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ADatum) associated with this controller.
ADatumView) associated with this controller.
TreeDatum the user selected in the
first of the two combo boxes.
TreeDatum the user selected in the
first of the two combo boxes.
node
BufferedReader,
creating one set of node names for each line.
- getNonstrictSubleaves() -
Method in class phylonet.network.characterization.NetworkTripartition
- This function returns an iterable list of leaves that are reachable from the root through _node, but
not necessarily through it.
- getNumberOfMinSolutions() -
Method in class phylonet.riatahgt.RiataHgt
- This function returns the number of minimal solutions.
- getNumInternalEdges1() -
Method in class phylonet.symmdiff.SymmetricDifference
-
- getNumInternalEdges2() -
Method in class phylonet.symmdiff.SymmetricDifference
-
- getOutboundEdges() -
Method in interface phylonet.graph.model.MutableNode
-
- getOutboundEdges() -
Method in interface phylonet.graph.model.Node
-
- getOutboundEdges() -
Method in class phylonet.graph.model.sgi.SGINode
-
- getOutboundNodes() -
Method in interface phylonet.graph.model.MutableNode
-
- getOutboundNodes() -
Method in interface phylonet.graph.model.Node
-
- getOutboundNodes() -
Method in class phylonet.graph.model.sgi.SGINode
-
- getOutdeg() -
Method in class phylonet.network.model.bni.BniNetNode
- This function computes the outdegree of a node.
- getOutdeg() -
Method in interface phylonet.network.model.NetNode
-
- getOutDegree() -
Method in interface phylonet.graph.model.MutableNode
-
- getOutDegree() -
Method in interface phylonet.graph.model.Node
-
- getOutDegree() -
Method in class phylonet.graph.model.sgi.SGINode
-
- getOutputEdgeWeightsAreSupports() -
Method in class phylonet.consensus.TreeConsensusCalculator
-
- getParameters() -
Static method in class phylonet.app.util.DialogsTestCase
-
- getParameters() -
Static method in class phylonet.maxclique.MaxCliqueParameterizedTestCase
-
- getParent() -
Method in class phylonet.tree.model.sti.STINode
-
- getParent() -
Method in interface phylonet.tree.model.TMutableNode
-
- getParent() -
Method in interface phylonet.tree.model.TNode
-
- getParentDistance(NetNode<T>) -
Method in class phylonet.network.model.bni.BniNetNode
- This function returns the distance from this node to one of its parent.
- getParentDistance(NetNode<T>) -
Method in interface phylonet.network.model.NetNode
-
- getParentDistance() -
Method in class phylonet.tree.model.sti.STINode
-
- getParentDistance() -
Method in interface phylonet.tree.model.TNode
-
- getParentNumber() -
Method in class phylonet.network.model.bni.BniNetNode
- This function returns the number of parent of a node.
- getParentNumber() -
Method in interface phylonet.network.model.NetNode
- This function returns the number of parent of a node.
- getParents() -
Method in class phylonet.network.model.bni.BniNetNode
- This function gets all (immediate) parents of this node.
- getParents() -
Method in interface phylonet.network.model.NetNode
-
- getPAUPFile() -
Method in class phylonet.app.tool.recomp.RECOMPParamsDialog
-
- getPOPSize() -
Method in class phylonet.app.tool.recomp.RECOMPParamsDialog
-
- getPositionToLeafNameMap(Map<String, Integer>) -
Static method in class phylonet.tree.util.Bipartitions
-
- getRefined() -
Method in class phylonet.app.tool.riatahgt.RiataHGTParamsDialog
- Returns whether or not the user has specified that the RIATA-HGT calculations
be refined.
- getRight() -
Method in class phylonet.tree.model.sti.STITreeBipartition
-
- getRightCount() -
Method in class phylonet.algorithms.bipartitemaching.HungarianBipartiteMatcher
-
- getRightLeaves() -
Method in class phylonet.tree.model.sti.STITreeBipartition
- Get the leaves in the right half of the bipartition LEFT | RIGHT.
- getRoot() -
Method in class phylonet.network.model.bni.BniNetwork
-
- getRoot() -
Method in interface phylonet.network.model.Network
-
- getRoot() -
Method in interface phylonet.tree.model.MutableTree
-
- getRoot() -
Method in class phylonet.tree.model.sti.STITree
-
- getRoot() -
Method in interface phylonet.tree.model.Tree
- If the tree is rooted, this returns the root.
- getSecondSelectedTreeDatum() -
Method in class phylonet.app.tool.countcoal.CountCoalParamsDialog
- Returns the
TreeDatum the user selected in the
second of the two combo boxes.
- getSecondSelectedTreeDatum() -
Method in class phylonet.app.tool.mast.MASTParamsDialog
- Returns the
TreeDatum the user selected in the
second of the two combo boxes.
- getSelectedComparisonFunction() -
Method in class phylonet.app.tool.recomp.RECOMPParamsDialog
-
- getSelectedComputationType() -
Method in class phylonet.app.tool.charnet.CharnetParamsDialog
- Returns the user's choice of computation type.
- getSelectedComputationType() -
Method in class phylonet.app.tool.cmpnets.CmpnetsParamsDialog
- Returns the user's choice of computation type.
- getSelectedCplexPath() -
Method in class phylonet.app.tool.inferst.subpanel.MdcIlpSubpanel
-
- getSelectedCplexPath() -
Method in class phylonet.app.tool.inferst.subpanel.MdcIlpTimeSubpanel
-
- getSelectedData() -
Method in class phylonet.app.tool.component.ExtendableComboBoxList
- Returns the list of data selected in this list of combo-boxes, in the same order
that the boxes are in.
- getSelectedDeepCoalescencesWeight() -
Method in class phylonet.app.tool.inferst.subpanel.MdcIlpTimeSubpanel
-
- getSelectedExhaust() -
Method in class phylonet.app.tool.inferst.subpanel.MdcDpSubpanel
-
- getSelectedExperimentalTreeDatum() -
Method in class phylonet.app.tool.rf.RFParamsDialog
- Returns the
TreeDatum the user selected in the
second of the two combo boxes.
- getSelectedExplore() -
Method in class phylonet.app.tool.inferst.subpanel.MdcDpSubpanel
-
- getSelectedGeneTreeData() -
Method in class phylonet.app.tool.inferst.InferSTParamsDialog
- Returns the current list of selected gene trees.
- getSelectedGeneTreeDatum() -
Method in class phylonet.app.tool.riatahgt.RiataHGTParamsDialog
- Returns the currently specified gene tree datum.
- getSelectedInferenceMethod() -
Method in class phylonet.app.tool.inferst.InferSTParamsDialog
- Returns the currently selected inference method.
- getSelectedModelTreeDatum() -
Method in class phylonet.app.tool.rf.RFParamsDialog
- Returns the
TreeDatum the user selected in the
first of the two combo boxes.
- getSelectedNetworkDatum() -
Method in class phylonet.app.tool.charnet.CharnetParamsDialog
- Returns the currently selected network datum.
- getSelectedNetworkDatum() -
Method in class phylonet.app.tool.netpars.NetparsParamsDialog
- Returns the network datum specified by the user in this parameters dialog.
- getSelectedNetworkDatum1() -
Method in class phylonet.app.tool.cmpnets.CmpnetsParamsDialog
- Returns the first currently selected network datum.
- getSelectedNetworkDatum2() -
Method in class phylonet.app.tool.cmpnets.CmpnetsParamsDialog
- Returns the second currently selected network datum.
- getSelectedNoCoalescencesWeight() -
Method in class phylonet.app.tool.inferst.subpanel.MdcIlpTimeSubpanel
-
- getSelectedNodeNames() -
Method in class phylonet.app.tool.component.ExtendableNodeSetsList
- Returns the list of currently specified node name sets.
- getSelectedNodeSets() -
Method in class phylonet.app.tool.lca.LCAParamsDialog
- Returns a list of the currently supplied sets of node names.
- getSelectedPrefix() -
Method in class phylonet.app.tool.lca.LCAParamsDialog
- Returns the currently specified prefix for automatic node labeling.
- getSelectedProportion() -
Method in class phylonet.app.tool.inferst.subpanel.MdcDpSubpanel
-
- getSelectedSequenceAlignment() -
Method in class phylonet.app.tool.netpars.NetparsParamsDialog
- Returns the sequence alignment specified by the user in this parameters dialog.
- getSelectedSequenceListDatum() -
Method in class phylonet.app.tool.recomp.RECOMPParamsDialog
- Returns the currently selected sequence list datum.
- getSelectedSpeciesTreeDatum() -
Method in class phylonet.app.tool.riatahgt.RiataHGTParamsDialog
- Returns the currently specified species tree datum.
- getSelectedTaxonMap() -
Method in class phylonet.app.tool.inferst.subpanel.MdcDpSubpanel
-
- getSelectedTreeDatum() -
Method in class phylonet.app.tool.lca.LCAParamsDialog
- Returns the currently selected tree datum.
- getSelectedUseTaxonMap() -
Method in class phylonet.app.tool.inferst.subpanel.MdcDpSubpanel
-
- getSequence() -
Method in class phylonet.sequence.io.FastaReader.FastaRecord
-
- getSequence() -
Method in class phylonet.sequence.io.PlainXReader.PlainXRecord
-
- getSequence1() -
Method in class phylonet.algorithms.pairalignment.SmithWaterman.Match
-
- getSequence2() -
Method in class phylonet.algorithms.pairalignment.SmithWaterman.Match
-
- getSequenceAlignment() -
Method in class phylonet.app.model.datum.SequenceAlignmentDatum
- Returns the sequence alignment contained in this datum.
- getSequenceCount() -
Method in class phylonet.sequence.io.PlainXReader
- If the header was read, then this method returns the number of sequences in the plain file.
- getSequenceCount() -
Method in class phylonet.sequence.model.SequenceAlignment
- Returns the number of sequences.
- getSequenceLength() -
Method in class phylonet.sequence.io.PlainXReader
- If the header was read, then this method returns the length of the sequences in the file - all sequences
must be of this size, though this requirement is not enforced by this reader.
- getSequenceLength() -
Method in class phylonet.sequence.model.SequenceAlignment
- Returns the sequence length.
- getSequences() -
Method in class phylonet.sequence.model.SequenceAlignment
- Returns the sequences contained by this sequence alignment.
- getSequenceStr() -
Method in class phylonet.sequence.io.FastaReader.FastaRecord
-
- getSequenceStr() -
Method in class phylonet.sequence.io.PlainXReader.PlainXRecord
-
- getShouldDisplayHelp() -
Method in class phylonet.cmdline.tool.CmdLineTool
-
- getSiblings() -
Method in class phylonet.tree.model.sti.STINode
-
- getSiblings() -
Method in interface phylonet.tree.model.TNode
-
- getSolutionTree() -
Method in class phylonet.riatahgt.RiataHgt
- This function returns the solution tree that contains HGT scenarios for a pair of species and gene trees.
- getSource() -
Method in interface phylonet.graph.model.Edge
-
- getSource() -
Method in interface phylonet.graph.model.MutableEdge
-
- getSource() -
Method in interface phylonet.graph.model.Path
-
- getSource() -
Method in class phylonet.graph.model.PathImpl
-
- getSource() -
Method in class phylonet.graph.model.sgi.SGIEdge
-
- getSourceEdge() -
Method in class phylonet.riatahgt.HgtEvent
-
- getSourceID() -
Method in interface phylonet.graph.model.Edge
-
- getSourceID() -
Method in class phylonet.graph.model.sgi.SGIEdge
-
- getSpeciesTree() -
Method in class phylonet.riatahgt.RiataHgt
- Returns the original, unmodified (except for labeling) species tree used
by the last RIATA-HGT calculation.
- getStepSize() -
Method in class phylonet.app.tool.recomp.RECOMPParamsDialog
- Returns the step size specified by the user in this parameters dialog.
- getStrictSubleaves() -
Method in class phylonet.network.characterization.NetworkTripartition
- This function returns an iterable list of leaves that are only reachable from the root through _node.
- getTail() -
Method in class phylonet.network.characterization.NetworkEdge
- This function returns the tail of this edge.
- getTarget() -
Method in interface phylonet.graph.model.Edge
-
- getTarget() -
Method in interface phylonet.graph.model.MutableEdge
-
- getTarget() -
Method in class phylonet.graph.model.sgi.SGIEdge
-
- getTargetID() -
Method in interface phylonet.graph.model.Edge
-
- getTargetID() -
Method in class phylonet.graph.model.sgi.SGIEdge
-
- getTaxa() -
Method in class phylonet.coalescent.TaxaDistanceMatrix
-
- getTaxa() -
Method in class phylonet.sequence.model.SequenceAlignment
- Returns the taxon names of this sequence alignment.
- getTaxa() -
Method in class phylonet.tree.model.sti.STITreeBipartition
-
- getTaxa() -
Method in class phylonet.tree.model.sti.STITreeCluster
-
- getTaxaDistanceMatrix() -
Method in class phylonet.app.tool.inferst.subpanel.GlassMatrixSubpanel
-
- getTaxaDistanceMatrix(File) -
Static method in class phylonet.coalescent.GLASSInference
-
- getTaxonFile() -
Method in class phylonet.app.tool.inferst.subpanel.GlassTreeSubpanel
-
- getTaxonFileText() -
Method in class phylonet.app.tool.inferst.subpanel.MdcDpRootedTimeSubpanel
-
- getTaxonMap() -
Method in class phylonet.app.tool.inferst.subpanel.GlassTreeSubpanel
-
- getTaxonMap() -
Method in class phylonet.app.tool.inferst.subpanel.MajoritySubpanel
-
- getTaxonMap() -
Method in class phylonet.app.tool.inferst.subpanel.MdcDpRootedTimeSubpanel
-
- getTaxonMapFile() -
Method in class phylonet.app.tool.inferst.subpanel.MajoritySubpanel
-
- getTaxonMapFromFile(File) -
Static method in class phylonet.coalescent.MajorityConsensusInference
- Returns a taxon map constructed from the contents of the specified file.
- getThumbnailView() -
Method in class phylonet.app.view.datum.ADatumView
- Returns the thumbnail view for this view.
- getToolTipText() -
Method in class phylonet.app.tool.APhyloTool
- Returns the explanatory tool-tip text for this tool.
- getTree() -
Method in class phylonet.app.model.datum.TreeDatum
- Returns the tree associated with this datum.
- getTree() -
Method in class phylonet.app.model.datum.TreeWithBranchLengthsDatum
-
- getTree() -
Method in class phylonet.coalescent.Solution
-
- getTree() -
Method in class phylonet.lca.SchieberVishkinLCA
-
- getTree() -
Method in class phylonet.riatahgt.viewer.TreeCanvas
-
- getTree() -
Method in class phylonet.tree.model.sti.STINode
-
- getTree() -
Method in interface phylonet.tree.model.TMutableNode
-
- getTree() -
Method in interface phylonet.tree.model.TNode
- Return the tree to which this node belongs.
- getTree() -
Method in class phylonet.tree.view.swing.TreeView
-
- getTreeNodes() -
Method in class phylonet.network.model.bni.BniNetwork
-
- getTreeNodes() -
Method in interface phylonet.network.model.Network
-
- getTrees(Network<T>) -
Static method in class phylonet.network.util.Networks
- This function returns a list of trees decomposed from the network.
- getTripartitionNode() -
Method in class phylonet.network.characterization.NetworkTripartition
- This function returns the head node v in edge e = (u, v) used to compute its tripartitions.
- getTripartitions(Network<T>) -
Static method in class phylonet.network.util.Networks
- This function returns an iterable list of network tripartitions.
- getType() -
Method in class phylonet.app.model.datum.ADatum
- Returns a string representation of this datum's type---"Tree",
for example.
- getType() -
Method in class phylonet.app.model.datum.BatchDatum
-
- getType() -
Method in class phylonet.app.model.datum.HGTDatum
-
- getType() -
Method in class phylonet.app.model.datum.NetworkDatum
-
- getType() -
Method in class phylonet.app.model.datum.SequenceAlignmentDatum
-
- getType() -
Method in class phylonet.app.model.datum.TreeDatum
-
- getType() -
Method in class phylonet.app.model.datum.TreeWithBranchLengthsDatum
-
- getUnreachableLeaves() -
Method in class phylonet.network.characterization.NetworkTripartition
- This function returns an iterable list of leaves that are not reachable from the root through _node.
- getUnweightedAverage() -
Method in class phylonet.symmdiff.SymmetricDifference
-
- getValidGeneTrees(String, String) -
Method in class phylonet.ilp.IlpGenerator
- This function filters from the set of gene trees those whose node times satisfy: time(parent) > time(children).
- getValue(int) -
Method in class phylonet.bits.BitVector
-
- getView() -
Method in class phylonet.app.controller.PhyloNetAppController
- Returns the top-level view belonging to this top-level controller.
- getWeight() -
Method in interface phylonet.graph.model.Edge
-
- getWeight() -
Method in interface phylonet.graph.model.Path
-
- getWeight() -
Method in class phylonet.graph.model.PathImpl
-
- getWeight() -
Method in class phylonet.graph.model.sgi.SGIEdge
-
- getWeightedAverage() -
Method in class phylonet.symmdiff.SymmetricDifference
-
- getWeightedFalseNegative() -
Method in class phylonet.symmdiff.SymmetricDifference
-
- getWeightedFalsePositive() -
Method in class phylonet.symmdiff.SymmetricDifference
-
- getWindowComparator() -
Method in class phylonet.app.tool.recomp.RECOMPParamsDialog
- Returns the window comparator defined by the user's selected parameters in
this dialog.
- getWindowSize() -
Method in class phylonet.app.tool.recomp.RECOMPParamsDialog
- Returns the window size specified by the user in this parameters dialog.
- GLASSInference - Class in phylonet.coalescent
- This class uses GLASS to infer the species tree from gene trees.
- GLASSInference() -
Constructor for class phylonet.coalescent.GLASSInference
-
- GlassMatrixSubpanel - Class in phylonet.app.tool.inferst.subpanel
-
- GlassMatrixSubpanel(Frame) -
Constructor for class phylonet.app.tool.inferst.subpanel.GlassMatrixSubpanel
-
- GlassTreeSubpanel - Class in phylonet.app.tool.inferst.subpanel
-
- GlassTreeSubpanel(Frame) -
Constructor for class phylonet.app.tool.inferst.subpanel.GlassTreeSubpanel
-
- Graph - Interface in phylonet.graph.model
- An interface defining a graph.
- GraphComponent - Interface in phylonet.graph.model
-
- GraphListener - Interface in phylonet.graph.model
- The methods used to notify an object that the graph has changed.
- gsi(String[]) -
Method in class phylonet.tree.model.sti.STITree
-
- gsi(String[]) -
Method in interface phylonet.tree.model.Tree
-
- GTDistributionInNetwork - Class in phylonet.network.gtdistribution
-
- GTDistributionInNetwork() -
Constructor for class phylonet.network.gtdistribution.GTDistributionInNetwork
- Constructor that initialize the variables.
- GTDistrInNetworkCmdLineTool - Class in phylonet.cmdline.tool
-
- GTDistrInNetworkCmdLineTool() -
Constructor for class phylonet.cmdline.tool.GTDistrInNetworkCmdLineTool
-
- GTRefineAndRootCmdLineTool - Class in phylonet.cmdline.tool
-
- GTRefineAndRootCmdLineTool() -
Constructor for class phylonet.cmdline.tool.GTRefineAndRootCmdLineTool
-
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