net.maizegenetics.dna.snp.score

Class HDF5AlleleDepth

java.lang.Object

net.maizegenetics.dna.snp.score.AlleleDepth

net.maizegenetics.dna.snp.score.HDF5AlleleDepth

All Implemented Interfaces:

SiteScore

public class HDF5AlleleDepth
extends AlleleDepth

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 inherited from class net.maizegenetics.dna.snp.score.AlleleDepth

ALLELE_DEPTH_TYPES, NUM_ALLELE_DEPTH_TYPES

Method Summary

Modifier and Type	Method and Description
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, 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[][]	valuesForTaxonByte(int taxon) Returns depth values (byte representation) of all nucleotides and sites for given taxon.

Methods inherited from class net.maizegenetics.dna.snp.score.AlleleDepth

depth, depthForAllele, depthForSite, depthForTaxon, numSites, numTaxa, siteScoreTypes, values, valuesForSiteByte

Methods inherited from class java.lang.Object

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

Method Detail

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().

Overrides:

valuesByte in class AlleleDepth

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.

Overrides:

valuesForTaxonByte in class AlleleDepth

Parameters:

taxon - taxon

Returns:

depths

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().

Overrides:

value in class AlleleDepth

Parameters:

taxon - taxon

site - site

scoreType - nucleotide

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().

Overrides:

values in class AlleleDepth

Parameters:

taxon - taxon

site - site

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().

Overrides:

valueByte in class AlleleDepth

Parameters:

taxon - taxon

site - site

scoreType - nucleotide

Returns:

depth