net.maizegenetics.dna.snp.byte2d

Class Byte2DBuilder

net.maizegenetics.dna.snp.byte2d.Byte2DBuilder

public class Byte2DBuilder

Builder to store 2 dimensional byte encoded values.

Method Detail

getInstance

public static Byte2DBuilder getInstance(int numTaxa,
                                        int numSites,
                                        net.maizegenetics.dna.snp.score.SiteScore.SITE_SCORE_TYPE siteScoreType,
                                        TaxaList taxaList)

getInstance

public static Byte2DBuilder getInstance(ch.systemsx.cisd.hdf5.IHDF5Writer writer,
                                        int numSites,
                                        net.maizegenetics.dna.snp.score.SiteScore.SITE_SCORE_TYPE siteScoreType,
                                        TaxaList taxaList)

getInstance

public static Byte2D getInstance(ch.systemsx.cisd.hdf5.IHDF5Reader reader,
                                 net.maizegenetics.dna.snp.score.SiteScore.SITE_SCORE_TYPE siteScoreType)

addTaxon

public Byte2DBuilder addTaxon(int taxon,
                              kotlin.Array[] values)

Add taxon and set values for all sites for that taxon.

Parameters:

taxon - taxon

values - values

Returns:

org.jetbrains.dokka.NodeRenderContent@56760bf6: builder

setDepthRangeForTaxon

public Byte2DBuilder setDepthRangeForTaxon(int taxon,
                                           int siteOffset,
                                           kotlin.Array[] values)

Set values for range of sites and alleles for a taxon simultaneously.

Parameters:

taxon - Index of taxon

siteOffset - site offset

values - array[sites] range of values

Returns:

org.jetbrains.dokka.NodeRenderContent@59965d34: builder

reorderPositions

public void reorderPositions(kotlin.Array[] newIndices)

build

public Byte2D build()