Package imp

Class RefHapHash

  • public class RefHapHash
extends java.lang.Object

    Class RefHapHash stores a hash code for each haplotype in a sublist of reference haplotypes. The hash code is computed from the allele sequence carried by the reference haplotype.

    Instances of class RefHapHash are immutable.

    • Constructor Summary

      Constructors 
      Constructor Description
      RefHapHash​(java.util.concurrent.atomic.AtomicReferenceArray<StateProbs> stateProbs, int targMarker, RefGT refHapPairs, int start, int end)
      Constructs a new RefHapHash instance for the specified data.

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      int end()
      Returns the ending reference marker index (exclusive) for the reference haplotype allele sequences.
      int hap​(int index)
      Return the specified haplotype in the sublist of reference haplotypes.
      int hap2Index​(int hap)
      Returns the index of the specified haplotype in the sublist of reference haplotypes.
      int hash​(int index)
      Return a hash code computed from the allele sequence of the specified haplotype in the sublist of reference haplotypes.
      int nHaps()
      Returns the size of the sublist of reference haplotypes.
      RefGT refGT()
      Returns the phased reference genotypes.
      void setAlleles​(int index, int[] alleles)
      Copies the alleles between this.start() (inclusive) and this.end() (exclusive) of the specified haplotype in the sublist of reference haplotypes to the specified array.
      int start()
      Returns the starting reference marker index (inclusive) for the reference haplotype allele sequences.
      int targMarker()
      Returns the target marker.

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Constructor Detail

      • RefHapHash

        public RefHapHash​(java.util.concurrent.atomic.AtomicReferenceArray<StateProbs> stateProbs,
                  int targMarker,
                  RefGT refHapPairs,
                  int start,
                  int end)
        Constructs a new RefHapHash instance for the specified data. The sublist of reference haplotypes is the ordered list of distinct reference haplotypes with stored state probability data at the specified target marker in the stateProbs parameter.
        Parameters:
        stateProbs - HMM state probabilities at the genotyped markers in the target samples
        targMarker - a target marker index
        refHapPairs - the reference haplotypes
        start - the starting reference marker index (inclusive) for the reference haplotype allele sequences
        end - the ending reference marker index (exclusive) for the reference haplotype allele sequences
        Throws:
        java.lang.IndexOutOfBoundsException - if targMarker < 0
        java.lang.IndexOutOfBoundsException - if there exists a j satisfying (0 <= j && j < stateProbs.size()) && (targMarker >= stateProbs.get(j).nMarkers())
        java.lang.IllegalArgumentException - if start < 0 || start >= end || end > refHapPairs.nMarkers()
        java.lang.NullPointerException - if stateProbs == null || refHapPairs == null
        java.lang.NullPointerException - if there exists a j satisfying (0 <= j && j < stateProbs.size()) && (stateProbs.get(j) == null)

    • Method Detail

      • targMarker

        public int targMarker()
        Returns the target marker.
        Returns:
        the target marker

      • refGT

        public RefGT refGT()
        Returns the phased reference genotypes.
        Returns:
        the phased reference genotypes

      • start

        public int start()
        Returns the starting reference marker index (inclusive) for the reference haplotype allele sequences.
        Returns:
        the starting reference marker index (inclusive) for the reference haplotype allele sequences

      • end

        public int end()
        Returns the ending reference marker index (exclusive) for the reference haplotype allele sequences.
        Returns:
        the ending reference marker index (exclusive) for the reference haplotype allele sequences

      • setAlleles

        public void setAlleles​(int index,
                       int[] alleles)
        Copies the alleles between this.start() (inclusive) and this.end() (exclusive) of the specified haplotype in the sublist of reference haplotypes to the specified array.
        Parameters:
        index - an index in the sublist of reference haplotypes
        alleles - the array to which haplotype alleles will be copied
        Throws:
        java.lang.IllegalArgumentException - if alleles.length < (this.end() - this.start())
        java.lang.NullPointerException - if alleles == null

      • nHaps

        public int nHaps()
        Returns the size of the sublist of reference haplotypes.
        Returns:
        the size of the sublist of reference haplotypes

      • hap2Index

        public int hap2Index​(int hap)
        Returns the index of the specified haplotype in the sublist of reference haplotypes. Returns (-insertionPoint - 1) if the specified haplotype is not found in the sublist of reference haplotypes.
        Parameters:
        hap - a reference haplotype index
        Returns:
        the index of the specified haplotype in the sublist of reference haplotypes

      • hap

        public int hap​(int index)
        Return the specified haplotype in the sublist of reference haplotypes.
        Parameters:
        index - an index in the sublist of reference haplotypes
        Returns:
        the specified haplotype in the sublist of reference haplotypes

      • hash

        public int hash​(int index)
        Return a hash code computed from the allele sequence of the specified haplotype in the sublist of reference haplotypes. The hash code is computed from the allele sequence between markers with index this.start() (inclusive) and this.end() (exclusive).
        Parameters:
        index - an index in the sublist of reference haplotypes
        Returns:
        a hash code computed from the allele sequence of the specified haplotype in the sublist of reference haplotypes