ibd

Class IbdSegment

java.lang.Object

ibd.IbdSegment

public final class IbdSegment
extends java.lang.Object

Class IbdSegment represents a pair of IBD haplotype segments.

Instances of class IbdSegment are immutable.

Constructor Summary

Constructors

Constructor and Description
IbdSegment(IntPair hapPair, Marker start, Marker end, float score, int startIndex, int endIndex) Constructs an new IbdSegment instance from the specified data.

Method Summary

Modifier and Type	Method and Description
Marker	end() Returns the ending marker (inclusive).
int	endIndex() Returns the ending marker index (inclusive) or -1 if the ending marker index is unknown.
boolean	equals(java.lang.Object o) Compares the specified object with this IbdSegment for equality.
int	hap1() Returns the first haplotype index.
int	hap2() Returns the second haplotype index.
IntPair	hapPair() Returns the ordered pair of haplotype indices.
int	hashCode() Returns the hash code value for this object.
float	score() Returns the IBD segment score.
Marker	start() Returns the starting marker (inclusive).
int	startIndex() Returns the starting marker index (inclusive) or -1 if the starting marker index is unknown.
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

IbdSegment

public IbdSegment(IntPair hapPair,
                  Marker start,
                  Marker end,
                  float score,
                  int startIndex,
                  int endIndex)

Constructs an new IbdSegment instance from the specified data.

Parameters:

hapPair - an ordered pair of haplotype indices

start - the starting marker for the IBD segment (inclusive)

end - the ending marker for the IBD segment (inclusive)

score - the score for the IBD segment

startIndex - the starting marker index (inclusive) or -1 if the starting marker index is unknown

endIndex - the ending marker index (inclusive) or -1 if the ending marker index is unknown

Throws:

java.lang.IllegalArgumentException - if hapPair.first() < 0 || hapPair.second() <= hapPair.first()

java.lang.IllegalArgumentException - if start.chromIndex() != end.chromIndex() || end.pos() < start.pos()

java.lang.IllegalArgumentException - if startIndex < -1 || endIndex < -1

java.lang.IllegalArgumentException - if Float.isNaN(score) == true

java.lang.NullPointerException - if hapPair == null || start == null || end == null

Method Detail

equals

public boolean equals(java.lang.Object o)

Compares the specified object with this IbdSegment for equality. Returns true if the specified object is an IbdSegment instance and if this IbdSegment is equal to the specified IbdSegment, and returns false otherwise. Two IbdSegment instances are equal if they have equal ordered pairs of haplotype indices, equal starting and ending markers, and equal scores.

Overrides:

equals in class java.lang.Object

Parameters:

o - the reference object with which to compare

Returns:

true if this IbdSegment is equal to the specified object.

hashCode

public int hashCode()

Returns the hash code value for this object. The hash code does not depend on the values of this.startIndex() or this.endIndex(). The hash code is defined by the following calculation:

  int hash = 5;
  hash = 67 * hash + this.hapPair().hashCode();
  hash = 67 * hash + this.start().hashCode();
  hash = 67 * hash + this.end().hashCode();
  hash = 67 * hash + Float.floatToIntBits(this.score());
     

Overrides:

hashCode in class java.lang.Object

Returns:

the hash code value for this object

hap1

public int hap1()

Returns the first haplotype index.

Returns:

the first haplotype index

hap2

public int hap2()

Returns the second haplotype index.

Returns:

the second haplotype index

hapPair

public IntPair hapPair()

Returns the ordered pair of haplotype indices.

Returns:

the ordered pair of haplotype indices

start

public Marker start()

Returns the starting marker (inclusive).

Returns:

the starting marker (inclusive)

end

public Marker end()

Returns the ending marker (inclusive).

Returns:

the ending marker (inclusive)

score

public float score()

Returns the IBD segment score.

Returns:

the IBD segment score

startIndex

public int startIndex()

Returns the starting marker index (inclusive) or -1 if the starting marker index is unknown.

Returns:

the starting marker index (inclusive)

endIndex

public int endIndex()

Returns the ending marker index (inclusive) or -1 if the ending marker index is unknown.

Returns:

the ending 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