Uses of Interface
net.maizegenetics.dna.tag.TaxaDistribution

Packages that use TaxaDistribution

Package	Description
net.maizegenetics.analysis.gbs.repgen
net.maizegenetics.dna.tag	Data structures for holding tags (contiguous DNA).

Uses of TaxaDistribution in net.maizegenetics.analysis.gbs.repgen

Method parameters in net.maizegenetics.analysis.gbs.repgen with type arguments of type TaxaDistribution

Modifier and Type	Method and Description
void	RepGenLDAnalysisPlugin.calculateCorrelations(com.google.common.collect.Multimap<Tag,TagCorrelationInfo> tagTagCorrelations, Map<Tag,TaxaDistribution> tagTaxaMap, Tag tag1, Tag tag2, double[] ddepths1, double[] depthsPrime1)

Uses of TaxaDistribution in net.maizegenetics.dna.tag

Methods in net.maizegenetics.dna.tag that return TaxaDistribution

Modifier and Type	Method and Description
static TaxaDistribution	TaxaDistBuilder.combine(TaxaDistribution taxaDist1, TaxaDistribution taxaDist2) Combines a TaxaDistribution to an expandable TaxaDistribution.
static TaxaDistribution	TaxaDistBuilder.create(byte[] encodedTaxaDistribution) Create an fixed TaxaDistribution with set values
static TaxaDistribution	TaxaDistBuilder.create(int maxTaxa) Create an expandable TaxaDistribution with no initial values
static TaxaDistribution	TaxaDistBuilder.create(int maxTaxa, int taxaWithTag) Create a TaxaDistribution with only a single taxa with a tag.
static TaxaDistribution	TaxaDistBuilder.create(int maxTaxa, int[] encodeTaxaDepths) Create expandable TaxaDistribution from encoded taxa distribution.
static TaxaDistribution	TaxaDistBuilder.create(int maxTaxa, int[] taxaWithTags, int[] depthOfTags) Create an fixed TaxaDistribution with set values
static TaxaDistribution	TaxaDistBuilder.create(TaxaDistribution srcTaxaDist) Copies a TaxaDistribution to an expandable TaxaDistribution.
TaxaDistribution	RepGenData.getTaxaDistribution(Tag tag) Returns the TaxaDistribution for a given taxa.
TaxaDistribution	RepGenSQLite.getTaxaDistribution(Tag tag)
TaxaDistribution	TagData.getTaxaDistribution(Tag tag) Returns the TaxaDistribution for a given taxa.
TaxaDistribution	TagDataSQLite.getTaxaDistribution(Tag tag)
TaxaDistribution	TaxaDistribution.increment(int taxaNum) Add the taxa to do the distribution, with an additional depth of 1

Methods in net.maizegenetics.dna.tag that return types with arguments of type TaxaDistribution

Modifier and Type	Method and Description
Stream<com.google.common.collect.ImmutableMultimap<Allele,TaxaDistribution>>	RepGenSQLite.getAllAllelesTaxaDistForSNP()
Stream<com.google.common.collect.ImmutableMultimap<Allele,TaxaDistribution>>	TagDataSQLite.getAllAllelesTaxaDistForSNP()
Stream<Map.Entry<Allele,TaxaDistribution>>	RepGenSQLite.getAllAllelesTaxaDistForSNPEntries()
Stream<Map.Entry<Allele,TaxaDistribution>>	TagDataSQLite.getAllAllelesTaxaDistForSNPEntries()
com.google.common.collect.Multimap<Allele,Map<Tag,TaxaDistribution>>	RepGenData.getAllelesTagTaxaDistForSNP(Position position) For a given snp position, Returns a Map of Allele with its associated Tag/TaxaDistribution
com.google.common.collect.Multimap<Allele,Map<Tag,TaxaDistribution>>	RepGenSQLite.getAllelesTagTaxaDistForSNP(Position position)
com.google.common.collect.Multimap<Allele,Map<Tag,TaxaDistribution>>	TagData.getAllelesTagTaxaDistForSNP(Position position) For a given snp position, Returns a Map of Allele with its associated Tag/TaxaDistribution
com.google.common.collect.Multimap<Allele,Map<Tag,TaxaDistribution>>	TagDataSQLite.getAllelesTagTaxaDistForSNP(Position position)
com.google.common.collect.Multimap<Allele,TaxaDistribution>	TagDataSQLite.getAllelesTaxaDistForSNP(Position position)
Map<Tag,TaxaDistribution>	RepGenData.getAllTagsTaxaMap() Return all tag/taxadistribution stored in database.
Map<Tag,TaxaDistribution>	RepGenSQLite.getAllTagsTaxaMap()
Map<Tag,TaxaDistribution>	TagData.getAllTagsTaxaMap() Return all tag/taxadistribution stored in database.
Map<Tag,TaxaDistribution>	TagDataSQLite.getAllTagsTaxaMap()
Map<Position,Map<Tag,TaxaDistribution>>	RepGenData.getCutPosForStrandTagTaxaMap(Chromosome chromosome, int firstPosition, int lastPosition, boolean strand) For a given snp position, Returns a Map of Allele with its associated Tag/TaxaDistribution Differs from getCutPositionTagTaxaMap() in that it now specifies on which strand the returned tags must appear.
Map<Position,Map<Tag,TaxaDistribution>>	RepGenSQLite.getCutPosForStrandTagTaxaMap(Chromosome chromosome, int firstPosition, int lastPosition, boolean direction)
Map<Position,Map<Tag,TaxaDistribution>>	TagData.getCutPosForStrandTagTaxaMap(Chromosome chromosome, int firstPosition, int lastPosition, boolean strand) For a given snp position, Returns a Map of Allele with its associated Tag/TaxaDistribution Differs from getCutPositionTagTaxaMap() in that it now specifies on which strand the returned tags must appear.
Map<Position,Map<Tag,TaxaDistribution>>	TagDataSQLite.getCutPosForStrandTagTaxaMap(Chromosome chromosome, int firstPosition, int lastPosition, boolean direction)
Map<Position,Map<Tag,Tuple<Boolean,TaxaDistribution>>>	RepGenData.getCutPositionTagTaxaMap(Chromosome chromosome, int firstPosition, int lastPosition) Map of positions and with associated map of Tags and their taxa distribution and their alignment direction.
Map<Position,Map<Tag,Tuple<Boolean,TaxaDistribution>>>	RepGenSQLite.getCutPositionTagTaxaMap(Chromosome chromosome, int firstPosition, int lastPosition)
Map<Position,Map<Tag,Tuple<Boolean,TaxaDistribution>>>	TagData.getCutPositionTagTaxaMap(Chromosome chromosome, int firstPosition, int lastPosition) Map of positions and with associated map of Tags and their taxa distribution and their alignment direction.
Map<Position,Map<Tag,Tuple<Boolean,TaxaDistribution>>>	TagDataSQLite.getCutPositionTagTaxaMap(Chromosome chromosome, int firstPosition, int lastPosition)
Map<Tag,TaxaDistribution>	TagData.getTagsTaxaMap(Position cutPosition) For a given genomic position returns of the map tags and their distribution.
Map<Tag,TaxaDistribution>	TagDataSQLite.getTagsTaxaMap(Position cutPosition)

Methods in net.maizegenetics.dna.tag with parameters of type TaxaDistribution

Modifier and Type	Method and Description
static TaxaDistribution	TaxaDistBuilder.combine(TaxaDistribution taxaDist1, TaxaDistribution taxaDist2) Combines a TaxaDistribution to an expandable TaxaDistribution.
static TaxaDistribution	TaxaDistBuilder.create(TaxaDistribution srcTaxaDist) Copies a TaxaDistribution to an expandable TaxaDistribution.

Method parameters in net.maizegenetics.dna.tag with type arguments of type TaxaDistribution

Modifier and Type	Method and Description
void	RepGenDataWriter.putTaxaDistribution(Map<Tag,TaxaDistribution> tagTaxaDistributionMap) Associates a map full of the specified Tag (key) with the specified TaxaDistribution (value).
void	RepGenSQLite.putTaxaDistribution(Map<Tag,TaxaDistribution> tagTaxaDistributionMap)
void	TagDataSQLite.putTaxaDistribution(Map<Tag,TaxaDistribution> tagTaxaDistributionMap)
void	TagDataWriter.putTaxaDistribution(Map<Tag,TaxaDistribution> tagTaxaDistributionMap) Associates a map full of the specified Tag (key) with the specified TaxaDistribution (value).