Package imp

Interface StateProbs

public interface StateProbs

Class StateProbs stores a subset of Li and Stephens HMM states and associated probabilities for a target haplotype.

All instances of interface StateProbs are required to be immutable.

  • Method Summary

    Modifier and Type
    Method
    Description
    int
    nStates(int targMarker)
    Returns the number of stored HMM states at the specified target marker.
    int
    nTargMarkers()
    Returns the number of target markers.
    float
    probs(int targMarker, int index)
    Returns the probability of the specified state at the specified target marker.
    float
    probsP1(int targMarker, int index)
    Returns the probability of the specified state at the marker following the specified target marker.
    int
    refHap(int targMarker, int index)
    Returns the specified reference haplotype index.
    int
    targHap()
    Returns the target haplotype index.

  • Method Details

    • targHap

      int targHap()
      Returns the target haplotype index.
      Returns:
      the target haplotype index

    • nTargMarkers

      int nTargMarkers()
      Returns the number of target markers.
      Returns:
      the number of target markers

    • nStates

      int nStates(int targMarker)
      Returns the number of stored HMM states at the specified target marker.
      Parameters:
      targMarker - a target marker index
      Returns:
      the number of stored HMM states at the specified target marker
      Throws:
      IndexOutOfBoundsException - if marker < 0 || marker >= this.nTargMarkers()

    • refHap

      int refHap(int targMarker, int index)
      Returns the specified reference haplotype index.
      Parameters:
      targMarker - a target marker index
      index - a stored state index at the specified target marker
      Returns:
      the specified reference haplotype index
      Throws:
      IndexOutOfBoundsException - if targMarker < 0 || targMarker >= this.nTargMarkers()
      IndexOutOfBoundsException - if index < 0 || index >= this.nStates(targMarker)

    • probs

      float probs(int targMarker, int index)
      Returns the probability of the specified state at the specified target marker.
      Parameters:
      targMarker - a target marker index
      index - a stored state index
      Returns:
      the probability of the specified state at the specified target marker
      Throws:
      IndexOutOfBoundsException - if targMarker < 0 || targMarker >= this.nTargMarkers()
      IndexOutOfBoundsException - if index < 0 || index >= this.nStates(targMarker)

    • probsP1

      float probsP1(int targMarker, int index)
      Returns the probability of the specified state at the marker following the specified target marker. If (targMarker + 1 == this.nTargMarkers()), the probability of the specified state at the specified target marker is returned.
      Parameters:
      targMarker - a target marker index
      index - a stored state index
      Returns:
      the probability of the specified state at the marker following the specified target marker
      Throws:
      IndexOutOfBoundsException - if targMarker < 0 || targMarker >= this.nTargMarkers()
      IndexOutOfBoundsException - if index < 0 || index >= this.nStates(targMarker)