Uses of Class
net.maizegenetics.dna.WHICH_ALLELE

Packages that use WHICH_ALLELE

Package	Description
net.maizegenetics.analysis.imputation	Methods for genotypic imputation including Viterbi HMM, FSFHap, and FILLIN
net.maizegenetics.dna	Data structures involved in genetics, genomes, and the representation of DNA variation.
net.maizegenetics.dna.map	Supports genetic and physical map representations of genomes including their annotation.
net.maizegenetics.dna.snp	Data structures for holding SNP and indel variation across taxa (samples) and genomic positions.
net.maizegenetics.dna.snp.bit	Support for bit level encoding of allele presence and absence.
net.maizegenetics.util	Provide basic utilities classes and methods used the entire code base.

Uses of WHICH_ALLELE in net.maizegenetics.analysis.imputation

Methods in net.maizegenetics.analysis.imputation with parameters of type WHICH_ALLELE

Modifier and Type	Method and Description
static ArrayList<Integer>	FILLINFindHaplotypesPlugin.maxMajorAllelesTaxa(GenotypeTable a, int numMaxTaxa, WHICH_ALLELE alleleNumber)
static ArrayList<Integer>	FindMergeHaplotypesPlugin.maxMajorAllelesTaxa(GenotypeTable a, int numMaxTaxa, WHICH_ALLELE alleleNumber)

Uses of WHICH_ALLELE in net.maizegenetics.dna

Methods in net.maizegenetics.dna that return WHICH_ALLELE

Modifier and Type	Method and Description
static WHICH_ALLELE[]	WHICH_ALLELE.frequencyAlleles()
static WHICH_ALLELE	WHICH_ALLELE.valueOf(String name) Returns the enum constant of this type with the specified name.
static WHICH_ALLELE[]	WHICH_ALLELE.values() Returns an array containing the constants of this enum type, in the order they are declared.

Uses of WHICH_ALLELE in net.maizegenetics.dna.map

Methods in net.maizegenetics.dna.map with parameters of type WHICH_ALLELE

Modifier and Type	Method and Description
GeneralPosition.Builder	GeneralPosition.Builder.allele(WHICH_ALLELE aT, byte val) Set allele annotation by Allele type (default=Alignment.UNKNOWN_ALLELE)
byte	PositionList.allele(WHICH_ALLELE alleleType, int site) Return the (haploid) reference allele at given site.
byte[]	PositionList.alleleForAllSites(WHICH_ALLELE alleleType) Returns sequence alleles.
byte[]	PositionList.alleles(WHICH_ALLELE alleleType, int startSite, int endSite) Returns reference sequence alleles in specified range.
byte	GeneralPosition.getAllele(WHICH_ALLELE alleleType)
byte	Position.getAllele(WHICH_ALLELE alleleType) Return the allele specified by alleleType, if unknown Alignment.Unknown is return

Uses of WHICH_ALLELE in net.maizegenetics.dna.snp

Methods in net.maizegenetics.dna.snp with parameters of type WHICH_ALLELE

Modifier and Type	Method and Description
BitSet	CombineGenotypeTable.allelePresenceForAllSites(int taxon, WHICH_ALLELE allele)
BitSet	CoreGenotypeTable.allelePresenceForAllSites(int taxon, WHICH_ALLELE allele)
BitSet	GenotypeTable.allelePresenceForAllSites(int taxon, WHICH_ALLELE allele) Returns sequence of true/false values indicating whether taxon at each site matches a specific allele (based on frequency).
BitSet	MergedGenotypeTable.allelePresenceForAllSites(int taxon, WHICH_ALLELE allele)
BitSet	TOPMGenotypeTable.allelePresenceForAllSites(int taxon, WHICH_ALLELE allele)
BitSet	CombineGenotypeTable.allelePresenceForAllTaxa(int site, WHICH_ALLELE allele)
BitSet	CoreGenotypeTable.allelePresenceForAllTaxa(int site, WHICH_ALLELE allele)
BitSet	GenotypeTable.allelePresenceForAllTaxa(int site, WHICH_ALLELE allele) Returns sequence of true/false values indicating whether site at each taxon matches a specific allele.
BitSet	MergedGenotypeTable.allelePresenceForAllTaxa(int site, WHICH_ALLELE allele)
BitSet	TOPMGenotypeTable.allelePresenceForAllTaxa(int site, WHICH_ALLELE allele)
long[]	CombineGenotypeTable.allelePresenceForSitesBlock(int taxon, WHICH_ALLELE allele, int startBlock, int endBlock)
long[]	CoreGenotypeTable.allelePresenceForSitesBlock(int taxon, WHICH_ALLELE allele, int startBlock, int endBlock)
long[]	GenotypeTable.allelePresenceForSitesBlock(int taxon, WHICH_ALLELE allele, int startBlock, int endBlock) Returns sequence of true/false values indicating whether taxon at sites (in given blocks, 64 sites per block including start block but excluding end block) matches a specific allele.
long[]	MergedGenotypeTable.allelePresenceForSitesBlock(int taxon, WHICH_ALLELE allele, int startBlock, int endBlock)
long[]	TOPMGenotypeTable.allelePresenceForSitesBlock(int taxon, WHICH_ALLELE allele, int startBlock, int endBlock)
BitStorage	CombineGenotypeTable.bitStorage(WHICH_ALLELE allele)
BitStorage	CoreGenotypeTable.bitStorage(WHICH_ALLELE allele)
BitStorage	GenotypeTable.bitStorage(WHICH_ALLELE allele) Returns BitStorage for this Genotype
BitStorage	MergedGenotypeTable.bitStorage(WHICH_ALLELE allele)
BitStorage	TOPMGenotypeTable.bitStorage(WHICH_ALLELE allele)
BitSet	CombineGenotypeTable.haplotypeAllelePresenceForAllSites(int taxon, boolean firstParent, WHICH_ALLELE allele)
BitSet	CoreGenotypeTable.haplotypeAllelePresenceForAllSites(int taxon, boolean firstParent, WHICH_ALLELE allele)
BitSet	GenotypeTable.haplotypeAllelePresenceForAllSites(int taxon, boolean firstParent, WHICH_ALLELE allele) Returns sequence of true/false values indicating whether taxon at each site for given parent matches a specific allele.
BitSet	MergedGenotypeTable.haplotypeAllelePresenceForAllSites(int taxon, boolean firstParent, WHICH_ALLELE allele)
BitSet	TOPMGenotypeTable.haplotypeAllelePresenceForAllSites(int taxon, boolean firstParent, WHICH_ALLELE allele)
BitSet	CombineGenotypeTable.haplotypeAllelePresenceForAllTaxa(int site, boolean firstParent, WHICH_ALLELE allele)
BitSet	CoreGenotypeTable.haplotypeAllelePresenceForAllTaxa(int site, boolean firstParent, WHICH_ALLELE allele)
BitSet	GenotypeTable.haplotypeAllelePresenceForAllTaxa(int site, boolean firstParent, WHICH_ALLELE allele) Returns sequence of true/false values indicating whether site at each taxon for given parent matches a specific allele (based on frequency).
BitSet	MergedGenotypeTable.haplotypeAllelePresenceForAllTaxa(int site, boolean firstParent, WHICH_ALLELE allele)
BitSet	TOPMGenotypeTable.haplotypeAllelePresenceForAllTaxa(int site, boolean firstParent, WHICH_ALLELE allele)
long[]	CombineGenotypeTable.haplotypeAllelePresenceForSitesBlock(int taxon, boolean firstParent, WHICH_ALLELE allele, int startBlock, int endBlock)
long[]	CoreGenotypeTable.haplotypeAllelePresenceForSitesBlock(int taxon, boolean firstParent, WHICH_ALLELE allele, int startBlock, int endBlock)
long[]	GenotypeTable.haplotypeAllelePresenceForSitesBlock(int taxon, boolean firstParent, WHICH_ALLELE allele, int startBlock, int endBlock) Returns sequence of true/false values indicating whether taxon at sites (in given blocks, 64 sites per block including start block but excluding end block) for given parent matches a specific allele (based on frequency).
long[]	MergedGenotypeTable.haplotypeAllelePresenceForSitesBlock(int taxon, boolean firstParent, WHICH_ALLELE allele, int startBlock, int endBlock)
long[]	TOPMGenotypeTable.haplotypeAllelePresenceForSitesBlock(int taxon, boolean firstParent, WHICH_ALLELE allele, int startBlock, int endBlock)

Uses of WHICH_ALLELE in net.maizegenetics.dna.snp.bit

Constructors in net.maizegenetics.dna.snp.bit with parameters of type WHICH_ALLELE

Constructor and Description
DynamicBitStorage(GenotypeCallTable genotype, WHICH_ALLELE allele, byte[] prefAllele)

Uses of WHICH_ALLELE in net.maizegenetics.util

Methods in net.maizegenetics.util with parameters of type WHICH_ALLELE

Modifier and Type	Method and Description
static byte[]	HDF5Utils.getHDF5Alleles(ch.systemsx.cisd.hdf5.IHDF5Reader reader, WHICH_ALLELE allele)