net.maizegenetics.dna.snp.score

Class AlleleDepth

java.lang.Object

net.maizegenetics.dna.snp.score.AlleleDepth

All Implemented Interfaces:

SiteScore

Direct Known Subclasses:

FilterAlleleDepth, FilterHDF5AlleleDepth, HDF5AlleleDepth, MaskAlleleDepth

public class AlleleDepth
extends Object
implements SiteScore

Author:

Terry Casstevens

Nested Class Summary

Nested classes/interfaces inherited from interface net.maizegenetics.dna.snp.score.SiteScore

SiteScore.SITE_SCORE_TYPE

Field Summary

Fields

Modifier and Type	Field and Description
static SiteScore.SITE_SCORE_TYPE[]	ALLELE_DEPTH_TYPES
static int	NUM_ALLELE_DEPTH_TYPES

Method Summary

Modifier and Type	Method and Description
int	depth(int taxon, int site) Returns sum of all nucleotide depths at given taxon and site.
int	depthForAllele(int taxon, int site, int allele) Same as value() but translates allele into scoreType
int	depthForSite(int site) Returns sum of all nucleotide depths across all taxa at given site.
int	depthForTaxon(int taxon) Returns sum of all nucleotide depths across all sites at given taxon.
int	numSites()
int	numTaxa()
Set<SiteScore.SITE_SCORE_TYPE>	siteScoreTypes() Return the site scores types.
int	value(int taxon, int site, SiteScore.SITE_SCORE_TYPE scoreType) Returns the depth of nucleotide (scoreType) at given taxon and site.
byte	valueByte(int taxon, int site, SiteScore.SITE_SCORE_TYPE scoreType) Returns the depth (byte representation) of nucleotide (scoreType) at given taxon and site.
int[][]	values(int taxon) Returns depth values of all nucleotides and sites for given taxon.
int[]	values(int taxon, int site) Returns the depth values of all nucleotides at given taxon and site.
byte[]	valuesByte(int taxon, int site) Returns the depth values (byte representation) of all nucleotides at given taxon and site.
byte[][]	valuesForSiteByte(int site) Returns depth values (byte representation) of all nucleotides and taxa for given site.
byte[][]	valuesForTaxonByte(int taxon) Returns depth values (byte representation) of all nucleotides and sites for given taxon.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

ALLELE_DEPTH_TYPES

public static final SiteScore.SITE_SCORE_TYPE[] ALLELE_DEPTH_TYPES

NUM_ALLELE_DEPTH_TYPES

public static final int NUM_ALLELE_DEPTH_TYPES

Method Detail

value

public int value(int taxon,
                 int site,
                 SiteScore.SITE_SCORE_TYPE scoreType)

Returns the depth of nucleotide (scoreType) at given taxon and site. Depth values are stored in bytes and translated to integer using AlleleDepthUtil.depthByteToInt().

Parameters:

taxon - taxon

site - site

scoreType - nucleotide

Returns:

depth

depthForAllele

public int depthForAllele(int taxon,
                          int site,
                          int allele)

Same as value() but translates allele into scoreType

Parameters:

taxon - taxon

site - site

allele - allele code (see NucleotideAlignmentConstants)

Returns:

depth

values

public int[] values(int taxon,
                    int site)

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().

Parameters:

taxon - taxon

site - site

Returns:

depths

values

public int[][] values(int taxon)

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.

Parameters:

taxon - taxon

Returns:

depths

valueByte

public byte valueByte(int taxon,
                      int site,
                      SiteScore.SITE_SCORE_TYPE scoreType)

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().

Parameters:

taxon - taxon

site - site

scoreType - nucleotide

Returns:

depth

valuesByte

public byte[] valuesByte(int taxon,
                         int 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().

Parameters:

taxon - taxon

site - site

Returns:

depths

valuesForTaxonByte

public byte[][] valuesForTaxonByte(int taxon)

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.

Parameters:

taxon - taxon

Returns:

depths

valuesForSiteByte

public byte[][] valuesForSiteByte(int site)

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.

Parameters:

site - site

Returns:

depths

depth

public int depth(int taxon,
                 int site)

Returns sum of all nucleotide depths at given taxon and site.

Parameters:

taxon - taxon

site - site

Returns:

sum of depths

depthForTaxon

public int depthForTaxon(int taxon)

Returns sum of all nucleotide depths across all sites at given taxon.

Parameters:

taxon - taxon

Returns:

sum of depths

depthForSite

public int depthForSite(int site)

Returns sum of all nucleotide depths across all taxa at given site.

Parameters:

site - site

Returns:

sum of depths

siteScoreTypes

public Set<SiteScore.SITE_SCORE_TYPE> siteScoreTypes()

Description copied from interface: SiteScore

Return the site scores types.

Specified by:

siteScoreTypes in interface SiteScore

Returns:

site score types.

numTaxa

public int numTaxa()

Specified by:

numTaxa in interface SiteScore

numSites

public int numSites()

Specified by:

numSites in interface SiteScore