Package com.compomics.util.experiment.personalization

Class ExperimentObject

java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
All Implemented Interfaces:
Serializable
Direct Known Subclasses:
AaSubstitutionMatrix, Advocate, AminoAcid, AminoAcidPattern, AminoAcidSequence, AndromedaParameters, AnnotationParameters, Atom, AtomChain, AtomImpl, BlobObject, BoxedObject, CacheElement, CometParameters, Contact, ContactGroup, CvTerm, DigestionParameters, DirecTagParameters, ElementaryElement, Enzyme, ExportScheme, FastaParameters, FilterParameters, FMIndex, FractionParameters, GeneMaps, GeneParameters, Header, Identification, IdentificationFeaturesCache, IdentificationKeys, IdentificationMatch, IdentificationMethod, IdentificationParameters, IdMatchValidationParameters, Instrument, Ion, IonMatch, JsonMarshaller, LastSelectedFolder, MassGap, MassIndexMap, MatchFilter, MatrixContent, MetaMorpheusParameters, Metrics, MgfIndex, Modification, ModificationLocalizationParameters, ModificationMatch, ModificationParameters, ModificationScoring, MsAmandaParameters, MsgfParameters, MyriMatchParameters, MzIdentMLIdfileSearchParametersConverter, NeutralLoss, NeutralLossesMap, NonSymmetricalNormalDistribution, NormalDistribution, NovorParameters, OmssaParameters, Peak, PepnovoAssumptionDetails, PepNovoIdfileReader, PepnovoParameters, Peptide, PeptideAssumptionFilter, PeptideVariantMatches, PeptideVariantsParameters, PNovoIdfileReader, PNovoParameters, Precursor, ProjectParameters, Protein, ProteinInferenceParameters, Protocol, PSModificationScores, PsmScoringParameters, PSParameter, PtmToPrideMap, Quantification, Reference, ReferenceGroup, ReporterMethodFactory, SageParameters, Sample, SearchParameters, SequenceMatchingParameters, SNPElement, Spectrum, SpectrumCountingParameters, SpectrumIdentificationAssumption, Tag, TagElement, TideIdfileReader, TideParameters, UnitOfMeasurement, UtilitiesUserParameters, ValidationQcParameters, XTandemIdfileReader, XtandemParameters
public abstract class ExperimentObject extends Object implements Serializable
This abstract class provides customization facilities. Tool-dependent parameters can be added to classes extending this class.
Author:
Marc Vaudel
See Also:

  • Field Details

    • NO_KEY

      public static final long NO_KEY
      Value for a key not set.

  • Constructor Details

    • ExperimentObject

      public ExperimentObject()
      Empty default constructor.

  • Method Details

    • getId

      public long getId()
      Returns the id of the object.
      Returns:
      the id of the object

    • setId

      public void setId(long id)
      Sets the id of the object.
      Parameters:
      id - the id of the object

    • addUrParam

      public void addUrParam(UrParameter parameter)
      Adds a user refinement parameter.
      Parameters:
      parameter - the parameter

    • removeUrParam

      public void removeUrParam(long paramterKey)
      Removes a user parameter from the user parameters map.
      Parameters:
      paramterKey - the key of the parameter

    • getUrParam

      public UrParameter getUrParam(UrParameter parameter)
      Returns the refinement parameter of the same type as the one provided. Null if not found.
      Parameters:
      parameter - the desired parameter
      Returns:
      the value stored. Null if not found.

    • clearParametersMap

      public void clearParametersMap()
      Clears the loaded parameters.

    • setUrParams

      public void setUrParams(HashMap<Long,UrParameter> urParams)
      Sets the user parameters map.
      Parameters:
      urParams - the user parameters map

    • getUrParams

      public HashMap<Long,UrParameter> getUrParams()
      Returns the user parameters map.
      Returns:
      the user parameters map

    • asLong

      public static long asLong(String key)
      Creating a unique 64 bit hash key from the original key of arbitrary length. The hashed key allows to search entries in the database or in dictionaries in constant time.
      Parameters:
      key - the original key
      Returns:
      the hashed key