A B C D E F G H I L M N O P Q R S T U V W X

A

AbstractCachingStrategy - Class in uk.ac.ebi.pride.utilities.data.controller.cache.strategy

AbstractCachingStrategy() - Constructor for class uk.ac.ebi.pride.utilities.data.controller.cache.strategy.AbstractCachingStrategy

AbstractDataAccessController - Class in uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl

AbstractDataAccessController provides an abstract implementation of DataAccessController.

AbstractDataAccessController() - Constructor for class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

AbstractDataAccessController(Object) - Constructor for class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

AbstractMzTabConverter - Class in uk.ac.ebi.pride.utilities.data.exporters

ms-data-core api will plan to export all the data to mztab files using the jmzTab library.

AbstractMzTabConverter(DataAccessController) - Constructor for class uk.ac.ebi.pride.utilities.data.exporters.AbstractMzTabConverter

AbundanceAssay - Class in uk.ac.ebi.pride.utilities.data.core

Abundance Assay is the Class to storage the abundance variables for each Protein.

AbundanceAssay(Comparable, String) - Constructor for class uk.ac.ebi.pride.utilities.data.core.AbundanceAssay

AbundanceAssay(ParamGroup, Comparable, String) - Constructor for class uk.ac.ebi.pride.utilities.data.core.AbundanceAssay

AbundanceAssay(Comparable, String, Assay, Double) - Constructor for class uk.ac.ebi.pride.utilities.data.core.AbundanceAssay

AbundanceAssay(ParamGroup, Comparable, String, Assay, Double) - Constructor for class uk.ac.ebi.pride.utilities.data.core.AbundanceAssay

AccessionFilter<T> - Interface in uk.ac.ebi.pride.utilities.data.filter

Filter for a protein accession

addCvParam(CvParam) - Method in class uk.ac.ebi.pride.utilities.data.core.ParamGroup

addCvParams(List<CvParam>) - Method in class uk.ac.ebi.pride.utilities.data.core.ParamGroup

addMSController(List<File>) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.ReferencedIdentificationController

Add a List of MS Files to the mzidentml.

addMSController(Map<SpectraData, File>) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.ReferencedIdentificationController

Check if the File format is supported and the spectrum Id and add a Set of DataAccessControllers.

addNewMSController(Map<SpectraData, File>, Map<Comparable, File>, Map<Comparable, String>) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.ReferencedIdentificationController

addOptionalColumnValue(MZTabRecord, MZTabColumnFactory, String, String) - Static method in class uk.ac.ebi.pride.utilities.data.utils.MzTabUtils

addRefParamGroup(String, ParamGroup) - Method in class uk.ac.ebi.pride.utilities.data.core.ReferenceableParamGroup

addScore(SearchEngineCvTermReference, SearchEngineScoreCvTermReference, Number) - Method in class uk.ac.ebi.pride.utilities.data.core.Score

Add a new peptide score

addsubSample(int) - Method in class uk.ac.ebi.pride.utilities.data.core.QuantitativeSample

addUserParam(UserParam) - Method in class uk.ac.ebi.pride.utilities.data.core.ParamGroup

addUserParams(List<UserParam>) - Method in class uk.ac.ebi.pride.utilities.data.core.ParamGroup

APL_EXT - Static variable in class uk.ac.ebi.pride.utilities.data.utils.Constants

apply(T) - Method in interface uk.ac.ebi.pride.utilities.data.filter.AccessionFilter

apply(String) - Method in class uk.ac.ebi.pride.utilities.data.filter.DecoyAccessionFilter

Assay - Class in uk.ac.ebi.pride.utilities.data.core

Assay In the mzTab experiment with the corresponding Reagent and sample

Assay(Comparable, String) - Constructor for class uk.ac.ebi.pride.utilities.data.core.Assay

Assay(ParamGroup, Comparable, String) - Constructor for class uk.ac.ebi.pride.utilities.data.core.Assay

Assay(Comparable, String, Sample) - Constructor for class uk.ac.ebi.pride.utilities.data.core.Assay

Assay(ParamGroup, Comparable, String, Sample) - Constructor for class uk.ac.ebi.pride.utilities.data.core.Assay

Assay(ParamGroup, Comparable, String, Sample, CvParam) - Constructor for class uk.ac.ebi.pride.utilities.data.core.Assay

B

BinaryDataArray - Class in uk.ac.ebi.pride.utilities.data.core

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.

BinaryDataArray(DataProcessing, double[], ParamGroup) - Constructor for class uk.ac.ebi.pride.utilities.data.core.BinaryDataArray

Constructor

BinaryDataArray(BinaryDataArray) - Constructor for class uk.ac.ebi.pride.utilities.data.core.BinaryDataArray

BinaryDataUtils - Class in uk.ac.ebi.pride.utilities.data.utils

This class need to be deleted in the future.

C

Cache - Interface in uk.ac.ebi.pride.utilities.data.controller.cache

Cache interface defines methods for storing data into cache and retrieving data from cache.

cache() - Method in interface uk.ac.ebi.pride.utilities.data.controller.cache.CachingStrategy

initialize the cache, it should clear the previous cache first, then createAttributedSequence the new cache.

cache - Variable in class uk.ac.ebi.pride.utilities.data.controller.cache.strategy.AbstractCachingStrategy

cache() - Method in class uk.ac.ebi.pride.utilities.data.controller.cache.strategy.MzDataCachingStrategy

For the moment, MzXmlCacheBuilder only caches spectrum ids and chromatogram ids.

cache() - Method in class uk.ac.ebi.pride.utilities.data.controller.cache.strategy.MzIdentMLCachingStrategy

Spectrum ids and identification ids are cached.

cache() - Method in class uk.ac.ebi.pride.utilities.data.controller.cache.strategy.MzMlCachingStrategy

For the moment, MzXmlCacheBuilder only caches spectrum ids and chromatogram ids.

cache() - Method in class uk.ac.ebi.pride.utilities.data.controller.cache.strategy.MzTabCachingStrategy

Spectrum ids and identification ids are cached.

cache() - Method in class uk.ac.ebi.pride.utilities.data.controller.cache.strategy.MzXmlCachingStrategy

For the moment, MzXmlCacheBuilder only caches spectrum ids and chromatogram ids.

cache() - Method in class uk.ac.ebi.pride.utilities.data.controller.cache.strategy.PeakCachingStrategy

For the moment, MzXmlCacheBuilder only caches spectrum ids and chromatogram ids.

cache() - Method in class uk.ac.ebi.pride.utilities.data.controller.cache.strategy.PrideXmlCachingStrategy

Spectrum ids and identification ids are cached.

CacheAccessor - Class in uk.ac.ebi.pride.utilities.data.controller.cache

CacheAccessor is the implementation of cache.

CacheAccessor() - Constructor for class uk.ac.ebi.pride.utilities.data.controller.cache.CacheAccessor

CacheAccessor constructor

cacheCvlookupMap(MzIdentMLUnmarshallerAdaptor) - Method in class uk.ac.ebi.pride.utilities.data.controller.cache.strategy.MzIdentMLCachingStrategy

CachedDataAccessController - Class in uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl

CachedDataAccessController is abstract class, which enables caching for DataAccessController.

CachedDataAccessController() - Constructor for class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

CachedDataAccessController(DataAccessMode) - Constructor for class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

CachedDataAccessController(Object, DataAccessMode) - Constructor for class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

CachedMap<K,V> - Class in uk.ac.ebi.pride.utilities.data.controller.cache

CachedMap is LRU map for caching.

CachedMap() - Constructor for class uk.ac.ebi.pride.utilities.data.controller.cache.CachedMap

CachedMap(int) - Constructor for class uk.ac.ebi.pride.utilities.data.controller.cache.CachedMap

CacheEntry - Enum in uk.ac.ebi.pride.utilities.data.controller.cache

CacheCategory provides a list of cache categories Each category defines the type of the data and the type of data structure to store the data.

cacheFragmentationTable(MzIdentMLUnmarshallerAdaptor) - Method in class uk.ac.ebi.pride.utilities.data.controller.cache.strategy.MzIdentMLCachingStrategy

cacheProtein(Protein) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.ReferencedIdentificationController

cacheSpectraData(MzIdentMLUnmarshallerAdaptor) - Method in class uk.ac.ebi.pride.utilities.data.controller.cache.strategy.MzIdentMLCachingStrategy

CachingStrategy - Interface in uk.ac.ebi.pride.utilities.data.controller.cache

Interface for building the cache.

checkMScontrollers(List<File>) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.ReferencedIdentificationController

Check if the ms File is supported and match with some of the par of the name in the Spectra Files This method should be used in high-throughput, when you add different files.

CHEMMOD - Static variable in class uk.ac.ebi.pride.utilities.data.exporters.MzIdentMLMzTabConverter

Chromatogram - Class in uk.ac.ebi.pride.utilities.data.core

Chromatogram object.

Chromatogram(Comparable, String, int, DataProcessing, int, List<BinaryDataArray>) - Constructor for class uk.ac.ebi.pride.utilities.data.core.Chromatogram

Chromatogram(ParamGroup, Comparable, String, int, DataProcessing, int, List<BinaryDataArray>) - Constructor for class uk.ac.ebi.pride.utilities.data.core.Chromatogram

CHROMATOGRAM_TYPE - Static variable in interface uk.ac.ebi.pride.utilities.data.controller.access.MzGraphDataAccess

fired when a chromatogram object has changed

clear(CacheEntry) - Method in interface uk.ac.ebi.pride.utilities.data.controller.cache.Cache

Clear all data assigned to CacheCategory

clear() - Method in interface uk.ac.ebi.pride.utilities.data.controller.cache.Cache

Clear all data

clear(CacheEntry) - Method in class uk.ac.ebi.pride.utilities.data.controller.cache.CacheAccessor

Clear a cache category

clear() - Method in class uk.ac.ebi.pride.utilities.data.controller.cache.CacheAccessor

Clear all cache

clearMSControllers() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.ReferencedIdentificationController

clone() - Method in class uk.ac.ebi.pride.utilities.data.core.Spectrum

close() - Method in interface uk.ac.ebi.pride.utilities.data.controller.DataAccessController

shutdown this controller, release all the resources.

close() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

close() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

Close data access controller by clearing the cache first

close() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzDataControllerImpl

Close data access controller by resetting the data reader first

close() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzIdentMLControllerImpl

close() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzMLControllerImpl

Close data access controller by resetting the data reader first

close() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzTabControllerImpl

close() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzXmlControllerImpl

Close data access controller by resetting the data reader first

close() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.PeakControllerImpl

Close data access controller by resetting the data reader first

close() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.PrideXmlControllerImpl

CollectionUtils - Class in uk.ac.ebi.pride.utilities.data.utils

A utility class to enhance Collections class in JDK

compareTo(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.PeptideSequence

compareTo(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.Sample

compress(byte[]) - Static method in class uk.ac.ebi.pride.utilities.data.utils.BinaryDataUtils

Compress byte array

Constants - Class in uk.ac.ebi.pride.utilities.data.utils

Constants contain a set of functions for SpectraData validation and also the constants used by mzTab and mzIdentML to reference the Ids and type file formats.

Constants.SpecFileFormat - Enum in uk.ac.ebi.pride.utilities.data.utils

An enum of the supported spectra file types

Constants.SpecIdFormat - Enum in uk.ac.ebi.pride.utilities.data.utils

Supported id format used in the spectrum file.

Contact - Class in uk.ac.ebi.pride.utilities.data.core

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.

Contact(Comparable, String) - Constructor for class uk.ac.ebi.pride.utilities.data.core.Contact

Contact(ParamGroup, Comparable, String) - Constructor for class uk.ac.ebi.pride.utilities.data.core.Contact

ContactRole - Class in uk.ac.ebi.pride.utilities.data.core

Contact Role is a class to define the role of an Specific Contact (Organization or Person)in the context of the Experiment a role is defined as CvParams () The role that a Contact plays in an organization or with respect to the associating class.

ContactRole(Contact, CvParam) - Constructor for class uk.ac.ebi.pride.utilities.data.core.ContactRole

containMGFTitleCVterm(List<CvParam>) - Static method in class uk.ac.ebi.pride.utilities.data.utils.MzIdentMLUtils

controller - Variable in class uk.ac.ebi.pride.utilities.data.controller.cache.strategy.AbstractCachingStrategy

convert(File) - Method in class uk.ac.ebi.pride.utilities.data.exporters.MzTabBedConverter

Performs the conversion of the mzTabFile into a bed file.

convertCvParamToCVParam(CvParam) - Static method in class uk.ac.ebi.pride.utilities.data.utils.MzTabUtils

This function takes the value of a CVParam and retrieve the corresponding CVParam

convertCvParamToCVParam(CvParam, Double) - Static method in class uk.ac.ebi.pride.utilities.data.utils.MzTabUtils

This function takes the value of a CVParam and retrieve the corresponding CVParam

convertMetadata() - Method in class uk.ac.ebi.pride.utilities.data.exporters.AbstractMzTabConverter

Generate Metadata

convertMetadata() - Method in class uk.ac.ebi.pride.utilities.data.exporters.MzIdentMLMzTabConverter

Returns the converted metadata, now including a check for chromosome information present, and if so, is set as a user param entry.

convertParamToCvParam(List<Param>) - Static method in class uk.ac.ebi.pride.utilities.data.utils.MzTabUtils

convertParamToCvParam(Param) - Static method in class uk.ac.ebi.pride.utilities.data.utils.MzTabUtils

convertProteinColumnFactory() - Method in class uk.ac.ebi.pride.utilities.data.exporters.AbstractMzTabConverter

Generate MZTabColumnFactory which maintain a couple of ProteinColumn

convertProteinColumnFactory() - Method in class uk.ac.ebi.pride.utilities.data.exporters.HQMzIdentMLMzTabConverter

convertProteinColumnFactory() - Method in class uk.ac.ebi.pride.utilities.data.exporters.MzIdentMLMzTabConverter

Generate MZTabColumnFactory which maintain a couple of ProteinColumn

convertProteinColumnFactory() - Method in class uk.ac.ebi.pride.utilities.data.exporters.PRIDEMzTabConverter

Generate MZTabColumnFactory which maintain a couple of ProteinColumn

convertPSMColumnFactory() - Method in class uk.ac.ebi.pride.utilities.data.exporters.AbstractMzTabConverter

Generate MZTabColumnFactory which maintain a couple of PSMColumn

convertPSMColumnFactory() - Method in class uk.ac.ebi.pride.utilities.data.exporters.MzIdentMLMzTabConverter

Generate MZTabColumnFactory which maintain a couple of PSMColumn

convertSoftwareNameToCvPram(String, String) - Static method in class uk.ac.ebi.pride.utilities.data.utils.PRIDEUtils

Conversion from PRIDE Software to CVParam using a general CVTerm like Analysis Software

convertStringListToUserParam(List<String>) - Static method in class uk.ac.ebi.pride.utilities.data.utils.MzTabUtils

convertStringToUserParam(String) - Static method in class uk.ac.ebi.pride.utilities.data.utils.MzTabUtils

convertUserParamToCVParam(UserParam) - Static method in class uk.ac.ebi.pride.utilities.data.utils.MzTabUtils

This function takes the value of a UserParam and returns a corresponding CVParam

createEmptyList() - Static method in class uk.ac.ebi.pride.utilities.data.utils.CollectionUtils

createListFromList(Collection<T>) - Static method in class uk.ac.ebi.pride.utilities.data.utils.CollectionUtils

createMapFromMap(Map<T, V>) - Static method in class uk.ac.ebi.pride.utilities.data.utils.MapUtils

CUSTOM_CHROM_INF_PARAM - Static variable in class uk.ac.ebi.pride.utilities.data.utils.MzTabUtils

CVLookup - Class in uk.ac.ebi.pride.utilities.data.core

CVLookup is referenced in every CvParam.

CVLookup(String, String, String, String) - Constructor for class uk.ac.ebi.pride.utilities.data.core.CVLookup

Constructor

CvParam - Class in uk.ac.ebi.pride.utilities.data.core

This object holds additional data in controlled vocabulary.

CvParam(String, String, String, String, String, String, String) - Constructor for class uk.ac.ebi.pride.utilities.data.core.CvParam

Constructor

CvUtilities - Class in uk.ac.ebi.pride.utilities.data.utils

This class is used for Metadata Terms transformation, including changes from one particular CVTerm to another type of CVTerm.

CvUtilities() - Constructor for class uk.ac.ebi.pride.utilities.data.utils.CvUtilities

D

DataAccessController - Interface in uk.ac.ebi.pride.utilities.data.controller

DataAccessController is an aggregate interface for data access.

DataAccessController.ContentCategory - Enum in uk.ac.ebi.pride.utilities.data.controller

ContentCategory defines the type of content a data access controller should have.

DataAccessController.Type - Enum in uk.ac.ebi.pride.utilities.data.controller

Type indicates the I/O of the data source.

DataAccessException - Exception in uk.ac.ebi.pride.utilities.data.controller

DataAccessException is thrown when there is an error during i/o via data access controller.

DataAccessException(String) - Constructor for exception uk.ac.ebi.pride.utilities.data.controller.DataAccessException

Create a DataAccessException using an specific text message

DataAccessException(String, Throwable) - Constructor for exception uk.ac.ebi.pride.utilities.data.controller.DataAccessException

Create a DataAccessException using an specific text message and the cause of the error

DataAccessMode - Enum in uk.ac.ebi.pride.utilities.data.controller

DataAccessMode is mainly to aid caching in data access controller, it can be use to cache the different objects of the source in memory or from the source.

DataAccessUtilities - Class in uk.ac.ebi.pride.utilities.data.controller

DataAccessUtilities provides methods for getting information out from the core objects.

DataBaseTranslation - Class in uk.ac.ebi.pride.utilities.data.core

DataBaseTranslation control and storage the information of Nucleotide Databases.

DataBaseTranslation(List<Integer>, List<IdentifiableParamGroup>) - Constructor for class uk.ac.ebi.pride.utilities.data.core.DataBaseTranslation

DataProcessing - Class in uk.ac.ebi.pride.utilities.data.core

Description of the way in which a List of Software were used.

DataProcessing(Comparable, List<ProcessingMethod>) - Constructor for class uk.ac.ebi.pride.utilities.data.core.DataProcessing

DataProcessing(Comparable, String, List<ProcessingMethod>) - Constructor for class uk.ac.ebi.pride.utilities.data.core.DataProcessing

DBSequence - Class in uk.ac.ebi.pride.utilities.data.core

A database sequence from the specified SearchDatabase (nucleic acid or amino acid).

DBSequence(String, SearchDataBase, String, String) - Constructor for class uk.ac.ebi.pride.utilities.data.core.DBSequence

DBSequence(ParamGroup, Comparable, String, int, String, SearchDataBase, String, String, String) - Constructor for class uk.ac.ebi.pride.utilities.data.core.DBSequence

decompress(byte[]) - Static method in class uk.ac.ebi.pride.utilities.data.utils.BinaryDataUtils

Decompress a compressed byte array

DecoyAccessionFilter - Class in uk.ac.ebi.pride.utilities.data.filter

Decoy filter for protein accession

DecoyAccessionFilter(DecoyAccessionFilter.Type, String) - Constructor for class uk.ac.ebi.pride.utilities.data.filter.DecoyAccessionFilter

DecoyAccessionFilter.Type - Enum in uk.ac.ebi.pride.utilities.data.filter

DEFAULT_CAPACITY - Static variable in class uk.ac.ebi.pride.utilities.data.controller.cache.CachedMap

DTA_EXT - Static variable in class uk.ac.ebi.pride.utilities.data.utils.Constants

DUP_PROTEINS_BEST_SEARCH_ENGINES_SCORE - Static variable in class uk.ac.ebi.pride.utilities.data.utils.PRIDEUtils

DUP_PROTEINS_HAD_QUANT - Static variable in class uk.ac.ebi.pride.utilities.data.utils.PRIDEUtils

DUP_PROTEINS_SEARCH_ENGINES - Static variable in class uk.ac.ebi.pride.utilities.data.utils.PRIDEUtils

DUP_PROTEINS_SEARCH_ENGINES_SCORES - Static variable in class uk.ac.ebi.pride.utilities.data.utils.PRIDEUtils

E

EMPAI - Static variable in class uk.ac.ebi.pride.utilities.data.exporters.PRIDEMzTabConverter

Enzyme - Class in uk.ac.ebi.pride.utilities.data.core

Enzyme used during the search in Databases.

Enzyme(String, String, boolean, int, int, ParamGroup, String) - Constructor for class uk.ac.ebi.pride.utilities.data.core.Enzyme

equals(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.BinaryDataArray

equals(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.ContactRole

equals(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.CVLookup

equals(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.CvParam

equals(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.DataBaseTranslation

equals(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.DataProcessing

equals(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.DBSequence

equals(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.Enzyme

equals(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.ExperimentMetaData

equals(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.ExperimentProtocol

equals(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.ExternalData

equals(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.Filter

equals(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.FragmentIon

equals(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.Gel

equals(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.Identifiable

equals(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.IdentifiableParamGroup

equals(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.IdentificationMetaData

equals(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.InstrumentComponent

equals(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.InstrumentConfiguration

equals(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.IonType

equals(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.MassTable

equals(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.Modification

equals(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.MzGraph

equals(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.MzGraphMetaData

equals(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.Organization

equals(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.Parameter

equals(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.ParamGroup

equals(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.Peptide

equals(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.PeptideEvidence

equals(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.PeptideSequence

equals(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.Person

equals(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.Precursor

equals(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.ProcessingMethod

equals(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.Protein

equals(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.Protocol

equals(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.Provider

equals(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.Quantification

equals(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.QuantitativeSample

equals(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.QuantScore

equals(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.Reference

equals(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.ReferenceableParamGroup

equals(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.Sample

equals(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.Scan

equals(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.ScanList

equals(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.ScanSetting

equals(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.Score

equals(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.SearchDataBase

equals(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.SearchModification

equals(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.Software

equals(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.SourceFile

equals(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.SpectraData

equals(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.Spectrum

equals(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentification

equals(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentificationList

equals(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentificationProtocol

equals(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.StudyVariable

equals(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.SubstitutionModification

equals(Object) - Method in class uk.ac.ebi.pride.utilities.data.core.UserParam

ExperimentMetaData - Class in uk.ac.ebi.pride.utilities.data.core

General descriptions shared or used for the whole file.

ExperimentMetaData(ParamGroup, Comparable, String, String, String, List<Sample>, List<Software>, List<Person>, List<SourceFile>, Provider, List<Organization>, List<Reference>, Date, Date, ExperimentProtocol) - Constructor for class uk.ac.ebi.pride.utilities.data.core.ExperimentMetaData

ExperimentMetaData(ParamGroup, Comparable, String, String, String, List<Sample>, List<Software>, List<Person>, List<SourceFile>, Provider, List<Organization>, List<Reference>, Date, Date, ExperimentProtocol, List<SpectraData>) - Constructor for class uk.ac.ebi.pride.utilities.data.core.ExperimentMetaData

ExperimentMetaData(ParamGroup, Comparable, String, String, String, List<Sample>, List<Software>, List<Person>, List<SourceFile>, Provider, List<Organization>, List<Reference>, Date, Date, ExperimentProtocol, List<SpectraData>, Map<Comparable, StudyVariable>) - Constructor for class uk.ac.ebi.pride.utilities.data.core.ExperimentMetaData

This controller is specially designed for mzTab files that contains Study Variables with description, etc.

ExperimentProtocol - Class in uk.ac.ebi.pride.utilities.data.core

Protocol used to generate the dataset, added by PRIDE XML 2.0.

ExperimentProtocol(Comparable, String) - Constructor for class uk.ac.ebi.pride.utilities.data.core.ExperimentProtocol

ExperimentProtocol(ParamGroup, String, String, List<ParamGroup>) - Constructor for class uk.ac.ebi.pride.utilities.data.core.ExperimentProtocol

ExternalData - Class in uk.ac.ebi.pride.utilities.data.core

Data external to the XML instance document.

ExternalData(String, String, String, CvParam, String) - Constructor for class uk.ac.ebi.pride.utilities.data.core.ExternalData

Constructor of External Data Objects

F

fillData() - Method in class uk.ac.ebi.pride.utilities.data.exporters.AbstractMzTabConverter

Fill records into model.

fillData() - Method in class uk.ac.ebi.pride.utilities.data.exporters.HQMzIdentMLMzTabConverter

Fill records into model.

fillData() - Method in class uk.ac.ebi.pride.utilities.data.exporters.MzIdentMLMzTabConverter

Fill records into model.

fillData() - Method in class uk.ac.ebi.pride.utilities.data.exporters.PRIDEMzTabConverter

Fill the data from the file, proteins and PSMs

Filter - Class in uk.ac.ebi.pride.utilities.data.core

Filter controlled the database filters with CVParams and UserParams.

Filter(ParamGroup, ParamGroup, ParamGroup) - Constructor for class uk.ac.ebi.pride.utilities.data.core.Filter

filter(List<Peptide>) - Method in class uk.ac.ebi.pride.utilities.data.filter.NoPeptideFilter

filter(List<Protein>) - Method in class uk.ac.ebi.pride.utilities.data.filter.NoProteinFilter

filter(List<Peptide>) - Method in interface uk.ac.ebi.pride.utilities.data.filter.PeptideFilter

filter(List<Protein>) - Method in interface uk.ac.ebi.pride.utilities.data.filter.ProteinFilter

filter(List<Peptide>) - Method in class uk.ac.ebi.pride.utilities.data.filter.RankOnePeptideFilter

filter(List<Peptide>) - Method in class uk.ac.ebi.pride.utilities.data.filter.ThresholdPeptideFilter

filter(List<Protein>) - Method in class uk.ac.ebi.pride.utilities.data.filter.ThresholdProteinFilter

FragmentIon - Class in uk.ac.ebi.pride.utilities.data.core

FragmentIon stores details about peptide fragment ion information.

FragmentIon(ParamGroup) - Constructor for class uk.ac.ebi.pride.utilities.data.core.FragmentIon

Constructor

G

Gel - Class in uk.ac.ebi.pride.utilities.data.core

Gel is a class to Describe the Gel Spot for each Protein.

Gel(ParamGroup, String, Double, Double, Double, Double) - Constructor for class uk.ac.ebi.pride.utilities.data.core.Gel

Constructor

GEL_COORDINATES - Static variable in class uk.ac.ebi.pride.utilities.data.exporters.PRIDEMzTabConverter

GEL_IDENTIFIER - Static variable in class uk.ac.ebi.pride.utilities.data.exporters.PRIDEMzTabConverter

GEL_SPOTIDENTIFIER - Static variable in class uk.ac.ebi.pride.utilities.data.exporters.PRIDEMzTabConverter

generateAccession(Protein) - Static method in class uk.ac.ebi.pride.utilities.data.exporters.AbstractMzTabConverter

generateAccession(Peptide) - Static method in class uk.ac.ebi.pride.utilities.data.exporters.AbstractMzTabConverter

generateHash(String) - Static method in class uk.ac.ebi.pride.utilities.data.utils.MD5Utils

Generate md5 hash from a given string

get(CacheEntry, Object) - Method in interface uk.ac.ebi.pride.utilities.data.controller.cache.Cache

Get data from cache using CacheCategory and key

get(CacheEntry) - Method in interface uk.ac.ebi.pride.utilities.data.controller.cache.Cache

Get data from cache using CacheCategory

get(CacheEntry, Object) - Method in class uk.ac.ebi.pride.utilities.data.controller.cache.CacheAccessor

Get the stored data using a key.

get(CacheEntry) - Method in class uk.ac.ebi.pride.utilities.data.controller.cache.CacheAccessor

Get the stored data set using a type.

getAccession() - Method in class uk.ac.ebi.pride.utilities.data.core.CvParam

getAccession() - Method in class uk.ac.ebi.pride.utilities.data.core.DBSequence

getAccessionVersion() - Method in class uk.ac.ebi.pride.utilities.data.core.DBSequence

getActivation() - Method in class uk.ac.ebi.pride.utilities.data.core.Precursor

getAdditional() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getAdditional() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzIdentMLControllerImpl

Additional is a concept that comes from PRIDE XML Files.

getAdditional() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzMLControllerImpl

In case of mzMl the additional parameters are related with the getFileContent This are a set of CVTerms related with the Content in the MzML File.

getAdditional() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzTabControllerImpl

Get custom parameters

getAdditional() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzXmlControllerImpl

Get additional details, the mzXML is like mzML the Additional is the combination of FileContent and StartTime.

getAdditional() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.PrideXmlControllerImpl

Get additional parameters

getAdditional() - Method in class uk.ac.ebi.pride.utilities.data.core.ExperimentMetaData

getAdditionalParams() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzTabUnmarshallerAdaptor

Retrieve a general description from the file

getAddress() - Method in class uk.ac.ebi.pride.utilities.data.core.CVLookup

getAdmin() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzDataUnmarshallerAdaptor

getAffiliation() - Method in class uk.ac.ebi.pride.utilities.data.core.Person

getAllowedFrames() - Method in class uk.ac.ebi.pride.utilities.data.core.DataBaseTranslation

getAllProteinAccessions() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzTabUnmarshallerAdaptor

Retrieve the Map of proteins with the corresponding list of PSMs for each protein.

getAllProteins() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzTabUnmarshallerAdaptor

getAllScoreValues() - Method in class uk.ac.ebi.pride.utilities.data.core.Score

Get all peptide scores, this will produce a sequential order list

getAmbiguousResidues() - Method in class uk.ac.ebi.pride.utilities.data.core.MassTable

getAminoAcidByPosition(int) - Method in class uk.ac.ebi.pride.utilities.data.core.PeptideSequence

getAminoAcidList() - Method in class uk.ac.ebi.pride.utilities.data.core.PeptideSequence

getAnalysisParam() - Method in class uk.ac.ebi.pride.utilities.data.core.Protocol

getAnalysisSoftware() - Method in class uk.ac.ebi.pride.utilities.data.core.Protocol

getAnalyzer() - Method in class uk.ac.ebi.pride.utilities.data.core.InstrumentConfiguration

getAssay() - Method in class uk.ac.ebi.pride.utilities.data.core.AbundanceAssay

getAssayAbundance() - Method in class uk.ac.ebi.pride.utilities.data.core.QuantScore

Returns the Assay Abundance

getAssays() - Method in class uk.ac.ebi.pride.utilities.data.core.StudyVariable

getAssays() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzTabUnmarshallerAdaptor

getAuthors() - Method in class uk.ac.ebi.pride.utilities.data.core.Reference

getAvailablePeptideLevelScores() - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.PeptideDataAccess

Get a collection of peptide scores in cv term reference format

getAvailablePeptideLevelScores() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getAvailablePeptideLevelScores() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

This function return the possible peptide scores in the Source.

getAvailableProteinLevelScores() - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.ProteinDataAccess

get a list of present protein scores in CV terms

getAvailableProteinLevelScores() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getAvailableProteinLevelScores() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

This function return the possible protein scores in the Source.

getAvailableQuantPeptideLevelScores() - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.QuantDataAccess

Get a collection of peptide scores in cv term reference format

getAvailableQuantPeptideLevelScores() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getAvgMassDelta() - Method in class uk.ac.ebi.pride.utilities.data.core.Modification

Get Average Mass Delta List

getAvgMassDelta() - Method in class uk.ac.ebi.pride.utilities.data.core.SubstitutionModification

getBinaryDataArray(String) - Method in class uk.ac.ebi.pride.utilities.data.core.MzGraph

Get either m/z array or intensity array

getBinaryDataArrays() - Method in class uk.ac.ebi.pride.utilities.data.core.MzGraph

getCache() - Method in class uk.ac.ebi.pride.utilities.data.controller.cache.strategy.AbstractCachingStrategy

getCache() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

getCachingStrategy() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

getCalculatedMassToCharge() - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentification

getCalculatedPI() - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentification

getCellLine(int) - Method in class uk.ac.ebi.pride.utilities.data.core.QuantitativeSample

Get cell line cv param of a sub sample with given index

getCharge() - Method in class uk.ac.ebi.pride.utilities.data.core.FragmentIon

getCharge() - Method in class uk.ac.ebi.pride.utilities.data.core.IonType

getChargeState() - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentification

getChromatogramById(Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.MzGraphDataAccess

Get a Chromatogram object

getChromatogramById(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

Get chromatogram object form cache It uses cache by default

getChromatogramById(Comparable, boolean) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

Get chromatogram using a chromatogram id, gives the option to choose whether to use cache.

getChromatogramById(Comparable, boolean) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzDataControllerImpl

Get chromatogram using a chromatogram id, gives the option to choose whether to use cache.

getChromatogramById(Comparable, boolean) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzMLControllerImpl

Get chromatogram using a chromatogram id, gives the option to choose whether to use cache.

getChromatogramById(Comparable, boolean) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzXmlControllerImpl

Get chromatogram using a chromatogram id, gives the option to choose whether to use cache.

getChromatogramById(Comparable, boolean) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.PeakControllerImpl

Get chromatogram using a chromatogram id, gives the option to choose whether to use cache.

getChromatogramByIndex(int, int) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.MzGraphDataAccess

Get a collection of chromatograms by its index and offset.

getChromatogramByIndex(int, int) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getChromatogramIds() - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.MzGraphDataAccess

Get a collection of chromatogram ids.

getChromatogramIds() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

Get chromatogram ids from cache

getChromatogramIds() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzMLUnmarshallerAdaptor

getChromatogramIndex(Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.MzGraphDataAccess

Get the index of a chromatogram by its id

getChromatogramIndex(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getContact() - Method in class uk.ac.ebi.pride.utilities.data.core.ContactRole

getContact() - Method in class uk.ac.ebi.pride.utilities.data.core.Provider

getContact() - Method in class uk.ac.ebi.pride.utilities.data.core.Software

getContactInfo() - Method in class uk.ac.ebi.pride.utilities.data.core.Person

getContactRoles() - Method in class uk.ac.ebi.pride.utilities.data.core.Sample

getContacts() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzTabUnmarshallerAdaptor

getContentCategories() - Method in interface uk.ac.ebi.pride.utilities.data.controller.DataAccessController

Return a collection of content categories

getContentCategories() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getController() - Method in class uk.ac.ebi.pride.utilities.data.controller.cache.strategy.AbstractCachingStrategy

getCreationDate() - Method in class uk.ac.ebi.pride.utilities.data.core.ExperimentMetaData

getCreationDate() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzIdentMLUnmarshallerAdaptor

getCreationDate() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzMLUnmarshallerAdaptor

getCriteria() - Method in class uk.ac.ebi.pride.utilities.data.filter.DecoyAccessionFilter

getcTermGain() - Method in class uk.ac.ebi.pride.utilities.data.core.Enzyme

getCustomization() - Method in class uk.ac.ebi.pride.utilities.data.core.Software

getCvLabel() - Method in class uk.ac.ebi.pride.utilities.data.core.CVLookup

getCvList() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzIdentMLUnmarshallerAdaptor

getCVList() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzMLUnmarshallerAdaptor

getCvLookupID() - Method in class uk.ac.ebi.pride.utilities.data.core.CvParam

getCvLookups() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzDataControllerImpl

Get a list of cvlookups, these are not cached

getCvLookups() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzIdentMLControllerImpl

Get a list of cv lookup objects.

getCvLookups() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzMLControllerImpl

Get a list of cvlookups, these are not cached

getCvLookups() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.PrideXmlControllerImpl

Get a list of cv lookup objects.

getCvLookups() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzDataUnmarshallerAdaptor

getCvParam(ParamGroup, String, String) - Static method in class uk.ac.ebi.pride.utilities.data.controller.DataAccessUtilities

Get cv param by accession number and cv label.

getCvParam(String, String, String, String) - Static method in class uk.ac.ebi.pride.utilities.data.controller.DataAccessUtilities

Create a List of Cv Params

getCvParams() - Method in class uk.ac.ebi.pride.utilities.data.core.ParamGroup

This method return a List of CvParam, the result List in a new Instance of the current List of CvParam

getCvParams() - Method in class uk.ac.ebi.pride.utilities.data.core.SearchModification

getCVTermFromCvReference(CvTermReference, String) - Static method in class uk.ac.ebi.pride.utilities.data.utils.CvUtilities

getDatabaseName(List<CvParam>, List<UserParam>) - Method in class uk.ac.ebi.pride.utilities.data.exporters.MzIdentMLMzTabConverter

getDatabases() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzTabUnmarshallerAdaptor

getDataBaseTranslation() - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentificationProtocol

getDataFormatFromFileExtension(SpectraData) - Static method in class uk.ac.ebi.pride.utilities.data.utils.Constants

Return the Spectrum File format beased onf the SpectraData object name

getDataProcessing() - Method in class uk.ac.ebi.pride.utilities.data.core.BinaryDataArray

getDataProcessing() - Method in class uk.ac.ebi.pride.utilities.data.core.MzGraph

getDataProcessing() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzDataUnmarshallerAdaptor

getDataProcessing() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzXmlUnmarshallerAdaptor

getDataProcessingList() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzMLUnmarshallerAdaptor

getDataProcessings() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzDataControllerImpl

Get a list of data processings by checking the cache first

getDataProcessings() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzMLControllerImpl

Get a list of data processings by checking the cache first

getDataProcessings() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzXmlControllerImpl

Get a list of data processings by checking the cache first

getDataProcessings() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.PrideXmlControllerImpl

Get a list of data processing objects

getDataProcessings() - Method in class uk.ac.ebi.pride.utilities.data.core.MzGraphMetaData

getDataSoftwares() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzTabUnmarshallerAdaptor

getDataStructType() - Method in enum uk.ac.ebi.pride.utilities.data.controller.cache.CacheEntry

getDbSequence() - Method in class uk.ac.ebi.pride.utilities.data.core.PeptideEvidence

getDbSequence() - Method in class uk.ac.ebi.pride.utilities.data.core.Protein

getDBSequenceById(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzIdentMLUnmarshallerAdaptor

getDefaultArrayLength() - Method in class uk.ac.ebi.pride.utilities.data.core.MzGraph

getDefaultScore() - Method in class uk.ac.ebi.pride.utilities.data.core.Score

Get the Default score for Search Engine

* @return score

getDefaultSearchEngine() - Method in class uk.ac.ebi.pride.utilities.data.core.Score

Get Default Search Engine for Scores.

getDescription(int) - Method in class uk.ac.ebi.pride.utilities.data.core.QuantitativeSample

Get description cv param of a sub sample with given index

getDescription() - Method in class uk.ac.ebi.pride.utilities.data.core.SearchDataBase

getDescription() - Method in class uk.ac.ebi.pride.utilities.data.core.StudyVariable

getDescriptionFromCVParams(List<CvParam>) - Method in class uk.ac.ebi.pride.utilities.data.exporters.MzIdentMLMzTabConverter

getDetector() - Method in class uk.ac.ebi.pride.utilities.data.core.InstrumentConfiguration

getDisease(int) - Method in class uk.ac.ebi.pride.utilities.data.core.QuantitativeSample

Get disease cv param of a sub sample with given index

getDoi() - Method in class uk.ac.ebi.pride.utilities.data.core.Reference

getDoubleArray() - Method in class uk.ac.ebi.pride.utilities.data.core.BinaryDataArray

getEditor() - Method in class uk.ac.ebi.pride.utilities.data.core.Reference

getElement(Collection<T>, int) - Static method in class uk.ac.ebi.pride.utilities.data.utils.CollectionUtils

getEndPosition() - Method in class uk.ac.ebi.pride.utilities.data.core.PeptideEvidence

getEnzymeName() - Method in class uk.ac.ebi.pride.utilities.data.core.Enzyme

getEnzymes() - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentificationProtocol

getExclude() - Method in class uk.ac.ebi.pride.utilities.data.core.Filter

getExpAccession() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzTabUnmarshallerAdaptor

getExperimentalMassToCharge() - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentification

getExperimentMetaData() - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.MetaDataAccess

Get a meta object

getExperimentMetaData() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getExperimentMetaData() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

Get the Experiment Meta Data

getExperimentMetaData() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzDataControllerImpl

getExperimentMetaData() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzIdentMLControllerImpl

Get meta data related to this experiment

getExperimentMetaData() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzMLControllerImpl

getExperimentMetaData() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzTabControllerImpl

Get meta data related to this experiment

getExperimentMetaData() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzXmlControllerImpl

The Experiment Metadata supported for MzXML is only the name of the files, the type of the file, the instrument, the person contacts.

getExperimentMetaData() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.PeakControllerImpl

getExperimentMetaData() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.PrideXmlControllerImpl

Get meta data related to this experiment

getExpTitle() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzTabUnmarshallerAdaptor

getExternalFormatDocumentationURI() - Method in class uk.ac.ebi.pride.utilities.data.core.ExternalData

getExternalFormatDocumentationURI() - Method in class uk.ac.ebi.pride.utilities.data.core.SourceFile

getExternalSpecRef() - Method in class uk.ac.ebi.pride.utilities.data.core.Scan

getExternalSpectrumID() - Method in class uk.ac.ebi.pride.utilities.data.core.Precursor

getFileContent() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzDataControllerImpl

File Content is extra parameters related with Source Files in case of mzData.

getFileContent() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzMLControllerImpl

This summarizes the different types of spectra that can be expected in the file.

getFileContent() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzXmlControllerImpl

This will be summarize the different parent file formats.

getFileContent() - Method in class uk.ac.ebi.pride.utilities.data.core.ExperimentMetaData

getFileContent() - Method in class uk.ac.ebi.pride.utilities.data.core.MzGraphMetaData

getFileDescription() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzMLUnmarshallerAdaptor

getFileFormat() - Method in class uk.ac.ebi.pride.utilities.data.core.ExternalData

getFileFormat() - Method in class uk.ac.ebi.pride.utilities.data.core.SourceFile

getFileFormatMGFTitle() - Static method in class uk.ac.ebi.pride.utilities.data.utils.MzIdentMLUtils

This CvParam override the current File format CVparam for those files that are native wiff but are mgf using title reference.

getFileType(File) - Static method in class uk.ac.ebi.pride.utilities.data.utils.Constants

Check the file type

getFileTypeSupported(SpectraData) - Static method in class uk.ac.ebi.pride.utilities.data.utils.Constants

Return the set of file format supported for an ambiguous SpectraData Object

getFilters() - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentificationProtocol

getFilterType() - Method in class uk.ac.ebi.pride.utilities.data.core.Filter

getFirstname() - Method in class uk.ac.ebi.pride.utilities.data.core.Person

getFragmentation() - Method in class uk.ac.ebi.pride.utilities.data.core.Peptide

getFragmentation() - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentification

getFragmentationTable() - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentificationList

getFragmentationTable() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzIdentMLUnmarshallerAdaptor

getFragmentIons(Comparable, Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.PeptideDataAccess

Get the fragment ions assigned to the peptide.

getFragmentIons(Comparable, Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getFragmentTolerance() - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentificationProtocol

getFrame() - Method in class uk.ac.ebi.pride.utilities.data.core.PeptideEvidence

getFullName() - Method in class uk.ac.ebi.pride.utilities.data.core.CVLookup

getFullReference() - Method in class uk.ac.ebi.pride.utilities.data.core.Reference

getGel() - Method in class uk.ac.ebi.pride.utilities.data.core.Protein

getGelLink() - Method in class uk.ac.ebi.pride.utilities.data.core.Gel

getGOTerm(int) - Method in class uk.ac.ebi.pride.utilities.data.core.QuantitativeSample

Get GO cv param of a sub sample with given index

getId() - Method in class uk.ac.ebi.pride.utilities.data.core.Identifiable

getId() - Method in class uk.ac.ebi.pride.utilities.data.core.IdentifiableParamGroup

getId() - Method in class uk.ac.ebi.pride.utilities.data.core.InstrumentConfiguration

getId() - Method in class uk.ac.ebi.pride.utilities.data.core.ScanSetting

getIdentificationById(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzIdentMLUnmarshallerAdaptor

getIdentificationMetaData() - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.MetaDataAccess

Get the MetaData Information for Identification Object.

getIdentificationMetaData() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getIdentificationMetaData() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

Get Identification Meta Data

getIdentificationMetaData() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzDataControllerImpl

getIdentificationMetaData() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzIdentMLControllerImpl

The IdentificationMetadata is a Combination of SpectrumIdentificationProtocol, a Protein Protocol and finally the Databases used in the Experiment.

getIdentificationMetaData() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzMLControllerImpl

The mzML do not contains Identification Metadata, just Spectrum Information

getIdentificationMetaData() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzTabControllerImpl

getIdentificationMetaData() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzXmlControllerImpl

The identification MetaData is not supported for mzXML files

getIdentificationMetaData() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.PeakControllerImpl

getIdentificationMetaData() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.PrideXmlControllerImpl

getIdMzData() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzDataUnmarshallerAdaptor

getInBatch(CacheEntry, Collection) - Method in interface uk.ac.ebi.pride.utilities.data.controller.cache.Cache

Get data from cache using CacheCategory and a collections of keys

getInBatch(CacheEntry, Collection) - Method in class uk.ac.ebi.pride.utilities.data.controller.cache.CacheAccessor

Get a collection of values using a collection of keys.

getInclude() - Method in class uk.ac.ebi.pride.utilities.data.core.Filter

getIndex() - Method in class uk.ac.ebi.pride.utilities.data.core.IonType

getIndex() - Method in class uk.ac.ebi.pride.utilities.data.core.MzGraph

getIndex(Collection<T>, T) - Static method in class uk.ac.ebi.pride.utilities.data.utils.CollectionUtils

Get the index of a element in a collection

getInstrument() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzDataUnmarshallerAdaptor

getInstrument() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzTabUnmarshallerAdaptor

getInstrumentConfiguration() - Method in class uk.ac.ebi.pride.utilities.data.core.Scan

getInstrumentConfigurationList() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzMLUnmarshallerAdaptor

getInstrumentConfigurations() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzDataControllerImpl

Get a list of instrument configurations by checking the cache first

getInstrumentConfigurations() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzMLControllerImpl

Get a list of instrument configurations by checking the cache first

getInstrumentConfigurations() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzTabControllerImpl

getInstrumentConfigurations() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzXmlControllerImpl

Get a list of instrument configurations.

getInstrumentConfigurations() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.PrideXmlControllerImpl

Get a list of instruments

getInstrumentConfigurations() - Method in class uk.ac.ebi.pride.utilities.data.core.MzGraphMetaData

getIntensity() - Method in class uk.ac.ebi.pride.utilities.data.core.FragmentIon

getIntensityArray() - Method in class uk.ac.ebi.pride.utilities.data.core.Chromatogram

getIntensityBinaryDataArray() - Method in class uk.ac.ebi.pride.utilities.data.core.Spectrum

getIonType() - Method in class uk.ac.ebi.pride.utilities.data.core.FragmentIon

getIonTypeAccession() - Method in class uk.ac.ebi.pride.utilities.data.core.FragmentIon

getIsolationWindow() - Method in class uk.ac.ebi.pride.utilities.data.core.Precursor

getIsotopeLabellingDeviation() - Method in class uk.ac.ebi.pride.utilities.data.core.Quantification

Get a list of standard deviations of isotope labelling

getIsotopeLabellingDeviation(int) - Method in class uk.ac.ebi.pride.utilities.data.core.Quantification

Get the standard deviation of a given sub sample

getIsotopeLabellingError() - Method in class uk.ac.ebi.pride.utilities.data.core.Quantification

Get a list of standard errors of isotope labelling

getIsotopeLabellingError(int) - Method in class uk.ac.ebi.pride.utilities.data.core.Quantification

Get the standard error of a given sub sample

getIsotopeLabellingMethod() - Method in class uk.ac.ebi.pride.utilities.data.core.Quantification

Get the isotope labelling method

getIsotopeLabellingQuantMethods() - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.QuantDataAccess

Get all the isotope labelling methods

getIsotopeLabellingQuantMethods() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getIsotopeLabellingResult(int) - Method in class uk.ac.ebi.pride.utilities.data.core.Quantification

Get the result of isotope labelling according to a given index

getIsotopeLabellingResults() - Method in class uk.ac.ebi.pride.utilities.data.core.Quantification

Get a list of results of isotope labelling

getIssue() - Method in class uk.ac.ebi.pride.utilities.data.core.Reference

getLabelFreeMethods() - Method in class uk.ac.ebi.pride.utilities.data.core.Quantification

Get a list of label free methods which are present

getLabelFreeQuantMethods() - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.QuantDataAccess

Get all the label free methods used

getLabelFreeQuantMethods() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getLabelFreeResults(Collection<QuantCvTermReference>) - Method in class uk.ac.ebi.pride.utilities.data.core.Quantification

Get the results of label free quantification methods

getLastElement(Collection<T>) - Static method in class uk.ac.ebi.pride.utilities.data.utils.CollectionUtils

getLastname() - Method in class uk.ac.ebi.pride.utilities.data.core.Person

getLength() - Method in class uk.ac.ebi.pride.utilities.data.core.DBSequence

getLocation() - Method in class uk.ac.ebi.pride.utilities.data.core.ExternalData

getLocation() - Method in class uk.ac.ebi.pride.utilities.data.core.FragmentIon

getLocation() - Method in class uk.ac.ebi.pride.utilities.data.core.Modification

Get Location of the Modification

getLocation() - Method in class uk.ac.ebi.pride.utilities.data.core.SubstitutionModification

getMail() - Method in class uk.ac.ebi.pride.utilities.data.core.Organization

getMailFromCvParam(ParamGroup) - Static method in class uk.ac.ebi.pride.utilities.data.utils.CvUtilities

getMassDelta() - Method in class uk.ac.ebi.pride.utilities.data.core.SearchModification

getMassError() - Method in class uk.ac.ebi.pride.utilities.data.core.FragmentIon

getMassIntensityMap() - Method in class uk.ac.ebi.pride.utilities.data.core.Spectrum

getMassTable() - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentification

getMassTables() - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentificationProtocol

getMeasures() - Method in class uk.ac.ebi.pride.utilities.data.core.IonType

getMetadata() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzTabUnmarshallerAdaptor

getMGFTitleReference(String) - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzIdentMLUnmarshallerAdaptor

getMidInitials() - Method in class uk.ac.ebi.pride.utilities.data.core.Person

getMinDistance() - Method in class uk.ac.ebi.pride.utilities.data.core.Enzyme

getMissedCleavages() - Method in class uk.ac.ebi.pride.utilities.data.core.Enzyme

getModDatabase() - Method in class uk.ac.ebi.pride.utilities.data.core.Modification

Get Modification DataBase Name

getModDatabaseVersion() - Method in class uk.ac.ebi.pride.utilities.data.core.Modification

Get Modification DataBase Version

getMode() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

Get the runtime mode

getModifications() - Method in class uk.ac.ebi.pride.utilities.data.core.Peptide

getModifications() - Method in class uk.ac.ebi.pride.utilities.data.core.PeptideSequence

getModifications() - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentification

getMolecularWeight() - Method in class uk.ac.ebi.pride.utilities.data.core.Gel

getMonoisotopicMassDelta() - Method in class uk.ac.ebi.pride.utilities.data.core.Modification

Get monoisotopic Mass Delta List

getMonoisotopicMassDelta() - Method in class uk.ac.ebi.pride.utilities.data.core.SubstitutionModification

getMRunMap() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzTabUnmarshallerAdaptor

getMsInstruments() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzXmlUnmarshallerAdaptor

getMsLevel(Spectrum) - Static method in class uk.ac.ebi.pride.utilities.data.controller.DataAccessUtilities

Get ms level of a spectrum

getMsLevel() - Method in class uk.ac.ebi.pride.utilities.data.core.MassTable

getMz() - Method in class uk.ac.ebi.pride.utilities.data.core.FragmentIon

getMzBinaryDataArray() - Method in class uk.ac.ebi.pride.utilities.data.core.Spectrum

getMzGraphMetaData() - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.MetaDataAccess

Get MetaData Information for Spectrum Experiment Object

getMzGraphMetaData() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getMzGraphMetaData() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

Get MzGraph Meta Data.

getMzGraphMetaData() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzDataControllerImpl

getMzGraphMetaData() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzIdentMLControllerImpl

MzidemtML files will support in the future Spectra MetaData if is present PRIDE Objects, also by other file Formats.

getMzGraphMetaData() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzMLControllerImpl

Get the Spectrum Metadata, the ScanSettings, The DataProcessing, and Instrument Configurations.

getMzGraphMetaData() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzTabControllerImpl

getMzGraphMetaData() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzXmlControllerImpl

Get the MzGraphMetaData support the dataProcessing Metadata, the Instrument Configuration and do not contains scanSetting information for mzXML files.

getMzGraphMetaData() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.PeakControllerImpl

getMzGraphMetaData() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.PrideXmlControllerImpl

getMzIdentMLName() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzIdentMLUnmarshallerAdaptor

getName() - Method in interface uk.ac.ebi.pride.utilities.data.controller.DataAccessController

Get the display name for this controller, for GUI

getName() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getName() - Method in class uk.ac.ebi.pride.utilities.data.core.Identifiable

getName() - Method in class uk.ac.ebi.pride.utilities.data.core.IdentifiableParamGroup

getName() - Method in class uk.ac.ebi.pride.utilities.data.core.Parameter

getNameDatabase() - Method in class uk.ac.ebi.pride.utilities.data.core.SearchDataBase

getnTermGain() - Method in class uk.ac.ebi.pride.utilities.data.core.Enzyme

getNumberOfChromatograms() - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.MzGraphDataAccess

Get number of chromatograms

getNumberOfChromatograms() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getNumberOfFragmentIons(Comparable, Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.PeptideDataAccess

Get the number of fragment ions for a peptide

getNumberOfFragmentIons(Comparable, Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getNumberOfFragmentIons(Comparable, Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

Get the number of fragment ions in a given peptide

getNumberOfIdentifiedSpectra() - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.MzGraphDataAccess

Get the number of identified spectra.

getNumberOfIdentifiedSpectra() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getNumberOfIdentifiedSpectra() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.ReferencedIdentificationController

Get the number of Spectra Identified in the DataAccessController

getNumberOfPeaks(Spectrum) - Static method in class uk.ac.ebi.pride.utilities.data.controller.DataAccessUtilities

Count the number of peaks of a spectrum

getNumberOfPeptides() - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.PeptideDataAccess

Get the total number of peptides

getNumberOfPeptides(Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.PeptideDataAccess

Get the number peptides of a identification.

getNumberOfPeptides(Protein) - Static method in class uk.ac.ebi.pride.utilities.data.controller.DataAccessUtilities

Convenient method for number of peptides

getNumberOfPeptides(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getNumberOfPeptides() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getNumberOfPeptides(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

Get number of peptides using identification id.

getNumberOfPeptides() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzIdentMLControllerImpl

Get the number of peptides.

getNumberOfPeptides() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzTabControllerImpl

Get the number of peptides.

getNumberOfPeptides() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.PrideXmlControllerImpl

Get the number of peptides.

getNumberOfPeptides(int) - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzTabUnmarshallerAdaptor

getNumberOfPeptidesByRank(int) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.PeptideDataAccess

Get the total number of peptides of a given Rank

getNumberOfPeptidesByRank(int) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getNumberOfPeptidesByRank(int) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzTabControllerImpl

Get the number of peptides by Rank, in MzTab all peptides are rank 1.

getNumberOfPeptidesByRank(int) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.PrideXmlControllerImpl

Get the number of peptides by Rank, in PRIDE XML all peptides are rank 1.

getNumberOfProteinAmbiguityGroups() - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.ProteinGroupDataAccess

Get the total number of protein ambiguity groups

getNumberOfProteinAmbiguityGroups() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getNumberOfProteins() - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.ProteinDataAccess

Get the total number of protein identifications.

getNumberOfProteins() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getNumberOfPTMs(Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.PeptideDataAccess

Get the number of ptms of a identification.

getNumberOfPTMs(Comparable, Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.PeptideDataAccess

Get the number of PTMs for a peptide

getNumberOfPTMs(Protein) - Static method in class uk.ac.ebi.pride.utilities.data.controller.DataAccessUtilities

Get the number of post translational modifications within a protein identification

getNumberOfPTMs(Peptide) - Static method in class uk.ac.ebi.pride.utilities.data.controller.DataAccessUtilities

Get the number of the modification of a peptide

getNumberOfPTMs(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getNumberOfPTMs(Comparable, Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getNumberOfPTMs(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

Get number of ptms using identification id.

getNumberOfPTMs(Comparable, Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

Get number of ptms using peptide id.

getNumberOfQuantPeptides() - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.QuantDataAccess

Get the total number of peptides

getNumberOfQuantPeptides(Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.QuantDataAccess

Get the number peptides of a identification.

getNumberOfQuantPeptides() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getNumberOfQuantPeptides(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getNumberOfQuantPTMs(Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.QuantDataAccess

Get the number of ptms of a identification.

getNumberOfQuantPTMs(Comparable, Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.QuantDataAccess

Get the number of PTMs for a peptide

getNumberOfQuantPTMs(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getNumberOfQuantPTMs(Comparable, Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getNumberOfReagents() - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.QuantDataAccess

Get the number of reagents

getNumberOfReagents() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getNumberOfSpectra() - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.MzGraphDataAccess

Get the number of spectra.

getNumberOfSpectra() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getNumberOfSpectra() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.ReferencedIdentificationController

Return the number of Spectra in the DataAccessController

getNumberOfSpectrabySpectraData(SpectraData) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.ReferencedIdentificationController

Get the number of Spectra by File associated with the mzidentml

getNumberOfSpectrumPeaks(Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.MzGraphDataAccess

Get the number peaks of a spectrum

getNumberOfSpectrumPeaks(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getNumberOfSpectrumPeaks(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

Get number of peaks using spectrum id.

getNumberOfSubSamples() - Method in class uk.ac.ebi.pride.utilities.data.core.QuantitativeSample

Get the number of valid sub samples

getNumberOfSubstitutionPTMs(Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.PeptideDataAccess

Get the number of Substitution ptms of a identification.

getNumberOfSubstitutionPTMs(Comparable, Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.PeptideDataAccess

Get the number of Substitution PTMs for a peptide

getNumberOfSubstitutionPTMs(Protein) - Static method in class uk.ac.ebi.pride.utilities.data.controller.DataAccessUtilities

Get the number of Substitution PTMs for an specific Protein Identification

getNumberOfSubstitutionPTMs(Peptide) - Static method in class uk.ac.ebi.pride.utilities.data.controller.DataAccessUtilities

Get the number of substitution modification of a peptide

getNumberOfSubstitutionPTMs(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getNumberOfSubstitutionPTMs(Comparable, Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getNumberOfUniquePeptides(Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.PeptideDataAccess

Get the number of unique peptides of a identification.

getNumberOfUniquePeptides(Protein) - Static method in class uk.ac.ebi.pride.utilities.data.controller.DataAccessUtilities

Convenient method for getting the number of unique peptides.

getNumberOfUniquePeptides(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getNumberOfUniquePeptides(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

Get number of unique peptides using identification id.

getNumberOfUniqueQuantPeptides(Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.QuantDataAccess

Get the number of unique peptides of a identification.

getNumberOfUniqueQuantPeptides(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getNumDatabaseResidue() - Method in class uk.ac.ebi.pride.utilities.data.core.SearchDataBase

getNumDatabaseSequence() - Method in class uk.ac.ebi.pride.utilities.data.core.SearchDataBase

getNumIdentifiedPeptides() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzIdentMLUnmarshallerAdaptor

getNumIdentifiedPeptides() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzTabUnmarshallerAdaptor

getNumSequenceSearched() - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentificationList

getOrder() - Method in class uk.ac.ebi.pride.utilities.data.core.InstrumentComponent

getOrder() - Method in class uk.ac.ebi.pride.utilities.data.core.ProcessingMethod

getOrganizationContacts() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzIdentMLControllerImpl

Get a list of Organization Contacts

getOrganizationContacts() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzMLControllerImpl

Get a list of Organization contacts

getOrganizationContacts() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzTabControllerImpl

Return the List of Organizations

getOrganizationContacts() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.PrideXmlControllerImpl

getOrganizationContacts() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzIdentMLUnmarshallerAdaptor

getOrganizations() - Method in class uk.ac.ebi.pride.utilities.data.core.ExperimentMetaData

getOriginalResidue() - Method in class uk.ac.ebi.pride.utilities.data.core.SubstitutionModification

getOriginalSpectrumId(SpectraData, String) - Static method in class uk.ac.ebi.pride.utilities.data.utils.MzTabUtils

getPages() - Method in class uk.ac.ebi.pride.utilities.data.core.Reference

getParamByName(ParamGroup, String) - Static method in class uk.ac.ebi.pride.utilities.data.controller.DataAccessUtilities

Get a list parameters using a given name.

getParentFiles() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzXmlUnmarshallerAdaptor

getParentOrganization() - Method in class uk.ac.ebi.pride.utilities.data.core.Organization

The containing organization (the university or business which a lab belongs to, etc.)

getParentSample() - Method in class uk.ac.ebi.pride.utilities.data.core.Sample

getParentTolerance() - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentificationProtocol

getPath() - Method in class uk.ac.ebi.pride.utilities.data.core.SourceFile

getPeptide(Protein, int) - Static method in class uk.ac.ebi.pride.utilities.data.controller.DataAccessUtilities

This is convenient method for accessing peptide.

getPeptide() - Method in class uk.ac.ebi.pride.utilities.data.core.Spectrum

getPeptideByIds(List<Comparable>) - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzTabUnmarshallerAdaptor

getPeptideByIndex(Comparable, Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.PeptideDataAccess

This is convenient method for accessing peptide.

getPeptideByIndex(Comparable, Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getPeptideByIndex(Comparable, Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

getPeptideByIndex(Comparable, Comparable, boolean) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

getPeptideByIndex(Comparable, Comparable, boolean) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.PrideXmlControllerImpl

Get peptide using a given identification id and a given peptide index

getPeptideByIndex(Comparable, Comparable, boolean) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.ReferencedIdentificationController

Get peptide using a given identification id and a given peptide index

getPeptideEvidence(List<Peptide>) - Static method in class uk.ac.ebi.pride.utilities.data.controller.DataAccessUtilities

Get peptide Evidence for a Lis of Peptide Identifications

getPeptideEvidence() - Method in class uk.ac.ebi.pride.utilities.data.core.Peptide

getPeptideEvidenceList() - Method in class uk.ac.ebi.pride.utilities.data.core.Peptide

getPeptideEvidenceList() - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentification

getPeptideEvidenceReferences(String, String) - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzIdentMLUnmarshallerAdaptor

getPeptideEvidences(Comparable, Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.PeptideDataAccess

Get all Peptide Evidence for a Peptide Identification

getPeptideEvidences(Comparable, Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getPeptideIds(Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.PeptideDataAccess

Get a collection of peptide ids belong to the identification.

getPeptideIds(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getPeptideIds(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

Get peptide ids using identification id.

getPeptideIsotopeLabellingQuantMethods() - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.QuantDataAccess

Get the isotope labelling methods at the peptide level

getPeptideIsotopeLabellingQuantMethods() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getPeptideLabelFreeQuantMethods() - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.QuantDataAccess

Get the label free methods at the peptide identification level

getPeptideLabelFreeQuantMethods() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getPeptidePrecursorCharge(Comparable, Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.PeptideDataAccess

Get precursor charge on peptide level Note: sometimes, precursor charge at the peptide level is different from the precursor charge at the spectrum level As the peptide-level precursor charge is often assigned by search engine rather than ms instrument

getPeptidePrecursorCharge(Comparable, Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

Get precursor charge on peptide level Note: sometimes, precursor charge at the peptide level is different from the precursor charge at the spectrum level As the peptide-level precursor charge is often assigned by search engine rather than ms instrument

getPeptidePrecursorCharge(Comparable, Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

Get precursor charge on peptide level Note: sometimes, precursor charge at the peptide level is different from the precursor charge at the spectrum level As the peptide-level precursor charge is often assigned by search engine rather than ms instrument

getPeptidePrecursorMz(Comparable, Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.PeptideDataAccess

Get precursor m/z on peptide level Note: sometimes, precursor m/z at the peptide level is different from the precursor charge at the spectrum level As the peptide-level precursor charge is often assigned by search engine rather than ms instrument

getPeptidePrecursorMz(Comparable, Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getPeptidePrecursorMz(Comparable, Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

Get precursor m/z from the peptide level

getPeptideQuantData(Comparable, Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.QuantDataAccess

Get quantitative data related to a given peptide

getPeptideQuantData(Comparable, Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getPeptideQuantStudyData(Comparable, Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.QuantDataAccess

Retrieve the Quantitation Score of peptides in Study Variables

getPeptideQuantStudyData(Comparable, Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getPeptideQuantUnit() - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.QuantDataAccess

Get the unit for peptide identification

getPeptideQuantUnit() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getPeptideQuantUnit() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

Get peptide quantification unit

getPeptideRank(Comparable, Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.PeptideDataAccess

Convenient method for accessing the rank of the peptide

getPeptideRank(Comparable, Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getPeptideRank(Comparable, Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.ReferencedIdentificationController

getPeptides() - Method in class uk.ac.ebi.pride.utilities.data.core.Protein

getPeptides() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzTabUnmarshallerAdaptor

getPeptidesBySpectrum(Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.MzGraphDataAccess

Retrieve the Identified Peptides related with one spectrum

getPeptidesBySpectrum(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

Retrieve the Identified Peptides related with one spectrum

getPeptidesBySpectrum(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

Retrieve the Identified Peptides related with one spectrum

getPeptidesBySpectrum(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.ReferencedIdentificationController

Retrieve the Identified Peptides related with one spectrum

getPeptideScore(Comparable, Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.PeptideDataAccess

Get peptide score generated by search engine.

getPeptideScore(Comparable, Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getPeptideScore(Comparable, Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

Get peptide score from search engine

getPeptideSequence(Comparable, Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.PeptideDataAccess

Get peptide sequence according to identification id and peptide id.

getPeptideSequence(Comparable, Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getPeptideSequence(Comparable, Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

Get peptide sequence using identification id and peptide id.

getPeptideSequence() - Method in class uk.ac.ebi.pride.utilities.data.core.Peptide

getPeptideSequence() - Method in class uk.ac.ebi.pride.utilities.data.core.PeptideEvidence

getPeptideSequence() - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentification

getPeptideSequenceEnd(Comparable, Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.PeptideDataAccess

Get peptide sequence stop

getPeptideSequenceEnd(Comparable, Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getPeptideSequenceEnd(Comparable, Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

Get peptide sequence stop using identification id and peptide id.

getPeptideSequences(Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.PeptideDataAccess

This method is to get a list of redundant peptide sequences

getPeptideSequences(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getPeptideSequences(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

Get peptide sequences using identification id.

getPeptideSequenceStart(Comparable, Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.PeptideDataAccess

Get peptide sequence start

getPeptideSequenceStart(Comparable, Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getPeptideSequenceStart(Comparable, Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

Get peptide sequence start using identification id and peptide id.

getPeptideSpectrumId(Comparable, Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.PeptideDataAccess

Get peptide's spectrum id

getPeptideSpectrumId(Comparable, Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getPeptideSpectrumId(Comparable, Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

Get peptide spectrum id using identification id and peptide id.

getPeptideSpectrumId(Comparable, Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.ReferencedIdentificationController

getPeptidesSequence() - Method in class uk.ac.ebi.pride.utilities.data.core.Protein

getPeptideTheoreticalMz(Comparable, Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.PeptideDataAccess

Get The Peptide Theoretical Mz from the file Note: sometimes, precursor m/z at the peptide level is different from the precursor charge at the spectrum level As the peptide-level precursor charge is often assigned by search engine rather than ms instrument

getPeptideTheoreticalMz(Comparable, Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getPersonContacts() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzDataControllerImpl

Get a list of person contacts

getPersonContacts() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzIdentMLControllerImpl

Get a list of Person Contacts

getPersonContacts() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzMLControllerImpl

Get a list of person contacts

getPersonContacts() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzTabControllerImpl

Return a List of Persons

getPersonContacts() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzXmlControllerImpl

Get a list of person contacts

getPersonContacts() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.PrideXmlControllerImpl

getPersonContacts() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzDataUnmarshallerAdaptor

getPersonContacts() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzIdentMLUnmarshallerAdaptor

getPersonContacts() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzXmlUnmarshallerAdaptor

getPersons() - Method in class uk.ac.ebi.pride.utilities.data.core.ExperimentMetaData

getPI() - Method in class uk.ac.ebi.pride.utilities.data.core.Gel

getPostResidue() - Method in class uk.ac.ebi.pride.utilities.data.core.PeptideEvidence

getPrecursorCharge(List<Precursor>) - Static method in class uk.ac.ebi.pride.utilities.data.controller.DataAccessUtilities

getPrecursorCharge() - Method in class uk.ac.ebi.pride.utilities.data.core.Peptide

getPrecursorChargeParamGroup(ParamGroup) - Static method in class uk.ac.ebi.pride.utilities.data.controller.DataAccessUtilities

Get precursor charge from param group

getPrecursorIntensity(Spectrum) - Static method in class uk.ac.ebi.pride.utilities.data.controller.DataAccessUtilities

Get precursor intensity

getPrecursorMz(Spectrum) - Static method in class uk.ac.ebi.pride.utilities.data.controller.DataAccessUtilities

Get precursor m/z value

getPrecursorMz(ParamGroup) - Static method in class uk.ac.ebi.pride.utilities.data.controller.DataAccessUtilities

Get precursor m/z value

getPrecursorMz() - Method in class uk.ac.ebi.pride.utilities.data.core.Peptide

getPrecursors() - Method in class uk.ac.ebi.pride.utilities.data.core.Spectrum

getPreResidue() - Method in class uk.ac.ebi.pride.utilities.data.core.PeptideEvidence

getProcessingMethods() - Method in class uk.ac.ebi.pride.utilities.data.core.DataProcessing

getProducts() - Method in class uk.ac.ebi.pride.utilities.data.core.Spectrum

getProjectName(ExperimentMetaData) - Static method in class uk.ac.ebi.pride.utilities.data.controller.DataAccessUtilities

Get the project of a experiment

getProteinAccession(Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.ProteinDataAccess

Get the protein accession of a identification

getProteinAccession(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getProteinAccession(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

Get protein accession value using identification id.

getProteinAccessionVersion(Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.ProteinDataAccess

Get the protein accession version of a identification

getProteinAccessionVersion(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getProteinAccessionVersion(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

Get protein accession version using identification id.

getProteinAmbiguityGroup(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzIdentMLUnmarshallerAdaptor

getProteinAmbiguityGroupById(Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.ProteinGroupDataAccess

Get protein ambiguity group using protein group id

getProteinAmbiguityGroupById(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getProteinAmbiguityGroupById(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

getProteinAmbiguityGroupById(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzIdentMLControllerImpl

Returns the ProteinAmbiguityGroup with an specific ID

getProteinAmbiguityGroupById(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzTabControllerImpl

The mzTab in the present version will not contains protein Groups because ambiguity members are not Protein Groups In the future we are thinking to support ambiguity groups in a different way

getProteinAmbiguityGroupIds() - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.ProteinGroupDataAccess

Get a collection of identification group ids

getProteinAmbiguityGroupIds() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getProteinAmbiguityGroupIds() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

Return a collection of the protein group identifiers

getProteinById(Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.ProteinDataAccess

Get a Identification object

getProteinById(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

Get identification object from cache It uses the cache by default

getProteinById(Comparable, boolean) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzIdentMLControllerImpl

Get identification using a identification id, gives the option to choose whether to use cache.

getProteinById(Comparable, boolean) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzTabControllerImpl

Get identification using a identification id, gives the option to choose whether to use cache.

getProteinById(Comparable, boolean) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.PrideXmlControllerImpl

Get identification using a identification id, gives the option to choose whether to use cache.

getProteinById(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzTabUnmarshallerAdaptor

It would look if the protein is in the file and retrieve the data, if the accession is not in the file with information it would create an empty entry Protein for it.

getProteinByIndex(int, int) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getProteinCoverage(Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.ProteinDataAccess

This function returns the protein coverage for a protein

getProteinCoverage(Protein) - Static method in class uk.ac.ebi.pride.utilities.data.controller.DataAccessUtilities

Number of amino acids covered

getProteinCoverage(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

The Coverage is compute as the number of identified (AminoAcid/TotalAminoAcids)*100

getProteinDetectionHypothesis() - Method in class uk.ac.ebi.pride.utilities.data.core.ProteinGroup

getProteinDetectionProtocol() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzIdentMLControllerImpl

The Protein Protocol is a relation of different Software and Processing Steps with the Identified Proteins.

getProteinDetectionProtocol() - Method in class uk.ac.ebi.pride.utilities.data.core.IdentificationMetaData

getProteinDetectionProtocol() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzIdentMLUnmarshallerAdaptor

getProteinGroupById(List<Protein>, ProteinFilter, PeptideFilter) - Method in class uk.ac.ebi.pride.utilities.data.exporters.HQMzIdentMLMzTabConverter

getProteinGroupIds() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzTabUnmarshallerAdaptor

getProteinIds() - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.ProteinDataAccess

Get a collection of identification ids

getProteinIds() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

Get identification ids from cache

getProteinIds() - Method in class uk.ac.ebi.pride.utilities.data.core.ProteinGroup

getProteinIsotopeLabellingQuantMethods() - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.QuantDataAccess

Get the isotope labelling methods at the protein level

getProteinIsotopeLabellingQuantMethods() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getProteinLabelFreeQuantMethods() - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.QuantDataAccess

Get the label free methods at the protein identification level

getProteinLabelFreeQuantMethods() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getProteinQuantData(Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.QuantDataAccess

Get quantitative data related to a given protein

getProteinQuantData(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getProteinQuantStudyData(Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.QuantDataAccess

Return the Quantitation Score for Study variables approach.

getProteinQuantStudyData(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getProteinQuantUnit() - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.QuantDataAccess

Get the unit for protein identifications

getProteinQuantUnit() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getProteinQuantUnit() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

Get protein quantification unit

getProteinScore(Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.ProteinDataAccess

Get the score of a identification.

getProteinScore(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getProteinScore(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

Get identification score using identification id.

getProteinScores(Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.ProteinDataAccess

Get protein identification score

getProteinScores(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getProteinSequence(Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.ProteinDataAccess

Get the sequence of the Identified Protein

getProteinSequence(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getProteinThreshold(Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.ProteinDataAccess

Get the threshold of a identification.

getProteinThreshold(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getProteinThreshold(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

Get identification threshold using identification id.

getProtocol() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzTabControllerImpl

Get the protocol object

getProtocol() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.PrideXmlControllerImpl

Get the protocol object

getProtocol() - Method in class uk.ac.ebi.pride.utilities.data.core.ExperimentMetaData

getProtocol() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzTabUnmarshallerAdaptor

getProtocolSteps() - Method in class uk.ac.ebi.pride.utilities.data.core.ExperimentProtocol

getProvider() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzIdentMLControllerImpl

Get provider of the experiment

getProvider() - Method in class uk.ac.ebi.pride.utilities.data.core.ExperimentMetaData

getProvider() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzIdentMLUnmarshallerAdaptor

getPSMs() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzTabUnmarshallerAdaptor

getPSMtoMsRunMap() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzTabUnmarshallerAdaptor

getPTMs(Comparable, Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.PeptideDataAccess

Get the ptms assigned to a peptide

getPTMs(Comparable, Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getPTMs(Comparable, Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

Get ptms using identification id nad peptide id

getPublication() - Method in class uk.ac.ebi.pride.utilities.data.core.Reference

getPublicDate() - Method in class uk.ac.ebi.pride.utilities.data.core.ExperimentMetaData

getPublisher() - Method in class uk.ac.ebi.pride.utilities.data.core.Reference

getQuantMethods() - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.QuantDataAccess

Get quantitative method type

getQuantMethods() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getQuantPeptide(Protein, int) - Static method in class uk.ac.ebi.pride.utilities.data.controller.DataAccessUtilities

This is convenient method for accessing peptide.

getQuantPeptideByIndex(Comparable, Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.QuantDataAccess

This is convenient method for accessing peptide.

getQuantPeptideByIndex(Comparable, Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getQuantPeptideEvidences(Comparable, Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.QuantDataAccess

Get all Peptide Evidence for a Peptide Identification

getQuantPeptideEvidences(Comparable, Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getQuantPeptideIds(Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.QuantDataAccess

Get a collection of peptide ids belong to the identification.

getQuantPeptideIds(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getQuantPeptideQuantScore(Comparable, Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.QuantDataAccess

Get peptide score generated by search engine.

getQuantPeptideQuantScore(Comparable, Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getQuantPeptides() - Method in class uk.ac.ebi.pride.utilities.data.core.Protein

getQuantPeptideScore(Comparable, Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.QuantDataAccess

Get peptide score generated by search engine.

getQuantPeptideScore(Comparable, Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getQuantPeptideSequence(Comparable, Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.QuantDataAccess

Get peptide sequence according to identification id and peptide id.

getQuantPeptideSequence(Comparable, Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getQuantPeptideSequences(Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.QuantDataAccess

This method is to get a list of redundant peptide sequences

getQuantPeptideSequences(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getQuantPeptideSpectrumId(Comparable, Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.QuantDataAccess

Get peptide's spectrum id

getQuantPeptideSpectrumId(Comparable, Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getQuantPTMs(Comparable, Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.QuantDataAccess

Get the ptms assigned to a peptide

getQuantPTMs(Comparable, Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getQuantSample() - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.QuantDataAccess

Get the mapping between sub samples and reagents

getQuantSample() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getQuantSample() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzTabControllerImpl

getQuantScore() - Method in class uk.ac.ebi.pride.utilities.data.core.Peptide

getQuantScore() - Method in class uk.ac.ebi.pride.utilities.data.core.Protein

getQuantScore() - Method in class uk.ac.ebi.pride.utilities.data.core.QuantPeptide

getQuantTermFromQuantReference(QuantCvTermReference, String) - Static method in class uk.ac.ebi.pride.utilities.data.utils.CvUtilities

getRank() - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentification

getReader() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzTabControllerImpl

Get the mzTab reader

getReader() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.PrideXmlControllerImpl

Get the pride xml reader

getReagent() - Method in class uk.ac.ebi.pride.utilities.data.core.Assay

getReagent(int) - Method in class uk.ac.ebi.pride.utilities.data.core.QuantitativeSample

Get reagent cv param of a sub sample with given index

getReferenceableParamGroup() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzMLControllerImpl

Get referenceable paramgroup, this concept is only available in mzML It is a paramgroup with id and this is not cached

getReferenceableParamGroupList() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzMLUnmarshallerAdaptor

getReferences() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzIdentMLControllerImpl

Get a list of references

getReferences() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzTabControllerImpl

Get a list of references

getReferences() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.PrideXmlControllerImpl

Get a list of references

getReferences() - Method in class uk.ac.ebi.pride.utilities.data.core.ExperimentMetaData

getReferences() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzIdentMLUnmarshallerAdaptor

getReferences() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzTabUnmarshallerAdaptor

Retrieve all publications from mzTab file

getReferenceSubSampleIndex() - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.QuantDataAccess

Get reference reagent's sub sample index

getReferenceSubSampleIndex() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getReferenceSubSampleIndex() - Method in class uk.ac.ebi.pride.utilities.data.core.Quantification

Get the index of reference sub sample

getRefMap() - Method in class uk.ac.ebi.pride.utilities.data.core.ReferenceableParamGroup

getRefParamGroup(String) - Method in class uk.ac.ebi.pride.utilities.data.core.ReferenceableParamGroup

getReleaseDate() - Method in class uk.ac.ebi.pride.utilities.data.core.SearchDataBase

getReplacementResidue() - Method in class uk.ac.ebi.pride.utilities.data.core.SubstitutionModification

getResidues() - Method in class uk.ac.ebi.pride.utilities.data.core.MassTable

getResidues() - Method in class uk.ac.ebi.pride.utilities.data.core.Modification

Get the Amino Acids associated with this modification

getRetentionTime(SpectrumIdentificationItem) - Static method in class uk.ac.ebi.pride.utilities.data.controller.DataAccessUtilities

getRetentionTime() - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentification

getRetentionTimeError() - Method in class uk.ac.ebi.pride.utilities.data.core.FragmentIon

getRole() - Method in class uk.ac.ebi.pride.utilities.data.core.ContactRole

getRole() - Method in class uk.ac.ebi.pride.utilities.data.core.Provider

getSample() - Method in class uk.ac.ebi.pride.utilities.data.core.Assay

getSample() - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentification

getSampleList() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzIdentMLUnmarshallerAdaptor

getSampleList() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzMLUnmarshallerAdaptor

getSamples() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getSamples() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzDataControllerImpl

Get a list of samples by checking the cache first

getSamples() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzIdentMLControllerImpl

Get a list of samples

getSamples() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzMLControllerImpl

Get a list of samples by checking the cache first

getSamples() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzTabControllerImpl

Get a list of samples

getSamples() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.PrideXmlControllerImpl

Get a list of samples

getSamples() - Method in class uk.ac.ebi.pride.utilities.data.core.ExperimentMetaData

getSamples() - Method in class uk.ac.ebi.pride.utilities.data.core.StudyVariable

getSamples() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzTabUnmarshallerAdaptor

getScanList() - Method in class uk.ac.ebi.pride.utilities.data.core.Spectrum

getScans() - Method in class uk.ac.ebi.pride.utilities.data.core.ScanList

getScanSetting() - Method in class uk.ac.ebi.pride.utilities.data.core.InstrumentConfiguration

getScanSettings() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzMLControllerImpl

Get a list of scan settings by checking the cache first

getScanSettings() - Method in class uk.ac.ebi.pride.utilities.data.core.MzGraphMetaData

getScanSettingsList() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzMLUnmarshallerAdaptor

getScanWindows() - Method in class uk.ac.ebi.pride.utilities.data.core.Scan

getScore(ParamGroup) - Static method in class uk.ac.ebi.pride.utilities.data.controller.DataAccessUtilities

getScore() - Method in class uk.ac.ebi.pride.utilities.data.core.Peptide

getScore() - Method in class uk.ac.ebi.pride.utilities.data.core.Protein

getScore(SearchEngineCvTermReference, SearchEngineScoreCvTermReference) - Method in class uk.ac.ebi.pride.utilities.data.core.Score

Get peptide score for a specified search engine and cv term reference

getScore() - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentification

getScores(SearchEngineCvTermReference) - Method in class uk.ac.ebi.pride.utilities.data.core.Score

Get scores for search engine

getScores(SearchEngineScoreCvTermReference) - Method in class uk.ac.ebi.pride.utilities.data.core.Score

Scan for scores using a given score cv term

getSearchDatabase(Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.ProteinDataAccess

Get the search database of a identification

getSearchDatabase(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getSearchDatabase(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

Get search database using identification id

getSearchDataBase() - Method in class uk.ac.ebi.pride.utilities.data.core.DBSequence

getSearchDataBases() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzIdentMLControllerImpl

Get the List of Databases used in the Experiment

getSearchDataBases() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzTabControllerImpl

getSearchDataBases() - Method in class uk.ac.ebi.pride.utilities.data.core.IdentificationMetaData

getSearchDatabases() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzIdentMLUnmarshallerAdaptor

getSearchDatabaseVersion(Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.ProteinDataAccess

Get the search database version of a identification

getSearchDatabaseVersion(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getSearchDatabaseVersion(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

Get search database version using identification id

getSearchEngineCvTermReference(ParamGroup) - Static method in class uk.ac.ebi.pride.utilities.data.controller.DataAccessUtilities

getSearchEngineCvTermReferences() - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.ProteinDataAccess

Get the search engine of a identification

getSearchEngineCvTermReferences() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getSearchEngineCvTermReferences() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

Get search engine type

getSearchEngineCvTermReferences() - Method in class uk.ac.ebi.pride.utilities.data.core.Score

Get all the search engine types within this peptide

getSearchEngineCvTermReferences(List<CvParam>) - Static method in class uk.ac.ebi.pride.utilities.data.utils.MzIdentMLUtils

Search and find a list of search engine types from input parameter group.

getSearchEngineScoreCvTermReferenceWithValues() - Method in class uk.ac.ebi.pride.utilities.data.core.Score

getSearchEngineScoresCvTermReference(ParamGroup) - Static method in class uk.ac.ebi.pride.utilities.data.controller.DataAccessUtilities

getSearchEngineScoreTerm(Score) - Static method in class uk.ac.ebi.pride.utilities.data.utils.MzTabUtils

Get the Search Engines Scores for a Proteins or Peptide

getSearchEngineTypes(ParamGroup) - Static method in class uk.ac.ebi.pride.utilities.data.controller.DataAccessUtilities

Deprecated.

getSearchModifications() - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentificationProtocol

getSearchType() - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentificationProtocol

getSelectedIonCharge(Precursor, int) - Static method in class uk.ac.ebi.pride.utilities.data.controller.DataAccessUtilities

Get the ion charge for a selected ion.

getSelectedIonIntensity(Precursor, int) - Static method in class uk.ac.ebi.pride.utilities.data.controller.DataAccessUtilities

Get the ion intensity value for a selected ion.

getSelectedIonMz(Precursor, int) - Static method in class uk.ac.ebi.pride.utilities.data.controller.DataAccessUtilities

Get the ion m/z value for a selected ion.

getSelectedIons() - Method in class uk.ac.ebi.pride.utilities.data.core.Precursor

getSequence() - Method in class uk.ac.ebi.pride.utilities.data.core.DBSequence

getSequence() - Method in class uk.ac.ebi.pride.utilities.data.core.Peptide

getSequence() - Method in class uk.ac.ebi.pride.utilities.data.core.PeptideSequence

getSequence() - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentification

getSequenceCoverage() - Method in class uk.ac.ebi.pride.utilities.data.core.Protein

getSequenceLength() - Method in class uk.ac.ebi.pride.utilities.data.core.Peptide

getSequenceLength() - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentification

getShortLabel() - Method in class uk.ac.ebi.pride.utilities.data.core.ExperimentMetaData

getSiteRegExp() - Method in class uk.ac.ebi.pride.utilities.data.core.Enzyme

getSize() - Method in enum uk.ac.ebi.pride.utilities.data.controller.cache.CacheEntry

getSoftware() - Method in class uk.ac.ebi.pride.utilities.data.core.InstrumentConfiguration

getSoftware() - Method in class uk.ac.ebi.pride.utilities.data.core.ProcessingMethod

getSoftware() - Method in class uk.ac.ebi.pride.utilities.data.core.Provider

getSoftware() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzDataUnmarshallerAdaptor

getSoftwares() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzDataControllerImpl

Get a List of Software

getSoftwares() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzIdentMLControllerImpl

Get a list of softwares

getSoftwares() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzMLControllerImpl

Get a List of Softwares

getSoftwares() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzTabControllerImpl

Get a list of software

getSoftwares() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzXmlControllerImpl

The softwares on mzXml are annotated with their names, the type, and the execution time processing the data.

getSoftwares() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.PrideXmlControllerImpl

Get a list of software

getSoftwares() - Method in class uk.ac.ebi.pride.utilities.data.core.ExperimentMetaData

getSoftwares() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzIdentMLUnmarshallerAdaptor

getSoftwares() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzMLUnmarshallerAdaptor

getSoftwares() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzXmlUnmarshallerAdaptor

getSource() - Method in interface uk.ac.ebi.pride.utilities.data.controller.DataAccessController

Get the original data source object

getSource() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getSource() - Method in class uk.ac.ebi.pride.utilities.data.core.InstrumentConfiguration

getSourceFile() - Method in class uk.ac.ebi.pride.utilities.data.core.Precursor

getSourceFile() - Method in class uk.ac.ebi.pride.utilities.data.core.Scan

getSourceFile() - Method in class uk.ac.ebi.pride.utilities.data.core.ScanSetting

getSourceFile() - Method in class uk.ac.ebi.pride.utilities.data.core.Spectrum

getSourceFiles() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzDataControllerImpl

Get the information of SourceFiles.

getSourceFiles() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzIdentMLControllerImpl

Get a list of source files.

getSourceFiles() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzMLControllerImpl

Get a List of SourceFiles

getSourceFiles() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzTabControllerImpl

Get a list of source files.

getSourceFiles() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzXmlControllerImpl

Get a list of Source Files.

getSourceFiles() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.PrideXmlControllerImpl

Get a list of source files.

getSourceFiles() - Method in class uk.ac.ebi.pride.utilities.data.core.ExperimentMetaData

getSourceFiles() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzDataUnmarshallerAdaptor

getSourceFiles() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzIdentMLUnmarshallerAdaptor

getSourceFiles() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzTabUnmarshallerAdaptor

getSpecFileFormat(String) - Static method in class uk.ac.ebi.pride.utilities.data.utils.Constants

Retrieve the Spectrum File format for an specific fileformat.

getSpecFileFormatFromLocation(String) - Static method in class uk.ac.ebi.pride.utilities.data.utils.Constants

Return the SpectrumFile format for an specific path such as: /myppath/spectrum_file.mgf

getSpecies(int) - Method in class uk.ac.ebi.pride.utilities.data.core.QuantitativeSample

Get the species information of sub sample with given index

getSpecificities() - Method in class uk.ac.ebi.pride.utilities.data.core.SearchModification

getSpecificityRules() - Method in class uk.ac.ebi.pride.utilities.data.core.SearchModification

getSpectraByIndex(int, int) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.MzGraphDataAccess

Get a collection of spectra by its index and offset.

getSpectraByIndex(int, int) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getSpectraData() - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentification

getSpectraData() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzIdentMLUnmarshallerAdaptor

getSpectraDataBasedOnTitle() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

In some cases (WIFF files) the spectrum is referenced using the TITLE instead of using the index.

getSpectraDataFiles() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzIdentMLControllerImpl

Get the List of File Spectra that the Mzidentml use to identified peptides

getSpectraDataFiles() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzTabControllerImpl

Get the List of File Spectra that the Mzidentml use to identified peptides

getSpectraDataFormat(SpectraData) - Static method in class uk.ac.ebi.pride.utilities.data.utils.Constants

This function returns the Spectrum File format for an specific SpectraData ob object

getSpectraDataFormat(SpectraData) - Static method in class uk.ac.ebi.pride.utilities.data.utils.MzTabUtils

getSpectraDataIdFormat(String) - Static method in class uk.ac.ebi.pride.utilities.data.utils.Constants

Spectrum Id format for an specific CVterm accession

getSpectraDataIdFormat(SpectraData) - Static method in class uk.ac.ebi.pride.utilities.data.utils.MzIdentMLUtils

getSpectraDataIdFormat(SpectraData) - Static method in class uk.ac.ebi.pride.utilities.data.utils.MzIdentMLUtils

getSpectraDataIdFormat(SpectraData) - Static method in class uk.ac.ebi.pride.utilities.data.utils.MzTabUtils

getSpectraDataMap() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzIdentMLUnmarshallerAdaptor

getSpectraDataMSControllers() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.ReferencedIdentificationController

getSpectraDataMSFiles() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.ReferencedIdentificationController

Get the Spectra Data Map with the corresponding File.

getSpectraDatas() - Method in class uk.ac.ebi.pride.utilities.data.core.ExperimentMetaData

getSpectrum() - Method in class uk.ac.ebi.pride.utilities.data.core.Peptide

getSpectrum() - Method in class uk.ac.ebi.pride.utilities.data.core.Precursor

getSpectrum() - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentification

getSpectrumById(Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.MzGraphDataAccess

Get a Spectrum object via an spectrum id

getSpectrumById(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

Get spectrum object from cache It uses cache by default

getSpectrumById(Comparable, boolean) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.PeakControllerImpl

Get spectrum using a spectrum id, gives the option to choose whether to use cache.

getSpectrumById(Comparable, boolean) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.ReferencedIdentificationController

Get spectrum using a spectrumIdentification id, gives the option to choose whether to use cache.

getSpectrumById(String) - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzDataUnmarshallerAdaptor

getSpectrumById(String) - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzXmlUnmarshallerAdaptor

getSpectrumById(String) - Method in class uk.ac.ebi.pride.utilities.data.io.file.PeakUnmarshallerAdaptor

getSpectrumDataAccessControllers() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.ReferencedIdentificationController

getSpectrumId(SpectraData, String) - Static method in class uk.ac.ebi.pride.utilities.data.utils.MzIdentMLUtils

getSpectrumId(SpectraData, String) - Static method in class uk.ac.ebi.pride.utilities.data.utils.MzTabUtils

getSpectrumIdBySpectrumIdentificationItemId(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.ReferencedIdentificationController

getSpectrumIdentification() - Method in class uk.ac.ebi.pride.utilities.data.core.Peptide

getSpectrumIdentificationItemIds(String) - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzIdentMLUnmarshallerAdaptor

getSpectrumIdentificationProtocol() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzIdentMLControllerImpl

The spectrum IdentificationProtocol is the Set of parameters Related with the Spectrum Identification Process in terms of Search Engines, Databases, Enzymes, Modifications and Database Filters, etc

getSpectrumIdentificationProtocol() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzIdentMLUnmarshallerAdaptor

getSpectrumIdentificationProtocols() - Method in class uk.ac.ebi.pride.utilities.data.core.IdentificationMetaData

getSpectrumIdentificationResultList() - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentificationList

getSpectrumIdentificationsByIds(List<Comparable>) - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzIdentMLUnmarshallerAdaptor

getSpectrumIdentificationsByIds(List<Comparable>) - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzTabUnmarshallerAdaptor

getSpectrumIdFormat() - Method in class uk.ac.ebi.pride.utilities.data.core.SpectraData

getSpectrumIdFormatMGFTitle() - Static method in class uk.ac.ebi.pride.utilities.data.utils.MzIdentMLUtils

getSpectrumIdForPeptide(Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.MzGraphDataAccess

Convert the PSM id to spectrum ID

getSpectrumIdForPeptide(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getSpectrumIdForPeptide(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

Convert PSM id to Spectrum ID

getSpectrumIds() - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.MzGraphDataAccess

Get a collection of spectrum ids

getSpectrumIds() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

Get spectrum ids from cache

getSpectrumIds() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.PeakControllerImpl

getSpectrumIds() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.ReferencedIdentificationController

getSpectrumIds() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzDataUnmarshallerAdaptor

getSpectrumIds() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzMLUnmarshallerAdaptor

getSpectrumIds() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzXmlUnmarshallerAdaptor

getSpectrumIds() - Method in class uk.ac.ebi.pride.utilities.data.io.file.PeakUnmarshallerAdaptor

getSpectrumIndex(Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.MzGraphDataAccess

Get the index of a spectrum using its id

getSpectrumIndex(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getSpectrumMsLevel(Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.MzGraphDataAccess

Get the ms level of a spectrum.

getSpectrumMsLevel(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getSpectrumMsLevel(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

Get ms level using spectrum id.

getSpectrumPrecursorCharge(Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.MzGraphDataAccess

Get the precursor charge of a spectrum.

getSpectrumPrecursorCharge(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

Get precursor charge of a spectrum.

getSpectrumPrecursorCharge(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

Get precursor charge of a spectrum.

getSpectrumPrecursorIntensity(Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.MzGraphDataAccess

Get the precursor's intensity of a spectrum.

getSpectrumPrecursorIntensity(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getSpectrumPrecursorIntensity(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

Get precursor intensity value using spectrum id.

getSpectrumPrecursorMz(Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.MzGraphDataAccess

Get the precursor's m/z value of a spectrum.

getSpectrumPrecursorMz(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getSpectrumPrecursorMz(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

Get precursor m/z value using spectrum id.

getSpectrumRef() - Method in class uk.ac.ebi.pride.utilities.data.core.Scan

getSpliceIsoform() - Method in class uk.ac.ebi.pride.utilities.data.core.DBSequence

getSpotID() - Method in class uk.ac.ebi.pride.utilities.data.core.Spectrum

getStartDate() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzXmlUnmarshallerAdaptor

getStartPosition() - Method in class uk.ac.ebi.pride.utilities.data.core.PeptideEvidence

getStudyVariables() - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.QuantDataAccess

In mzTab files the information of Quantitation is store in StudyVariables and not in Samples

getStudyVariables() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getStudyVariables() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzTabControllerImpl

Returns StudyVariables for mzTab files.

getStudyVariables() - Method in class uk.ac.ebi.pride.utilities.data.core.ExperimentMetaData

getStudyVariables() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzTabUnmarshallerAdaptor

getStudyVariableScores() - Method in class uk.ac.ebi.pride.utilities.data.core.QuantScore

Return Study variables map

getSubstitutionModifications() - Method in class uk.ac.ebi.pride.utilities.data.core.PeptideSequence

getSubstitutionPTMs(Comparable, Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.PeptideDataAccess

Get the ptms assigned to a peptide

getSubstitutionPTMs(Comparable, Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getSumOfIntensity(Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.MzGraphDataAccess

Get the sum of intensity of a spectrum.

getSumOfIntensity(Spectrum) - Static method in class uk.ac.ebi.pride.utilities.data.controller.DataAccessUtilities

Get the sum of all the peak intensities within a spectrum

getSumOfIntensity(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getSumOfIntensity(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

Get sum of intensity value using spectrum id.

getSupportedSpectraData() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.ReferencedIdentificationController

getTargets() - Method in class uk.ac.ebi.pride.utilities.data.core.ScanSetting

getTaxonomy(ExperimentMetaData) - Static method in class uk.ac.ebi.pride.utilities.data.controller.DataAccessUtilities

Get a list of taxonomy accessions based on a given metadata

getThreshold() - Method in class uk.ac.ebi.pride.utilities.data.core.Protein

getThreshold() - Method in class uk.ac.ebi.pride.utilities.data.core.Protocol

getTimeArray() - Method in class uk.ac.ebi.pride.utilities.data.core.Chromatogram

getTissue(int) - Method in class uk.ac.ebi.pride.utilities.data.core.QuantitativeSample

Get tissue cv param of a sub sample with given index

getTitle() - Method in class uk.ac.ebi.pride.utilities.data.core.Reference

getTitleReferenceFile(Map<Comparable, SpectraData>) - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzIdentMLUnmarshallerAdaptor

Check for all the SpectraData if they are referenced by title instead of using the normal index.

getTranslationTable() - Method in class uk.ac.ebi.pride.utilities.data.core.PeptideEvidence

getTranslationTables() - Method in class uk.ac.ebi.pride.utilities.data.core.DataBaseTranslation

getType() - Method in interface uk.ac.ebi.pride.utilities.data.controller.DataAccessController

Get the type of database access controller.

getType() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getType() - Method in class uk.ac.ebi.pride.utilities.data.core.Quantification

getType() - Method in class uk.ac.ebi.pride.utilities.data.core.UserParam

getType() - Method in class uk.ac.ebi.pride.utilities.data.filter.DecoyAccessionFilter

getUid() - Method in interface uk.ac.ebi.pride.utilities.data.controller.DataAccessController

Get the unique id represent the uniqueness of the data source

getUid() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getUid() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzDataControllerImpl

Get the unique id for this data access controller It generates a MD5 hash using the absolute path of the file This will guarantee the same id if the file path is the same

getUid() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzIdentMLControllerImpl

Get the unique id of the data access controller

getUid() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzMLControllerImpl

Get the unique id for this data access controller It generates a MD5 hash using the absolute path of the file This will guarantee the same id if the file path is the same

getUid() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzTabControllerImpl

Get md5 hash unique id

getUid() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzXmlControllerImpl

Get the unique id for this data access controller It generates a MD5 hash using the absolute path of the file This will guarantee the same id if the file path is the same

getUid() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.PeakControllerImpl

Get the unique id for this data access controller It generates a MD5 hash using the absolute path of the file This will guarantee the same id if the file path is the same

getUid() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.PrideXmlControllerImpl

Get md5 hash unique id

getUnit() - Method in class uk.ac.ebi.pride.utilities.data.core.Quantification

Get the unit of the quantification

getUnitAcc() - Method in class uk.ac.ebi.pride.utilities.data.core.Parameter

getUnitCVLookupID() - Method in class uk.ac.ebi.pride.utilities.data.core.Parameter

getUnitName() - Method in class uk.ac.ebi.pride.utilities.data.core.Parameter

getUnmarshaller() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzDataControllerImpl

Get the backend data reader

getUnmarshaller() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzIdentMLControllerImpl

Return the mzidentml unmarshall adaptor to be used by the CacheBuilder Implementation.

getUnmarshaller() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzMLControllerImpl

Get the backend data reader

getUnmarshaller() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzXmlControllerImpl

Get the backend data reader

getUnmarshaller() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.PeakControllerImpl

Get the backend data reader

getUnmarshaller() - Method in class uk.ac.ebi.pride.utilities.data.io.file.PeakUnmarshallerAdaptor

getUri() - Method in class uk.ac.ebi.pride.utilities.data.core.Software

getUserParams() - Method in class uk.ac.ebi.pride.utilities.data.core.ParamGroup

getValue() - Method in class uk.ac.ebi.pride.utilities.data.core.Parameter

getValueBySearchEngineScoreTerm(String) - Method in class uk.ac.ebi.pride.utilities.data.core.Score

Retrieve the value of one score for an specific search engine term

getValueFromParmGroup(List<CvParam>, String) - Static method in class uk.ac.ebi.pride.utilities.data.utils.CvUtilities

getVersion() - Method in class uk.ac.ebi.pride.utilities.data.core.CVLookup

getVersion() - Method in class uk.ac.ebi.pride.utilities.data.core.ExperimentMetaData

getVersion() - Method in class uk.ac.ebi.pride.utilities.data.core.SearchDataBase

getVersion() - Method in class uk.ac.ebi.pride.utilities.data.core.Software

getVersion() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzTabUnmarshallerAdaptor

getVersionMzData() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzDataUnmarshallerAdaptor

getVolume() - Method in class uk.ac.ebi.pride.utilities.data.core.Reference

getXCoordinate() - Method in class uk.ac.ebi.pride.utilities.data.core.Gel

getYCoordinate() - Method in class uk.ac.ebi.pride.utilities.data.core.Gel

getYear() - Method in class uk.ac.ebi.pride.utilities.data.core.Reference

H

hasCacheEntry(CacheEntry) - Method in interface uk.ac.ebi.pride.utilities.data.controller.cache.Cache

Check whether the cache already has the cache category

hasCacheEntry(CacheEntry) - Method in class uk.ac.ebi.pride.utilities.data.controller.cache.CacheAccessor

Check the cachecategory availability

hasCellLine() - Method in class uk.ac.ebi.pride.utilities.data.core.QuantitativeSample

Get whether cell line information exists

hasChromatogram() - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.MzGraphDataAccess

Whether this controller contains chromatogram.

hasChromatogram() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

hasDecoyInformation() - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.ProteinDataAccess

This function return true if the controller contains decoy information and false if the controller do not contain decoy information.

hasDecoyInformation() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

hasDecoyInformation() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzIdentMLControllerImpl

Check if the DataAccessController contains the ProteinSequence

hasDecoyInformation() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzIdentMLUnmarshallerAdaptor

hasDescription() - Method in class uk.ac.ebi.pride.utilities.data.core.QuantitativeSample

Get whether description exists

hasDisease() - Method in class uk.ac.ebi.pride.utilities.data.core.QuantitativeSample

Get whether disease information exists

hasFragmentIon(Spectrum) - Static method in class uk.ac.ebi.pride.utilities.data.controller.DataAccessUtilities

Check whether spectrum has fragment ion information

hasFragmentIon(Peptide) - Static method in class uk.ac.ebi.pride.utilities.data.controller.DataAccessUtilities

Check whether peptide has fragment ion information

hasGOTerm() - Method in class uk.ac.ebi.pride.utilities.data.core.QuantitativeSample

Get whether GO information exists

hashCode() - Method in class uk.ac.ebi.pride.utilities.data.core.BinaryDataArray

hashCode() - Method in class uk.ac.ebi.pride.utilities.data.core.ContactRole

hashCode() - Method in class uk.ac.ebi.pride.utilities.data.core.CVLookup

hashCode() - Method in class uk.ac.ebi.pride.utilities.data.core.CvParam

hashCode() - Method in class uk.ac.ebi.pride.utilities.data.core.DataBaseTranslation

hashCode() - Method in class uk.ac.ebi.pride.utilities.data.core.DataProcessing

hashCode() - Method in class uk.ac.ebi.pride.utilities.data.core.DBSequence

hashCode() - Method in class uk.ac.ebi.pride.utilities.data.core.Enzyme

hashCode() - Method in class uk.ac.ebi.pride.utilities.data.core.ExperimentMetaData

hashCode() - Method in class uk.ac.ebi.pride.utilities.data.core.ExperimentProtocol

hashCode() - Method in class uk.ac.ebi.pride.utilities.data.core.ExternalData

hashCode() - Method in class uk.ac.ebi.pride.utilities.data.core.Filter

hashCode() - Method in class uk.ac.ebi.pride.utilities.data.core.FragmentIon

hashCode() - Method in class uk.ac.ebi.pride.utilities.data.core.Gel

hashCode() - Method in class uk.ac.ebi.pride.utilities.data.core.Identifiable

hashCode() - Method in class uk.ac.ebi.pride.utilities.data.core.IdentifiableParamGroup

hashCode() - Method in class uk.ac.ebi.pride.utilities.data.core.IdentificationMetaData

hashCode() - Method in class uk.ac.ebi.pride.utilities.data.core.InstrumentComponent

hashCode() - Method in class uk.ac.ebi.pride.utilities.data.core.InstrumentConfiguration

hashCode() - Method in class uk.ac.ebi.pride.utilities.data.core.IonType

hashCode() - Method in class uk.ac.ebi.pride.utilities.data.core.MassTable

hashCode() - Method in class uk.ac.ebi.pride.utilities.data.core.Modification

hashCode() - Method in class uk.ac.ebi.pride.utilities.data.core.MzGraph

hashCode() - Method in class uk.ac.ebi.pride.utilities.data.core.MzGraphMetaData

hashCode() - Method in class uk.ac.ebi.pride.utilities.data.core.Organization

hashCode() - Method in class uk.ac.ebi.pride.utilities.data.core.Parameter

hashCode() - Method in class uk.ac.ebi.pride.utilities.data.core.ParamGroup

hashCode() - Method in class uk.ac.ebi.pride.utilities.data.core.Peptide

hashCode() - Method in class uk.ac.ebi.pride.utilities.data.core.PeptideEvidence

hashCode() - Method in class uk.ac.ebi.pride.utilities.data.core.PeptideSequence

hashCode() - Method in class uk.ac.ebi.pride.utilities.data.core.Person

hashCode() - Method in class uk.ac.ebi.pride.utilities.data.core.Precursor

hashCode() - Method in class uk.ac.ebi.pride.utilities.data.core.ProcessingMethod

hashCode() - Method in class uk.ac.ebi.pride.utilities.data.core.Protein

hashCode() - Method in class uk.ac.ebi.pride.utilities.data.core.Protocol

hashCode() - Method in class uk.ac.ebi.pride.utilities.data.core.Provider

hashCode() - Method in class uk.ac.ebi.pride.utilities.data.core.Quantification

hashCode() - Method in class uk.ac.ebi.pride.utilities.data.core.QuantitativeSample

hashCode() - Method in class uk.ac.ebi.pride.utilities.data.core.QuantScore

hashCode() - Method in class uk.ac.ebi.pride.utilities.data.core.Reference

hashCode() - Method in class uk.ac.ebi.pride.utilities.data.core.ReferenceableParamGroup

hashCode() - Method in class uk.ac.ebi.pride.utilities.data.core.Sample

hashCode() - Method in class uk.ac.ebi.pride.utilities.data.core.Scan

hashCode() - Method in class uk.ac.ebi.pride.utilities.data.core.ScanList

hashCode() - Method in class uk.ac.ebi.pride.utilities.data.core.ScanSetting

hashCode() - Method in class uk.ac.ebi.pride.utilities.data.core.Score

hashCode() - Method in class uk.ac.ebi.pride.utilities.data.core.SearchDataBase

hashCode() - Method in class uk.ac.ebi.pride.utilities.data.core.SearchModification

hashCode() - Method in class uk.ac.ebi.pride.utilities.data.core.Software

hashCode() - Method in class uk.ac.ebi.pride.utilities.data.core.SourceFile

hashCode() - Method in class uk.ac.ebi.pride.utilities.data.core.SpectraData

hashCode() - Method in class uk.ac.ebi.pride.utilities.data.core.Spectrum

hashCode() - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentification

hashCode() - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentificationList

hashCode() - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentificationProtocol

hashCode() - Method in class uk.ac.ebi.pride.utilities.data.core.StudyVariable

hashCode() - Method in class uk.ac.ebi.pride.utilities.data.core.SubstitutionModification

hashCode() - Method in class uk.ac.ebi.pride.utilities.data.core.UserParam

hasIsotopeLabellingMethod() - Method in class uk.ac.ebi.pride.utilities.data.core.Quantification

Check whether the results of isotope labelling methods are present

hasIsotopeLabellingQuantMethods() - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.QuantDataAccess

Check whether the experiment contains quantitative data using isotope labelling methods

hasIsotopeLabellingQuantMethods() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

hasLabelFreeMethod() - Method in class uk.ac.ebi.pride.utilities.data.core.Quantification

Check whether the results of label free quantification methods are present

hasLabelFreeQuantMethods() - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.QuantDataAccess

Check whether the experiment contains quantitative data using label free methods

hasLabelFreeQuantMethods() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

hasMetaDataInformation() - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.MetaDataAccess

This function give the user the possibility to know if the controller contains MetaData.

hasMetaDataInformation() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

hasMetaDataInformation() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.PeakControllerImpl

The only file format that not contain any MetaData are the pure peak files.

hasModification() - Method in class uk.ac.ebi.pride.utilities.data.core.Peptide

hasModification() - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentification

hasPeptide() - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.PeptideDataAccess

Whether this controller contains peptides

hasPeptide() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

hasPeptideQuantData() - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.QuantDataAccess

Check whether the experiment contains quantitative data at the peptide level

hasPeptideQuantData() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

hasPeptideTotalIntensities() - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.QuantDataAccess

Check whether the experiment contains total intensities at the protein level

hasPeptideTotalIntensities() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

hasProtein() - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.ProteinDataAccess

Whether this controller contains identifications

hasProtein() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

hasProtein() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzMLControllerImpl

This method provide the way to know if the controller contain Identification Data and IdentificationMetadata.

hasProteinAmbiguityGroup() - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.ProteinGroupDataAccess

Whether this controller contains protein groups information

hasProteinAmbiguityGroup() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

hasProteinAmbiguityGroup() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.ReferencedIdentificationController

Check if the PROTEIN_GROUP Cache contains any element

hasProteinGroup() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzIdentMLUnmarshallerAdaptor

hasProteinGroup() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzTabUnmarshallerAdaptor

hasProteinQuantData() - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.QuantDataAccess

Check whether the experiment contains quantitative data at the protein level

hasProteinQuantData() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

hasProteinSequence() - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.ProteinDataAccess

Whether this controller contains protein sequences

hasProteinSequence() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

hasProteinSequence() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzIdentMLControllerImpl

Check if the DataAccessController contains the ProteinSequence

hasProteinSequence() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzTabControllerImpl

Check if the file contains Protein Sequence by looking inside the CVTerms in the MzTab Unmarshaller

hasProteinSequence() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzIdentMLUnmarshallerAdaptor

hasProteinSequence() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzTabUnmarshallerAdaptor

hasProteinTotalIntensities() - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.QuantDataAccess

Check whether the experiment contains total intensities at the protein level

hasProteinTotalIntensities() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

hasQuantData() - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.QuantDataAccess

Check whether the experiment contains quantitative data

hasQuantData() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

hasQuantData() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzIdentMLControllerImpl

The mzidentml do not support Quatitation Data

hasQuantData() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzTabControllerImpl

hasQuantitationData() - Method in class uk.ac.ebi.pride.utilities.data.io.file.MzTabUnmarshallerAdaptor

hasQuantPeptide() - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.QuantDataAccess

Whether this controller contains peptides

hasQuantPeptide() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

hasReagent() - Method in class uk.ac.ebi.pride.utilities.data.core.QuantitativeSample

Get whether reagent information exists

hasSpecies() - Method in class uk.ac.ebi.pride.utilities.data.core.QuantitativeSample

Get whether species information exists

hasSpectrum() - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.MzGraphDataAccess

Whether this controller contains spectra

hasSpectrum() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

hasSpectrum() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.ReferencedIdentificationController

If the spectrum information associated with the identification files is provided then the mzidentml contains spectra.

hasSubSample(int) - Method in class uk.ac.ebi.pride.utilities.data.core.QuantitativeSample

Check whether a subsample exist with a given index

hasTissue() - Method in class uk.ac.ebi.pride.utilities.data.core.QuantitativeSample

Get whether tissue information exists

hasTotalIntensities() - Method in class uk.ac.ebi.pride.utilities.data.core.Quantification

Convenient method to check whether the reported value is total intensity These values can be used for calculating ratios.

HQMzIdentMLMzTabConverter - Class in uk.ac.ebi.pride.utilities.data.exporters

The filtering when exporting a mzIdentML to mzTab is done follows the next set of rules: If there is not protein detection protocol in mzIdentML (e.

HQMzIdentMLMzTabConverter(MzIdentMLControllerImpl) - Constructor for class uk.ac.ebi.pride.utilities.data.exporters.HQMzIdentMLMzTabConverter

Default constructor

I

Identifiable - Class in uk.ac.ebi.pride.utilities.data.core

Other classes in the model can be specified as sub-classes, inheriting from Identifiable.

Identifiable(Comparable, String) - Constructor for class uk.ac.ebi.pride.utilities.data.core.Identifiable

IdentifiableParamGroup - Class in uk.ac.ebi.pride.utilities.data.core

Other classes in the model can be specified as sub-classes, inheriting from IdentifiablePraramGroup.

IdentifiableParamGroup(Comparable, String) - Constructor for class uk.ac.ebi.pride.utilities.data.core.IdentifiableParamGroup

IdentifiableParamGroup(ParamGroup, Comparable, String) - Constructor for class uk.ac.ebi.pride.utilities.data.core.IdentifiableParamGroup

IdentificationMetaData - Class in uk.ac.ebi.pride.utilities.data.core

This class is used to manage and store the information of the metadata for protein and spectrum identifications.

IdentificationMetaData(Comparable, String, List<SpectrumIdentificationProtocol>, Protocol, List<SearchDataBase>) - Constructor for class uk.ac.ebi.pride.utilities.data.core.IdentificationMetaData

IdentificationMetaData(ParamGroup, Comparable, String, List<SpectrumIdentificationProtocol>, Protocol, List<SearchDataBase>) - Constructor for class uk.ac.ebi.pride.utilities.data.core.IdentificationMetaData

indexOfProtein(Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.ProteinDataAccess

Get the index of identification by its id

indexOfProtein(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

init() - Method in class uk.ac.ebi.pride.utilities.data.exporters.AbstractMzTabConverter

initialize(boolean, boolean) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzIdentMLControllerImpl

This function initialize all the Categories in which the Controller used the Cache System.

initialize() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzTabControllerImpl

Initialize the mzTab file reader

initialize() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.PrideXmlControllerImpl

InstrumentComponent - Class in uk.ac.ebi.pride.utilities.data.core

InstrumentComponent is key to keep the order of different instrument component.

InstrumentComponent(int, ParamGroup) - Constructor for class uk.ac.ebi.pride.utilities.data.core.InstrumentComponent

constructor

InstrumentConfiguration - Class in uk.ac.ebi.pride.utilities.data.core

Description of a particular hardware configuration of a mass spectrometer.

InstrumentConfiguration(String, ScanSetting, Software, List<InstrumentComponent>, List<InstrumentComponent>, List<InstrumentComponent>, ParamGroup) - Constructor for class uk.ac.ebi.pride.utilities.data.core.InstrumentConfiguration

Constructor

INTEGER - Static variable in class uk.ac.ebi.pride.utilities.data.utils.Constants

integer expression

IonType - Class in uk.ac.ebi.pride.utilities.data.core

IonType defines the index of fragmentation ions being reported, importing a CV term for the type of ion e.g.

IonType(String, String, String, String, String, String, String) - Constructor for class uk.ac.ebi.pride.utilities.data.core.IonType

Constructor

isDecoy() - Method in class uk.ac.ebi.pride.utilities.data.core.PeptideEvidence

isDecoyHit(ParamGroup) - Static method in class uk.ac.ebi.pride.utilities.data.utils.CvUtilities

Checks whether the passed identification object is a decoy hit.

isEmpty() - Method in class uk.ac.ebi.pride.utilities.data.core.ParamGroup

isEnzymeIndependent() - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentificationProtocol

isFixedMod() - Method in class uk.ac.ebi.pride.utilities.data.core.SearchModification

isFragmentIonsChargeAnnotated() - Method in class uk.ac.ebi.pride.utilities.data.core.Peptide

isIdentification() - Method in class uk.ac.ebi.pride.utilities.data.exporters.AbstractMzTabConverter

Only one sample means this file is Identification and Complete.

isIdentification() - Method in class uk.ac.ebi.pride.utilities.data.exporters.MzIdentMLMzTabConverter

MzIdentML is always an Identification File

isIdentifiedSpectrum(Comparable) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.MzGraphDataAccess

Check whether the given spectrum is identified.

isIdentifiedSpectrum(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

isIdentifiedSpectrum(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.PrideXmlControllerImpl

Check whether the spectrum has been identified.

isIdentifiedSpectrum(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.ReferencedIdentificationController

Is identified Spectrum return true if the spectrum was identified

isPassThreshold() - Method in class uk.ac.ebi.pride.utilities.data.core.Protein

isPassThreshold() - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentification

isSemiSpecific() - Method in class uk.ac.ebi.pride.utilities.data.core.Enzyme

isSpectraDataReferencedByTitle(SpectraData) - Static method in class uk.ac.ebi.pride.utilities.data.utils.MzIdentMLUtils

isSpectraDataSupported(SpectraData) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.ReferencedIdentificationController

isSpectrumBasedOnTitle() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

In some cases (WIFF files) the spectrum is referenced using the TITLE instead of using the index.

isSupported(DataAccessController) - Static method in class uk.ac.ebi.pride.utilities.data.exporters.AbstractMzTabConverter

This function validate if the file is supported in this case it only supports MZIdentML, PRIDE XML and MzTab

isSupported(DataAccessController) - Static method in class uk.ac.ebi.pride.utilities.data.exporters.MzIdentMLMzTabConverter

isUseTitle() - Method in class uk.ac.ebi.pride.utilities.data.io.file.PeakUnmarshallerAdaptor

isValidFormat(File) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzDataControllerImpl

Check a file is mzML file

isValidFormat(File) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzIdentMLControllerImpl

Check a file is MZIdentML XML file

isValidFormat(File) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzMLControllerImpl

Check a file is mzML file

isValidFormat(File) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzTabControllerImpl

Check a file is mzTab File is supported, it should contain the protein and psm sections, it must be mztab version 1.0 and finally it should be mzTab extension file.

isValidFormat(File) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzXmlControllerImpl

Check a file is mzML file

isValidFormat(File) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.PeakControllerImpl

Check a file is mzML file

isValidFormat(File) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.PrideXmlControllerImpl

Check a file is PRIDE XML file

L

length() - Method in class uk.ac.ebi.pride.utilities.data.core.PeptideSequence

loadContacts() - Method in class uk.ac.ebi.pride.utilities.data.exporters.AbstractMzTabConverter

Converts a list of Contacts into an ArrayList of mzTab Contacts.

loadExperimentParams() - Method in class uk.ac.ebi.pride.utilities.data.exporters.AbstractMzTabConverter

Processes the experiment additional params: (f.e.

loadExperimentParams() - Method in class uk.ac.ebi.pride.utilities.data.exporters.MzIdentMLMzTabConverter

Processes the experiment additional params: (f.e.

loadExperimentParams() - Method in class uk.ac.ebi.pride.utilities.data.exporters.PRIDEMzTabConverter

loadGelData() - Method in class uk.ac.ebi.pride.utilities.data.exporters.AbstractMzTabConverter

Load Gel Data

loadGelData() - Method in class uk.ac.ebi.pride.utilities.data.exporters.MzIdentMLMzTabConverter

loadGelData() - Method in class uk.ac.ebi.pride.utilities.data.exporters.PRIDEMzTabConverter

loadInstrument() - Method in class uk.ac.ebi.pride.utilities.data.exporters.AbstractMzTabConverter

Load Instrument should be implemented by different controllers

loadInstrument() - Method in class uk.ac.ebi.pride.utilities.data.exporters.MzIdentMLMzTabConverter

loadInstrument() - Method in class uk.ac.ebi.pride.utilities.data.exporters.PRIDEMzTabConverter

Retrieve the data for instrument in and Instrument Processing (Analyzer, Source and Detector)

loadMetadataModifications() - Method in class uk.ac.ebi.pride.utilities.data.exporters.MzIdentMLMzTabConverter

loadModifications(Protein, List<Peptide>) - Method in class uk.ac.ebi.pride.utilities.data.exporters.MzIdentMLMzTabConverter

loadMsRun() - Method in class uk.ac.ebi.pride.utilities.data.exporters.AbstractMzTabConverter

Load all the files related with the original Identification file

loadMsRun() - Method in class uk.ac.ebi.pride.utilities.data.exporters.MzIdentMLMzTabConverter

loadMsRun() - Method in class uk.ac.ebi.pride.utilities.data.exporters.PRIDEMzTabConverter

loadProtein(Protein, List<Peptide>) - Method in class uk.ac.ebi.pride.utilities.data.exporters.MzIdentMLMzTabConverter

loadPSMs(List<Comparable>) - Method in class uk.ac.ebi.pride.utilities.data.exporters.MzIdentMLMzTabConverter

loadPSMs(Protein, List<Peptide>) - Method in class uk.ac.ebi.pride.utilities.data.exporters.MzIdentMLMzTabConverter

Converts the passed Identification object into an MzTab PSM.

loadReferences() - Method in class uk.ac.ebi.pride.utilities.data.exporters.AbstractMzTabConverter

Converts the experiment's references into a couple of PublicationItem (including DOIs and PubMed ids)

loadSampleProcessing() - Method in class uk.ac.ebi.pride.utilities.data.exporters.AbstractMzTabConverter

Load Sample Processing should be implemented by different controllers

loadSampleProcessing() - Method in class uk.ac.ebi.pride.utilities.data.exporters.MzIdentMLMzTabConverter

loadSampleProcessing() - Method in class uk.ac.ebi.pride.utilities.data.exporters.PRIDEMzTabConverter

loadSamples() - Method in class uk.ac.ebi.pride.utilities.data.exporters.AbstractMzTabConverter

Adds the sample parameters (species, tissue, cell type, disease) to the unit and the various sub-samples.

loadSamples() - Method in class uk.ac.ebi.pride.utilities.data.exporters.MzIdentMLMzTabConverter

Adds the sample parameters (species, tissue, cell type, disease) to the unit and the various sub-samples.

loadSamples() - Method in class uk.ac.ebi.pride.utilities.data.exporters.PRIDEMzTabConverter

loadSearchEngineScores() - Method in class uk.ac.ebi.pride.utilities.data.exporters.AbstractMzTabConverter

loadSoftware() - Method in class uk.ac.ebi.pride.utilities.data.exporters.AbstractMzTabConverter

Load software information

loadSoftware() - Method in class uk.ac.ebi.pride.utilities.data.exporters.MzIdentMLMzTabConverter

loadSoftware() - Method in class uk.ac.ebi.pride.utilities.data.exporters.PRIDEMzTabConverter

logger - Static variable in class uk.ac.ebi.pride.utilities.data.controller.DataAccessUtilities

logger - Static variable in class uk.ac.ebi.pride.utilities.data.exporters.AbstractMzTabConverter

logger - Static variable in class uk.ac.ebi.pride.utilities.data.exporters.HQMzIdentMLMzTabConverter

logger - Static variable in class uk.ac.ebi.pride.utilities.data.exporters.MzIdentMLMzTabConverter

M

MapUtils - Class in uk.ac.ebi.pride.utilities.data.utils

MassSpecObject - Interface in uk.ac.ebi.pride.utilities.data.core

All core objects should implement this interface.

MassTable - Class in uk.ac.ebi.pride.utilities.data.core

MassTable(List<Integer>, Map<String, Float>, Map<String, ParamGroup>) - Constructor for class uk.ac.ebi.pride.utilities.data.core.MassTable

MAX_SUB_SAMPLE_SIZE - Static variable in class uk.ac.ebi.pride.utilities.data.core.QuantitativeSample

MD5Utils - Class in uk.ac.ebi.pride.utilities.data.utils

MD5Utils provides static method

metadata - Variable in class uk.ac.ebi.pride.utilities.data.exporters.AbstractMzTabConverter

MetaDataAccess - Interface in uk.ac.ebi.pride.utilities.data.controller.access

MGF_EXT - Static variable in class uk.ac.ebi.pride.utilities.data.utils.Constants

MGFTitleCVtermValue(List<CvParam>) - Static method in class uk.ac.ebi.pride.utilities.data.utils.MzIdentMLUtils

Modification - Class in uk.ac.ebi.pride.utilities.data.core

A molecule modification specification.

Modification(String, String, int, List<String>, List<Double>, List<Double>, String, String) - Constructor for class uk.ac.ebi.pride.utilities.data.core.Modification

Constructor for PRIDE Modification Object

Modification(ParamGroup, String, String, int, List<String>, List<Double>, List<Double>, String, String) - Constructor for class uk.ac.ebi.pride.utilities.data.core.Modification

Constructor for Modification Objects

MS2_EXT - Static variable in class uk.ac.ebi.pride.utilities.data.utils.Constants

msDataAccessControllers - Variable in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.ReferencedIdentificationController

MzDataCachingStrategy - Class in uk.ac.ebi.pride.utilities.data.controller.cache.strategy

Class to Create the Cache for MzData Files.

MzDataCachingStrategy() - Constructor for class uk.ac.ebi.pride.utilities.data.controller.cache.strategy.MzDataCachingStrategy

MzDataControllerImpl - Class in uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl

This controller is used to retrieve the information from mzData files.

MzDataControllerImpl(File) - Constructor for class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzDataControllerImpl

MzDataTransformer - Class in uk.ac.ebi.pride.utilities.data.controller.impl.Transformer

This class provide the functions to convert and transform mzData objects to ms-core-api objetcs.

MzDataUnmarshallerAdaptor - Class in uk.ac.ebi.pride.utilities.data.io.file

The UnmarshallerAdaptor for MzData files retrieve the mzData objects from the mzdata_parser.

MzDataUnmarshallerAdaptor(MzDataFile) - Constructor for class uk.ac.ebi.pride.utilities.data.io.file.MzDataUnmarshallerAdaptor

MzGraph - Class in uk.ac.ebi.pride.utilities.data.core

Abstract object can be extended by both Spectrum and Chromatogram.

MzGraph(Comparable, String, int, DataProcessing, int, List<BinaryDataArray>) - Constructor for class uk.ac.ebi.pride.utilities.data.core.MzGraph

MzGraph(ParamGroup, Comparable, String, int, DataProcessing, int, List<BinaryDataArray>) - Constructor for class uk.ac.ebi.pride.utilities.data.core.MzGraph

MZGRAPH_TYPE - Static variable in interface uk.ac.ebi.pride.utilities.data.controller.access.MzGraphDataAccess

fired when a mz graph object has changed

MzGraphDataAccess - Interface in uk.ac.ebi.pride.utilities.data.controller.access

MzGraphDataAccess defines the interface for accessing mzgraph data.

MzGraphMetaData - Class in uk.ac.ebi.pride.utilities.data.core

This class storage the information related with metadata at the spectrum level.

MzGraphMetaData(Comparable, String, List<ScanSetting>, List<InstrumentConfiguration>, List<DataProcessing>) - Constructor for class uk.ac.ebi.pride.utilities.data.core.MzGraphMetaData

MzGraphMetaData(ParamGroup, Comparable, String, List<ScanSetting>, List<InstrumentConfiguration>, List<DataProcessing>) - Constructor for class uk.ac.ebi.pride.utilities.data.core.MzGraphMetaData

MzIdentMLCachingStrategy - Class in uk.ac.ebi.pride.utilities.data.controller.cache.strategy

The MzIdentMLCacheBuilder initialize the cache for mzidentml file reading.

MzIdentMLCachingStrategy() - Constructor for class uk.ac.ebi.pride.utilities.data.controller.cache.strategy.MzIdentMLCachingStrategy

MzIdentMLControllerImpl - Class in uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl

The MzIdentMLControllerImpl is the controller that retrieve the information from the mzidentml files.

MzIdentMLControllerImpl(File) - Constructor for class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzIdentMLControllerImpl

MzIdentMLControllerImpl(File, boolean) - Constructor for class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzIdentMLControllerImpl

MzIdentMLControllerImpl(File, boolean, boolean) - Constructor for class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzIdentMLControllerImpl

MzIdentMLMzTabConverter - Class in uk.ac.ebi.pride.utilities.data.exporters

MzIdentMLMzTabConverter(MzIdentMLControllerImpl) - Constructor for class uk.ac.ebi.pride.utilities.data.exporters.MzIdentMLMzTabConverter

Default constructor

MzIdentMLTransformer - Class in uk.ac.ebi.pride.utilities.data.controller.impl.Transformer

This class is the Transformer class from a jmzidml object to a core object.

MzIdentMLUnmarshallerAdaptor - Class in uk.ac.ebi.pride.utilities.data.io.file

MzMLIdentMLUnmarshallerAdaptor provides a list of convenient methods to access mzidentML files.

MzIdentMLUnmarshallerAdaptor(File, boolean) - Constructor for class uk.ac.ebi.pride.utilities.data.io.file.MzIdentMLUnmarshallerAdaptor

MzIdentMLUnmarshallerAdaptor(File, boolean, boolean) - Constructor for class uk.ac.ebi.pride.utilities.data.io.file.MzIdentMLUnmarshallerAdaptor

MzIdentMLUtils - Class in uk.ac.ebi.pride.utilities.data.utils

MzIdentML utilities class.

MZML_EXT - Static variable in class uk.ac.ebi.pride.utilities.data.utils.Constants

MzMlCachingStrategy - Class in uk.ac.ebi.pride.utilities.data.controller.cache.strategy

The CacheBuilder class provides the functionality to initialize the cache categories for mzML files.

MzMlCachingStrategy() - Constructor for class uk.ac.ebi.pride.utilities.data.controller.cache.strategy.MzMlCachingStrategy

MzMLControllerImpl - Class in uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl

MzMlControllerImpl provides methods to access mzML files.

MzMLControllerImpl(File) - Constructor for class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzMLControllerImpl

Construct a data access controller using a given mzML file

MzMLTransformer - Class in uk.ac.ebi.pride.utilities.data.controller.impl.Transformer

This class contains a set of static methods for converting jmzML object to the pride inspector core objects

MzMLUnmarshallerAdaptor - Class in uk.ac.ebi.pride.utilities.data.io.file

MzMLUnmarshallerHelper provides a list of convenient methods to access mzML files

MzMLUnmarshallerAdaptor(File) - Constructor for class uk.ac.ebi.pride.utilities.data.io.file.MzMLUnmarshallerAdaptor

MZTAB_EXT - Static variable in class uk.ac.ebi.pride.utilities.data.utils.Constants

MzTabBedConverter - Class in uk.ac.ebi.pride.utilities.data.exporters

Class to convert MzTab files to Bed files.

MzTabBedConverter(MzTabControllerImpl) - Constructor for class uk.ac.ebi.pride.utilities.data.exporters.MzTabBedConverter

Constructor to setup conversion of an mzTabFile into a bed file.

MzTabCachingStrategy - Class in uk.ac.ebi.pride.utilities.data.controller.cache.strategy

Cache the mzTab structures such as proteins, peptide evidences and spectrum references //Todo: No way to match PSMs and Peptides which means that the current model is only for Protein + PMSs for identifications and Protein + Peptides for Quantitation.

MzTabCachingStrategy() - Constructor for class uk.ac.ebi.pride.utilities.data.controller.cache.strategy.MzTabCachingStrategy

MzTabControllerImpl - Class in uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl

MzTab DataAccessController for MzTab Files.

MzTabControllerImpl(File) - Constructor for class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzTabControllerImpl

MzTabTransformer - Class in uk.ac.ebi.pride.utilities.data.controller.impl.Transformer

MzTab Transformer to ms-data-core-api Objects.

MzTabTransformer() - Constructor for class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzTabTransformer

MzTabUnmarshallerAdaptor - Class in uk.ac.ebi.pride.utilities.data.io.file

Unmarshaller an MZTab file

MzTabUnmarshallerAdaptor(File, OutputStream) - Constructor for class uk.ac.ebi.pride.utilities.data.io.file.MzTabUnmarshallerAdaptor

MzTabUtils - Class in uk.ac.ebi.pride.utilities.data.utils

MzTabUtils() - Constructor for class uk.ac.ebi.pride.utilities.data.utils.MzTabUtils

MZXML_EXT - Static variable in class uk.ac.ebi.pride.utilities.data.utils.Constants

MzXmlCachingStrategy - Class in uk.ac.ebi.pride.utilities.data.controller.cache.strategy

MzMlAccessCacheBuilder initialize the cache for mzML reading.

MzXmlCachingStrategy() - Constructor for class uk.ac.ebi.pride.utilities.data.controller.cache.strategy.MzXmlCachingStrategy

MzXmlControllerImpl - Class in uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl

This class is the controller to parse an retrieve the information from mzXML files, It retrieve the spectrum information, and also the most important metadata, the relevant and portable to the ms-core-api information from the mzXML files.

MzXmlControllerImpl(File) - Constructor for class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzXmlControllerImpl

MzXmlTransformer - Class in uk.ac.ebi.pride.utilities.data.controller.impl.Transformer

MZXml transformer provides the methods to convert MzXml objects to ms-core-api objetcs.

MzXmlUnmarshallerAdaptor - Class in uk.ac.ebi.pride.utilities.data.io.file

The MzXML Unmarshaller Adaptor provides the methods to retrieve the information form the mzxml_parser library.

MzXmlUnmarshallerAdaptor(MzXMLFile) - Constructor for class uk.ac.ebi.pride.utilities.data.io.file.MzXmlUnmarshallerAdaptor

N

NO_THRESHOLD - Static variable in class uk.ac.ebi.pride.utilities.data.exporters.HQMzIdentMLMzTabConverter

NO_THRESHOLD_MS_AC - Static variable in class uk.ac.ebi.pride.utilities.data.exporters.HQMzIdentMLMzTabConverter

NoPeptideFilter - Class in uk.ac.ebi.pride.utilities.data.filter

NoPeptideFilter() - Constructor for class uk.ac.ebi.pride.utilities.data.filter.NoPeptideFilter

NoProteinFilter - Class in uk.ac.ebi.pride.utilities.data.filter

NoProteinFilter() - Constructor for class uk.ac.ebi.pride.utilities.data.filter.NoProteinFilter

NOT_AVAILABLE - Static variable in class uk.ac.ebi.pride.utilities.data.utils.Constants

NUM_MERGE_PROTEINS - Static variable in class uk.ac.ebi.pride.utilities.data.utils.PRIDEUtils

O

OPTIONAL_CHROM_COLUMN - Static variable in class uk.ac.ebi.pride.utilities.data.utils.MzTabUtils

OPTIONAL_CHROMEND_COLUMN - Static variable in class uk.ac.ebi.pride.utilities.data.utils.MzTabUtils

OPTIONAL_CHROMSTART_COLUMN - Static variable in class uk.ac.ebi.pride.utilities.data.utils.MzTabUtils

OPTIONAL_DECOY_COLUMN - Static variable in class uk.ac.ebi.pride.utilities.data.utils.MzTabUtils

OPTIONAL_ID_COLUMN - Static variable in class uk.ac.ebi.pride.utilities.data.utils.MzTabUtils

OPTIONAL_PREDICTION_COLUMN - Static variable in class uk.ac.ebi.pride.utilities.data.utils.MzTabUtils

OPTIONAL_PROTEIN_NAME_COLUMN - Static variable in class uk.ac.ebi.pride.utilities.data.utils.MzTabUtils

OPTIONAL_PSM_FDRSCORE_COLUMN - Static variable in class uk.ac.ebi.pride.utilities.data.utils.MzTabUtils

OPTIONAL_RANK_COLUMN - Static variable in class uk.ac.ebi.pride.utilities.data.utils.MzTabUtils

OPTIONAL_SEQUENCE_COLUMN - Static variable in class uk.ac.ebi.pride.utilities.data.utils.MzTabUtils

OPTIONAL_STRAND_COLUMN - Static variable in class uk.ac.ebi.pride.utilities.data.utils.MzTabUtils

Organization - Class in uk.ac.ebi.pride.utilities.data.core

Organizations are entities like companies, universities, government agencies.

Organization(ParamGroup, String, String) - Constructor for class uk.ac.ebi.pride.utilities.data.core.Organization

Organization(Comparable, String, String, Organization) - Constructor for class uk.ac.ebi.pride.utilities.data.core.Organization

Organization(ParamGroup, Comparable, String, Organization, String) - Constructor for class uk.ac.ebi.pride.utilities.data.core.Organization

P

Parameter - Class in uk.ac.ebi.pride.utilities.data.core

Parameter exist in neither PRIDE XML nor mzML, it created for method sharing.

Parameter(String, String, String, String, String) - Constructor for class uk.ac.ebi.pride.utilities.data.core.Parameter

Constructor

ParamGroup - Class in uk.ac.ebi.pride.utilities.data.core

ParamGroup is a container for CvParams and UserParams.

ParamGroup() - Constructor for class uk.ac.ebi.pride.utilities.data.core.ParamGroup

Constructor creates an empty param group

ParamGroup(ParamGroup) - Constructor for class uk.ac.ebi.pride.utilities.data.core.ParamGroup

ParamGroup(CvParam, UserParam) - Constructor for class uk.ac.ebi.pride.utilities.data.core.ParamGroup

ParamGroup(List<CvParam>, List<UserParam>) - Constructor for class uk.ac.ebi.pride.utilities.data.core.ParamGroup

Constructor

parseQuantitationReagentCvParam(Param) - Static method in class uk.ac.ebi.pride.utilities.data.utils.MzTabUtils

Param for the reagent to retrieve the PRIDE Term for that, is important that most of the fields can be null, for that reason we look through all the the information looking for patterns.

PeakCachingStrategy - Class in uk.ac.ebi.pride.utilities.data.controller.cache.strategy

PeakCacheBuilder provides the methods to initialize the Cache Categories for pure peaks list file formats.

PeakCachingStrategy() - Constructor for class uk.ac.ebi.pride.utilities.data.controller.cache.strategy.PeakCachingStrategy

PeakControllerImpl - Class in uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl

Peak Controller keep the information from different Peak files.

PeakControllerImpl(File) - Constructor for class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.PeakControllerImpl

Construct a data access controller using a given mzML file

PeakControllerImpl(File, boolean) - Constructor for class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.PeakControllerImpl

PeakTransformer - Class in uk.ac.ebi.pride.utilities.data.controller.impl.Transformer

PeakTransformer provides the functionality to convert peak objects to ms-core-api objects.

PeakUnmarshallerAdaptor - Class in uk.ac.ebi.pride.utilities.data.io.file

Retrieve the information from different pure file formats using the JMzReader library.

PeakUnmarshallerAdaptor(JMzReader, boolean) - Constructor for class uk.ac.ebi.pride.utilities.data.io.file.PeakUnmarshallerAdaptor

Peptide - Class in uk.ac.ebi.pride.utilities.data.core

The class Peptide Manage the information for peptide Identifications

Peptide(PeptideEvidence, SpectrumIdentification) - Constructor for class uk.ac.ebi.pride.utilities.data.core.Peptide

PEPTIDE_C_TERM - Static variable in class uk.ac.ebi.pride.utilities.data.exporters.MzIdentMLMzTabConverter

PEPTIDE_N_TERM - Static variable in class uk.ac.ebi.pride.utilities.data.exporters.MzIdentMLMzTabConverter

PeptideDataAccess - Interface in uk.ac.ebi.pride.utilities.data.controller.access

PeptideDataAccess defines methods for accessing peptide related information.

PeptideEvidence - Class in uk.ac.ebi.pride.utilities.data.core

PeptideEvidence links a specific Peptide Element to a specific position in a DBSequence.

PeptideEvidence(String, String, Integer, Integer, Boolean, PeptideSequence, DBSequence) - Constructor for class uk.ac.ebi.pride.utilities.data.core.PeptideEvidence

PeptideEvidence(ParamGroup, String, String, Integer, Integer, boolean, PeptideSequence, DBSequence) - Constructor for class uk.ac.ebi.pride.utilities.data.core.PeptideEvidence

PeptideFilter - Interface in uk.ac.ebi.pride.utilities.data.filter

PeptideSequence - Class in uk.ac.ebi.pride.utilities.data.core

One (poly)peptide (a sequence with modifications).

PeptideSequence(String, List<Modification>) - Constructor for class uk.ac.ebi.pride.utilities.data.core.PeptideSequence

PeptideSequence(String, String, String, List<Modification>) - Constructor for class uk.ac.ebi.pride.utilities.data.core.PeptideSequence

PeptideSequence(ParamGroup, String, String, String, List<Modification>) - Constructor for class uk.ac.ebi.pride.utilities.data.core.PeptideSequence

PeptideSequence(String, String, String, List<Modification>, List<SubstitutionModification>) - Constructor for class uk.ac.ebi.pride.utilities.data.core.PeptideSequence

PeptideSequence(List<CvParam>, List<UserParam>, String, String, String, List<Modification>) - Constructor for class uk.ac.ebi.pride.utilities.data.core.PeptideSequence

PeptideSequence(List<CvParam>, List<UserParam>, String, String, String, List<Modification>, List<SubstitutionModification>) - Constructor for class uk.ac.ebi.pride.utilities.data.core.PeptideSequence

PeptideSequence(ParamGroup, String, String, String, List<Modification>, List<SubstitutionModification>) - Constructor for class uk.ac.ebi.pride.utilities.data.core.PeptideSequence

Person - Class in uk.ac.ebi.pride.utilities.data.core

A person's name and contact details.

Person(ParamGroup, String, String) - Constructor for class uk.ac.ebi.pride.utilities.data.core.Person

Person(Comparable, String, String, String, String, List<Organization>, String) - Constructor for class uk.ac.ebi.pride.utilities.data.core.Person

Person(ParamGroup, Comparable, String, String, String, String, List<Organization>, String) - Constructor for class uk.ac.ebi.pride.utilities.data.core.Person

PKL_EXT - Static variable in class uk.ac.ebi.pride.utilities.data.utils.Constants

populateCache() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

Precursor - Class in uk.ac.ebi.pride.utilities.data.core

The method of precursor ion selection and activation

Precursor(Spectrum, SourceFile, String, ParamGroup, List<ParamGroup>, ParamGroup) - Constructor for class uk.ac.ebi.pride.utilities.data.core.Precursor

Constructor

PRIDEMzTabConverter - Class in uk.ac.ebi.pride.utilities.data.exporters

PRIDEMzTabConverter(DataAccessController) - Constructor for class uk.ac.ebi.pride.utilities.data.exporters.PRIDEMzTabConverter

PRIDEUtils - Class in uk.ac.ebi.pride.utilities.data.utils

PRIDEUtils() - Constructor for class uk.ac.ebi.pride.utilities.data.utils.PRIDEUtils

PrideXmlCachingStrategy - Class in uk.ac.ebi.pride.utilities.data.controller.cache.strategy

PrideXmlAccessCacheBuilder initialize the cache for pride xml reading.

PrideXmlCachingStrategy() - Constructor for class uk.ac.ebi.pride.utilities.data.controller.cache.strategy.PrideXmlCachingStrategy

PrideXmlControllerImpl - Class in uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl

PrideXmlControllerImpl is responsible for reading Pride Xml files.

PrideXmlControllerImpl(File) - Constructor for class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.PrideXmlControllerImpl

PrideXmlTransformer - Class in uk.ac.ebi.pride.utilities.data.controller.impl.Transformer

PrideXmlTransformer contains a list of static methods which convert pride-jaxb objects to pride inspector core objects

ProcessingMethod - Class in uk.ac.ebi.pride.utilities.data.core

Description of the default peak processing method.

ProcessingMethod(int, Software, ParamGroup) - Constructor for class uk.ac.ebi.pride.utilities.data.core.ProcessingMethod

Constructor

Protein - Class in uk.ac.ebi.pride.utilities.data.core

Abstract class for both GelFreeIdentification and TwoDimIdentification

Protein(Comparable, String, DBSequence, boolean, List<Peptide>, Score, double, double, Gel) - Constructor for class uk.ac.ebi.pride.utilities.data.core.Protein

Constructor for Protein Entity Identification

Protein(ParamGroup, Comparable, String, DBSequence, boolean, List<Peptide>, Score, double, double, Gel) - Constructor for class uk.ac.ebi.pride.utilities.data.core.Protein

Constructor for Protein Entity Identification with CVParams

Protein(ParamGroup, Comparable, String, DBSequence, boolean, List<Peptide>, Score, double, double, Gel, QuantScore) - Constructor for class uk.ac.ebi.pride.utilities.data.core.Protein

Constructor for Protein Entity Identification with CVParams and Quantitation Score based on mzTab model

Protein(ParamGroup, Comparable, String, DBSequence, boolean, List<Peptide>, Score, double, double, Gel, QuantScore, List<QuantPeptide>) - Constructor for class uk.ac.ebi.pride.utilities.data.core.Protein

Constructor for Protein Entity Identification with CVParams and Quantitation Score based on mzTab model

PROTEIN_C_TERM - Static variable in class uk.ac.ebi.pride.utilities.data.exporters.MzIdentMLMzTabConverter

PROTEIN_N_TERM - Static variable in class uk.ac.ebi.pride.utilities.data.exporters.MzIdentMLMzTabConverter

proteinColumnFactory - Variable in class uk.ac.ebi.pride.utilities.data.exporters.AbstractMzTabConverter

ProteinDataAccess - Interface in uk.ac.ebi.pride.utilities.data.controller.access

ProteinDataAccess defines the interface for accessing identification data.

ProteinFilter - Interface in uk.ac.ebi.pride.utilities.data.filter

ProteinGroup - Class in uk.ac.ebi.pride.utilities.data.core

A set of logically related results from a protein detection, for example to represent conflicting assignments of peptides to proteins

ProteinGroup(Comparable, String, List<Protein>) - Constructor for class uk.ac.ebi.pride.utilities.data.core.ProteinGroup

ProteinGroup(ParamGroup, Comparable, String, List<Protein>) - Constructor for class uk.ac.ebi.pride.utilities.data.core.ProteinGroup

ProteinGroupDataAccess - Interface in uk.ac.ebi.pride.utilities.data.controller.access

ProteinAmbiguityGroupDataAccess defines the interface for accessing protein grouping information.

proteinIds - Variable in class uk.ac.ebi.pride.utilities.data.exporters.MzIdentMLMzTabConverter

proteinsAreInferred() - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

returns true if the proteins are inferred externally

proteinScoreToScoreIndex - Variable in class uk.ac.ebi.pride.utilities.data.exporters.AbstractMzTabConverter

Protocol - Class in uk.ac.ebi.pride.utilities.data.core

The collection of protocols which include the parameters and settings of the performed analyses.

Protocol(Comparable, String, ParamGroup) - Constructor for class uk.ac.ebi.pride.utilities.data.core.Protocol

Protocol(ParamGroup, Comparable, String, Software, ParamGroup) - Constructor for class uk.ac.ebi.pride.utilities.data.core.Protocol

Provider - Class in uk.ac.ebi.pride.utilities.data.core

Provider object.

Provider(Comparable, String, Software, Contact, CvParam) - Constructor for class uk.ac.ebi.pride.utilities.data.core.Provider

psmColumnFactory - Variable in class uk.ac.ebi.pride.utilities.data.exporters.AbstractMzTabConverter

psmScoreToScoreIndex - Variable in class uk.ac.ebi.pride.utilities.data.exporters.AbstractMzTabConverter

Q

QuantDataAccess - Interface in uk.ac.ebi.pride.utilities.data.controller.access

QuantDataAccess defines methods for accessing quantitative proteomics data

Quantification - Class in uk.ac.ebi.pride.utilities.data.core

Quantitation object is a pseudo object which contains all the cv params related to quantitative data for PRIDE XMLs.

Quantification(Quantification.Type, List<CvParam>) - Constructor for class uk.ac.ebi.pride.utilities.data.core.Quantification

Quantification.Type - Enum in uk.ac.ebi.pride.utilities.data.core

The type of the identification;

QuantitativeSample - Class in uk.ac.ebi.pride.utilities.data.core

QuantitativeSample which contains quantitative related information This is mainly for PRIDE XMl

QuantitativeSample() - Constructor for class uk.ac.ebi.pride.utilities.data.core.QuantitativeSample

QuantPeptide - Class in uk.ac.ebi.pride.utilities.data.core

Quantitative Peptide is a Peptide with Quantitation information and is used in mzTab file formats.

QuantPeptide(PeptideEvidence, SpectrumIdentification, QuantScore) - Constructor for class uk.ac.ebi.pride.utilities.data.core.QuantPeptide

QuantScore - Class in uk.ac.ebi.pride.utilities.data.core

The QuantScore is the List of StudyVariable Scores and the Abundance by Assays.

QuantScore(Comparable, String, Map<Comparable, Double>, Map<Comparable, Double>) - Constructor for class uk.ac.ebi.pride.utilities.data.core.QuantScore

Default Constructor for QuantScore.

QuantScore(ParamGroup, Comparable, String, Map<Comparable, Double>, Map<Comparable, Double>) - Constructor for class uk.ac.ebi.pride.utilities.data.core.QuantScore

Default Constructor for QuantScore.

QuantScore(Map<Comparable, Double>, Map<Comparable, Double>) - Constructor for class uk.ac.ebi.pride.utilities.data.core.QuantScore

Default Constructor for QuantScore without Cv Params

R

RankOnePeptideFilter - Class in uk.ac.ebi.pride.utilities.data.filter

RankOnePeptideFilter() - Constructor for class uk.ac.ebi.pride.utilities.data.filter.RankOnePeptideFilter

Reference - Class in uk.ac.ebi.pride.utilities.data.core

Reference is added by PRIDE XML 2.0., also a generic reference for mzIdentML References.

Reference(ParamGroup, String) - Constructor for class uk.ac.ebi.pride.utilities.data.core.Reference

Reference(List<CvParam>, List<UserParam>, String, String, String) - Constructor for class uk.ac.ebi.pride.utilities.data.core.Reference

Reference(String, String, String, String, String, String, String, String, String, String, String, String, String) - Constructor for class uk.ac.ebi.pride.utilities.data.core.Reference

Reference(ParamGroup, String, String, String, String, String, String, String, String, String, String, String, String, String) - Constructor for class uk.ac.ebi.pride.utilities.data.core.Reference

Reference(List<CvParam>, List<UserParam>, String, String, String, String, String, String, String, String, String, String, String, String, String) - Constructor for class uk.ac.ebi.pride.utilities.data.core.Reference

ReferenceableParamGroup - Class in uk.ac.ebi.pride.utilities.data.core

Referenceable param group stores a map of reference string to param group.

ReferenceableParamGroup(Map<String, ParamGroup>) - Constructor for class uk.ac.ebi.pride.utilities.data.core.ReferenceableParamGroup

ReferencedIdentificationController - Class in uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl

Abstract Class that contains methods shared by mzTab controller and mzIdentML controller and also some data structures share for both classes.

ReferencedIdentificationController(File, DataAccessMode) - Constructor for class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.ReferencedIdentificationController

removeCvParam(CvParam) - Method in class uk.ac.ebi.pride.utilities.data.core.ParamGroup

removeCvParams(List<CvParam>) - Method in class uk.ac.ebi.pride.utilities.data.core.ParamGroup

removeEldestEntry(Map.Entry) - Method in class uk.ac.ebi.pride.utilities.data.controller.cache.CachedMap

removeNewLineAndTab(String) - Static method in class uk.ac.ebi.pride.utilities.data.utils.MzTabUtils

If there exists reserved characters in value, remove them all.

removeRefParamGroup(String) - Method in class uk.ac.ebi.pride.utilities.data.core.ReferenceableParamGroup

removeScore(SearchEngineCvTermReference) - Method in class uk.ac.ebi.pride.utilities.data.core.Score

Remove all the scores assigned to the input search engine.

removeScore(SearchEngineCvTermReference, SearchEngineScoreCvTermReference) - Method in class uk.ac.ebi.pride.utilities.data.core.Score

Remove peptide score with specified search engine and cv term reference

removeUserParam(UserParam) - Method in class uk.ac.ebi.pride.utilities.data.core.ParamGroup

removeUserParams(List<UserParam>) - Method in class uk.ac.ebi.pride.utilities.data.core.ParamGroup

replaceValuesInCollection(Collection<T>, Collection<T>) - Static method in class uk.ac.ebi.pride.utilities.data.utils.CollectionUtils

replaceValuesInMap(Map<T, V>, Map<T, V>) - Static method in class uk.ac.ebi.pride.utilities.data.utils.MapUtils

S

Sample - Class in uk.ac.ebi.pride.utilities.data.core

Description of the sample used to generate the Dataset.

Sample(ParamGroup, String, String) - Constructor for class uk.ac.ebi.pride.utilities.data.core.Sample

Sample(ParamGroup, String, String, List<Sample>, Map<Contact, CvParam>) - Constructor for class uk.ac.ebi.pride.utilities.data.core.Sample

Scan - Class in uk.ac.ebi.pride.utilities.data.core

Scan or acquisition from original raw file used to create this peak list, as specified in sourceFile.

Scan(String, String, SourceFile, InstrumentConfiguration, List<ParamGroup>, ParamGroup) - Constructor for class uk.ac.ebi.pride.utilities.data.core.Scan

Constructor

ScanList - Class in uk.ac.ebi.pride.utilities.data.core

List and descriptions of scans.

ScanList(List<Scan>, ParamGroup) - Constructor for class uk.ac.ebi.pride.utilities.data.core.ScanList

Constructor

ScanSetting - Class in uk.ac.ebi.pride.utilities.data.core

Description of the acquisition settings or the instrument prior to the start of the run.

ScanSetting(String, List<SourceFile>, List<ParamGroup>, ParamGroup) - Constructor for class uk.ac.ebi.pride.utilities.data.core.ScanSetting

Constructor

Score - Class in uk.ac.ebi.pride.utilities.data.core

Score stores a number of scores from a list of search engines.

Score() - Constructor for class uk.ac.ebi.pride.utilities.data.core.Score

Score(Map<SearchEngineCvTermReference, Map<SearchEngineScoreCvTermReference, Number>>) - Constructor for class uk.ac.ebi.pride.utilities.data.core.Score

SearchDataBase - Class in uk.ac.ebi.pride.utilities.data.core

A database for searching mass spectra.

SearchDataBase(String, String) - Constructor for class uk.ac.ebi.pride.utilities.data.core.SearchDataBase

Constructor with name and database Version

SearchDataBase(String, String, ParamGroup) - Constructor for class uk.ac.ebi.pride.utilities.data.core.SearchDataBase

Database with name, version, DatabaseName in the form of CvParam

SearchDataBase(String, String, String, CvParam, String, String, String, int, long, ParamGroup, List<CvParam>) - Constructor for class uk.ac.ebi.pride.utilities.data.core.SearchDataBase

SearchModification - Class in uk.ac.ebi.pride.utilities.data.core

Search Modification is the variable or fixed modification defined in the Identification Search by the user.

SearchModification(boolean, double, List<String>, List<CvParam>, List<CvParam>) - Constructor for class uk.ac.ebi.pride.utilities.data.core.SearchModification

setAccession(String) - Method in class uk.ac.ebi.pride.utilities.data.core.CvParam

setAccession(String) - Method in class uk.ac.ebi.pride.utilities.data.core.DBSequence

setAccessionVersion(String) - Method in class uk.ac.ebi.pride.utilities.data.core.DBSequence

setActivation(ParamGroup) - Method in class uk.ac.ebi.pride.utilities.data.core.Precursor

setAddress(String) - Method in class uk.ac.ebi.pride.utilities.data.core.CVLookup

setAffiliation(List<Organization>) - Method in class uk.ac.ebi.pride.utilities.data.core.Person

setAllowedFrames(List<Integer>) - Method in class uk.ac.ebi.pride.utilities.data.core.DataBaseTranslation

setAmbiguousResidues(Map<String, ParamGroup>) - Method in class uk.ac.ebi.pride.utilities.data.core.MassTable

setAnalysisParam(ParamGroup) - Method in class uk.ac.ebi.pride.utilities.data.core.Protocol

setAnalysisSoftware(Software) - Method in class uk.ac.ebi.pride.utilities.data.core.Protocol

setAnalyzer(List<InstrumentComponent>) - Method in class uk.ac.ebi.pride.utilities.data.core.InstrumentConfiguration

setAssay(Assay) - Method in class uk.ac.ebi.pride.utilities.data.core.AbundanceAssay

setAssayAbundance(Map<Comparable, Double>) - Method in class uk.ac.ebi.pride.utilities.data.core.QuantScore

Return the Assay Abundance

setAssays(List<Assay>) - Method in class uk.ac.ebi.pride.utilities.data.core.StudyVariable

setAuthors(String) - Method in class uk.ac.ebi.pride.utilities.data.core.Reference

setAvgMassDelta(List<Double>) - Method in class uk.ac.ebi.pride.utilities.data.core.Modification

Get Average Mass Delta List

setAvgMassDelta(double) - Method in class uk.ac.ebi.pride.utilities.data.core.SubstitutionModification

setBinaryDataArrays(List<BinaryDataArray>) - Method in class uk.ac.ebi.pride.utilities.data.core.MzGraph

setCache(Cache) - Method in interface uk.ac.ebi.pride.utilities.data.controller.cache.CachingStrategy

setCache(Cache) - Method in class uk.ac.ebi.pride.utilities.data.controller.cache.strategy.AbstractCachingStrategy

setCachingStrategy(CachingStrategy) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

setCalculatedMassToCharge(double) - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentification

setCalculatedPI(double) - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentification

setCellLine(CvParam) - Method in class uk.ac.ebi.pride.utilities.data.core.QuantitativeSample

Add cell line information to a subsample

setCellLine(int, CvParam) - Method in class uk.ac.ebi.pride.utilities.data.core.QuantitativeSample

Add cell line information to a subsample

setCharge(int) - Method in class uk.ac.ebi.pride.utilities.data.core.FragmentIon

setCharge(int) - Method in class uk.ac.ebi.pride.utilities.data.core.IonType

setChargeState(int) - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentification

setContact(Contact) - Method in class uk.ac.ebi.pride.utilities.data.core.ContactRole

setContact(Contact) - Method in class uk.ac.ebi.pride.utilities.data.core.Provider

setContact(Contact) - Method in class uk.ac.ebi.pride.utilities.data.core.Software

setContactInfo(String) - Method in class uk.ac.ebi.pride.utilities.data.core.Person

setContactRoles(Map<Contact, CvParam>) - Method in class uk.ac.ebi.pride.utilities.data.core.Sample

setContentCategories(DataAccessController.ContentCategory...) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

setController(DataAccessController) - Method in class uk.ac.ebi.pride.utilities.data.controller.cache.strategy.AbstractCachingStrategy

setCreationDate(Date) - Method in class uk.ac.ebi.pride.utilities.data.core.ExperimentMetaData

setcTermGain(String) - Method in class uk.ac.ebi.pride.utilities.data.core.Enzyme

setCustomization(String) - Method in class uk.ac.ebi.pride.utilities.data.core.Software

setCvLabel(String) - Method in class uk.ac.ebi.pride.utilities.data.core.CVLookup

setCvLookupID(String) - Method in class uk.ac.ebi.pride.utilities.data.core.CvParam

setCvLookupMap(Map<String, CVLookup>) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzIdentMLTransformer

setCvParams(List<CvParam>) - Method in class uk.ac.ebi.pride.utilities.data.core.ParamGroup

setCvParams(List<CvParam>) - Method in class uk.ac.ebi.pride.utilities.data.core.SearchModification

setDataAccessController(DataAccessController) - Method in interface uk.ac.ebi.pride.utilities.data.controller.cache.CachingStrategy

setDataAccessController(DataAccessController) - Method in class uk.ac.ebi.pride.utilities.data.controller.cache.strategy.AbstractCachingStrategy

setDataBaseTranslation(DataBaseTranslation) - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentificationProtocol

setDataProcessing(DataProcessing) - Method in class uk.ac.ebi.pride.utilities.data.core.BinaryDataArray

setDataProcessing(DataProcessing) - Method in class uk.ac.ebi.pride.utilities.data.core.MzGraph

setDataProcessings(List<DataProcessing>) - Method in class uk.ac.ebi.pride.utilities.data.core.MzGraphMetaData

setDbSequence(DBSequence) - Method in class uk.ac.ebi.pride.utilities.data.core.PeptideEvidence

setDbSequence(DBSequence) - Method in class uk.ac.ebi.pride.utilities.data.core.Protein

setDecoy(boolean) - Method in class uk.ac.ebi.pride.utilities.data.core.PeptideEvidence

setDefaultArrayLength(int) - Method in class uk.ac.ebi.pride.utilities.data.core.MzGraph

setDescription(CvParam) - Method in class uk.ac.ebi.pride.utilities.data.core.QuantitativeSample

Add description to a subsample

setDescription(int, CvParam) - Method in class uk.ac.ebi.pride.utilities.data.core.QuantitativeSample

Add description to a subsample

setDescription(List<CvParam>) - Method in class uk.ac.ebi.pride.utilities.data.core.SearchDataBase

setDescription(String) - Method in class uk.ac.ebi.pride.utilities.data.core.StudyVariable

setDetector(List<InstrumentComponent>) - Method in class uk.ac.ebi.pride.utilities.data.core.InstrumentConfiguration

setDisease(CvParam) - Method in class uk.ac.ebi.pride.utilities.data.core.QuantitativeSample

Add disease information to a subsample

setDisease(int, CvParam) - Method in class uk.ac.ebi.pride.utilities.data.core.QuantitativeSample

Add disease information to a subsample

setDoi(String) - Method in class uk.ac.ebi.pride.utilities.data.core.Reference

setDoubleArray(double[]) - Method in class uk.ac.ebi.pride.utilities.data.core.BinaryDataArray

setEditor(String) - Method in class uk.ac.ebi.pride.utilities.data.core.Reference

setEndPosition(int) - Method in class uk.ac.ebi.pride.utilities.data.core.PeptideEvidence

setEnzymeIndependent(boolean) - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentificationProtocol

setEnzymeName(ParamGroup) - Method in class uk.ac.ebi.pride.utilities.data.core.Enzyme

setEnzymes(List<Enzyme>) - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentificationProtocol

setExclude(ParamGroup) - Method in class uk.ac.ebi.pride.utilities.data.core.Filter

setExperimentalMassToCharge(double) - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentification

setExternalFormatDocumentationURI(String) - Method in class uk.ac.ebi.pride.utilities.data.core.ExternalData

setExternalFormatDocumentationURI(String) - Method in class uk.ac.ebi.pride.utilities.data.core.SourceFile

setExternalSpecRef(String) - Method in class uk.ac.ebi.pride.utilities.data.core.Scan

setExternalSpectrumID(String) - Method in class uk.ac.ebi.pride.utilities.data.core.Precursor

setFileContent(ParamGroup) - Method in class uk.ac.ebi.pride.utilities.data.core.MzGraphMetaData

setFileFormat(CvParam) - Method in class uk.ac.ebi.pride.utilities.data.core.ExternalData

setFileFormat(CvParam) - Method in class uk.ac.ebi.pride.utilities.data.core.SourceFile

setFilters(List<Filter>) - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentificationProtocol

setFilterType(ParamGroup) - Method in class uk.ac.ebi.pride.utilities.data.core.Filter

setFirstname(String) - Method in class uk.ac.ebi.pride.utilities.data.core.Person

setFixedMod(boolean) - Method in class uk.ac.ebi.pride.utilities.data.core.SearchModification

setFragmentation(List<FragmentIon>) - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentification

setFragmentationTable(Map<String, IdentifiableParamGroup>) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzIdentMLTransformer

setFragmentationTable(List<IdentifiableParamGroup>) - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentificationList

setFragmentTolerance(List<CvParam>) - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentificationProtocol

setFrame(int) - Method in class uk.ac.ebi.pride.utilities.data.core.PeptideEvidence

setFullName(String) - Method in class uk.ac.ebi.pride.utilities.data.core.CVLookup

setFullReference(String) - Method in class uk.ac.ebi.pride.utilities.data.core.Reference

setGel(Gel) - Method in class uk.ac.ebi.pride.utilities.data.core.Protein

setGelLink(String) - Method in class uk.ac.ebi.pride.utilities.data.core.Gel

setGOTerm(CvParam) - Method in class uk.ac.ebi.pride.utilities.data.core.QuantitativeSample

Add GO information to a subsample

setGOTerm(int, CvParam) - Method in class uk.ac.ebi.pride.utilities.data.core.QuantitativeSample

Add GO information to a subsample

setId(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.core.Identifiable

setId(Comparable) - Method in class uk.ac.ebi.pride.utilities.data.core.IdentifiableParamGroup

setId(String) - Method in class uk.ac.ebi.pride.utilities.data.core.InstrumentConfiguration

setId(String) - Method in class uk.ac.ebi.pride.utilities.data.core.ScanSetting

setInclude(ParamGroup) - Method in class uk.ac.ebi.pride.utilities.data.core.Filter

setIndex(List<Integer>) - Method in class uk.ac.ebi.pride.utilities.data.core.IonType

setIndex(int) - Method in class uk.ac.ebi.pride.utilities.data.core.MzGraph

setInferredProteinGroups(Map<Comparable, Map<Comparable, List<Comparable>>>) - Method in interface uk.ac.ebi.pride.utilities.data.controller.access.ProteinGroupDataAccess

This method sets the protein groups calculated by a protein inference.

setInferredProteinGroups(Map<Comparable, Map<Comparable, List<Comparable>>>) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

setInstrumentConfiguration(InstrumentConfiguration) - Method in class uk.ac.ebi.pride.utilities.data.core.Scan

setInstrumentConfigurations(List<InstrumentConfiguration>) - Method in class uk.ac.ebi.pride.utilities.data.core.MzGraphMetaData

setIntensity(double) - Method in class uk.ac.ebi.pride.utilities.data.core.FragmentIon

setIonType(String) - Method in class uk.ac.ebi.pride.utilities.data.core.FragmentIon

setIonTypeAccession(String) - Method in class uk.ac.ebi.pride.utilities.data.core.FragmentIon

setIsolationWindow(ParamGroup) - Method in class uk.ac.ebi.pride.utilities.data.core.Precursor

setIssue(String) - Method in class uk.ac.ebi.pride.utilities.data.core.Reference

setLastname(String) - Method in class uk.ac.ebi.pride.utilities.data.core.Person

setLength(int) - Method in class uk.ac.ebi.pride.utilities.data.core.DBSequence

setLocation(String) - Method in class uk.ac.ebi.pride.utilities.data.core.ExternalData

setLocation(int) - Method in class uk.ac.ebi.pride.utilities.data.core.FragmentIon

setLocation(int) - Method in class uk.ac.ebi.pride.utilities.data.core.Modification

Set Location of the Modification

setLocation(int) - Method in class uk.ac.ebi.pride.utilities.data.core.SubstitutionModification

setMail(String) - Method in class uk.ac.ebi.pride.utilities.data.core.Organization

setMassDelta(double) - Method in class uk.ac.ebi.pride.utilities.data.core.SearchModification

setMassError(double) - Method in class uk.ac.ebi.pride.utilities.data.core.FragmentIon

setMassIntensityMap(double[][]) - Method in class uk.ac.ebi.pride.utilities.data.core.Spectrum

setMassTable(MassTable) - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentification

setMassTables(List<MassTable>) - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentificationProtocol

setMeasures(Map<IdentifiableParamGroup, List<Integer>>) - Method in class uk.ac.ebi.pride.utilities.data.core.IonType

setMidInitials(String) - Method in class uk.ac.ebi.pride.utilities.data.core.Person

setMinDistance(int) - Method in class uk.ac.ebi.pride.utilities.data.core.Enzyme

setMissedCleavages(int) - Method in class uk.ac.ebi.pride.utilities.data.core.Enzyme

setModDatabase(String) - Method in class uk.ac.ebi.pride.utilities.data.core.Modification

Set Modification DataBase Name

setModDatabaseVersion(String) - Method in class uk.ac.ebi.pride.utilities.data.core.Modification

Set Modification DataBase Version

setMode(DataAccessMode) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

Set the runtime mode

setModifications(List<Modification>) - Method in class uk.ac.ebi.pride.utilities.data.core.PeptideSequence

setMolecularWeight(Double) - Method in class uk.ac.ebi.pride.utilities.data.core.Gel

setMonoisotopicMassDelta(List<Double>) - Method in class uk.ac.ebi.pride.utilities.data.core.Modification

Set monoisotopic mass delta List

setMonoisotopicMassDelta(double) - Method in class uk.ac.ebi.pride.utilities.data.core.SubstitutionModification

setMsLevel(List<Integer>) - Method in class uk.ac.ebi.pride.utilities.data.core.MassTable

setMz(double) - Method in class uk.ac.ebi.pride.utilities.data.core.FragmentIon

setName(String) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

setName(String) - Method in class uk.ac.ebi.pride.utilities.data.core.Identifiable

setName(String) - Method in class uk.ac.ebi.pride.utilities.data.core.IdentifiableParamGroup

setName(String) - Method in class uk.ac.ebi.pride.utilities.data.core.Parameter

setNameDatabase(ParamGroup) - Method in class uk.ac.ebi.pride.utilities.data.core.SearchDataBase

setnTermGain(String) - Method in class uk.ac.ebi.pride.utilities.data.core.Enzyme

setNumDatabaseResidue(long) - Method in class uk.ac.ebi.pride.utilities.data.core.SearchDataBase

setNumDatabaseSequence(int) - Method in class uk.ac.ebi.pride.utilities.data.core.SearchDataBase

setNumSequenceSearched(int) - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentificationList

setOrder(int) - Method in class uk.ac.ebi.pride.utilities.data.core.InstrumentComponent

setOrder(int) - Method in class uk.ac.ebi.pride.utilities.data.core.ProcessingMethod

setOrganizations(List<Organization>) - Method in class uk.ac.ebi.pride.utilities.data.core.ExperimentMetaData

setOriginalResidue(String) - Method in class uk.ac.ebi.pride.utilities.data.core.SubstitutionModification

setPages(String) - Method in class uk.ac.ebi.pride.utilities.data.core.Reference

setParentOrganization(Organization) - Method in class uk.ac.ebi.pride.utilities.data.core.Organization

setParentSample(List<Sample>) - Method in class uk.ac.ebi.pride.utilities.data.core.Sample

setParentTolerance(List<CvParam>) - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentificationProtocol

setPassThreshold(boolean) - Method in class uk.ac.ebi.pride.utilities.data.core.Protein

setPassThreshold(boolean) - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentification

setPath(String) - Method in class uk.ac.ebi.pride.utilities.data.core.SourceFile

setPeptide(List<Peptide>) - Method in class uk.ac.ebi.pride.utilities.data.core.Spectrum

setPeptideEvidence(PeptideEvidence) - Method in class uk.ac.ebi.pride.utilities.data.core.Peptide

setPeptideEvidenceList(List<PeptideEvidence>) - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentification

setPeptides(List<Peptide>) - Method in class uk.ac.ebi.pride.utilities.data.core.Protein

setPeptideSequence(PeptideSequence) - Method in class uk.ac.ebi.pride.utilities.data.core.PeptideEvidence

setPeptideSequence(PeptideSequence) - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentification

setPersons(List<Person>) - Method in class uk.ac.ebi.pride.utilities.data.core.ExperimentMetaData

setPI(Double) - Method in class uk.ac.ebi.pride.utilities.data.core.Gel

setPostResidue(char) - Method in class uk.ac.ebi.pride.utilities.data.core.PeptideEvidence

setPrecursors(List<Precursor>) - Method in class uk.ac.ebi.pride.utilities.data.core.Spectrum

setPreResidue(char) - Method in class uk.ac.ebi.pride.utilities.data.core.PeptideEvidence

setProcessingMethods(List<ProcessingMethod>) - Method in class uk.ac.ebi.pride.utilities.data.core.DataProcessing

setProducts(List<ParamGroup>) - Method in class uk.ac.ebi.pride.utilities.data.core.Spectrum

setProteinDetectionHypothesis(Collection<Protein>) - Method in class uk.ac.ebi.pride.utilities.data.core.ProteinGroup

setProteinDetectionProtocol(Protocol) - Method in class uk.ac.ebi.pride.utilities.data.core.IdentificationMetaData

setProtocol(ExperimentProtocol) - Method in class uk.ac.ebi.pride.utilities.data.core.ExperimentMetaData

setProtocolSteps(List<ParamGroup>) - Method in class uk.ac.ebi.pride.utilities.data.core.ExperimentProtocol

setProvider(Provider) - Method in class uk.ac.ebi.pride.utilities.data.core.ExperimentMetaData

setPublication(String) - Method in class uk.ac.ebi.pride.utilities.data.core.Reference

setPublicDate(Date) - Method in class uk.ac.ebi.pride.utilities.data.core.ExperimentMetaData

setPublisher(String) - Method in class uk.ac.ebi.pride.utilities.data.core.Reference

setQuantScore(QuantScore) - Method in class uk.ac.ebi.pride.utilities.data.core.Protein

setQuantScore(QuantScore) - Method in class uk.ac.ebi.pride.utilities.data.core.QuantPeptide

setRank(int) - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentification

setReagent(CvParam) - Method in class uk.ac.ebi.pride.utilities.data.core.Assay

setReagent(CvParam) - Method in class uk.ac.ebi.pride.utilities.data.core.QuantitativeSample

Add reagent information to a subsample

setReagent(int, CvParam) - Method in class uk.ac.ebi.pride.utilities.data.core.QuantitativeSample

Add reagent information to a subsample

setReferences(List<Reference>) - Method in class uk.ac.ebi.pride.utilities.data.core.ExperimentMetaData

setRefMap(Map<String, ParamGroup>) - Method in class uk.ac.ebi.pride.utilities.data.core.ReferenceableParamGroup

setReleaseDate(String) - Method in class uk.ac.ebi.pride.utilities.data.core.SearchDataBase

setReplacementResidue(String) - Method in class uk.ac.ebi.pride.utilities.data.core.SubstitutionModification

setResidues(Map<String, Float>) - Method in class uk.ac.ebi.pride.utilities.data.core.MassTable

setResidues(List<String>) - Method in class uk.ac.ebi.pride.utilities.data.core.Modification

Set the Amino Acids associated with this modification

setRetentionTime(String) - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentification

setRetentionTimeError(double) - Method in class uk.ac.ebi.pride.utilities.data.core.FragmentIon

setRole(CvParam) - Method in class uk.ac.ebi.pride.utilities.data.core.ContactRole

setRole(CvParam) - Method in class uk.ac.ebi.pride.utilities.data.core.Provider

setSample(Sample) - Method in class uk.ac.ebi.pride.utilities.data.core.Assay

setSample(Sample) - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentification

setSamples(List<Sample>) - Method in class uk.ac.ebi.pride.utilities.data.core.ExperimentMetaData

setSamples(List<Sample>) - Method in class uk.ac.ebi.pride.utilities.data.core.StudyVariable

setScanList(ScanList) - Method in class uk.ac.ebi.pride.utilities.data.core.Spectrum

setScans(List<Scan>) - Method in class uk.ac.ebi.pride.utilities.data.core.ScanList

setScanSetting(ScanSetting) - Method in class uk.ac.ebi.pride.utilities.data.core.InstrumentConfiguration

setScanSettings(List<ScanSetting>) - Method in class uk.ac.ebi.pride.utilities.data.core.MzGraphMetaData

setScanWindows(List<ParamGroup>) - Method in class uk.ac.ebi.pride.utilities.data.core.Scan

setScore(Score) - Method in class uk.ac.ebi.pride.utilities.data.core.Protein

setScore(Score) - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentification

setSearchDataBase(SearchDataBase) - Method in class uk.ac.ebi.pride.utilities.data.core.DBSequence

setSearchDataBases(List<SearchDataBase>) - Method in class uk.ac.ebi.pride.utilities.data.core.IdentificationMetaData

setSearchModifications(List<SearchModification>) - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentificationProtocol

setSearchType(ParamGroup) - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentificationProtocol

setSelectedIons(List<ParamGroup>) - Method in class uk.ac.ebi.pride.utilities.data.core.Precursor

setSemiSpecific(boolean) - Method in class uk.ac.ebi.pride.utilities.data.core.Enzyme

setSequence(String) - Method in class uk.ac.ebi.pride.utilities.data.core.DBSequence

setSequence(String) - Method in class uk.ac.ebi.pride.utilities.data.core.PeptideSequence

setSequenceCoverage(double) - Method in class uk.ac.ebi.pride.utilities.data.core.Protein

setShortLabel(String) - Method in class uk.ac.ebi.pride.utilities.data.core.ExperimentMetaData

setSiteRegExp(String) - Method in class uk.ac.ebi.pride.utilities.data.core.Enzyme

setSoftware(Software) - Method in class uk.ac.ebi.pride.utilities.data.core.InstrumentConfiguration

setSoftware(Software) - Method in class uk.ac.ebi.pride.utilities.data.core.ProcessingMethod

setSoftware(Software) - Method in class uk.ac.ebi.pride.utilities.data.core.Provider

setSoftwares(List<Software>) - Method in class uk.ac.ebi.pride.utilities.data.core.ExperimentMetaData

setSource(Object) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

setSource(List<InstrumentComponent>) - Method in class uk.ac.ebi.pride.utilities.data.core.InstrumentConfiguration

setSourceFile(SourceFile) - Method in class uk.ac.ebi.pride.utilities.data.core.Precursor

setSourceFile(SourceFile) - Method in class uk.ac.ebi.pride.utilities.data.core.Scan

setSourceFile(List<SourceFile>) - Method in class uk.ac.ebi.pride.utilities.data.core.ScanSetting

setSourceFile(SourceFile) - Method in class uk.ac.ebi.pride.utilities.data.core.Spectrum

setSourceFiles(List<SourceFile>) - Method in class uk.ac.ebi.pride.utilities.data.core.ExperimentMetaData

setSpecies(CvParam) - Method in class uk.ac.ebi.pride.utilities.data.core.QuantitativeSample

Add species information to a subsample

setSpecies(int, CvParam) - Method in class uk.ac.ebi.pride.utilities.data.core.QuantitativeSample

Add species information to a subsample

setSpecificities(List<String>) - Method in class uk.ac.ebi.pride.utilities.data.core.SearchModification

setSpecificityRules(List<CvParam>) - Method in class uk.ac.ebi.pride.utilities.data.core.SearchModification

setSpectraData(SpectraData) - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentification

setSpectraDatas(List<SpectraData>) - Method in class uk.ac.ebi.pride.utilities.data.core.ExperimentMetaData

setSpectrum(Spectrum) - Method in class uk.ac.ebi.pride.utilities.data.core.Peptide

setSpectrum(Spectrum) - Method in class uk.ac.ebi.pride.utilities.data.core.Precursor

setSpectrum(Spectrum) - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentification

setSpectrumIdentification(SpectrumIdentification) - Method in class uk.ac.ebi.pride.utilities.data.core.Peptide

setSpectrumIdentificationProtocols(List<SpectrumIdentificationProtocol>) - Method in class uk.ac.ebi.pride.utilities.data.core.IdentificationMetaData

setSpectrumIdentificationResultList(List<Peptide>) - Method in class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentificationList

setSpectrumIdFormat(CvParam) - Method in class uk.ac.ebi.pride.utilities.data.core.SpectraData

setSpectrumRef(String) - Method in class uk.ac.ebi.pride.utilities.data.core.Scan

setSpliceIsoform(String) - Method in class uk.ac.ebi.pride.utilities.data.core.DBSequence

setSpotID(String) - Method in class uk.ac.ebi.pride.utilities.data.core.Spectrum

setStartPosition(int) - Method in class uk.ac.ebi.pride.utilities.data.core.PeptideEvidence

setStudyVariables(Map<Comparable, StudyVariable>) - Method in class uk.ac.ebi.pride.utilities.data.core.ExperimentMetaData

setStudyVariableScores(Map<Comparable, Double>) - Method in class uk.ac.ebi.pride.utilities.data.core.QuantScore

Set abundance Study Variable Map

setSubstitutionModifications(List<SubstitutionModification>) - Method in class uk.ac.ebi.pride.utilities.data.core.PeptideSequence

setTargets(List<ParamGroup>) - Method in class uk.ac.ebi.pride.utilities.data.core.ScanSetting

setThreshold(double) - Method in class uk.ac.ebi.pride.utilities.data.core.Protein

setThreshold(ParamGroup) - Method in class uk.ac.ebi.pride.utilities.data.core.Protocol

setTissue(CvParam) - Method in class uk.ac.ebi.pride.utilities.data.core.QuantitativeSample

Add tissue information to a subsample

setTissue(int, CvParam) - Method in class uk.ac.ebi.pride.utilities.data.core.QuantitativeSample

Add tissue information to a subsample

setTitle(String) - Method in class uk.ac.ebi.pride.utilities.data.core.Reference

setTranslationTable(IdentifiableParamGroup) - Method in class uk.ac.ebi.pride.utilities.data.core.PeptideEvidence

setTranslationTables(List<IdentifiableParamGroup>) - Method in class uk.ac.ebi.pride.utilities.data.core.DataBaseTranslation

setType(DataAccessController.Type) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

setType(Quantification.Type) - Method in class uk.ac.ebi.pride.utilities.data.core.Quantification

setType(String) - Method in class uk.ac.ebi.pride.utilities.data.core.UserParam

setUid(String) - Method in class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

setUnitAcc(String) - Method in class uk.ac.ebi.pride.utilities.data.core.Parameter

setUnitCVLookupID(String) - Method in class uk.ac.ebi.pride.utilities.data.core.Parameter

setUnitName(String) - Method in class uk.ac.ebi.pride.utilities.data.core.Parameter

setUnmarshaller(JMzReader) - Method in class uk.ac.ebi.pride.utilities.data.io.file.PeakUnmarshallerAdaptor

setUri(String) - Method in class uk.ac.ebi.pride.utilities.data.core.Software

setUserParams(List<UserParam>) - Method in class uk.ac.ebi.pride.utilities.data.core.ParamGroup

setUseTitle(boolean) - Method in class uk.ac.ebi.pride.utilities.data.io.file.PeakUnmarshallerAdaptor

setValue(String) - Method in class uk.ac.ebi.pride.utilities.data.core.Parameter

setVersion(String) - Method in class uk.ac.ebi.pride.utilities.data.core.CVLookup

setVersion(String) - Method in class uk.ac.ebi.pride.utilities.data.core.ExperimentMetaData

setVersion(String) - Method in class uk.ac.ebi.pride.utilities.data.core.SearchDataBase

setVersion(String) - Method in class uk.ac.ebi.pride.utilities.data.core.Software

setVolume(String) - Method in class uk.ac.ebi.pride.utilities.data.core.Reference

setXCoordinate(Double) - Method in class uk.ac.ebi.pride.utilities.data.core.Gel

setYCoordinate(Double) - Method in class uk.ac.ebi.pride.utilities.data.core.Gel

setYear(String) - Method in class uk.ac.ebi.pride.utilities.data.core.Reference

Software - Class in uk.ac.ebi.pride.utilities.data.core

Software details.

Software(Comparable, String, Contact, String, String, String) - Constructor for class uk.ac.ebi.pride.utilities.data.core.Software

Create a Software object with all the attributes

Software(ParamGroup, Comparable, String, Contact, String, String, String) - Constructor for class uk.ac.ebi.pride.utilities.data.core.Software

SourceFile - Class in uk.ac.ebi.pride.utilities.data.core

Description of source file, including identification file, location and type.

SourceFile(String, String) - Constructor for class uk.ac.ebi.pride.utilities.data.core.SourceFile

SourceFile(ParamGroup, String, String, String) - Constructor for class uk.ac.ebi.pride.utilities.data.core.SourceFile

SourceFile(ParamGroup, String, String, String, CvParam, String) - Constructor for class uk.ac.ebi.pride.utilities.data.core.SourceFile

SpectraData - Class in uk.ac.ebi.pride.utilities.data.core

A data set containing spectra data (consisting of one or more spectra).

SpectraData(String, String, String, CvParam, String, CvParam) - Constructor for class uk.ac.ebi.pride.utilities.data.core.SpectraData

spectraToRun - Variable in class uk.ac.ebi.pride.utilities.data.exporters.MzIdentMLMzTabConverter

Spectrum - Class in uk.ac.ebi.pride.utilities.data.core

A peak list including the underlying acquisitions.

Spectrum(Comparable, String, int, DataProcessing, int, List<BinaryDataArray>, String, SourceFile, ScanList, List<Precursor>, List<ParamGroup>, List<Peptide>) - Constructor for class uk.ac.ebi.pride.utilities.data.core.Spectrum

Spectrum(ParamGroup, Comparable, String, int, DataProcessing, int, List<BinaryDataArray>, String, SourceFile, ScanList, List<Precursor>, List<ParamGroup>) - Constructor for class uk.ac.ebi.pride.utilities.data.core.Spectrum

Spectrum(ParamGroup, Comparable, String, int, DataProcessing, int, List<BinaryDataArray>, String, SourceFile, ScanList, List<Precursor>, List<ParamGroup>, List<Peptide>) - Constructor for class uk.ac.ebi.pride.utilities.data.core.Spectrum

Spectrum(Spectrum) - Constructor for class uk.ac.ebi.pride.utilities.data.core.Spectrum

SPECTRUM_TYPE - Static variable in interface uk.ac.ebi.pride.utilities.data.controller.access.MzGraphDataAccess

fired when a spectrum object has changed

SpectrumIdentification - Class in uk.ac.ebi.pride.utilities.data.core

PSM Spectrum identification match.

SpectrumIdentification(Comparable, String, int, double, double, double, PeptideSequence, int, boolean, MassTable, Sample, List<PeptideEvidence>, List<FragmentIon>, Score, Spectrum, SpectraData) - Constructor for class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentification

Spectrum Identification Item

SpectrumIdentification(ParamGroup, Comparable, String, int, double, double, double, PeptideSequence, int, boolean, MassTable, Sample, List<PeptideEvidence>, List<FragmentIon>, Score, Spectrum, SpectraData) - Constructor for class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentification

Spectrum Identification Item

SpectrumIdentificationList - Class in uk.ac.ebi.pride.utilities.data.core

Represents the set of all search results from SpectrumIdentification.

SpectrumIdentificationList(Comparable, String, int, List<IdentifiableParamGroup>, List<Peptide>) - Constructor for class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentificationList

SpectrumIdentificationList(ParamGroup, Comparable, String, int, List<IdentifiableParamGroup>, List<Peptide>) - Constructor for class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentificationList

SpectrumIdentificationProtocol - Class in uk.ac.ebi.pride.utilities.data.core

The parameters and settings of a SpectrumIdentification analysis.

SpectrumIdentificationProtocol(Comparable, String, Software, ParamGroup, ParamGroup, ParamGroup, List<SearchModification>, boolean, List<Enzyme>, List<MassTable>, List<CvParam>, List<CvParam>, List<Filter>, DataBaseTranslation) - Constructor for class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentificationProtocol

SpectrumIdentificationProtocol(ParamGroup, Comparable, String, Software, ParamGroup, ParamGroup, List<SearchModification>, boolean, List<Enzyme>, List<MassTable>, List<CvParam>, List<CvParam>, List<Filter>, DataBaseTranslation) - Constructor for class uk.ac.ebi.pride.utilities.data.core.SpectrumIdentificationProtocol

store(CacheEntry, Object, Object) - Method in interface uk.ac.ebi.pride.utilities.data.controller.cache.Cache

Store data into cache by key-value pairs

store(CacheEntry, Object) - Method in interface uk.ac.ebi.pride.utilities.data.controller.cache.Cache

Store data into cache by key only

store(CacheEntry, Object) - Method in class uk.ac.ebi.pride.utilities.data.controller.cache.CacheAccessor

Store key into cache, type should be a collection type.

store(CacheEntry, Object, Object) - Method in class uk.ac.ebi.pride.utilities.data.controller.cache.CacheAccessor

Store a key-value pair into cache, type should be a map type.

storeInBatch(CacheEntry, Map) - Method in interface uk.ac.ebi.pride.utilities.data.controller.cache.Cache

Store a map of data into the cache

storeInBatch(CacheEntry, Collection) - Method in interface uk.ac.ebi.pride.utilities.data.controller.cache.Cache

Store a collection into the cache

storeInBatch(CacheEntry, Map) - Method in class uk.ac.ebi.pride.utilities.data.controller.cache.CacheAccessor

Store a map of values

storeInBatch(CacheEntry, Collection) - Method in class uk.ac.ebi.pride.utilities.data.controller.cache.CacheAccessor

Store a collection of values

StudyVariable - Class in uk.ac.ebi.pride.utilities.data.core

Study variable is use for Quantitation on mzTab files.

StudyVariable(Comparable, String) - Constructor for class uk.ac.ebi.pride.utilities.data.core.StudyVariable

StudyVariable(ParamGroup, Comparable, String) - Constructor for class uk.ac.ebi.pride.utilities.data.core.StudyVariable

SubstitutionModification - Class in uk.ac.ebi.pride.utilities.data.core

Substitution Modification is a Modification where One amino acid is replaced by another amino acid.

SubstitutionModification(String, String, int, double, double) - Constructor for class uk.ac.ebi.pride.utilities.data.core.SubstitutionModification

T

TabProteinList - Class in uk.ac.ebi.pride.utilities.data.exporters

Exporter to Protein List

TabProteinList() - Constructor for class uk.ac.ebi.pride.utilities.data.exporters.TabProteinList

ThresholdPeptideFilter - Class in uk.ac.ebi.pride.utilities.data.filter

ThresholdPeptideFilter() - Constructor for class uk.ac.ebi.pride.utilities.data.filter.ThresholdPeptideFilter

ThresholdProteinFilter - Class in uk.ac.ebi.pride.utilities.data.filter

ThresholdProteinFilter() - Constructor for class uk.ac.ebi.pride.utilities.data.filter.ThresholdProteinFilter

toDoubleArray(byte[], CvTermReference, ByteOrder) - Static method in class uk.ac.ebi.pride.utilities.data.utils.BinaryDataUtils

Convert to double array

toNumberArray(byte[], CvTermReference, ByteOrder) - Static method in class uk.ac.ebi.pride.utilities.data.utils.BinaryDataUtils

Convert a byte array to a number array

toString() - Method in class uk.ac.ebi.pride.utilities.data.core.ContactRole

toString() - Method in class uk.ac.ebi.pride.utilities.data.core.CvParam

toString() - Method in class uk.ac.ebi.pride.utilities.data.core.IdentifiableParamGroup

toString() - Method in class uk.ac.ebi.pride.utilities.data.core.Parameter

toString() - Method in class uk.ac.ebi.pride.utilities.data.core.PeptideSequence

toString() - Method in class uk.ac.ebi.pride.utilities.data.core.StudyVariable

toString() - Method in class uk.ac.ebi.pride.utilities.data.core.UserParam

transformAdditional(List<Param>) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzTabTransformer

transformAdditional(Param) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.PrideXmlTransformer

Transform additional params from pride xml to core data model format.

transformAffiliationToOrganization(List<Affiliation>) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzIdentMLTransformer

transformBinaryDataArray(PeakListBinary, CvTermReference) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.PrideXmlTransformer

Transform BinaryDataArray from pride xml to core data model

transformChromatogram(Chromatogram) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzMLTransformer

Convert chromatogram

transformContacts(Admin) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.PrideXmlTransformer

Transform a list of contacts from pride xml to core data model format

transformContactToOrganization(Map<Integer, Contact>) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzTabTransformer

transformContactToOrganization(Contact) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzTabTransformer

transformContactToOrganization(Admin) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.PrideXmlTransformer

Transform a list of contacts from person contact

transformContactToPerson(Contact) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzTabTransformer

transformContactToPerson(Admin) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.PrideXmlTransformer

Transform a list of contacts from person contact

transformContactToPersons(Map<Integer, Contact>) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzTabTransformer

transformCVList(List<CvLookup>) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzDataTransformer

Convert cv loopups

transformCVList(List<Cv>) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzIdentMLTransformer

transformCVList(CVList) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzMLTransformer

Convert cv loopups

transformCVLookup(CvLookup) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzDataTransformer

Convert cv lookups

transformCVLookup(CV) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzMLTransformer

Convert cv lookups

transformCvLookups(List<CvLookup>) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.PrideXmlTransformer

Transform a list of cvlookup object from pride Xml format to core data model format.

transformCvParam(CvParam) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.PrideXmlTransformer

Transform a cv parameter from pride xml format to core data model format.

transformCvParams(List<CvParam>) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.PrideXmlTransformer

Convert a list of cv params

transformDatabases(Set<Tuple<String, String>>) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzTabTransformer

transformDataProcessing(DataProcessing) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzDataTransformer

Convert data processing

transformDataProcessing(DataProcessing) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzMLTransformer

Convert data processing

transformDataProcessing(int, DataProcessing) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzXmlTransformer

Convert data processing

transformDataProcessing(DataProcessing) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.PrideXmlTransformer

Transform data processing from pride xml to core data model format.

transformDataProcessingList(DataProcessingList) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzMLTransformer

Convert a list of data prcessings

transformDataProcessingList(List<DataProcessing>) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzXmlTransformer

Convert a list of data prcessings

transformDateToCvParam(Date) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzIdentMLTransformer

transformDateToCvParam(Date) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzMLTransformer

transformDurationToCvParam(Duration, CvTermReference) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzXmlTransformer

transformFileDescriptionOrganization(FileDescription) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzMLTransformer

Method to transform FileDescription in the MzMl file to an Organization Objet List

transformFileDescriptionToFileContent(FileDescription) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzMLTransformer

Retrieve the file content

transformFileDescriptionToFileSource(FileDescription) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzMLTransformer

Transform FileDescription object to List of SourceFile

transformFileDescriptionToPerson(FileDescription) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzMLTransformer

Method to retrieve the Contact Persons From the FileDescription Object in the MzMl Files

transformFileSources(List<ParentFile>) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzXmlTransformer

transformGelFreeIdent(GelFreeIdentification) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.PrideXmlTransformer

Convert gel free protein identification

transformIdent(Protein, Integer, Map<String, PSM>, Map<String, Peptide>, Metadata, boolean) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzTabTransformer

transformIdentification(Protein, Integer, Map<String, PSM>, Map<String, Peptide>, Metadata, boolean) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzTabTransformer

Convert gel free protein identification

transformIdentification(Identification) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.PrideXmlTransformer

Convert protein identification

transformInstrument(Map<Integer, Instrument>) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzTabTransformer

transformInstrument(Instrument, DataProcessing) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.PrideXmlTransformer

Transform an instrument from pride xml to core data model format.

transformInstrumentConfiguration(InstrumentDescription) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzDataTransformer

Convert instrument configuration

transformInstrumentConfiguration(InstrumentConfiguration) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzMLTransformer

Convert instrument configuration

transformInstrumentConfigurationList(InstrumentConfigurationList) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzMLTransformer

Convert instrument configuration list

transformMsInstrument(List<MsInstrument>) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzXmlTransformer

transformMsRunMap(Map<Integer, MsRun>) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzTabTransformer

transformParamGroup(T) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzDataTransformer

Convert param group

transformParamGroup(T) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzMLTransformer

Convert param group

transformParamGroup(Param) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.PrideXmlTransformer

Transform a paramgroup from pride xml format to core data model format.

transformParamGroupList(List<T>) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzDataTransformer

Convert a list of param groups

transformParamGroupList(List<T>) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzMLTransformer

Convert a list of param groups

transformPeptide(PSM, DBSequence, Comparable, Metadata) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzTabTransformer

Transform peptide from pride xml to core data model.

transformPeptide(PeptideItem, DBSequence, Comparable) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.PrideXmlTransformer

Transform peptide from pride xml to core data model.

transformPersonContacts(List<Operator>) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzXmlTransformer

transformPrecursor(Precursor) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.PrideXmlTransformer

transform precursors from pride xml to core data model

Note: In MzData schema, there are experimentRef, this is not included in pride xml schema.

transformPrecursorList(PrecursorList) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.PrideXmlTransformer

Convert precursor list

transformProteinAmbiguityGroupToProteinGroup(ProteinAmbiguityGroup) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzIdentMLTransformer

transformProteinHypothesisToIdentification(ProteinDetectionHypothesis) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzIdentMLTransformer

transformProtocol(SortedMap<Integer, SplitList<Param>>) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzTabTransformer

transformProtocol(Protocol) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.PrideXmlTransformer

transform protocol from pride xml to core data model.

transformQuantPeptide(Peptide, DBSequence, Comparable, Metadata) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzTabTransformer

Transform quantitative peptide from pride xml to core data model.

transformReferenceableParamGroupList(ReferenceableParamGroupList) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzMLTransformer

Convert referenceable param group

transformReferences(Map<Integer, Publication>) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzTabTransformer

transformReferences(List<Reference>) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.PrideXmlTransformer

Transform references from pride xml format to core data model format

transformSample(Sample) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzMLTransformer

Convert sample

transformSample(Admin) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.PrideXmlTransformer

Transform sample from pride xml format to core data model format

transformSampleList(Admin) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzDataTransformer

Convert sample list

transformSampleList(SampleList) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzMLTransformer

Convert sample list

transformSamples(Map<Integer, Sample>, Metadata, boolean) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzTabTransformer

transformScanSetting(ScanSettings) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzMLTransformer

Convert scan setting

transformScanSettingList(ScanSettingsList) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzMLTransformer

Convert scan settings

transformSoftware(Software) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzDataTransformer

Convert software list

transformSoftware(Software) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzMLTransformer

Convert software

transformSoftware(Software) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzTabTransformer

Transform a Software Object

transformSoftware(Software) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzXmlTransformer

transformSoftware(DataProcessing) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.PrideXmlTransformer

Transform an software object from pride xml format to core data model format.

transformSoftwareList(SoftwareList) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzMLTransformer

Convert software list

transformSoftwares(Map<Integer, Software>) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzTabTransformer

Transform a List of softwares

transformSoftwares(List<Software>) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzXmlTransformer

transformSourceFile(MsRun) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzTabTransformer

Convert an msRun to SourceFile

transformSourceFile(Admin) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.PrideXmlTransformer

Transform source file from pride xml to core data model

transformSourceFileList(SourceFileList) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzMLTransformer

Convert source file list

transformSourceFiles(Map<Integer, MsRun>) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzTabTransformer

transformSpectrum(Spectrum) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzDataTransformer

Convert spectrum

transformSpectrum(Spectrum) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzMLTransformer

Convert spectrum

transformSpectrum(Spectrum) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzXmlTransformer

Convert spectrum

transformSpectrum(Spectrum) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.PeakTransformer

Convert spectrum

transformSpectrum(Spectrum) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.PrideXmlTransformer

Convert spectrum

Note: supDes, supDataArrayBinary are ignored.

transformSpectrumIdentificationItemToIdentification(DBSequence, List<SpectrumIdentificationItem>) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzIdentMLTransformer

transformStudyVariables(Metadata, boolean) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzTabTransformer

transformSubSampleToSample(List<SubSample>) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzIdentMLTransformer

transformToCVLookup(Cv) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzIdentMLTransformer

transformToFileSource(SourceFile) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzDataTransformer

Transform FileDescription object to List of SourceFile

transformToFragmentationTable(FragmentationTable) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzIdentMLTransformer

transformToOrganization(List<Organization>) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzIdentMLTransformer

transformToOrganization(Organization) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzIdentMLTransformer

transformToPeptideIdentification(SpectrumIdentificationItem) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzIdentMLTransformer

transformToPeptideIdentificationsFromSpectrumItems(List<SpectrumIdentificationItem>) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzIdentMLTransformer

transformToPerson(List<Person>) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzDataTransformer

Method to retrieve the Contact Persons From the FileDescription Object in the mzData Files

transformToPerson(List<Person>) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzIdentMLTransformer

transformToPerson(Person) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzIdentMLTransformer

transformToProteinDetectionProtocol(ProteinDetectionProtocol) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzIdentMLTransformer

transformToProvider(Provider) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzIdentMLTransformer

transformToReference(Iterator<BibliographicReference>) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzIdentMLTransformer

transformToSample(List<Sample>) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzIdentMLTransformer

Transform old Samples to Samples

transformToSample(Sample) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzIdentMLTransformer

transformToSearchDataBase(List<SearchDatabase>) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzIdentMLTransformer

transformToSoftware(List<AnalysisSoftware>) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzIdentMLTransformer

transformToSoftware(AnalysisSoftware) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzIdentMLTransformer

transformToSourceFile(List<SourceFile>) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzIdentMLTransformer

transformToSpectraData(SpectraData, boolean) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzIdentMLTransformer

transformToSpectraData(List<SpectraData>, List<Comparable>) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzIdentMLTransformer

transformToSpectrumIdentificationProtocol(List<SpectrumIdentificationProtocol>) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzIdentMLTransformer

transformToSpectrumIdentificationProtocol(SpectrumIdentificationProtocol) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzIdentMLTransformer

transformTwoDimIdent(TwoDimensionalIdentification) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.PrideXmlTransformer

Convert two dimensional identification

ToDo: there are code duplication between transformTwoDimIdent and transformGelFreeIdent

transformUserParam(UserParam) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.PrideXmlTransformer

Transform a user parameter from pride xml format to core data model format.

transformUserParams(List<UserParam>) - Static method in class uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.PrideXmlTransformer

Convert a list of user params

U

uk.ac.ebi.pride.utilities.data.controller - package uk.ac.ebi.pride.utilities.data.controller

uk.ac.ebi.pride.utilities.data.controller.access - package uk.ac.ebi.pride.utilities.data.controller.access

uk.ac.ebi.pride.utilities.data.controller.cache - package uk.ac.ebi.pride.utilities.data.controller.cache

uk.ac.ebi.pride.utilities.data.controller.cache.strategy - package uk.ac.ebi.pride.utilities.data.controller.cache.strategy

uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl - package uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl

uk.ac.ebi.pride.utilities.data.controller.impl.Transformer - package uk.ac.ebi.pride.utilities.data.controller.impl.Transformer

uk.ac.ebi.pride.utilities.data.core - package uk.ac.ebi.pride.utilities.data.core

uk.ac.ebi.pride.utilities.data.exporters - package uk.ac.ebi.pride.utilities.data.exporters

uk.ac.ebi.pride.utilities.data.filter - package uk.ac.ebi.pride.utilities.data.filter

uk.ac.ebi.pride.utilities.data.io.file - package uk.ac.ebi.pride.utilities.data.io.file

uk.ac.ebi.pride.utilities.data.utils - package uk.ac.ebi.pride.utilities.data.utils

UNKNOWN_MODIFICATION - Static variable in class uk.ac.ebi.pride.utilities.data.exporters.MzIdentMLMzTabConverter

UserParam - Class in uk.ac.ebi.pride.utilities.data.core

Uncontrolled user parameters, allowing free text.

UserParam(String, String, String, String, String, String) - Constructor for class uk.ac.ebi.pride.utilities.data.core.UserParam

Constructor

V

validateMzIdentMLSchema(File) - Static method in class uk.ac.ebi.pride.utilities.data.utils.MzIdentMLUtils

valueOf(String) - Static method in enum uk.ac.ebi.pride.utilities.data.controller.cache.CacheEntry

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum uk.ac.ebi.pride.utilities.data.controller.DataAccessController.ContentCategory

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum uk.ac.ebi.pride.utilities.data.controller.DataAccessController.Type

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum uk.ac.ebi.pride.utilities.data.controller.DataAccessMode

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum uk.ac.ebi.pride.utilities.data.core.Quantification.Type

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum uk.ac.ebi.pride.utilities.data.filter.DecoyAccessionFilter.Type

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum uk.ac.ebi.pride.utilities.data.utils.Constants.SpecFileFormat

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum uk.ac.ebi.pride.utilities.data.utils.Constants.SpecIdFormat

Returns the enum constant of this type with the specified name.

values() - Static method in enum uk.ac.ebi.pride.utilities.data.controller.cache.CacheEntry

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum uk.ac.ebi.pride.utilities.data.controller.DataAccessController.ContentCategory

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum uk.ac.ebi.pride.utilities.data.controller.DataAccessController.Type

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum uk.ac.ebi.pride.utilities.data.controller.DataAccessMode

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum uk.ac.ebi.pride.utilities.data.core.Quantification.Type

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum uk.ac.ebi.pride.utilities.data.filter.DecoyAccessionFilter.Type

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum uk.ac.ebi.pride.utilities.data.utils.Constants.SpecFileFormat

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum uk.ac.ebi.pride.utilities.data.utils.Constants.SpecIdFormat

Returns an array containing the constants of this enum type, in the order they are declared.

variableModifications - Variable in class uk.ac.ebi.pride.utilities.data.exporters.MzIdentMLMzTabConverter

W

WIFF_EXT - Static variable in class uk.ac.ebi.pride.utilities.data.utils.Constants

X

XML_EXT - Static variable in class uk.ac.ebi.pride.utilities.data.utils.Constants

A B C D E F G H I L M N O P Q R S T U V W X