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

C

calculateGroups(boolean, double) - Method in class phylonet.maxclique.MaxClique

Returns the set of maximal cliques or maximal independent sets, determined by the supplied cutoff value.

calculateGTDistribution(Network<Double>, List<Tree>, Map<String, String>) - Method in class phylonet.network.gtdistribution.GTDistributionInNetwork

The public function for calculating the probabilities.

canMakeBranch(STITreeClusterWD<D>, List<STITreeClusterWD<D>>) - Method in class phylonet.tree.model.sti.STITreeClusterWD

CharnetClusterResultsDialog - Class in phylonet.app.tool.charnet

Represents a results dialog for the CHARNET tool, after it has been used to calculate the clusters induced from a network.

CharnetClusterResultsDialog(Frame, Date, PhyloNetAppController, NetworkDatum, List<NetworkCluster<Object>>) - Constructor for class phylonet.app.tool.charnet.CharnetClusterResultsDialog

Instantiates a new results dialog for the CHARNET tool that has been used to calculate the clusters of a network.

CharnetCmdLineTool - Class in phylonet.cmdline.tool

This class provides the command line interface to functions that compute the clusters, trees, and tripartitions in a network.

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

CharnetParamsDialog - Class in phylonet.app.tool.charnet

Represents a parameters dialog for the CHARNET tool.

CharnetParamsDialog(Frame, PhyloNetAppModel) - Constructor for class phylonet.app.tool.charnet.CharnetParamsDialog

Instantiates a new parameters dialog for the charnet tool.

CharnetResultsDialog - Class in phylonet.app.tool.charnet

Represents a results dialog for the CHARNET tool.

CharnetResultsDialog(Frame, Date) - Constructor for class phylonet.app.tool.charnet.CharnetResultsDialog

A default constructor used by subclasses of this class.

CharnetTool - Class in phylonet.app.tool.charnet

Represents the CHARNET tool.

CharnetTool(PhyloNetAppController) - Constructor for class phylonet.app.tool.charnet.CharnetTool

Instantiates a new CHARNET tool.

CharnetTreeResultsDialog - Class in phylonet.app.tool.charnet

Represents a results dialog for the CHARNET tool, after it has been used to calculate the trees induced from a network.

CharnetTreeResultsDialog(Frame, Date, PhyloNetAppController, NetworkDatum, List<Tree>) - Constructor for class phylonet.app.tool.charnet.CharnetTreeResultsDialog

Instantiates a new results dialog for the CHARNET tool that has been used to calculate the trees of a network.

CharnetTripartitionResultsDialog - Class in phylonet.app.tool.charnet

Represents a results dialog for the CHARNET tool, after it has been used to calculate the tripartitions induced from a network.

CharnetTripartitionResultsDialog(Frame, Date, PhyloNetAppController, NetworkDatum, List<NetworkTripartition<Object>>) - Constructor for class phylonet.app.tool.charnet.CharnetTripartitionResultsDialog

Instantiates a new results dialog for the CHARNET tool that has been used to calculate the tripartitions of a network.

checkMapping(List<Tree>, Map<String, String>) - Static method in class phylonet.tree.util.Trees

cleanUp() - Static method in class phylonet.ilp.IlpGeneratorTestCase

cleanUp() - Static method in class phylonet.maxclique.MaxCliqueParameterizedTestCase

cleanUpSilently() - Method in class phylonet.cmdline.tool.BootstrapCmdLineTool

cleanUpSilently() - Method in class phylonet.cmdline.tool.CharnetCmdLineTool

cleanUpSilently() - Method in class phylonet.cmdline.tool.CmdLineTool

cleanUpSilently() - Method in class phylonet.cmdline.tool.CmpnetsCmdLineTool

cleanUpSilently() - Method in class phylonet.cmdline.tool.CompatCmdLineTool

cleanUpSilently() - Method in class phylonet.cmdline.tool.CountCoalCmdLineTool

cleanUpSilently() - Method in class phylonet.cmdline.tool.DeepCoalCountCmdLineTool

cleanUpSilently() - Method in class phylonet.cmdline.tool.GenCplexCmdLineTool

cleanUpSilently() - Method in class phylonet.cmdline.tool.GenstCmdLineTool

cleanUpSilently() - Method in class phylonet.cmdline.tool.GTDistrInNetworkCmdLineTool

cleanUpSilently() - Method in class phylonet.cmdline.tool.GTRefineAndRootCmdLineTool

cleanUpSilently() - Method in class phylonet.cmdline.tool.InferStCmdLineTool

cleanUpSilently() - Method in class phylonet.cmdline.tool.LcaCmdLineTool

cleanUpSilently() - Method in class phylonet.cmdline.tool.MastCmdLineTool

cleanUpSilently() - Method in class phylonet.cmdline.tool.NetparsCmdLineTool

cleanUpSilently() - Method in class phylonet.cmdline.tool.RecompCmdLineTool

cleanUpSilently() - Method in class phylonet.cmdline.tool.RfCmdLineTool

cleanUpSilently() - Method in class phylonet.cmdline.tool.RiataHgtCmdLineTool

cleanUpSilently() - Method in class phylonet.cmdline.tool.SimGTInNetworkCmdLineTool

clear() - Method in class phylonet.network.model.bni.BniNetwork

This function clears all nodes in the network.

clear() - Method in interface phylonet.network.model.Network

This function clears all nodes in the network.

clear() - Method in interface phylonet.util.ImmutableCollection

This method is not supported.

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

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

clearData() - Method in class phylonet.app.model.PhyloNetAppModel

Clears the list of imported data.

clearDatumViews() - Method in class phylonet.app.view.PhyloNetAppView

Clears and disposes of all added views, including thumbnails.

clearNonTreeEdges() - Method in class phylonet.riatahgt.viewer.TreeCanvas

clearScenarioTree() - Method in class phylonet.riatahgt.viewer.RiataViewerFrame

CLIQUES - Static variable in class phylonet.maxclique.MaxClique

Used with calculateGroups to indicate that this finder should find maximal cliques.

clone() - Method in class phylonet.network.model.bni.BniNetwork

This function creates an identical copy of this current network.

clone() - Method in interface phylonet.network.model.Network

This function creates an identical copy of this current network.

Clustering - Class in phylonet.tree.util

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

ClusteringInference - Class in phylonet.coalescent

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

ClustersReader<T> - Class in phylonet.network.io

This class is for reading a list of clusters from an input stream.

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

CmdLineTool - Class in phylonet.cmdline.tool

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

CmpnetsCmdLineTool - Class in phylonet.cmdline.tool

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

CmpnetsParamsDialog - Class in phylonet.app.tool.cmpnets

Represents a parameters dialog for the CMPNETS tool.

CmpnetsParamsDialog(Frame, PhyloNetAppModel) - Constructor for class phylonet.app.tool.cmpnets.CmpnetsParamsDialog

Instantiates a new parameters dialog for the CMPNETS tool.

CmpnetsResultsDialog - Class in phylonet.app.tool.cmpnets

Represents a results dialog for the CMPNETS tool.

CmpnetsResultsDialog(Frame, Date, NetworkDatum, NetworkDatum, NetworkCharacterizationMeasure, double[]) - Constructor for class phylonet.app.tool.cmpnets.CmpnetsResultsDialog

Instantiates a new results dialog for the CMPNETS tool.

CmpnetsTool - Class in phylonet.app.tool.cmpnets

Represents the CMPNETS tool.

CmpnetsTool(PhyloNetAppController) - Constructor for class phylonet.app.tool.cmpnets.CmpnetsTool

Instantiates a new CMPNETS tool.

CoalescentCounter - Class in phylonet.coalescent

This class counts the number of coalescents supported by two trees.

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

CoalescentCounterTestCase - Class in phylonet.coalescent

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

collapse(Tree, Tree) - Method in class phylonet.riatahgt.ExMultipleMasts

This method collapses the two trees tr1 and tr2.

Collapse - Class in phylonet.tree.util

This class provides functionality to collapse and restore the shared structure within trees.

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

collapse(MutableTree, MutableTree) - Static method in class phylonet.tree.util.Collapse

Collapse all clades that occur in both t1 and t2.

collapse(List<Tree>) - Static method in class phylonet.tree.util.Collapse

Collapse.CollapseDescriptor - Class in phylonet.tree.util

This class contains the description of what was collapsed by a call to collapse.

Collapse.CollapseDescriptor() - Constructor for class phylonet.tree.util.Collapse.CollapseDescriptor

collapseChains(MutableTree, MutableTree, List<Chain>, List<Chain>) - Method in class phylonet.riatahgt.RiataHgt

Replace identical chains found by findChains by abc-chains.

CollapseTestCase - Class in phylonet.tree.util

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

CommandLineApp - Class in phylonet.cmdline

Provides a general command-line interface to PhyloNet functionality.

CommandLineApp() - Constructor for class phylonet.cmdline.CommandLineApp

CommandLineAppTestCase - Class in phylonet.cmdline

CommandLineAppTestCase() - Constructor for class phylonet.cmdline.CommandLineAppTestCase

compare(int, int, char[][], char[][]) - Method in class phylonet.recomp.comparator.PAUPAvgMaxComparator

compare(int, int, char[][], char[][]) - Method in class phylonet.recomp.comparator.PAUPAvgMinComparator

compare(int, int, char[][], char[][]) - Method in class phylonet.recomp.comparator.PAUPIntersectionComparator

compare(int, int, char[][], char[][]) - Method in class phylonet.recomp.comparator.PAUPParsDiffComparator

compare(int, int, char[][], char[][]) - Method in interface phylonet.recomp.WindowComparator

This method compares two adjacent windows.

compare(N, N) - Static method in class phylonet.util.LIDAMath

A method to compare two numbers.

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

Compares this datum to another datum based on the ordering of their unique IDs.

CompatCmdLineTool - Class in phylonet.cmdline.tool

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

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

computeAllClusters(List<Tree>) - Method in class phylonet.ilp.IlpGenerator

Compute all clusters induced by a list of trees.

computeBipartitions(Tree, Map<String, Integer>, Map<BitVector, TNode>) - Static method in class phylonet.tree.util.Bipartitions

This method computes all the bipartitions contained in a tree and stores them and the node below the edge that induces them in the map h.

computeBipartitions(Tree, String[], Map<BitVector, TNode>) - Static method in class phylonet.tree.util.Bipartitions

computeBipartitions(Tree, Map<String, Integer>) - Static method in class phylonet.tree.util.Bipartitions

This method computes all the bipartitions contained in a tree and returns them in an array.

computeBootstrap() - Method in class phylonet.riatahgt.EventBootstrap

Compute bootstrap values for events in the solution tree.

computeClusterDistance(Network<T>, Network<T>) - Static method in class phylonet.network.util.Networks

This function compute the cluster-based distance between two networks.

computeClusterDistance(List<NetworkCluster<T>>, List<NetworkCluster<T>>) - Static method in class phylonet.network.util.Networks

Compute the cluter-based distance between two networks represented as two lists of clusters.

computeDifference(Tree, Tree) - Method in class phylonet.symmdiff.SymmetricDifference

Compute the symmetric difference between two trees.

computeEdgeSupports(MutableTree, Iterable<Tree>) - Static method in class phylonet.tree.util.Trees

Compute the support for each edge in support_tree to be the fraction of trees in trees that contain that edges.

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

Computes the weights of events returned by computeHgt.

computeHgt(Tree, Tree) - Method in class phylonet.riatahgt.RiataHgt

This function computes all HGT scenarios for the two species and gene trees.

computeMultipleMasts(Tree, Tree) - Method in class phylonet.riatahgt.ExMultipleMasts

This method computes MASTs between the two trees tr1 and tr2.

computeMultipleRMasts(Tree, Tree) - Static method in class phylonet.mast.MastWrapper

This function returns all rooted MASTs for two (rooted) trees.

computeMultipleUMasts(Tree, Tree) - Static method in class phylonet.mast.MastWrapper

This function computes all unrooted MASTs for two (unrooted) trees.

computeNormalizedTreeDistance(Network<T>, Network<T>) - Static method in class phylonet.network.util.Networks

computeNormalizedTreeDistance(List<Tree>, List<Tree>) - Static method in class phylonet.network.util.Networks

computeNumCompatibleBipartitions(STITree<Object>, STITree<Object>) - Static method in class phylonet.tree.util.Trees

Compute the number of incompatible bipartitions.

computeNumCompatibleClusters(STITree<Object>, STITree<Object>) - Static method in class phylonet.tree.util.Trees

Compute the incompatibility of two trees.

computeParsimony(MutableTree, String[], String[]) - Method in class phylonet.fitchpars.ParsimonyCalculator

Compute the parsimony score of the tree given the specified set of sequences.

computeParsimony(MutableTree, String[], String[], Hashtable<TNode, String>) - Method in class phylonet.fitchpars.ParsimonyCalculator

This method computes the parsimony score of the tree and also returns the assignment of sequences to the internal nodes.

computeParsimony(Network<T>, String, int) - Static method in class phylonet.network.util.Networks

This function computes the parsimony for a network N and and a list of sequences.

computeParsimony(Network<T>, SequenceAlignment, int) - Static method in class phylonet.network.util.Networks

This function computes the parsimony for a network N and and a list of sequences.

computeRMAST(Iterable<? extends Tree>) - Method in class phylonet.mast.SteelWarnowMAST

This method computes the rooted mast for a set of trees.

computeRMAST(Tree, Tree) - Method in class phylonet.mast.SteelWarnowMAST

This method computes the rooted maximum agreement subtree for two trees.

computeRootedConsensus(Set<? extends Tree>, double) - Method in class phylonet.consensus.TreeConsensusCalculator

This method computes the consensus of a set of trees.

computeRootedConsensus(Tree[], double) - Method in class phylonet.consensus.TreeConsensusCalculator

Compute the consensus for all the trees in the array.

computeRootedConsensus(Tree[], int, double) - Method in class phylonet.consensus.TreeConsensusCalculator

Compute the consensus for only a subset of the trees in the array.

computeRootedMCLS(Tree, Tree) - Method in class phylonet.mct.GaneshkumarWarnowMCT

This method computes the maximum compatible leaf set (MCLS) of the two trees for their current root.

computeRootedMCT(Tree, Tree) - Method in class phylonet.mct.GaneshkumarWarnowMCT

This method computes the rooted Maximum Compatibility Tree for two trees at their current roots.

computeShortestPaths(double) - Method in class phylonet.algorithms.shortestpath.HershbergerMaxelSuriKSSP

Find all paths with length shorter than or equal to threshold

computeShortestPaths(int) - Method in class phylonet.algorithms.shortestpath.HershbergerMaxelSuriKSSP

Find the k shortest paths in the graph between the specified source and sink.

computeSingleHgt(Tree, Tree) - Method in class phylonet.riatahgt.RiataHgt

computeSingleRMast(Tree, Tree) - Static method in class phylonet.mast.MastWrapper

This function computes a rooted MAST for two rooted trees.

computeSingleUMast(Tree, Tree) - Static method in class phylonet.mast.MastWrapper

This function computes an unrooted MAST for the two (unrooted) trees.

computeSpan(Tree) - Static method in class phylonet.tree.util.Trees

This method computes the maximum distance across the tree specified.

computeTreeClusters(Tree) - Method in class phylonet.ilp.IlpGenerator

Computer clusters induced by a tree.

computeTreeDistance(Network<T>, Network<T>) - Static method in class phylonet.network.util.Networks

This function computes the tree-based distance between two networks.

computeTreeDistance(List<Tree>, List<Tree>) - Static method in class phylonet.network.util.Networks

This function computes the tree-based distance between two networks represented as two lists of trees.

computeTripartitionDistance(Network<T>, Network<T>) - Static method in class phylonet.network.util.Networks

This function computes the tripartition-based distance between two networks.

computeTripartitionDistance(List<NetworkTripartition<T>>, List<NetworkTripartition<T>>) - Static method in class phylonet.network.util.Networks

This function computes the distance between two networks represented as two lists of tripartitions.

computeUMAST(Iterable<? extends Tree>) - Method in class phylonet.mast.SteelWarnowMAST

This method computes the unrooted mast for a set of trees.

computeUMAST(Tree, Tree) - Method in class phylonet.mast.SteelWarnowMAST

This method computes the unrooted maximum agreement subtree for two trees.

computeUnrootedConsensus(Tree[], double) - Method in class phylonet.consensus.TreeConsensusCalculator

computeUnrootedConsensus(Tree[], int, double) - Method in class phylonet.consensus.TreeConsensusCalculator

computeUnrootedConsensus(Set<? extends Tree>, double) - Method in class phylonet.consensus.TreeConsensusCalculator

computeUnrootedMCLS(Tree, Tree) - Method in class phylonet.mct.GaneshkumarWarnowMCT

This method computes the maximum compatible leaf set (MCLS) of the two trees in the unrooted case.

computeUnrootedMCT(Tree, Tree) - Method in class phylonet.mct.GaneshkumarWarnowMCT

This method computes the maximum compatible tree (MCT) for the two trees for any possible rooting.

ConsensusTestCase - Class in phylonet.consensus

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

Consolidate - Class in phylonet.tree.util

This class provides static methods to combine a set of leaves occurring together within two trees to be collapsed into a single leaf.

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

consolidate(MutableTree, MutableTree) - Static method in class phylonet.tree.util.Consolidate

Collapse leaves that are grouped together into a single node.

Consolidate.ConsolidateDescriptor - Class in phylonet.tree.util

This class contains a description of the consolidate operation that can then be used to undo the consolidation.

Consolidate.ConsolidateDescriptor() - Constructor for class phylonet.tree.util.Consolidate.ConsolidateDescriptor

CONSOLIDATE_POSTFIX - Static variable in class phylonet.tree.util.Consolidate

CONSOLIDATE_PREFIX - Static variable in class phylonet.tree.util.Consolidate

constrainByLeaves(Iterable<String>) - Method in interface phylonet.tree.model.MutableTree

constrainByLeaves(Iterable<String>) - Method in class phylonet.tree.model.sti.STITree

This method prunes the tree so that it only contains leaves whose names are in the set leaf_names.

construct(double[][], String[]) - Method in class phylonet.nj.NeighborJoining

This method constructs a tree from the distances given.

contains(Node) - Method in interface phylonet.graph.model.Path

contains(Node) - Method in class phylonet.graph.model.PathImpl

contains(Object) - Method in class phylonet.util.ImmutableCollectionWrapper

contains(Object) - Method in class phylonet.util.ImmutableSetWrapper

containsAll(Collection) - Method in class phylonet.util.ImmutableCollectionWrapper

containsAll(Collection) - Method in class phylonet.util.ImmutableSetWrapper

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

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

Return true if this cluster contains another cluster.

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

Return true if this cluster contains cluster bs.

containsCluster(STITreeClusterWD<D>) - Method in class phylonet.tree.model.sti.STITreeClusterWD

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

Return true if the cluster contains leaf l.

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

This function counts the number of bad events.

CountCoalCmdLineTool - Class in phylonet.cmdline.tool

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

countCoalescents(Tree, Tree) - Method in class phylonet.coalescent.CoalescentCounter

This method counts the number of coalescents that are congruent with the two trees specified.

CountCoalParamsDialog - Class in phylonet.app.tool.countcoal

Represents the parameters dialog for the 'countcoal' tool.

CountCoalParamsDialog(Frame, PhyloNetAppModel) - Constructor for class phylonet.app.tool.countcoal.CountCoalParamsDialog

Instantiates a new parameters dialog for the 'countcoal' tool.

CountCoalResultsDialog - Class in phylonet.app.tool.countcoal

Represents a results dialog for the 'countcoal' tool.

CountCoalResultsDialog(Frame, Date, TreeDatum, TreeDatum, int) - Constructor for class phylonet.app.tool.countcoal.CountCoalResultsDialog

Instantiates a new results dialog for the 'countcoal' tool.

CountCoalTool - Class in phylonet.app.tool.countcoal

Represents the COUNTCOAL tool.

CountCoalTool(PhyloNetAppController) - Constructor for class phylonet.app.tool.countcoal.CountCoalTool

Instantiates a new COUNTCOAL tool.

countExtraCoal(List<Tree>, Tree, boolean, double) - Static method in class phylonet.coalescent.DeepCoalescencesCounter

Compute the number of extra lineages contributed by a species tree and a set of gene tree when single allele is contained

countExtraCoal(List<Tree>, Tree, Map<String, String>, boolean, double) - Static method in class phylonet.coalescent.DeepCoalescencesCounter

Compute the number of extra lineages contributed by a species tree and a set of gene tree when multiple alleles are contained

countExtraCoal(List<Tree>, Network, Map<String, String>) - Static method in class phylonet.coalescent.DeepCoalescencesCounter

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

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

This function counts the number of violated events.

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

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

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

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

Create a new child beneath this node.

createChild(String) - Method in interface phylonet.tree.model.TMutableNode

Create a new child with a specific name beneath this node.

createChild(TNode) - Method in interface phylonet.tree.model.TMutableNode

Create a new child and any subchildren as a child of this node based on a pre-existing node either in this tree or in some other tree.

createDummyNetwork(List<String>) - Static method in class phylonet.network.util.Networks

This function creates a dummy network, which contains just the root and a set of leaves directly connected to the root.

createEdge(int, int) - Method in interface phylonet.graph.model.MutableGraph

Creates an edge between two nodes.

createEdge(int, int, double) - Method in interface phylonet.graph.model.MutableGraph

Creates a weighted edge between two nodes.

createEdge(String, int, int, double) - Method in interface phylonet.graph.model.MutableGraph

Creates a weighted edge between two nodes.

createEdge(MutableNode, MutableNode) - Method in interface phylonet.graph.model.MutableGraph

Creates an edge between two edges.

createEdge(MutableNode, MutableNode, double) - Method in interface phylonet.graph.model.MutableGraph

Creates a weighted edge between two nodes.

createEdge(String, MutableNode, MutableNode, double) - Method in interface phylonet.graph.model.MutableGraph

Creates a weighted edge between two nodes.

createEdge(int, int) - Method in class phylonet.graph.model.sgi.SGIGraph

createEdge(int, int, double) - Method in class phylonet.graph.model.sgi.SGIGraph

createEdge(String, int, int, double) - Method in class phylonet.graph.model.sgi.SGIGraph

createEdge(MutableNode, MutableNode) - Method in class phylonet.graph.model.sgi.SGIGraph

createEdge(MutableNode, MutableNode, double) - Method in class phylonet.graph.model.sgi.SGIGraph

createEdge(String, MutableNode, MutableNode, double) - Method in class phylonet.graph.model.sgi.SGIGraph

createNode() - Method in interface phylonet.graph.model.MutableGraph

createNode(String) - Method in interface phylonet.graph.model.MutableGraph

Create a node with a unique name.

createNode() - Method in class phylonet.graph.model.sgi.SGIGraph

createNode(String, ND) - Method in class phylonet.graph.model.sgi.SGIGraph

createNode(String) - Method in class phylonet.graph.model.sgi.SGIGraph

createRoot(String) - Method in class phylonet.network.model.bni.BniNetwork

This function creates the root for a network.

createRoot(String) - Method in interface phylonet.network.model.Network

This function creates the root for a network.

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

In an empty tree, this method creates a new node which is the root.

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

createToolFromName(String) - Static method in class phylonet.cmdline.tool.CmdLineTool