Package ubic.gemma.model.genome

Class Gene

java.lang.Object
ubic.gemma.model.common.AbstractIdentifiable
ubic.gemma.model.common.AbstractDescribable
ubic.gemma.model.genome.ChromosomeFeature
ubic.gemma.model.genome.Gene
All Implemented Interfaces:
Describable, Identifiable
@Indexed public class Gene extends ChromosomeFeature
Represents a functionally transcribed unit in the genome, recognized by other databases (NCBI, Ensembl).

  • Constructor Details

    • Gene

      public Gene()
      No-arg constructor added to satisfy javabean contract

  • Method Details

    • equals

      public boolean equals(Object object)
      Description copied from class: AbstractIdentifiable
      Important note: Two objects with the same class and non-null ID must be considered equal. If one or both IDs are nulls, the rest of the state can be used to determine equality.
      Specified by:
      equals in class AbstractIdentifiable

    • toString

      public String toString()
      Overrides:
      toString in class AbstractDescribable

    • getId

      @DocumentId public Long getId()
      Specified by:
      getId in interface Identifiable
      Overrides:
      getId in class AbstractIdentifiable

    • getName

      @Field public String getName()
      Description copied from interface: Describable
      Obtain the name of an object is a possibly ambiguous human-readable identifier that need not be an external database reference.
      Specified by:
      getName in interface Describable
      Overrides:
      getName in class AbstractDescribable

    • getAccessions

      @IndexedEmbedded public Set<DatabaseEntry> getAccessions()

    • setAccessions

      public void setAccessions(Set<DatabaseEntry> accessions)

    • getAliases

      @IndexedEmbedded public Set<GeneAlias> getAliases()

    • setAliases

      public void setAliases(Set<GeneAlias> aliases)

    • getEnsemblId

      @Nullable @Field(analyze=NO) public String getEnsemblId()
      Returns:
      An Ensembl ID for the gene.

    • setEnsemblId

      public void setEnsemblId(@Nullable String ensemblId)

    • getMultifunctionality

      public Multifunctionality getMultifunctionality()

    • setMultifunctionality

      public void setMultifunctionality(Multifunctionality multifunctionality)

    • getNcbiGeneId

      @Field(analyze=NO) public Integer getNcbiGeneId()

    • setNcbiGeneId

      public void setNcbiGeneId(Integer ncbiGeneId)

    • getOfficialName

      @Field(analyze=NO) public String getOfficialName()

    • setOfficialName

      public void setOfficialName(String officialName)

    • getOfficialSymbol

      @Field(analyze=NO) public String getOfficialSymbol()

    • setOfficialSymbol

      public void setOfficialSymbol(String officialSymbol)

    • getProducts

      @IndexedEmbedded public Set<GeneProduct> getProducts()

    • setProducts

      public void setProducts(Set<GeneProduct> products)

    • getTaxon

      @IndexedEmbedded public Taxon getTaxon()
      Returns:
      Note that a Gene also has a chromosome, so the organism can be inferred that way as well. This direct association is a denormalization for queries that don't care about location, just species-membership.

    • setTaxon

      public void setTaxon(Taxon taxon)