Package org.biopax.paxtools.impl.level3

Class BioSourceImpl

java.lang.Object
org.biopax.paxtools.impl.BioPAXElementImpl
org.biopax.paxtools.impl.level3.L3ElementImpl
org.biopax.paxtools.impl.level3.XReferrableImpl
org.biopax.paxtools.impl.level3.NamedImpl
org.biopax.paxtools.impl.level3.BioSourceImpl
All Implemented Interfaces:
Serializable, Cloneable, BioPAXElement, BioSource, Level3Element, Named, UtilityClass, XReferrable
public class BioSourceImpl extends NamedImpl implements BioSource
See Also:

  • Constructor Details

    • BioSourceImpl

      public BioSourceImpl()

  • Method Details

    • getModelInterface

      public Class<? extends BioSource> getModelInterface()
      Description copied from interface: BioPAXElement
      This method returns the actual model interface that a class implements.
      Specified by:
      getModelInterface in interface BioPAXElement
      Returns:
      an interface from org.biopax.paxtools.model package corresponding to a BioPAX class.

    • semanticallyEquivalent

      protected boolean semanticallyEquivalent(BioPAXElement element)
      Overrides:
      semanticallyEquivalent in class BioPAXElementImpl

    • equivalenceCode

      public int equivalenceCode()
      Description copied from interface: BioPAXElement
      If two elements are equivalent, then their equivalence code should be the same.
      Specified by:
      equivalenceCode in interface BioPAXElement
      Overrides:
      equivalenceCode in class XReferrableImpl
      Returns:
      an integer that is same across all equivalent entities.

    • getCellType

      public CellVocabulary getCellType()
      Description copied from interface: BioSource
      A cell type, e.g. 'HeLa'. This should reference a term in a controlled vocabulary of cell types. Best practice is to refer to OBOCell Ontology.
      Specified by:
      getCellType in interface BioSource
      Returns:
      cell type if this biosource is a cell line or a specific tissue. Null otherwise.

    • setCellType

      public void setCellType(CellVocabulary celltype)
      Description copied from interface: BioSource
      A cell type, e.g. 'HeLa'. This should reference a term in a controlled vocabulary of cell types. Best practice is to refer to OBOCell Ontology.
      Specified by:
      setCellType in interface BioSource
      Parameters:
      celltype - if this biosource is a cell line or a specific tissue. Null for n/a.

    • getTissue

      public TissueVocabulary getTissue()
      Description copied from interface: BioSource
      An external controlled vocabulary of tissue types. A reference to the BRENDA
      Specified by:
      getTissue in interface BioSource
      Returns:
      An external controlled vocabulary of tissue types.

    • setTissue

      public void setTissue(TissueVocabulary tissue)
      Description copied from interface: BioSource
      An external controlled vocabulary of tissue types. A reference to the BRENDA
      Specified by:
      setTissue in interface BioSource
      Parameters:
      tissue - An external controlled vocabulary of tissue types.

    • toString

      public String toString()
      Overrides:
      toString in class BioPAXElementImpl