Interface Marker

Method Details

• chrom

  String chrom()

  Returns the chromosome.

  Returns:

  the chromosome

• chromIndex

  int chromIndex()

  Returns the chromosome index.

  Returns:

  the chromosome index

• pos

  int pos()

  Returns the chromosome position coordinate.

  Returns:

  the chromosome position coordinate

• nIds

  int nIds()

  Returns the number of marker identifiers.

  Returns:

  the number of marker identifiers

• id

  String id(int index)

  Returns the specified marker identifier.

  Parameters:

  index - a marker identifier index

  Returns:

  the specified marker identifier

  Throws:

  IndexOutOfBoundsException - if index < 0 || index >= this.nIds()

• id

  String id()

  Returns the first marker identifier if there is at least one identifier in the VCF record ID field, and returns this.chr() + ":" + this.pos() otherwise.

  Returns:

  a marker identifier

• nAlleles

  int nAlleles()

  Returns the number of alleles for the marker, including the REF allele.

  Returns:

  the number of alleles for the marker, including the REF allele

• bitsPerAllele

  int bitsPerAllele()

  Returns the minimum number of bits required to store a non-missing allele.

  Returns:

  the minimum number of bits required to store a non-missing allele

• allele

  String allele(int index)

  Returns the specified allele. The reference allele has index 0.

  Parameters:

  index - an allele index

  Returns:

  the specified allele

  Throws:

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

• alleles

  String[] alleles()

  Returns the alleles. The k-th element of the returned array is equal to this.allele(k).

  Returns:

  the alleles

• nGenotypes

  int nGenotypes()

  Returns the number of distinct genotypes, which equals this.nAlleles()*(1 + this.nAlleles())/2.

  Returns:

  the number of distinct genotypes

• end

  int end()

  Returns the INFO END field, or -1 if there is no INFO END field.

  Returns:

  the INFO END field, or -1 if there is no INFO END field

• equals

  boolean equals(Object obj)

  Returns true if the specified object is a Marker with the same chromosome, position, allele lists, and INFO END field, and returns false otherwise. Equality does not depend on value of the VCF record ID field.

  Overrides:

  equals in class Object

  Parameters:

  obj - object to be compared with this for equality

  Returns:

  true if the specified object is a Marker with the same chromosome, position, and allele lists, and INFO END field

• hashCode

  int hashCode()

  Returns the hash code value for this object. The hash code does not depend on value of the VCF record ID field. The hash code is defined by the following calculation:

     int hash = 5;
     hash = 29 * hash + this.chromIndex();
     hash = 29 * hash + this.pos();
     for (int j=0, n=this.nAlleles(); j<n; ++j) {
         hash = 29 * hash + alleles[j].hashCode();
     }
     hash = 29 * hash + end();
   

  Overrides:

  hashCode in class Object

  Returns:

  the hash code value for this marker

• compareTo

  int compareTo(Marker other)

  Compares this marker with the specified marker for order, and returns a negative integer, 0, or a positive integer depending on whether this marker is less than, equal to, or greater than the specified marker. Comparison is on chromosome index, position, allele identifier lists, and end value in that order. Allele identifier lists are compared for lexicographical order, and alleles are compared using the String compareTo() method.

  Specified by:

  compareTo in interface Comparable<Marker>

  Parameters:

  other - the Marker to be compared

  Returns:

  a negative integer, 0, or a positive integer depending on whether this marker is less than, equal, or greater than the specified marker

• toString

  String toString()

  Returns a string equal to the first five tab-delimited fields of a VCF record corresponding to this marker.

  Overrides:

  toString in class Object

  Returns:

  a string equal to the first five tab-delimited fields of a VCF record corresponding to this marker