Class Markers

Method Details

• 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:

  IllegalArgumentException - if markers on a chromosome are not in chromosome order

  IllegalArgumentException - if there are duplicate markers

  IllegalArgumentException - if the markers on a chromosome do not form a contiguous set of entries within the array

  NullPointerException - if markers == null or if markers[j] == null for any j satisfying (0 <= j && j < markers.length)

• cumSumGenotypes

  public int[] cumSumGenotypes()

  Return an array of length this.size() + 1 whose k-th value is the the sum of the number of possible genotypes for markers with index less than k

  Returns:

  an array whose k-th value is the the sum of the number of possible genotypes for markers with index less than k

• 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 Object

  Returns:

  a hash code value for the object

• equals

  public boolean equals(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 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:

  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:

  IndexOutOfBoundsException - if start < 0 || end > this.nMarkers()

  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:

  IndexOutOfBoundsException - if there exists j such that (0 <= j && j < indices.length) such that (indices[j] < 0 || indices[j] >= this.nMarkers())

  IllegalArgumentException - if there exists j such that (1 <= j && j < indices.length) such that (indices[j] <= indice[j - 1])

  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:

  IndexOutOfBoundsException - if marker < 0 || marker > this.nMarkers()

• sumAlleles

  public int sumAlleles()

  Returns this.sumAlleles(this.nMarkers()).

  Returns:

  this.sumAlleles(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:

  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:

  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:

  IllegalArgumentException - if alleles.length != this.nMarkers()

  IllegalArgumentException - if bitList.size() != this.sumHaplotypeBits()

  IllegalArgumentException - if there exists a k such that (0 < k && k < alleles.length) and (alleles[k] < 0 || alleles[k] >= this.marker(k).nAlleles())

  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:

  IllegalArgumentException - if alleles.length != this.nMarkers()

  IllegalArgumentException - if bitList.size() != this.sumHaplotypeBits()

  IndexOutOfBoundsException - if marker < 0 || marker >= this.nMarkers()

  IndexOutOfBoundsException - if allele < 0 || allele >= this.marker(marker).nAlleles()

  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:

  IndexOutOfBoundsException - if marker < 0 || marker >= this.nMarkers()

  IndexOutOfBoundsException - if hapBits.size() < this.sumHaplotypeBits(marker + 1)

  NullPointerException - if hapBits == null

• toString

  public String toString()

  Returns a string representation of this. The exact details of the representation are unspecified and subject to change.

  Overrides:

  toString in class Object

  Returns:

  a string representation of this