A B C D E F G H I L M N O P R S T U V W X Y _

T

t1 - Static variable in class phylonet.simulator.SimGTInNetwork

t2 - Static variable in class phylonet.simulator.SimGTInNetwork

TaxaDistanceMatrix - Class in phylonet.coalescent

TaxaDistanceMatrix(String[]) - Constructor for class phylonet.coalescent.TaxaDistanceMatrix

test1() - Method in class phylonet.fitchpars.ParsimonyCalculatorTestCase

test1() - Method in class phylonet.lca.SchieberVishkinLCATestCase

test2() - Method in class phylonet.lca.SchieberVishkinLCATestCase

testAndOr() - Method in class phylonet.bits.BitVectorTestCase

testBadEvents() - Method in class phylonet.riatahgt.ExRiataMultipleHgtTestCase

testBasic() - Method in class phylonet.algorithms.shortestpath.DijkstraTestCase

testBasic() - Method in class phylonet.algorithms.shortestpath.HershbergerMaxelSuriKSSPTestCase

testBasic() - Method in class phylonet.consensus.ConsensusTestCase

testBasic() - Method in class phylonet.heaps.MinFibonacciHeapTestCase

testBasic() - Method in class phylonet.mast.SteelWarnowMASTTestCase

Test some of the basic settings

testBasic() - Method in class phylonet.nj.NJTestCase

Run some basic tests for correctness

testBasic() - Method in class phylonet.tree.util.CollapseTestCase

testBasic2() - Method in class phylonet.algorithms.shortestpath.DijkstraTestCase

testBasicUnrooted() - Method in class phylonet.consensus.ConsensusTestCase

testBigDifferent() - Method in class phylonet.mast.SteelWarnowMASTTestCase

testBigIdentical() - Method in class phylonet.mast.SteelWarnowMASTTestCase

This dataset tests the MAST performance with a big (100 taxa) identical data set.

testComputeBipartitions() - Method in class phylonet.tree.util.TreesTestCase

testComputeMultipleRMastsRick1() - Method in class phylonet.mast.MastWrapperTestCase

testComputeMultipleRMastsRick2() - Method in class phylonet.mast.MastWrapperTestCase

testConstrainLeaves() - Method in class phylonet.riatahgt.ExRiataMultipleHgtTestCase

testCountCoalescentsRick1() - Method in class phylonet.coalescent.CoalescentCounterTestCase

testCountCoalescentsRick1Reversed() - Method in class phylonet.coalescent.CoalescentCounterTestCase

testDecrement() - Method in class phylonet.bits.BitVectorTestCase

testDerek() - Method in class phylonet.riatahgt.ExRiataMultipleHgtTestCase

testDiff1() - Method in class phylonet.symmdiff.SymmetricDifferenceTestCase

testDifferentLeafSets() - Method in class phylonet.mast.SteelWarnowMASTTestCase

testDiffRoot() - Method in class phylonet.symmdiff.SymmetricDifferenceTestCase

testDuplicateNodes() - Method in class phylonet.network.io.ExNewickReaderTestCase

testEqual() - Method in class phylonet.symmdiff.SymmetricDifferenceTestCase

Test two trees that are identical.

testExplicitRooted() - Method in class phylonet.tree.io.NewickReaderTestCase

testExplicitUnrooted() - Method in class phylonet.tree.io.NewickReaderTestCase

testExtraCharactersAfterSemicolon() - Method in class phylonet.network.io.ExNewickReaderTestCase

testGenerateSpeciesTreesBig() - Method in class phylonet.ilp.IlpGeneratorTestCase

testGenerateSpeciesTreesSmall() - Method in class phylonet.ilp.IlpGeneratorTestCase

testGetSet() - Method in class phylonet.bits.BitVectorTestCase

testHaplotype() - Method in class phylonet.mast.SteelWarnowMASTTestCase

testHaplotypeGraph() - Method in class phylonet.algorithms.shortestpath.HershbergerMaxelSuriKSSPTestCase

This test case came from some research on a haplotype in which we were looking for the shortest paths.

testHidekiUMAST() - Method in class phylonet.mast.SteelWarnowMASTTestCase

testImproperNames() - Method in class phylonet.network.io.ExNewickReaderTestCase

testImproperRootingCharacters() - Method in class phylonet.tree.io.NewickReaderTestCase

testIncrement() - Method in class phylonet.bits.BitVectorTestCase

testLargeTrees() - Method in class phylonet.mast.SteelWarnowMASTTestCase

testLuay1() - Method in class phylonet.riatahgt.RiataHGTTestCase

Pre v.

testMaxClique() - Method in class phylonet.maxclique.MaxCliqueParameterizedTestCase

testMissingEquals() - Method in class phylonet.network.io.ExNewickReaderTestCase

testMissingSemicolons() - Method in class phylonet.network.io.ExNewickReaderTestCase

testNoAmpersand() - Method in class phylonet.tree.io.NewickReaderTestCase

testNoClosingSquareBrace() - Method in class phylonet.tree.io.NewickReaderTestCase

testNonOverlappingTrees() - Method in class phylonet.riatahgt.RiataHGTTestCase

testNonSquareMatrix() - Method in class phylonet.maxclique.MaxCliqueNonParameterizedTestCase

testNumberNames() - Method in class phylonet.tree.io.NewickReaderTestCase

testOneNodeTree() - Method in class phylonet.mast.SteelWarnowMASTTestCase

testOrphanedSubtrees() - Method in class phylonet.network.io.ExNewickReaderTestCase

testOutgroup() - Method in class phylonet.riatahgt.ExMultipleMastsTestCase

The purpose of this function is to test the function addOutgroup and removeOutgroup of SteelWarnowMAST.

testReadingAnotherSequenceAlignment() - Method in class phylonet.sequence.model.SequenceAlignmentTestCase

testReadNetworks() - Method in class phylonet.network.io.ExNewickReaderTestCase

testReadNewickFormatSingleLine() - Method in class phylonet.network.io.ExNewickReaderTestCase

testReadSequencesFromFile() - Method in class phylonet.sequence.model.SequenceAlignmentTestCase

testReadSequencesString() - Method in class phylonet.sequence.model.SequenceAlignmentTestCase

testReadSequencesString2() - Method in class phylonet.sequence.model.SequenceAlignmentTestCase

testRiataViewer() - Method in class phylonet.riatahgt.viewer.RiataViewerFrameTestCase

testRooted() - Method in class phylonet.riatahgt.RiataHGTTestCase

testSimpleRooted() - Method in class phylonet.mct.GaneshkumarWarnowMCTTestCase

testSimpleUnrootedMCLS() - Method in class phylonet.mct.GaneshkumarWarnowMCTTestCase

testSimpleUnrootedMCT() - Method in class phylonet.mct.GaneshkumarWarnowMCTTestCase

testSmallIdentity() - Method in class phylonet.mast.SteelWarnowMASTTestCase

testSomethingElse() - Method in class phylonet.algorithms.bipartitemaching.HungarianTestCase

testSquare() - Method in class phylonet.algorithms.bipartitemaching.HungarianTestCase

testToolCharnetCluster() - Method in class phylonet.cmdline.CommandLineAppTestCase

testToolCharnetTree() - Method in class phylonet.cmdline.CommandLineAppTestCase

testToolCharnetTripartition() - Method in class phylonet.cmdline.CommandLineAppTestCase

testToolCmpNetsCluster() - Method in class phylonet.cmdline.CommandLineAppTestCase

testToolCmpNetsClusterWithoutMeasureArgument() - Method in class phylonet.cmdline.CommandLineAppTestCase

testToolCmpNetsTree() - Method in class phylonet.cmdline.CommandLineAppTestCase

testToolCmpNetsTreeWithoutMeasureArgument() - Method in class phylonet.cmdline.CommandLineAppTestCase

testToolCmpNetsTripartition() - Method in class phylonet.cmdline.CommandLineAppTestCase

testToolCmpNetsTripartitionWithoutMeasureArgument() - Method in class phylonet.cmdline.CommandLineAppTestCase

testToolCountCoal() - Method in class phylonet.cmdline.CommandLineAppTestCase

testToolInferSTInvalidMethod() - Method in class phylonet.cmdline.CommandLineAppTestCase

testToolLCA() - Method in class phylonet.cmdline.CommandLineAppTestCase

testToolMASTMultiple() - Method in class phylonet.cmdline.CommandLineAppTestCase

testToolMASTSingle() - Method in class phylonet.cmdline.CommandLineAppTestCase

testToolNetparsMultiple() - Method in class phylonet.cmdline.CommandLineAppTestCase

testToolRF() - Method in class phylonet.cmdline.CommandLineAppTestCase

testToolRIATAHGT() - Method in class phylonet.cmdline.CommandLineAppTestCase

testTree118() - Method in class phylonet.riatahgt.RiataHGTTestCase

Pre v1.0 RIATA-HGT predicted 2 HGT events on this when the algorithm should have returned one.

testTree31() - Method in class phylonet.riatahgt.RiataHGTTestCase

Pre v1.0 RIATA-HGT predicted 5 HGT events on this when the algorithm should have returned 3.

testTree35() - Method in class phylonet.riatahgt.RiataHGTTestCase

Pre v1.0 RIATA-HGT failed on this case.

testUnderscore() - Method in class phylonet.tree.io.NewickReaderTestCase

testUnrootedException() - Method in class phylonet.lca.SchieberVishkinLCATestCase

testVariousUnexpectedCharacters() - Method in class phylonet.network.io.ExNewickReaderTestCase

testWeird() - Method in class phylonet.lca.SchieberVishkinLCATestCase

testWordWrap() - Method in class phylonet.app.util.DialogsTestCase

TMutableNode - Interface in phylonet.tree.model

This class defines the methods and attributes of a node in a MutableTree.

TNode - Interface in phylonet.tree.model

This class represents a node in a Tree.

toArray() - Method in class phylonet.util.ImmutableCollectionWrapper

toArray(Object[]) - Method in class phylonet.util.ImmutableCollectionWrapper

toArray() - Method in class phylonet.util.ImmutableSetWrapper

toArray(Object[]) - Method in class phylonet.util.ImmutableSetWrapper

toBitSet() - Method in class phylonet.bits.BitVector

toNewick() - Method in class phylonet.tree.model.sti.STINode

toNewick() - Method in class phylonet.tree.model.sti.STITree

toNewick() - Method in interface phylonet.tree.model.Tree

toNewickWD() - Method in class phylonet.tree.model.sti.STITree

toNewickWD() - Method in interface phylonet.tree.model.Tree

toolCharnetShouldRejectInvalidInputFile() - Method in class phylonet.cmdline.CommandLineAppTestCase

toolCharnetShouldRejectInvalidMeasure() - Method in class phylonet.cmdline.CommandLineAppTestCase

toolCharnetShouldRejectMissingFilename() - Method in class phylonet.cmdline.CommandLineAppTestCase

toolCharnetShouldRejectMissingMeasureType() - Method in class phylonet.cmdline.CommandLineAppTestCase

ToolException - Exception in phylonet.cmdline.tool

ToolException(String) - Constructor for exception phylonet.cmdline.tool.ToolException

ToolInitializationException - Exception in phylonet.cmdline.tool

ToolInitializationException(String) - Constructor for exception phylonet.cmdline.tool.ToolInitializationException

toString() - Method in class phylonet.app.model.datum.ADatum

toString() - Method in enum phylonet.app.tool.inferst.InferenceMethod

toString() - Method in class phylonet.bits.BitVector

toString(int) - Method in class phylonet.bits.BitVector

toString() - Method in class phylonet.network.characterization.NetworkCluster

This function prints this cluster.

toString() - Method in class phylonet.network.characterization.NetworkTripartition

This function prints a network to a string.

toString() - Method in class phylonet.recomp.comparator.PAUPAvgMaxComparator

toString() - Method in class phylonet.recomp.comparator.PAUPAvgMinComparator

toString() - Method in class phylonet.recomp.comparator.PAUPIntersectionComparator

toString() - Method in class phylonet.recomp.comparator.PAUPParsDiffComparator

toString() - Method in class phylonet.riatahgt.HgtEvent

toString() - Method in class phylonet.riatahgt.HgtScenario

The method prints events in the list of events.

toString(int) - Method in class phylonet.riatahgt.HgtScenario

toString() - Method in class phylonet.riatahgt.RiataHgt

This function prints the solution.

toString() - Method in interface phylonet.rpt.Printable

toString(int) - Method in interface phylonet.rpt.Printable

toString() - Method in class phylonet.tree.model.sti.STINode

The string version of a node is its name, if it has one.

toString(int) - Method in class phylonet.tree.model.sti.STINode

toString() - Method in class phylonet.tree.model.sti.STITree

toString(int) - Method in class phylonet.tree.model.sti.STITree

toString() - Method in class phylonet.tree.model.sti.STITreeBipartition

Returns the string representation of this biapartition.

toString() - Method in class phylonet.tree.model.sti.STITreeCluster

Returns the string representation of this cluster.

toString() - Method in class phylonet.tree.model.sti.STITreeClusterWD

toString(int) - Method in interface phylonet.tree.model.Tree

Returns a string representation of this tree.

toStringWD() - Method in interface phylonet.tree.model.MutableTree

toStringWD() - Method in class phylonet.tree.model.sti.STITree

toStringWD() - Method in interface phylonet.tree.model.Tree

Tree - Interface in phylonet.tree.model

This interface defines the methods that all trees must implement.

TreeCanvas - Class in phylonet.riatahgt.viewer

TreeCanvas() - Constructor for class phylonet.riatahgt.viewer.TreeCanvas

TreeCompatibility - Class in phylonet.compatibility

TreeCompatibility() - Constructor for class phylonet.compatibility.TreeCompatibility

TreeConsensusCalculator - Class in phylonet.consensus

TreeConsensusCalculator() - Constructor for class phylonet.consensus.TreeConsensusCalculator

TreeDatum - Class in phylonet.app.model.datum

Represents a single tree and its associated identifier.

TreeDatum(Tree) - Constructor for class phylonet.app.model.datum.TreeDatum

Instantiates a new TreeDatum containing the given Tree.

TreeDatumController - Class in phylonet.app.controller.datum

The controller for the TreeDatum model and view.

TreeDatumController(PhyloNetAppController, TreeDatum, TreeDatumView) - Constructor for class phylonet.app.controller.datum.TreeDatumController

Instantiates a new TreeDatumController with the given parent controller, model, and view elements.

TreeDatumView - Class in phylonet.app.view.datum

A concrete implementation of ADatumView to display a full-sized representation of a tree.

TreeDatumView(TreeDatum) - Constructor for class phylonet.app.view.datum.TreeDatumView

Instantiates a new TreeDatumView to be associated with the given datum.

TREES - Static variable in interface phylonet.app.model.DataCriterion

A criterion that matches all types of trees.

Trees - Class in phylonet.tree.util

This class contains some basic routines that are commonly performed on trees.

TREES_OR_BATCHES - Static variable in interface phylonet.app.model.DataCriterion

A criterion that matches all types of trees AND batches of trees.

TREES_WITH_BOOTSTRAPS - Static variable in interface phylonet.app.model.DataCriterion

A criterion that matches trees that contain bootstrap information.

TreesReader - Class in phylonet.network.io

This class reads a network entered as a list of trees represented in the Newick format.

TreesReader(Reader) - Constructor for class phylonet.network.io.TreesReader

TreesTestCase - Class in phylonet.tree.util

TreesTestCase() - Constructor for class phylonet.tree.util.TreesTestCase

TreeView - Class in phylonet.tree.view.swing

This class provides a component that visualizes a tree.

TreeView(Tree, TreeView.TreeStyle) - Constructor for class phylonet.tree.view.swing.TreeView

TreeView.TreeStyle - Enum in phylonet.tree.view.swing

TreeWithBranchLengthsDatum - Class in phylonet.app.model.datum

Represents a single tree, containing bootstrap information, and its associated identifier.

TreeWithBranchLengthsDatum(STITree<Double>) - Constructor for class phylonet.app.model.datum.TreeWithBranchLengthsDatum

Instantiates a new datum associated with the given tree.

TripartitionsReader - Class in phylonet.network.io

This class reads a list of tripartitions.

TripartitionsReader() - Constructor for class phylonet.network.io.TripartitionsReader