java.lang.Object
- picard.fingerprint.HaplotypeBlock

All Implemented Interfaces:

Comparable<HaplotypeBlock>
```
public class HaplotypeBlock
extends Object
implements Comparable<HaplotypeBlock>
```
Represents information about a group of SNPs that form a haplotype in perfect LD with one another.

Constructor Summary

Constructors
Constructor Description

HaplotypeBlock(double maf)
Constructs a haplotype block with the provided minor allele frequency.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`addSnp(Snp snp)`	Adds a SNP to the haplotype.
`int`	`compareTo(HaplotypeBlock that)`
`boolean`	`contains(Snp snp)`	Returns true if the SNP is contained within the haplotype block, false otherwise.
`boolean`	`equals(Object o)`
`DiploidHaplotype`	`getDiploidHaplotype(Snp snp, DiploidGenotype gt)`	Gets the diploid haplotype for this haplotype block given the provided SNP and SNP genotype.
`Snp`	`getFirstSnp()`	Gets the arbitrarily first SNP in the haplotype.
`double[]`	`getHaplotypeFrequencies()`	Gets the set of haplotype frequencies.
`double`	`getHaplotypeFrequency(int i)`	Gets the frequency of the i'th diploid haplotype where haplotypes are ordered accorinding to DiploidHaplotype.
`double`	`getMaf()`	Returns the minor allele frequency of this haplotype.
`Snp`	`getSnp(String name)`	Gets a SNP by name if it belongs to this haplotype.
`DiploidGenotype`	`getSnpGenotype(Snp snp, DiploidHaplotype haplotype)`	Gets the expected genotype of the provided SNP given the provided haplotype of this haplotype block.
`Collection<Snp>`	`getSnps()`	Returns an unmodifiable, unordered, collection of all SNPs in this haplotype block.
`int`	`hashCode()`
`int`	`size()`	Returns the number of SNPs within the haplotype block.
`String`	`toString()`

Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait

- Constructor Detail
  - HaplotypeBlock
```
public HaplotypeBlock(double maf)
```
    Constructs a haplotype block with the provided minor allele frequency.
- Method Detail
  - getHaplotypeFrequencies
```
public double[] getHaplotypeFrequencies()
```
    Gets the set of haplotype frequencies.
  - addSnp
```
public void addSnp(Snp snp)
```
    Adds a SNP to the haplotype. Will throw an exception if the SNP is on the wrong chromosome.
  - getSnp
```
public Snp getSnp(String name)
```
    Gets a SNP by name if it belongs to this haplotype.
  - getFirstSnp
```
public Snp getFirstSnp()
```
    Gets the arbitrarily first SNP in the haplotype.
  - contains
```
public boolean contains(Snp snp)
```
    Returns true if the SNP is contained within the haplotype block, false otherwise.
  - size
```
public int size()
```
    Returns the number of SNPs within the haplotype block.
  - getSnps
```
public Collection<Snp> getSnps()
```
    Returns an unmodifiable, unordered, collection of all SNPs in this haplotype block.
  - getHaplotypeFrequency
```
public double getHaplotypeFrequency(int i)
```
    Gets the frequency of the i'th diploid haplotype where haplotypes are ordered accorinding to DiploidHaplotype.
  - getMaf
```
public double getMaf()
```
    Returns the minor allele frequency of this haplotype.
  - getSnpGenotype
```
public DiploidGenotype getSnpGenotype(Snp snp,
                                      DiploidHaplotype haplotype)
```
    Gets the expected genotype of the provided SNP given the provided haplotype of this haplotype block.
  - getDiploidHaplotype
```
public DiploidHaplotype getDiploidHaplotype(Snp snp,
                                            DiploidGenotype gt)
```
    Gets the diploid haplotype for this haplotype block given the provided SNP and SNP genotype.
  - compareTo
```
public int compareTo(HaplotypeBlock that)
```
    Specified by:
    
    compareTo in interface Comparable<HaplotypeBlock>
  - equals
```
public boolean equals(Object o)
```
    Overrides:
    
    equals in class Object
  - hashCode
```
public int hashCode()
```
    Overrides:
    
    hashCode in class Object
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Object

Class HaplotypeBlock

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

HaplotypeBlock

Method Detail

getHaplotypeFrequencies

addSnp

getSnp

getFirstSnp

contains

size

getSnps

getHaplotypeFrequency

getMaf

getSnpGenotype

getDiploidHaplotype

compareTo

equals

hashCode

toString