Package ubic.gemma.model.genome.biosequence

Class BioSequence

java.lang.Object
ubic.gemma.model.common.AbstractIdentifiable
ubic.gemma.model.common.AbstractDescribable
ubic.gemma.model.genome.biosequence.BioSequence
All Implemented Interfaces:
Describable, Identifiable
@Indexed public class BioSequence extends AbstractDescribable

The sequence of a biological polymer such as a protein or DNA. BioSequences may be artificial, such as Affymetrix reporter oligonucleotide chains, or they may be the sequence

of nucleotides associated with a gene product. This class only represents the sequence itself ("ATCGCCG..."), not the physical item, and not the database entry for the sequence.

  • Constructor Details

    • BioSequence

      public BioSequence()

  • Method Details

    • 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

    • getBioSequence2GeneProduct

      public Set<BioSequence2GeneProduct> getBioSequence2GeneProduct()

    • setBioSequence2GeneProduct

      public void setBioSequence2GeneProduct(Set<BioSequence2GeneProduct> bioSequence2GeneProduct)

    • getFractionRepeats

      public Double getFractionRepeats()
      Returns:
      The fraction of the sequences determined to be made up of repeats (e.g., via repeat masker)

    • setFractionRepeats

      public void setFractionRepeats(Double fractionRepeats)

    • getIsApproximateLength

      public Boolean getIsApproximateLength()

    • setIsApproximateLength

      public void setIsApproximateLength(Boolean isApproximateLength)

    • getIsCircular

      public Boolean getIsCircular()

    • setIsCircular

      public void setIsCircular(Boolean isCircular)

    • getLength

      public Long getLength()

    • setLength

      public void setLength(Long length)

    • getPolymerType

      @Nullable public PolymerType getPolymerType()

    • setPolymerType

      public void setPolymerType(@Nullable PolymerType polymerType)

    • getSequence

      public String getSequence()

    • setSequence

      public void setSequence(String sequence)
      Parameters:
      sequence - The actual nucleotic sequence as in ATGC

    • getSequenceDatabaseEntry

      @IndexedEmbedded public DatabaseEntry getSequenceDatabaseEntry()

    • setSequenceDatabaseEntry

      public void setSequenceDatabaseEntry(DatabaseEntry sequenceDatabaseEntry)

    • getTaxon

      public Taxon getTaxon()

    • setTaxon

      public void setTaxon(Taxon taxon)

    • getType

      @Nullable public SequenceType getType()

    • setType

      public void setType(@Nullable SequenceType type)

    • hashCode

      public int hashCode()
      Description copied from class: AbstractIdentifiable
      Important note: Never use the ID in the hashCode() implementation since it can be assigned when the object is persisted.
      Overrides:
      hashCode in class AbstractDescribable

    • 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