Package pal.alignment

Interface AnnotationAlignment

    • Method Detail

      • getChromosomePosition

        float getChromosomePosition​(int site)
        Return the position along chromosome
      • getChromosome

        int getChromosome​(int site)
        Returns chromosome
      • getWeightedLocusPosition

        float getWeightedLocusPosition​(int site)
        Return the weighted position along the locus (handles gaps)
      • getLocusPosition

        int getLocusPosition​(int site)
        Return the position along the locus (ignores gaps)
      • getPositionType

        char getPositionType​(int site)
        Returns position type (eg. I=intron, E=exon, P=promoter, 1=first, 2=second, 3=third, etc.
      • getLocusName

        java.lang.String getLocusName​(int site)
        Returns the name of the locus
      • getDataType

        DataType getDataType​(int site)
        Returns the datatype for a specific site, which could differ by site in complex alignments
      • report

        void report​(java.io.PrintWriter out)
        Returns a report for the alignment
        Specified by:
        report in interface Report
        Parameters:
        out - output stream