Index

_

__init__() (TASSELpy.java.lang.Boolean.Boolean method) (TASSELpy.java.lang.Byte.Byte method) (TASSELpy.java.lang.Comparable.Comparable method) (TASSELpy.java.lang.Double.Double method) (TASSELpy.java.lang.Enum.Enum method) (TASSELpy.java.lang.Enum.enum method) (TASSELpy.java.lang.Float.Float method) (TASSELpy.java.lang.Integer.Integer method) (TASSELpy.java.lang.Iterable.Iterable method) (TASSELpy.java.lang.Long.Long method) (TASSELpy.java.lang.Number.Number method) (TASSELpy.java.lang.Object.Class method) (TASSELpy.java.lang.Object.Object method) (TASSELpy.java.lang.Runnable.Runnable method) (TASSELpy.java.lang.String.String method) (TASSELpy.java.lang.Thread.Thread method) (TASSELpy.java.util.AbstractMap.AbstractMap method) (TASSELpy.java.util.AbstractSequentialList.AbstractSequentialList method) (TASSELpy.java.util.ArrayList.ArrayList method) (TASSELpy.java.util.Collection.Collection method) (TASSELpy.java.util.Collection.metaCollection method) (TASSELpy.java.util.Deque.Deque method) (TASSELpy.java.util.FilterList.FilterList method) (TASSELpy.java.util.HashMap.HashMap method) (TASSELpy.java.util.Iterator.Iterator method) (TASSELpy.java.util.LinkedList.LinkedList method) (TASSELpy.java.util.List.List method) (TASSELpy.java.util.List.metaList method) (TASSELpy.java.util.ListIterator.ListIterator method) (TASSELpy.java.util.Map.Map method) (TASSELpy.java.util.Map.Map.Entry method) (TASSELpy.java.util.Queue.Queue method) (TASSELpy.java.util.Set.Set method) (TASSELpy.javaObj.genericJavaObj method) (TASSELpy.net.maizegenetics.analysis.association.FixedEffectLMPlugin.FixedEffectLMPlugin method) (TASSELpy.net.maizegenetics.analysis.association.FixedEffectLMPlugin.easy_GLM method) (TASSELpy.net.maizegenetics.analysis.data.IntersectionAlignmentPlugin.IntersectionAlignmentPlugin method) (TASSELpy.net.maizegenetics.analysis.data.UnionAlignmentPlugin.UnionAlignmentPlugin method) (TASSELpy.net.maizegenetics.analysis.distance.IBSDistanceMatrix.IBSDistanceMatrix method) (TASSELpy.net.maizegenetics.analysis.distance.Kinship.Kinship method) (TASSELpy.net.maizegenetics.analysis.popgen.LDResult.LDResult method) (TASSELpy.net.maizegenetics.analysis.popgen.LDResult.LDResult.Builder method) (TASSELpy.net.maizegenetics.analysis.popgen.LinkageDisequilibrium.LinkageDisequilibrium method) (TASSELpy.net.maizegenetics.dna.map.Chromosome.Chromosome method) (TASSELpy.net.maizegenetics.dna.map.Position.Position method) (TASSELpy.net.maizegenetics.dna.map.PositionList.PositionList method) (TASSELpy.net.maizegenetics.dna.snp.CoreGenotypeTable.CoreGenotypeTable method) (TASSELpy.net.maizegenetics.dna.snp.FilterGenotypeTable.FilterGenotypeTable method) (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) (TASSELpy.net.maizegenetics.dna.snp.GenotypeTableUtils.GenotypeTableUtils method) (TASSELpy.net.maizegenetics.dna.snp.ImportUtils.ImportUtils method) (TASSELpy.net.maizegenetics.dna.snp.byte2d.Byte2D.Byte2D method) (TASSELpy.net.maizegenetics.dna.snp.depth.AlleleDepth.AlleleDepth method) (TASSELpy.net.maizegenetics.dna.snp.genotypecall.AbstractGenotypeCallTable.AbstractGenotypeCallTable method) (TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable.GenotypeCallTable method) (TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeMergeRule.GenotypeMergeRule method) (TASSELpy.net.maizegenetics.dna.snp.score.AlleleProbability.AlleleProbability method) (TASSELpy.net.maizegenetics.dna.snp.score.Dosage.Dosage method) (TASSELpy.net.maizegenetics.dna.snp.score.ReferenceProbability.ReferenceProbability method) (TASSELpy.net.maizegenetics.dna.snp.score.SiteScore.SiteScore method) (TASSELpy.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix.DoubleMatrix method) (TASSELpy.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixFactory.DoubleMatrixFactory method) (TASSELpy.net.maizegenetics.matrixalgebra.decomposition.EigenvalueDecomposition.EigenvalueDecomposition method) (TASSELpy.net.maizegenetics.matrixalgebra.decomposition.SingularValueDecomposition.SingularValueDecomposition method) (TASSELpy.net.maizegenetics.plugindef.AbstractPlugin.AbstractPlugin method) (TASSELpy.net.maizegenetics.plugindef.Datum.Datum method) (TASSELpy.net.maizegenetics.plugindef.Plugin.DataSet method) (TASSELpy.net.maizegenetics.plugindef.Plugin.Plugin method) (TASSELpy.net.maizegenetics.plugindef.PluginParameter.PluginParameter method) (TASSELpy.net.maizegenetics.stats.statistics.FisherExact.FisherExact method) (TASSELpy.net.maizegenetics.taxa.TaxaList.TaxaList method) (TASSELpy.net.maizegenetics.taxa.TaxaListBuilder.TaxaListBuilder method) (TASSELpy.net.maizegenetics.taxa.Taxon.Taxon method) (TASSELpy.net.maizegenetics.taxa.distance.DistanceMatrix.DistanceMatrix method) (TASSELpy.net.maizegenetics.taxa.distance.TaxaListMatrix.TaxaListMatrix method) (TASSELpy.net.maizegenetics.trait.AbstractPhenotype.AbstractPhenotype method) (TASSELpy.net.maizegenetics.trait.CombinePhenotype.CombinePhenotype method) (TASSELpy.net.maizegenetics.trait.FilterPhenotype.FilterPhenotype method) (TASSELpy.net.maizegenetics.trait.MarkerPhenotype.MarkerPhenotype method) (TASSELpy.net.maizegenetics.trait.MarkerPhenotypeAdapter.MarkerPhenotypeAdapter method) (TASSELpy.net.maizegenetics.trait.Phenotype.Phenotype method) (TASSELpy.net.maizegenetics.trait.ReadPhenotypeUtils.ReadPhenotypeUtils method) (TASSELpy.net.maizegenetics.trait.SimplePhenotype.SimplePhenotype method) (TASSELpy.net.maizegenetics.trait.Trait.Trait method) (TASSELpy.net.maizegenetics.util.GeneralAnnotationStorage.GeneralAnnotationStorage.Builder method) (TASSELpy.net.maizegenetics.util.OpenBitSet.OpenBitSet method) (TASSELpy.net.maizegenetics.util.ProgressListener.ProgressListener method) (TASSELpy.net.maizegenetics.util.TableReport.TableReport method) (TASSELpy.net.maizegenetics.util.UnmodifiableBitSet.UnmodifiableBitSet method) (TASSELpy.test.java.lang.langTestSuite.langTestSuite method) (TASSELpy.test.java.util.utilTestSuite.utilTestSuite method) (TASSELpy.test.mainTestSuite.mainTestSuite method) (TASSELpy.test.net.maizegenetics.analysis.analysisTestSuite.analysisTestSuite method) (TASSELpy.test.net.maizegenetics.analysis.association.associationTestSuite.associationTestSuite method) (TASSELpy.test.net.maizegenetics.analysis.distance.distanceTestSuite.distanceTestSuite method) (TASSELpy.test.net.maizegenetics.analysis.popgen.popgenTestSuite.popgenTestSuite method) (TASSELpy.test.net.maizegenetics.dna.snp.snpTestSuite.snpTestSuite method) (TASSELpy.test.net.maizegenetics.matrixalgebra.Matrix.MatrixTestSuite.MatrixTestSuite method) (TASSELpy.test.net.maizegenetics.matrixalgebra.decomposition.decompositionTestSuite.decompositionTestSuite method) (TASSELpy.test.net.maizegenetics.stats.statistics.statisticsTestSuite.statisticsTestSuite method) (TASSELpy.test.net.maizegenetics.taxa.distance.distanceTestSuite.distanceTestSuite method) (TASSELpy.test.net.maizegenetics.taxa.taxaTestSuite.taxaTestSuite method) (TASSELpy.test.net.maizegenetics.trait.traitTestSuite.traitTestSuite method) (TASSELpy.test.net.maizegenetics.util.utilTestSuite.utilTestSuite method) (TASSELpy.test.utils.utilsTestSuite.utilsTestSuite method) (TASSELpy.utils.DocInherit.DocInherit method) (TASSELpy.utils.OrderedSet.OrderedSet method) (TASSELpy.utils.OrderedSet.lruOrderedSet method) (TASSELpy.utils.Overloading.bidirectional_dict method) (TASSELpy.utils.Overloading.javaConstructorOverload method) (TASSELpy.utils.Overloading.javaGenericOverload method) (TASSELpy.utils.Overloading.javaOverload method) (TASSELpy.utils.Overloading.javaStaticOverload method) (TASSELpy.utils.caching.LRUcache method) (TASSELpy.utils.caching.doubleLinkedList method) (TASSELpy.utils.caching.doubleLinkedListNode method)

A

absoluteDistance() (TASSELpy.net.maizegenetics.taxa.distance.DistanceMatrix.DistanceMatrix method) AbstractGenotypeCallTable (class in TASSELpy.net.maizegenetics.dna.snp.genotypecall.AbstractGenotypeCallTable) AbstractMap (class in TASSELpy.java.util.AbstractMap) AbstractPhenotype (class in TASSELpy.net.maizegenetics.trait.AbstractPhenotype) AbstractPlugin (class in TASSELpy.net.maizegenetics.plugindef.AbstractPlugin) AbstractSequentialList (class in TASSELpy.java.util.AbstractSequentialList) add() (TASSELpy.java.util.ArrayList.ArrayList method) (TASSELpy.java.util.Collection.Collection method) (TASSELpy.java.util.ListIterator.ListIterator method) (TASSELpy.java.util.Queue.Queue method) (TASSELpy.net.maizegenetics.taxa.TaxaListBuilder.TaxaListBuilder method) (TASSELpy.utils.OrderedSet.OrderedSet method) (TASSELpy.utils.OrderedSet.lruOrderedSet method) addAll() (TASSELpy.java.util.Collection.Collection method) (TASSELpy.java.util.LinkedList.LinkedList method) (TASSELpy.net.maizegenetics.taxa.TaxaListBuilder.TaxaListBuilder method) addAnnotation() (TASSELpy.net.maizegenetics.util.GeneralAnnotationStorage.GeneralAnnotationStorage.Builder method) addCovariate() (TASSELpy.net.maizegenetics.analysis.association.FixedEffectLMPlugin.easy_GLM method) addFactor() (TASSELpy.net.maizegenetics.trait.Trait.Trait method) addFirst() (TASSELpy.java.util.Deque.Deque method) addLast() (TASSELpy.java.util.Deque.Deque method) addMarkers() (TASSELpy.net.maizegenetics.analysis.association.FixedEffectLMPlugin.easy_GLM method) addPhenotype() (TASSELpy.net.maizegenetics.analysis.association.FixedEffectLMPlugin.easy_GLM method) ALLELE_SORT_TYPE (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable attribute)

alleleDefinitions() (TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable.GenotypeCallTable method) (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) AlleleDepth (class in TASSELpy.net.maizegenetics.dna.snp.depth.AlleleDepth) allelePresenceForAllSites() (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) allelePresenceForAllTaxa() (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) allelePresenceForSitesBlock() (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) AlleleProbability (class in TASSELpy.net.maizegenetics.dna.snp.score.AlleleProbability) alleles() (TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable.GenotypeCallTable method) (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) allelesBySortType() (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) allelesSortedByFrequency() (TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable.GenotypeCallTable method) (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) analysisTestSuite (class in TASSELpy.test.net.maizegenetics.analysis.analysisTestSuite) andNot() (TASSELpy.net.maizegenetics.util.BitSet.BitSet method) append() (TASSELpy.utils.caching.doubleLinkedList method) areTraitFactorsConsistent() (TASSELpy.net.maizegenetics.trait.MarkerPhenotypeAdapter.MarkerPhenotypeAdapter method) Array (class in TASSELpy.java.lang.reflect.Array) ArrayList (class in TASSELpy.java.util.ArrayList) associationTestSuite (class in TASSELpy.test.net.maizegenetics.analysis.association.associationTestSuite)

B

bidirectional_dict (class in TASSELpy.utils.Overloading) BitSet (class in TASSELpy.net.maizegenetics.util.BitSet) bitStorage() (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) Boolean (class in TASSELpy.java.lang.Boolean) BooleanTest (class in TASSELpy.test.java.lang.BooleanTest)

build() (TASSELpy.net.maizegenetics.analysis.popgen.LDResult.LDResult.Builder method) (TASSELpy.net.maizegenetics.taxa.TaxaListBuilder.TaxaListBuilder method) (TASSELpy.net.maizegenetics.util.GeneralAnnotationStorage.GeneralAnnotationStorage.Builder method) Byte (class in TASSELpy.java.lang.Byte) Byte2D (class in TASSELpy.net.maizegenetics.dna.snp.byte2d.Byte2D) ByteTest (class in TASSELpy.test.java.lang.ByteTest) byteValue() (TASSELpy.java.lang.Number.Number method)

C

calcBitPresenceFromGenotype() (TASSELpy.net.maizegenetics.dna.snp.GenotypeTableUtils.GenotypeTableUtils static method) calculateBitLDForHaplotype() (TASSELpy.net.maizegenetics.analysis.popgen.LinkageDisequilibrium.LinkageDisequilibrium static method) calculateDPrime() (TASSELpy.net.maizegenetics.analysis.popgen.LinkageDisequilibrium.LinkageDisequilibrium static method) calculateRSqr() (TASSELpy.net.maizegenetics.analysis.popgen.LinkageDisequilibrium.LinkageDisequilibrium static method) callBasedOnDepth() (TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeMergeRule.GenotypeMergeRule method) capacity() (TASSELpy.net.maizegenetics.util.BitSet.BitSet method) cardinality() (TASSELpy.net.maizegenetics.util.BitSet.BitSet method) cast() (TASSELpy.java.lang.Object.Class method) castTo() (TASSELpy.java.lang.Object.Object method) checkFactorCovariateEnvironments() (TASSELpy.net.maizegenetics.trait.MarkerPhenotypeAdapter.MarkerPhenotypeAdapter method) chromosomalPosition() (TASSELpy.net.maizegenetics.dna.map.PositionList.PositionList method) (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) Chromosome (class in TASSELpy.net.maizegenetics.dna.map.Chromosome) chromosome() (TASSELpy.net.maizegenetics.dna.map.PositionList.PositionList method) (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) chromosomeName() (TASSELpy.net.maizegenetics.dna.map.PositionList.PositionList method) (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) chromosomes() (TASSELpy.net.maizegenetics.dna.map.PositionList.PositionList method) (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) chromosomeSiteCount() (TASSELpy.net.maizegenetics.dna.map.PositionList.PositionList method) (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) chromosomesOffsets() (TASSELpy.net.maizegenetics.dna.map.PositionList.PositionList method) (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) Class (class in TASSELpy.java.lang.Object) clear() (TASSELpy.java.util.Collection.Collection method) (TASSELpy.java.util.Map.Map method) (TASSELpy.net.maizegenetics.util.BitSet.BitSet method)

clone() (TASSELpy.java.lang.Object.Object method) Collection (class in TASSELpy.java.util.Collection) column() (TASSELpy.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix.DoubleMatrix method) columnRank() (TASSELpy.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix.DoubleMatrix method) columnSum() (TASSELpy.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix.DoubleMatrix method) CombinePhenotype (class in TASSELpy.net.maizegenetics.trait.CombinePhenotype) Comparable (class in TASSELpy.java.lang.Comparable) compareTo() (TASSELpy.java.lang.Boolean.Boolean static method) (TASSELpy.java.lang.Byte.Byte static method) (TASSELpy.java.lang.Comparable.Comparable method) (TASSELpy.java.lang.Double.Double method) (TASSELpy.java.lang.Enum.Enum method) (TASSELpy.java.lang.Float.Float static method) (TASSELpy.java.lang.Integer.Integer static method) (TASSELpy.java.lang.Long.Long static method) compose() (TASSELpy.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixFactory.DoubleMatrixFactory method) compositeAlignments() (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) computeHetBitDistances() (TASSELpy.net.maizegenetics.analysis.distance.IBSDistanceMatrix.IBSDistanceMatrix static method) concatenate() (TASSELpy.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix.DoubleMatrix method) contains() (TASSELpy.java.util.Collection.Collection method) containsAll() (TASSELpy.java.util.Collection.Collection method) containsKey() (TASSELpy.java.util.Map.Map method) containsValue() (TASSELpy.java.util.Map.Map method) copy() (TASSELpy.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix.DoubleMatrix method) CoreGenotypeTable (class in TASSELpy.net.maizegenetics.dna.snp.CoreGenotypeTable) crossproduct() (TASSELpy.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix.DoubleMatrix method)

D

DataSet (class in TASSELpy.net.maizegenetics.plugindef.Plugin) Datum (class in TASSELpy.net.maizegenetics.plugindef.Datum) decompositionTestSuite (class in TASSELpy.test.net.maizegenetics.matrixalgebra.decomposition.decompositionTestSuite) depth() (TASSELpy.net.maizegenetics.dna.snp.depth.AlleleDepth.AlleleDepth method) (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) depthAllSitesByte() (TASSELpy.net.maizegenetics.dna.snp.depth.AlleleDepth.AlleleDepth method) depthForAllele() (TASSELpy.net.maizegenetics.dna.snp.depth.AlleleDepth.AlleleDepth method) depthForAlleleByte() (TASSELpy.net.maizegenetics.dna.snp.depth.AlleleDepth.AlleleDepth method) depthForAlleles() (TASSELpy.net.maizegenetics.dna.snp.depth.AlleleDepth.AlleleDepth method) (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) depthForSite() (TASSELpy.net.maizegenetics.dna.snp.depth.AlleleDepth.AlleleDepth method) depthForTaxon() (TASSELpy.net.maizegenetics.dna.snp.depth.AlleleDepth.AlleleDepth method) Deque (class in TASSELpy.java.util.Deque) descendingIterator() (TASSELpy.java.util.Deque.Deque method) diagonal() (TASSELpy.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixFactory.DoubleMatrixFactory method) diploidAsString() (TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable.GenotypeCallTable method) (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) discard() (TASSELpy.utils.OrderedSet.OrderedSet method) DistanceMatrix (class in TASSELpy.net.maizegenetics.taxa.distance.DistanceMatrix) DistanceMatrixTest (class in TASSELpy.test.net.maizegenetics.taxa.distance.DistanceMatrixTest)

distanceTestSuite (class in TASSELpy.test.net.maizegenetics.analysis.distance.distanceTestSuite) (class in TASSELpy.test.net.maizegenetics.taxa.distance.distanceTestSuite) doc_inherit (in module TASSELpy.utils.DocInherit) DocInherit (class in TASSELpy.utils.DocInherit) Dosage (class in TASSELpy.net.maizegenetics.dna.snp.score.Dosage) Double (class in TASSELpy.java.lang.Double) doubleFromCharacterTrait() (TASSELpy.net.maizegenetics.trait.ReadPhenotypeUtils.ReadPhenotypeUtils static method) doubleLinkedList (class in TASSELpy.utils.caching) doubleLinkedListNode (class in TASSELpy.utils.caching) doubleLinkedListTest (class in TASSELpy.test.utils.cachingTest) DoubleMatrix (class in TASSELpy.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix) DoubleMatrixFactory (class in TASSELpy.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixFactory) DoubleMatrixFactoryTest (class in TASSELpy.test.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixFactoryTest) DoubleMatrixTest (class in TASSELpy.test.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixTest) DoubleTest (class in TASSELpy.test.java.lang.DoubleTest) doubleValue() (TASSELpy.java.lang.Number.Number method) dPrime() (TASSELpy.net.maizegenetics.analysis.popgen.LDResult.LDResult method) dprime() (TASSELpy.net.maizegenetics.analysis.popgen.LDResult.LDResult.Builder method)

E

easy_GLM (class in TASSELpy.net.maizegenetics.analysis.association.FixedEffectLMPlugin) easy_GLMTest (class in TASSELpy.test.net.maizegenetics.analysis.association.FixedEffectLMPlugin) EigenvalueDecomposition (class in TASSELpy.net.maizegenetics.matrixalgebra.decomposition.EigenvalueDecomposition) EigenvalueDecompositionTest (class in TASSELpy.test.net.maizegenetics.matrixalgebra.decomposition.EigenvalueDecompositionTest) element() (TASSELpy.java.util.Queue.Queue method) ensureCapacity() (TASSELpy.net.maizegenetics.util.BitSet.BitSet method)

ensureCapacityWords() (TASSELpy.net.maizegenetics.util.BitSet.BitSet method) entrySet() (TASSELpy.java.util.Map.Map method) Enum (class in TASSELpy.java.lang.Enum) enum (class in TASSELpy.java.lang.Enum) equals() (TASSELpy.java.lang.Enum.Enum method) (TASSELpy.java.lang.Object.Object method)

F

FactoryType (TASSELpy.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixFactory.DoubleMatrixFactory attribute) fastClear() (TASSELpy.net.maizegenetics.util.BitSet.BitSet method) fastFlip() (TASSELpy.net.maizegenetics.util.BitSet.BitSet method) fastGet() (TASSELpy.net.maizegenetics.util.BitSet.BitSet method) fastSet() (TASSELpy.net.maizegenetics.util.BitSet.BitSet method) filterEnumerator() (TASSELpy.java.util.FilterList.FilterList method) FilterGenotypeTable (class in TASSELpy.net.maizegenetics.dna.snp.FilterGenotypeTable) filterIterator() (TASSELpy.java.util.FilterList.FilterList method) FilterList (class in TASSELpy.java.util.FilterList) FilterPhenotype (class in TASSELpy.net.maizegenetics.trait.FilterPhenotype)

firstLastSiteOfChromosome() (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) FisherExact (class in TASSELpy.net.maizegenetics.stats.statistics.FisherExact) FisherExactTest (class in TASSELpy.test.net.maizegenetics.stats.statistics.FisherExactTest) FixedEffectLMPlugin (class in TASSELpy.net.maizegenetics.analysis.association.FixedEffectLMPlugin) flip() (TASSELpy.net.maizegenetics.util.BitSet.BitSet method) flipAndGet() (TASSELpy.net.maizegenetics.util.BitSet.BitSet method) Float (class in TASSELpy.java.lang.Float) FloatTest (class in TASSELpy.test.java.lang.FloatTest) floatValue() (TASSELpy.java.lang.Number.Number method) functionalFilters() (TASSELpy.net.maizegenetics.dna.snp.FilterGenotypeTable.FilterGenotypeTable static method)

G

GeneralAnnotation (class in TASSELpy.net.maizegenetics.util.GeneralAnnotation) GeneralAnnotationStorage (class in TASSELpy.net.maizegenetics.util.GeneralAnnotationStorage) GeneralAnnotationStorage.Builder (class in TASSELpy.net.maizegenetics.util.GeneralAnnotationStorage) generalizedInverse() (TASSELpy.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix.DoubleMatrix method) generalizedInverseWithRank() (TASSELpy.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix.DoubleMatrix method) genericJavaObj (class in TASSELpy.javaObj) genericJavaObjTest (class in TASSELpy.test.javaObjTest) genoCounts() (TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable.GenotypeCallTable method) (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) genomeVersion() (TASSELpy.net.maizegenetics.dna.map.PositionList.PositionList method) (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) genosSortedByFrequency() (TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable.GenotypeCallTable method) (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) genotype() (TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable.GenotypeCallTable method) (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) genotypeAllSites() (TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable.GenotypeCallTable method) (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) genotypeAllTaxa() (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) genotypeArray() (TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable.GenotypeCallTable method) (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) genotypeAsString() (TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable.GenotypeCallTable method) (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) genotypeAsStringArray() (TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable.GenotypeCallTable method) (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) genotypeAsStringRange() (TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable.GenotypeCallTable method) (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) genotypeAsStringRow() (TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable.GenotypeCallTable method) (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) GenotypeCallTable (class in TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable) genotypeForAllSites() (TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable.GenotypeCallTable method) genotypeForAllTaxa() (TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable.GenotypeCallTable method) genotypeForSiteRange() (TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable.GenotypeCallTable method) genotypeMatrix() (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) GenotypeMergeRule (class in TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeMergeRule) genotypeRange() (TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable.GenotypeCallTable method) (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) GenotypeTable (class in TASSELpy.net.maizegenetics.dna.snp.GenotypeTable) GenotypeTableTest (class in TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest) GenotypeTableUtils (class in TASSELpy.net.maizegenetics.dna.snp.GenotypeTableUtils) get() (TASSELpy.java.lang.reflect.Array.Array static method) (TASSELpy.java.util.List.List method) (TASSELpy.java.util.Map.Map method) (TASSELpy.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix.DoubleMatrix method) (TASSELpy.net.maizegenetics.util.BitSet.BitSet method) get_array_type() (TASSELpy.javaObj.javaArray static method) (TASSELpy.utils.primativeArray.javaPrimativeArray static method) get_no_inst() (TASSELpy.utils.DocInherit.DocInherit method) get_with_inst() (TASSELpy.utils.DocInherit.DocInherit method) getAlignment() (TASSELpy.net.maizegenetics.analysis.popgen.LinkageDisequilibrium.LinkageDisequilibrium method) (TASSELpy.net.maizegenetics.trait.MarkerPhenotype.MarkerPhenotype method) getAllAnnotationEntries() (TASSELpy.net.maizegenetics.util.GeneralAnnotation.GeneralAnnotation method) getAllele() (TASSELpy.net.maizegenetics.dna.map.Position.Position method) getAlleles() (TASSELpy.net.maizegenetics.dna.snp.GenotypeTableUtils.GenotypeTableUtils static method) getAllelesSortedByFrequency() (TASSELpy.net.maizegenetics.dna.snp.GenotypeTableUtils.GenotypeTableUtils static method) getAlleleStates() (TASSELpy.net.maizegenetics.dna.snp.GenotypeTableUtils.GenotypeTableUtils static method) getAndSet() (TASSELpy.net.maizegenetics.util.BitSet.BitSet method) getAnnotation() (TASSELpy.net.maizegenetics.util.GeneralAnnotation.GeneralAnnotation method) getAnnotationAsMap() (TASSELpy.net.maizegenetics.util.GeneralAnnotation.GeneralAnnotation method) getArray() (TASSELpy.java.lang.String.String class method) (TASSELpy.javaObj.javaObj class method) getAverageAnnotation() (TASSELpy.net.maizegenetics.util.GeneralAnnotation.GeneralAnnotation method) getAverageTotalSites() (TASSELpy.net.maizegenetics.analysis.distance.IBSDistanceMatrix.IBSDistanceMatrix method) getBaseAlignment() (TASSELpy.net.maizegenetics.dna.snp.FilterGenotypeTable.FilterGenotypeTable method) getBaseSitesShown() (TASSELpy.net.maizegenetics.dna.snp.FilterGenotypeTable.FilterGenotypeTable method) getBit() (TASSELpy.net.maizegenetics.util.BitSet.BitSet method) getBits() (TASSELpy.net.maizegenetics.util.BitSet.BitSet method) getBoolean() (TASSELpy.java.lang.reflect.Array.Array static method) getBuilder() (TASSELpy.net.maizegenetics.util.GeneralAnnotationStorage.GeneralAnnotationStorage static method) getByte() (TASSELpy.java.lang.reflect.Array.Array static method) getCanonicalChromosome() (TASSELpy.net.maizegenetics.dna.map.Chromosome.Chromosome static method) getChar() (TASSELpy.java.lang.reflect.Array.Array static method) getChecked() (TASSELpy.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix.DoubleMatrix method) getChromosome() (TASSELpy.net.maizegenetics.dna.map.Position.Position method) getChromosomeNumber() (TASSELpy.net.maizegenetics.dna.map.Chromosome.Chromosome method) getCitation() (TASSELpy.net.maizegenetics.plugindef.Plugin.Plugin method) getClass() (TASSELpy.java.lang.Object.Object method) getClonedDistances() (TASSELpy.net.maizegenetics.taxa.distance.TaxaListMatrix.TaxaListMatrix method) getClosestIndex() (TASSELpy.net.maizegenetics.taxa.distance.DistanceMatrix.DistanceMatrix method) getCM() (TASSELpy.net.maizegenetics.dna.map.Position.Position method) getColumnCount() (TASSELpy.net.maizegenetics.util.TableReport.TableReport method) getColumnName() (TASSELpy.net.maizegenetics.taxa.distance.DistanceMatrix.DistanceMatrix method) getComment() (TASSELpy.net.maizegenetics.plugindef.Datum.Datum method) getConsensusAnnotation() (TASSELpy.net.maizegenetics.util.GeneralAnnotation.GeneralAnnotation method) getCovariateName() (TASSELpy.net.maizegenetics.trait.MarkerPhenotypeAdapter.MarkerPhenotypeAdapter method) getCovariateValues() (TASSELpy.net.maizegenetics.trait.MarkerPhenotypeAdapter.MarkerPhenotypeAdapter method) getCreator() (TASSELpy.net.maizegenetics.plugindef.Plugin.DataSet method) getCumulativeP() (TASSELpy.net.maizegenetics.stats.statistics.FisherExact.FisherExact method) getData() (TASSELpy.net.maizegenetics.plugindef.Datum.Datum method) (TASSELpy.net.maizegenetics.plugindef.Plugin.DataSet method) (TASSELpy.net.maizegenetics.trait.Phenotype.Phenotype method) getDataBytes() (TASSELpy.net.maizegenetics.dna.snp.GenotypeTableUtils.GenotypeTableUtils static method) getDataOfType() (TASSELpy.net.maizegenetics.plugindef.Plugin.DataSet method) getDataOfTypeWithName() (TASSELpy.net.maizegenetics.plugindef.Plugin.DataSet method) getDataSet() (TASSELpy.net.maizegenetics.plugindef.Plugin.DataSet method) getDataType() (TASSELpy.net.maizegenetics.plugindef.Datum.Datum method) getDataWithName() (TASSELpy.net.maizegenetics.plugindef.Plugin.DataSet method) getDblArray() (TASSELpy.java.lang.String.String class method) (TASSELpy.javaObj.javaObj class method) getDiploidsSortedByFrequency() (TASSELpy.net.maizegenetics.dna.snp.GenotypeTableUtils.GenotypeTableUtils static method) getDiploidValue() (TASSELpy.net.maizegenetics.dna.snp.GenotypeTableUtils.GenotypeTableUtils static method) getDiploidValuePhased() (TASSELpy.net.maizegenetics.dna.snp.GenotypeTableUtils.GenotypeTableUtils static method) getDiploidValues() (TASSELpy.net.maizegenetics.dna.snp.GenotypeTableUtils.GenotypeTableUtils static method) getDistance() (TASSELpy.net.maizegenetics.taxa.distance.TaxaListMatrix.TaxaListMatrix method) getDistances() (TASSELpy.net.maizegenetics.taxa.distance.DistanceMatrix.DistanceMatrix method) getDm() (TASSELpy.net.maizegenetics.analysis.distance.Kinship.Kinship method) getDouble() (TASSELpy.java.lang.reflect.Array.Array static method) getDPrime() (TASSELpy.net.maizegenetics.analysis.popgen.LinkageDisequilibrium.LinkageDisequilibrium method) getEigenvalue() (TASSELpy.net.maizegenetics.matrixalgebra.decomposition.EigenvalueDecomposition.EigenvalueDecomposition method) getEigenvalueDecomposition() (TASSELpy.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix.DoubleMatrix method) getEigenvalueMatrix() (TASSELpy.net.maizegenetics.matrixalgebra.decomposition.EigenvalueDecomposition.EigenvalueDecomposition method) getEigenvalues() (TASSELpy.net.maizegenetics.matrixalgebra.decomposition.EigenvalueDecomposition.EigenvalueDecomposition method) getEigenvectors() (TASSELpy.net.maizegenetics.matrixalgebra.decomposition.EigenvalueDecomposition.EigenvalueDecomposition method) getElement() (TASSELpy.utils.caching.doubleLinkedListNode method) getElementCount() (TASSELpy.net.maizegenetics.util.TableReport.TableReport method) getFactorName() (TASSELpy.net.maizegenetics.trait.MarkerPhenotypeAdapter.MarkerPhenotypeAdapter method)

getFactorNames() (TASSELpy.net.maizegenetics.trait.Trait.Trait method) getFactorValue() (TASSELpy.net.maizegenetics.trait.Trait.Trait method) getFactorValues() (TASSELpy.net.maizegenetics.trait.MarkerPhenotypeAdapter.MarkerPhenotypeAdapter method) getFirst() (TASSELpy.java.util.Deque.Deque method) (TASSELpy.utils.caching.doubleLinkedList method) getFloat() (TASSELpy.java.lang.reflect.Array.Array static method) getGlobalMAF() (TASSELpy.net.maizegenetics.dna.map.Position.Position method) getGlobalSiteCoverage() (TASSELpy.net.maizegenetics.dna.map.Position.Position method) getIncludedSitesBasedOnFreqIgnoreMissing() (TASSELpy.net.maizegenetics.dna.snp.GenotypeTableUtils.GenotypeTableUtils static method) getIndicesOfSetBits() (TASSELpy.net.maizegenetics.util.BitSet.BitSet method) getInputs() (TASSELpy.net.maizegenetics.plugindef.AbstractPlugin.AbstractPlugin method) getInstance() (TASSELpy.net.maizegenetics.dna.snp.FilterGenotypeTable.FilterGenotypeTable static method) (TASSELpy.net.maizegenetics.trait.CombinePhenotype.CombinePhenotype static method) (TASSELpy.net.maizegenetics.trait.FilterPhenotype.FilterPhenotype static method) (TASSELpy.net.maizegenetics.trait.MarkerPhenotype.MarkerPhenotype static method) (TASSELpy.net.maizegenetics.trait.Trait.Trait static method) (TASSELpy.net.maizegenetics.util.UnmodifiableBitSet.UnmodifiableBitSet static method) getInstanceRemoveIDs() (TASSELpy.net.maizegenetics.dna.snp.FilterGenotypeTable.FilterGenotypeTable static method) (TASSELpy.net.maizegenetics.trait.FilterPhenotype.FilterPhenotype static method) getInstanceRemoveSiteNames() (TASSELpy.net.maizegenetics.dna.snp.FilterGenotypeTable.FilterGenotypeTable static method) getInt() (TASSELpy.java.lang.reflect.Array.Array static method) getKey() (TASSELpy.java.util.Map.Map.Entry method) getKnownVariants() (TASSELpy.net.maizegenetics.dna.map.Position.Position method) getLast() (TASSELpy.java.util.Deque.Deque method) (TASSELpy.utils.caching.doubleLinkedList method) getLDForSitePair() (TASSELpy.net.maizegenetics.analysis.popgen.LinkageDisequilibrium.LinkageDisequilibrium static method) getLeftTailedP() (TASSELpy.net.maizegenetics.stats.statistics.FisherExact.FisherExact method) getLength() (TASSELpy.java.lang.reflect.Array.Array static method) (TASSELpy.net.maizegenetics.dna.map.Chromosome.Chromosome method) getLevelLabel() (TASSELpy.net.maizegenetics.trait.Trait.Trait method) getLevelLabels() (TASSELpy.net.maizegenetics.trait.Trait.Trait method) getLocusName() (TASSELpy.net.maizegenetics.trait.MarkerPhenotypeAdapter.MarkerPhenotypeAdapter method) getLocusPosition() (TASSELpy.net.maizegenetics.trait.MarkerPhenotypeAdapter.MarkerPhenotypeAdapter method) getLong() (TASSELpy.java.lang.reflect.Array.Array static method) getMarkerChromosome() (TASSELpy.net.maizegenetics.trait.MarkerPhenotypeAdapter.MarkerPhenotypeAdapter method) getMarkerChromosomePosition() (TASSELpy.net.maizegenetics.trait.MarkerPhenotypeAdapter.MarkerPhenotypeAdapter method) getMarkerName() (TASSELpy.net.maizegenetics.trait.MarkerPhenotypeAdapter.MarkerPhenotypeAdapter method) getMarkerValue() (TASSELpy.net.maizegenetics.trait.MarkerPhenotypeAdapter.MarkerPhenotypeAdapter method) getMissingCovariates() (TASSELpy.net.maizegenetics.trait.MarkerPhenotypeAdapter.MarkerPhenotypeAdapter method) getMissingFactors() (TASSELpy.net.maizegenetics.trait.MarkerPhenotypeAdapter.MarkerPhenotypeAdapter method) getMissingMarkers() (TASSELpy.net.maizegenetics.trait.MarkerPhenotypeAdapter.MarkerPhenotypeAdapter method) getMissingPhenotypes() (TASSELpy.net.maizegenetics.trait.MarkerPhenotypeAdapter.MarkerPhenotypeAdapter method) getName() (TASSELpy.java.lang.Object.Class method) (TASSELpy.net.maizegenetics.dna.map.Chromosome.Chromosome method) (TASSELpy.net.maizegenetics.plugindef.Datum.Datum method) (TASSELpy.net.maizegenetics.taxa.Taxon.Taxon method) (TASSELpy.net.maizegenetics.trait.Trait.Trait method) getNumberOfBlocks() (TASSELpy.net.maizegenetics.trait.MarkerPhenotypeAdapter.MarkerPhenotypeAdapter method) getNumberOfCovariates() (TASSELpy.net.maizegenetics.trait.MarkerPhenotypeAdapter.MarkerPhenotypeAdapter method) getNumberOfFactors() (TASSELpy.net.maizegenetics.trait.MarkerPhenotypeAdapter.MarkerPhenotypeAdapter method) (TASSELpy.net.maizegenetics.trait.Trait.Trait method) getNumberOfLevels() (TASSELpy.net.maizegenetics.trait.Trait.Trait method) getNumberOfMarkers() (TASSELpy.net.maizegenetics.trait.MarkerPhenotypeAdapter.MarkerPhenotypeAdapter method) getNumberOfPhenotypes() (TASSELpy.net.maizegenetics.trait.MarkerPhenotypeAdapter.MarkerPhenotypeAdapter method) getNumberOfProperties() (TASSELpy.net.maizegenetics.trait.Trait.Trait method) getNumberOfRows() (TASSELpy.net.maizegenetics.trait.MarkerPhenotypeAdapter.MarkerPhenotypeAdapter method) getNumberOfTaxa() (TASSELpy.net.maizegenetics.trait.Phenotype.Phenotype method) getNumberOfTraits() (TASSELpy.net.maizegenetics.trait.Phenotype.Phenotype method) getNumWords() (TASSELpy.net.maizegenetics.util.BitSet.BitSet method) getP() (TASSELpy.net.maizegenetics.stats.statistics.FisherExact.FisherExact method) getParameter() (TASSELpy.net.maizegenetics.plugindef.Plugin.Plugin method) getPhenotype() (TASSELpy.net.maizegenetics.trait.MarkerPhenotype.MarkerPhenotype method) getPhenotypeName() (TASSELpy.net.maizegenetics.trait.MarkerPhenotypeAdapter.MarkerPhenotypeAdapter method) getPhenotypeValues() (TASSELpy.net.maizegenetics.trait.MarkerPhenotypeAdapter.MarkerPhenotypeAdapter method) getPosition() (TASSELpy.net.maizegenetics.dna.map.Position.Position method) getPredecessor() (TASSELpy.utils.caching.doubleLinkedListNode method) getProperties() (TASSELpy.net.maizegenetics.trait.Trait.Trait method) getProperty() (TASSELpy.net.maizegenetics.trait.Trait.Trait method) getPropertyNames() (TASSELpy.net.maizegenetics.trait.Trait.Trait method) getPval() (TASSELpy.net.maizegenetics.analysis.popgen.LinkageDisequilibrium.LinkageDisequilibrium method) getQuantAnnotation() (TASSELpy.net.maizegenetics.util.GeneralAnnotation.GeneralAnnotation method) getRank() (TASSELpy.net.maizegenetics.matrixalgebra.decomposition.SingularValueDecomposition.SingularValueDecomposition method) getRightTailedP() (TASSELpy.net.maizegenetics.stats.statistics.FisherExact.FisherExact method) getRightTailedPQuick() (TASSELpy.net.maizegenetics.stats.statistics.FisherExact.FisherExact method) getRow() (TASSELpy.net.maizegenetics.util.TableReport.TableReport method) getRowCount() (TASSELpy.net.maizegenetics.util.TableReport.TableReport method) getRSqr() (TASSELpy.net.maizegenetics.analysis.popgen.LinkageDisequilibrium.LinkageDisequilibrium method) getS() (TASSELpy.net.maizegenetics.matrixalgebra.decomposition.SingularValueDecomposition.SingularValueDecomposition method) getSampleSize() (TASSELpy.net.maizegenetics.analysis.popgen.LinkageDisequilibrium.LinkageDisequilibrium method) getSelection() (TASSELpy.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix.DoubleMatrix method) getShort() (TASSELpy.java.lang.reflect.Array.Array static method) getSingularValueDecomposition() (TASSELpy.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix.DoubleMatrix method) getSingularValues() (TASSELpy.net.maizegenetics.matrixalgebra.decomposition.SingularValueDecomposition.SingularValueDecomposition method) getSiteCount() (TASSELpy.net.maizegenetics.analysis.popgen.LinkageDisequilibrium.LinkageDisequilibrium method) getSize() (TASSELpy.net.maizegenetics.plugindef.Plugin.DataSet method) (TASSELpy.net.maizegenetics.taxa.distance.TaxaListMatrix.TaxaListMatrix method) getSNPID() (TASSELpy.net.maizegenetics.dna.map.Position.Position method) getStrand() (TASSELpy.net.maizegenetics.dna.map.Position.Position method) getSuccessor() (TASSELpy.utils.caching.doubleLinkedListNode method) getTableColumnNames() (TASSELpy.net.maizegenetics.util.TableReport.TableReport method) getTableTitle() (TASSELpy.net.maizegenetics.util.TableReport.TableReport method) getTaxa() (TASSELpy.net.maizegenetics.trait.MarkerPhenotypeAdapter.MarkerPhenotypeAdapter method) (TASSELpy.net.maizegenetics.trait.Phenotype.Phenotype method) getTaxaList() (TASSELpy.net.maizegenetics.taxa.distance.TaxaListMatrix.TaxaListMatrix method) getTaxon() (TASSELpy.net.maizegenetics.taxa.distance.DistanceMatrix.DistanceMatrix method) (TASSELpy.net.maizegenetics.trait.Phenotype.Phenotype method) getTextAnnotation() (TASSELpy.net.maizegenetics.util.GeneralAnnotation.GeneralAnnotation method) getTrait() (TASSELpy.net.maizegenetics.trait.Phenotype.Phenotype method) getTraits() (TASSELpy.net.maizegenetics.trait.Phenotype.Phenotype method) getTwoTailedP() (TASSELpy.net.maizegenetics.stats.statistics.FisherExact.FisherExact method) getType() (TASSELpy.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixFactory.DoubleMatrixFactory method) (TASSELpy.net.maizegenetics.trait.Trait.Trait method) getU() (TASSELpy.net.maizegenetics.matrixalgebra.decomposition.SingularValueDecomposition.SingularValueDecomposition method) getUnphasedDiploidValue() (TASSELpy.net.maizegenetics.dna.snp.GenotypeTableUtils.GenotypeTableUtils static method) getUnphasedDiploidValueNoHets() (TASSELpy.net.maizegenetics.dna.snp.GenotypeTableUtils.GenotypeTableUtils static method) getV() (TASSELpy.net.maizegenetics.matrixalgebra.decomposition.SingularValueDecomposition.SingularValueDecomposition method) getValue() (TASSELpy.java.util.Map.Map.Entry method) getValueAt() (TASSELpy.net.maizegenetics.util.TableReport.TableReport method) getX() (TASSELpy.net.maizegenetics.analysis.popgen.LinkageDisequilibrium.LinkageDisequilibrium method) getXtXGM() (TASSELpy.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix.DoubleMatrix method) getY() (TASSELpy.net.maizegenetics.analysis.popgen.LinkageDisequilibrium.LinkageDisequilibrium method)

H

haplotypeAllelePresenceForAllSites() (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) haplotypeAllelePresenceForAllTaxa() (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) haplotypeAllelePresenceForSitesBlock() (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) hasAlleleProbabilities() (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) hasDepth() (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) hashCode() (TASSELpy.java.lang.Object.Object method) HashMap (class in TASSELpy.java.util.HashMap) hasLevels() (TASSELpy.net.maizegenetics.trait.Trait.Trait method)

hasMarkerNames() (TASSELpy.net.maizegenetics.trait.MarkerPhenotypeAdapter.MarkerPhenotypeAdapter method) hasNext() (TASSELpy.java.util.Iterator.Iterator method) hasPrevious() (TASSELpy.java.util.ListIterator.ListIterator method) hasReference() (TASSELpy.net.maizegenetics.dna.map.PositionList.PositionList method) (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) hasSiteScores() (TASSELpy.net.maizegenetics.dna.snp.score.SiteScore.SiteScore method) heterozygousCount() (TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable.GenotypeCallTable method) (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) heterozygousCountForTaxon() (TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable.GenotypeCallTable method) (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) HetTreatment (TASSELpy.net.maizegenetics.analysis.popgen.LinkageDisequilibrium.LinkageDisequilibrium attribute)

I

IBSDistanceMatrix (class in TASSELpy.net.maizegenetics.analysis.distance.IBSDistanceMatrix) IBSDistanceMatrixTest (class in TASSELpy.test.net.maizegenetics.analysis.IBSDistanceMatrixTest) identity() (TASSELpy.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixFactory.DoubleMatrixFactory method) ImportUtils (class in TASSELpy.net.maizegenetics.dna.snp.ImportUtils) indelSize() (TASSELpy.net.maizegenetics.dna.map.PositionList.PositionList method) (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) indexOf() (TASSELpy.java.util.List.List method) (TASSELpy.net.maizegenetics.taxa.TaxaList.TaxaList method) indexOfNthSetBit() (TASSELpy.net.maizegenetics.util.BitSet.BitSet method) Integer (class in TASSELpy.java.lang.Integer) IntegerTest (class in TASSELpy.test.java.lang.IntegerTest) intersect() (TASSELpy.net.maizegenetics.util.BitSet.BitSet method) IntersectionAlignmentPlugin (class in TASSELpy.net.maizegenetics.analysis.data.IntersectionAlignmentPlugin) intersects() (TASSELpy.net.maizegenetics.util.BitSet.BitSet method) intValue() (TASSELpy.java.lang.Number.Number method) inverse() (TASSELpy.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix.DoubleMatrix method) invert() (TASSELpy.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix.DoubleMatrix method) isAllPolymorphic() (TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable.GenotypeCallTable method) (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) isDiscrete() (TASSELpy.net.maizegenetics.trait.Trait.Trait method) isEmpty() (TASSELpy.java.util.Collection.Collection method) (TASSELpy.java.util.Map.Map method) (TASSELpy.net.maizegenetics.util.BitSet.BitSet method) isEqual() (TASSELpy.net.maizegenetics.dna.snp.GenotypeTableUtils.GenotypeTableUtils static method) isEqualOrUnknown() (TASSELpy.net.maizegenetics.dna.snp.GenotypeTableUtils.GenotypeTableUtils static method)

isHeterozygous() (TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable.GenotypeCallTable method) (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) (TASSELpy.net.maizegenetics.dna.snp.GenotypeTableUtils.GenotypeTableUtils static method) isIndel() (TASSELpy.net.maizegenetics.dna.map.Position.Position method) (TASSELpy.net.maizegenetics.dna.map.PositionList.PositionList method) (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) isInteractive() (TASSELpy.net.maizegenetics.plugindef.Plugin.Plugin method) isMarkerDiscrete() (TASSELpy.net.maizegenetics.trait.MarkerPhenotypeAdapter.MarkerPhenotypeAdapter method) isMergePossible() (TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeMergeRule.GenotypeMergeRule method) isNucleotide() (TASSELpy.net.maizegenetics.dna.map.Position.Position method) isPartiallyEqual() (TASSELpy.net.maizegenetics.dna.snp.GenotypeTableUtils.GenotypeTableUtils static method) isPhased() (TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable.GenotypeCallTable method) (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) isPolymorphic() (TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable.GenotypeCallTable method) (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) isPositiveStrand() (TASSELpy.net.maizegenetics.dna.map.PositionList.PositionList method) (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) isPrimitive() (TASSELpy.java.lang.Object.Class method) isSiteFilter() (TASSELpy.net.maizegenetics.dna.snp.FilterGenotypeTable.FilterGenotypeTable method) isSiteFilterByRange() (TASSELpy.net.maizegenetics.dna.snp.FilterGenotypeTable.FilterGenotypeTable method) isSymmetric() (TASSELpy.net.maizegenetics.taxa.distance.TaxaListMatrix.TaxaListMatrix method) isTaxaFilter() (TASSELpy.net.maizegenetics.dna.snp.FilterGenotypeTable.FilterGenotypeTable method) isTrueIBS() (TASSELpy.net.maizegenetics.analysis.distance.IBSDistanceMatrix.IBSDistanceMatrix method) Iterable (class in TASSELpy.java.lang.Iterable) Iterator (class in TASSELpy.java.util.Iterator) iterator() (TASSELpy.java.lang.Iterable.Iterable method)

J

java_arr_type (TASSELpy.utils.primativeArray.meta_byte_array attribute) (TASSELpy.utils.primativeArray.meta_double_array attribute) (TASSELpy.utils.primativeArray.meta_float_array attribute) (TASSELpy.utils.primativeArray.meta_int_array attribute) (TASSELpy.utils.primativeArray.meta_long_array attribute) javaArray (class in TASSELpy.javaObj) javaArrayTest (class in TASSELpy.test.javaObjTest) javaConstructorOverload (class in TASSELpy.utils.Overloading) javaGenericOverload (class in TASSELpy.utils.Overloading)

javaObj (class in TASSELpy.javaObj) javaObjTest (class in TASSELpy.test.javaObjTest) javaOverload (class in TASSELpy.utils.Overloading) javaPrimativeArray (class in TASSELpy.utils.primativeArray) javaStaticOverload (class in TASSELpy.utils.Overloading)

K

keySet() (TASSELpy.java.util.Map.Map method) Kinship (class in TASSELpy.net.maizegenetics.analysis.distance.Kinship)

KinshipTest (class in TASSELpy.test.net.maizegenetics.analysis.distance.KinshipTest)

L

langTestSuite (class in TASSELpy.test.java.lang.langTestSuite) lastIndexOf() (TASSELpy.java.util.List.List method) LDResult (class in TASSELpy.net.maizegenetics.analysis.popgen.LDResult) LDResult.Builder (class in TASSELpy.net.maizegenetics.analysis.popgen.LDResult) LDResultTest (class in TASSELpy.test.net.maizegenetics.analysis.popgen.LDResultTest) LinkageDisequilibrium (class in TASSELpy.net.maizegenetics.analysis.popgen.LinkageDisequilibrium) LinkageDisequilibriumTest (class in TASSELpy.test.net.maizegenetics.analysis.popgen.LinkageDisequilibriumTest) LinkedList (class in TASSELpy.java.util.LinkedList) List (class in TASSELpy.java.util.List)

list_builder (TASSELpy.test.net.maizegenetics.taxa.TaxaListTest.TaxaListTest attribute) ListIterator (class in TASSELpy.java.util.ListIterator) listIterator() (TASSELpy.java.util.List.List method) Long (class in TASSELpy.java.lang.Long) LongTest (class in TASSELpy.test.java.lang.LongTest) longValue() (TASSELpy.java.lang.Number.Number method) LRUcache (class in TASSELpy.utils.caching) LRUcacheTest (class in TASSELpy.test.utils.cachingTest) lruOrderedSet (class in TASSELpy.utils.OrderedSet)

M

mainTestSuite (class in TASSELpy.test.mainTestSuite) majorAllele() (TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable.GenotypeCallTable method) (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) majorAlleleAsString() (TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable.GenotypeCallTable method) (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) majorAlleleCount() (TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable.GenotypeCallTable method) (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) majorAlleleForAllSites() (TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable.GenotypeCallTable method) majorAlleleFrequency() (TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable.GenotypeCallTable method) (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) majorMinorCounts() (TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable.GenotypeCallTable method) (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) make() (TASSELpy.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixFactory.DoubleMatrixFactory method) make_array() (TASSELpy.java.lang.String.String static method) (TASSELpy.javaObj.javaArray static method) (TASSELpy.utils.primativeArray.javaPrimativeArray static method) make_array_from_obj() (TASSELpy.utils.primativeArray.javaPrimativeArray static method) make_constructor_sig() (in module TASSELpy.utils.helper) make_dbl_array() (TASSELpy.utils.primativeArray.javaPrimativeArray static method) make_sig() (in module TASSELpy.utils.helper) make_string_array() (in module TASSELpy.utils.Overloading) makeCharacterTrait() (TASSELpy.net.maizegenetics.trait.ReadPhenotypeUtils.ReadPhenotypeUtils static method) Map (class in TASSELpy.java.util.Map) Map.Entry (class in TASSELpy.java.util.Map) MapTest (class in TASSELpy.test.java.util.MapTest) MarkerPhenotype (class in TASSELpy.net.maizegenetics.trait.MarkerPhenotype) MarkerPhenotypeAdapter (class in TASSELpy.net.maizegenetics.trait.MarkerPhenotypeAdapter) MarkerPhenotypeTest (class in TASSELpy.test.net.maizegenetics.trait.MarkerPhenotypeTest) MatrixTestSuite (class in TASSELpy.test.net.maizegenetics.matrixalgebra.Matrix.MatrixTestSuite) maxNumAlleles() (TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable.GenotypeCallTable method) (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) meanDistance() (TASSELpy.net.maizegenetics.taxa.distance.TaxaListMatrix.TaxaListMatrix method) mergeCalls() (TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeMergeRule.GenotypeMergeRule method) mergeWithDepth() (TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeMergeRule.GenotypeMergeRule method) meta_byte_array (class in TASSELpy.utils.primativeArray) meta_double_array (class in TASSELpy.utils.primativeArray) meta_float_array (class in TASSELpy.utils.primativeArray) meta_int_array (class in TASSELpy.utils.primativeArray) meta_long_array (class in TASSELpy.utils.primativeArray)

MetaBitSet (class in TASSELpy.net.maizegenetics.util.BitSet) metaBoolean (class in TASSELpy.java.lang.Boolean) metaByte (class in TASSELpy.java.lang.Byte) MetaChromosome (class in TASSELpy.net.maizegenetics.dna.map.Chromosome) metaCollection (class in TASSELpy.java.util.Collection) metaDistanceMatrix (class in TASSELpy.net.maizegenetics.taxa.distance.DistanceMatrix) metaDouble (class in TASSELpy.java.lang.Double) metaDoubleMatrix (class in TASSELpy.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix) metaEnum (class in TASSELpy.java.lang.Enum) metaFloat (class in TASSELpy.java.lang.Float) MetaGenotypeTable (class in TASSELpy.net.maizegenetics.dna.snp.GenotypeTable) metaInteger (class in TASSELpy.java.lang.Integer) metaList (class in TASSELpy.java.util.List) metaLong (class in TASSELpy.java.lang.Long) metaMap (class in TASSELpy.java.util.Map) metaMarkerPhenotype (class in TASSELpy.net.maizegenetics.trait.MarkerPhenotype) metaNumber (class in TASSELpy.java.lang.Number) metaPlugin (class in TASSELpy.net.maizegenetics.plugindef.Plugin) metaString (class in TASSELpy.java.lang.String) metaTrait (class in TASSELpy.net.maizegenetics.trait.Trait) minorAllele() (TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable.GenotypeCallTable method) (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) minorAlleleAsString() (TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable.GenotypeCallTable method) (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) minorAlleleCount() (TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable.GenotypeCallTable method) (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) minorAlleleForAllSites() (TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable.GenotypeCallTable method) minorAlleleFrequency() (TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable.GenotypeCallTable method) (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) minorAlleles() (TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable.GenotypeCallTable method) (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) minus() (TASSELpy.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix.DoubleMatrix method) minusEquals() (TASSELpy.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix.DoubleMatrix method) mult() (TASSELpy.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix.DoubleMatrix method) multadd() (TASSELpy.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix.DoubleMatrix method)

N

n() (TASSELpy.net.maizegenetics.analysis.popgen.LDResult.LDResult method) (TASSELpy.net.maizegenetics.analysis.popgen.LDResult.LDResult.Builder method) name() (TASSELpy.java.lang.Enum.Enum method) newInstance() (TASSELpy.java.lang.Object.Class method) next() (TASSELpy.java.util.Iterator.Iterator method) nextIndex() (TASSELpy.java.util.ListIterator.ListIterator method) nextSetBit() (TASSELpy.net.maizegenetics.util.BitSet.BitSet method) Number (class in TASSELpy.java.lang.Number)

numberOfColumns() (TASSELpy.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix.DoubleMatrix method) numberOfRows() (TASSELpy.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix.DoubleMatrix method) numberOfSites() (TASSELpy.net.maizegenetics.dna.map.PositionList.PositionList method) (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) (TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable.GenotypeCallTable method) numberOfTaxa() (TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable.GenotypeCallTable method) (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) (TASSELpy.net.maizegenetics.taxa.TaxaList.TaxaList method) (TASSELpy.net.maizegenetics.taxa.distance.DistanceMatrix.DistanceMatrix method) numChromosomes() (TASSELpy.net.maizegenetics.dna.map.PositionList.PositionList method) (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) numSites() (TASSELpy.net.maizegenetics.dna.snp.byte2d.Byte2D.Byte2D method) numTaxa() (TASSELpy.net.maizegenetics.dna.snp.byte2d.Byte2D.Byte2D method)

O

Object (class in TASSELpy.java.lang.Object) offer() (TASSELpy.java.util.Queue.Queue method) offerFirst() (TASSELpy.java.util.Deque.Deque method) offerLast() (TASSELpy.java.util.Deque.Deque method)

OpenBitSet (class in TASSELpy.net.maizegenetics.util.OpenBitSet) OrderedSet (class in TASSELpy.utils.OrderedSet) ordinal() (TASSELpy.java.lang.Enum.Enum method)

P

p() (TASSELpy.net.maizegenetics.analysis.popgen.LDResult.LDResult method) (TASSELpy.net.maizegenetics.analysis.popgen.LDResult.LDResult.Builder method) peek() (TASSELpy.java.util.Queue.Queue method) peekFirst() (TASSELpy.java.util.Deque.Deque method) peekLast() (TASSELpy.java.util.Deque.Deque method) performFunction() (TASSELpy.net.maizegenetics.plugindef.Plugin.Plugin method) Phenotype (class in TASSELpy.net.maizegenetics.trait.Phenotype) PhenotypeTest (class in TASSELpy.test.net.maizegenetics.trait.PhenotypeTest) physicalPositions() (TASSELpy.net.maizegenetics.dna.map.PositionList.PositionList method) (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) Plugin (class in TASSELpy.net.maizegenetics.plugindef.Plugin) pluginDescription() (TASSELpy.net.maizegenetics.plugindef.Plugin.Plugin method) PluginParameter (class in TASSELpy.net.maizegenetics.plugindef.PluginParameter) plus() (TASSELpy.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix.DoubleMatrix method) plusEquals() (TASSELpy.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix.DoubleMatrix method) poll() (TASSELpy.java.util.Queue.Queue method) pollFirst() (TASSELpy.java.util.Deque.Deque method) pollLast() (TASSELpy.java.util.Deque.Deque method)

pop() (TASSELpy.java.util.Deque.Deque method) (TASSELpy.utils.OrderedSet.OrderedSet method) (TASSELpy.utils.caching.doubleLinkedList method) popgenTestSuite (class in TASSELpy.test.net.maizegenetics.analysis.popgen.popgenTestSuite) popleft() (TASSELpy.utils.caching.doubleLinkedList method) Position (class in TASSELpy.net.maizegenetics.dna.map.Position) PositionList (class in TASSELpy.net.maizegenetics.dna.map.PositionList) positions() (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) previous() (TASSELpy.java.util.ListIterator.ListIterator method) previousIndex() (TASSELpy.java.util.ListIterator.ListIterator method) previousSetBit() (TASSELpy.net.maizegenetics.util.BitSet.BitSet method) primativeArrayTest (class in TASSELpy.test.utils.primativeArrayTest) processData() (TASSELpy.net.maizegenetics.plugindef.Plugin.Plugin method) progress() (TASSELpy.net.maizegenetics.util.ProgressListener.ProgressListener method) ProgressListener (class in TASSELpy.net.maizegenetics.util.ProgressListener) push() (TASSELpy.java.util.Deque.Deque method) put() (TASSELpy.java.util.Map.Map method) putAll() (TASSELpy.java.util.Map.Map method)

Q

Queue (class in TASSELpy.java.util.Queue)

R

r2() (TASSELpy.net.maizegenetics.analysis.popgen.LDResult.LDResult method) (TASSELpy.net.maizegenetics.analysis.popgen.LDResult.LDResult.Builder method) readFasta() (TASSELpy.net.maizegenetics.dna.snp.ImportUtils.ImportUtils static method) readFromHapmap() (TASSELpy.net.maizegenetics.dna.snp.ImportUtils.ImportUtils static method) readFromPLink() (TASSELpy.net.maizegenetics.dna.snp.ImportUtils.ImportUtils static method) readFromVCF() (TASSELpy.net.maizegenetics.dna.snp.ImportUtils.ImportUtils static method) readGenericFile() (TASSELpy.net.maizegenetics.trait.ReadPhenotypeUtils.ReadPhenotypeUtils static method) readGuessFormat() (TASSELpy.net.maizegenetics.dna.snp.ImportUtils.ImportUtils static method) readNumericalAlignment() (TASSELpy.net.maizegenetics.trait.ReadPhenotypeUtils.ReadPhenotypeUtils static method) ReadPhenotypeUtils (class in TASSELpy.net.maizegenetics.trait.ReadPhenotypeUtils) readPolymorphismAlignment() (TASSELpy.net.maizegenetics.trait.ReadPhenotypeUtils.ReadPhenotypeUtils static method) receiveInput() (TASSELpy.net.maizegenetics.plugindef.Plugin.Plugin method) referenceAllele() (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) referenceAlleleForAllSites() (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) referenceAlleles() (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) referenceGenotype() (TASSELpy.net.maizegenetics.dna.map.PositionList.PositionList method) referenceGenotypeForAllSites() (TASSELpy.net.maizegenetics.dna.map.PositionList.PositionList method) referenceGenotypes() (TASSELpy.net.maizegenetics.dna.map.PositionList.PositionList method) ReferenceProbability (class in TASSELpy.net.maizegenetics.dna.snp.score.ReferenceProbability)

remove() (TASSELpy.java.util.Collection.Collection method) (TASSELpy.java.util.Deque.Deque method) (TASSELpy.java.util.Iterator.Iterator method) (TASSELpy.java.util.Map.Map method) (TASSELpy.net.maizegenetics.util.BitSet.BitSet method) removeAll() (TASSELpy.java.util.Collection.Collection method) removeFirst() (TASSELpy.java.util.Deque.Deque method) removeFirstOccurrence() (TASSELpy.java.util.Deque.Deque method) removeLast() (TASSELpy.java.util.Deque.Deque method) removeLastOccurrence() (TASSELpy.java.util.Deque.Deque method) removeNode() (TASSELpy.utils.caching.doubleLinkedList method) removeSitesBasedOnFreqIgnoreMissing() (TASSELpy.net.maizegenetics.dna.snp.GenotypeTableUtils.GenotypeTableUtils static method) removeSitesOutsideRange() (TASSELpy.net.maizegenetics.dna.snp.GenotypeTableUtils.GenotypeTableUtils static method) retainAll() (TASSELpy.java.util.Collection.Collection method) retainsRareAlleles() (TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable.GenotypeCallTable method) (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) reverseTranslateSite() (TASSELpy.net.maizegenetics.dna.snp.FilterGenotypeTable.FilterGenotypeTable method) row() (TASSELpy.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix.DoubleMatrix method) rowSum() (TASSELpy.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix.DoubleMatrix method) run() (TASSELpy.java.lang.Runnable.Runnable method) run_glm() (TASSELpy.net.maizegenetics.analysis.association.FixedEffectLMPlugin.easy_GLM method) Runnable (class in TASSELpy.java.lang.Runnable)

S

scalarAdd() (TASSELpy.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix.DoubleMatrix method) scalarAddEquals() (TASSELpy.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix.DoubleMatrix method) scalarMult() (TASSELpy.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix.DoubleMatrix method) scalarMultEquals() (TASSELpy.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix.DoubleMatrix method) send_to_java() (in module TASSELpy.utils.helper) Set (class in TASSELpy.java.util.Set) set() (TASSELpy.java.lang.reflect.Array.Array static method) (TASSELpy.java.util.List.List method) (TASSELpy.java.util.ListIterator.ListIterator method) (TASSELpy.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix.DoubleMatrix method) (TASSELpy.net.maizegenetics.util.BitSet.BitSet method) setBits() (TASSELpy.net.maizegenetics.util.BitSet.BitSet method) setBoolean() (TASSELpy.java.lang.reflect.Array.Array static method) setByte() (TASSELpy.java.lang.reflect.Array.Array static method) setChecked() (TASSELpy.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix.DoubleMatrix method) setData() (TASSELpy.net.maizegenetics.trait.CombinePhenotype.CombinePhenotype method) (TASSELpy.net.maizegenetics.trait.FilterPhenotype.FilterPhenotype method) (TASSELpy.net.maizegenetics.trait.Phenotype.Phenotype method) setDefault() (TASSELpy.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixFactory.DoubleMatrixFactory static method) setDouble() (TASSELpy.java.lang.reflect.Array.Array static method) setElement() (TASSELpy.utils.caching.doubleLinkedListNode method) setFloat() (TASSELpy.java.lang.reflect.Array.Array static method) setInt() (TASSELpy.java.lang.reflect.Array.Array static method) setLevelLabels() (TASSELpy.net.maizegenetics.trait.Trait.Trait method) setLong() (TASSELpy.java.lang.reflect.Array.Array static method) (TASSELpy.net.maizegenetics.util.BitSet.BitSet method) setMaxP() (TASSELpy.net.maizegenetics.analysis.association.FixedEffectLMPlugin.FixedEffectLMPlugin method) setName() (TASSELpy.net.maizegenetics.plugindef.Datum.Datum method) setNumberOfPermutations() (TASSELpy.net.maizegenetics.analysis.association.FixedEffectLMPlugin.FixedEffectLMPlugin method) setNumWords() (TASSELpy.net.maizegenetics.util.BitSet.BitSet method) setOutputFile() (TASSELpy.net.maizegenetics.analysis.association.FixedEffectLMPlugin.FixedEffectLMPlugin method) setParameter() (TASSELpy.net.maizegenetics.plugindef.Plugin.Plugin method) setParameters() (TASSELpy.net.maizegenetics.plugindef.Plugin.Plugin method) setPermute() (TASSELpy.net.maizegenetics.analysis.association.FixedEffectLMPlugin.FixedEffectLMPlugin method) setPredecessor() (TASSELpy.utils.caching.doubleLinkedListNode method) setProperty() (TASSELpy.net.maizegenetics.trait.Trait.Trait method) setRandomizer() (TASSELpy.net.maizegenetics.analysis.association.FixedEffectLMPlugin.FixedEffectLMPlugin method) setRestrictOutput() (TASSELpy.net.maizegenetics.analysis.association.FixedEffectLMPlugin.FixedEffectLMPlugin method)

setSuccessor() (TASSELpy.utils.caching.doubleLinkedListNode method) setType() (TASSELpy.net.maizegenetics.trait.Trait.Trait method) setUp() (TASSELpy.test.java.util.MapTest.MapTest method) (TASSELpy.test.javaObjTest.javaArrayTest method) (TASSELpy.test.net.maizegenetics.analysis.distance.KinshipTest.KinshipTest method) (TASSELpy.test.net.maizegenetics.analysis.popgen.LDResultTest.LDResultTest method) (TASSELpy.test.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixFactoryTest.DoubleMatrixFactoryTest method) (TASSELpy.test.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixTest.DoubleMatrixTest method) (TASSELpy.test.net.maizegenetics.matrixalgebra.decomposition.EigenvalueDecompositionTest.EigenvalueDecompositionTest method) (TASSELpy.test.net.maizegenetics.matrixalgebra.decomposition.SingularValueDecompositionTest.SingularValueDecompositionTest method) (TASSELpy.test.net.maizegenetics.stats.statistics.FisherExactTest.FisherExactTest method) (TASSELpy.test.net.maizegenetics.trait.PhenotypeTest.PhenotypeTest method) (TASSELpy.test.net.maizegenetics.trait.TraitTest.TraitTest method) (TASSELpy.test.utils.cachingTest.doubleLinkedListTest method) setUpClass() (TASSELpy.test.net.maizegenetics.analysis.IBSDistanceMatrixTest.IBSDistanceMatrixTest class method) (TASSELpy.test.net.maizegenetics.analysis.popgen.LinkageDisequilibriumTest.LinkageDisequilibriumTest class method) (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest class method) (TASSELpy.test.net.maizegenetics.taxa.TaxaListBuilderTest.TaxaListBuilderTest class method) (TASSELpy.test.net.maizegenetics.taxa.TaxonTest.TaxonTest class method) (TASSELpy.test.net.maizegenetics.taxa.distance.TaxaListMatrixTest.TaxaListMatrixTest class method) (TASSELpy.test.net.maizegenetics.trait.MarkerPhenotypeTest.MarkerPhenotypeTest class method) (TASSELpy.test.net.maizegenetics.util.TableReportTest.TableReportTest class method) setValue() (TASSELpy.java.util.Map.Map.Entry method) shortValue() (TASSELpy.java.lang.Number.Number method) signature_dict (class in TASSELpy.utils.Overloading) simpleCopy() (TASSELpy.net.maizegenetics.trait.CombinePhenotype.CombinePhenotype method) (TASSELpy.net.maizegenetics.trait.FilterPhenotype.FilterPhenotype method) SimplePhenotype (class in TASSELpy.net.maizegenetics.trait.SimplePhenotype) SingularValueDecomposition (class in TASSELpy.net.maizegenetics.matrixalgebra.decomposition.SingularValueDecomposition) SingularValueDecompositionTest (class in TASSELpy.test.net.maizegenetics.matrixalgebra.decomposition.SingularValueDecompositionTest) site1() (TASSELpy.net.maizegenetics.analysis.popgen.LDResult.LDResult method) site2() (TASSELpy.net.maizegenetics.analysis.popgen.LDResult.LDResult method) SITE_SCORE_TYPE (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable attribute) (TASSELpy.net.maizegenetics.dna.snp.score.SiteScore.SiteScore attribute) siteName() (TASSELpy.net.maizegenetics.dna.map.PositionList.PositionList method) (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) siteOfPhysicalPosition() (TASSELpy.net.maizegenetics.dna.map.PositionList.PositionList method) (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) SiteScore (class in TASSELpy.net.maizegenetics.dna.snp.score.SiteScore) siteScore() (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) (TASSELpy.net.maizegenetics.dna.snp.score.SiteScore.SiteScore method) siteScores() (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) (TASSELpy.net.maizegenetics.dna.snp.score.SiteScore.SiteScore method) siteScoreType() (TASSELpy.net.maizegenetics.dna.snp.byte2d.Byte2D.Byte2D method) (TASSELpy.net.maizegenetics.dna.snp.score.SiteScore.SiteScore method) size() (TASSELpy.java.util.ArrayList.ArrayList method) (TASSELpy.java.util.Collection.Collection method) (TASSELpy.java.util.Map.Map method) (TASSELpy.net.maizegenetics.util.BitSet.BitSet method) snpTestSuite (class in TASSELpy.test.net.maizegenetics.dna.snp.snpTestSuite) solve() (TASSELpy.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix.DoubleMatrix method) squaredDistance() (TASSELpy.net.maizegenetics.taxa.distance.DistanceMatrix.DistanceMatrix method) start() (TASSELpy.TASSELbridge.TASSELbridge static method) startAndEndOfChromosome() (TASSELpy.net.maizegenetics.dna.map.PositionList.PositionList method) statisticsTestSuite (class in TASSELpy.test.net.maizegenetics.stats.statistics.statisticsTestSuite) stop() (TASSELpy.TASSELbridge.TASSELbridge static method) String (class in TASSELpy.java.lang.String) subList() (TASSELpy.java.util.List.List method)

T

TableReport (class in TASSELpy.net.maizegenetics.util.TableReport) TableReportTest (class in TASSELpy.test.net.maizegenetics.util.TableReportTest) TASSELbridge (class in TASSELpy.TASSELbridge) TASSELpy (module) TASSELpy.data (module) TASSELpy.data.data_constants (module) TASSELpy.java (module) TASSELpy.java.lang (module) TASSELpy.java.lang.Boolean (module) TASSELpy.java.lang.Byte (module) TASSELpy.java.lang.Class (module) TASSELpy.java.lang.Comparable (module) TASSELpy.java.lang.Double (module) TASSELpy.java.lang.Enum (module) TASSELpy.java.lang.Float (module) TASSELpy.java.lang.Integer (module) TASSELpy.java.lang.Iterable (module) TASSELpy.java.lang.Long (module) TASSELpy.java.lang.Number (module) TASSELpy.java.lang.Object (module) TASSELpy.java.lang.reflect (module) TASSELpy.java.lang.reflect.Array (module) TASSELpy.java.lang.Runnable (module) TASSELpy.java.lang.String (module) TASSELpy.java.lang.Thread (module) TASSELpy.java.util (module) TASSELpy.java.util.AbstractMap (module) TASSELpy.java.util.AbstractSequentialList (module) TASSELpy.java.util.ArrayList (module) TASSELpy.java.util.Collection (module) TASSELpy.java.util.Deque (module) TASSELpy.java.util.FilterList (module) TASSELpy.java.util.HashMap (module) TASSELpy.java.util.Iterator (module) TASSELpy.java.util.LinkedList (module) TASSELpy.java.util.List (module) TASSELpy.java.util.ListIterator (module) TASSELpy.java.util.Map (module) TASSELpy.java.util.Queue (module) TASSELpy.java.util.Set (module) TASSELpy.javaObj (module) TASSELpy.net (module) TASSELpy.net.maizegenetics (module) TASSELpy.net.maizegenetics.analysis (module) TASSELpy.net.maizegenetics.analysis.association (module) TASSELpy.net.maizegenetics.analysis.association.FixedEffectLMPlugin (module) TASSELpy.net.maizegenetics.analysis.data (module) TASSELpy.net.maizegenetics.analysis.data.IntersectionAlignmentPlugin (module) TASSELpy.net.maizegenetics.analysis.data.UnionAlignmentPlugin (module) TASSELpy.net.maizegenetics.analysis.distance (module) TASSELpy.net.maizegenetics.analysis.distance.IBSDistanceMatrix (module) TASSELpy.net.maizegenetics.analysis.distance.Kinship (module) TASSELpy.net.maizegenetics.analysis.popgen (module) TASSELpy.net.maizegenetics.analysis.popgen.LDResult (module) TASSELpy.net.maizegenetics.analysis.popgen.LinkageDisequilibrium (module) TASSELpy.net.maizegenetics.dna (module) TASSELpy.net.maizegenetics.dna.map (module) TASSELpy.net.maizegenetics.dna.map.Chromosome (module) TASSELpy.net.maizegenetics.dna.map.Position (module) TASSELpy.net.maizegenetics.dna.map.PositionList (module) TASSELpy.net.maizegenetics.dna.snp (module) TASSELpy.net.maizegenetics.dna.snp.byte2d (module) TASSELpy.net.maizegenetics.dna.snp.byte2d.Byte2D (module) TASSELpy.net.maizegenetics.dna.snp.CoreGenotypeTable (module) TASSELpy.net.maizegenetics.dna.snp.depth (module) TASSELpy.net.maizegenetics.dna.snp.depth.AlleleDepth (module) TASSELpy.net.maizegenetics.dna.snp.FilterGenotypeTable (module) TASSELpy.net.maizegenetics.dna.snp.genotypecall (module) TASSELpy.net.maizegenetics.dna.snp.genotypecall.AbstractGenotypeCallTable (module) TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable (module) TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeMergeRule (module) TASSELpy.net.maizegenetics.dna.snp.GenotypeTable (module) TASSELpy.net.maizegenetics.dna.snp.GenotypeTableUtils (module) TASSELpy.net.maizegenetics.dna.snp.ImportUtils (module) TASSELpy.net.maizegenetics.dna.snp.score (module) TASSELpy.net.maizegenetics.dna.snp.score.AlleleProbability (module) TASSELpy.net.maizegenetics.dna.snp.score.Dosage (module) TASSELpy.net.maizegenetics.dna.snp.score.ReferenceProbability (module) TASSELpy.net.maizegenetics.dna.snp.score.SiteScore (module) TASSELpy.net.maizegenetics.dna.tag (module) TASSELpy.net.maizegenetics.dna.WHICH_ALLELE (module) TASSELpy.net.maizegenetics.matrixalgebra (module) TASSELpy.net.maizegenetics.matrixalgebra.decomposition (module) TASSELpy.net.maizegenetics.matrixalgebra.decomposition.EigenvalueDecomposition (module) TASSELpy.net.maizegenetics.matrixalgebra.decomposition.SingularValueDecomposition (module) TASSELpy.net.maizegenetics.matrixalgebra.Matrix (module) TASSELpy.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix (module) TASSELpy.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixFactory (module) TASSELpy.net.maizegenetics.plugindef (module) TASSELpy.net.maizegenetics.plugindef.AbstractPlugin (module) TASSELpy.net.maizegenetics.plugindef.DataSet (module) TASSELpy.net.maizegenetics.plugindef.Datum (module) TASSELpy.net.maizegenetics.plugindef.Plugin (module) TASSELpy.net.maizegenetics.plugindef.PluginParameter (module) TASSELpy.net.maizegenetics.stats (module) TASSELpy.net.maizegenetics.stats.statistics (module) TASSELpy.net.maizegenetics.stats.statistics.FisherExact (module) TASSELpy.net.maizegenetics.taxa (module) TASSELpy.net.maizegenetics.taxa.distance (module) TASSELpy.net.maizegenetics.taxa.distance.DistanceMatrix (module) TASSELpy.net.maizegenetics.taxa.distance.TaxaListMatrix (module) TASSELpy.net.maizegenetics.taxa.TaxaList (module) TASSELpy.net.maizegenetics.taxa.TaxaListBuilder (module) TASSELpy.net.maizegenetics.taxa.Taxon (module) TASSELpy.net.maizegenetics.trait (module) TASSELpy.net.maizegenetics.trait.AbstractPhenotype (module) TASSELpy.net.maizegenetics.trait.CombinePhenotype (module) TASSELpy.net.maizegenetics.trait.FilterPhenotype (module) TASSELpy.net.maizegenetics.trait.MarkerPhenotype (module) TASSELpy.net.maizegenetics.trait.MarkerPhenotypeAdapter (module) TASSELpy.net.maizegenetics.trait.Phenotype (module) TASSELpy.net.maizegenetics.trait.ReadPhenotypeUtils (module) TASSELpy.net.maizegenetics.trait.SimplePhenotype (module) TASSELpy.net.maizegenetics.trait.Trait (module) TASSELpy.net.maizegenetics.util (module) TASSELpy.net.maizegenetics.util.BitSet (module) TASSELpy.net.maizegenetics.util.GeneralAnnotation (module) TASSELpy.net.maizegenetics.util.GeneralAnnotationStorage (module) TASSELpy.net.maizegenetics.util.OpenBitSet (module) TASSELpy.net.maizegenetics.util.ProgressListener (module) TASSELpy.net.maizegenetics.util.TableReport (module) TASSELpy.net.maizegenetics.util.UnmodifiableBitSet (module) TASSELpy.TASSELbridge (module) TASSELpy.test (module) TASSELpy.test.java (module) TASSELpy.test.java.lang (module) TASSELpy.test.java.lang.BooleanTest (module) TASSELpy.test.java.lang.ByteTest (module) TASSELpy.test.java.lang.DoubleTest (module) TASSELpy.test.java.lang.FloatTest (module) TASSELpy.test.java.lang.IntegerTest (module) TASSELpy.test.java.lang.langTestSuite (module) TASSELpy.test.java.lang.LongTest (module) TASSELpy.test.java.util (module) TASSELpy.test.java.util.MapTest (module) TASSELpy.test.java.util.utilTestSuite (module) TASSELpy.test.javaObjTest (module) TASSELpy.test.mainTestSuite (module) TASSELpy.test.net (module) TASSELpy.test.net.maizegenetics (module) TASSELpy.test.net.maizegenetics.analysis (module) TASSELpy.test.net.maizegenetics.analysis.analysisTestSuite (module) TASSELpy.test.net.maizegenetics.analysis.association (module) TASSELpy.test.net.maizegenetics.analysis.association.associationTestSuite (module) TASSELpy.test.net.maizegenetics.analysis.association.FixedEffectLMPlugin (module) TASSELpy.test.net.maizegenetics.analysis.distance (module) TASSELpy.test.net.maizegenetics.analysis.distance.distanceTestSuite (module) TASSELpy.test.net.maizegenetics.analysis.distance.KinshipTest (module) TASSELpy.test.net.maizegenetics.analysis.IBSDistanceMatrixTest (module) TASSELpy.test.net.maizegenetics.analysis.popgen (module) TASSELpy.test.net.maizegenetics.analysis.popgen.LDResultTest (module) TASSELpy.test.net.maizegenetics.analysis.popgen.LinkageDisequilibriumTest (module) TASSELpy.test.net.maizegenetics.analysis.popgen.popgenTestSuite (module) TASSELpy.test.net.maizegenetics.dna (module) TASSELpy.test.net.maizegenetics.dna.snp (module) TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest (module) TASSELpy.test.net.maizegenetics.dna.snp.snpTestSuite (module) TASSELpy.test.net.maizegenetics.matrixalgebra (module) TASSELpy.test.net.maizegenetics.matrixalgebra.decomposition (module) TASSELpy.test.net.maizegenetics.matrixalgebra.decomposition.decompositionTestSuite (module) TASSELpy.test.net.maizegenetics.matrixalgebra.decomposition.EigenvalueDecompositionTest (module) TASSELpy.test.net.maizegenetics.matrixalgebra.decomposition.SingularValueDecompositionTest (module) TASSELpy.test.net.maizegenetics.matrixalgebra.Matrix (module) TASSELpy.test.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixFactoryTest (module) TASSELpy.test.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixTest (module) TASSELpy.test.net.maizegenetics.matrixalgebra.Matrix.MatrixTestSuite (module) TASSELpy.test.net.maizegenetics.stats (module) TASSELpy.test.net.maizegenetics.stats.statistics (module) TASSELpy.test.net.maizegenetics.stats.statistics.FisherExactTest (module) TASSELpy.test.net.maizegenetics.stats.statistics.statisticsTestSuite (module) TASSELpy.test.net.maizegenetics.taxa (module) TASSELpy.test.net.maizegenetics.taxa.distance (module) TASSELpy.test.net.maizegenetics.taxa.distance.DistanceMatrixTest (module) TASSELpy.test.net.maizegenetics.taxa.distance.distanceTestSuite (module) TASSELpy.test.net.maizegenetics.taxa.distance.TaxaListMatrixTest (module) TASSELpy.test.net.maizegenetics.taxa.TaxaListBuilderTest (module) TASSELpy.test.net.maizegenetics.taxa.TaxaListTest (module) TASSELpy.test.net.maizegenetics.taxa.taxaTestSuite (module) TASSELpy.test.net.maizegenetics.taxa.TaxonTest (module) TASSELpy.test.net.maizegenetics.trait (module) TASSELpy.test.net.maizegenetics.trait.MarkerPhenotypeTest (module) TASSELpy.test.net.maizegenetics.trait.PhenotypeTest (module) TASSELpy.test.net.maizegenetics.trait.TraitTest (module) TASSELpy.test.net.maizegenetics.trait.traitTestSuite (module) TASSELpy.test.net.maizegenetics.util (module) TASSELpy.test.net.maizegenetics.util.TableReportTest (module) TASSELpy.test.net.maizegenetics.util.utilTestSuite (module) TASSELpy.test.utils (module) TASSELpy.test.utils.cachingTest (module) TASSELpy.test.utils.primativeArrayTest (module) TASSELpy.test.utils.utilsTestSuite (module) TASSELpy.utils (module) TASSELpy.utils.caching (module) TASSELpy.utils.DocInherit (module) TASSELpy.utils.helper (module) TASSELpy.utils.OrderedSet (module) TASSELpy.utils.Overloading (module) TASSELpy.utils.primativeArray (module) taxa() (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) taxa_list (TASSELpy.test.net.maizegenetics.taxa.TaxaListTest.TaxaListTest attribute) TaxaList (class in TASSELpy.net.maizegenetics.taxa.TaxaList) TaxaListBuilder (class in TASSELpy.net.maizegenetics.taxa.TaxaListBuilder) TaxaListBuilderTest (class in TASSELpy.test.net.maizegenetics.taxa.TaxaListBuilderTest) TaxaListMatrix (class in TASSELpy.net.maizegenetics.taxa.distance.TaxaListMatrix) TaxaListMatrixTest (class in TASSELpy.test.net.maizegenetics.taxa.distance.TaxaListMatrixTest) TaxaListTest (class in TASSELpy.test.net.maizegenetics.taxa.TaxaListTest) taxaName() (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) (TASSELpy.net.maizegenetics.taxa.TaxaList.TaxaList method) taxaTestSuite (class in TASSELpy.test.net.maizegenetics.taxa.taxaTestSuite) Taxon (class in TASSELpy.net.maizegenetics.taxa.Taxon) TaxonTest (class in TASSELpy.test.net.maizegenetics.taxa.TaxonTest) tcrossproduct() (TASSELpy.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix.DoubleMatrix method) test___init__() (TASSELpy.test.net.maizegenetics.taxa.TaxaListTest.TaxaListTest method) test__init__() (TASSELpy.test.net.maizegenetics.taxa.TaxonTest.TaxonTest method) test_absoluteDistance() (TASSELpy.test.net.maizegenetics.taxa.distance.DistanceMatrixTest.DistanceMatrixTest method) test_add() (TASSELpy.test.net.maizegenetics.taxa.TaxaListBuilderTest.TaxaListBuilderTest method) test_addAll() (TASSELpy.test.net.maizegenetics.taxa.TaxaListBuilderTest.TaxaListBuilderTest method) test_addFactor() (TASSELpy.test.net.maizegenetics.trait.TraitTest.TraitTest method) test_addition() (TASSELpy.test.java.lang.ByteTest.ByteTest method) (TASSELpy.test.java.lang.DoubleTest.DoubleTest method) (TASSELpy.test.java.lang.FloatTest.FloatTest method) (TASSELpy.test.java.lang.IntegerTest.IntegerTest method) (TASSELpy.test.java.lang.LongTest.LongTest method) test_all() (TASSELpy.test.utils.cachingTest.LRUcacheTest method) test_alleleDefinitions() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_allelePresenceForAllSites() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_allelePresenceForAllTaxa() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_allelePresenceForSitesBlock() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_alleles() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_allelesBySortType() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_allelesSortedByFrequency() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_Boolean() (TASSELpy.test.java.lang.BooleanTest.BooleanTest method) test_Byte() (TASSELpy.test.java.lang.ByteTest.ByteTest method) test_byteArray() (TASSELpy.test.utils.primativeArrayTest.primativeArrayTest method) test_byteDblArray() (TASSELpy.test.utils.primativeArrayTest.primativeArrayTest method) test_calculateBitLDForHaplotype() (TASSELpy.test.net.maizegenetics.analysis.popgen.LinkageDisequilibriumTest.LinkageDisequilibriumTest method) test_calculateDPrime() (TASSELpy.test.net.maizegenetics.analysis.popgen.LinkageDisequilibriumTest.LinkageDisequilibriumTest method) test_calculateRSqr() (TASSELpy.test.net.maizegenetics.analysis.popgen.LinkageDisequilibriumTest.LinkageDisequilibriumTest method) test_chromosomalPosition() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_chromosome() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_chromosomeName() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_chromosomes() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_chromosomeSiteCount() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_chromosomesOffsets() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_clear() (TASSELpy.test.java.util.MapTest.MapTest method) test_column() (TASSELpy.test.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixTest.DoubleMatrixTest method) test_columnRank() (TASSELpy.test.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixTest.DoubleMatrixTest method) test_columnSum() (TASSELpy.test.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixTest.DoubleMatrixTest method) test_compareTo() (TASSELpy.test.java.lang.BooleanTest.BooleanTest method) (TASSELpy.test.java.lang.ByteTest.ByteTest method) (TASSELpy.test.java.lang.DoubleTest.DoubleTest method) (TASSELpy.test.java.lang.FloatTest.FloatTest method) (TASSELpy.test.java.lang.IntegerTest.IntegerTest method) (TASSELpy.test.java.lang.LongTest.LongTest method) test_compose() (TASSELpy.test.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixFactoryTest.DoubleMatrixFactoryTest method)

test_compositeAlignments() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_computeHetBitDistances() (TASSELpy.test.net.maizegenetics.analysis.IBSDistanceMatrixTest.IBSDistanceMatrixTest method) test_concatenate() (TASSELpy.test.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixTest.DoubleMatrixTest method) test_constructor() (TASSELpy.test.javaObjTest.genericJavaObjTest method) (TASSELpy.test.net.maizegenetics.analysis.popgen.LinkageDisequilibriumTest.LinkageDisequilibriumTest method) test_constructor1() (TASSELpy.test.net.maizegenetics.analysis.IBSDistanceMatrixTest.IBSDistanceMatrixTest method) (TASSELpy.test.net.maizegenetics.taxa.distance.DistanceMatrixTest.DistanceMatrixTest method) test_constructor2() (TASSELpy.test.net.maizegenetics.analysis.IBSDistanceMatrixTest.IBSDistanceMatrixTest method) (TASSELpy.test.net.maizegenetics.taxa.distance.DistanceMatrixTest.DistanceMatrixTest method) test_constructor3() (TASSELpy.test.net.maizegenetics.analysis.IBSDistanceMatrixTest.IBSDistanceMatrixTest method) (TASSELpy.test.net.maizegenetics.taxa.distance.DistanceMatrixTest.DistanceMatrixTest method) test_constructor4() (TASSELpy.test.net.maizegenetics.analysis.IBSDistanceMatrixTest.IBSDistanceMatrixTest method) (TASSELpy.test.net.maizegenetics.taxa.distance.DistanceMatrixTest.DistanceMatrixTest method) test_containsKey() (TASSELpy.test.java.util.MapTest.MapTest method) test_containsValue() (TASSELpy.test.java.util.MapTest.MapTest method) test_copy() (TASSELpy.test.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixTest.DoubleMatrixTest method) test_crossproduct() (TASSELpy.test.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixTest.DoubleMatrixTest method) test_depth() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_depthForAlleles() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_diagonal() (TASSELpy.test.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixFactoryTest.DoubleMatrixFactoryTest method) test_diploidAsString() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_Double() (TASSELpy.test.java.lang.DoubleTest.DoubleTest method) test_doubleArray() (TASSELpy.test.utils.primativeArrayTest.primativeArrayTest method) test_doubleDblArray() (TASSELpy.test.utils.primativeArrayTest.primativeArrayTest method) test_dPrime() (TASSELpy.test.net.maizegenetics.analysis.popgen.LDResultTest.LDResultTest method) test_duild() (TASSELpy.test.net.maizegenetics.taxa.TaxaListBuilderTest.TaxaListBuilderTest method) test_easy_GLM() (TASSELpy.test.net.maizegenetics.analysis.association.FixedEffectLMPlugin.easy_GLMTest method) test_entrySet() (TASSELpy.test.java.util.MapTest.MapTest method) test_firstLastSiteOfChromosome() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_Float() (TASSELpy.test.java.lang.FloatTest.FloatTest method) test_floatArray() (TASSELpy.test.utils.primativeArrayTest.primativeArrayTest method) test_floatDblArray() (TASSELpy.test.utils.primativeArrayTest.primativeArrayTest method) test_generalizedInverse() (TASSELpy.test.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixTest.DoubleMatrixTest method) test_generalizedInverseWithRank() (TASSELpy.test.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixTest.DoubleMatrixTest method) test_generic_getitem() (TASSELpy.test.javaObjTest.genericJavaObjTest method) test_generic_setitem() (TASSELpy.test.javaObjTest.genericJavaObjTest method) test_genoCount() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_genomeVersion() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_genosSortedByFrequency() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_genotype() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_genotypeAllSites() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_genotypeAllTaxa() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_genotypeArray() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_genotypeAsString() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_genotypeAsStringArray() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_genotypeAsStringRange() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_genotypeAsStringRow() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_genotypeRange() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_get() (TASSELpy.test.java.util.MapTest.MapTest method) (TASSELpy.test.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixTest.DoubleMatrixTest method) test_get_array_type() (TASSELpy.test.javaObjTest.javaArrayTest method) test_getAlignment() (TASSELpy.test.net.maizegenetics.analysis.popgen.LinkageDisequilibriumTest.LinkageDisequilibriumTest method) (TASSELpy.test.net.maizegenetics.trait.MarkerPhenotypeTest.MarkerPhenotypeTest method) test_getArray() (TASSELpy.test.javaObjTest.javaObjTest method) test_getAverageTotalSits() (TASSELpy.test.net.maizegenetics.analysis.IBSDistanceMatrixTest.IBSDistanceMatrixTest method) test_getChecked() (TASSELpy.test.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixTest.DoubleMatrixTest method) test_getClonedDistances() (TASSELpy.test.net.maizegenetics.taxa.distance.TaxaListMatrixTest.TaxaListMatrixTest method) test_getClosestIndex() (TASSELpy.test.net.maizegenetics.taxa.distance.DistanceMatrixTest.DistanceMatrixTest method) test_getColumnCount() (TASSELpy.test.net.maizegenetics.util.TableReportTest.TableReportTest method) test_getColumnName() (TASSELpy.test.net.maizegenetics.taxa.distance.DistanceMatrixTest.DistanceMatrixTest method) test_getCumulativeP() (TASSELpy.test.net.maizegenetics.stats.statistics.FisherExactTest.FisherExactTest method) test_getData() (TASSELpy.test.net.maizegenetics.trait.PhenotypeTest.PhenotypeTest method) test_getDblArray() (TASSELpy.test.javaObjTest.javaObjTest method) test_getDistance() (TASSELpy.test.net.maizegenetics.taxa.distance.TaxaListMatrixTest.TaxaListMatrixTest method) test_getDistances() (TASSELpy.test.net.maizegenetics.taxa.distance.DistanceMatrixTest.DistanceMatrixTest method) test_getDm() (TASSELpy.test.net.maizegenetics.analysis.distance.KinshipTest.KinshipTest method) test_getDPrime() (TASSELpy.test.net.maizegenetics.analysis.popgen.LinkageDisequilibriumTest.LinkageDisequilibriumTest method) test_getEigenvalue() (TASSELpy.test.net.maizegenetics.matrixalgebra.decomposition.EigenvalueDecompositionTest.EigenvalueDecompositionTest method) test_getEigenvalueDecomposition() (TASSELpy.test.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixTest.DoubleMatrixTest method) test_getEigenvalueMatrix() (TASSELpy.test.net.maizegenetics.matrixalgebra.decomposition.EigenvalueDecompositionTest.EigenvalueDecompositionTest method) test_getEigenvalues() (TASSELpy.test.net.maizegenetics.matrixalgebra.decomposition.EigenvalueDecompositionTest.EigenvalueDecompositionTest method) test_getEigenvectors() (TASSELpy.test.net.maizegenetics.matrixalgebra.decomposition.EigenvalueDecompositionTest.EigenvalueDecompositionTest method) test_getElementCount() (TASSELpy.test.net.maizegenetics.util.TableReportTest.TableReportTest method) test_getFactorNames() (TASSELpy.test.net.maizegenetics.trait.TraitTest.TraitTest method) test_getFactorValue() (TASSELpy.test.net.maizegenetics.trait.TraitTest.TraitTest method) test_getFirst() (TASSELpy.test.utils.cachingTest.doubleLinkedListTest method) test_getInstance() (TASSELpy.test.net.maizegenetics.trait.MarkerPhenotypeTest.MarkerPhenotypeTest method) (TASSELpy.test.net.maizegenetics.trait.TraitTest.TraitTest method) test_getLast() (TASSELpy.test.utils.cachingTest.doubleLinkedListTest method) test_getLDForSitePair() (TASSELpy.test.net.maizegenetics.analysis.popgen.LinkageDisequilibriumTest.LinkageDisequilibriumTest method) test_getLeftTailedP() (TASSELpy.test.net.maizegenetics.stats.statistics.FisherExactTest.FisherExactTest method) test_getLevelLabel() (TASSELpy.test.net.maizegenetics.trait.TraitTest.TraitTest method) test_getName() (TASSELpy.test.net.maizegenetics.taxa.TaxonTest.TaxonTest method) test_getNumberOfLevels() (TASSELpy.test.net.maizegenetics.trait.TraitTest.TraitTest method) test_getNumberOfProperties() (TASSELpy.test.net.maizegenetics.trait.TraitTest.TraitTest method) test_getNumberOfTaxa() (TASSELpy.test.net.maizegenetics.trait.PhenotypeTest.PhenotypeTest method) test_getNumberOfTraits() (TASSELpy.test.net.maizegenetics.trait.PhenotypeTest.PhenotypeTest method) test_getP() (TASSELpy.test.net.maizegenetics.stats.statistics.FisherExactTest.FisherExactTest method) test_getPhenotype() (TASSELpy.test.net.maizegenetics.trait.MarkerPhenotypeTest.MarkerPhenotypeTest method) test_getProperties() (TASSELpy.test.net.maizegenetics.trait.TraitTest.TraitTest method) test_getProperty() (TASSELpy.test.net.maizegenetics.trait.TraitTest.TraitTest method) test_getPropertyNames() (TASSELpy.test.net.maizegenetics.trait.TraitTest.TraitTest method) test_getPVal() (TASSELpy.test.net.maizegenetics.analysis.popgen.LinkageDisequilibriumTest.LinkageDisequilibriumTest method) test_getRank() (TASSELpy.test.net.maizegenetics.matrixalgebra.decomposition.SingularValueDecompositionTest.SingularValueDecompositionTest method) test_getRightTailedP() (TASSELpy.test.net.maizegenetics.stats.statistics.FisherExactTest.FisherExactTest method) test_getRightTailedPQuick() (TASSELpy.test.net.maizegenetics.stats.statistics.FisherExactTest.FisherExactTest method) test_getRow() (TASSELpy.test.net.maizegenetics.util.TableReportTest.TableReportTest method) test_getRowCount() (TASSELpy.test.net.maizegenetics.util.TableReportTest.TableReportTest method) test_getRSqr() (TASSELpy.test.net.maizegenetics.analysis.popgen.LinkageDisequilibriumTest.LinkageDisequilibriumTest method) test_getS() (TASSELpy.test.net.maizegenetics.matrixalgebra.decomposition.SingularValueDecompositionTest.SingularValueDecompositionTest method) test_getSampleSize() (TASSELpy.test.net.maizegenetics.analysis.popgen.LinkageDisequilibriumTest.LinkageDisequilibriumTest method) test_getSelection() (TASSELpy.test.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixTest.DoubleMatrixTest method) test_getSingularValueDecomposition() (TASSELpy.test.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixTest.DoubleMatrixTest method) test_getSingularValues() (TASSELpy.test.net.maizegenetics.matrixalgebra.decomposition.SingularValueDecompositionTest.SingularValueDecompositionTest method) test_getSiteCount() (TASSELpy.test.net.maizegenetics.analysis.popgen.LinkageDisequilibriumTest.LinkageDisequilibriumTest method) test_getSize() (TASSELpy.test.net.maizegenetics.taxa.distance.TaxaListMatrixTest.TaxaListMatrixTest method) test_getTableColumnNames() (TASSELpy.test.net.maizegenetics.util.TableReportTest.TableReportTest method) test_getTableTitle() (TASSELpy.test.net.maizegenetics.util.TableReportTest.TableReportTest method) test_getTaxa() (TASSELpy.test.net.maizegenetics.trait.PhenotypeTest.PhenotypeTest method) test_getTaxaList() (TASSELpy.test.net.maizegenetics.taxa.distance.TaxaListMatrixTest.TaxaListMatrixTest method) test_getTaxon() (TASSELpy.test.net.maizegenetics.taxa.distance.DistanceMatrixTest.DistanceMatrixTest method) (TASSELpy.test.net.maizegenetics.trait.PhenotypeTest.PhenotypeTest method) test_getTrait() (TASSELpy.test.net.maizegenetics.trait.PhenotypeTest.PhenotypeTest method) test_getTraits() (TASSELpy.test.net.maizegenetics.trait.PhenotypeTest.PhenotypeTest method) test_getTwoTailedP() (TASSELpy.test.net.maizegenetics.stats.statistics.FisherExactTest.FisherExactTest method) test_getType() (TASSELpy.test.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixFactoryTest.DoubleMatrixFactoryTest method) (TASSELpy.test.net.maizegenetics.trait.TraitTest.TraitTest method) test_getU() (TASSELpy.test.net.maizegenetics.matrixalgebra.decomposition.SingularValueDecompositionTest.SingularValueDecompositionTest method) test_getV() (TASSELpy.test.net.maizegenetics.matrixalgebra.decomposition.SingularValueDecompositionTest.SingularValueDecompositionTest method) test_getValueAt() (TASSELpy.test.net.maizegenetics.util.TableReportTest.TableReportTest method) test_getX() (TASSELpy.test.net.maizegenetics.analysis.popgen.LinkageDisequilibriumTest.LinkageDisequilibriumTest method) test_getXtXGM() (TASSELpy.test.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixTest.DoubleMatrixTest method) test_getY() (TASSELpy.test.net.maizegenetics.analysis.popgen.LinkageDisequilibriumTest.LinkageDisequilibriumTest method) test_haplotypeAllelePresenceForAllSites() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_haplotypeAllelePresenceForAllTaxa() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_haplotypeAllelePresenceForSitesBlock() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_hasAlleleProbabilities() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_hasDepth() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_hasLevels() (TASSELpy.test.net.maizegenetics.trait.TraitTest.TraitTest method) test_hasReference() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_heterozygousCount() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_heterozygousCountForTaxon() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_identity() (TASSELpy.test.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixFactoryTest.DoubleMatrixFactoryTest method) test_indelSize() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_intArray() (TASSELpy.test.utils.primativeArrayTest.primativeArrayTest method) test_intDblArray() (TASSELpy.test.utils.primativeArrayTest.primativeArrayTest method) test_Integer() (TASSELpy.test.java.lang.IntegerTest.IntegerTest method) test_inverse() (TASSELpy.test.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixTest.DoubleMatrixTest method) test_invert() (TASSELpy.test.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixTest.DoubleMatrixTest method) test_isAllPolymorphic() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_isDiscrete() (TASSELpy.test.net.maizegenetics.trait.TraitTest.TraitTest method) test_isEmpty() (TASSELpy.test.java.util.MapTest.MapTest method) test_isHeterozygous() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_isIndel() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_isPhased() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_isPolymorphic() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_isPositiveStrand() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_isSymmetric() (TASSELpy.test.net.maizegenetics.taxa.distance.TaxaListMatrixTest.TaxaListMatrixTest method) test_isTrueIBS() (TASSELpy.test.net.maizegenetics.analysis.IBSDistanceMatrixTest.IBSDistanceMatrixTest method) test_iter() (TASSELpy.test.javaObjTest.javaArrayTest method) test_javaObjType() (TASSELpy.test.javaObjTest.javaObjTest method) test_keySet() (TASSELpy.test.java.util.MapTest.MapTest method) test_len() (TASSELpy.test.javaObjTest.javaArrayTest method) test_Long() (TASSELpy.test.java.lang.LongTest.LongTest method) test_longArray() (TASSELpy.test.utils.primativeArrayTest.primativeArrayTest method) test_longDblArray() (TASSELpy.test.utils.primativeArrayTest.primativeArrayTest method) test_majorAllele() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_majorAlleleAsString() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_majorAlleleCount() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_majorAlleleFrequency() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_majorMinorCounts() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_make() (TASSELpy.test.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixFactoryTest.DoubleMatrixFactoryTest method) test_maxNumAlleles() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_meanDistance() (TASSELpy.test.net.maizegenetics.taxa.distance.TaxaListMatrixTest.TaxaListMatrixTest method) test_metaBoolean() (TASSELpy.test.java.lang.BooleanTest.BooleanTest method) test_metaByte() (TASSELpy.test.java.lang.ByteTest.ByteTest method) test_metaDouble() (TASSELpy.test.java.lang.DoubleTest.DoubleTest method) test_metaFloat() (TASSELpy.test.java.lang.FloatTest.FloatTest method) test_metaInteger() (TASSELpy.test.java.lang.IntegerTest.IntegerTest method) test_metaLong() (TASSELpy.test.java.lang.LongTest.LongTest method) test_minorAllele() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_minorAlleleAsString() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_minorAlleleCount() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_minorAlleleFrequency() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_minorAlleles() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_minus() (TASSELpy.test.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixTest.DoubleMatrixTest method) test_minusEquals() (TASSELpy.test.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixTest.DoubleMatrixTest method) test_mult() (TASSELpy.test.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixTest.DoubleMatrixTest method) test_multadd() (TASSELpy.test.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixTest.DoubleMatrixTest method) test_n() (TASSELpy.test.net.maizegenetics.analysis.popgen.LDResultTest.LDResultTest method) test_numberOfRowsAndCols() (TASSELpy.test.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixTest.DoubleMatrixTest method) test_numberOfTaxa() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) (TASSELpy.test.net.maizegenetics.taxa.TaxaListTest.TaxaListTest method) (TASSELpy.test.net.maizegenetics.taxa.distance.DistanceMatrixTest.DistanceMatrixTest method) test_numChromosomes() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_p() (TASSELpy.test.net.maizegenetics.analysis.popgen.LDResultTest.LDResultTest method) test_physicalPosition() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_plus() (TASSELpy.test.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixTest.DoubleMatrixTest method) test_plusEquals() (TASSELpy.test.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixTest.DoubleMatrixTest method) test_pop() (TASSELpy.test.utils.cachingTest.doubleLinkedListTest method) test_popleft() (TASSELpy.test.utils.cachingTest.doubleLinkedListTest method) test_positions() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_putAll() (TASSELpy.test.java.util.MapTest.MapTest method) test_r2() (TASSELpy.test.net.maizegenetics.analysis.popgen.LDResultTest.LDResultTest method) test_referenceAllele() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_referenceAlleleForAllSites() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_referenceAlleles() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_remove() (TASSELpy.test.java.util.MapTest.MapTest method) test_removeNode() (TASSELpy.test.utils.cachingTest.doubleLinkedListTest method) test_retainsRareAlleles() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_rowSum() (TASSELpy.test.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixTest.DoubleMatrixTest method) test_scalarAdd() (TASSELpy.test.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixTest.DoubleMatrixTest method) test_scalarMult() (TASSELpy.test.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixTest.DoubleMatrixTest method) test_scalarMultEquals() (TASSELpy.test.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixTest.DoubleMatrixTest method) test_set() (TASSELpy.test.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixTest.DoubleMatrixTest method) test_setData() (TASSELpy.test.net.maizegenetics.trait.PhenotypeTest.PhenotypeTest method) test_setitem() (TASSELpy.test.javaObjTest.javaArrayTest method) test_setLevelLabels() (TASSELpy.test.net.maizegenetics.trait.TraitTest.TraitTest method) test_setProperty() (TASSELpy.test.net.maizegenetics.trait.TraitTest.TraitTest method) test_setType() (TASSELpy.test.net.maizegenetics.trait.TraitTest.TraitTest method) test_site1() (TASSELpy.test.net.maizegenetics.analysis.popgen.LDResultTest.LDResultTest method) test_site2() (TASSELpy.test.net.maizegenetics.analysis.popgen.LDResultTest.LDResultTest method) test_siteName() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_siteOfPhysicalPosition() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_size() (TASSELpy.test.java.util.MapTest.MapTest method) test_solve() (TASSELpy.test.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixTest.DoubleMatrixTest method) test_squaredDistance() (TASSELpy.test.net.maizegenetics.taxa.distance.DistanceMatrixTest.DistanceMatrixTest method) test_taxa() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_taxaName() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) (TASSELpy.test.net.maizegenetics.taxa.TaxaListTest.TaxaListTest method) test_tcrossproduct() (TASSELpy.test.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixTest.DoubleMatrixTest method) test_to_numpy_array() (TASSELpy.test.javaObjTest.javaArrayTest method) (TASSELpy.test.utils.primativeArrayTest.primativeArrayTest method) test_toDict() (TASSELpy.test.net.maizegenetics.util.TableReportTest.TableReportTest method) test_toString() (TASSELpy.test.net.maizegenetics.taxa.distance.TaxaListMatrixTest.TaxaListMatrixTest method) test_toStringWithVCFAnnotation() (TASSELpy.test.net.maizegenetics.taxa.TaxonTest.TaxonTest method) test_totalGametesNonMissingForSites() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_totalGametesNonMissingForTaxon() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_totalNonMissingForSite() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_totalNonMissingForTaxon() (TASSELpy.test.net.maizegenetics.dna.snp.GenotypeTableTest.GenotypeTableTest method) test_transpose() (TASSELpy.test.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixTest.DoubleMatrixTest method) test_values() (TASSELpy.test.java.util.MapTest.MapTest method) test_whichIdNumber() (TASSELpy.test.net.maizegenetics.taxa.distance.DistanceMatrixTest.DistanceMatrixTest method) test_whichTaxon() (TASSELpy.test.net.maizegenetics.trait.PhenotypeTest.PhenotypeTest method) test_whichTrait() (TASSELpy.test.net.maizegenetics.trait.PhenotypeTest.PhenotypeTest method) test_wrap_existing_array() (TASSELpy.test.javaObjTest.javaObjTest method) testDesign (TASSELpy.net.maizegenetics.analysis.popgen.LinkageDisequilibrium.LinkageDisequilibrium attribute) Thread (class in TASSELpy.java.lang.Thread) to_java_string() (in module TASSELpy.utils.Overloading) to_numpy_array() (TASSELpy.javaObj.javaArray method) (TASSELpy.utils.primativeArray.javaPrimativeArray method) to_wrapped_array() (TASSELpy.javaObj.javaArray static method) (TASSELpy.utils.primativeArray.javaPrimativeArray static method) toArray() (TASSELpy.java.util.Collection.Collection method) toDict() (TASSELpy.net.maizegenetics.util.TableReport.TableReport method) toPrimative() (TASSELpy.java.lang.Byte.Byte static method) (TASSELpy.java.lang.Double.Double static method) (TASSELpy.java.lang.Float.Float static method) (TASSELpy.java.lang.Integer.Integer static method) (TASSELpy.java.lang.Long.Long static method) (TASSELpy.java.lang.Number.Number method) toString() (TASSELpy.java.lang.Enum.Enum method) (TASSELpy.java.lang.Object.Object method) (TASSELpy.net.maizegenetics.analysis.distance.IBSDistanceMatrix.IBSDistanceMatrix method) (TASSELpy.net.maizegenetics.taxa.distance.TaxaListMatrix.TaxaListMatrix method) (TASSELpy.test.net.maizegenetics.analysis.IBSDistanceMatrixTest.IBSDistanceMatrixTest method) toStringWithVCFAnnotation() (TASSELpy.net.maizegenetics.taxa.Taxon.Taxon method) totalGametesNonMissingForSite() (TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable.GenotypeCallTable method) (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) totalGametesNonMissingForTaxon() (TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable.GenotypeCallTable method) (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) totalNonMissingForSite() (TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable.GenotypeCallTable method) (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) totalNonMissingForTaxon() (TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable.GenotypeCallTable method) (TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable method) Trait (class in TASSELpy.net.maizegenetics.trait.Trait) TraitTest (class in TASSELpy.test.net.maizegenetics.trait.TraitTest) traitTestSuite (class in TASSELpy.test.net.maizegenetics.trait.traitTestSuite) translateSite() (TASSELpy.net.maizegenetics.dna.snp.FilterGenotypeTable.FilterGenotypeTable method) translateTaxon() (TASSELpy.net.maizegenetics.dna.snp.FilterGenotypeTable.FilterGenotypeTable method) transpose() (TASSELpy.net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix.DoubleMatrix method) transposeData() (TASSELpy.net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable.GenotypeCallTable method) trimTrailingZeros() (TASSELpy.net.maizegenetics.util.BitSet.BitSet method)

U

union() (TASSELpy.net.maizegenetics.util.BitSet.BitSet method) UnionAlignmentPlugin (class in TASSELpy.net.maizegenetics.analysis.data.UnionAlignmentPlugin) UnmodifiableBitSet (class in TASSELpy.net.maizegenetics.util.UnmodifiableBitSet)

use_parent_doc() (TASSELpy.utils.DocInherit.DocInherit method) utilsTestSuite (class in TASSELpy.test.utils.utilsTestSuite) utilTestSuite (class in TASSELpy.test.java.util.utilTestSuite) (class in TASSELpy.test.net.maizegenetics.util.utilTestSuite)

V

value() (TASSELpy.net.maizegenetics.dna.snp.score.AlleleProbability.AlleleProbability method) (TASSELpy.net.maizegenetics.dna.snp.score.Dosage.Dosage method) (TASSELpy.net.maizegenetics.dna.snp.score.ReferenceProbability.ReferenceProbability method) valueForAllele() (TASSELpy.net.maizegenetics.dna.snp.byte2d.Byte2D.Byte2D method)

values() (TASSELpy.java.util.Map.Map method) valuesForAllSites() (TASSELpy.net.maizegenetics.dna.snp.byte2d.Byte2D.Byte2D method)

W

whichIdNumber() (TASSELpy.net.maizegenetics.taxa.distance.DistanceMatrix.DistanceMatrix method) whichTaxon() (TASSELpy.net.maizegenetics.trait.Phenotype.Phenotype method)

whichTrait() (TASSELpy.net.maizegenetics.trait.Phenotype.Phenotype method) wrap_existing_array() (TASSELpy.java.lang.String.String class method) (TASSELpy.javaObj.javaObj class method) (TASSELpy.utils.primativeArray.javaPrimativeArray class method)

X

xor() (TASSELpy.net.maizegenetics.util.BitSet.BitSet method)