Class SpliceSiteAcceptor

All Implemented Interfaces:
Serializable, Cloneable, Comparable<Interval>, TxtSerializable

public class SpliceSiteAcceptor extends SpliceSite
Interval for a splice site acceptor Note: Splice sites donnor are defined as the last 2 bases of an intron Reference: http://en.wikipedia.org/wiki/RNA_splicing
Author:
pcingola
See Also:
  • Constructor Details

    • SpliceSiteAcceptor

      public SpliceSiteAcceptor()
    • SpliceSiteAcceptor

      public SpliceSiteAcceptor(Intron parent, int start, int end, boolean strandMinus, String id)
  • Method Details

    • 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