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

P

paintComponent(Graphics) - Method in class phylonet.riatahgt.viewer.TreeCanvas

PAM250 - Static variable in class phylonet.algorithms.pairalignment.SmithWaterman

PAM_CHAR_MAP - Static variable in class phylonet.algorithms.pairalignment.SmithWaterman

ParseException - Exception in phylonet.tree.io

This exception is thrown by readers when a tree is incorrectedly formatted.

ParseException(String) - Constructor for exception phylonet.tree.io.ParseException

parseOptions(String[]) - Method in class phylonet.cmdline.tool.BootstrapCmdLineTool

parseOptions(String[]) - Method in class phylonet.cmdline.tool.CharnetCmdLineTool

parseOptions(String[]) - Method in class phylonet.cmdline.tool.CmdLineTool

parseOptions(String[]) - Method in class phylonet.cmdline.tool.CmpnetsCmdLineTool

parseOptions(String[]) - Method in class phylonet.cmdline.tool.CompatCmdLineTool

parseOptions(String[]) - Method in class phylonet.cmdline.tool.CountCoalCmdLineTool

parseOptions(String[]) - Method in class phylonet.cmdline.tool.DeepCoalCountCmdLineTool

parseOptions(String[]) - Method in class phylonet.cmdline.tool.GenCplexCmdLineTool

parseOptions(String[]) - Method in class phylonet.cmdline.tool.GenstCmdLineTool

parseOptions(String[]) - Method in class phylonet.cmdline.tool.GTDistrInNetworkCmdLineTool

parseOptions(String[]) - Method in class phylonet.cmdline.tool.GTRefineAndRootCmdLineTool

parseOptions(String[]) - Method in class phylonet.cmdline.tool.InferStCmdLineTool

parseOptions(String[]) - Method in class phylonet.cmdline.tool.LcaCmdLineTool

parseOptions(String[]) - Method in class phylonet.cmdline.tool.MastCmdLineTool

parseOptions(String[]) - Method in class phylonet.cmdline.tool.NetparsCmdLineTool

parseOptions(String[]) - Method in class phylonet.cmdline.tool.RecompCmdLineTool

parseOptions(String[]) - Method in class phylonet.cmdline.tool.RfCmdLineTool

parseOptions(String[]) - Method in class phylonet.cmdline.tool.RiataHgtCmdLineTool

parseOptions(String[]) - Method in class phylonet.cmdline.tool.SimGTInNetworkCmdLineTool

ParsimonyCalculator - Class in phylonet.fitchpars

This class computes the parsimony score of a tree as well as along all edges in the tree.

Algorithm reference:
W.

ParsimonyCalculator() - Constructor for class phylonet.fitchpars.ParsimonyCalculator

ParsimonyCalculatorTestCase - Class in phylonet.fitchpars

ParsimonyCalculatorTestCase() - Constructor for class phylonet.fitchpars.ParsimonyCalculatorTestCase

Path - Interface in phylonet.graph.model

This interface defines an abstract representation of a path within a graph.

PathImpl - Class in phylonet.graph.model

This class provides a basic implementation of the Path interface.

PathImpl(Edge[]) - Constructor for class phylonet.graph.model.PathImpl

Build the path from an array of edges.

PAUPAvgMaxComparator - Class in phylonet.recomp.comparator

PAUPAvgMaxComparator(File, int, int, int, PAUPWindowComparator.DistanceMeasure) - Constructor for class phylonet.recomp.comparator.PAUPAvgMaxComparator

PAUPAvgMinComparator - Class in phylonet.recomp.comparator

PAUPAvgMinComparator(File, int, int, int, PAUPWindowComparator.DistanceMeasure) - Constructor for class phylonet.recomp.comparator.PAUPAvgMinComparator

PAUPIntersectionComparator - Class in phylonet.recomp.comparator

PAUPIntersectionComparator(File, int, int, int, PAUPWindowComparator.DistanceMeasure) - Constructor for class phylonet.recomp.comparator.PAUPIntersectionComparator

PAUPParsDiffComparator - Class in phylonet.recomp.comparator

This class implements a Parsimony difference window comparator that uses PAUP's implementation of maximum parsimony.

PAUPParsDiffComparator(File, int, int, int) - Constructor for class phylonet.recomp.comparator.PAUPParsDiffComparator

Construct a comparator that uses the top num_levels of the parsimony trees for a window.

PAUPWindowComparator - Class in phylonet.recomp.comparator

This class provides useful PAUP methods for use by window comparators.

PAUPWindowComparator(File, int, int, PAUPWindowComparator.DistanceMeasure) - Constructor for class phylonet.recomp.comparator.PAUPWindowComparator

PAUPWindowComparator.DistanceMeasure - Enum in phylonet.recomp.comparator

This enumeration is used to specify the standard tree distance measure that will be used by the window comparator

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

PhyloComboBox - Class in phylonet.app.tool.component

An extension of the normal JComboBox that shows only data matching a particular criterion.

PhyloComboBox(DataCriterion, PhyloNetAppModel) - Constructor for class phylonet.app.tool.component.PhyloComboBox

Instantiates a new PhyloComboBox having the given criterion.

PhyloLogger - Class in phylonet.app.util

A utility class for storing logged messages (informational or error-related) which can later be recalled in order to, for example, generate an error log.

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

phylonet.algorithms.bipartitemaching - package phylonet.algorithms.bipartitemaching

phylonet.algorithms.pairalignment - package phylonet.algorithms.pairalignment

phylonet.algorithms.shortestpath - package phylonet.algorithms.shortestpath

phylonet.app.controller - package phylonet.app.controller

phylonet.app.controller.datum - package phylonet.app.controller.datum

phylonet.app.model - package phylonet.app.model

phylonet.app.model.datum - package phylonet.app.model.datum

phylonet.app.tool - package phylonet.app.tool

phylonet.app.tool.charnet - package phylonet.app.tool.charnet

phylonet.app.tool.cmpnets - package phylonet.app.tool.cmpnets

phylonet.app.tool.component - package phylonet.app.tool.component

phylonet.app.tool.countcoal - package phylonet.app.tool.countcoal

phylonet.app.tool.inferst - package phylonet.app.tool.inferst

phylonet.app.tool.inferst.subpanel - package phylonet.app.tool.inferst.subpanel

phylonet.app.tool.lca - package phylonet.app.tool.lca

phylonet.app.tool.mast - package phylonet.app.tool.mast

phylonet.app.tool.netpars - package phylonet.app.tool.netpars

phylonet.app.tool.recomp - package phylonet.app.tool.recomp

phylonet.app.tool.rf - package phylonet.app.tool.rf

phylonet.app.tool.riatahgt - package phylonet.app.tool.riatahgt

phylonet.app.util - package phylonet.app.util

phylonet.app.view - package phylonet.app.view

phylonet.app.view.datum - package phylonet.app.view.datum

phylonet.bits - package phylonet.bits

phylonet.cmdline - package phylonet.cmdline

phylonet.cmdline.tool - package phylonet.cmdline.tool

phylonet.coalescent - package phylonet.coalescent

phylonet.compatibility - package phylonet.compatibility

phylonet.consensus - package phylonet.consensus

phylonet.fitchpars - package phylonet.fitchpars

phylonet.graph.io - package phylonet.graph.io

phylonet.graph.model - package phylonet.graph.model

phylonet.graph.model.sgi - package phylonet.graph.model.sgi

phylonet.heaps - package phylonet.heaps

phylonet.ilp - package phylonet.ilp

phylonet.lca - package phylonet.lca

This package contains implementations of algorithms that solve the Lowest Common Ancestor Retrieval (LCA) Problem.

phylonet.mast - package phylonet.mast

This package contains an implementations of algorithms that solve the Maximum Agreement Subtree (MAST) Problem.

phylonet.maxclique - package phylonet.maxclique

phylonet.mct - package phylonet.mct

phylonet.network.characterization - package phylonet.network.characterization

phylonet.network.gtdistribution - package phylonet.network.gtdistribution

phylonet.network.io - package phylonet.network.io

phylonet.network.model - package phylonet.network.model

phylonet.network.model.bni - package phylonet.network.model.bni

phylonet.nj - package phylonet.nj

phylonet.recomp - package phylonet.recomp

This package contains an implementation of the RECOMP method - a technique for detecting regions of recombination among a set of sequences.

phylonet.recomp.comparator - package phylonet.recomp.comparator

phylonet.riatahgt - package phylonet.riatahgt

phylonet.riatahgt.viewer - package phylonet.riatahgt.viewer

phylonet.rpt - package phylonet.rpt

phylonet.rpt.io - package phylonet.rpt.io

phylonet.sequence.io - package phylonet.sequence.io

phylonet.sequence.model - package phylonet.sequence.model

phylonet.simulator - package phylonet.simulator

phylonet.symmdiff - package phylonet.symmdiff

This package contains implementations of the Symmetric Difference that is calculated on pairs of trees.

phylonet.tree.io - package phylonet.tree.io

phylonet.tree.model - package phylonet.tree.model

phylonet.tree.model.sti - package phylonet.tree.model.sti

phylonet.tree.util - package phylonet.tree.util

phylonet.tree.view.swing - package phylonet.tree.view.swing

phylonet.util - package phylonet.util

PhyloNetApp - Class in phylonet.app

The main executing class for the GUI-based PhyloNet application.

PhyloNetApp() - Constructor for class phylonet.app.PhyloNetApp

PhyloNetAppController - Class in phylonet.app.controller

Represents the main controller of the application.

PhyloNetAppController(PhyloNetAppModel, PhyloNetAppView) - Constructor for class phylonet.app.controller.PhyloNetAppController

Instantiates a new controller for the given model and view.

PhyloNetAppModel - Class in phylonet.app.model

Encapsulates the top-level state (model) of the PhyloNet application.

PhyloNetAppModel() - Constructor for class phylonet.app.model.PhyloNetAppModel

Instantiates a new model, which begins with an empty list of data.

PhyloNetAppView - Class in phylonet.app.view

Represents the view of the application's main screen, the workspace screen.

PhyloNetAppView() - Constructor for class phylonet.app.view.PhyloNetAppView

Instantiates a new view for the application.

PhyloTestCase - Class in phylonet

This class provides assert methods for more advanced data-types, including trees.

PhyloTestCase() - Constructor for class phylonet.PhyloTestCase

PhyloTextArea - Class in phylonet.app.tool.component

Represents a monospaced, uneditable text area.

PhyloTextArea(String) - Constructor for class phylonet.app.tool.component.PhyloTextArea

Instantiates a new monospaced, uneditable text area with the given text.

PhyloTextField - Class in phylonet.app.tool.component

Represents a monospaced, uneditable text field.

PhyloTextField(String) - Constructor for class phylonet.app.tool.component.PhyloTextField

Instantiates a new monospaced, uneditable text field with the given text.

PlainXReader - Class in phylonet.sequence.io

This reader can extract sequences from plain file formats - files that contain one sequence per line.

PlainXReader(File) - Constructor for class phylonet.sequence.io.PlainXReader

PlainXReader(Reader) - Constructor for class phylonet.sequence.io.PlainXReader

PlainXReader(String) - Constructor for class phylonet.sequence.io.PlainXReader

PlainXReader.PlainXRecord - Class in phylonet.sequence.io

This class holds the data for a single Plain sequence.

PostTraversal<D> - Class in phylonet.tree.util

An iterable class that allows us to visit the tree in the post order.

PostTraversal(TNode) - Constructor for class phylonet.tree.util.PostTraversal

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

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

Traverse the tree in the post order.

postTraverse() - Method in interface phylonet.tree.model.TNode

postTraverse() - Method in interface phylonet.tree.model.Tree

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

This function preprocesses the two trees before RiataHgt computes HGT events.

Printable - Interface in phylonet.rpt

This interface provides quick methods for printing a representation of the object for debugging or text inspection.

printAdjacencyLists(PrintStream) - Method in class phylonet.maxclique.MaxClique

Prints the current adjacency lists to the supplied output stream.

printDebugMsg(String) - Static method in class phylonet.cmdline.CommandLineApp

printMatrix(PrintStream) - Method in class phylonet.maxclique.MaxClique

Prints the current adjacency matrix to the supplied output stream.

printNameAndComputations(Network<String>, PrintStream) - Method in enum phylonet.network.characterization.NetworkCharacterizationMeasure

printUsage(PrintStream) - Method in class phylonet.cmdline.tool.BootstrapCmdLineTool

printUsage(PrintStream) - Method in class phylonet.cmdline.tool.CharnetCmdLineTool

printUsage(PrintStream) - Method in class phylonet.cmdline.tool.CmdLineTool

printUsage(PrintStream) - Method in class phylonet.cmdline.tool.CmpnetsCmdLineTool

printUsage(PrintStream) - Method in class phylonet.cmdline.tool.CompatCmdLineTool

printUsage(PrintStream) - Method in class phylonet.cmdline.tool.CountCoalCmdLineTool

printUsage(PrintStream) - Method in class phylonet.cmdline.tool.DeepCoalCountCmdLineTool

printUsage(PrintStream) - Method in class phylonet.cmdline.tool.GenCplexCmdLineTool

printUsage(PrintStream) - Method in class phylonet.cmdline.tool.GenstCmdLineTool

printUsage(PrintStream) - Method in class phylonet.cmdline.tool.GTDistrInNetworkCmdLineTool

printUsage(PrintStream) - Method in class phylonet.cmdline.tool.GTRefineAndRootCmdLineTool

printUsage(PrintStream) - Method in class phylonet.cmdline.tool.InferStCmdLineTool

printUsage(PrintStream) - Method in class phylonet.cmdline.tool.LcaCmdLineTool

printUsage(PrintStream) - Method in class phylonet.cmdline.tool.MastCmdLineTool

printUsage(PrintStream) - Method in class phylonet.cmdline.tool.NetparsCmdLineTool

printUsage(PrintStream) - Method in class phylonet.cmdline.tool.RecompCmdLineTool

printUsage(PrintStream) - Method in class phylonet.cmdline.tool.RfCmdLineTool

printUsage(PrintStream) - Method in class phylonet.cmdline.tool.RiataHgtCmdLineTool

printUsage(PrintStream) - Method in class phylonet.cmdline.tool.SimGTInNetworkCmdLineTool

printUsage() - Static method in class phylonet.coalescent.Bootstrap

Print the help information of the command format

printUsage(PrintStream) - Static method in class phylonet.coalescent.CoalescentCounter

printUsage() - Static method in class phylonet.coalescent.DeepCoalescencesCounter

Print the help information of the command format

printUsage() - Static method in class phylonet.coalescent.GeneTreeRefinement

Print the help information of the command format

printUsage() - Static method in class phylonet.compatibility.TreeCompatibility

printUsage() - Static method in class phylonet.ilp.IlpGenerator

Print help message about how to use

printUsage() - Static method in class phylonet.lca.SchieberVishkinLCA

printUsage(PrintStream) - Static method in class phylonet.recomp.RECOMP

printUsage() - Static method in class phylonet.riatahgt.ExMultipleMasts

This method prints the usage information for the command-line MAST interface.

printUsage() - Static method in class phylonet.riatahgt.RiataHgt

Print the usage for the RiataHGT command-line tool

printUsage(boolean) - Static method in class phylonet.simulator.SimGTInNetwork

Print the help information of the command format

printUsage() - Static method in class phylonet.symmdiff.SymmetricDifference

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

Refine and root a set of gene trees optimally with respect to a given species tree

pruneLeaves(MutableTree, MutableTree) - Static method in class phylonet.tree.util.Trees

This function prunes leaves that are in either one of the two trees, but not both.

pruneNetworks(Network<T>, Network<T>) - Method in class phylonet.network.util.Networks

Restrict network 1 and network 2 on the common set of leaves.

put(STITreeCluster, double) - Method in class phylonet.coalescent.TaxaDistanceMatrix