Package beagleutil

Class CompHapSegment

  • All Implemented Interfaces:
    java.lang.Comparable<CompHapSegment>
    public class CompHapSegment
extends java.lang.Object
implements java.lang.Comparable<CompHapSegment>

    Class CompHapSegment represents a copied haplotype segment in a composite reference haplotype.

    Instances of class CompHapSegment are not thread-safe.

    • Constructor Summary

      Constructors 
      Constructor Description
      CompHapSegment​(int hap, int start, int ibsStep, int compHapIndex)
      Constructs a new CompHapSegment from the specified data.

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      int compareTo​(CompHapSegment seg)
      Compares the specified segment to this for order.
      int compHapIndex()
      Returns the composite haplotype index.
      int hap()
      Returns the haplotype.
      int ibsStep()
      Returns the last recorded IBS ibsStep for this.hap().
      int startMarker()
      Returns the first marker in the haplotype segment
      void updateSegment​(int hap, int start, int ibsStep)
      Update the haplotype, the first marker in the haplotype segment, and the last recorded IBS ibsStep.
      void updateStep​(int ibsStep)
      Updates the last recorded IBS ibsStep to the specified value

      • Methods inherited from class java.lang.Object

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

    • Constructor Detail

      • CompHapSegment

        public CompHapSegment​(int hap,
                      int start,
                      int ibsStep,
                      int compHapIndex)
        Constructs a new CompHapSegment from the specified data.
        Parameters:
        hap - the haplotype
        start - the index of the first marker in the haplotype segment
        ibsStep - the last recorded IBS ibsStep
        compHapIndex - the composite haplotype index

    • Method Detail

      • updateSegment

        public void updateSegment​(int hap,
                          int start,
                          int ibsStep)
        Update the haplotype, the first marker in the haplotype segment, and the last recorded IBS ibsStep.
        Parameters:
        hap - the haplotype
        start - the index of the first marker in the haplotype segment
        ibsStep - the last recorded IBS ibsStep

      • updateStep

        public void updateStep​(int ibsStep)
        Updates the last recorded IBS ibsStep to the specified value
        Parameters:
        ibsStep - the last recorded IBS ibsStep

      • hap

        public int hap()
        Returns the haplotype.
        Returns:
        the haplotype

      • startMarker

        public int startMarker()
        Returns the first marker in the haplotype segment
        Returns:
        the first marker in the haplotype segment

      • ibsStep

        public int ibsStep()
        Returns the last recorded IBS ibsStep for this.hap().
        Returns:
        the last recorded IBS ibsStep for this.hap()

      • compHapIndex

        public int compHapIndex()
        Returns the composite haplotype index.
        Returns:
        the composite haplotype index

      • compareTo

        public int compareTo​(CompHapSegment seg)
        Compares the specified segment to this for order. Returns -1, 0, or 1 according to whether this.end() is less than, equal, or greater than seg.end().
        Specified by:
        compareTo in interface java.lang.Comparable<CompHapSegment>
        Parameters:
        seg - the object to be compared
        Returns:
        -1, 0, or 1 according to whether this.end() is less than, equal, or greater than seg.end()