Package ubic.gemma.model.expression.experiment

Class ExpressionExperimentValueObject

java.lang.Object
ubic.gemma.model.common.IdentifiableValueObject<ExpressionExperiment>
ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject<ExpressionExperiment>
ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject
All Implemented Interfaces:
gemma.gsec.model.Securable, gemma.gsec.model.SecureValueObject, Serializable, Describable, Identifiable, BioAssaySetValueObject
Direct Known Subclasses:
DatasetsWebService.ExpressionExperimentWithSearchResultValueObject, ExpressionExperimentDetailsValueObject
public class ExpressionExperimentValueObject extends AbstractCuratableValueObject<ExpressionExperiment> implements BioAssaySetValueObject
See Also:

  • Field Details

    • numberOfBioAssays

      protected Integer numberOfBioAssays

    • description

      protected String description

    • name

      protected String name

  • Constructor Details

    • ExpressionExperimentValueObject

      public ExpressionExperimentValueObject()
      Required when using the class as a spring bean.

    • ExpressionExperimentValueObject

      public ExpressionExperimentValueObject(Long id)

    • ExpressionExperimentValueObject

      public ExpressionExperimentValueObject(ExpressionExperiment ee, boolean ignoreDesign, boolean ignoreAccession)
      Creates a new value object out of given Expression Experiment.
      Parameters:
      ee - the experiment to convert into a value object.
      ignoreDesign - exclude the experimental design from serialization
      ignoreAccession - exclude accession from serialization

    • ExpressionExperimentValueObject

      public ExpressionExperimentValueObject(ExpressionExperiment ee)

    • ExpressionExperimentValueObject

      public ExpressionExperimentValueObject(ExpressionExperiment ee, gemma.gsec.acl.domain.AclObjectIdentity aoi, gemma.gsec.acl.domain.AclSid sid)
      Creates a new ExpressionExperiment value object with additional information about ownership.

    • ExpressionExperimentValueObject

      protected ExpressionExperimentValueObject(ExpressionExperimentValueObject vo)

  • Method Details

    • getBioAssayCount

      @Deprecated public int getBioAssayCount()
      Deprecated.
      use getNumberOfBioAssays() instead.
      Obtain the number of BioAssay in this experiment.

    • getIsPublic

      public boolean getIsPublic()
      Specified by:
      getIsPublic in interface gemma.gsec.model.SecureValueObject

    • getIsShared

      public boolean getIsShared()
      Specified by:
      getIsShared in interface gemma.gsec.model.SecureValueObject

    • getTaxon

      public String getTaxon()

    • getTaxonId

      @Deprecated public Long getTaxonId()
      Deprecated.
      use getTaxonObject() instead

    • getSecurableClass

      public Class<? extends Securable> getSecurableClass()
      Specified by:
      getSecurableClass in interface gemma.gsec.model.SecureValueObject

    • getUserCanWrite

      public boolean getUserCanWrite()
      Specified by:
      getUserCanWrite in interface gemma.gsec.model.SecureValueObject

    • getUserOwned

      public boolean getUserOwned()
      Specified by:
      getUserOwned in interface gemma.gsec.model.SecureValueObject

    • setIsPublic

      public void setIsPublic(boolean b)
      Specified by:
      setIsPublic in interface gemma.gsec.model.SecureValueObject

    • setIsShared

      public void setIsShared(boolean b)
      Specified by:
      setIsShared in interface gemma.gsec.model.SecureValueObject

    • setUserCanWrite

      public void setUserCanWrite(boolean userCanWrite)
      Specified by:
      setUserCanWrite in interface gemma.gsec.model.SecureValueObject

    • setUserOwned

      public void setUserOwned(boolean isUserOwned)
      Specified by:
      setUserOwned in interface gemma.gsec.model.SecureValueObject

    • getCurrentUserHasWritePermission

      public boolean getCurrentUserHasWritePermission()

    • getCurrentUserIsOwner

      public boolean getCurrentUserIsOwner()

    • toString

      public String toString()
      Overrides:
      toString in class IdentifiableValueObject<ExpressionExperiment>

    • getNumberOfBioAssays

      public Integer getNumberOfBioAssays()
      Description copied from interface: BioAssaySetValueObject
      Obtain the number of assays in this set.
      Specified by:
      getNumberOfBioAssays in interface BioAssaySetValueObject

    • getDescription

      public String getDescription()
      Description copied from interface: Describable
      Obtain a human-readable description of the object
      Specified by:
      getDescription in interface Describable

    • getName

      public String getName()
      Description copied from interface: Describable
      Obtain the name of an object is a possibly ambiguous human-readable identifier that need not be an external database reference.
      Specified by:
      getName in interface Describable

    • getAccession

      public String getAccession()
      Description copied from interface: BioAssaySetValueObject
      Obtain the accession of this set if one exists.
      Specified by:
      getAccession in interface BioAssaySetValueObject

    • getArrayDesignCount

      public Long getArrayDesignCount()

    • getBatchConfound

      public String getBatchConfound()

    • getBatchEffect

      public String getBatchEffect()
      Batch effect type. See BatchEffectType enum for possible values.

    • getBatchEffectStatistics

      @Nullable public String getBatchEffectStatistics()
      Summary statistics of a batch effect is present.

    • getBioMaterialCount

      public Integer getBioMaterialCount()

    • getExperimentalDesign

      public Long getExperimentalDesign()

    • getExternalDatabase

      public String getExternalDatabase()

    • getExternalDatabaseUri

      public String getExternalDatabaseUri()

    • getExternalUri

      public String getExternalUri()

    • getGeeq

      public GeeqValueObject getGeeq()

    • getMetadata

      public String getMetadata()

    • getProcessedExpressionVectorCount

      public Integer getProcessedExpressionVectorCount()

    • getShortName

      public String getShortName()

    • getSource

      public String getSource()

    • getSuitableForDEA

      public Boolean getSuitableForDEA()

    • getTaxonObject

      @Nullable public TaxonValueObject getTaxonObject()
      FIXME: this should be named simply "taxon", but that field is already taken for Gemma Web, see getTaxon().

    • getTechnologyType

      public String getTechnologyType()

    • getCharacteristics

      @Nullable public Set<CharacteristicValueObject> getCharacteristics()
      Specified by:
      getCharacteristics in interface BioAssaySetValueObject

    • getMinPvalue

      @Nullable public Double getMinPvalue()

    • setNumberOfBioAssays

      public void setNumberOfBioAssays(Integer numberOfBioAssays)

    • setDescription

      public void setDescription(String description)

    • setName

      public void setName(String name)

    • setAccession

      public void setAccession(String accession)

    • setArrayDesignCount

      public void setArrayDesignCount(Long arrayDesignCount)

    • setBatchConfound

      public void setBatchConfound(String batchConfound)

    • setBatchEffect

      public void setBatchEffect(String batchEffect)
      Batch effect type. See BatchEffectType enum for possible values.

    • setBatchEffectStatistics

      public void setBatchEffectStatistics(@Nullable String batchEffectStatistics)
      Summary statistics of a batch effect is present.

    • setBioMaterialCount

      public void setBioMaterialCount(Integer bioMaterialCount)

    • setExperimentalDesign

      public void setExperimentalDesign(Long experimentalDesign)

    • setExternalDatabase

      public void setExternalDatabase(String externalDatabase)

    • setExternalDatabaseUri

      public void setExternalDatabaseUri(String externalDatabaseUri)

    • setExternalUri

      public void setExternalUri(String externalUri)

    • setGeeq

      public void setGeeq(GeeqValueObject geeq)

    • setMetadata

      public void setMetadata(String metadata)

    • setProcessedExpressionVectorCount

      public void setProcessedExpressionVectorCount(Integer processedExpressionVectorCount)

    • setShortName

      public void setShortName(String shortName)

    • setSource

      public void setSource(String source)

    • setSuitableForDEA

      public void setSuitableForDEA(Boolean suitableForDEA)

    • setTaxonObject

      public void setTaxonObject(@Nullable TaxonValueObject taxonObject)
      FIXME: this should be named simply "taxon", but that field is already taken for Gemma Web, see getTaxon().

    • setTechnologyType

      public void setTechnologyType(String technologyType)

    • setCharacteristics

      public void setCharacteristics(@Nullable Set<CharacteristicValueObject> characteristics)

    • setMinPvalue

      public void setMinPvalue(@Nullable Double minPvalue)