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/*
* AlleleDepth
*/
package net.maizegenetics.dna.snp.score;
import net.maizegenetics.dna.snp.byte2d.Byte2D;
import java.util.*;
/**
* @author Terry Casstevens
*/
public class AlleleDepth implements SiteScore {
public static final SiteScore.SITE_SCORE_TYPE[] ALLELE_DEPTH_TYPES = new SiteScore.SITE_SCORE_TYPE[]{
SiteScore.SITE_SCORE_TYPE.DepthA, SiteScore.SITE_SCORE_TYPE.DepthC,
SiteScore.SITE_SCORE_TYPE.DepthG, SiteScore.SITE_SCORE_TYPE.DepthT,
SiteScore.SITE_SCORE_TYPE.DepthInsertion, SiteScore.SITE_SCORE_TYPE.DepthGap};
public static final int NUM_ALLELE_DEPTH_TYPES = ALLELE_DEPTH_TYPES.length;
private final Map myValues;
private final int myNumTaxa;
private final int myNumSites;
AlleleDepth(Byte2D[] values) {
if (values.length == 0) {
throw new IllegalArgumentException("AlleleDepth: init: no values provided.");
}
myValues = new HashMap<>();
myNumTaxa = values[0].numTaxa();
myNumSites = values[0].numSites();
for (int i = 0; i < values.length; i++) {
if ((myNumTaxa != values[i].numTaxa()) || (myNumSites != values[i].numSites())) {
throw new IllegalArgumentException("AlleleDepth: init: number of taxa or sites don't match for all values.");
}
myValues.put(values[i].siteScoreType(), values[i]);
}
}
AlleleDepth(int numTaxa, int numSites) {
myNumTaxa = numTaxa;
myNumSites = numSites;
myValues = null;
}
/**
* Returns the depth of nucleotide (scoreType) at given taxon and site.
* Depth values are stored in bytes and translated to integer using
* AlleleDepthUtil.depthByteToInt().
*
* @param taxon taxon
* @param site site
* @param scoreType nucleotide
*
* @return depth
*/
public int value(int taxon, int site, SITE_SCORE_TYPE scoreType) {
return AlleleDepthUtil.depthByteToInt(myValues.get(scoreType).valueForAllele(taxon, site));
}
/**
* Same as value() but translates allele into scoreType
*
* @param taxon taxon
* @param site site
* @param allele allele code (see NucleotideAlignmentConstants)
*
* @return depth
*/
public int depthForAllele(int taxon, int site, int allele) {
return value(taxon, site, ALLELE_DEPTH_TYPES[allele]);
}
/**
* Returns the depth values of all nucleotides at given taxon and site.
* Depth values are stored in bytes and translated to integer using
* AlleleDepthUtil.depthByteToInt().
*
* @param taxon taxon
* @param site site
*
* @return depths
*/
public int[] values(int taxon, int site) {
int[] result = new int[NUM_ALLELE_DEPTH_TYPES];
int count = 0;
for (SITE_SCORE_TYPE current : ALLELE_DEPTH_TYPES) {
result[count++] = value(taxon, site, current);
}
return result;
}
/**
* Returns depth values of all nucleotides and sites for given taxon. The
* first dimension of returned array is nucleotides (ALLELE_DEPTH_TYPES) and
* second dimension is sites.
*
* @param taxon taxon
*
* @return depths
*/
public int[][] values(int taxon) {
int[][] result = new int[NUM_ALLELE_DEPTH_TYPES][numSites()];
int count = 0;
for (SITE_SCORE_TYPE current : ALLELE_DEPTH_TYPES) {
for (int site = 0; site < numSites(); site++) {
result[count][site] = value(taxon, site, current);
}
count++;
}
return result;
}
/**
* Returns the depth (byte representation) of nucleotide (scoreType) at
* given taxon and site. Depth values are stored in bytes and translated to
* integer using AlleleDepthUtil.depthByteToInt().
*
* @param taxon taxon
* @param site site
* @param scoreType nucleotide
*
* @return depth
*/
public byte valueByte(int taxon, int site, SITE_SCORE_TYPE scoreType) {
return myValues.get(scoreType).valueForAllele(taxon, site);
}
/**
* Returns the depth values (byte representation) of all nucleotides at
* given taxon and site. Depth values are stored in bytes and translated to
* integer using AlleleDepthUtil.depthByteToInt().
*
* @param taxon taxon
* @param site site
*
* @return depths
*/
public byte[] valuesByte(int taxon, int site) {
byte[] result = new byte[NUM_ALLELE_DEPTH_TYPES];
int count = 0;
for (SITE_SCORE_TYPE current : ALLELE_DEPTH_TYPES) {
result[count++] = valueByte(taxon, site, current);
}
return result;
}
/**
* Returns depth values (byte representation) of all nucleotides and sites
* for given taxon. The first dimension of returned array is nucleotides
* (ALLELE_DEPTH_TYPES) and second dimension is sites.
*
* @param taxon taxon
*
* @return depths
*/
public byte[][] valuesForTaxonByte(int taxon) {
byte[][] result = new byte[NUM_ALLELE_DEPTH_TYPES][numSites()];
int count = 0;
for (SITE_SCORE_TYPE current : ALLELE_DEPTH_TYPES) {
for (int site = 0; site < numSites(); site++) {
result[count][site] = valueByte(taxon, site, current);
}
count++;
}
return result;
}
/**
* Returns depth values (byte representation) of all nucleotides and taxa
* for given site. The first dimension of returned array is nucleotides
* (ALLELE_DEPTH_TYPES) and second dimension is taxa.
*
* @param site site
*
* @return depths
*/
public byte[][] valuesForSiteByte(int site) {
byte[][] result = new byte[NUM_ALLELE_DEPTH_TYPES][numTaxa()];
int count = 0;
for (SITE_SCORE_TYPE current : ALLELE_DEPTH_TYPES) {
for (int taxon = 0; taxon < numTaxa(); taxon++) {
result[count][taxon] = valueByte(taxon, site, current);
}
count++;
}
return result;
}
/**
* Returns sum of all nucleotide depths at given taxon and site.
*
* @param taxon taxon
* @param site site
*
* @return sum of depths
*/
public int depth(int taxon, int site) {
int result = 0;
for (SITE_SCORE_TYPE current : ALLELE_DEPTH_TYPES) {
result += value(taxon, site, current);
}
return result;
}
/**
* Returns sum of all nucleotide depths across all sites at given taxon.
*
* @param taxon taxon
*
* @return sum of depths
*/
public int depthForTaxon(int taxon) {
int result = 0;
for (int site = 0; site < numSites(); site++) {
result += depth(taxon, site);
}
return result;
}
/**
* Returns sum of all nucleotide depths across all taxa at given site.
*
* @param site site
*
* @return sum of depths
*/
public int depthForSite(int site) {
int result = 0;
for (int taxon = 0; taxon < numTaxa(); taxon++) {
result += depth(taxon, site);
}
return result;
}
Collection byteStorage() {
return myValues.values();
}
@Override
public Set siteScoreTypes() {
return new HashSet<>(Arrays.asList(ALLELE_DEPTH_TYPES));
}
@Override
public int numTaxa() {
return myNumTaxa;
}
@Override
public int numSites() {
return myNumSites;
}
}
