Class BioSequence

  • All Implemented Interfaces:
    Serializable, Describable, Identifiable

    @Indexed
    public class BioSequence
    extends AbstractDescribable
    implements Serializable

    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.

    See Also:
    Serialized Form
    • Constructor Detail

      • BioSequence

        public BioSequence()
        No-arg constructor added to satisfy javabean contract
    • Method Detail

      • 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
      • 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)
      • 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)
      • equals

        public boolean equals​(Object object)
        Description copied from class: AbstractDescribable
        Returns true if the argument is an Describable instance and all identifiers for this entity equal the identifiers of the argument entity. Returns false otherwise.
        Overrides:
        equals in class AbstractDescribable