java.lang.Object
- vcf.Markers

```
public final class Markers
extends java.lang.Object
```
Class Markers represent a list of markers in chromosome order.

Instances of class Markers are immutable.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`int`	`allele(BitArray hapBits, int marker)`	Returns the specified allele
`void`	`allelesToBits(int[] alleles, BitArray bitList)`	Stores the specified alleles in the specified `bitList`
`int[]`	`bitsToAlleles(BitArray hapBits)`	Returns the specified allele stored in the specified `hapBits` array.
`boolean`	`contains(Marker marker)`	Returns `true` if the specified marker is not `null` and is an element in the list of markers represented by `this`, and returns `false` otherwise.
`static Markers`	`create(Marker[] markers)`	Returns a new `Markers` instance that is constructed from the specified data.
`boolean`	`equals(java.lang.Object obj)`	Returns `true` if the specified object is a `Markers` instance which represents the same list of markers as `this`, and returns `false` otherwise.
`int`	`hashCode()`	Returns a hash code value for the object.
`Marker`	`marker(int marker)`	Returns the specified marker.
`Marker[]`	`markers()`	Returns the list of markers.
`Markers`	`restrict(int[] indices)`	Returns a `Markers` instance that represents the specified markers.
`Markers`	`restrict(int start, int end)`	Returns a `Markers` instance that represents the specified range of marker indices.
`void`	`setAllele(int marker, int allele, BitArray bitList)`	Stores the specified alleles in the specified `bitList`
`int`	`size()`	Returns the number of markers.
`int`	`sumAlleles()`	Returns `this.sumAlleles(this.nMarkers())`.
`int`	`sumAlleles(int marker)`	Returns the sum of the number of alleles for the markers with index less than the specified index.
`int`	`sumGenotypes()`	Returns `this.sumGenotypes(this.nMarkers())`.
`int`	`sumGenotypes(int marker)`	Returns the sum of the number of possible genotypes for the markers with index less than the specified index.
`int`	`sumHapBits()`	Returns `this.sumHaplotypeBits(this.nMarkers())`.
`int`	`sumHapBits(int marker)`	Returns the number of bits requires to store a haplotype for the markers with index less than the specified index.
`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

- Method Detail
  - create
```
public static Markers create(Marker[] markers)
```
    Returns a new Markers instance that is constructed from the specified data.
    
    Parameters:
    
    markers - a list of markers in chromosome order
    
    Returns:
    
    a new Markers instance corresponding to the specified list of markers
    
    Throws:
    
    java.lang.IllegalArgumentException - if markers on a chromosome are not in chromosome order
    
    java.lang.IllegalArgumentException - if there are duplicate markers
    
    java.lang.IllegalArgumentException - if the markers on a chromosome do not form a contiguous set of entries within the array
    
    java.lang.NullPointerException - if markers == null or if markers[j] == null for any j satisfying (0 <= j && j < markers.length)
  - hashCode
```
public int hashCode()
```
    Returns a hash code value for the object. The returned hash code equals Arrays.deepHashCode(this.markers()).
    
    Overrides:
    
    hashCode in class java.lang.Object
    
    Returns:
    
    a hash code value for the object
  - equals
```
public boolean equals(java.lang.Object obj)
```
    Returns true if the specified object is a Markers instance which represents the same list of markers as this, and returns false otherwise. Two lists of markers are the same if the lists have the same size and if markers with the same index in the two lists are equal.
    
    Overrides:
    
    equals in class java.lang.Object
    
    Parameters:
    
    obj - the object to be tested for equality with this
    
    Returns:
    
    true if the specified object is a Markers instance which represents the same list of markers as this
  - size
```
public int size()
```
    Returns the number of markers.
    
    Returns:
    
    the number of markers
  - marker
```
public Marker marker(int marker)
```
    Returns the specified marker.
    
    Parameters:
    
    marker - a marker index
    
    Returns:
    
    the specified marker
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if marker < 0 || marker >= this.nMarkers()
  - markers
```
public Marker[] markers()
```
    Returns the list of markers.
    
    Returns:
    
    the list of markers
  - contains
```
public boolean contains(Marker marker)
```
    Returns true if the specified marker is not null and is an element in the list of markers represented by this, and returns false otherwise.
    
    Parameters:
    
    marker - a marker
    
    Returns:
    
    true if the specified marker is not null and is an element in the list of markers represented by this
  - restrict
```
public Markers restrict(int start,
                        int end)
```
    Returns a Markers instance that represents the specified range of marker indices.
    
    Parameters:
    
    start - the starting marker index (inclusive)
    
    end - the ending marker index (exclusive)
    
    Returns:
    
    a Markers instance that represents the specified range of marker indices
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if start < 0 || end > this.nMarkers()
    
    java.lang.IllegalArgumentException - if start >= end
  - restrict
```
public Markers restrict(int[] indices)
```
    Returns a Markers instance that represents the specified markers.
    
    Parameters:
    
    indices - a list of distinct marker indices in increasing order
    
    Returns:
    
    a new Markers instance that represents the specified markers
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if there exists j such that (0 <= j && j < indices.length) such that (indices[j] < 0 || indices[j] >= this.nMarkers())
    
    java.lang.IllegalArgumentException - if there exists j such that (1 <= j && j < indices.length) such that (indices[j] <= indice[j - 1])
    
    java.lang.NullPointerException - if indices == null
  - sumAlleles
```
public int sumAlleles(int marker)
```
    Returns the sum of the number of alleles for the markers with index less than the specified index.
    
    Parameters:
    
    marker - a marker index
    
    Returns:
    
    the sum of the number of alleles for the markers with index less than the specified index
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if marker < 0 || marker > this.nMarkers()
  - sumAlleles
```
public int sumAlleles()
```
    Returns this.sumAlleles(this.nMarkers()).
    
    Returns:
    
    this.sumAlleles(this.nMarkers())
  - sumGenotypes
```
public int sumGenotypes(int marker)
```
    Returns the sum of the number of possible genotypes for the markers with index less than the specified index.
    
    Parameters:
    
    marker - a marker index
    
    Returns:
    
    the sum of the number of possible genotypes for the markers with index less than the specified index
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if marker < 0 || marker > this.nMarkers()
  - sumGenotypes
```
public int sumGenotypes()
```
    Returns this.sumGenotypes(this.nMarkers()).
    
    Returns:
    
    this.sumGenotypes(this.nMarkers())
  - sumHapBits
```
public int sumHapBits(int marker)
```
    Returns the number of bits requires to store a haplotype for the markers with index less than the specified index.
    
    Parameters:
    
    marker - a marker index
    
    Returns:
    
    the number of bits requires to store a haplotype for the markers with index less than the specified index
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if marker < 0 || marker > this.nMarkers()
  - sumHapBits
```
public int sumHapBits()
```
    Returns this.sumHaplotypeBits(this.nMarkers()).
    
    Returns:
    
    this.sumHaplotypeBits(this.nMarkers())
  - bitsToAlleles
```
public int[] bitsToAlleles(BitArray hapBits)
```
    Returns the specified allele stored in the specified hapBits array. The contract for this method is undefined if the specified hapBits array was not created with the this.allelesToBits() method.
    
    Parameters:
    
    hapBits - the bit array storing the haplotype alleles
    
    Returns:
    
    the specified allele stored in the specified hapBits array.
    
    Throws:
    
    java.lang.NullPointerException - if hapBits == null
  - allelesToBits
```
public void allelesToBits(int[] alleles,
                          BitArray bitList)
```
    Stores the specified alleles in the specified bitList
    
    Parameters:
    
    alleles - a sequence of alleles
    
    bitList - a sequence of bits
    
    Throws:
    
    java.lang.IllegalArgumentException - if alleles.length != this.nMarkers()
    
    java.lang.IllegalArgumentException - if bitList.size() != this.sumHaplotypeBits()
    
    java.lang.IllegalArgumentException - if there exists a k such that (0 < k && k < alleles.length) and (alleles[k] < 0 || alleles[k] >= this.marker(k).nAlleles())
    
    java.lang.NullPointerException - if alleles == null || bitList == null
  - setAllele
```
public void setAllele(int marker,
                      int allele,
                      BitArray bitList)
```
    Stores the specified alleles in the specified bitList
    
    Parameters:
    
    marker - a marker index
    
    allele - an allele index
    
    bitList - a sequence of bits
    
    Throws:
    
    java.lang.IllegalArgumentException - if alleles.length != this.nMarkers()
    
    java.lang.IllegalArgumentException - if bitList.size() != this.sumHaplotypeBits()
    
    java.lang.IndexOutOfBoundsException - if marker < 0 || marker >= this.nMarkers()
    
    java.lang.IndexOutOfBoundsException - if allele < 0 || allele >= this.marker(marker).nAlleles()
    
    java.lang.NullPointerException - if bitList == null
  - allele
```
public int allele(BitArray hapBits,
                  int marker)
```
    Returns the specified allele
    
    Parameters:
    
    hapBits - a haplotype encoded as bits with the this.allelesToBits() method
    
    marker - a marker index
    
    Returns:
    
    the specified allele
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if marker < 0 || marker >= this.nMarkers()
    
    java.lang.IndexOutOfBoundsException - if hapBits.size() < this.sumHaplotypeBits(marker + 1)
    
    java.lang.NullPointerException - if hapBits == null
  - 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

Class Markers

Method Summary

Methods inherited from class java.lang.Object

Method Detail

create

hashCode

equals

size

marker

markers

contains

restrict

restrict

sumAlleles

sumAlleles

sumGenotypes

sumGenotypes

sumHapBits

sumHapBits

bitsToAlleles

allelesToBits

setAllele

allele

toString