net.maizegenetics.dna.snp

Class FilterGenotypeTable

net.maizegenetics.dna.snp.FilterGenotypeTable

public class FilterGenotypeTable

Taxa and site filtering of GenotypeTables. The class essentially creates views of the baseGenotypeTable through arrays for indirection.

Method Detail

getInstance

public static GenotypeTable getInstance(GenotypeTable base,
                                        TaxaList taxa,
                                        PositionList positions,
                                        Translate translate)

createPositions

public static PositionList createPositions(GenotypeTable genotypes,
                                           Translate translate)

createTaxa

public static TaxaList createTaxa(GenotypeTable genotypes,
                                  Translate translate)

getInstance

public static GenotypeTable getInstance(GenotypeTable genotypes,
                                        PositionList positions,
                                        kotlin.Array[] redirectSites)

For use when converting between coordinate systems.

Parameters:

genotypes - base genotypes

positions - new position list

redirectSites - redirected sites from positions to base genotypes

Returns:

org.jetbrains.dokka.NodeRenderContent@74d370bc: new reordered genotype table

getInstance

public static GenotypeTable getInstance(GenotypeTable a,
                                        TaxaList subTaxaList)

This returns GenotypeTable with only specified subTaxaList. Defaults to retain unknown taxa.

Parameters:

a - original genotype table

subTaxaList - taxa list subset

Returns:

org.jetbrains.dokka.NodeRenderContent@3415e921: genotype table

getInstanceSortTaxaAlphabetically

public static GenotypeTable getInstanceSortTaxaAlphabetically(GenotypeTable genotypes)

getInstanceTaxaOrderedByGeneticDistance

public static Tuple<net.maizegenetics.dna.snp.GenotypeTable,kotlin.Array[]> getInstanceTaxaOrderedByGeneticDistance(GenotypeTable genotypes,
                                                                                                                    int taxon)

getInstance

public static GenotypeTable getInstance(GenotypeTable genotype,
                                        TaxaList subTaxaList,
                                        boolean retainUnknownTaxa)

This returns FilterGenotypeTable with only specified subTaxaList. If retainUnknownTaxa is true then Alignment will return unknown values for missing taxa.

Parameters:

genotype - original genotype table

subTaxaList - taxa list subset

retainUnknownTaxa - whether to retain unknown taxa

Returns:

org.jetbrains.dokka.NodeRenderContent@4ef23d8a: genotype table

getInstanceRemoveIDs

public static GenotypeTable getInstanceRemoveIDs(GenotypeTable a,
                                                 TaxaList subTaxaList)

Removes specified IDs.

Parameters:

a - alignment to getInstance

subTaxaList - specified IDs

Returns:

org.jetbrains.dokka.NodeRenderContent@6b5d55af: Filtered Alignment

getInstance

public static GenotypeTable getInstance(GenotypeTable genotypes,
                                        kotlin.Array[] subSites)

getInstance

public static GenotypeTable getInstance(GenotypeTable genotypes,
                                        BitSet subSites,
                                        boolean includeSites)

getInstance

public static GenotypeTable getInstance(GenotypeTable a,
                                        java.util.List<java.lang.String> siteNamesToKeep)

getInstance

public static GenotypeTable getInstance(GenotypeTable a,
                                        java.lang.String[] siteNamesToKeep)

getInstanceRemoveSiteNames

public static GenotypeTable getInstanceRemoveSiteNames(GenotypeTable a,
                                                       java.util.List<java.lang.String> siteNamesToRemove)

getInstanceRemoveSiteNames

public static GenotypeTable getInstanceRemoveSiteNames(GenotypeTable a,
                                                       java.lang.String[] siteNamesToRemove)

getInstance

public static GenotypeTable getInstance(GenotypeTable a,
                                        PositionList subPositionList)

getInstance

public static GenotypeTable getInstance(GenotypeTable a,
                                        java.lang.String chromosome,
                                        int startPhysicalPos,
                                        int endPhysicalPos)

getInstance

public static GenotypeTable getInstance(GenotypeTable a,
                                        Chromosome chromosome,
                                        int startPhysicalPos,
                                        int endPhysicalPos)

getInstance

public static GenotypeTable getInstance(GenotypeTable a,
                                        Chromosome chromosome)

getInstance

public static GenotypeTable getInstance(GenotypeTable genotypes,
                                        int startSite,
                                        int endSite)

Factory method that returns genotypes FilterGenotypeTable viewing sites between start site (inclusive) and end site (inclusive).

Parameters:

genotypes - alignment

startSite - start site

endSite - end site

Returns:

org.jetbrains.dokka.NodeRenderContent@4649ee8: Genotype Table

getInstance

public static GenotypeTable getInstance(GenotypeTable a,
                                        int startSite,
                                        int endSite,
                                        boolean includeSites)