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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saveImage(File) - Method in class phylonet.app.view.datum.HGTDatumView

Saves the currently-shown tree image to the specified file.

saveImage(File) - Method in class phylonet.riatahgt.viewer.TreeCanvas

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

Scale the branch lengths of the tree by a specified amount.

SchieberVishkinLCA - Class in phylonet.lca

This class implements the LCA algorithm first described by Harel and Tarjan in their 1984 paper Fast algorithms for finding nearest common ancestors and then simplified by Schieber and Vishkin in 1988 in their paper On finding lowest common ancestors: simplications and parallelization.

SchieberVishkinLCA(Tree) - Constructor for class phylonet.lca.SchieberVishkinLCA

Construct an object that will return the LCA for nodes in the specified tree.

SchieberVishkinLCATestCase - Class in phylonet.lca

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

selectRandomNode(boolean, boolean) - Method in class phylonet.tree.model.sti.STITree

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

A criterion that matches all sequence alignments.

SequenceAlignment - Class in phylonet.sequence.model

This class defines a sequence alignment for computing the network parsimony.

SequenceAlignment(String[], String[]) - Constructor for class phylonet.sequence.model.SequenceAlignment

This constructor constructs a sequence alignment from an array of taxon names and an array of strings representing sequences.

SequenceAlignment() - Constructor for class phylonet.sequence.model.SequenceAlignment

Instantiates a new, empty sequence alignment.

SequenceAlignmentDatum - Class in phylonet.app.model.datum

Represents a single list of genetic sequences.

SequenceAlignmentDatum(SequenceAlignment) - Constructor for class phylonet.app.model.datum.SequenceAlignmentDatum

Instantiates a new sequence list datum representing the given sequence alignment.

SequenceAlignmentDatumController - Class in phylonet.app.controller.datum

The controller element for the sequence list datum model and view.

SequenceAlignmentDatumController(PhyloNetAppController, SequenceAlignmentDatum, SequenceAlignmentDatumView) - Constructor for class phylonet.app.controller.datum.SequenceAlignmentDatumController

Instantiates a new controller for the given model and view.

SequenceAlignmentDatumView - Class in phylonet.app.view.datum

Represents the full-sized view of a single sequence alignment.

SequenceAlignmentDatumView(SequenceAlignmentDatum) - Constructor for class phylonet.app.view.datum.SequenceAlignmentDatumView

Instantiates a new full-sized view of the supplied sequence alignment.

SequenceAlignmentTestCase - Class in phylonet.sequence.model

SequenceAlignmentTestCase() - Constructor for class phylonet.sequence.model.SequenceAlignmentTestCase

SequenceException - Exception in phylonet.sequence.model

An Exception type used by SequenceAlignment whenever an invalidly-formatted sequence is parsed.

SequenceException(String) - Constructor for exception phylonet.sequence.model.SequenceException

SequenceException(String, Throwable) - Constructor for exception phylonet.sequence.model.SequenceException

SequenceException(Throwable) - Constructor for exception phylonet.sequence.model.SequenceException

setBipartition(BitSet, BitSet) - Method in class phylonet.tree.model.sti.STITreeBipartition

Set left and right halves of this bipartition.

setClearWorkspaceAction(Action) - Method in class phylonet.app.view.PhyloNetAppView

Sets the action to be performed when the user selects the "Clear Workspace" menu item.

setCloseAction(Action) - Method in class phylonet.app.view.datum.ADatumView

Sets the Action to be performed when the user selects the "Close" menu item.

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

Set a bit vector that represents this cluster.

setCountNodesAction(Action) - Method in class phylonet.app.view.datum.TreeDatumView

Sets the action to be performed when the user selects the "Count Nodes" menu item.

setCplexPath(String) - Method in class phylonet.coalescent.MDCInference_ILP

Set the path to the CPLEX program.

setData(List<ADatum>) - Method in class phylonet.app.model.PhyloNetAppModel

Sets the list of data to the supplied list.

setData(ED) - Method in class phylonet.graph.model.sgi.SGIEdge

setData(ED) - Method in class phylonet.graph.model.sgi.SGIGraph

setData(ND) - Method in class phylonet.graph.model.sgi.SGINode

setData(T) - Method in class phylonet.network.model.bni.BniNetNode

This function updates the data stored in this node.

setData(T) - Method in interface phylonet.network.model.NetNode

This function updates data stored in this node.

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

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

setDeleteDatumAction(Action) - Method in class phylonet.app.view.datum.ADatumView

Sets the Action to be performed when the user selects the "Delete Datum" menu item.

setDimensions(int, int) - Method in class phylonet.algorithms.bipartitemaching.HungarianBipartiteMatcher

setExportDatumAction(Action) - Method in class phylonet.app.view.datum.ADatumView

Sets the action to be performed when the user selects the "Export Datum" menu item.

setGamma(int, double) - Method in class phylonet.network.model.bni.BniNetNode

This function resets the gamma value of the index_th child

setGamma(int, double) - Method in interface phylonet.network.model.NetNode

This function updates the gamma value stored in this node.

setId(String) - Method in class phylonet.app.model.datum.ADatum

Sets the unique ID of this datum.

setImportNetworkAction(Action) - Method in class phylonet.app.view.PhyloNetAppView

Sets the action to be performed when the user selects the "Import > Network..." menu item.

setImportSequenceAlignmentAction(Action) - Method in class phylonet.app.view.PhyloNetAppView

Sets the action to be performed when the user selects the "Import > Sequence Alignment..." menu item.

setImportTreeAction(Action) - Method in class phylonet.app.view.PhyloNetAppView

Sets the action to be performed when the user selects the "Import > Tree(s)" menu item.

setImportTreeWithBranchLengthsAction(Action) - Method in class phylonet.app.view.PhyloNetAppView

Sets the action to be performed when the user selects the "Import > Tree(s) with Branch Lengths..." menu item.

setInputEdgeWeightsAreSupports(boolean) - Method in class phylonet.consensus.TreeConsensusCalculator

If this property is set to true, then edge weights on input trees are interpretted as existing edge supports.

setLoadWorkspaceAction(Action) - Method in class phylonet.app.view.PhyloNetAppView

Sets the action to be performed when the user selects the "Load Workspace" menu item.

setMissingCharacter(char) - Method in class phylonet.fitchpars.ParsimonyCalculator

Set the character that will be treated as a missing or gap character.

setName(String) - Method in class phylonet.network.model.bni.BniNetNode

This function changes the name of this node.

setName(String) - Method in interface phylonet.network.model.NetNode

This function changes the name of an existing node.

setName(String) - Method in interface phylonet.tree.model.MutableTree

Set the name of the tree.

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

Duplicate node names are not allowed.

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

setName(String) - Method in interface phylonet.tree.model.TMutableNode

Set the name of this node.

setOutputEdgeWeightsAreSupports(boolean) - Method in class phylonet.consensus.TreeConsensusCalculator

setParentDistance(NetNode<T>, double) - Method in class phylonet.network.model.bni.BniNetNode

This functions sets the distance from this calling node to parent with the new value newDistance.

setParentDistance(NetNode<T>, double) - Method in interface phylonet.network.model.NetNode

This functions sets the distance from this calling node to parent with the new value newDistance.

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

setParentDistance(double) - Method in interface phylonet.tree.model.TMutableNode

Set the distance between this node and its parent.

setParentDistance(double) - Method in interface phylonet.tree.model.TNode

set the distance between this node and its parent.

setPath(String) - Method in class phylonet.coalescent.MDCURInference_ILP

setPrefix(String) - Method in class phylonet.riatahgt.RiataHgt

This function sets a string used to label internal node.

setPrinting(boolean) - Static method in class phylonet.coalescent.DemocraticVoteInference

setPrinting(boolean) - Static method in class phylonet.coalescent.GLASSInference

setPrinting(boolean) - Static method in class phylonet.coalescent.MajorityConsensusInference

setPrinting(boolean) - Static method in class phylonet.coalescent.MDCInference_DP

setPrinting(boolean) - Static method in class phylonet.coalescent.MDCInference_ILP

setPrinting(boolean) - Static method in class phylonet.coalescent.MDCURInference_DP

setPrinting(boolean) - Static method in class phylonet.coalescent.MDCURInference_ILP

setPrinting(boolean) - Static method in class phylonet.coalescent.MDCWithTime

setQuitAction(Action) - Method in class phylonet.app.view.PhyloNetAppView

Sets the action to be performed when the user selects the "Quit" menu item.

setRenameDatumAction(Action) - Method in class phylonet.app.view.datum.ADatumView

Sets the Action to be performed when the user selects the "Rename Datum" menu item.

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

setSaveImageAction(Action) - Method in class phylonet.app.view.datum.HGTDatumView

Sets the action to be performed when the user selects the "File > Save Image..." menu item.

setSaveWorkspaceAction(Action) - Method in class phylonet.app.view.PhyloNetAppView

Sets the action to be performed when the user selects the "Save Workspace" menu item.

setScenarioTree(STITree<List<HgtScenario>>) - Method in class phylonet.app.view.datum.HGTDatumView

Sets the tree of HGT events to be displayed by this view.

setScenarioTree(STITree<List<HgtScenario>>) - Method in class phylonet.riatahgt.viewer.RiataViewerFrame

setSfWeight(double) - Method in class phylonet.ilp.IlpGenerator

Set weight for sf.

setSgWeight(double) - Method in class phylonet.ilp.IlpGenerator

Set weight for sg.

setSpeciesTree(STITree) - Method in class phylonet.riatahgt.viewer.RiataViewerFrame

setTaxa(List<String>) - Method in class phylonet.ilp.IlpGenerator

setText(String) - Method in class phylonet.app.view.datum.DatumThumbnailView

Sets the text to be displayed by this thumbnail.

setTree(Tree) - Method in class phylonet.riatahgt.viewer.TreeCanvas

setTree(Tree) - Method in class phylonet.tree.view.swing.TreeView

setValue(int, boolean) - Method in class phylonet.bits.BitVector

Set the value of a single bit in this vector.

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

Set the value of this bit vector to exactly the value of the provided vector.

setVisible(boolean) - Method in class phylonet.app.tool.AParamsDialog

SGIEdge<ND,ED> - Class in phylonet.graph.model.sgi

SGIGraph<ND,ED> - Class in phylonet.graph.model.sgi

This class provides a generic implementation of the MutableGraph class so that new types of graphs can be quickly created.

SGIGraph(boolean) - Constructor for class phylonet.graph.model.sgi.SGIGraph

SGINode<ND,ED> - Class in phylonet.graph.model.sgi

SGINode() - Constructor for class phylonet.graph.model.sgi.SGINode

SGINode(String) - Constructor for class phylonet.graph.model.sgi.SGINode

showConfirm(Component, String, String) - Static method in class phylonet.app.util.Dialogs

Reveals a confirmation dialog displaying the provided message and title.

showError(Component, String, String) - Static method in class phylonet.app.util.Dialogs

Reveals an error dialog displaying the provided error message and title.

showErrorWithSubmission(Frame, String, String, Throwable) - Static method in class phylonet.app.util.Dialogs

Reveals a special error dialog displaying the provided error message and title, along with an extra line asking the user to aid PhyloNet's development by submitting an error report.

showInput(Component, String, String) - Static method in class phylonet.app.util.Dialogs

Reveals an input dialog displaying the provided message and title.

showLoadFileDialog(Frame, String) - Static method in class phylonet.app.util.Dialogs

Reveals a file-loading dialog displaying the provided message.

showOptionDialog(Component, String, String, int, int, Object[], Object) - Static method in class phylonet.app.util.Dialogs

Reveals an option dialog with the specified type allowing the user to select from among the specified options.

showPlainMessageDialog(Component, String, String) - Static method in class phylonet.app.util.Dialogs

Reveals a plain message dialog displaying the provided message and title.

showSaveFileDialog(Frame, String, String) - Static method in class phylonet.app.util.Dialogs

Reveals a file-saving dialog displaying the provided message.

showWarning(Component, String, String) - Static method in class phylonet.app.util.Dialogs

Reveals an warning dialog displaying the provided warning message and title.

SimGTInNetwork - Class in phylonet.simulator

SimGTInNetwork() - Constructor for class phylonet.simulator.SimGTInNetwork

SimGTInNetworkCmdLineTool - Class in phylonet.cmdline.tool

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

size() - Method in class phylonet.util.ImmutableCollectionWrapper

size() - Method in class phylonet.util.ImmutableSetWrapper

SmithWaterman - Class in phylonet.algorithms.pairalignment

This class provides an implementation of the Smith-Waterman pairwise local sequence alignment algorithm.

SmithWaterman(int[][], String, int) - Constructor for class phylonet.algorithms.pairalignment.SmithWaterman

SmithWaterman.Match - Class in phylonet.algorithms.pairalignment

This class is used to report a single match in an alignment.

Solution - Class in phylonet.coalescent

This class saves the result of multiple versions of MDC

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

SteelWarnowMAST - Class in phylonet.mast

This class implements the algorithm for solving the Maximum Agreement Subtree Problem (MAST) described in the paper by Mike Steel and Tandy Warnow entitled Kaikoura tree theorems: Computing the maximum agreement subtree.

SteelWarnowMAST() - Constructor for class phylonet.mast.SteelWarnowMAST

SteelWarnowMASTTestCase - Class in phylonet.mast

SteelWarnowMASTTestCase() - Constructor for class phylonet.mast.SteelWarnowMASTTestCase

STINode<D> - Class in phylonet.tree.model.sti

STITree<D> - Class in phylonet.tree.model.sti

This class provides an implementation of a mutable tree whose nodes contain a specific type of data.

STITree() - Constructor for class phylonet.tree.model.sti.STITree

Create a rooted tree with only one node.

STITree(String) - Constructor for class phylonet.tree.model.sti.STITree

Construct a tree from the newick string.

STITree(boolean) - Constructor for class phylonet.tree.model.sti.STITree

Create a tree with a specified rootedness.

STITree(String, boolean) - Constructor for class phylonet.tree.model.sti.STITree

Creates a new tree.

STITree(Tree) - Constructor for class phylonet.tree.model.sti.STITree

Make a copy of the specified tree.

STITree(TNode) - Constructor for class phylonet.tree.model.sti.STITree

Creates a new rooted tree with root as the root of the tree.

STITree(TNode, boolean) - Constructor for class phylonet.tree.model.sti.STITree

Creates a new tree with root as the root of the tree.

STITreeBipartition - Class in phylonet.tree.model.sti

A class for representing a tree bipartition.

STITreeBipartition(String[]) - Constructor for class phylonet.tree.model.sti.STITreeBipartition

Create a trivial bipartition, that is, \emptyset | X.

STITreeCluster - Class in phylonet.tree.model.sti

A class for representing a tree cluster.

STITreeCluster(String[]) - Constructor for class phylonet.tree.model.sti.STITreeCluster

Create an empty cluster.

STITreeCluster(STITreeCluster) - Constructor for class phylonet.tree.model.sti.STITreeCluster

Make the same copy of this cluster

STITreeClusterWD<D> - Class in phylonet.tree.model.sti

STITreeClusterWD(STITreeCluster) - Constructor for class phylonet.tree.model.sti.STITreeClusterWD

STITreeClusterWD(STITreeClusterWD<D>) - Constructor for class phylonet.tree.model.sti.STITreeClusterWD

STITreeClusterWD(STITreeCluster, D) - Constructor for class phylonet.tree.model.sti.STITreeClusterWD

STITreeClusterWD(String[]) - Constructor for class phylonet.tree.model.sti.STITreeClusterWD

SymmetricDifference - Class in phylonet.symmdiff

This is an implementation of the Symmetric Difference tree metric.

SymmetricDifference() - Constructor for class phylonet.symmdiff.SymmetricDifference

SymmetricDifferenceTestCase - Class in phylonet.symmdiff

SymmetricDifferenceTestCase() - Constructor for class phylonet.symmdiff.SymmetricDifferenceTestCase