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

D

DataCriterion - Interface in phylonet.app.model

This interface provides methods to match data elements in PhyloNet against certain criteria.

DatumThumbnailView - Class in phylonet.app.view.datum

Represents the thumbnail view of an individual datum in the workspace.

DatumThumbnailView(ADatum) - Constructor for class phylonet.app.view.datum.DatumThumbnailView

Instantiates a new thumbnail view to be associated with the supplied datum.

decreaseKey(MinFibonacciHeap<N, D>.FibonacciHeapEntry, N) - Method in class phylonet.heaps.MinFibonacciHeap

This call decreases the key value of the pair n to the specified value.

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

Decrement the value of this bit-vector

DeepCoalCountCmdLineTool - Class in phylonet.cmdline.tool

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

DeepCoalescencesCounter - Class in phylonet.coalescent

This class counts the number of deep coalescences for a species tree given a set of gene trees.

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

DEFAULT_INSETS - Static variable in class phylonet.app.tool.AParamsDialog

DEFAULT_LABEL_ALIGNMENT - Static variable in class phylonet.app.tool.AParamsDialog

DEFAULT_WRAP_WIDTH - Static variable in class phylonet.app.util.Dialogs

The default maximum number of characters do display in a single line of any dialog.

DemocraticVoteInference - Class in phylonet.coalescent

This class uses democratic vote to infer the species tree from gene trees

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

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

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

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

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

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

Dialogs - Class in phylonet.app.util

Provides convenience methods for displaying common dialogs used throughout PhlyoNet.

Dialogs() - Constructor for class phylonet.app.util.Dialogs

DialogsTestCase - Class in phylonet.app.util

DialogsTestCase(String, int, String) - Constructor for class phylonet.app.util.DialogsTestCase

Dijkstra - Class in phylonet.algorithms.shortestpath

This class implements a version of Dijkstra's single-source shortest path algorithm for both directed and undirected graphs.

Dijkstra(Graph) - Constructor for class phylonet.algorithms.shortestpath.Dijkstra

DijkstraTestCase - Class in phylonet.algorithms.shortestpath

DijkstraTestCase() - Constructor for class phylonet.algorithms.shortestpath.DijkstraTestCase

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

This function tells RiataHgt not to collapse the trees before computing HGT events.

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

This function tells RiataHgt not to refine the trees before computing HGT events.

doClustering(List<Tree>, int, int, int, double, int) - Method in class phylonet.tree.util.Clustering

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