Package uk.ac.ebi.kraken.interfaces.uniprot.comments

Interface Comment

All Superinterfaces:
HasCommentStatus, HasEvidences, Serializable
All Known Subinterfaces:
AllergenComment, AlternativeProductsComment, BioPhysicoChemicalPropertiesComment, BiotechnologyComment, CatalyticActivityComment, CatalyticActivityCommentStructured, CautionComment, CofactorCommentStructured, DevelopmentalStageComment, DiseaseCommentStructured, DisruptionPhenotypeComment, DomainComment, EnzymeRegulationComment, FunctionComment, InductionComment, Interaction, InteractionComment, MassSpectrometryComment, MiscellaneousComment, PAGEDataComment, PathwayComment, PharmaceuticalComment, PolymorphismComment, PtmComment, RnaEditingComment, SequenceCautionComment, SimilarityComment, SubcellularLocationComment, SubunitComment, TextOnlyComment, TissueSpecificityComment, ToxicDoseComment, WebResourceComment
public interface Comment extends HasEvidences, Serializable, HasCommentStatus
A Comment in the UniProtEntry.

Notes:
  • public void setCommentType(CommentType type);
    removed because it causes havoc if textual comments change into structured ones. Hence, a comment does not change type once it is built.
  • To build a comment, use CommentFactory.buildComment(CommentType)
  • Some Comments have further strucutrs such as the Interaction Comment.
  • The getValue() method of each Comment implementation will return the UniProt flat file representation of the Comment without linewrapping or "CC -!- " / "CC " prefixes.
  • The setValue(String) method of each of the implementations of the further structured Comments will set the the corresponding fields simultaneously.


These values can be found in the CC lines of the flat file on the marked position. 
    RT   "Cytochrome c in the apoptotic and antioxidant cascades.";
 RL   FEBS Lett. 423:275-280(1998).
 CC   -!- INTERACTION:
 CC       O14727:APAF1; NbExp=2; IntAct=EBI-446479, EBI-446492;
 CC   -!- SUBCELLULAR LOCATION: Mitochondrial matrix.
 CC   -!- PTM: Binds 1 heme group per subunit.
 DR   EMBL; M22877; AAA35732.1; -; Genomic_DNA.
 DR   PIR; A31764; CCHU.
 ...
In XML: 
  ...
 <scope>REVIEW ON ROLE IN APOPTOSIS.</scope>
 </reference>
 <comment type="interaction">
 <interactant intactId="EBI-446479"/>
 <interactant intactId="EBI-446492">
 <id>O14727</id>
 <label>APAF1</label>
 </interactant>
 <organismsDiffer>false</organismsDiffer>
 <experiments>2</experiments>
 </comment>
 <comment type="subcellular location">
 <text>Mitochondrial matrix</text>
 </comment>
 <comment type="PTM">
 <text>Binds 1 heme group per subunit</text>
 </comment>
 <dbReference type="EMBL" id="M22877" key="24">
 <property type="protein sequence ID" value="AAA35732.1"/>
 ...

  • Method Details

    • getCommentType

      CommentType getCommentType()
      Returns the type of this comment.
      Returns:
      The type of this comment.

    • setCommentType

      void setCommentType(CommentType type)

    • setMolecule

      void setMolecule(String molecule)

    • getMolecule

      String getMolecule()