Package ubic.gemma.model.expression.biomaterial

Class BioMaterialValueObject

java.lang.Object
ubic.gemma.model.common.IdentifiableValueObject<BioMaterial>
ubic.gemma.model.expression.biomaterial.BioMaterialValueObject
All Implemented Interfaces:
Serializable, Identifiable
public class BioMaterialValueObject extends IdentifiableValueObject<BioMaterial>
Author:
lukem
See Also:

  • Constructor Details

    • BioMaterialValueObject

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

    • BioMaterialValueObject

      public BioMaterialValueObject(Long id)

    • BioMaterialValueObject

      public BioMaterialValueObject(BioMaterial bm)

    • BioMaterialValueObject

      public BioMaterialValueObject(BioMaterial bm, BioAssay ba)

    • BioMaterialValueObject

      public BioMaterialValueObject(BioMaterial bm, boolean basic, boolean allFactorValuesAndCharacteristics)
      Parameters:
      basic - if true, populate fVBasicVOs instead of factorValueObjects. Note that basic FVs should be preferred for new code.
      allFactorValuesAndCharacteristics - whether to include all factor values and characteristics, including those inherited from the source biomaterial, otherwise only those from the sample will be included

  • Method Details

    • getFactorValues

      public Collection<? extends IdentifiableValueObject> getFactorValues()

    • getFactorValueObjects

      @Deprecated public Collection<? extends IdentifiableValueObject> getFactorValueObjects()
      Deprecated.
      use getFactorValues()

    • toString

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

    • getName

      public String getName()

    • getDescription

      public String getDescription()

    • getAssayName

      public String getAssayName()

    • getAssayDescription

      public String getAssayDescription()

    • getFastqHeaders

      public String getFastqHeaders()

    • getBioAssayIds

      public Collection<Long> getBioAssayIds()
      Related BioAssay IDs.

    • getCharacteristics

      public Collection<CharacteristicValueObject> getCharacteristics()

    • getSourceBioMaterialId

      @Nullable public Long getSourceBioMaterialId()

    • getCharacteristicValues

      public Map<String,String> getCharacteristicValues()

    • getCharacteristicOriginalValues

      public Map<String,String> getCharacteristicOriginalValues()
      Map of categories to original text values (for this biomaterial). This is only used for display and will only be populated if the original value is different from the value.

    • isBasicFVs

      public boolean isBasicFVs()
      Indicate if this is using the fVBasicVOs or factorValueObjects for representing factor values.

    • getFVBasicVOs

      public Collection<FactorValueBasicValueObject> getFVBasicVOs()

    • getFactorIdToFactorValueId

      public Map<String,String> getFactorIdToFactorValueId()
      Map of factor ids (factor232) to factor value (id or the actual value) for this biomaterial.

    • getFactors

      @Deprecated public Map<String,String> getFactors()
      Deprecated.
      Map of ids (factor232) to a representation of the factor (e.g., the name).

    • getAssayProcessingDate

      public Date getAssayProcessingDate()

    • setName

      public void setName(String name)

    • setDescription

      public void setDescription(String description)

    • setAssayName

      public void setAssayName(String assayName)

    • setAssayDescription

      public void setAssayDescription(String assayDescription)

    • setFastqHeaders

      public void setFastqHeaders(String fastqHeaders)

    • setBioAssayIds

      public void setBioAssayIds(Collection<Long> bioAssayIds)
      Related BioAssay IDs.

    • setCharacteristics

      public void setCharacteristics(Collection<CharacteristicValueObject> characteristics)

    • setSourceBioMaterialId

      public void setSourceBioMaterialId(@Nullable Long sourceBioMaterialId)

    • setCharacteristicValues

      public void setCharacteristicValues(Map<String,String> characteristicValues)

    • setCharacteristicOriginalValues

      public void setCharacteristicOriginalValues(Map<String,String> characteristicOriginalValues)
      Map of categories to original text values (for this biomaterial). This is only used for display and will only be populated if the original value is different from the value.

    • setBasicFVs

      public void setBasicFVs(boolean basicFVs)
      Indicate if this is using the fVBasicVOs or factorValueObjects for representing factor values.

    • setFVBasicVOs

      public void setFVBasicVOs(Collection<FactorValueBasicValueObject> fVBasicVOs)

    • setFactorValueObjects

      public void setFactorValueObjects(Collection<FactorValueValueObject> factorValueObjects)

    • setFactorValues

      public void setFactorValues(Map<String,String> factorValues)
      Map of ids (fv133) to a representation of the value (for this biomaterial.)

    • setFactorIdToFactorValueId

      public void setFactorIdToFactorValueId(Map<String,String> factorIdToFactorValueId)
      Map of factor ids (factor232) to factor value (id or the actual value) for this biomaterial.

    • setFactors

      @Deprecated public void setFactors(Map<String,String> factors)
      Deprecated.
      Map of ids (factor232) to a representation of the factor (e.g., the name).

    • setAssayProcessingDate

      public void setAssayProcessingDate(Date assayProcessingDate)

    • equals

      public boolean equals(Object o)
      Overrides:
      equals in class IdentifiableValueObject<BioMaterial>

    • canEqual

      protected boolean canEqual(Object other)
      Overrides:
      canEqual in class IdentifiableValueObject<BioMaterial>

    • hashCode

      public int hashCode()
      Overrides:
      hashCode in class IdentifiableValueObject<BioMaterial>