Package org.biopax.paxtools.model.level3

Interface SequenceEntityReference

All Superinterfaces:
BioPAXElement, Cloneable, EntityReference, Level3Element, Named, Observable, Serializable, UtilityClass, XReferrable
All Known Subinterfaces:
DnaReference, DnaRegionReference, NucleicAcidReference, NucleicAcidRegionReference, ProteinReference, RnaReference, RnaRegionReference
All Known Implementing Classes:
DnaReferenceImpl, DnaRegionReferenceImpl, NucleicAcidReferenceImpl, NucleicAcidRegionReferenceImpl, ProteinReferenceImpl, RnaReferenceImpl, RnaRegionReferenceImpl, SequenceEntityReferenceImpl
public interface SequenceEntityReference extends EntityReference
Tagger interface for protein, dna and rna entities

  • Method Details

    • getOrganism

      BioSource getOrganism()
      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.
      Returns:
      the organism for this gene.

    • setOrganism

      void setOrganism(BioSource source)
      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.
      Parameters:
      source - new organism for this gene

    • getSequence

      String getSequence()
      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.
      Returns:
      sequence - primary structure of a biopolymer.

    • setSequence

      void setSequence(String sequence)
      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.
      Parameters:
      sequence - Polymer sequence in uppercase letters.