net.maizegenetics.dna.tag

Class TaxaDistBuilder

net.maizegenetics.dna.tag.TaxaDistBuilder

public class TaxaDistBuilder

Builder for TaxaDistribution. Deals with the

Method Detail

create

public static TaxaDistribution create(int maxTaxa,
                                      int taxaWithTag)

Create a TaxaDistribution with only a single taxa with a tag. Very memory efficient, but needs conversion add an additional taxon with a tag

Parameters:

maxTaxa -

taxaWithTag -

Returns:

org.jetbrains.dokka.NodeRenderContent@208661f0:

create

public static TaxaDistribution create(int maxTaxa)

Create an expandable TaxaDistribution with no initial values

Parameters:

maxTaxa -

Returns:

org.jetbrains.dokka.NodeRenderContent@489304e9:

create

public static TaxaDistribution create(int maxTaxa,
                                      kotlin.Array[] taxaWithTags,
                                      kotlin.Array[] depthOfTags)

Create an fixed TaxaDistribution with set values

Parameters:

maxTaxa -

Returns:

org.jetbrains.dokka.NodeRenderContent@66683ec:

create

public static TaxaDistribution create(kotlin.Array[] encodedTaxaDistribution)

Create an fixed TaxaDistribution with set values

Parameters:

encodedTaxaDistribution - byte array of encoded TaxaDistribution

Returns:

org.jetbrains.dokka.NodeRenderContent@16e6484e:

create

public static TaxaDistribution create(TaxaDistribution srcTaxaDist)

Copies a TaxaDistribution to an expandable TaxaDistribution. Can be used to convert a single TaxaDistribution to an expandable version

Parameters:

srcTaxaDist -

Returns:

org.jetbrains.dokka.NodeRenderContent@5fc3283:

combine

public static TaxaDistribution combine(TaxaDistribution taxaDist1,
                                       TaxaDistribution taxaDist2)

Combines a TaxaDistribution to an expandable TaxaDistribution. Can be used to convert a single TaxaDistribution to an expandable version

Parameters:

taxaDist1 -

Returns:

org.jetbrains.dokka.NodeRenderContent@5518ca99:

create

public static TaxaDistribution create(int maxTaxa,
                                      kotlin.Array[] encodeTaxaDepths)

Create expandable TaxaDistribution from encoded taxa distribution. The int[] encoding use first three bytes for taxa index, and last byte for depth as unsigned byte. Depths greater than 256 just increase.

Parameters:

maxTaxa -

encodeTaxaDepths -

Returns:

org.jetbrains.dokka.NodeRenderContent@67d35a35:

getDepthMatrixForEncodedDepths

public static kotlin.Array[] getDepthMatrixForEncodedDepths(kotlin.Array[] input)