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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handle(Throwable) - Method in class phylonet.app.util.PhyloLogger

Handles Throwables not caught by PhyloNet's main method.

handleBootStrapInTree(Tree, double) - Static method in class phylonet.tree.util.Trees

Extract a tree with a given bootstrap threshold

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

This function checks if the network has duplicate names or not.

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

This function checks if the network has duplicate names or not.

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

hashCode() - Method in class phylonet.riatahgt.HgtEvent

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

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

hasReadError() - Method in class phylonet.sequence.io.FastaReader

hasReadError() - Method in class phylonet.sequence.io.PlainXReader

HershbergerMaxelSuriKSSP - Class in phylonet.algorithms.shortestpath

This class implements the algorithm for finding the K-Shortest Simple Path (KSSP) described by Hershberger, Maxel, and Suri in their 2004 paper entitled Finding the k Shortest Simple Paths: A New Algorithm and its Implementation.
This implementation was adapted from a C++ implementation written by Matthew Maxel.

HershbergerMaxelSuriKSSP(Graph, Node, Node) - Constructor for class phylonet.algorithms.shortestpath.HershbergerMaxelSuriKSSP

HershbergerMaxelSuriKSSP.HMSPath - Class in phylonet.algorithms.shortestpath

HershbergerMaxelSuriKSSP.HMSPath(HershbergerMaxelSuriKSSP.Path) - Constructor for class phylonet.algorithms.shortestpath.HershbergerMaxelSuriKSSP.HMSPath

HershbergerMaxelSuriKSSPTestCase - Class in phylonet.algorithms.shortestpath

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

HGTDatum - Class in phylonet.app.model.datum

Represents a set of solutions resulting from the RIATA-HGT tool.

HGTDatum(RiataHgt) - Constructor for class phylonet.app.model.datum.HGTDatum

Instantiates a new datum containing the supplied RIATA-HGT solution set.

HGTDatumController - Class in phylonet.app.controller.datum

The controller element of the HGT result model-view-controller trio.

HGTDatumController(PhyloNetAppController, HGTDatum, HGTDatumView) - Constructor for class phylonet.app.controller.datum.HGTDatumController

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

HGTDatumView - Class in phylonet.app.view.datum

The full-sized view of a HGT (horizontal gene transfer) solution set.

HGTDatumView(HGTDatum) - Constructor for class phylonet.app.view.datum.HGTDatumView

Instantiates a new view linked to the supplied HGT solution set.

HgtEvent - Class in phylonet.riatahgt

This class models a single HGT event.

HgtEvent(TNode, TNode) - Constructor for class phylonet.riatahgt.HgtEvent

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

This class is for reading and constructing a network from a tree and a set of HGT events.

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

HgtScenario - Class in phylonet.riatahgt

HgtScenario() - Constructor for class phylonet.riatahgt.HgtScenario

HungarianBipartiteMatcher - Class in phylonet.algorithms.bipartitemaching

This class provides an implementation of the Hungarian method for computing the maximum weight matching for a bipartite graph.

HungarianBipartiteMatcher(int, int) - Constructor for class phylonet.algorithms.bipartitemaching.HungarianBipartiteMatcher

This constructor allows the bipartite graph to be manually specified.

HungarianTestCase - Class in phylonet.algorithms.bipartitemaching

HungarianTestCase() - Constructor for class phylonet.algorithms.bipartitemaching.HungarianTestCase