Package ubic.gemma.model.genome.biosequence

Class 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 Detail

      • BioSequence

        public BioSequence()

    • 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)

      • 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