net.maizegenetics.pangenome.api

Class HaplotypeNode

java.lang.Object

net.maizegenetics.pangenome.api.HaplotypeNode

All Implemented Interfaces:

Comparable<HaplotypeNode>

public class HaplotypeNode
extends Object
implements Comparable<HaplotypeNode>

Author:

Terry Casstevens Created June 19, 2017, Zack Miller, Karl Kremling, Jacob Washburn Class for representing haplotype nodes (HaplotypNode) , also known as anchor or inner anchor haplotypes. Haplotype nodes contain are the basic unit of the graph and represent sequence blocks of a given single haplotype. They are derived from a single chromosome from a single line/genotype/variety. In many cases, a haplotype node may also use the consensus sequence of very similar haplotypes from multiple lines/genotypes/varieties.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	HaplotypeNode.VariantInfo These are instantiated only when requested.

Constructor Summary

Constructors

Constructor and Description
HaplotypeNode(HaplotypeSequence haplotypeSequence, net.maizegenetics.taxa.TaxaList taxaList)
HaplotypeNode(HaplotypeSequence haplotypeSequence, net.maizegenetics.taxa.TaxaList taxaList, int id)
HaplotypeNode(HaplotypeSequence haplotypeSequence, net.maizegenetics.taxa.TaxaList taxaList, int id, byte[] variantContexts)

Method Summary

Modifier and Type	Method and Description
int	compareTo(HaplotypeNode o)
HaplotypeSequence	haplotypeSequence() HaplotypeSequence object containing the nucleotide sequence and other sequence related information for a given HaplotypeNode object.
int	id()
int	numTaxa() Number of taxa used when consensus sequence was created or one if this is an original sequence.
ReferenceRange	referenceRange() Object containing the range of genomic coordinate values associated with a given HaplotypeNode and other details associated with that range of values.
net.maizegenetics.taxa.TaxaList	taxaList() List of taxa used when the consensus sequence was created or a single taxon.
String	toString()
Optional<List<htsjdk.variant.variantcontext.VariantContext>>	variantContexts() Returns variant contexts for this node.
Optional<List<HaplotypeNode.VariantInfo>>	variantInfos() These correspond to the VariantContext but holds less information for memory efficiency.

Methods inherited from class java.lang.Object

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

Constructor Detail

HaplotypeNode

public HaplotypeNode(HaplotypeSequence haplotypeSequence,
                     net.maizegenetics.taxa.TaxaList taxaList,
                     int id,
                     byte[] variantContexts)

HaplotypeNode

public HaplotypeNode(HaplotypeSequence haplotypeSequence,
                     net.maizegenetics.taxa.TaxaList taxaList,
                     int id)

HaplotypeNode

public HaplotypeNode(HaplotypeSequence haplotypeSequence,
                     net.maizegenetics.taxa.TaxaList taxaList)

Method Detail

haplotypeSequence

public HaplotypeSequence haplotypeSequence()

HaplotypeSequence object containing the nucleotide sequence and other sequence related information for a given HaplotypeNode object.

taxaList

public net.maizegenetics.taxa.TaxaList taxaList()

List of taxa used when the consensus sequence was created or a single taxon.

id

public int id()

referenceRange

public ReferenceRange referenceRange()

Object containing the range of genomic coordinate values associated with a given HaplotypeNode and other details associated with that range of values. These values correspond to the reference genome being used (Generally B73 in Maize).

numTaxa

public int numTaxa()

Number of taxa used when consensus sequence was created or one if this is an original sequence.

Returns:

number of taxa

variantContexts

public Optional<List<htsjdk.variant.variantcontext.VariantContext>> variantContexts()

Returns variant contexts for this node.

Returns:

variant contexts

toString

public String toString()

Overrides:

toString in class Object

variantInfos

public Optional<List<HaplotypeNode.VariantInfo>> variantInfos()

These correspond to the VariantContext but holds less information for memory efficiency.

Returns:

variant infos

compareTo

public int compareTo(HaplotypeNode o)

Specified by:

compareTo in interface Comparable<HaplotypeNode>