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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 beagleutil;
import ints.IntArray;
import ints.IntList;
import java.util.Arrays;
import java.util.stream.IntStream;
/**
* <p>Class {@code PbwtDivUpdater} updates prefix and divergence arrays using
* the positional Burrows-Wheeler transform (PBWT).</p>
*
* <p>Instances of {@code PbwtDivUpdater} are not thread-safe.</p>
*
* <p>Reference: Durbin, Richard (2014) Efficient haplotype matching and storage
* using the positional Burrows-Wheeler transform (PBWT).
* Bioinformatics 30(9):166-1272. doi: 10.1093/bioinformatics/btu014</p>
*
* @author Brian L. Browning {@code <browning@uw.edu>}
*/
public class PbwtDivUpdater {
private final int nHaps;
private IntList[] a; // data for updated prefix array
private IntList[] d; // data for updated div array
private int[] p;
/**
* Constructs a new {@code PbwtUpdater} instance for the specified data.
* @param nHaps the number of haplotypes at each position
* @throws NegativeArraySizeException if {@code nHaps < 0}
*/
public PbwtDivUpdater(int nHaps) {
int initNumAlleles = 4;
this.nHaps = nHaps;
this.p = new int[initNumAlleles];
this.a = IntStream.range(0, initNumAlleles)
.mapToObj(i -> new IntList())
.toArray(IntList[]::new);
this.d = IntStream.range(0, initNumAlleles)
.mapToObj(i -> new IntList())
.toArray(IntList[]::new);
}
/**
* Returns the number of haplotypes.
* @return the number of haplotypes
*/
public int nHaps() {
return nHaps;
}
/**
* Update the specified prefix and divergence arrays using the forward
* Positional Burrows-Wheeler Transform. The contract for this method is
* undefined if the specified {@code prefix} array is not a permutation of
* {@code 0, 1, 2, ..., (nHaps - 1)}, or if the elements of the
* specified {@code div} arrays are not all less than or equal to
* the specified {@code marker}.
*
* @param rec the haplotype alleles
* @param nAlleles the number of alleles
* @param marker the marker index for the specified haplotype alleles
* @param prefix the prefix array
* @param div the divergence array
*
* @throws IllegalArgumentException if {@code nAlleles < 1}
* @throws IllegalArgumentException if
* {@code rec.size() != this.nHaps() || prefix.length != this.nHaps()}
* @throws IndexOutOfBoundsException if
* {@code (prefix[j] < 0 || prefix[j] >= rec.size()}
* for any {@code j} satisfying {@code (0 <= j && j < prefix.length)}
* @throws IndexOutOfBoundsException if
* {@code (rec.get[j] < 0 || rec.get(j) >= nAlleles)}
* for any {@code j} satisfying {@code (0 <= j && j < this.nHaps())}
* @throws IndexOutOfBoundsException if {@code div.length < this.nHaps()}
* @throws NullPointerException if
* {@code rec == null || prefix == null || div == null}
*/
public void fwdUpdate(IntArray rec, int nAlleles, int marker, int[] prefix,
int[] div) {
if (rec.size()!=nHaps) {
throw new IllegalArgumentException(String.valueOf(rec.size()));
}
if (prefix.length!=nHaps) {
throw new IllegalArgumentException(String.valueOf(prefix.length));
}
initPArray(nAlleles, marker+1);
for (int i=0; i<nHaps; ++i) {
int allele = rec.get(prefix[i]);
if (allele>=nAlleles) {
throw new IndexOutOfBoundsException(String.valueOf(nAlleles));
}
for (int j=0; j<nAlleles; ++j) {
if (div[i]>p[j]) {
p[j] = div[i];
}
}
a[allele].add(prefix[i]);
d[allele].add(p[allele]);
p[allele] = Integer.MIN_VALUE;
}
updatePrefixAndDiv(nAlleles, prefix, div);
}
/**
* Update the specified prefix and divergence arrays using the backward
* Positional Burrows-Wheeler Transform. The contract for this method is
* undefined if the specified {@code prefix} array is not a permutation of
* {@code 0, 1, 2, ..., (nHaps - 1)}, or if the elements of the
* specified {@code div} arrays are not all greater than or equal to
* the specified {@code marker}.
*
* @param rec the haplotype alleles
* @param nAlleles the number of alleles
* @param marker the marker index for the specified haplotype alleles
* @param prefix the prefix array
* @param div the divergence array
*
* @throws IllegalArgumentException if {@code nAlleles < 1}
* @throws IllegalArgumentException if
* {@code rec.size() != this.nHaps() || prefix.length != this.nHaps()}
* @throws IndexOutOfBoundsException if
* {@code (prefix[j] < 0 || prefix[j] >= rec.size()}
* for any {@code j} satisfying {@code (0 <= j && j < prefix.length)}
* @throws IndexOutOfBoundsException if
* {@code (rec.get[j] < 0 || rec.get(j) >= nAlleles)}
* for any {@code j} satisfying {@code (0 <= j && j < this.nHaps())}
* @throws IndexOutOfBoundsException if {@code div.length < this.nHaps()}
* @throws NullPointerException if
* {@code rec == null || prefix == null || div == null}
*/
public void bwdUpdate(IntArray rec, int nAlleles, int marker, int[] prefix,
int[] div) {
if (rec.size()!=nHaps) {
throw new IllegalArgumentException(String.valueOf(rec.size()));
}
if (prefix.length!=nHaps) {
throw new IllegalArgumentException(String.valueOf(prefix.length));
}
initPArray(nAlleles, marker-1);
for (int i=0; i<nHaps; ++i) {
int allele = rec.get(prefix[i]);
if (allele>=nAlleles) {
throw new IndexOutOfBoundsException(String.valueOf(nAlleles));
}
for (int j=0; j<nAlleles; ++j) {
if (div[i]<p[j]) {
p[j] = div[i];
}
}
a[allele].add(prefix[i]);
d[allele].add(p[allele]);
p[allele] = Integer.MAX_VALUE;
}
updatePrefixAndDiv(nAlleles, prefix, div);
}
private void updatePrefixAndDiv(int nAlleles, int[] prefix, int[] div) {
int start = 0;
for (int al=0; al<nAlleles; ++al) {
int size = a[al].size();
System.arraycopy(a[al].toArray(), 0, prefix, start, size);
System.arraycopy(d[al].toArray(), 0, div, start, size);
start += size;
a[al].clear();
d[al].clear();
}
assert start == nHaps;
}
private void initPArray(int nAlleles, int initValue) {
if (nAlleles<1) {
throw new IllegalArgumentException(String.valueOf(nAlleles));
}
ensureArrayCapacity(nAlleles);
Arrays.fill(p, 0, nAlleles, initValue);
}
private void ensureArrayCapacity(int nAlleles) {
if (nAlleles>a.length) {
int oldLength = a.length;
p = Arrays.copyOf(p, nAlleles);
a = Arrays.copyOf(a, nAlleles);
d = Arrays.copyOf(d, nAlleles);
for (int j = oldLength; j<a.length; ++j) {
a[j] = new IntList();
d[j] = new IntList();
}
}
}
}
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