Uses of Class
net.maizegenetics.pangenome.api.HaplotypeNode

Packages that use HaplotypeNode

Package	Description
net.maizegenetics.pangenome.api
net.maizegenetics.pangenome.db_loading
net.maizegenetics.pangenome.gui
net.maizegenetics.pangenome.hapCalling
net.maizegenetics.pangenome.hapcollapse

Uses of HaplotypeNode in net.maizegenetics.pangenome.api

Methods in net.maizegenetics.pangenome.api that return HaplotypeNode

Modifier and Type	Method and Description
HaplotypeNode	HaplotypeEdge.leftHapNode() HaplotypeNode to the left of the current edge.
HaplotypeNode	HaplotypeEdge.rightHapNode() HaplotypeNode to the right of the current edge

Methods in net.maizegenetics.pangenome.api that return types with arguments of type HaplotypeNode

Modifier and Type	Method and Description
static List<HaplotypeNode>	CreateHaplotypeNodeListFromFasta.createHaplotypeNodeList(String fastaFile, String intervalFile)
static List<HaplotypeNode>	CreateHaplotypeNodeListFromFasta.createHaplotypeNodeListFromDirectory(String fastaDir, String intervalFile)
static TreeMap<ReferenceRange,List<HaplotypeNode>>	CreateGraphUtils.createHaplotypeNodes(Connection database, Map<Integer,ReferenceRange> referenceRangeMap, Map<Integer,net.maizegenetics.taxa.TaxaList> taxaListMap, String method, boolean onlyAnchors, boolean includeVariantContext, SortedSet<Integer> includeHapids) Creates lists of HaplotypeNodes organized by reference Range based on the given method.
static TreeMap<ReferenceRange,List<HaplotypeNode>>	CreateGraphUtils.createHaplotypeNodes(Connection database, String method, boolean onlyAnchors, boolean includeVariantContext, SortedSet<Integer> includeHapids) Creates HaplotypeNode Lists with keys as ReferenceRanges.
static TreeMap<ReferenceRange,List<HaplotypeNode>>	CreateGraphUtils.createHaplotypeNodesWithVariants(Connection database, Set<HaplotypeNode> includeHapNodes) Creates lists of HaplotypeNodes with variant contexts corresponding to the specified nodes organized by reference Range.
List<HaplotypeNode>	HaplotypeGraph.endNodes() Returns list of HaplotypeNodes that end graph.
List<HaplotypeNode>	HaplotypeGraph.endNodes(net.maizegenetics.dna.map.Chromosome chr)
List<HaplotypeNode>	HaplotypePath.nodes()
static List<HaplotypeNode>	GraphUtils.nodes(HaplotypeGraph graph, SortedSet<Integer> hapids) Returns a list of HaplotypeNodes corresponding to the given hapids in the given graph.
List<HaplotypeNode>	HaplotypeGraph.nodes(ReferenceRange range) Returns list of HaplotypeNodes for given ReferenceRange
static List<HaplotypeNode>	GraphUtils.nodesContainingExactly(net.maizegenetics.taxa.TaxaList taxa, HaplotypeGraph graph) Gets list of HaplotypeNodes containing exact list of taxa.
Stream<HaplotypeNode>	HaplotypeGraph.nodeStream()
static SortedSet<HaplotypeNode>	GraphUtils.pathsToNodes(TreeMap<net.maizegenetics.dna.map.Chromosome,HaplotypePath> paths)
List<HaplotypeNode>	HaplotypeGraph.startNodes() Returns list of HaplotypeNodes that start graph.
List<HaplotypeNode>	HaplotypeGraph.startNodes(net.maizegenetics.dna.map.Chromosome chr)
TreeMap<ReferenceRange,List<HaplotypeNode>>	HaplotypeGraph.tree(net.maizegenetics.dna.map.Chromosome chr) Creates a sorted (on keys ReferenceRanges) map to list of HaplotypeNodes for given chromosome.
static TreeMap<ReferenceRange,List<HaplotypeNode>>	CreateGraphUtils.tree(HaplotypeGraph graph)

Methods in net.maizegenetics.pangenome.api with parameters of type HaplotypeNode

Modifier and Type	Method and Description
int	HaplotypeNode.compareTo(HaplotypeNode o)
Optional<HaplotypeEdge>	HaplotypeGraph.edge(HaplotypeNode node1, HaplotypeNode node2) Returns optional edge between given nodes.
List<HaplotypeEdge>	HaplotypeGraph.leftEdges(HaplotypeNode node) Returns List of Left HaplotypeEdges for given HaplotypeNode
int	HaplotypeGraph.numberOfLeftEdges(HaplotypeNode node) Return number of left edges for given node.
int	HaplotypeGraph.numberOfRightEdges(HaplotypeNode node) Return number of right edges for given node.
List<HaplotypeEdge>	HaplotypeGraph.rightEdges(HaplotypeNode node) Returns List of Right HaplotypeEdges for given HaplotypeNode

Method parameters in net.maizegenetics.pangenome.api with type arguments of type HaplotypeNode

Modifier and Type	Method and Description
static int	CreateGraphUtils.addInnerAnchorNodes(TreeMap<ReferenceRange,List<HaplotypeNode>> result, Connection database, Map<Integer,ReferenceRange> referenceRangeMap, Map<Integer,net.maizegenetics.taxa.TaxaList> taxaListMap, boolean includeVariantContext, int hapMethodId)
static int	CreateGraphUtils.addMissingSequenceNodes(TreeMap<ReferenceRange,List<HaplotypeNode>> result)
static void	CreateGraphUtils.addUnconsolidatedNodes(Connection database, Map<ReferenceRange,List<HaplotypeNode>> consensusNodes, Map<Integer,ReferenceRange> referenceRangeMap, Map<Integer,net.maizegenetics.taxa.TaxaList> taxaListMap, boolean onlyAnchors) Adds HaplotypeNodes to the given map for sequences that wasn't consolidated into a consensus sequence.
static List<HaplotypeEdge>	CreateGraphUtils.createEdges(Collection<HaplotypeNode> haplotypeNodes) Generates Edges based on HaplotypeNodes.
static List<HaplotypeEdge>	CreateGraphUtils.createEdges(TreeMap<ReferenceRange,List<HaplotypeNode>> rangeToNode) Generates Edges based on HaplotypeNodes.
static TreeMap<ReferenceRange,List<HaplotypeNode>>	CreateGraphUtils.createHaplotypeNodesWithVariants(Connection database, Set<HaplotypeNode> includeHapNodes) Creates lists of HaplotypeNodes with variant contexts corresponding to the specified nodes organized by reference Range.
static ReferenceRangeEmissionProbability	ReferenceRangeEmissionProbability.getInstanceFromHapidCountMap(TreeMap<ReferenceRange,List<HaplotypeNode>> nodes, Map<Integer,Integer> hapidCountMap, double probCorrect)
static ReferenceRangeEmissionProbability	ReferenceRangeEmissionProbability.getInstanceFromHapidCounts(TreeMap<ReferenceRange,List<HaplotypeNode>> nodes, com.google.common.collect.Multiset<Integer> hapidCounts, double probCorrect)
static ReferenceRangeEmissionProbability	ReferenceRangeEmissionProbability.getInstanceFromNodeCounts(TreeMap<ReferenceRange,List<HaplotypeNode>> nodes, com.google.common.collect.Multiset<HaplotypeNode> nodeCounts, double probCorrect)
static ReferenceRangeEmissionProbability	ReferenceRangeEmissionProbability.getInstanceFromNodeCounts(TreeMap<ReferenceRange,List<HaplotypeNode>> nodes, com.google.common.collect.Multiset<HaplotypeNode> nodeCounts, double probCorrect)
ReferenceRangeEmissionProbability.Builder	ReferenceRangeEmissionProbability.Builder.nodeMap(TreeMap<ReferenceRange,List<HaplotypeNode>> nodeMap)
TreeMap<net.maizegenetics.dna.map.Chromosome,HaplotypePath>	HaplotypeGraph.path(List<HaplotypeNode> nodes) Returns most probable HaplotypePath for each Chromosome given the specified list of known HaplotypeNodes.
TreeMap<net.maizegenetics.dna.map.Chromosome,HaplotypePath>	HaplotypeGraph.path(String taxon, List<HaplotypeNode> nodes) Returns most probable HaplotypePath for each Chromosome given the specified taxon and list of known HaplotypeNodes.
TreeMap<net.maizegenetics.dna.map.Chromosome,HaplotypePath>	HaplotypeGraph.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.
static net.maizegenetics.taxa.TaxaList	CreateGraphUtils.taxaInNodes(TreeMap<ReferenceRange,List<HaplotypeNode>> nodes)

Constructors in net.maizegenetics.pangenome.api with parameters of type HaplotypeNode

Constructor and Description
HaplotypeEdge(HaplotypeNode leftHapNode, HaplotypeNode rightHapNode, double edgeProbability) Constructor

Constructor parameters in net.maizegenetics.pangenome.api with type arguments of type HaplotypeNode

Constructor and Description
ReferenceRangeTransitionProbability(ArrayList<List<HaplotypeNode>> anchorNodeList, HaplotypeGraph hapGraph, double minTransitionProb)

Uses of HaplotypeNode in net.maizegenetics.pangenome.db_loading

Method parameters in net.maizegenetics.pangenome.db_loading with type arguments of type HaplotypeNode

Modifier and Type	Method and Description
static byte[]	DBLoadingUtils.encodeHapCountsArrayFromMultiset(com.google.common.collect.Multiset<HaplotypeNode> perfectHitSet, com.google.common.collect.Multiset<HaplotypeNode> exclusionHitSet) THis method takes 2 multisets of HaplotypeNode objects: one indicating inclusion counts for a haplotype, the other indicating exclusion counts.
static byte[]	DBLoadingUtils.encodeHapCountsArrayFromMultiset(com.google.common.collect.Multiset<HaplotypeNode> perfectHitSet, com.google.common.collect.Multiset<HaplotypeNode> exclusionHitSet) THis method takes 2 multisets of HaplotypeNode objects: one indicating inclusion counts for a haplotype, the other indicating exclusion counts.
static byte[]	DBLoadingUtils.encodePathArrayFromSet(Set<HaplotypeNode> paths)
void	PHGDataWriter.putPathsData(String method, String methodDetails, com.google.common.collect.Multimap<Integer,HaplotypeNode> paths) This method stores paths data to the paths table.
void	PHGdbAccess.putPathsData(String method, String methodDetails, com.google.common.collect.Multimap<Integer,HaplotypeNode> paths)

Uses of HaplotypeNode in net.maizegenetics.pangenome.gui

Method parameters in net.maizegenetics.pangenome.gui with type arguments of type HaplotypeNode

Modifier and Type	Method and Description
static void	CreateStreamGraph.view(HaplotypeGraph graph, com.google.common.collect.Multimap<String,HaplotypeNode> paths)

Uses of HaplotypeNode in net.maizegenetics.pangenome.hapCalling

Methods in net.maizegenetics.pangenome.hapCalling that return types with arguments of type HaplotypeNode

Modifier and Type	Method and Description
List<HaplotypeNode>	ConvertGBSUtils.chooseBestNode(HaplotypeGraph hapgraph, com.google.common.collect.Multiset<Integer> hapidCounts)
List<HaplotypeNode>	ConvertGBSToSNPs.haplotypeCountsToPath()
List<HaplotypeNode>	ConvertGBSToSNPs.nodeListFromProbabilities(double minP)
List<HaplotypeNode>	ConvertGBSToSNPs.nodeListFromProbabilities(double minP, String infoFilename)
List<HaplotypeNode>	ConvertGBSToSNPs.nodesOnPath()
com.google.common.collect.Multiset<HaplotypeNode>	FastqToHapCountPlugin.runPlugin(net.maizegenetics.plugindef.DataSet input) Convenience method to run plugin with one return object.

Method parameters in net.maizegenetics.pangenome.hapCalling with type arguments of type HaplotypeNode

Modifier and Type	Method and Description
static void	HapCallingUtils.callSNPsFromHaplotypeNodes(List<HaplotypeNode> listOfNodes, HashMap<Integer,String> hapIdToFileNameMapping, String vcfFileDir, String exportVCFFileName, String referenceFileName, String taxonName)
static void	ConvertGBSUtils.countNodesWithW22(List<HaplotypeNode> myNodes)
void	FastqToHapCountPlugin.generateMetrics(com.google.common.collect.Multiset<HaplotypeNode> perfectHitSet, com.google.common.collect.Multiset<HaplotypeNode> exlusionSet)
void	FastqToHapCountPlugin.generateMetrics(com.google.common.collect.Multiset<HaplotypeNode> perfectHitSet, com.google.common.collect.Multiset<HaplotypeNode> exlusionSet)
static List<htsjdk.variant.variantcontext.VariantContext>	HapCallingUtils.getVariantContextFromHaplotypeNodeList(List<HaplotypeNode> nodeList) Method to extract the VCF VariantContexts from a List of HaplotypeNodes
double[]	ConvertGBSToSNPs.probabilityOfBeingCorrect(Map<Integer,Integer> hapidCountMap, TreeMap<ReferenceRange,List<HaplotypeNode>> rangeToNodesMap)
double[]	ConvertGBSToSNPs.probabilityOfBeingCorrect(com.google.common.collect.Multiset<Integer> hapidCounts, TreeMap<ReferenceRange,List<HaplotypeNode>> rangeToNodesMap)
double[]	ConvertGBSToSNPs.startProbabilities(List<HaplotypeNode> nodeList)
void	HapCountBestPathPlugin.writeGraphInfoFilesForChr(String outbase, List<HaplotypeNode> path, HaplotypeGraph graph, Map<Integer,Integer> inclusionMap, Map<Integer,Integer> exclusionMap, net.maizegenetics.dna.map.Chromosome chr, String target)
static void	ConvertGBSUtils.writeNodeStatistics(HaplotypeGraph graph, List<HaplotypeNode> path, Map<Integer,Integer> inclusionCountMap, Map<Integer,Integer> exclusionCountMap, String target)
void	HapCountBestPathPlugin.writePathInformation(String outFilename, List<HaplotypeNode> nodeList, HaplotypeGraph filteredGraph, Map<Integer,Integer> inclusionMap, Map<Integer,Integer> exclusionMap) Method is used to write diagnostic information about a path to a file.

Uses of HaplotypeNode in net.maizegenetics.pangenome.hapcollapse

Method parameters in net.maizegenetics.pangenome.hapcollapse with type arguments of type HaplotypeNode

Modifier and Type	Method and Description
static net.maizegenetics.dna.snp.GenotypeTable	MergeGVCFUtils.createGenotypeTableFromHaplotypeNodes(ReferenceRange refRange, List<HaplotypeNode> nodesWithVariantContexts, net.maizegenetics.dna.map.GenomeSequence referenceSequence) Method to make a genotypeTable from a list of Haplotype Nodes.