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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IlpGenerator - Class in phylonet.ilp

IlpGenerator defines methods for generating CPLEX inputs.

IlpGenerator() - Constructor for class phylonet.ilp.IlpGenerator

IlpGeneratorTestCase - Class in phylonet.ilp

IlpGeneratorTestCase() - Constructor for class phylonet.ilp.IlpGeneratorTestCase

ImmutableCollection - Interface in phylonet.util

This interface specifies the attributes of a collection that cannot be changed by the holder.

ImmutableCollectionWrapper - Class in phylonet.util

This class wraps an existing collection as an immutable set.

ImmutableCollectionWrapper(Collection) - Constructor for class phylonet.util.ImmutableCollectionWrapper

ImmutableSet - Interface in phylonet.util

This interface specifies the attributes of a set that cannot be changed by the holder.

ImmutableSetWrapper - Class in phylonet.util

This class wraps an existing set as an immutable set.

ImmutableSetWrapper(Set) - Constructor for class phylonet.util.ImmutableSetWrapper

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

Adds the given datum to the model and the view.

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

Increment the value of this bit-vector

INDEPENDENT_SETS - Static variable in class phylonet.maxclique.MaxClique

Used with calculateGroups to indicated that this finder should find maximal independent sets.

InferenceMethod - Enum in phylonet.app.tool.inferst

Represents the different methods by which PhyloNet may infer species trees from a set of gene trees.

InferenceMethodParametersSubpanel - Class in phylonet.app.tool.inferst.subpanel

InferenceMethodParametersSubpanel() - Constructor for class phylonet.app.tool.inferst.subpanel.InferenceMethodParametersSubpanel

inferSpeciesTree(List<String>, String, int, double, List<String>) - Method in class phylonet.coalescent.Bootstrap

The public function for infer species tree by bootstrap

inferSpeciesTree(List<Tree>, int, int, int, double, int, double[], List<Integer>) - Method in class phylonet.coalescent.ClusteringInference

inferSpeciesTree(List<Tree>) - Method in class phylonet.coalescent.DemocraticVoteInference

inferSpeciesTree(List<Tree>, Map<String, String>) - Method in class phylonet.coalescent.GLASSInference

Infers the species tree from the given list of unrooted gene trees with multiple alleles

inferSpeciesTree(List<Tree>) - Method in class phylonet.coalescent.GLASSInference

Infers the species tree from the given list of unrooted gene trees with single alleles

inferSpeciesTree(List<Tree>, boolean) - Method in class phylonet.coalescent.MajorityConsensusInference

inferSpeciesTree(List<Tree>, boolean, Map<String, String>) - Method in class phylonet.coalescent.MajorityConsensusInference

inferSpeciesTree(List<Tree>, boolean, double, boolean, double, boolean, double) - Method in class phylonet.coalescent.MDCInference_DP

Infers the species tree from the given list of rooted gene trees with single allele.

inferSpeciesTree(List<Tree>, Map<String, String>, boolean, double, boolean, double, boolean, double) - Method in class phylonet.coalescent.MDCInference_DP

Infers the species tree from the given list of rooted gene trees with multiple alleles.

inferSpeciesTree(List<Tree>) - Method in class phylonet.coalescent.MDCInference_ILP

Infer the species tree from gene trees under the coalescent.

inferSpeciesTree(List<Tree>, boolean, double, boolean) - Method in class phylonet.coalescent.MDCURInference

Infers the species tree from the given list of unrooted gene trees with single allele.

inferSpeciesTree(List<Tree>, Map<String, String>, boolean, double, boolean) - Method in class phylonet.coalescent.MDCURInference

Infers the species tree from the given list of unrooted gene trees with multiple alleles.

inferSpeciesTree(List<Tree>, boolean, double, boolean, double, boolean, double) - Method in class phylonet.coalescent.MDCURInference_DP

Infers the species tree from the given list of unrooted gene trees with single allele.

inferSpeciesTree(List<Tree>, Map<String, String>, boolean, double, boolean, double, boolean, double) - Method in class phylonet.coalescent.MDCURInference_DP

Infers the species tree from the given list of unrooted gene trees with multiple alleles.

inferSpeciesTree(String, List<Tree>) - Method in class phylonet.coalescent.MDCURInference_ILP

inferSpeciesTree(String, List<Tree>, Map<String, String>) - Method in class phylonet.coalescent.MDCURInference_ILP

inferSpeciesTree(List<Tree>, double) - Method in class phylonet.coalescent.MDCWithTime

Infers the species tree from the given list of rooted gene trees with single allele by dynamic programming.

inferSpeciesTree(List<Tree>, Map<String, String>, double) - Method in class phylonet.coalescent.MDCWithTime

Infers the species tree from the given list of rooted gene trees with multiple alleles by dynamic programming.

inferSpeciesTree2(List<SequenceAlignment>) - Method in class phylonet.coalescent.GLASSInference

inferSpeciesTree2(List<SequenceAlignment>, double) - Method in class phylonet.coalescent.GLASSInference

inferSpeciesTree2(List<SequenceAlignment>, Map<String, String>) - Method in class phylonet.coalescent.GLASSInference

inferSpeciesTree2(List<SequenceAlignment>, Map<String, String>, double) - Method in class phylonet.coalescent.GLASSInference

inferSpeciesTreeFromTaxa(TaxaDistanceMatrix) - Method in class phylonet.coalescent.GLASSInference

Infers the species tree from the given distances of taxon pairs

inferSpeciesTreeWithTime(List<Tree>, double, double) - Method in class phylonet.coalescent.MDCInference_ILP

InferStCmdLineTool - Class in phylonet.cmdline.tool

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

InferSTParamsDialog - Class in phylonet.app.tool.inferst

Represents the parameters dialog for the INFER_ST tool.

InferSTParamsDialog(Frame, PhyloNetAppModel) - Constructor for class phylonet.app.tool.inferst.InferSTParamsDialog

Instantiates a new INFER_ST parameters dialog.

InferStResultsDialog - Class in phylonet.app.tool.inferst

Represents a results dialog for the INFER_ST tool.

InferStResultsDialog(Frame, Date, List<TreeDatum>, List<Tree>, InferenceMethod, long) - Constructor for class phylonet.app.tool.inferst.InferStResultsDialog

Instantiates a new results dialog for the INFER_ST tool.

InferSTTool - Class in phylonet.app.tool.inferst

Represents the INFER_ST tool.

InferSTTool(PhyloNetAppController) - Constructor for class phylonet.app.tool.inferst.InferSTTool

Instantiates a new INFER_ST tool.

info(String, Throwable) - Static method in class phylonet.app.util.PhyloLogger

Appends an informational log to the current list of logs.

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

Appends an informational log to the current list of logs.

insert(N, D) - Method in class phylonet.heaps.BinaryMaxHeap

insert(N, D) - Method in class phylonet.heaps.BinaryMinHeap

insert(double, Object) - Method in class phylonet.heaps.MaxDoubleHeap

insert(N, D) - Method in class phylonet.heaps.MaxHeap

Insert a new (key,value) pair in to the heap.

insert(int, int) - Method in class phylonet.heaps.MaxIntHeap

insert(N, D) - Method in class phylonet.heaps.MinFibonacciHeap

insert(N, D) - Method in class phylonet.heaps.MinHeap

Insert a new (key,value) pair in to the heap.

insertEx(N, D) - Method in class phylonet.heaps.MinFibonacciHeap

This method is an extended version of the insert method in that it inserts the (key,value) pair and returns an object that can be used to manage the key value of this entry in the heap via calls to decreaseKey.

InvalidParameterException - Exception in phylonet.app.tool

Used by PhyloNet tools to indicate that a provided set of parameters is not valid.

InvalidParameterException(String) - Constructor for exception phylonet.app.tool.InvalidParameterException

invertNormalizedScore() - Method in class phylonet.recomp.comparator.PAUPIntersectionComparator

invertNormalizedScore() - Method in class phylonet.recomp.comparator.PAUPWindowComparator

invertNormalizedScore() - Method in interface phylonet.recomp.WindowComparator

If this method returns true, then the comparison function must be inverted (1-score) after normalization in order for the high value to be taken as an indicator of recombination.

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

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

isBad() - Method in class phylonet.riatahgt.HgtEvent

If an event is bad, this function returns true.

isBinary(Tree) - Static method in class phylonet.tree.util.Trees

compute if a tree is binary

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

Checks if two bipartitions are compatible or not.

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

Check if another cluster is compatible with this cluster.

isCompatible(BitVector, BitVector) - Static method in class phylonet.tree.util.Bipartitions

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

Check if two clusters are complementary to each other (i.e., they are a partition of the taxon set).

isDirected() - Method in interface phylonet.graph.model.Edge

isDirected() - Method in interface phylonet.graph.model.Graph

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

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

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

Check if this cluster is disjoint with another cluster.

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

isEmpty() - Method in interface phylonet.graph.model.Graph

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

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

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

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

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

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

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

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

isEmpty() - Method in class phylonet.network.characterization.NetworkCluster

This function tests if this cluster is empty, i.e.

isEmpty() - Method in class phylonet.network.model.bni.BniNetwork

isEmpty() - Method in interface phylonet.network.model.Network

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

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

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

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

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

Checks if two bipartitions are equal or not.

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

This function checks if a node is a leaf of a network.

isLeaf() - Method in interface phylonet.network.model.NetNode

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

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

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

This function checks if a node is a network node, i.e.

isNetworkNode() - Method in interface phylonet.network.model.NetNode

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

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

This function checks if a node is the root of the network it belongs.

isRoot() - Method in interface phylonet.network.model.NetNode

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

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

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

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

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

This function checks if a node is a tree node, i.e.

isTreeNode() - Method in interface phylonet.network.model.NetNode

isTrivial() - Method in class phylonet.network.characterization.NetworkCluster

This function tests if a cluster is trivial.

isUseTaxonMapSelected() - Method in class phylonet.app.tool.inferst.subpanel.GlassTreeSubpanel

isUseTaxonMapSelected() - Method in class phylonet.app.tool.inferst.subpanel.MajoritySubpanel

isUseTaxonMapSelected() - Method in class phylonet.app.tool.inferst.subpanel.MdcDpRootedTimeSubpanel

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

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

isViolated() - Method in class phylonet.riatahgt.HgtEvent

If an event is time-violated, this function returns true.

Iterating - Class in phylonet.rpt

This class contains methods that use Java's ability to write quick iteration code to speed up writing looping code.

Iterating() - Constructor for class phylonet.rpt.Iterating

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

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

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

iterator() - Method in class phylonet.network.characterization.NetworkTreeEnumerator

iterator() - Method in class phylonet.network.model.bni.BfsSearch

iterator() - Method in class phylonet.network.model.bni.DfsSearch

iterator() - Method in class phylonet.rpt.io.LineReader

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

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

iterator() - Method in class phylonet.tree.util.PostTraversal

iterator() - Method in interface phylonet.util.ImmutableCollection

This method returns an iterator that does not supported the Iterator.remove operation, as this would modify the underlying set.

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

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