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/*
* Copyright (C) 2014-2021 Brian L. Browning
*
* This file is part of Beagle
*
* Beagle is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* Beagle is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package vcf;
/**
* <p>Interface {@code Marker} represents a genetic marker.
* </p>
* <p>All instances of class {@code Marker} are required to be immutable.
* </p>
*
* @author Brian L. Browning {@code <browning@uw.edu>}
*/
public interface Marker extends Comparable<Marker> {
/**
* Returns the chromosome.
* @return the chromosome
*/
String chrom();
/**
* Returns the chromosome index.
* @return the chromosome index
*/
int chromIndex();
/**
* Returns the chromosome position coordinate.
* @return the chromosome position coordinate
*/
int pos();
/**
* Returns the number of marker identifiers.
* @return the number of marker identifiers
*/
int nIds();
/**
* Returns the specified marker identifier.
* @param index a marker identifier index
* @return the specified marker identifier
*
* @throws IndexOutOfBoundsException if
* {@code index < 0 || index >= this.nIds()}
*/
String id(int index);
/**
* Returns the first marker identifier if there is at least
* one identifier in the VCF record ID field, and returns
* {@code this.chr() + ":" + this.pos()} otherwise.
*
* @return a marker identifier
*/
String id();
/**
* Returns the number of alleles for the marker, including the REF
* allele.
* @return the number of alleles for the marker, including the REF
* allele
*/
int nAlleles();
/**
* Returns the minimum number of bits required to store a non-missing
* allele.
* @return the minimum number of bits required to store a non-missing
* allele
*/
int bitsPerAllele();
/**
* Returns the specified allele. The reference allele has index 0.
* @param index an allele index
* @return the specified allele
*
* @throws IndexOutOfBoundsException if
* {@code index < 0 || index >= this.nAlleles()}
*/
String allele(int index);
/**
* Returns the alleles. The {@code k}-th element of the returned array
* is equal to {@code this.allele(k)}.
* @return the alleles
*/
String[] alleles();
/**
* Returns the number of distinct genotypes, which equals
* {@code this.nAlleles()*(1 + this.nAlleles())/2}.
*
* @return the number of distinct genotypes
*/
int nGenotypes();
/**
* Returns the INFO END field, or -1 if there is no INFO END field.
*
* @return the INFO END field, or -1 if there is no INFO END field
*/
int end();
/**
* Returns {@code true} if the specified object is a
* {@code Marker} with the same chromosome,
* position, allele lists, and INFO END field, and
* returns {@code false} otherwise. Equality does not
* depend on value of the VCF record ID field.
*
* @param obj object to be compared with {@code this} for equality
*
* @return {@code true} if the specified object is a
* {@code Marker} with the same chromosome,
* position, and allele lists, and INFO END field
*/
@Override
boolean equals(Object obj);
/**
* <p>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:
* </p>
* <pre>
* 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();
* </pre>
*
* @return the hash code value for this marker
*/
@Override
int hashCode();
/**
* 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
* {@code String compareTo()} method.
*
* @param other the {@code Marker} to be compared
* @return a negative integer, 0, or a positive integer
* depending on whether this marker is less than, equal,
* or greater than the specified marker
*/
@Override
int compareTo(Marker other);
/**
* Returns a string equal to the first five tab-delimited fields
* of a VCF record corresponding to this marker.
*
* @return a string equal to the first five tab-delimited fields
* of a VCF record corresponding to this marker
*/
@Override
String toString();
}
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