net.maizegenetics.taxa

Class TaxaListBuilder

net.maizegenetics.taxa.TaxaListBuilder

public class TaxaListBuilder

A builder for creating immutable interface TaxaList instances. Example:

   TaxaListBuilder tlb=new TaxaListBuilder();
    for (int i = 0; i < 10; i++) {
       Taxon at= new Taxon.Builder("Z"+i+":Line:mays:Zea")
            .inbreedF(0.99f)
            .parents("B73","B97")
            .pedigree("(B73xB97)S6I1")
            .build();
        tlb.add(at);
        }
    TaxaList tl=tlb.build();

If building from HDF5:

    TaxaList tl=new TaxaListBuilder().buildFromHDF5Genotypes(testMutFile);
    

See Also:

interface TaxaList

Constructor Detail

TaxaListBuilder

public TaxaListBuilder()

Method Detail

getInstance

public static TaxaList getInstance(int numTaxa)

add

public TaxaListBuilder add(Taxon taxon)

add

public TaxaListBuilder add(java.lang.String taxon)

contains

public boolean contains(Taxon taxon)

addOrMerge

public TaxaListBuilder addOrMerge(Taxon taxon)

addAll

public TaxaListBuilder addAll(java.util.Collection<net.maizegenetics.taxa.Taxon> taxa)

addAll

public TaxaListBuilder addAll(GenotypeTable a)

addAll

public TaxaListBuilder addAll(java.lang.String[] taxa)

addAll

public TaxaListBuilder addAll(java.util.List<java.lang.String> taxa)

addAll

public TaxaListBuilder addAll(Taxon[] taxa)

addAll

public TaxaListBuilder addAll(TaxaListBuilder builder)

noIndex

public TaxaListBuilder noIndex()

build

public TaxaList build()

buildFromHDF5Genotypes

public TaxaList buildFromHDF5Genotypes(ch.systemsx.cisd.hdf5.IHDF5Reader reader)

Builds TaxaList with annotations from an HDF5 file. The list of Taxa come from the those taxa that have been genotyped (in /Genotypes/ path), while the annotations come from the /Taxa/ path. Frequently these two lists are identical, but sometimes this can Genotypes can have a subset of the taxa in /Taxa/

Parameters:

reader -

Returns:

org.jetbrains.dokka.NodeRenderContent@2758e97d:

buildFromHDF5

public TaxaList buildFromHDF5(ch.systemsx.cisd.hdf5.IHDF5Reader reader)

Builds TaxaList with annotations from an HDF5 file. The list of Taxa and annotations come from the /Taxa/ path. This maybe a super set of what is present in the /Genotypes/ or /TBT/ paths.

Parameters:

reader -

Returns:

org.jetbrains.dokka.NodeRenderContent@2ffcba07:

createHDF5TaxaList

public static void createHDF5TaxaList(ch.systemsx.cisd.hdf5.IHDF5Writer writer,
                                      TaxaList exportList)

sortTaxaAlphabetically

public TaxaListBuilder sortTaxaAlphabetically(GenotypeCallTableBuilder genotypes)

sortTaxaAlphabetically

public TaxaListBuilder sortTaxaAlphabetically()

sortAlphabetically

public kotlin.Array[] sortAlphabetically()

numberOfTaxa

public int numberOfTaxa()