net.maizegenetics.dna.snp

Class ProjectionBuilder

java.lang.Object

net.maizegenetics.dna.snp.ProjectionBuilder

public class ProjectionBuilder
extends Object

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.

Author:

Ed Buckler

Constructor Summary

Constructors

Constructor and Description
ProjectionBuilder(GenotypeTable myBaseAlignment)

Method Summary

Modifier and Type	Method and Description
ProjectionBuilder	addTaxon(Taxon taxon, Collection<DonorHaplotypes> breakPoints)
ProjectionBuilder	addTaxon(Taxon taxon, Map<Position,Taxon[]> breakPoints)
ProjectionBuilder	addTaxon(Taxon taxon, NavigableSet<DonorHaplotypes> breakPoints)
GenotypeTable	build()
static GenotypeTable	getInstance(GenotypeTable baseAlignment, com.google.common.collect.ImmutableMap<Taxon,NavigableSet<DonorHaplotypes>> allBreakPoints)

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ProjectionBuilder

public ProjectionBuilder(GenotypeTable myBaseAlignment)

Method Detail

getInstance

public static GenotypeTable getInstance(GenotypeTable baseAlignment,
                                        com.google.common.collect.ImmutableMap<Taxon,NavigableSet<DonorHaplotypes>> allBreakPoints)

addTaxon

public ProjectionBuilder addTaxon(Taxon taxon,
                                  Map<Position,Taxon[]> breakPoints)

addTaxon

public ProjectionBuilder addTaxon(Taxon taxon,
                                  NavigableSet<DonorHaplotypes> breakPoints)

addTaxon

public ProjectionBuilder addTaxon(Taxon taxon,
                                  Collection<DonorHaplotypes> breakPoints)

build

public GenotypeTable build()