net.maizegenetics.dna.snp.score

Class AlleleDepth

net.maizegenetics.dna.snp.score.AlleleDepth

All Implemented Interfaces:

SiteScore

Direct Known Subclasses:

FilterAlleleDepth, FilterHDF5AlleleDepth, HDF5AlleleDepth, MaskAlleleDepth

public class AlleleDepth
implements SiteScore

Field Detail

ALLELE_DEPTH_TYPES

public static net.maizegenetics.dna.snp.score.SiteScore.SITE_SCORE_TYPE[] ALLELE_DEPTH_TYPES

NUM_ALLELE_DEPTH_TYPES

public static int NUM_ALLELE_DEPTH_TYPES

Method Detail

value

public int value(int taxon,
                 int site,
                 net.maizegenetics.dna.snp.score.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:

org.jetbrains.dokka.NodeRenderContent@227f991d: 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:

org.jetbrains.dokka.NodeRenderContent@d2125f8: depth

values

public kotlin.Array[] 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:

org.jetbrains.dokka.NodeRenderContent@10048252: depths

values

public kotlin.Array[] 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:

org.jetbrains.dokka.NodeRenderContent@591a3d1: depths

valueByte

public byte valueByte(int taxon,
                      int site,
                      net.maizegenetics.dna.snp.score.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:

org.jetbrains.dokka.NodeRenderContent@5b78750f: depth

valuesByte

public kotlin.Array[] 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:

org.jetbrains.dokka.NodeRenderContent@5f72857d: depths

valuesForTaxonByte

public kotlin.Array[] 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:

org.jetbrains.dokka.NodeRenderContent@6bd09ad3: depths

valuesForSiteByte

public kotlin.Array[] 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:

org.jetbrains.dokka.NodeRenderContent@63573353: 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:

org.jetbrains.dokka.NodeRenderContent@7b9fe23b: 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:

org.jetbrains.dokka.NodeRenderContent@308dd958: 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:

org.jetbrains.dokka.NodeRenderContent@5f64db98: sum of depths

siteScoreTypes

public java.util.Set<net.maizegenetics.dna.snp.score.SiteScore.SITE_SCORE_TYPE> siteScoreTypes()

numTaxa

public int numTaxa()

numSites

public int numSites()