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

R

randomSeq(Double, Double) - Static method in class phylonet.rpt.Iterating

Produces an iterable sequence of random numbers in a certain range.

range(Integer, Integer) - Static method in class phylonet.rpt.Iterating

range(Integer, Integer, Integer) - Static method in class phylonet.rpt.Iterating

Produces an iterable object that produces numbers from start up to (not including) end.

reachedEOF() - Method in class phylonet.tree.io.NewickReader

Indicates whether the end of the reader has been reached.

readClusters() - Method in class phylonet.network.io.ClustersReader

readFastaSequences(Reader) - Method in class phylonet.sequence.model.SequenceAlignment

Reads a set of sequences in the FASTA format from the supplied Reader.

readHgt() - Method in class phylonet.network.io.HgtReader

This function builds a network from a tree and a set of HGT events.

readNetwork() - Method in class phylonet.network.io.ExNewickReader

This function reads a set of lines representing the network and builds the corresponding network.

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

Read the next Fasta sequence entry in this file.

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

readPhylipSequences(Reader) - Method in class phylonet.sequence.model.SequenceAlignment

Implementation to read sequences in PHYLIP format (either sequential or interleaved).

readPhyloNetSequences(Reader) - Method in class phylonet.sequence.model.SequenceAlignment

Reads sequences, together with their corresponding taxa names.

readSequences(String) - Method in class phylonet.sequence.model.SequenceAlignment

Parse the raw input sequence input.

readTree() - Method in class phylonet.tree.io.NewickReader

This method reads in a tree and returns the tree read in.

readTree(STITree<Double>) - Method in class phylonet.tree.io.NewickReader

This method reads a tree from the reader.

readTree(MutableTree) - Method in class phylonet.tree.io.NewickReader

This method reads a tree from the reader.

readTreeName() - Method in class phylonet.tree.io.NewickReader

readTrees() - Method in class phylonet.network.io.TreesReader

RECOMP - Class in phylonet.recomp

This class provides an implementation of the RECOMP algorithm described in the publication: D.

RECOMP(String[], WindowComparator) - Constructor for class phylonet.recomp.RECOMP

Construct an instance of RECOMP that will run on the set of sequences and use the designated window comparator.

RecompCmdLineTool - Class in phylonet.cmdline.tool

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

RECOMPParamsDialog - Class in phylonet.app.tool.recomp

Represents the parameters for the 'RECOMP' tool.

RECOMPParamsDialog(Frame, PhyloNetAppModel) - Constructor for class phylonet.app.tool.recomp.RECOMPParamsDialog

Instantiates a new parameters dialog for the 'RECOMP' tool.

RECOMPParamsDialog.ComparisonFunction - Enum in phylonet.app.tool.recomp

RECOMPResultsDialog - Class in phylonet.app.tool.recomp

Represents a results dialog for the "RECOMP" tool.

RECOMPResultsDialog(PhyloNetAppView, Date, SequenceAlignmentDatum, int, int, RECOMPParamsDialog.ComparisonFunction, PAUPWindowComparator.DistanceMeasure, File, int, int, int, double[]) - Constructor for class phylonet.app.tool.recomp.RECOMPResultsDialog

Instantiates a new results dialog for the "RECOMP" tool.

RecompTool - Class in phylonet.app.tool.recomp

Represents the RECOMP tool.

RecompTool(PhyloNetAppController) - Constructor for class phylonet.app.tool.recomp.RecompTool

Instantiates a new RECOMP tool.

refine(Tree, Tree) - Method in class phylonet.riatahgt.ExMultipleMasts

This method refines two trees tr1 and tr2.

refineRootedGeneTrees(List<Tree>, Tree, HashSet<STITreeCluster>) - Static method in class phylonet.coalescent.GeneTreeRefinement

Refine a set of rooted gene trees with respect to a species tree

registerAsExceptionHandler() - Static method in class phylonet.app.util.PhyloLogger

Tells this class to register itself as the system's exception handler for uncaught exceptions.

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

This method is not supported.

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

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

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

This method is not supported.

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

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

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

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

This function removes all binary nodes from the network.

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

Remove all nodes with only one child in this tree.

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

This function makes child no longer a child of this node.

removeChild(NetNode<T>) - Method in interface phylonet.network.model.NetNode

This function makes child no longer a child of this node.

removeChild(TMutableNode, boolean) - Method in class phylonet.tree.model.sti.STINode

removeChild(TMutableNode, boolean) - Method in interface phylonet.tree.model.TMutableNode

Remove the specified child from this node.

removeDatum(ADatumController) - Method in class phylonet.app.controller.PhyloNetAppController

Removes the given controller, its corresponding model, and its corresponding view, from PhyloNet.

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

Removes the given datum from the current list of data.

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

Removes and disposes of the given datum view.

removeEdge(int) - Method in interface phylonet.graph.model.MutableGraph

Remove an edge by its unique id.

removeEdge(MutableEdge) - Method in interface phylonet.graph.model.MutableGraph

Removes this edge from the graph.

removeEdge(int) - Method in class phylonet.graph.model.sgi.SGIGraph

removeEdge(MutableEdge) - Method in class phylonet.graph.model.sgi.SGIGraph

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

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

This function removes an event from the list _events of this scenario.

removeGamma(int) - Method in class phylonet.network.model.bni.BniNetNode

This function removes the gamma value of the index_th child

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

Remove an object from the group that is notified when the graph changes.

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

removeMax() - Method in class phylonet.heaps.BinaryMaxHeap

removeMax() - Method in class phylonet.heaps.MaxDoubleHeap

removeMax() - Method in class phylonet.heaps.MaxHeap

Remove the maximum (key,value) pair from the heap.

removeMax() - Method in class phylonet.heaps.MaxIntHeap

removeMin() - Method in class phylonet.heaps.BinaryMinHeap

removeMin() - Method in class phylonet.heaps.MinFibonacciHeap

removeMin() - Method in class phylonet.heaps.MinHeap

Remove the maximum (key,value) pair from the heap.

removeNode(int) - Method in interface phylonet.graph.model.MutableGraph

Removes the node from this graph.

removeNode(String) - Method in interface phylonet.graph.model.MutableGraph

Removes the node from this graph.

removeNode(MutableNode) - Method in interface phylonet.graph.model.MutableGraph

Removes the node from this graph.

removeNode(int) - Method in class phylonet.graph.model.sgi.SGIGraph

removeNode(String) - Method in class phylonet.graph.model.sgi.SGIGraph

removeNode(MutableNode) - Method in class phylonet.graph.model.sgi.SGIGraph

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

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

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

This method removes this node and all its children from the tree.

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

rename(String) - Method in class phylonet.app.controller.datum.ADatumController

Sets the name of the datum managed by this controller, and updates the view to display the new name.

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

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

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

rerootTreeAtEdge(int) - Method in interface phylonet.tree.model.Tree

Root a tree at an edge.

rerootTreeAtEdge(String) - Method in interface phylonet.tree.model.Tree

Root a tree at a node.

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

rerootTreeAtNode(TNode) - Method in interface phylonet.tree.model.Tree

Root a tree at a node.

Resolve - Class in phylonet.tree.util

Implements functionality to resolve compatible trees using each others structure.

Resolve() - Constructor for class phylonet.tree.util.Resolve

resolveRooted(MutableTree, MutableTree) - Static method in class phylonet.tree.util.Resolve

This method refines two rooted trees tr1 and tr2.

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

This method is not supported.

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

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

RfCmdLineTool - Class in phylonet.cmdline.tool

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

RFParamsDialog - Class in phylonet.app.tool.rf

Represents the parameters dialog for the 'rf' tool.

RFParamsDialog(Frame, PhyloNetAppModel) - Constructor for class phylonet.app.tool.rf.RFParamsDialog

Instantiates a new parameters dialog for the 'rf' tool.

RFResultsDialog - Class in phylonet.app.tool.rf

Represents a results dialog for the 'rf' tool.

RFResultsDialog(Frame, Date, TreeDatum, TreeDatum, SymmetricDifference) - Constructor for class phylonet.app.tool.rf.RFResultsDialog

Instantiates a new results dialog for the 'rf' tool.

RFTool - Class in phylonet.app.tool.rf

Represents the RF tool.

RFTool(PhyloNetAppController) - Constructor for class phylonet.app.tool.rf.RFTool

Instantiates a new RF tool.

RiataHgt - Class in phylonet.riatahgt

This class is a wrapper class for the two classes SingleRiataHgt and MultipleRiataHgt, which computes single and multiple HGT scenarios.

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

This function constructs an object of RiataHgt for computing HGT events.

RiataHgtCmdLineTool - Class in phylonet.cmdline.tool

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

RiataHGTParamsDialog - Class in phylonet.app.tool.riatahgt

Represents a parameters dialog for the 'riatahgt' tool.

RiataHGTParamsDialog(Frame, PhyloNetAppModel) - Constructor for class phylonet.app.tool.riatahgt.RiataHGTParamsDialog

Instantiates a new parameters dialog for the RIATA-HGT tool.

RiataHGTResultsDialog - Class in phylonet.app.tool.riatahgt

Represents a results dialog for the RIATA-HGT tool.

RiataHGTResultsDialog(Frame, Date, TreeDatum, TreeDatum, RiataHgt) - Constructor for class phylonet.app.tool.riatahgt.RiataHGTResultsDialog

Instantiates a new results dialog for the RIATA-HGT tool.

RiataHGTTestCase - Class in phylonet.riatahgt

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

RIATAHGTTool - Class in phylonet.app.tool.riatahgt

Represents the RIATA-HGT tool.

RIATAHGTTool(PhyloNetAppController) - Constructor for class phylonet.app.tool.riatahgt.RIATAHGTTool

Instantiates a new RIATA-HGT tool.

RiataViewerFrame - Class in phylonet.riatahgt.viewer

RiataViewerFrame(String) - Constructor for class phylonet.riatahgt.viewer.RiataViewerFrame

RiataViewerFrameTestCase - Class in phylonet.riatahgt.viewer

RiataViewerFrameTestCase() - Constructor for class phylonet.riatahgt.viewer.RiataViewerFrameTestCase

RIGHT_COLUMN_WIDTH - Static variable in class phylonet.app.tool.inferst.InferSTParamsDialog

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

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

A criterion that matches all rooted trees.

rootGeneTrees(List<Tree>, Tree) - Static method in class phylonet.coalescent.GeneTreeRefinement

Root a set of unrooted gene trees with respect to a species tree

run(int, int) - Method in class phylonet.recomp.RECOMP

Perform the window comparison across the entire dataset.