Class SpliceSiteRegion

  • All Implemented Interfaces:
    java.io.Serializable, java.lang.Cloneable, java.lang.Comparable<Interval>, TxtSerializable

    public class SpliceSiteRegion
    extends SpliceSite
    Interval for a splice site acceptor From Sequence Ontology: A sequence variant in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8 bases of the intron.
    Author:
    pcingola
    See Also:
    Serialized Form
    • Constructor Detail

      • SpliceSiteRegion

        public SpliceSiteRegion()
      • SpliceSiteRegion

        public SpliceSiteRegion​(Exon parent,
                                int start,
                                int end,
                                boolean strandMinus,
                                java.lang.String id)
      • SpliceSiteRegion

        public SpliceSiteRegion​(Intron parent,
                                int start,
                                int end,
                                boolean strandMinus,
                                java.lang.String id)
    • Method Detail

      • intersectsCoreSpliceSite

        public boolean intersectsCoreSpliceSite​(Marker marker)
        Description copied from class: SpliceSite
        Core splice sites are defined as CORE_SPLICE_SITE_SIZE bases after exon end or before exon begins. Usually CORE_SPLICE_SITE_SIZE is 2 bases. Other spice sites are considered "non-core".
        Specified by:
        intersectsCoreSpliceSite in class SpliceSite
      • isExonPart

        public boolean isExonPart()
      • isIntronPart

        public boolean isIntronPart()