Class Exon

    • Field Detail

      • ToStringVersion

        public static int ToStringVersion
    • Constructor Detail

      • Exon

        public Exon()
      • Exon

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

      • add

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

        public Exon apply​(Variant variant)
        Apply variant to exon WARNING: There might be conditions which change the exon type (e.g. an intron is deleted). Nevertheless ExonSpliceType is not updated since it reflects the exon type before a sequence change.
        Overrides:
        apply in class MarkerSeq
        Returns:
        The marker result after applying variant
      • createSpliceSiteRegionEnd

        public SpliceSiteRegion createSpliceSiteRegionEnd​(int size)
        Create splice site regions
      • createSpliceSiteRegionStart

        public SpliceSiteRegion createSpliceSiteRegionStart​(int size)
        Create splice site regions
      • frameCorrection

        public boolean frameCorrection​(int frameCorrection)
        Correct exons according to frame information Shift the start position one base
      • getAaIdxEnd

        public int getAaIdxEnd()
      • getAaIdxStart

        public int getAaIdxStart()
      • getRank

        public int getRank()
      • getSpliceSites

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

        protected boolean isAdjustIfParentDoesNotInclude​(Marker parent)
        Description copied from class: Marker
        Adjust parent if it does not include child?
        Overrides:
        isAdjustIfParentDoesNotInclude in class Marker
      • query

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

        public void reset()
      • setAaIdx

        public void setAaIdx​(int aaIdxStart,
                             int aaIdxEnd)
      • setFrame

        public void setFrame​(int frame)
        Frame can be {-1, 0, 1, 2}, where '-1' means unknown
        Specified by:
        setFrame in interface MarkerWithFrame
      • setRank

        public void setRank​(int rank)
      • toString

        public java.lang.String toString()
        Overrides:
        toString in class MarkerSeq
      • variantEffect

        public boolean variantEffect​(Variant variant,
                                     VariantEffects variantEffects)
        Note: This only adds spliceSites effects, for detailed codon changes effects we use 'CodonChange' class
        Overrides:
        variantEffect in class Marker