ibd

Class Haplotype

java.lang.Object

ibd.Haplotype

public class Haplotype
extends java.lang.Object

Class Haplotype represents a haplotype segment.

Instances of class Haplotype are immutable.

Constructor Summary

Constructors

Constructor and Description
Haplotype(SampleHapPairs haps, int hap) Constructs a new Haplotype instance.
Haplotype(SampleHapPairs haps, int hap, int start, int end) Constructs a new Haplotype instance.

Method Summary

Modifier and Type	Method and Description
int	allele(int index) Returns the specified allele on the haplotype.
boolean	equals(java.lang.Object obj) Compares the specified object with this Haplotype for equality.
int	hapIndex() Returns the index of the haplotype.
int	hashCode() Returns a hash code value for the object.
int	length() Returns the number of alleles in this haplotype segment.
Marker	marker(int index) Returns the specified marker.
Haplotype	restrict(int start, int end) Returns a new Haplotype instance that is obtained by restricting this haplotype to the specified marker interval.
SampleHapPairs	sampleHapPairs() Returns the sample haplotype pairs.
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

Haplotype

public Haplotype(SampleHapPairs haps,
                 int hap)

Constructs a new Haplotype instance. The haplotype will include all markers in the specified SampleHapPairs parameter.

Parameters:

haps - sample haplotype pairs

hap - a haplotype index

Throws:

java.lang.IndexOutOfBoundsException - if hap < 0 || hap >= haps.nHaps()

java.lang.NullPointerException - if haps == null

Haplotype

public Haplotype(SampleHapPairs haps,
                 int hap,
                 int start,
                 int end)

Constructs a new Haplotype instance.

Parameters:

haps - sample haplotype pairs

hap - a haplotype index

start - the starting marker index for the haplotype segment (inclusive)

end - the ending marker index for the haplotype segment (exclusive)

Throws:

java.lang.IndexOutOfBoundsException - if hap < 0 || hap >= haps.nHaps()

java.lang.IndexOutOfBoundsException - if start < 0 || start > end || end > haps.nMarkers()

java.lang.NullPointerException - if haps == null

Method Detail

restrict

public Haplotype restrict(int start,
                          int end)

Returns a new Haplotype instance that is obtained by restricting this haplotype to the specified marker interval.

Parameters:

start - the starting marker index for the haplotype segment (inclusive)

end - the ending marker index for the haplotype segment (exclusive)

Returns:

the restricted haplotype segment

Throws:

java.lang.IndexOutOfBoundsException - if start < 0 || start > end || end > this.length()

length

public int length()

Returns the number of alleles in this haplotype segment.

Returns:

the number of alleles in this haplotype segment

hapIndex

public int hapIndex()

Returns the index of the haplotype.

Returns:

the index of the haplotype

sampleHapPairs

public SampleHapPairs sampleHapPairs()

Returns the sample haplotype pairs.

Returns:

the sample haplotype pairs

marker

public Marker marker(int index)

Returns the specified marker. The first marker on the haplotype segment has index 0.

Parameters:

index - a marker index

Returns:

the specified marker

Throws:

java.lang.IndexOutOfBoundsException - if index < 0 || index >= this.length()

allele

public int allele(int index)

Returns the specified allele on the haplotype. The first allele on the haplotype segment has index 0.

Parameters:

index - a marker index

Returns:

the specified allele on the haplotype

Throws:

java.lang.IndexOutOfBoundsException - if index < 0 || index >= this.length()

equals

public boolean equals(java.lang.Object obj)

Compares the specified object with this Haplotype for equality. Returns true if the specified object is a Haplotype that represents the same haplotype segment as this, and returns false otherwise.

Overrides:

equals in class java.lang.Object

Parameters:

obj - the object to be compared for equality with this Haplotype

Returns:

true if the specified object is an Haplotype that represents the same haplotype segment as this

hashCode

public int hashCode()

Returns a hash code value for the object.

The hash code is defined by the following calculation:

        int hash = 17;
        for (int j=0; j<this.length(); ++j) {
            hash += 29 * hash + haps.allele(j, this.hapIndex());
            hash += 29 * hash + haps.marker(j).hashCode();
        }
 

Overrides:

hashCode in class java.lang.Object

Returns:

a hash code value for the object

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