net.maizegenetics.dna.snp

Class ProjectionBuilder

net.maizegenetics.dna.snp.ProjectionBuilder

public class ProjectionBuilder

Builder for a projection alignment. Projection alignments use defined haplotypes and breakpoints that point to high density genotypes (base GenotypeTable). These are used to efficiently store and connect low density maps with imputed high density genotypes.

The alignment built by this builder is a CoreGenotypeTable with a ProjectionGenotypeCallTable. The taxa come from the projection alignment file, while the sites and positions are the same as the base alignment.

Constructor Detail

ProjectionBuilder

public ProjectionBuilder(GenotypeTable myBaseAlignment)

Method Detail

getInstance

public static GenotypeTable getInstance(GenotypeTable baseAlignment,
                                        com.google.common.collect.ImmutableMap<net.maizegenetics.taxa.Taxon,java.util.NavigableSet> allBreakPoints)

addTaxon

public ProjectionBuilder addTaxon(Taxon taxon,
                                  java.util.Map<net.maizegenetics.dna.map.Position,kotlin.Array[]> breakPoints)

addTaxon

public ProjectionBuilder addTaxon(Taxon taxon,
                                  java.util.NavigableSet<net.maizegenetics.dna.map.DonorHaplotypes> breakPoints)

addTaxon

public ProjectionBuilder addTaxon(Taxon taxon,
                                  java.util.Collection<net.maizegenetics.dna.map.DonorHaplotypes> breakPoints)

build

public GenotypeTable build()