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

A

actionPerformed(ActionEvent) - Method in class phylonet.app.tool.APhyloTool

Initializes this tool's parameters dialog, if necessary, and displays it.

ADatum - Class in phylonet.app.model.datum

Represents a single piece of data in the PhyloNet model, along with its identifying name given by the user.

ADatum() - Constructor for class phylonet.app.model.datum.ADatum

ADatumController - Class in phylonet.app.controller.datum

The controller class for an individual datum.

ADatumController(PhyloNetAppController, ADatum, ADatumView) - Constructor for class phylonet.app.controller.datum.ADatumController

Instantiates a new ADatumController with the given parent, model, and view.

ADatumView - Class in phylonet.app.view.datum

Abstract representation of a full-sized window showing a single datum.

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

Instantiates a new datum view with the given title.

add(Object) - Method in interface phylonet.util.ImmutableCollection

This method is not supported.

add(Object) - Method in class phylonet.util.ImmutableCollectionWrapper

add(Object) - Method in class phylonet.util.ImmutableSetWrapper

addActionListener(ActionListener) - Method in class phylonet.app.view.datum.DatumThumbnailView

Adds an ActionListener to the button contained in this thumbnail.

addAll(Collection) - Method in interface phylonet.util.ImmutableCollection

This method is not supported.

addAll(Collection) - Method in class phylonet.util.ImmutableCollectionWrapper

addAll(Collection) - Method in class phylonet.util.ImmutableSetWrapper

addDatum(ADatum) - Method in class phylonet.app.model.PhyloNetAppModel

Adds the given datum to the list of imported data.

addDatumView(ADatumView) - Method in class phylonet.app.view.PhyloNetAppView

Adds the given datum view to the list of views.

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

Add edge (i,j) to the graph that the matching will be computed over where i is the index of the left node, j is the index of the right node, and weight is the weight associated with the edge.

addEvent(HgtEvent) - Method in class phylonet.riatahgt.HgtScenario

This function adds a new event to the list of events contained in this scenario.

addEvents(HgtScenario) - Method in class phylonet.riatahgt.HgtScenario

Add all events from another scenario to this scenario.

addGamma(double) - Method in class phylonet.network.model.bni.BniNetNode

This function adds a new gamma value to the gamma list

addGamma(double) - Method in interface phylonet.network.model.NetNode

This function adds the gamma value stored in this node.

addGraphListener(GraphListener) - Method in interface phylonet.graph.model.MutableGraph

Add an object to be notified when the graph changes.

addGraphListener(GraphListener) - Method in class phylonet.graph.model.sgi.SGIGraph

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

Add a leaf to this cluster.

addLeafToLeft(String) - Method in class phylonet.tree.model.sti.STITreeBipartition

Add a leaf to the left half of the bipartition LEFT | RIGHT.

addLeafToRight(String) - Method in class phylonet.tree.model.sti.STITreeBipartition

Add a leaf to the right half of the bipartition LEFT | RIGHT.

addNonTreeEdge(STINode, STINode) - Method in class phylonet.riatahgt.viewer.TreeCanvas

addThumbnailClickedActionListener(ActionListener) - Method in class phylonet.app.view.datum.ADatumView

Adds an ActionListener to the thumbnail representation of the datum associated with this view.

addTool(APhyloTool) - Method in class phylonet.app.controller.PhyloNetAppController

Adds the supplied tool to this controller's view and this controller's list of managed tools.

addTool(APhyloTool) - Method in class phylonet.app.view.PhyloNetAppView

Creates a new menu item for the supplied tool and adds it to this view's "Calculate" menu.

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

This function connects an existing node (the node that makes a call to this function) to another node child.

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

This function connects an existing node (the node that makes a call to this function) to another node child.

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

This function connects an existing node (the node that makes a call to this function) to another node child.

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

This function connects an existing node (the node that makes a call to this function) to another node child.

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

adoptChild(TMutableNode) - Method in interface phylonet.tree.model.TMutableNode

Move an existing node beneath this node.

align(String, String) - Method in class phylonet.algorithms.pairalignment.SmithWaterman

Perform the local alignment of the two sequences

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

AND the value of this bit vector with another bit vector.

AParamsDialog - Class in phylonet.app.tool

An abstract representation of the parameters dialogs in which the user can supply options to the various PhyloNet tools.

AParamsDialog(Frame, String, PhyloNetAppModel) - Constructor for class phylonet.app.tool.AParamsDialog

Instantiates a new parameters dialog with the given parent frame and tool name.

APhyloTool - Class in phylonet.app.tool

Represents a generalized PhyloNet tool.

APhyloTool(PhyloNetAppController, String, String) - Constructor for class phylonet.app.tool.APhyloTool

Instantiates a new PhyloNet tool using the given top-level controller.

AResultsDialog - Class in phylonet.app.tool

An abstract representation of a results dialog for a calculation.

AResultsDialog(Frame, Date, String) - Constructor for class phylonet.app.tool.AResultsDialog

Creates a new results dialog for a tool with the given title.

ARROW_LENGTH - Static variable in class phylonet.riatahgt.viewer.TreeCanvas

assertEqualsFileContents(File, String) - Static method in class phylonet.PhyloTestCase

assertSetContainsTree(Set<Tree>, Tree) - Static method in class phylonet.PhyloTestCase

Checks whether the supplied set contains the supplied tree.

assertTreeEquals(Tree, Tree) - Static method in class phylonet.PhyloTestCase

Checks whether trees t1 and t2 are identical.

assertTreeEquals(String, Tree, Tree) - Static method in class phylonet.PhyloTestCase

assertTreeEquals(String, String, Tree) - Static method in class phylonet.PhyloTestCase

This method compares a tree to the tree described by a newick string.

assertTreeEquals(String, Tree) - Static method in class phylonet.PhyloTestCase

assignLeafPositions(Tree) - Static method in class phylonet.tree.util.Bipartitions

Generates an assignment of the leaves of the tree to positions in a BitVector.

assignLeafPositions(Tree, Map<String, Integer>) - Static method in class phylonet.tree.util.Bipartitions

Generate an assignment of leaves to positions in a BitVector.

assignNodeTime(STITree<Double>) - Method in class phylonet.ilp.IlpGenerator

Convert the tree with branch lengths into the tree with time.

autoLabelNodes(Network<T>) - Static method in class phylonet.network.util.Networks

This function names internal nodes so that they all have non-empty names.

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

Apply a labeling to ensure that all nodes are labeled in the tree.

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

Apply a labeling to ensure that all nodes are labeled in the tree.