Package vcf

Interface XGT1

  • All Known Implementing Classes:
    XBasicGT1

    public interface XGT1

    Interface XGT1 (Genotype Likelihoods) represents genotype likelihoods for one sample.

    Instances of XGT1 are required to be immutable.

    • Method Summary

      All Methods Instance Methods Abstract Methods 
      Modifier and Type Method Description
      int allele1​(int marker)
      Returns the first allele for the specified marker if the observed data include a non-missing allele, and returns -1 otherwise.
      int allele2​(int marker)
      Returns the second allele for the specified marker if the observed data include a non-missing allele, and returns -1 otherwise.
      float gl​(int marker, int allele1, int allele2)
      Returns the probability of the observed data for the specified marker if the specified pair of ordered alleles is the true ordered genotype.
      int idIndex()
      Returns the sample identifier index.
      Marker marker​(int marker)
      Returns the specified marker.
      Markers markers()
      Returns the list of markers.
      int nMarkers()
      Returns the number of markers.
      java.lang.String toString()
      Returns a string representation of this.
    • Method Detail

      • gl

        float gl​(int marker,
                 int allele1,
                 int allele2)
        Returns the probability of the observed data for the specified marker if the specified pair of ordered alleles is the true ordered genotype.
        Parameters:
        marker - the marker index
        allele1 - the first allele index
        allele2 - the second allele index
        Returns:
        the probability of the observed data for the specified marker and sample if the specified pair of ordered alleles is the true ordered genotype
        Throws:
        java.lang.IndexOutOfBoundsException - if marker < 0 || marker >= this.nMarkers()
        java.lang.IndexOutOfBoundsException - if allele1 < 0 || allele1 >= this.marker(marker).nAlleles()
        java.lang.IndexOutOfBoundsException - if allele2 < 0 || allele2 >= this.marker(marker).nAlleles()
      • allele1

        int allele1​(int marker)
        Returns the first allele for the specified marker if the observed data include a non-missing allele, and returns -1 otherwise. Alleles are arbitrarily ordered if the genotype is unphased.
        Parameters:
        marker - the marker index
        Returns:
        the first allele for the specified marker if the observed data include a non-missing allele, and -1 otherwise
        Throws:
        java.lang.IndexOutOfBoundsException - if marker < 0 || marker >= this.nMarkers()
      • allele2

        int allele2​(int marker)
        Returns the second allele for the specified marker if the observed data include a non-missing allele, and returns -1 otherwise. Alleles are arbitrarily ordered if the genotype is unphased.
        Parameters:
        marker - the marker index
        Returns:
        the second allele for the specified marker if the observed data include a non-missing allele, and -1 otherwise
        Throws:
        java.lang.IndexOutOfBoundsException - if marker < 0 || marker >= this.nMarkers()
      • nMarkers

        int nMarkers()
        Returns the number of markers.
        Returns:
        the number of markers
      • marker

        Marker marker​(int marker)
        Returns the specified marker.
        Parameters:
        marker - the marker index
        Returns:
        the specified marker
        Throws:
        java.lang.IndexOutOfBoundsException - if marker < 0 || marker >= this.nMarkers()
      • markers

        Markers markers()
        Returns the list of markers.
        Returns:
        the list of markers
      • idIndex

        int idIndex()
        Returns the sample identifier index.
        Returns:
        the sample identifier index
      • toString

        java.lang.String toString()
        Returns a string representation of this. The exact details of the representation are unspecified and subject to change.
        Overrides:
        toString in class java.lang.Object
        Returns:
        a string representation of this