net.maizegenetics.pangenome.api

Class GraphUtils

java.lang.Object

net.maizegenetics.pangenome.api.GraphUtils

public class GraphUtils
extends Object

Author:

Terry Casstevens Created August 30, 2017

Method Summary

Modifier and Type	Method and Description
static int[]	distributionTaxaRepresented(HaplotypeGraph graph)
static List<HaplotypeNode>	nodes(HaplotypeGraph graph, SortedSet<Integer> hapids) Returns a list of HaplotypeNodes corresponding to the given hapids in the given graph.
static List<HaplotypeNode>	nodesContainingExactly(net.maizegenetics.taxa.TaxaList taxa, HaplotypeGraph graph) Gets list of HaplotypeNodes containing exact list of taxa.
static void	nodeTaxaPairs(HaplotypeGraph graph, String filename)
static SortedSet<Integer>	path(TreeMap<net.maizegenetics.dna.map.Chromosome,HaplotypePath> paths) Returns sorted set of haplotype ids from the given paths.
static SortedSet<HaplotypeNode>	pathsToNodes(TreeMap<net.maizegenetics.dna.map.Chromosome,HaplotypePath> paths)
static void	presenceAbsenceTaxonByNode(HaplotypeGraph graph, String filename)
static SortedSet<net.maizegenetics.dna.map.Position>	snpPositions(HaplotypeGraph graph) Return sorted set of positions that are variant (SNP) positions in given graph.
static SortedSet<net.maizegenetics.dna.map.Position>	snpPositions(HaplotypeGraph graph, Collection<Integer> referenceRanges) Return sorted set of positions that are variant (SNP) positions in given graph.
static void	tagNodePairCounts(String tagTaxaFile, HaplotypeGraph graph, String outputFile)

Methods inherited from class java.lang.Object

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

Method Detail

path

public static SortedSet<Integer> path(TreeMap<net.maizegenetics.dna.map.Chromosome,HaplotypePath> paths)

Returns sorted set of haplotype ids from the given paths.

Parameters:

paths - paths

Returns:

sorted set of haplotype ids

pathsToNodes

public static SortedSet<HaplotypeNode> pathsToNodes(TreeMap<net.maizegenetics.dna.map.Chromosome,HaplotypePath> paths)

nodes

public static List<HaplotypeNode> nodes(HaplotypeGraph graph,
                                        SortedSet<Integer> hapids)

Returns a list of HaplotypeNodes corresponding to the given hapids in the given graph.

Parameters:

graph - graph

hapids - haplotype ids

Returns:

list of HaplotypeNodes

presenceAbsenceTaxonByNode

public static void presenceAbsenceTaxonByNode(HaplotypeGraph graph,
                                              String filename)

distributionTaxaRepresented

public static int[] distributionTaxaRepresented(HaplotypeGraph graph)

nodesContainingExactly

public static List<HaplotypeNode> nodesContainingExactly(net.maizegenetics.taxa.TaxaList taxa,
                                                         HaplotypeGraph graph)

Gets list of HaplotypeNodes containing exact list of taxa.

Parameters:

taxa - taxa list

graph - graph

Returns:

list of nodes

tagNodePairCounts

public static void tagNodePairCounts(String tagTaxaFile,
                                     HaplotypeGraph graph,
                                     String outputFile)

nodeTaxaPairs

public static void nodeTaxaPairs(HaplotypeGraph graph,
                                 String filename)

snpPositions

public static SortedSet<net.maizegenetics.dna.map.Position> snpPositions(HaplotypeGraph graph)

Return sorted set of positions that are variant (SNP) positions in given graph.

Parameters:

graph - graph

Returns:

sorted set of positions

snpPositions

public static SortedSet<net.maizegenetics.dna.map.Position> snpPositions(HaplotypeGraph graph,
                                                                         Collection<Integer> referenceRanges)

Return sorted set of positions that are variant (SNP) positions in given graph.

Parameters:

graph - graph

referenceRanges - set of reference ranges (ids) that are included in result. If null, all ranges are included.

Returns:

sorted set of positions