Hierarchy For All Packages

Package Hierarchies:

• uk.ac.ebi.pride.utilities.data.controller,
• uk.ac.ebi.pride.utilities.data.controller.access,
• uk.ac.ebi.pride.utilities.data.controller.cache,
• uk.ac.ebi.pride.utilities.data.controller.cache.strategy,
• uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl,
• uk.ac.ebi.pride.utilities.data.controller.impl.Transformer,
• uk.ac.ebi.pride.utilities.data.core,
• uk.ac.ebi.pride.utilities.data.exporters,
• uk.ac.ebi.pride.utilities.data.filter,
• uk.ac.ebi.pride.utilities.data.io.file,
• uk.ac.ebi.pride.utilities.data.utils

Class Hierarchy

• java.lang.Object
  • uk.ac.ebi.pride.utilities.data.controller.cache.strategy.AbstractCachingStrategy (implements uk.ac.ebi.pride.utilities.data.controller.cache.CachingStrategy)
    • uk.ac.ebi.pride.utilities.data.controller.cache.strategy.MzDataCachingStrategy
    • uk.ac.ebi.pride.utilities.data.controller.cache.strategy.MzIdentMLCachingStrategy
    • uk.ac.ebi.pride.utilities.data.controller.cache.strategy.MzMlCachingStrategy
    • uk.ac.ebi.pride.utilities.data.controller.cache.strategy.MzTabCachingStrategy
    • uk.ac.ebi.pride.utilities.data.controller.cache.strategy.MzXmlCachingStrategy
    • uk.ac.ebi.pride.utilities.data.controller.cache.strategy.PeakCachingStrategy
    • uk.ac.ebi.pride.utilities.data.controller.cache.strategy.PrideXmlCachingStrategy
  • uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController (implements uk.ac.ebi.pride.utilities.data.controller.DataAccessController)
    • uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController
      • uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzDataControllerImpl
      • uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzMLControllerImpl
      • uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzXmlControllerImpl
      • uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.PeakControllerImpl
      • uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.PrideXmlControllerImpl
      • uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.ReferencedIdentificationController
        • uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzIdentMLControllerImpl
        • uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzTabControllerImpl
  • java.util.AbstractMap<K,V> (implements java.util.Map<K,V>)
    • java.util.HashMap<K,V> (implements java.lang.Cloneable, java.util.Map<K,V>, java.io.Serializable)
      • java.util.LinkedHashMap<K,V> (implements java.util.Map<K,V>)
        • uk.ac.ebi.pride.utilities.data.controller.cache.CachedMap<K,V>
  • uk.ac.ebi.pride.utilities.data.utils.BinaryDataUtils
  • uk.ac.ebi.pride.utilities.data.controller.cache.CacheAccessor (implements uk.ac.ebi.pride.utilities.data.controller.cache.Cache)
  • uk.ac.ebi.pride.utilities.data.utils.CollectionUtils
  • uk.ac.ebi.pride.utilities.data.utils.Constants
  • uk.ac.ebi.pride.utilities.data.core.ContactRole
  • uk.ac.ebi.pride.jmztab.utils.convert.ConvertProvider<T,V>
    • uk.ac.ebi.pride.utilities.data.exporters.AbstractMzTabConverter
      • uk.ac.ebi.pride.utilities.data.exporters.MzIdentMLMzTabConverter
        • uk.ac.ebi.pride.utilities.data.exporters.HQMzIdentMLMzTabConverter
      • uk.ac.ebi.pride.utilities.data.exporters.PRIDEMzTabConverter
  • uk.ac.ebi.pride.utilities.data.core.CVLookup (implements uk.ac.ebi.pride.utilities.data.core.MassSpecObject)
  • uk.ac.ebi.pride.utilities.data.utils.CvUtilities
  • uk.ac.ebi.pride.utilities.data.controller.DataAccessUtilities
  • uk.ac.ebi.pride.utilities.data.core.DataBaseTranslation
  • uk.ac.ebi.pride.utilities.data.filter.DecoyAccessionFilter (implements uk.ac.ebi.pride.utilities.data.filter.AccessionFilter<T>)
  • uk.ac.ebi.pride.utilities.data.core.Filter
  • uk.ac.ebi.pride.utilities.data.core.Identifiable (implements uk.ac.ebi.pride.utilities.data.core.MassSpecObject)
    • uk.ac.ebi.pride.utilities.data.core.DataProcessing
    • uk.ac.ebi.pride.utilities.data.core.Enzyme
    • uk.ac.ebi.pride.utilities.data.core.ExternalData
      • uk.ac.ebi.pride.utilities.data.core.SearchDataBase
      • uk.ac.ebi.pride.utilities.data.core.SpectraData
    • uk.ac.ebi.pride.utilities.data.core.Provider
  • uk.ac.ebi.pride.utilities.data.utils.MapUtils
  • uk.ac.ebi.pride.utilities.data.utils.MD5Utils
  • uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzDataTransformer
  • uk.ac.ebi.pride.utilities.data.io.file.MzDataUnmarshallerAdaptor
  • uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzIdentMLTransformer
  • uk.ac.ebi.jmzidml.xml.io.MzIdentMLUnmarshaller
    • uk.ac.ebi.pride.utilities.data.io.file.MzIdentMLUnmarshallerAdaptor
  • uk.ac.ebi.pride.utilities.data.utils.MzIdentMLUtils
  • uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzMLTransformer
  • uk.ac.ebi.jmzml.xml.io.MzMLUnmarshaller
    • uk.ac.ebi.pride.utilities.data.io.file.MzMLUnmarshallerAdaptor
  • uk.ac.ebi.pride.utilities.data.exporters.MzTabBedConverter
  • uk.ac.ebi.pride.jmztab.utils.MZTabFileParser
    • uk.ac.ebi.pride.utilities.data.io.file.MzTabUnmarshallerAdaptor
  • uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzTabTransformer
  • uk.ac.ebi.pride.utilities.data.utils.MzTabUtils
  • uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzXmlTransformer
  • uk.ac.ebi.pride.utilities.data.io.file.MzXmlUnmarshallerAdaptor
  • uk.ac.ebi.pride.utilities.data.filter.NoPeptideFilter (implements uk.ac.ebi.pride.utilities.data.filter.PeptideFilter)
  • uk.ac.ebi.pride.utilities.data.filter.NoProteinFilter (implements uk.ac.ebi.pride.utilities.data.filter.ProteinFilter)
  • uk.ac.ebi.pride.utilities.data.core.Parameter (implements uk.ac.ebi.pride.utilities.data.core.MassSpecObject)
    • uk.ac.ebi.pride.utilities.data.core.CvParam
      • uk.ac.ebi.pride.utilities.data.core.IonType
    • uk.ac.ebi.pride.utilities.data.core.UserParam
  • uk.ac.ebi.pride.utilities.data.core.ParamGroup (implements uk.ac.ebi.pride.utilities.data.core.MassSpecObject)
    • uk.ac.ebi.pride.utilities.data.core.BinaryDataArray
    • uk.ac.ebi.pride.utilities.data.core.FragmentIon
    • uk.ac.ebi.pride.utilities.data.core.Gel
    • uk.ac.ebi.pride.utilities.data.core.IdentifiableParamGroup
      • uk.ac.ebi.pride.utilities.data.core.AbundanceAssay
      • uk.ac.ebi.pride.utilities.data.core.Assay
      • uk.ac.ebi.pride.utilities.data.core.Contact
        • uk.ac.ebi.pride.utilities.data.core.Organization
        • uk.ac.ebi.pride.utilities.data.core.Person
      • uk.ac.ebi.pride.utilities.data.core.DBSequence
      • uk.ac.ebi.pride.utilities.data.core.ExperimentMetaData
      • uk.ac.ebi.pride.utilities.data.core.ExperimentProtocol
      • uk.ac.ebi.pride.utilities.data.core.IdentificationMetaData
      • uk.ac.ebi.pride.utilities.data.core.Modification
      • uk.ac.ebi.pride.utilities.data.core.MzGraph
        • uk.ac.ebi.pride.utilities.data.core.Chromatogram
        • uk.ac.ebi.pride.utilities.data.core.Spectrum (implements java.lang.Cloneable)
      • uk.ac.ebi.pride.utilities.data.core.MzGraphMetaData
      • uk.ac.ebi.pride.utilities.data.core.PeptideEvidence
      • uk.ac.ebi.pride.utilities.data.core.PeptideSequence (implements java.lang.Comparable<T>)
      • uk.ac.ebi.pride.utilities.data.core.Protein
      • uk.ac.ebi.pride.utilities.data.core.ProteinGroup
      • uk.ac.ebi.pride.utilities.data.core.Protocol
        • uk.ac.ebi.pride.utilities.data.core.SpectrumIdentificationProtocol
      • uk.ac.ebi.pride.utilities.data.core.QuantScore
      • uk.ac.ebi.pride.utilities.data.core.Reference
      • uk.ac.ebi.pride.utilities.data.core.Sample (implements java.lang.Comparable<T>)
      • uk.ac.ebi.pride.utilities.data.core.Software
      • uk.ac.ebi.pride.utilities.data.core.SourceFile
      • uk.ac.ebi.pride.utilities.data.core.SpectrumIdentification
      • uk.ac.ebi.pride.utilities.data.core.SpectrumIdentificationList
      • uk.ac.ebi.pride.utilities.data.core.StudyVariable
    • uk.ac.ebi.pride.utilities.data.core.InstrumentComponent
    • uk.ac.ebi.pride.utilities.data.core.InstrumentConfiguration
    • uk.ac.ebi.pride.utilities.data.core.MassTable
    • uk.ac.ebi.pride.utilities.data.core.ProcessingMethod
    • uk.ac.ebi.pride.utilities.data.core.Scan
    • uk.ac.ebi.pride.utilities.data.core.ScanList
    • uk.ac.ebi.pride.utilities.data.core.ScanSetting
  • uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.PeakTransformer
  • uk.ac.ebi.pride.utilities.data.io.file.PeakUnmarshallerAdaptor
  • uk.ac.ebi.pride.utilities.data.core.Peptide
    • uk.ac.ebi.pride.utilities.data.core.QuantPeptide
  • uk.ac.ebi.pride.utilities.data.core.Precursor (implements uk.ac.ebi.pride.utilities.data.core.MassSpecObject)
  • uk.ac.ebi.pride.utilities.data.utils.PRIDEUtils
  • uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.PrideXmlTransformer
  • uk.ac.ebi.pride.utilities.data.core.Quantification
  • uk.ac.ebi.pride.utilities.data.core.QuantitativeSample
  • uk.ac.ebi.pride.utilities.data.filter.RankOnePeptideFilter (implements uk.ac.ebi.pride.utilities.data.filter.PeptideFilter)
  • uk.ac.ebi.pride.utilities.data.core.ReferenceableParamGroup (implements uk.ac.ebi.pride.utilities.data.core.MassSpecObject)
  • uk.ac.ebi.pride.utilities.data.core.Score
  • uk.ac.ebi.pride.utilities.data.core.SearchModification
  • uk.ac.ebi.pride.utilities.data.core.SubstitutionModification
  • uk.ac.ebi.pride.utilities.data.exporters.TabProteinList
  • uk.ac.ebi.pride.utilities.data.filter.ThresholdPeptideFilter (implements uk.ac.ebi.pride.utilities.data.filter.PeptideFilter)
  • uk.ac.ebi.pride.utilities.data.filter.ThresholdProteinFilter (implements uk.ac.ebi.pride.utilities.data.filter.ProteinFilter)
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • java.lang.RuntimeException
        • uk.ac.ebi.pride.utilities.data.controller.DataAccessException

Interface Hierarchy

• uk.ac.ebi.pride.utilities.data.filter.AccessionFilter<T>
• uk.ac.ebi.pride.utilities.data.controller.cache.Cache
• uk.ac.ebi.pride.utilities.data.controller.cache.CachingStrategy
• uk.ac.ebi.pride.utilities.data.controller.access.MetaDataAccess
  • uk.ac.ebi.pride.utilities.data.controller.DataAccessController (also extends uk.ac.ebi.pride.utilities.data.controller.access.MzGraphDataAccess, uk.ac.ebi.pride.utilities.data.controller.access.PeptideDataAccess, uk.ac.ebi.pride.utilities.data.controller.access.ProteinDataAccess, uk.ac.ebi.pride.utilities.data.controller.access.ProteinGroupDataAccess, uk.ac.ebi.pride.utilities.data.controller.access.QuantDataAccess)
• uk.ac.ebi.pride.utilities.data.controller.access.MzGraphDataAccess
  • uk.ac.ebi.pride.utilities.data.controller.DataAccessController (also extends uk.ac.ebi.pride.utilities.data.controller.access.MetaDataAccess, uk.ac.ebi.pride.utilities.data.controller.access.PeptideDataAccess, uk.ac.ebi.pride.utilities.data.controller.access.ProteinDataAccess, uk.ac.ebi.pride.utilities.data.controller.access.ProteinGroupDataAccess, uk.ac.ebi.pride.utilities.data.controller.access.QuantDataAccess)
• uk.ac.ebi.pride.utilities.data.controller.access.PeptideDataAccess
  • uk.ac.ebi.pride.utilities.data.controller.DataAccessController (also extends uk.ac.ebi.pride.utilities.data.controller.access.MetaDataAccess, uk.ac.ebi.pride.utilities.data.controller.access.MzGraphDataAccess, uk.ac.ebi.pride.utilities.data.controller.access.ProteinDataAccess, uk.ac.ebi.pride.utilities.data.controller.access.ProteinGroupDataAccess, uk.ac.ebi.pride.utilities.data.controller.access.QuantDataAccess)
• uk.ac.ebi.pride.utilities.data.filter.PeptideFilter
• uk.ac.ebi.pride.utilities.data.controller.access.ProteinDataAccess
  • uk.ac.ebi.pride.utilities.data.controller.DataAccessController (also extends uk.ac.ebi.pride.utilities.data.controller.access.MetaDataAccess, uk.ac.ebi.pride.utilities.data.controller.access.MzGraphDataAccess, uk.ac.ebi.pride.utilities.data.controller.access.PeptideDataAccess, uk.ac.ebi.pride.utilities.data.controller.access.ProteinGroupDataAccess, uk.ac.ebi.pride.utilities.data.controller.access.QuantDataAccess)
• uk.ac.ebi.pride.utilities.data.filter.ProteinFilter
• uk.ac.ebi.pride.utilities.data.controller.access.ProteinGroupDataAccess
  • uk.ac.ebi.pride.utilities.data.controller.DataAccessController (also extends uk.ac.ebi.pride.utilities.data.controller.access.MetaDataAccess, uk.ac.ebi.pride.utilities.data.controller.access.MzGraphDataAccess, uk.ac.ebi.pride.utilities.data.controller.access.PeptideDataAccess, uk.ac.ebi.pride.utilities.data.controller.access.ProteinDataAccess, uk.ac.ebi.pride.utilities.data.controller.access.QuantDataAccess)
• uk.ac.ebi.pride.utilities.data.controller.access.QuantDataAccess
  • uk.ac.ebi.pride.utilities.data.controller.DataAccessController (also extends uk.ac.ebi.pride.utilities.data.controller.access.MetaDataAccess, uk.ac.ebi.pride.utilities.data.controller.access.MzGraphDataAccess, uk.ac.ebi.pride.utilities.data.controller.access.PeptideDataAccess, uk.ac.ebi.pride.utilities.data.controller.access.ProteinDataAccess, uk.ac.ebi.pride.utilities.data.controller.access.ProteinGroupDataAccess)
• java.io.Serializable
  • uk.ac.ebi.pride.utilities.data.core.MassSpecObject

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • uk.ac.ebi.pride.utilities.data.controller.cache.CacheEntry
    • uk.ac.ebi.pride.utilities.data.controller.DataAccessMode
    • uk.ac.ebi.pride.utilities.data.controller.DataAccessController.ContentCategory
    • uk.ac.ebi.pride.utilities.data.controller.DataAccessController.Type
    • uk.ac.ebi.pride.utilities.data.core.Quantification.Type
    • uk.ac.ebi.pride.utilities.data.filter.DecoyAccessionFilter.Type
    • uk.ac.ebi.pride.utilities.data.utils.Constants.SpecIdFormat
    • uk.ac.ebi.pride.utilities.data.utils.Constants.SpecFileFormat