HaplotypeGraph (net.maizegenetics:phg 0.0.1 API)

java.lang.Object
- net.maizegenetics.pangenome.api.HaplotypeGraph

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

Author:

Terry Casstevens Created August 03, 2017

Constructor Summary

Constructors
Constructor and Description

HaplotypeGraph(Collection<HaplotypeEdge> edges)
Constructor for HaplotypeGraph.

Constructors
Constructor and Description
`HaplotypeGraph(Collection<HaplotypeEdge> edges)` Constructor for HaplotypeGraph.

Method Summary

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

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

- Constructor Detail
  - HaplotypeGraph
```
public HaplotypeGraph(Collection<HaplotypeEdge> edges)
```
    Constructor for HaplotypeGraph. See HaplotypeGraphBuilderPlugin
    
    Parameters:
    
    edges - HaplotypeEdges
- Method Detail
  - numberOfNodes
```
public int numberOfNodes()
```
  - chromosomes
```
public List<net.maizegenetics.dna.map.Chromosome> chromosomes()
```
  - numberOfChromosomes
```
public int numberOfChromosomes()
```
  - path
```
public TreeMap<net.maizegenetics.dna.map.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
    
    Returns:
    
    paths for each chromosome
  - path
```
public TreeMap<net.maizegenetics.dna.map.Chromosome,HaplotypePath> path(net.maizegenetics.taxa.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
    
    Returns:
    
    paths for each chromosome
  - path
```
public TreeMap<net.maizegenetics.dna.map.Chromosome,HaplotypePath> path(List<HaplotypeNode> nodes)
```
    Returns most probable HaplotypePath for each Chromosome given the specified list of known HaplotypeNodes. List of nodes can have at most one node per ReferenceRange.
    
    Parameters:
    
    nodes - list of known nodes
    
    Returns:
    
    paths for each chromosome
  - path
```
public TreeMap<net.maizegenetics.dna.map.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
    
    Returns:
    
    paths for each chromosome
  - path
```
public HaplotypePath path(net.maizegenetics.taxa.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
    
    Returns:
    
    paths for each chromosome
  - path
```
public TreeMap<net.maizegenetics.dna.map.Chromosome,HaplotypePath> path()
```
    Returns most probable HaplotypePath for each Chromosome.
    
    Returns:
    
    paths for each chromosome
  - startNodes
```
public List<HaplotypeNode> startNodes()
```
    Returns list of HaplotypeNodes that start graph.
    
    Returns:
    
    Starting HaplotypeNodes
  - startNodes
```
public List<HaplotypeNode> startNodes(net.maizegenetics.dna.map.Chromosome chr)
```
  - endNodes
```
public List<HaplotypeNode> endNodes()
```
    Returns list of HaplotypeNodes that end graph.
    
    Returns:
    
    Ending HaplotypeNodes
  - endNodes
```
public List<HaplotypeNode> endNodes(net.maizegenetics.dna.map.Chromosome chr)
```
  - nodes
```
public List<HaplotypeNode> nodes(ReferenceRange range)
```
    Returns list of HaplotypeNodes for given ReferenceRange
    
    Parameters:
    
    range - ReferenceRange
    
    Returns:
    
    List of HaplotypeNodes
  - nodeStream
```
public Stream<HaplotypeNode> nodeStream()
```
  - tree
```
public TreeMap<ReferenceRange,List<HaplotypeNode>> tree(net.maizegenetics.dna.map.Chromosome chr)
```
    Creates a sorted (on keys ReferenceRanges) map to list of HaplotypeNodes for given chromosome.
    
    Parameters:
    
    chr - chromosome
    
    Returns:
    
    map of ReferenceRanges to Lists of HaplotypeNodes
  - numberOfLeftEdges
```
public int numberOfLeftEdges(HaplotypeNode node)
```
    Return number of left edges for given node.
    
    Parameters:
    
    node - node
    
    Returns:
    
    number of left edges
  - numberOfRightEdges
```
public int numberOfRightEdges(HaplotypeNode node)
```
    Return number of right edges for given node.
    
    Parameters:
    
    node - node
    
    Returns:
    
    number of right edges
  - leftEdges
```
public List<HaplotypeEdge> leftEdges(HaplotypeNode node)
```
    Returns List of Left HaplotypeEdges for given HaplotypeNode
    
    Parameters:
    
    node - HaplotypeNode
    
    Returns:
    
    List of Left HaplotypeEdges
  - rightEdges
```
public List<HaplotypeEdge> rightEdges(HaplotypeNode node)
```
    Returns List of Right HaplotypeEdges for given HaplotypeNode
    
    Parameters:
    
    node - HaplotypeNode
    
    Returns:
    
    List of Right HaplotypeEdges
  - edge
```
public Optional<HaplotypeEdge> edge(HaplotypeNode node1,
                                    HaplotypeNode node2)
```
    Returns optional edge between given nodes.
    
    Parameters:
    
    node1 - first node
    
    node2 - second node
    
    Returns:
    
    edge
  - numberOfRanges
```
public int numberOfRanges()
```
    Returns number of reference ranges in this graph.
    
    Returns:
    
    number of reference ranges
  - referenceRanges
```
public Set<ReferenceRange> referenceRanges()
```
    Returns sorted set of reference ranges for whole graph. Consider using referenceRangeStream()
    
    Returns:
    
    sorted set of all reference ranges
  - referenceRangeList
```
public List<ReferenceRange> referenceRangeList()
```
    Returns list of reference ranges for whole graph. Consider using referenceRangeStream()
    
    Returns:
    
    list of all reference ranges
  - referenceRangeStream
```
public Stream<ReferenceRange> referenceRangeStream()
```
    Returns stream of reference ranges for entire graph.
    
    Returns:
    
    stream of reference ranges
  - referenceRangeStream
```
public Stream<ReferenceRange> referenceRangeStream(net.maizegenetics.dna.map.Chromosome chr)
```
    Returns stream of reference ranges for given chromosome.
    
    Parameters:
    
    chr - chromosome
    
    Returns:
    
    stream of reference ranges
  - firstReferenceRange
```
public ReferenceRange firstReferenceRange()
```
    Returns the first reference range in this graph.
    
    Returns:
    
    first reference range
  - lastReferenceRange
```
public ReferenceRange lastReferenceRange()
```
    Returns the last reference range in this graph.
    
    Returns:
    
    last reference range
  - firstReferenceRange
```
public ReferenceRange firstReferenceRange(net.maizegenetics.dna.map.Chromosome chr)
```
    Returns the first reference range for the given chromosome.
    
    Parameters:
    
    chr - chromosome
    
    Returns:
    
    first reference range
  - lastReferenceRange
```
public ReferenceRange lastReferenceRange(net.maizegenetics.dna.map.Chromosome chr)
```
    Returns the last reference range for the given chromosome.
    
    Parameters:
    
    chr - chromosome
    
    Returns:
    
    last reference range
  - taxaInGraph
```
public net.maizegenetics.taxa.TaxaList taxaInGraph()
```
    Return all taxa represented in this graph.
    
    Returns:
    
    all taxa
  - totalNumberTaxa
```
public int totalNumberTaxa()
```
    Returns total number of taxa represented by this graph
    
    Returns:
    
    total number of taxa
  - taxaInRange
```
public net.maizegenetics.taxa.TaxaList taxaInRange(ReferenceRange range)
```
    Returns taxa represented by given reference range.
    
    Parameters:
    
    range - reference range
    
    Returns:
    
    taxa in reference range
  - numberTaxa
```
public int numberTaxa(ReferenceRange range)
```
    Returns number of taxa represented by given reference range.
    
    Parameters:
    
    range - reference range
    
    Returns:
    
    number of taxa in reference range

Class HaplotypeGraph

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

HaplotypeGraph

Method Detail

numberOfNodes

chromosomes

numberOfChromosomes

path

path

path

path

path

path

startNodes

startNodes

endNodes

endNodes

nodes

nodeStream

tree

numberOfLeftEdges

numberOfRightEdges

leftEdges

rightEdges

edge

numberOfRanges

referenceRanges

referenceRangeList

referenceRangeStream

referenceRangeStream

firstReferenceRange

lastReferenceRange

firstReferenceRange

lastReferenceRange

taxaInGraph

totalNumberTaxa

taxaInRange

numberTaxa