net.maizegenetics.dna.snp

Class TOPMGenotypeTable

net.maizegenetics.dna.snp.TOPMGenotypeTable

All Implemented Interfaces:

GenotypeTable

public class TOPMGenotypeTable
implements GenotypeTable

Constructor Detail

TOPMGenotypeTable

public TOPMGenotypeTable(TOPMInterface topm)

Method Detail

genotypeMatrix

public GenotypeCallTable genotypeMatrix()

isSNP

public boolean isSNP(int taxon,
                     int site)

genotype

public byte genotype(int taxon,
                     int site)

genotypeArray

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

genotype

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

genotypeRange

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

genotypeAllSites

public kotlin.Array[] genotypeAllSites(int taxon)

genotypeAllTaxa

public kotlin.Array[] genotypeAllTaxa(int site)

allelePresenceForAllSites

public BitSet allelePresenceForAllSites(int taxon,
                                        WHICH_ALLELE allele)

allelePresenceForSitesBlock

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

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)

genotypeAsString

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

genotypeAsStringRange

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

genotypeAsStringRow

public java.lang.String genotypeAsStringRow(int taxon)

genotypeAsStringArray

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

hasReference

public boolean hasReference()

isHeterozygous

public boolean isHeterozygous(int taxon,
                              int site)

heterozygousCount

public int heterozygousCount(int site)

siteName

public java.lang.String siteName(int site)

numberOfSites

public int numberOfSites()

chromosomeSiteCount

public int chromosomeSiteCount(Chromosome chromosome)

firstLastSiteOfChromosome

public kotlin.Array[] firstLastSiteOfChromosome(Chromosome chromosome)

numberOfTaxa

public int numberOfTaxa()

positions

public PositionList positions()

chromosomalPosition

public int chromosomalPosition(int site)

siteOfPhysicalPosition

public int siteOfPhysicalPosition(int physicalPosition,
                                  Chromosome chromosome)

siteOfPhysicalPosition

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

physicalPositions

public kotlin.Array[] physicalPositions()

chromosomeName

public java.lang.String chromosomeName(int site)

chromosome

public Chromosome chromosome(int site)

chromosome

public Chromosome chromosome(java.lang.String name)

chromosomes

public Chromosome[] chromosomes()

numChromosomes

public int numChromosomes()

chromosomesOffsets

public kotlin.Array[] chromosomesOffsets()

hasGenotype

public boolean hasGenotype()

hasDepth

public boolean hasDepth()

siteScoreTypes

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

hasAlleleProbabilities

public boolean hasAlleleProbabilities()

hasReferenceProbablity

public boolean hasReferenceProbablity()

hasDosage

public boolean hasDosage()

indelSize

public int indelSize(int site)

isIndel

public boolean isIndel(int site)

isAllPolymorphic

public boolean isAllPolymorphic()

isPolymorphic

public boolean isPolymorphic(int site)

majorAllele

public byte majorAllele(int site)

majorAlleleAsString

public java.lang.String majorAlleleAsString(int site)

minorAllele

public byte minorAllele(int site)

minorAlleleAsString

public java.lang.String minorAlleleAsString(int site)

minorAlleles

public kotlin.Array[] minorAlleles(int site)

alleles

public kotlin.Array[] alleles(int site)

minorAlleleFrequency

public double minorAlleleFrequency(int site)

majorAlleleFrequency

public double majorAlleleFrequency(int site)

taxa

public TaxaList taxa()

taxaName

public java.lang.String taxaName(int index)

genomeVersion

public java.lang.String genomeVersion()

isPositiveStrand

public boolean isPositiveStrand(int site)

compositeAlignments

public GenotypeTable[] compositeAlignments()

allelesSortedByFrequency

public kotlin.Array[] allelesSortedByFrequency(int site)

genosSortedByFrequency

public java.lang.Object[] genosSortedByFrequency(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)

diploidAsString

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

maxNumAlleles

public int maxNumAlleles()

totalGametesNonMissingForSite

public int totalGametesNonMissingForSite(int site)

totalNonMissingForSite

public int totalNonMissingForSite(int site)

minorAlleleCount

public int minorAlleleCount(int site)

majorAlleleCount

public int majorAlleleCount(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)

depth

public AlleleDepth depth()

depthForAlleles

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

bitStorage

public BitStorage bitStorage(WHICH_ALLELE allele)

referenceAllele

public byte referenceAllele(int site)

alternateAllele

public byte alternateAllele(int site)

referenceAlleles

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

referenceAlleleForAllSites

public kotlin.Array[] referenceAlleleForAllSites()

alleleProbability

public AlleleProbability alleleProbability()

alleleProbability

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

dosage

public Dosage dosage()

dosage

public byte dosage(int taxon,
                   int site)

annotations

public GeneralAnnotationStorage annotations()

referenceProbability

public ReferenceProbability referenceProbability()

referenceProbability

public float referenceProbability(int taxon,
                                  int site)

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()