Package org.biopax.paxtools.impl.level3

Class SequenceEntityReferenceImpl

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.EntityReferenceImpl
org.biopax.paxtools.impl.level3.SequenceEntityReferenceImpl
All Implemented Interfaces:
Serializable, Cloneable, BioPAXElement, EntityReference, Level3Element, Named, Observable, SequenceEntityReference, UtilityClass, XReferrable
Direct Known Subclasses:
NucleicAcidReferenceImpl, ProteinReferenceImpl
public abstract class SequenceEntityReferenceImpl extends EntityReferenceImpl implements SequenceEntityReference
See Also:

  • Constructor Details

    • SequenceEntityReferenceImpl

      public SequenceEntityReferenceImpl()

  • Method Details

    • getOrganism

      public BioSource getOrganism()
      Description copied from interface: SequenceEntityReference
      An organism, e.g. 'Homo sapiens'. This is the organism that the entity is found in. Pathways may not have an organism associated with them, for instance, reference pathways from KEGG. Sequence-based entities (DNA, protein, RNA) may contain an xref to a sequence database that contains organism information, in which case the information should be consistent with the value for ORGANISM.
      Specified by:
      getOrganism in interface SequenceEntityReference
      Returns:
      the organism for this gene.

    • setOrganism

      public void setOrganism(BioSource organism)
      Description copied from interface: SequenceEntityReference
      An organism, e.g. 'Homo sapiens'. This is the organism that the entity is found in. Pathways may not have an organism associated with them, for instance, reference pathways from KEGG. Sequence-based entities (DNA, protein, RNA) may contain an xref to a sequence database that contains organism information, in which case the information should be consistent with the value for ORGANISM.
      Specified by:
      setOrganism in interface SequenceEntityReference
      Parameters:
      organism - new organism for this gene

    • getSequence

      public String getSequence()
      Description copied from interface: SequenceEntityReference
      Polymer sequence in uppercase letters. For DNA, usually A,C,G,T letters representing the nucleosides of adenine, cytosine, guanine and thymine, respectively; for RNA, usually A, C, U, G; for protein, usually the letters corresponding to the 20 letter IUPAC amino acid code.
      Specified by:
      getSequence in interface SequenceEntityReference
      Returns:
      sequence - primary structure of a biopolymer.

    • setSequence

      public void setSequence(String sequence)
      Description copied from interface: SequenceEntityReference
      Polymer sequence in uppercase letters. For DNA, usually A,C,G,T letters representing the nucleosides of adenine, cytosine, guanine and thymine, respectively; for RNA, usually A, C, U, G; for protein, usually the letters corresponding to the 20 letter IUPAC amino acid code.
      Specified by:
      setSequence in interface SequenceEntityReference
      Parameters:
      sequence - Polymer sequence in uppercase letters.

    • 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.