Class Intron

    • Constructor Detail

      • Intron

        public Intron()
      • Intron

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

      • add

        public void add​(SpliceSite ss)
        Add a splice site to the collection
      • apply

        public Intron apply​(Variant variant)
        Description copied from class: Marker
        Apply a variant to a marker.

        Calculate a the result of a marker, such that newMarker = marker.apply( variant ) variant = Diff( newMarker , marker ) // Differences in sequence

        Note: This method may return: - The same marker (this) when genetic coordinates remain unchanged - 'null' if the whole marker is removed by the variant (e.g. a deletion spanning the whole marker)

        For these reasons, the method should never be invoked directly. This is why the method is 'private' and 'final'

        Overrides:
        apply in class Marker
        Returns:
        The marker result after applying variant
      • cloneShallow

        public Intron cloneShallow()
        Description copied from class: Marker
        Perform a shallow clone
        Overrides:
        cloneShallow in class Marker
      • createSpliceSiteAcceptor

        public SpliceSiteAcceptor createSpliceSiteAcceptor​(int maxSpliceSiteSize)
        Create a splice site acceptor of 'size' length Acceptor site: 3' end of the intron
      • createSpliceSiteDonor

        public SpliceSiteDonor createSpliceSiteDonor​(int maxSpliceSiteSize)
        Create a splice site donor of 'maxSize' length Donor site: 5' end of the intron
      • createSpliceSiteRegionEnd

        public SpliceSiteRegion createSpliceSiteRegionEnd​(int sizeMin,
                                                          int sizeMax)
        Create splice site region
      • createSpliceSiteRegionStart

        public SpliceSiteRegion createSpliceSiteRegionStart​(int sizeMin,
                                                            int sizeMax)
        Create splice site region
      • getExonAfter

        public Exon getExonAfter()
      • getExonBefore

        public Exon getExonBefore()
      • getRank

        public int getRank()
      • getSpliceSites

        public java.util.ArrayList<SpliceSite> getSpliceSites()
      • getSpliceType

        public java.lang.String getSpliceType()
      • query

        public Markers query​(Marker marker)
        Query all genomic regions that intersect 'marker'
        Overrides:
        query in class Marker
      • reset

        public void reset()
      • setRank

        public void setRank​(int rank)