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

N

n - Static variable in class phylonet.simulator.SimGTInNetwork

NAME_PREFIX - Static variable in class phylonet.network.util.Networks

nameAndImportData(List<? extends ADatum>) - Method in class phylonet.app.controller.PhyloNetAppController

Names and imports the supplied set of data, either as individual data or a single batch of data, based on their number, sameness, and user choice.

nameDatumFromUser(Component, ADatumController) - Method in class phylonet.app.controller.PhyloNetAppController

Renames the given datum and updates the appropriate elements of the view.

nameDatumNumerically(ADatumController, String) - Method in class phylonet.app.controller.PhyloNetAppController

Names the supplied datum with the given name, appending a number if the supplied name is not unique.

NeighborJoining - Class in phylonet.nj

This class implements the Neighbor-Joining algorithm.

NeighborJoining() - Constructor for class phylonet.nj.NeighborJoining

NetNode<T> - Interface in phylonet.network.model

This interface defines basic methods that a network node must implement.

NetNodes - Class in phylonet.network.util

This method implements utility methods on network nodes.

NetNodes() - Constructor for class phylonet.network.util.NetNodes

NetparsCmdLineTool - Class in phylonet.cmdline.tool

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

NetparsParamsDialog - Class in phylonet.app.tool.netpars

Represents a parameters dialog for the NETPARS tool.

NetparsParamsDialog(Frame, PhyloNetAppModel) - Constructor for class phylonet.app.tool.netpars.NetparsParamsDialog

Instantiates a new parameters dialog for the NETPARS tool.

NetparsResultsDialog - Class in phylonet.app.tool.netpars

Represents a results dialog for the NETPARS tool.

NetparsResultsDialog(Frame, Date, NetworkDatum, SequenceAlignmentDatum, int, double) - Constructor for class phylonet.app.tool.netpars.NetparsResultsDialog

Instantiates a new results dialog for the NETPARS tool.

NetparsTool - Class in phylonet.app.tool.netpars

Represents the NETPARS tool.

NetparsTool(PhyloNetAppController) - Constructor for class phylonet.app.tool.netpars.NetparsTool

Instantiates a new NETPARS tool.

Network<T> - Interface in phylonet.network.model

This interface defines methods that a network must implement.

NetworkCharacterizationMeasure - Enum in phylonet.network.characterization

NetworkCluster<T> - Class in phylonet.network.characterization

This class defines a tree cluster, which is essentially a set of leaves under a node.

NetworkCluster(Network<T>, List<NetNode<T>>) - Constructor for class phylonet.network.characterization.NetworkCluster

This function constructs a cluster for a given node in a tree generated from a network.

NetworkDatum - Class in phylonet.app.model.datum

Represents a single network and its associated identifier.

NetworkDatum(Network<Object>) - Constructor for class phylonet.app.model.datum.NetworkDatum

Instantiates a new datum for the given network.

NetworkDatumController - Class in phylonet.app.controller.datum

The controller element of the network model-view-controller trio.

NetworkDatumController(PhyloNetAppController, NetworkDatum, NetworkDatumView) - Constructor for class phylonet.app.controller.datum.NetworkDatumController

Instantiates a new controller to manage the supplied model and view.

NetworkDatumView - Class in phylonet.app.view.datum

Represents the full-sized view of a single network datum.

NetworkDatumView(NetworkDatum) - Constructor for class phylonet.app.view.datum.NetworkDatumView

Instantiates a new network datum view to display the supplied network datum.

NetworkEdge<T> - Class in phylonet.network.characterization

This class defines an edge in a network.

NetworkEdge(NetNode<T>, NetNode<T>) - Constructor for class phylonet.network.characterization.NetworkEdge

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

A criterion that matches all networks.

Networks - Class in phylonet.network.util

This class implements methods for decomposing the network into trees, clusters and tripartitions.

Networks() - Constructor for class phylonet.network.util.Networks

NetworkTree<T> - Class in phylonet.network.characterization

This class defines a network configuration from which a tree is built.

NetworkTree(Network<T>, List<NetworkEdge<T>>) - Constructor for class phylonet.network.characterization.NetworkTree

This constructor initializes a network tree.

NetworkTreeEnumerator<T> - Class in phylonet.network.characterization

This class is for enumerating all different sets of network edges chosen to build trees.

NetworkTreeEnumerator(Network<T>) - Constructor for class phylonet.network.characterization.NetworkTreeEnumerator

NetworkTripartition<T> - Class in phylonet.network.characterization

This class defines a network tripartition for a given internal node.

NetworkTripartition(Network<T>, NetNode<T>) - Constructor for class phylonet.network.characterization.NetworkTripartition

This function constructs a network tripartition.

NEWICK_FORMAT - Static variable in interface phylonet.tree.model.Tree

When used with the Printable.toString method, the tree prints itself in newick format.

NewickReader - Class in phylonet.tree.io

This class reads trees in newick format from a stream provided as a Reader.

NewickReader(Reader) - Constructor for class phylonet.tree.io.NewickReader

NewickReaderTestCase - Class in phylonet.tree.io

NewickReaderTestCase() - Constructor for class phylonet.tree.io.NewickReaderTestCase

NewickViewer - Class in phylonet.tree.view.swing

A simple tool for visualizing newick strings as trees.

NewickViewer(String) - Constructor for class phylonet.tree.view.swing.NewickViewer

NewickViewer(Tree) - Constructor for class phylonet.tree.view.swing.NewickViewer

NewickViewer() - Constructor for class phylonet.tree.view.swing.NewickViewer

NewickWriter - Class in phylonet.tree.io

This class writes trees in newick format to a writer.

NewickWriter(Writer) - Constructor for class phylonet.tree.io.NewickWriter

NJTestCase - Class in phylonet.nj

NJTestCase() - Constructor for class phylonet.nj.NJTestCase

NO_DISTANCE - Static variable in interface phylonet.network.model.NetNode

NO_DISTANCE - Static variable in interface phylonet.tree.model.TNode

NO_EDGE - Static variable in class phylonet.algorithms.bipartitemaching.HungarianBipartiteMatcher

NO_NAME - Static variable in interface phylonet.graph.model.GraphComponent

NO_NAME - Static variable in interface phylonet.network.model.NetNode

NO_NAME - Static variable in class phylonet.tree.model.sti.STITree

NO_NAME - Static variable in interface phylonet.tree.model.TNode

NO_NAME - Static variable in interface phylonet.tree.model.Tree

The value returned by getName when the tree does not have a name.

NO_WEIGHT - Static variable in interface phylonet.graph.model.Edge

Node - Interface in phylonet.graph.model

This interface represents a Node that belongs to a single instance of a @link{Graph}.

NODE_WIDTH - Static variable in class phylonet.riatahgt.viewer.TreeCanvas

nodeAdded(int, String) - Method in interface phylonet.graph.model.GraphListener

NodeListReader - Class in phylonet.lca

Provides methods for the reading and parsing of lists of tree or network nodes.

NodeListReader() - Constructor for class phylonet.lca.NodeListReader

nodeRemoved(int, String) - Method in interface phylonet.graph.model.GraphListener

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

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

not() - Method in class phylonet.bits.BitVector

Flip the bits of each bit in this vector