Package pal.alignment

Class IndelAnnotatedAlignment

    • Field Detail

      • chromosomePosition

        public float chromosomePosition
        used to designate position along chromosome
      • chromosome

        public int chromosome
        used to designate chromosome
      • weightedLocusPosition

        public float[] weightedLocusPosition
        used to designate weighted position; accounts for gaps
      • locusPosition

        public int[] locusPosition
        used to designate position; do not account for gaps
      • positionType

        public char[] positionType
        used to designate position Type
      • locusName

        public java.lang.String locusName
        used to designate locus name
    • Constructor Detail

      • IndelAnnotatedAlignment

        public IndelAnnotatedAlignment​(AnnotationAlignment a,
                                       boolean anchored)
        Basic constructor. All annotation is based off the first site in the AnnotationAlignment. This Alignment should not span multiple loci.
        Parameters:
        anchored - sets to score anchored indels as same position
    • Method Detail

      • setChromosomePosition

        public void setChromosomePosition​(float position)
        Set the position along chromosome
      • setChromosome

        public void setChromosome​(int chromosome)
        Sets chromosome
      • getLocusPosition

        public int getLocusPosition​(int site)
        Return the position along the locus (ignores gaps)
        Specified by:
        getLocusPosition in interface AnnotationAlignment
      • getPositionType

        public char getPositionType​(int site)
        Returns position type (eg. I=intron, E-exon, P=promoter, 1=first, 2=second, 3=third, etc.
        Specified by:
        getPositionType in interface AnnotationAlignment
      • getLocusName

        public java.lang.String getLocusName​(int site)
        Returns the name of the locus
        Specified by:
        getLocusName in interface AnnotationAlignment
      • setLocusName

        public void setLocusName​(java.lang.String locusName)
        Sets the name of the locus