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tagCountsByTaxaFile() - function in net.maizegenetics.pangenome.hapCalling.ConvertRampSeqTagsToMapPlugin

File holding the tag counts for each taxa

tagCountsByTaxaFile(String) - function in net.maizegenetics.pangenome.hapCalling.ConvertRampSeqTagsToMapPlugin

Set Tag Count By Taxa File.

tagNodePairCounts(String,HaplotypeGraph,String) - function in net.maizegenetics.pangenome.api.GraphUtils

 

tagToHapIdMapFile() - function in net.maizegenetics.pangenome.hapCalling.ConvertRampSeqTagsToMapPlugin

tagToHapIDMappingFile

tagToHapIdMapFile(String) - function in net.maizegenetics.pangenome.hapCalling.ConvertRampSeqTagsToMapPlugin

Set Hap Id Mapping File.

target() - function in net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin

Name of target in mummer query, this is usually the reference

target(String) - function in net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin

Set Target name.

targetName() - function in net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin

The name of the taxon to which the path will be compared.

targetName(String) - function in net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin

Set Taxon name.

targetTaxon(String) - function in net.maizegenetics.pangenome.hapCalling.ConvertReadsToPathUsingHMM

 

targetTaxon() - function in net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin

The taxon that will be used to evaluate the node list returned.

targetTaxon(String) - function in net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin

Set Target.

targetTaxon() - function in net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin

The taxon that will be used to evaluate the node list returned.

targetTaxon(String) - function in net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin

Set Target.

taxaFilter(TaxaList) - function in net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin

Set Taxa.

taxaFilterList(String) - function in net.maizegenetics.pangenome.hapCalling.ConvertReadsToPathUsingHMM

 

taxaFilterList(TaxaList) - function in net.maizegenetics.pangenome.hapCalling.ConvertReadsToPathUsingHMM

 

taxaFilterString() - function in net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin

A comma delimited list of taxa (no spaces allowed) to include in graph.

taxaFilterString(String) - function in net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin

Set Taxa.

taxaFilterString() - function in net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin

A comma delimited list of taxa (no spaces allowed) to include in graph.

taxaFilterString(String) - function in net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin

Set Taxa.

taxaFilterString() - function in net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin

A list of taxa to include in graph.

taxaInGraph() - function in net.maizegenetics.pangenome.api.HaplotypeGraph

Return all taxa represented in this graph.

taxaInNodes(TreeMap) - function in net.maizegenetics.pangenome.api.CreateGraphUtils

 

taxaInRange(ReferenceRange) - function in net.maizegenetics.pangenome.api.HaplotypeGraph

Returns taxa represented by given reference range.

taxaList() - function in net.maizegenetics.pangenome.api.FilterGraphPlugin

Optional list of taxa to include.

taxaList(String) - function in net.maizegenetics.pangenome.api.FilterGraphPlugin

Set Taxa List.

taxaList(TaxaList) - function in net.maizegenetics.pangenome.api.FilterGraphPlugin

Set Taxa List.

taxaList() - function in net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin

Optional list of taxa to include.

taxaList(String) - function in net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin

 

taxaList(TaxaList) - function in net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin

Set Taxa.

taxaList() - function in net.maizegenetics.pangenome.api.HaplotypeNode

List of taxa used when the consensus sequence was created or a single taxon.

taxaListMap(Connection) - function in net.maizegenetics.pangenome.api.CreateGraphUtils

Retrieves all groups of taxa.

taxon() - function in net.maizegenetics.pangenome.hapCalling.ExportVCForTaxonMethodPlugin

Name of taxon whose variant contexts should be pulled.

taxon(String) - function in net.maizegenetics.pangenome.hapCalling.ExportVCForTaxonMethodPlugin

Set Taxon.

taxon() - function in net.maizegenetics.pangenome.processAssemblyGenomes.ResizeRefBlockPlugin

Name to be assigned for the taxon

taxon(String) - function in net.maizegenetics.pangenome.processAssemblyGenomes.ResizeRefBlockPlugin

Set Taxon Name.

taxonName() - function in net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin

The name of the taxon for which the path is requested.

taxonName(String) - function in net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin

Set Taxon name.

TEST_ANCHOR_HAPLOTYPES - enum entry in net.maizegenetics.pangenome.db_loading.DBLoadingUtils.MethodType

 

TEST_ASSEMBLY_HAPLOTYPES - enum entry in net.maizegenetics.pangenome.db_loading.DBLoadingUtils.MethodType

 

TEST_CONSENSUS_ANCHOR_SEQUENCE - enum entry in net.maizegenetics.pangenome.db_loading.DBLoadingUtils.MethodType

 

TEST_PATHS - enum entry in net.maizegenetics.pangenome.db_loading.DBLoadingUtils.MethodType

 

TEST_READ_MAPPING - enum entry in net.maizegenetics.pangenome.db_loading.DBLoadingUtils.MethodType

 

testChrMatch() - function in net.maizegenetics.pangenome.db_loading.TestPHGStuff

 

testChromLength(String) - function in net.maizegenetics.pangenome.db_loading.TestPHGStuff

 

testDataFrame() - function in net.maizegenetics.pangenome.api.RMethods

A test function to verify that DataFrameVectors works correctly for R

testMafftfromJava() - function in net.maizegenetics.pangenome.db_loading.TestPHGStuff

 

testMatrix() - function in net.maizegenetics.pangenome.api.RMethods

A test function to verify that MatrixWithNames works correctly for R

testObjectAssignment() - function in net.maizegenetics.pangenome.db_loading.TestPHGStuff

 

TestPHGStuff - class in net.maizegenetics.pangenome.db_loading

 

testPythonLD(String,String,String,String) - function in net.maizegenetics.pangenome.db_loading.TestPHGStuff

 

testSortedRange() - function in net.maizegenetics.pangenome.db_loading.TestPHGStuff

 

toBuilder() - function in net.maizegenetics.pangenome.io.Haplotypegraph.GVCFIDToFileProto

 

toBuilder() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeEdgeProto

 

toBuilder() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto

 

toBuilder() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto

 

toBuilder() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeSequenceProto

 

toBuilder() - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProto

 

toByteArray() - function in com.google.protobuf.AbstractMessageLite

 

toByteString() - function in com.google.protobuf.AbstractMessageLite

 

toLong() - function in net.maizegenetics.pangenome.api.HaplotypeNode.VariantInfo

 

toString() - function in com.google.protobuf.AbstractMessage

 

toString() - function in com.google.protobuf.AbstractMessage.Builder

 

toString() - function in net.maizegenetics.pangenome.api.HaplotypeEdge

 

toString() - function in net.maizegenetics.pangenome.api.HaplotypeNode

 

toString() - function in net.maizegenetics.pangenome.api.HaplotypePath

 

toString() - function in net.maizegenetics.pangenome.api.HaplotypeSequence

 

toString() - function in net.maizegenetics.pangenome.api.ReferenceRange

 

toString() - function in net.maizegenetics.pangenome.api.ReferenceRangeEmissionProbability

 

toString() - function in net.maizegenetics.pangenome.db_loading.GeneGFFData

 

totalNumberTaxa() - function in net.maizegenetics.pangenome.api.HaplotypeGraph

Returns total number of taxa represented by this graph

toTextFile(String) - function in net.maizegenetics.pangenome.api.RMethods.DataFrameVectors

 

trace(int) - function in net.maizegenetics.plugindef.AbstractPlugin

 

transitionProbabilitySameTaxon(double) - function in net.maizegenetics.pangenome.hapCalling.ConvertReadsToPathUsingHMM

 

tree(HaplotypeGraph) - function in net.maizegenetics.pangenome.api.CreateGraphUtils

 

tree(Chromosome) - function in net.maizegenetics.pangenome.api.HaplotypeGraph

Creates a sorted (on keys ReferenceRanges) map to list of HaplotypeNodes for given chromosome.

TrimGenotypeTableAnchors - class in net.maizegenetics.pangenome.trimAnchors

Simple class holding utilities to trim a genotype table by identity and coverage thresholds TODO needs to be refractored and have a standardized api Created by zrm22 on 7/6/17.

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