net.maizegenetics.dna.snp

Class CombineGenotypeTable

net.maizegenetics.dna.snp.CombineGenotypeTable

All Implemented Interfaces:

GenotypeTable

public class CombineGenotypeTable
implements GenotypeTable

Combines multiple GenotypeTables together.

Method Detail

getInstance

public static GenotypeTable getInstance(GenotypeTable[] genoTables)

This factory method combines given genoTables. If only one genotypeTable, then it is returned unchanged. Otherwise, this requires that each genotypeTable has the same Taxa in the same order.

Parameters:

genoTables -

Returns:

org.jetbrains.dokka.NodeRenderContent@5e00f608:

getInstance

public static GenotypeTable getInstance(GenotypeTable[] genoTables,
                                        boolean isUnion)

This factory method combines given genoTables. If only one genotypeTable, then it is returned unchanged. If isUnion equals true, a union join of the Identifiers will be used to construct the combination. Any genotypeTable not containing one of the Identifiers will return unknown value for those locations. If isUnion equals false, a intersect join of the Identifiers will be used.

Parameters:

genoTables - genoTables to combine

isUnion - whether to union or intersect join

Returns:

org.jetbrains.dokka.NodeRenderContent@21170df3:

genotype

public byte genotype(int taxon,
                     int site)

genotypeRange

public kotlin.Array[] genotypeRange(int taxon,
                                    int startSite,
                                    int endSite)

genotype

public byte genotype(int taxon,
                     Chromosome locus,
                     int physicalPosition)

translateSite

public int translateSite(int site)

Returns which genotypeTable to use.

Parameters:

site -

Returns:

org.jetbrains.dokka.NodeRenderContent@54832471: genotypeTable index.

hasReference

public boolean hasReference()

siteName

public java.lang.String siteName(int site)

numberOfSites

public int numberOfSites()

chromosomeSiteCount

public int chromosomeSiteCount(Chromosome locus)

chromosomalPosition

public int chromosomalPosition(int site)

siteOfPhysicalPosition

public int siteOfPhysicalPosition(int physicalPosition,
                                  Chromosome locus)

siteOfPhysicalPosition

public int siteOfPhysicalPosition(int physicalPosition,
                                  Chromosome locus,
                                  java.lang.String snpName)

chromosome

public Chromosome chromosome(int site)

chromosomes

public Chromosome[] chromosomes()

numChromosomes

public int numChromosomes()

indelSize

public int indelSize(int site)

isIndel

public boolean isIndel(int site)

referenceAllele

public byte referenceAllele(int site)

alternateAllele

public byte alternateAllele(int site)

compositeAlignments

public GenotypeTable[] compositeAlignments()

majorAllele

public byte majorAllele(int site)

minorAllele

public byte minorAllele(int site)

minorAlleles

public kotlin.Array[] minorAlleles(int site)

alleles

public kotlin.Array[] alleles(int site)

minorAlleleFrequency

public double minorAlleleFrequency(int site)

allelesSortedByFrequency

public kotlin.Array[] allelesSortedByFrequency(int site)

genotypeArray

public kotlin.Array[] genotypeArray(int taxon,
                                    int site)

genotypeAllTaxa

public kotlin.Array[] genotypeAllTaxa(int site)

genotypeAllSites

public kotlin.Array[] genotypeAllSites(int taxon)

allelePresenceForAllSites

public BitSet allelePresenceForAllSites(int taxon,
                                        WHICH_ALLELE allele)

allelePresenceForSitesBlock

public kotlin.Array[] allelePresenceForSitesBlock(int taxon,
                                                  WHICH_ALLELE allele,
                                                  int startBlock,
                                                  int endBlock)

genotypeAsString

public java.lang.String genotypeAsString(int taxon,
                                         int site)

genotypeAsStringArray

public java.lang.String[] genotypeAsStringArray(int taxon,
                                                int site)

referenceAlleles

public kotlin.Array[] referenceAlleles(int startSite,
                                       int endSite)

referenceAlleleForAllSites

public kotlin.Array[] referenceAlleleForAllSites()

isHeterozygous

public boolean isHeterozygous(int taxon,
                              int site)

physicalPositions

public kotlin.Array[] physicalPositions()

chromosomeName

public java.lang.String chromosomeName(int site)

chromosomesOffsets

public kotlin.Array[] chromosomesOffsets()

siteScoreTypes

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

isAllPolymorphic

public boolean isAllPolymorphic()

isPolymorphic

public boolean isPolymorphic(int site)

majorAlleleFrequency

public double majorAlleleFrequency(int site)

genomeVersion

public java.lang.String genomeVersion()

isPositiveStrand

public boolean isPositiveStrand(int site)

isPhased

public boolean isPhased()

retainsRareAlleles

public boolean retainsRareAlleles()

alleleDefinitions

public java.lang.String[] alleleDefinitions()

alleleDefinitions

public java.lang.String[] alleleDefinitions(int site)

genotypeAsString

public java.lang.String genotypeAsString(int site,
                                         byte value)

maxNumAlleles

public int maxNumAlleles()

totalGametesNonMissingForSite

public int totalGametesNonMissingForSite(int site)

heterozygousCount

public int heterozygousCount(int site)

minorAlleleCount

public int minorAlleleCount(int site)

majorAlleleCount

public int majorAlleleCount(int site)

genosSortedByFrequency

public java.lang.Object[] genosSortedByFrequency(int site)

allelesBySortType

public kotlin.Array[] allelesBySortType(net.maizegenetics.dna.snp.GenotypeTable.ALLELE_SORT_TYPE scope,
                                        int site)

allelePresenceForAllTaxa

public BitSet allelePresenceForAllTaxa(int site,
                                       WHICH_ALLELE allele)

haplotypeAllelePresenceForAllSites

public BitSet haplotypeAllelePresenceForAllSites(int taxon,
                                                 boolean firstParent,
                                                 WHICH_ALLELE allele)

haplotypeAllelePresenceForAllTaxa

public BitSet haplotypeAllelePresenceForAllTaxa(int site,
                                                boolean firstParent,
                                                WHICH_ALLELE allele)

haplotypeAllelePresenceForSitesBlock

public kotlin.Array[] haplotypeAllelePresenceForSitesBlock(int taxon,
                                                           boolean firstParent,
                                                           WHICH_ALLELE allele,
                                                           int startBlock,
                                                           int endBlock)

genotypeAsStringRange

public java.lang.String genotypeAsStringRange(int taxon,
                                              int startSite,
                                              int endSite)

genotypeAsStringRow

public java.lang.String genotypeAsStringRow(int taxon)

firstLastSiteOfChromosome

public kotlin.Array[] firstLastSiteOfChromosome(Chromosome chromosome)

numberOfTaxa

public int numberOfTaxa()

chromosome

public Chromosome chromosome(java.lang.String name)

majorAlleleAsString

public java.lang.String majorAlleleAsString(int site)

minorAlleleAsString

public java.lang.String minorAlleleAsString(int site)

taxa

public TaxaList taxa()

taxaName

public java.lang.String taxaName(int index)

diploidAsString

public java.lang.String diploidAsString(int site,
                                        byte value)

totalNonMissingForSite

public int totalNonMissingForSite(int site)

genoCounts

public java.lang.Object[] genoCounts()

majorMinorCounts

public java.lang.Object[] majorMinorCounts()

totalGametesNonMissingForTaxon

public int totalGametesNonMissingForTaxon(int taxon)

heterozygousCountForTaxon

public int heterozygousCountForTaxon(int taxon)

totalNonMissingForTaxon

public int totalNonMissingForTaxon(int taxon)

hasGenotype

public boolean hasGenotype()

hasDepth

public boolean hasDepth()

hasAlleleProbabilities

public boolean hasAlleleProbabilities()

hasReferenceProbablity

public boolean hasReferenceProbablity()

hasDosage

public boolean hasDosage()

depth

public AlleleDepth depth()

depthForAlleles

public kotlin.Array[] depthForAlleles(int taxon,
                                      int site)

bitStorage

public BitStorage bitStorage(WHICH_ALLELE allele)

positions

public PositionList positions()

genotypeMatrix

public GenotypeCallTable genotypeMatrix()

alleleProbability

public AlleleProbability alleleProbability()

alleleProbability

public float alleleProbability(int taxon,
                               int site,
                               net.maizegenetics.dna.snp.score.SiteScore.SITE_SCORE_TYPE type)

referenceProbability

public ReferenceProbability referenceProbability()

referenceProbability

public float referenceProbability(int taxon,
                                  int site)

dosage

public Dosage dosage()

dosage

public byte dosage(int taxon,
                   int site)

annotations

public GeneralAnnotationStorage annotations()

streamGenotype

public java.util.stream.Stream<java.lang.Byte> streamGenotype()

streamGenotype

public java.util.stream.Stream<java.lang.Byte> streamGenotype(int taxon)

hasSiteTranslations

public boolean hasSiteTranslations()

siteTranslations

public kotlin.Array[] siteTranslations()