All Implemented Interfaces:
```
public class HaplotypeGraph

                    
```
This Class is a wrapper around a complete Practical Haplotype Graph (PHG). Including HaplotypeNodes, HaplotypeEdges, HaplotypePaths, HaplotypeSequences, ReferenceRanges, etc.

Nested Class Summary

Nested Classes
Modifier and Type	Class	Description

Field Summary

Fields
Modifier and Type	Field	Description

Constructor Summary

Constructors
Constructor	Description
`HaplotypeGraph(Collection<HaplotypeEdge> edges)`	Constructor for HaplotypeGraph.
`HaplotypeGraph(NavigableMap<ReferenceRange, List<HaplotypeNode>> nodes)`
`HaplotypeGraph(NavigableMap<ReferenceRange, List<HaplotypeNode>> nodes, BiFunction<List<HaplotypeNode>, List<HaplotypeNode>, List<HaplotypeEdge>> edgeFunction)`	Constructor for HaplotypeGraph.

Enum Constant Summary

Enum Constants
Enum Constant	Description

Method Summary

Modifier and Type	Method	Description
`boolean`	`hasSequences()`
`int`	`numberOfNodes()`
`List<Chromosome>`	`chromosomes()`
`int`	`numberOfChromosomes()`
`NavigableMap<Chromosome, HaplotypePath>`	`path(String taxon, List<HaplotypeNode> nodes)`	Returns most probable HaplotypePath for each Chromosome given the specified taxon and list of known HaplotypeNodes.
`NavigableMap<Chromosome, HaplotypePath>`	`path(Taxon taxon, List<HaplotypeNode> nodes)`	Returns most probable HaplotypePath for each Chromosome given the specified Taxon and list of known HaplotypeNodes.
`NavigableMap<Chromosome, HaplotypePath>`	`path(List<HaplotypeNode> nodes)`	Returns most probable HaplotypePath for each Chromosome given the specified list of known s.
`NavigableMap<Chromosome, HaplotypePath>`	`path(String taxon)`	Returns most probable HaplotypePath for each Chromosome given the specified taxon.
`NavigableMap<Chromosome, HaplotypePath>`	`path(Taxon taxon)`	Returns most probable HaplotypePath for each Chromosome given the specified Taxon.
`NavigableMap<Chromosome, HaplotypePath>`	`path()`	Returns most probable HaplotypePath for each Chromosome.
`List<HaplotypeNode>`	`startNodes()`	Returns list of HaplotypeNodes that start graph.
`List<HaplotypeNode>`	`startNodes(Chromosome chr)`
`List<HaplotypeNode>`	`endNodes()`	Returns list of HaplotypeNodes that end graph.
`List<HaplotypeNode>`	`endNodes(Chromosome chr)`
`List<HaplotypeNode>`	`nodes(ReferenceRange range)`	Returns list of HaplotypeNodes for given ReferenceRange
`Stream<HaplotypeNode>`	`nodeStream()`
`NavigableMap<ReferenceRange, List<HaplotypeNode>>`	`tree(Chromosome chr)`	Creates a sorted (on keys ReferenceRanges) map to list of HaplotypeNodes for given chromosome.
`int`	`numberOfLeftEdges(HaplotypeNode node)`	Return number of left edges for given node.
`int`	`numberOfRightEdges(HaplotypeNode node)`	Return number of right edges for given node.
`List<HaplotypeEdge>`	`leftEdges(HaplotypeNode node)`	Returns List of Left HaplotypeEdges for given HaplotypeNode
`List<HaplotypeEdge>`	`rightEdges(HaplotypeNode node)`	Returns List of Right HaplotypeEdges for given HaplotypeNode
`ReferenceRange`	`previousRange(ReferenceRange range)`
`ReferenceRange`	`nextRange(ReferenceRange range)`
`Optional<HaplotypeEdge>`	`edge(HaplotypeNode node1, HaplotypeNode node2)`	Returns optional edge between given nodes.
`int`	`numberOfRanges()`	Returns number of reference ranges in this graph.
`Set<ReferenceRange>`	`referenceRanges()`	Returns sorted set of reference ranges for whole graph.
`List<ReferenceRange>`	`referenceRangeList()`	Returns list of reference ranges for whole graph.
`Stream<ReferenceRange>`	`referenceRangeStream()`	Returns stream of reference ranges for entire graph.
`Stream<ReferenceRange>`	`referenceRangeStream(Chromosome chr)`	Returns stream of reference ranges for given chromosome.
`ReferenceRange`	`firstReferenceRange()`	Returns the first reference range in this graph.
`ReferenceRange`	`lastReferenceRange()`	Returns the last reference range in this graph.
`ReferenceRange`	`firstReferenceRange(Chromosome chr)`	Returns the first reference range for the given chromosome.
`ReferenceRange`	`lastReferenceRange(Chromosome chr)`	Returns the last reference range for the given chromosome.
`TaxaList`	`taxaInGraph()`	Return all taxa represented in this graph.
`int`	`totalNumberTaxa()`	Returns total number of taxa represented by this graph
`TaxaList`	`taxaInRange(ReferenceRange range)`	Returns taxa represented by given reference range.
`int`	`numberTaxa(ReferenceRange range)`	Returns number of taxa represented by given reference range.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - HaplotypeGraph
```
HaplotypeGraph(Collection<HaplotypeEdge> edges)
```
    Constructor for HaplotypeGraph.
    
    Parameters:
    
    edges - HaplotypeEdges
  - HaplotypeGraph
```
HaplotypeGraph(NavigableMap<ReferenceRange, List<HaplotypeNode>> nodes)
```
  - HaplotypeGraph
```
HaplotypeGraph(NavigableMap<ReferenceRange, List<HaplotypeNode>> nodes, BiFunction<List<HaplotypeNode>, List<HaplotypeNode>, List<HaplotypeEdge>> edgeFunction)
```
    Constructor for HaplotypeGraph.
    
    Parameters:
    
    nodes - HaplotypeNodes
    
    edgeFunction - function used to create edges
- Method Detail
  - hasSequences
```
 boolean hasSequences()
```
  - numberOfNodes
```
 int numberOfNodes()
```
  - chromosomes
```
 List<Chromosome> chromosomes()
```
  - numberOfChromosomes
```
 int numberOfChromosomes()
```
  - path
```
 NavigableMap<Chromosome, HaplotypePath> path(String taxon, List<HaplotypeNode> nodes)
```
    Returns most probable HaplotypePath for each Chromosome given the specified taxon and list of known HaplotypeNodes. List of nodes can have at most one node per ReferenceRange. Nodes constructed with specified taxon will always be used in resulting paths. Specified nodes must either have been constructed with specified taxon or reside in a reference range that has no node constructed with specified taxon.
    
    Parameters:
    
    taxon - taxon
    
    nodes - list of known nodes
  - path
```
 NavigableMap<Chromosome, HaplotypePath> path(Taxon taxon, List<HaplotypeNode> nodes)
```
    Returns most probable HaplotypePath for each Chromosome given the specified Taxon and list of known HaplotypeNodes. List of nodes can have at most one node per ReferenceRange. Nodes constructed with specified taxon will always be used in resulting paths. Specified nodes must either have been constructed with specified taxon or reside in a reference range that has no node constructed with specified taxon.
    
    Parameters:
    
    taxon - taxon
    
    nodes - list of known nodes
  - path
```
 NavigableMap<Chromosome, HaplotypePath> path(List<HaplotypeNode> nodes)
```
    Returns most probable HaplotypePath for each Chromosome given the specified list of known s. List of nodes can have at most one node per ReferenceRange.
    
    Parameters:
    
    nodes - list of known nodes
  - path
```
 NavigableMap<Chromosome, HaplotypePath> path(String taxon)
```
    Returns most probable HaplotypePath for each Chromosome given the specified taxon. Nodes constructed with specified taxon will always be used in resulting paths.
    
    Parameters:
    
    taxon - taxon
  - path
```
 NavigableMap<Chromosome, HaplotypePath> path(Taxon taxon)
```
    Returns most probable HaplotypePath for each Chromosome given the specified Taxon. Nodes constructed with specified taxon will always be used in resulting paths.
    
    Parameters:
    
    taxon - taxon
  - path
```
 NavigableMap<Chromosome, HaplotypePath> path()
```
    Returns most probable HaplotypePath for each Chromosome.
  - startNodes
```
 List<HaplotypeNode> startNodes()
```
    Returns list of HaplotypeNodes that start graph.
  - startNodes
```
 List<HaplotypeNode> startNodes(Chromosome chr)
```
  - endNodes
```
 List<HaplotypeNode> endNodes()
```
    Returns list of HaplotypeNodes that end graph.
  - endNodes
```
 List<HaplotypeNode> endNodes(Chromosome chr)
```
  - nodes
```
 List<HaplotypeNode> nodes(ReferenceRange range)
```
    Returns list of HaplotypeNodes for given ReferenceRange
    
    Parameters:
    
    range - ReferenceRange
  - nodeStream
```
 Stream<HaplotypeNode> nodeStream()
```
  - tree
```
 NavigableMap<ReferenceRange, List<HaplotypeNode>> tree(Chromosome chr)
```
    Creates a sorted (on keys ReferenceRanges) map to list of HaplotypeNodes for given chromosome.
    
    Parameters:
    
    chr - chromosome
  - numberOfLeftEdges
```
 int numberOfLeftEdges(HaplotypeNode node)
```
    Return number of left edges for given node.
    
    Parameters:
    
    node - node
  - numberOfRightEdges
```
 int numberOfRightEdges(HaplotypeNode node)
```
    Return number of right edges for given node.
    
    Parameters:
    
    node - node
  - leftEdges
```
 List<HaplotypeEdge> leftEdges(HaplotypeNode node)
```
    Returns List of Left HaplotypeEdges for given HaplotypeNode
    
    Parameters:
    
    node - HaplotypeNode
  - rightEdges
```
 List<HaplotypeEdge> rightEdges(HaplotypeNode node)
```
    Returns List of Right HaplotypeEdges for given HaplotypeNode
    
    Parameters:
    
    node - HaplotypeNode
  - previousRange
```
 ReferenceRange previousRange(ReferenceRange range)
```
  - nextRange
```
 ReferenceRange nextRange(ReferenceRange range)
```
  - edge
```
 Optional<HaplotypeEdge> edge(HaplotypeNode node1, HaplotypeNode node2)
```
    Returns optional edge between given nodes.
    
    Parameters:
    
    node1 - first node
    
    node2 - second node
  - numberOfRanges
```
 int numberOfRanges()
```
    Returns number of reference ranges in this graph.
  - referenceRanges
```
 Set<ReferenceRange> referenceRanges()
```
    Returns sorted set of reference ranges for whole graph. Consider using referenceRangeStream
  - referenceRangeList
```
 List<ReferenceRange> referenceRangeList()
```
    Returns list of reference ranges for whole graph. Consider using referenceRangeStream
  - referenceRangeStream
```
 Stream<ReferenceRange> referenceRangeStream()
```
    Returns stream of reference ranges for entire graph.
  - referenceRangeStream
```
 Stream<ReferenceRange> referenceRangeStream(Chromosome chr)
```
    Returns stream of reference ranges for given chromosome.
    
    Parameters:
    
    chr - chromosome
  - firstReferenceRange
```
 ReferenceRange firstReferenceRange()
```
    Returns the first reference range in this graph.
  - lastReferenceRange
```
 ReferenceRange lastReferenceRange()
```
    Returns the last reference range in this graph.
  - firstReferenceRange
```
 ReferenceRange firstReferenceRange(Chromosome chr)
```
    Returns the first reference range for the given chromosome.
    
    Parameters:
    
    chr - chromosome
  - lastReferenceRange
```
 ReferenceRange lastReferenceRange(Chromosome chr)
```
    Returns the last reference range for the given chromosome.
    
    Parameters:
    
    chr - chromosome
  - taxaInGraph
```
 TaxaList taxaInGraph()
```
    Return all taxa represented in this graph.
  - totalNumberTaxa
```
 int totalNumberTaxa()
```
    Returns total number of taxa represented by this graph
  - taxaInRange
```
 TaxaList taxaInRange(ReferenceRange range)
```
    Returns taxa represented by given reference range.
    
    Parameters:
    
    range - reference range
  - numberTaxa
```
 int numberTaxa(ReferenceRange range)
```
    Returns number of taxa represented by given reference range.
    
    Parameters:
    
    range - reference range

Class HaplotypeGraph

Nested Class Summary

Field Summary

Constructor Summary

Enum Constant Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

HaplotypeGraph

HaplotypeGraph

HaplotypeGraph

Method Detail

hasSequences

numberOfNodes

chromosomes

numberOfChromosomes

path

path

path

path

path

path

startNodes

startNodes

endNodes

endNodes

nodes

nodeStream

tree

numberOfLeftEdges

numberOfRightEdges

leftEdges

rightEdges

previousRange

nextRange

edge

numberOfRanges

referenceRanges

referenceRangeList

referenceRangeStream

referenceRangeStream

firstReferenceRange

lastReferenceRange

firstReferenceRange

lastReferenceRange

taxaInGraph

totalNumberTaxa

taxaInRange

numberTaxa