Package imp

Class ImpStates

  • public final class ImpStates
extends java.lang.Object

    Class ImpStates identifies a list of pseudo-reference haplotypes for a target haplotype. Each pseudo-reference haplotype is a one-dimensional mosaic of reference haplotype segments.

    Instances of ImpStates are not thread-safe.

    • Constructor Summary

      Constructors 
      Constructor Description
      ImpStates​(ImpIbs ibsHaps)
      Constructs a new ImpStates object from the specified data.

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      int ibsStates​(int targHap, int[][] hapIndices, boolean[][] alMatch)
      Stores the reference haplotype for the j-th state at the m-th marker in hapIndices[m][j], and stores the equality of the allele carried by the reference haplotype for the j-th state and the allele carried by the target haplotype at the m-th marker in alMatch[m][j].
      int nStates()
      Returns the number of HMM states per marker.

      • Methods inherited from class java.lang.Object

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

    • Constructor Detail

      • ImpStates

        public ImpStates​(ImpIbs ibsHaps)
        Constructs a new ImpStates object from the specified data.
        Parameters:
        ibsHaps - the IBS haplotype segments
        Throws:
        java.lang.NullPointerException - if impData == null || ibsStates == null

    • Method Detail

      • nStates

        public int nStates()
        Returns the number of HMM states per marker.
        Returns:
        the number of HMM states per marker

      • ibsStates

        public int ibsStates​(int targHap,
                     int[][] hapIndices,
                     boolean[][] alMatch)
        Stores the reference haplotype for the j-th state at the m-th marker in hapIndices[m][j], and stores the equality of the allele carried by the reference haplotype for the j-th state and the allele carried by the target haplotype at the m-th marker in alMatch[m][j]. The number of HMM states states at each marker is returned.
        Parameters:
        targHap - the haplotype index
        hapIndices - the two-dimensional array in which reference haplotype indices for each HMM state will be stored
        alMatch - the two-dimensional array in which allele match status between the target haplotype and HMM state will be stored
        Returns:
        the number of HMM states at each marker
        Throws:
        java.lang.IndexOutOfBoundsException - if targHap < 0 || targHap >= this.nTargHaps()
        java.lang.IndexOutOfBoundsException - if (hapIndices.length < this.impData().nClusters()) or if any hapIndices[j].length is less than the number of HMM states at a marker for any j satisfying (0 <= j && j < this.nClusters())
        java.lang.IndexOutOfBoundsException - if (alMatch.length < this.impdata().nClusters()) or if any alMatch[j].length is less than the number of HMM states at a marker for any j satisfying (0 <= j && j < this.nClusters())
        java.lang.NullPointerException - if (hapIndices == null) or if (hapIndices[j] == null) for any j satisfying (0 <= j && j < this.nClusters())
        java.lang.NullPointerException - if (alMatch == null) or if (alMatch[j] == null) for any j satisfying (0 <= j && j < this.nClusters())