Package phase

Class SampleSeg

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

    Class SampleSeg represents a segment of genotype data in a sample.

    Instances of class SampleSeg are immutable

    • Constructor Summary

      Constructors 
      Constructor Description
      SampleSeg​(int sample, int start, int inclEnd)
      Constructs a new SampleSeg instance from the specified data.

    • Method Summary

      All Methods Static Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      int compareTo​(SampleSeg ss)
      Compares this SampleSeg with the specified SampleSeg for order.
      boolean equals​(java.lang.Object o)
      Compares the specified object with this SampleSeg for equality.
      int hashCode()
      Returns the hash code value for this object.
      int inclEnd()
      Returns the end marker index (inclusive).
      int sample()
      Returns the sample index.
      static java.util.Comparator<SampleSeg> sampleComp()
      Returns a comparator that orders first by this.sample(), then by this.start(), and finally by this.end().
      int start()
      Returns the start marker index (inclusive).
      java.lang.String toString()
      Returns a string representation of this.

      • Methods inherited from class java.lang.Object

        clone, finalize, getClass, notify, notifyAll, wait, wait, wait

    • Constructor Detail

      • SampleSeg

        public SampleSeg​(int sample,
                 int start,
                 int inclEnd)
        Constructs a new SampleSeg instance from the specified data.
        Parameters:
        sample - the sample index
        start - the start marker index (inclusive)
        inclEnd - the end marker index (inclusive)
        Throws:
        java.lang.IllegalArgumentException - if start > inclEnd

    • Method Detail

      • sample

        public int sample()
        Returns the sample index.
        Returns:
        the sample index

      • start

        public int start()
        Returns the start marker index (inclusive).
        Specified by:
        start in interface IntInterval
        Returns:
        the start marker index (inclusive)

      • inclEnd

        public int inclEnd()
        Returns the end marker index (inclusive).
        Specified by:
        inclEnd in interface IntInterval
        Returns:
        the end marker index (inclusive)

      • toString

        public 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

      • hashCode

        public int hashCode()

        Returns the hash code value for this object. The hash code is defined by the following calculation: 

          int hash = 5;
  hash = 89 * hash + this.hap();
  hash = 89 * hash + this.start();
  hash = 89 * hash + this.inclEnd();
        Overrides:
        hashCode in class java.lang.Object
        Returns:
        the hash code value for this object

      • equals

        public boolean equals​(java.lang.Object o)
        Compares the specified object with this SampleSeg for equality. Returns true if the specified object is a SampleSeg instance and if this SampleSeg is equal to the specified SampleSeg, and returns false otherwise. Two SampleSeg instances are equal if they have equal sample indices, equal start marker indices, and equal end marker indices.
        Overrides:
        equals in class java.lang.Object
        Parameters:
        o - the object to be compared with this SampleSeg for equality
        Returns:
        true if the specified object is equal to this

      • compareTo

        public int compareTo​(SampleSeg ss)
        Compares this SampleSeg with the specified SampleSeg for order. Returns a negative integer, zero, or a positive integer as this object is less than, equal to, or greater than the specified object. SampleSeg instances are ordered first by this.start(), then by this.end(), and finally by tthis.sample().
        Specified by:
        compareTo in interface java.lang.Comparable<SampleSeg>
        Parameters:
        ss - the SampleSeg to be compared with this SampleSeg
        Returns:
        a negative integer, zero, or a positive integer as this SampleSeg is less than, equal to, or greater than the specified SampleSeg
        Throws:
        java.lang.NullPointerException - if ss == null

      • sampleComp

        public static java.util.Comparator<SampleSeg> sampleComp()
        Returns a comparator that orders first by this.sample(), then by this.start(), and finally by this.end().
        Returns:
        a comparator that orders first by this.sample(), then by this.start(), and finally by this.end()