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

Packages that use HaplotypeGraph

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

Uses of HaplotypeGraph in net.maizegenetics.pangenome.api

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

Modifier and Type	Method and Description
static HaplotypeGraph	CreateGraphUtils.addMissingSequenceNodes(HaplotypeGraph graph)
HaplotypeGraph	HaplotypeGraphBuilderPlugin.build()
static HaplotypeGraph	CreateGraphUtils.createHaplotypeNodesWithVariants(Connection database, HaplotypeGraph graph) Creates HaplotypeGraph with variant contexts corresponding to the given HaplotypeGraph.
HaplotypeGraph	FilterGraphPlugin.filter(HaplotypeGraph graph)
static HaplotypeGraph	CreateGraphUtils.keepRefRanges(HaplotypeGraph graph, List<ReferenceRange> ranges) Creates graph that includes specified reference ranges.
static HaplotypeGraph	CreateGraphUtils.nodesSplitByIndividualTaxa(HaplotypeGraph graph, double sameTaxonPercent)
static HaplotypeGraph	CreateGraphUtils.removeRefRanges(HaplotypeGraph graph, double minPercentTaxa) Removes reference ranges from given graph that represent less than given minimum percent of total taxa.
static HaplotypeGraph	CreateGraphUtils.removeRefRanges(HaplotypeGraph graph, int minCountTaxa) Removes reference ranges from given graph that represent less than given minimum number of taxa.
static HaplotypeGraph	CreateGraphUtils.removeRefRanges(HaplotypeGraph graph, List<ReferenceRange> ranges) Removes specified reference ranges from graph.
static HaplotypeGraph	CreateGraphUtils.subsetGraph(HaplotypeGraph graph, net.maizegenetics.taxa.TaxaList taxa) Create graph that's a subset of the given graph which contains only nodes from the taxa list.

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

Modifier and Type	Method and Description
static HaplotypeGraph	CreateGraphUtils.addMissingSequenceNodes(HaplotypeGraph graph)
static HaplotypeGraph	CreateGraphUtils.createHaplotypeNodesWithVariants(Connection database, HaplotypeGraph graph) Creates HaplotypeGraph with variant contexts corresponding to the given HaplotypeGraph.
static int[]	GraphUtils.distributionTaxaRepresented(HaplotypeGraph graph)
HaplotypeGraph	FilterGraphPlugin.filter(HaplotypeGraph graph)
static HaplotypeGraph	CreateGraphUtils.keepRefRanges(HaplotypeGraph graph, List<ReferenceRange> ranges) Creates graph that includes specified reference ranges.
static List<HaplotypeNode>	GraphUtils.nodes(HaplotypeGraph graph, SortedSet<Integer> hapids) Returns a list of HaplotypeNodes corresponding to the given hapids in the given graph.
static List<HaplotypeNode>	GraphUtils.nodesContainingExactly(net.maizegenetics.taxa.TaxaList taxa, HaplotypeGraph graph) Gets list of HaplotypeNodes containing exact list of taxa.
static HaplotypeGraph	CreateGraphUtils.nodesSplitByIndividualTaxa(HaplotypeGraph graph, double sameTaxonPercent)
static void	GraphUtils.nodeTaxaPairs(HaplotypeGraph graph, String filename)
static void	GraphUtils.presenceAbsenceTaxonByNode(HaplotypeGraph graph, String filename)
static HaplotypeGraph	CreateGraphUtils.removeRefRanges(HaplotypeGraph graph, double minPercentTaxa) Removes reference ranges from given graph that represent less than given minimum percent of total taxa.
static HaplotypeGraph	CreateGraphUtils.removeRefRanges(HaplotypeGraph graph, int minCountTaxa) Removes reference ranges from given graph that represent less than given minimum number of taxa.
static HaplotypeGraph	CreateGraphUtils.removeRefRanges(HaplotypeGraph graph, List<ReferenceRange> ranges) Removes specified reference ranges from graph.
static SortedSet<net.maizegenetics.dna.map.Position>	GraphUtils.snpPositions(HaplotypeGraph graph) Return sorted set of positions that are variant (SNP) positions in given graph.
static SortedSet<net.maizegenetics.dna.map.Position>	GraphUtils.snpPositions(HaplotypeGraph graph, Collection<Integer> referenceRanges) Return sorted set of positions that are variant (SNP) positions in given graph.
static HaplotypeGraph	CreateGraphUtils.subsetGraph(HaplotypeGraph graph, net.maizegenetics.taxa.TaxaList taxa) Create graph that's a subset of the given graph which contains only nodes from the taxa list.
static void	GraphUtils.tagNodePairCounts(String tagTaxaFile, HaplotypeGraph graph, String outputFile)
static TreeMap<ReferenceRange,List<HaplotypeNode>>	CreateGraphUtils.tree(HaplotypeGraph graph)
static void	GraphIO.writeAnchorsFasta(HaplotypeGraph graph, String filename) Writes only anchor sequences from HaplotypeNodes in given graph to fasta format.
static void	GraphIO.writeFasta(HaplotypeGraph graph, String filename) Writes all sequences from HaplotypeNodes in given graph to fasta format.
static void	GraphIO.writeFasta(HaplotypeGraph graph, String filename, boolean includeAnchors, boolean includeInnerAnchors)
static void	GraphIO.writeInnerAnchorsFasta(HaplotypeGraph graph, String filename) Writes only inner-anchor sequences from HaplotypeNodes in given graph to fasta format.

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

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

Uses of HaplotypeGraph in net.maizegenetics.pangenome.gui

Methods in net.maizegenetics.pangenome.gui with parameters of type HaplotypeGraph

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

Uses of HaplotypeGraph in net.maizegenetics.pangenome.hapCalling

Methods in net.maizegenetics.pangenome.hapCalling that return HaplotypeGraph

Modifier and Type	Method and Description
static HaplotypeGraph	ConvertGBSUtils.buildHaplotypeGraph()
HaplotypeGraph	ConvertGBSToSNPs.filteredGraph()

Methods in net.maizegenetics.pangenome.hapCalling with parameters of type HaplotypeGraph

Modifier and Type	Method and Description
static void	HapCallingUtils.callSNPsFromHaplotypePath(HaplotypeGraph graph, HaplotypePath bestPath, String vcfFileDir, String exportVCFFileName, String referenceFileName, String taxonName)
List<HaplotypeNode>	ConvertGBSUtils.chooseBestNode(HaplotypeGraph hapgraph, com.google.common.collect.Multiset<Integer> hapidCounts)
static void	ConvertGBSUtils.countW22NodesFullGraph(HaplotypeGraph hapgraph)
static HashMap<Integer,String>	HapCallingUtils.createHapIdToFileNameMapping(HaplotypeGraph graph, String pangenomeDir)
void	ConvertGBSUtils.evaluateOneBestNodeRanges(HaplotypeGraph hapgraph, com.google.common.collect.Multiset<Integer> hapidCounts)
ConvertGBSToSNPs	ConvertGBSToSNPs.filterHaplotypeGraph(HaplotypeGraph hapGraph) This method filters a HaplotypeGraph and sets the myGraph field of the class to the result.
ConvertGBSToSNPs	ConvertGBSToSNPs.filterHaplotypeGraph(HaplotypeGraph hapGraph, List<Integer> rangesToKeep) This method filters a HaplotypeGraph and sets the myGraph field of the class to the result.
static void	ConvertGBSUtils.howManyAnchorsHaveW22InMostFrequentNode(HaplotypeGraph hapgraph, com.google.common.collect.Multiset<Integer> hapidCounts)
static void	ConvertGBSUtils.listTaxa(HaplotypeGraph hapgraph)
static int	ConvertGBSUtils.maxTaxaPerRange(HaplotypeGraph graph)
double[]	ConvertGBSToSNPs.probabilityOfBeingCorrect(HaplotypeGraph hapGraph, com.google.common.collect.Multiset<Integer> hapidCounts)
void	ConvertGBSToSNPs.testHapidCounts(HaplotypeGraph graph, String taxonName)
void	PathToIgraphPlugin.writeGraphInfoAllChr(String outbase, int[] pathids, HaplotypeGraph graph, int[][] inclusionExclusionCounts, String target)
void	PathToIgraphPlugin.writeGraphInfoFilesForChr(String outbase, int[] pathids, HaplotypeGraph graph, Map<Integer,Integer> inclusionMap, Map<Integer,Integer> exclusionMap, net.maizegenetics.dna.map.Chromosome chr, String target)
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 HaplotypeGraph in net.maizegenetics.pangenome.hapcollapse

Methods in net.maizegenetics.pangenome.hapcollapse with parameters of type HaplotypeGraph

Modifier and Type	Method and Description
void	RunHapCollapsePipelinePlugin.runCollapsePipeline(HaplotypeGraph graph, String referenceFasta) This method will loop through each reference range in the graph and will: 1.