilities.data.core

Classes in uk.ac.ebi.pride.utilities.data.core that implement MassSpecObject

Modifier and Type	Class and Description
class	AbundanceAssay Abundance Assay is the Class to storage the abundance variables for each Protein.
class	Assay Assay In the mzTab experiment with the corresponding Reagent and sample
class	BinaryDataArray BinaryDataArray is a slim down version of binaryDataArray in mzML ParamGroup of this object must have the followings in mzML 1.1.0.1 definition: For Chromatograms (once each): 1.
class	Chromatogram Chromatogram object.
class	Contact This class is just to organize the code, the ConstantRole class have to kind of instance, one of then is Organization and the Other one if the person both objects extend the IdentifiableParamGroup in order to organize the code we create a new abstract class named AbstractContact to separate the Contacts types from the IdentifiableParamGroup.
class	CVLookup CVLookup is referenced in every CvParam.
class	CvParam This object holds additional data in controlled vocabulary.
class	DataProcessing Description of the way in which a List of Software were used.
class	DBSequence A database sequence from the specified SearchDatabase (nucleic acid or amino acid).
class	Enzyme Enzyme used during the search in Databases.
class	ExperimentMetaData General descriptions shared or used for the whole file.
class	ExperimentProtocol Protocol used to generate the dataset, added by PRIDE XML 2.0.
class	ExternalData Data external to the XML instance document.
class	FragmentIon FragmentIon stores details about peptide fragment ion information.
class	Gel Gel is a class to Describe the Gel Spot for each Protein.
class	Identifiable Other classes in the model can be specified as sub-classes, inheriting from Identifiable.
class	IdentifiableParamGroup Other classes in the model can be specified as sub-classes, inheriting from IdentifiablePraramGroup.
class	IdentificationMetaData This class is used to manage and store the information of the metadata for protein and spectrum identifications.
class	InstrumentComponent InstrumentComponent is key to keep the order of different instrument component.
class	InstrumentConfiguration Description of a particular hardware configuration of a mass spectrometer.
class	IonType IonType defines the index of fragmentation ions being reported, importing a CV term for the type of ion e.g.
class	MassTable
class	Modification A molecule modification specification.
class	MzGraph Abstract object can be extended by both Spectrum and Chromatogram.
class	MzGraphMetaData This class storage the information related with metadata at the spectrum level.
class	Organization Organizations are entities like companies, universities, government agencies.
class	Parameter Parameter exist in neither PRIDE XML nor mzML, it created for method sharing.
class	ParamGroup ParamGroup is a container for CvParams and UserParams.
class	PeptideEvidence PeptideEvidence links a specific Peptide Element to a specific position in a DBSequence.
class	PeptideSequence One (poly)peptide (a sequence with modifications).
class	Person A person's name and contact details.
class	Precursor The method of precursor ion selection and activation
class	ProcessingMethod Description of the default peak processing method.
class	Protein Abstract class for both GelFreeIdentification and TwoDimIdentification
class	ProteinGroup A set of logically related results from a protein detection, for example to represent conflicting assignments of peptides to proteins
class	Protocol The collection of protocols which include the parameters and settings of the performed analyses.
class	Provider Provider object.
class	QuantScore The QuantScore is the List of StudyVariable Scores and the Abundance by Assays.
class	Reference Reference is added by PRIDE XML 2.0., also a generic reference for mzIdentML References.
class	ReferenceableParamGroup Referenceable param group stores a map of reference string to param group.
class	Sample Description of the sample used to generate the Dataset.
class	Scan Scan or acquisition from original raw file used to create this peak list, as specified in sourceFile.
class	ScanList List and descriptions of scans.
class	ScanSetting Description of the acquisition settings or the instrument prior to the start of the run.
class	SearchDataBase A database for searching mass spectra.
class	Software Software details.
class	SourceFile Description of source file, including identification file, location and type.
class	SpectraData A data set containing spectra data (consisting of one or more spectra).
class	Spectrum A peak list including the underlying acquisitions.
class	SpectrumIdentification PSM Spectrum identification match.
class	SpectrumIdentificationList Represents the set of all search results from SpectrumIdentification.
class	SpectrumIdentificationProtocol The parameters and settings of a SpectrumIdentification analysis.
class	StudyVariable Study variable is use for Quantitation on mzTab files.
class	UserParam Uncontrolled user parameters, allowing free text.