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

B

BatchDatum - Class in phylonet.app.model.datum

A class to represent sets of data that will be operated upon as a group.

BatchDatum(List<? extends ADatum>) - Constructor for class phylonet.app.model.datum.BatchDatum

Instantiates a new BatchDatum containing the given list of data.

BatchDatumController - Class in phylonet.app.controller.datum

The controller element of the MVC trio for a batch of data.

BatchDatumController(PhyloNetAppController, BatchDatum, BatchDatumView) - Constructor for class phylonet.app.controller.datum.BatchDatumController

Instantiates a new BatchDatumController using the given parent controller, batch datum, and batch datum view.

BatchDatumView - Class in phylonet.app.view.datum

Represents the full-sized window representing a batch of data.

BatchDatumView(BatchDatum) - Constructor for class phylonet.app.view.datum.BatchDatumView

Instantiates a new full-sized view for the given batch of data.

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

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

BfsSearch<T> - Class in phylonet.network.model.bni

This class allows us to visit all nodes under a start node in a network.

BfsSearch(NetNode<T>) - Constructor for class phylonet.network.model.bni.BfsSearch

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

An implementation of a MaxHeap that contains arbitary kinds of data.

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

Construct a heap with a fixed capacity.

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

An implementation of a binary MinHeap.

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

Bipartitions - Class in phylonet.tree.util

This class contains methods related to the bipartitions contained within a tree.
Unless otherwise noted, bipartitions are represented using BitVectors in which each bit represents a leaf in the tree.

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

BITSTRING_FORMAT - Static variable in class phylonet.bits.BitVector

BitVector - Class in phylonet.bits

This class provides an implementation of an arbitrarily long bit vector.

BitVector(int) - Constructor for class phylonet.bits.BitVector

Creates a zero-ed out bit vector of length len.

BitVector(String) - Constructor for class phylonet.bits.BitVector

Creates a bit vector from the string specified.

BitVector(BitVector) - Constructor for class phylonet.bits.BitVector

Creates a bit vector with the same length and value as the specified bit vector.

BitVectorTestCase - Class in phylonet.bits

BitVectorTestCase() - Constructor for class phylonet.bits.BitVectorTestCase

BniNetNode<T> - Class in phylonet.network.model.bni

This class implements the methodes declared in the interface NetNode.

BniNetNode() - Constructor for class phylonet.network.model.bni.BniNetNode

This constructor instantiates an isolated, no-name node.

BniNetNode(String, T) - Constructor for class phylonet.network.model.bni.BniNetNode

This constructor instantiates an isolated node.

BniNetwork<T> - Class in phylonet.network.model.bni

This class implements the methodes declared in the interface Network.

BniNetwork() - Constructor for class phylonet.network.model.bni.BniNetwork

This constructor creates an empty network.

BniNetwork(BniNetNode<T>) - Constructor for class phylonet.network.model.bni.BniNetwork

This constructor creates a network with root as the network's root.

Bootstrap - Class in phylonet.coalescent

This class use bootstrap to infer species tree

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

BootstrapCmdLineTool - Class in phylonet.cmdline.tool

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

breakEdge(NetNode<T>, NetNode<T>, double) - Static method in class phylonet.network.util.NetNodes

This function inserts a binary nodes between nodes tail and head.

BrowseButton - Class in phylonet.app.tool.component

Represents a "Browse" button associated with a given text field.

BrowseButton(Frame, JTextField...) - Constructor for class phylonet.app.tool.component.BrowseButton

Instantiates a new Browse button to be associated with the given text field.

buildCompatibilityGraph(List<Tree>, String[], List<STITreeCluster>) - Method in class phylonet.coalescent.MDCInference_ILP

Construct the compatibility graph.

buildTreeFromClusters(List<STITreeCluster>) - Static method in class phylonet.tree.util.Trees

Build a tree from a list of clusters.