Package vcf

Interface Marker

All Superinterfaces:

java.lang.Comparable<Marker>

All Known Implementing Classes:

BasicMarker

public interface Marker
extends java.lang.Comparable<Marker>

Interface Marker represents a genetic marker.

All instances of class Marker are required to be immutable.

Method Summary

Modifier and Type	Method	Description
java.lang.String	allele(int index)	Returns the specified allele.
java.lang.String[]	alleles()	Returns the alleles.
int	bitsPerAllele()	Returns the minimum number of bits required to store a non-missing allele.
java.lang.String	chrom()	Returns the chromosome.
int	chromIndex()	Returns the chromosome index.
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.
int	end()	Returns the INFO END field, or -1 if there is no INFO END field.
boolean	equals(java.lang.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.
int	hashCode()	Returns the hash code value for this object.
java.lang.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.
java.lang.String	id(int index)	Returns the specified marker identifier.
int	nAlleles()	Returns the number of alleles for the marker, including the REF allele.
int	nGenotypes()	Returns the number of distinct genotypes, which equals this.nAlleles()*(1 + this.nAlleles())/2.
int	nIds()	Returns the number of marker identifiers.
int	pos()	Returns the chromosome position coordinate.
java.lang.String	toString()	Returns a string equal to the first five tab-delimited fields of a VCF record corresponding to this marker.

Method Detail

chrom

java.lang.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

java.lang.String id(int index)

Returns the specified marker identifier.

Parameters:

index - a marker identifier index

Returns:

the specified marker identifier

Throws:

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

id

java.lang.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

java.lang.String allele(int index)

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

Parameters:

index - an allele index

Returns:

the specified allele

Throws:

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

alleles

java.lang.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(java.lang.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 java.lang.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 java.lang.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 java.lang.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

java.lang.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 java.lang.Object

Returns:

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