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

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main(String[]) - Static method in class phylonet.app.PhyloNetApp

The PhyloNet application entry point.

main(String[]) - Static method in class phylonet.cmdline.CommandLineApp

main(String[]) - Static method in class phylonet.coalescent.Bootstrap

main(String[]) - Static method in class phylonet.coalescent.ClusteringInference

main(String[]) - Static method in class phylonet.coalescent.CoalescentCounter

main(String[]) - Static method in class phylonet.coalescent.DeepCoalescencesCounter

main(String[]) - Static method in class phylonet.coalescent.DemocraticVoteInference

main(String[]) - Static method in class phylonet.coalescent.GeneTreeRefinement

main(String[]) - Static method in class phylonet.coalescent.GLASSInference

main(String[]) - Static method in class phylonet.coalescent.MajorityConsensusInference

main(String[]) - Static method in class phylonet.coalescent.MDCInference_DP

main(String[]) - Static method in class phylonet.coalescent.MDCInference_ILP

main(String[]) - Static method in class phylonet.coalescent.MDCURInference

main(String[]) - Static method in class phylonet.coalescent.MDCURInference_DP

main(String[]) - Static method in class phylonet.coalescent.MDCURInference_ILP

main(String[]) - Static method in class phylonet.coalescent.MDCWithTime

main(String[]) - Static method in class phylonet.compatibility.TreeCompatibility

main(String[]) - Static method in class phylonet.lca.SchieberVishkinLCA

main(String[]) - Static method in class phylonet.mast.SteelWarnowMAST

This method implements the command-line interface for this class.

main(String[]) - Static method in class phylonet.recomp.RECOMP

main(String[]) - Static method in class phylonet.riatahgt.ExMultipleMasts

This method implements the command-line interface for this class.

main(String[]) - Static method in class phylonet.riatahgt.RiataHgt

main(String[]) - Static method in class phylonet.simulator.SimGTInNetwork

main(String[]) - Static method in class phylonet.symmdiff.SymmetricDifference

main(String[]) - Static method in class phylonet.tree.util.Clustering

main(String[]) - Static method in class phylonet.tree.view.swing.NewickViewer

MajorityConsensusInference - Class in phylonet.coalescent

This class use extended Majority Consensus to infer the species tree from gene trees

MajorityConsensusInference() - Constructor for class phylonet.coalescent.MajorityConsensusInference

MajoritySubpanel - Class in phylonet.app.tool.inferst.subpanel

MajoritySubpanel(Frame) - Constructor for class phylonet.app.tool.inferst.subpanel.MajoritySubpanel

makeDatumController(PhyloNetAppController, ADatum, ADatumView) - Static method in class phylonet.app.controller.datum.ADatumController

Returns a controller of the correct type for the supplied ADatum.

makeDatumView(ADatum) - Static method in class phylonet.app.view.datum.ADatumView

Returns a datum view of the correct type for the supplied datum.

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

makeRoot() - Method in interface phylonet.tree.model.TMutableNode

Reorganize the tree to which this node belongs so that this node is the root of the tree.

makeTree() - Method in class phylonet.network.characterization.NetworkTree

This class returns a STITree counterpart for this network tree.

MastCmdLineTool - Class in phylonet.cmdline.tool

MastCmdLineTool() - Constructor for class phylonet.cmdline.tool.MastCmdLineTool

MASTParamsDialog - Class in phylonet.app.tool.mast

Represents the parameters dialog for the 'mast' tool.

MASTParamsDialog(Frame, PhyloNetAppModel) - Constructor for class phylonet.app.tool.mast.MASTParamsDialog

Instantiates a new parameters dialog with the given parent window.

MASTResultsDialog - Class in phylonet.app.tool.mast

A dialog to display the results of a MAST calculation.

MASTResultsDialog(Frame, Date, TreeDatum, TreeDatum, List<TreeDatum>) - Constructor for class phylonet.app.tool.mast.MASTResultsDialog

Creates a new MAST results dialog based on the given input and output trees.

MastTool - Class in phylonet.app.tool.mast

Represents the MAST tool.

MastTool(PhyloNetAppController) - Constructor for class phylonet.app.tool.mast.MastTool

Instantiates a new MAST tool.

MastWrapper - Class in phylonet.mast

This class is a wrapper class for the two classes SteelWarowMAST and ExMultipleMasts.

MastWrapper() - Constructor for class phylonet.mast.MastWrapper

MastWrapperTestCase - Class in phylonet.mast

MastWrapperTestCase() - Constructor for class phylonet.mast.MastWrapperTestCase

matches(ADatum) - Method in interface phylonet.app.model.DataCriterion

Determines whether a given ADatum meets a set of criteria for data.

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

Returns true if this datum matches the given criterion, or false otherwise.

MaxClique - Class in phylonet.maxclique

Finds maximal cliques and independent sets of graphs.

MaxClique(double[][]) - Constructor for class phylonet.maxclique.MaxClique

Instantiates a new maximum-clique/independent-set finder using the given matrix of data.

MaxCliqueNonParameterizedTestCase - Class in phylonet.maxclique

MaxCliqueNonParameterizedTestCase() - Constructor for class phylonet.maxclique.MaxCliqueNonParameterizedTestCase

MaxCliqueParameterizedTestCase - Class in phylonet.maxclique

MaxCliqueParameterizedTestCase(double[][], double, boolean) - Constructor for class phylonet.maxclique.MaxCliqueParameterizedTestCase

MaxDoubleHeap - Class in phylonet.heaps

An implementation of a MaxHeap that contains key/value pairs that are both primative int types.

MaxDoubleHeap(int) - Constructor for class phylonet.heaps.MaxDoubleHeap

Construct a heap with a fixed capacity.

MaxHeap<N extends java.lang.Number,D> - Class in phylonet.heaps

Basic interface for a max heap.

MaxHeap() - Constructor for class phylonet.heaps.MaxHeap

MaxIntHeap - Class in phylonet.heaps

An implementation of a MaxHeap that contains key/value pairs that are both primative int types.

MaxIntHeap(int) - Constructor for class phylonet.heaps.MaxIntHeap

Construct a heap with a fixed capacity.

MdcDpRootedTimeSubpanel - Class in phylonet.app.tool.inferst.subpanel

MdcDpRootedTimeSubpanel(Frame) - Constructor for class phylonet.app.tool.inferst.subpanel.MdcDpRootedTimeSubpanel

MdcDpSubpanel - Class in phylonet.app.tool.inferst.subpanel

MdcDpSubpanel(Frame) - Constructor for class phylonet.app.tool.inferst.subpanel.MdcDpSubpanel

MdcIlpSubpanel - Class in phylonet.app.tool.inferst.subpanel

MdcIlpSubpanel(Frame) - Constructor for class phylonet.app.tool.inferst.subpanel.MdcIlpSubpanel

MdcIlpTimeSubpanel - Class in phylonet.app.tool.inferst.subpanel

MdcIlpTimeSubpanel(Frame) - Constructor for class phylonet.app.tool.inferst.subpanel.MdcIlpTimeSubpanel

MDCInference_DP - Class in phylonet.coalescent

Class for inferring the species tree from a set of rooted gene trees by minimizing deep coalescence number.

MDCInference_DP() - Constructor for class phylonet.coalescent.MDCInference_DP

MDCInference_ILP - Class in phylonet.coalescent

This class is for inferring the species tree from gene trees, by minimizing the number of coalescences.

MDCInference_ILP() - Constructor for class phylonet.coalescent.MDCInference_ILP

MDCURInference - Class in phylonet.coalescent

Class for inferring the species tree from a set of unrooted gene trees by minimizing deep coalescence number.

MDCURInference() - Constructor for class phylonet.coalescent.MDCURInference

MDCURInference_DP - Class in phylonet.coalescent

Class for inferring the species tree from a set of unrooted gene trees by minimizing deep coalescence number.

MDCURInference_DP() - Constructor for class phylonet.coalescent.MDCURInference_DP

MDCURInference_ILP - Class in phylonet.coalescent

MDCURInference_ILP() - Constructor for class phylonet.coalescent.MDCURInference_ILP

MDCWithTime - Class in phylonet.coalescent

Class for inferring the species tree from a set of unrooted gene trees by minimizing deep coalescence number.

MDCWithTime() - Constructor for class phylonet.coalescent.MDCWithTime

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

Merge with another cluster.

METHOD_SPECIFIC_LEFT_COLUMN_SIZE - Static variable in class phylonet.app.tool.inferst.InferSTParamsDialog

METHOD_SPECIFIC_PARAMETERS_PANEL_SIZE - Static variable in class phylonet.app.tool.inferst.InferSTParamsDialog

MinFibonacciHeap<N extends java.lang.Number,D> - Class in phylonet.heaps

Implementation of a Fibonacci Heap.

MinFibonacciHeap() - Constructor for class phylonet.heaps.MinFibonacciHeap

MinFibonacciHeap.FibonacciHeapEntry - Class in phylonet.heaps

MinFibonacciHeap.FibonacciHeapEntry() - Constructor for class phylonet.heaps.MinFibonacciHeap.FibonacciHeapEntry

MinFibonacciHeapTestCase - Class in phylonet.heaps

MinFibonacciHeapTestCase() - Constructor for class phylonet.heaps.MinFibonacciHeapTestCase

MinHeap<N extends java.lang.Number,D> - Class in phylonet.heaps

MinHeap() - Constructor for class phylonet.heaps.MinHeap

MutableEdge - Interface in phylonet.graph.model

MutableGraph - Interface in phylonet.graph.model

MutableNode - Interface in phylonet.graph.model

MutableTree - Interface in phylonet.tree.model

This interface defines the methods that a tree that can be changed.