Package org.biopax.paxtools.impl.level3

Class ChemicalStructureImpl

java.lang.Object
org.biopax.paxtools.impl.BioPAXElementImpl
org.biopax.paxtools.impl.level3.L3ElementImpl
org.biopax.paxtools.impl.level3.ChemicalStructureImpl
All Implemented Interfaces:
Serializable, Cloneable, BioPAXElement, ChemicalStructure, Level3Element, UtilityClass
public class ChemicalStructureImpl extends L3ElementImpl implements ChemicalStructure
See Also:

  • Constructor Details

    • ChemicalStructureImpl

      public ChemicalStructureImpl()

  • Method Details

    • getModelInterface

      public Class<? extends ChemicalStructure> 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 BioPAXElementImpl
      Returns:
      an integer that is same across all equivalent entities.

    • getStructureData

      public String getStructureData()
      Description copied from interface: ChemicalStructure
      This property holds a string defining chemical structure,in one of the three formats: CML, SMILES or InChI. If, for example,the CML format is used, then the value of this property is a string containing the XML encoding of the CML data.
      Specified by:
      getStructureData in interface ChemicalStructure
      Returns:
      a string defining chemical structure

    • setStructureData

      public void setStructureData(String structureData)
      Description copied from interface: ChemicalStructure
      This property holds a string of data defining chemical structure,in one of the three formats: CML, SMILES or InChI. If, for example,the CML format is used, then the value of this property is a string containing the XML encoding of the CML data.
      Specified by:
      setStructureData in interface ChemicalStructure
      Parameters:
      structureData - a string defining chemical structure

    • getStructureFormat

      public StructureFormatType getStructureFormat()
      Description copied from interface: ChemicalStructure
      This property specifies which format is used to define chemical structure.
      Specified by:
      getStructureFormat in interface ChemicalStructure
      Returns:
      format used to define chemical structure

    • setStructureFormat

      public void setStructureFormat(StructureFormatType structureFormat)
      Description copied from interface: ChemicalStructure
      This property specifies which format is used to define chemical structure.
      Specified by:
      setStructureFormat in interface ChemicalStructure
      Parameters:
      structureFormat - format used to define chemical structure