Uses of Interface
jebl.evolution.trees.Tree
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Packages that use Tree Package Description jebl.evolution.align Provides classes and interfaces for pairwise alignment of two sequences.jebl.evolution.io jebl.evolution.parsimony jebl.evolution.trees -
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Uses of Tree in jebl.evolution.align
Fields in jebl.evolution.align declared as Tree Modifier and Type Field Description Tree
AlignmentTreeBuilderFactory.Result. tree
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Uses of Tree in jebl.evolution.io
Methods in jebl.evolution.io that return Tree Modifier and Type Method Description Tree
NewickImporter. importNextTree()
Tree
NexusImporter. importNextTree()
If not currently reading a TREES block then read ahead to the next TREES block, parsing TRANSLATE and TAXA blocks in the process if necessary.Tree
TreeImporter. importNextTree()
Import a single treeMethods in jebl.evolution.io that return types with arguments of type Tree Modifier and Type Method Description java.util.List<Tree>
NewickImporter. importTrees()
java.util.List<Tree>
NexusImporter. importTrees()
Import all trees in the file from the current position.java.util.List<Tree>
TreeImporter. importTrees()
Import all the treesjava.util.Iterator<Tree>
NewickImporter. iterator()
Returns an iterator over a set of elements of type T.java.util.Iterator<Tree>
NexusImporter. iterator()
java.util.List<Tree>
NexusImporter. parseTreesBlock(java.util.List<Taxon> taxonList)
Parse the next 'TREES' block encountered in the input.Methods in jebl.evolution.io with parameters of type Tree Modifier and Type Method Description void
NewickExporter. exportTree(Tree tree)
Export a single treevoid
NexusExporter. exportTree(Tree tree)
Export a single treevoid
PHYLIPExporter. exportTree(Tree tree)
void
TreeExporter. exportTree(Tree tree)
Export a single treeMethod parameters in jebl.evolution.io with type arguments of type Tree Modifier and Type Method Description void
NewickExporter. exportTrees(java.util.Collection<? extends Tree> trees)
Export a collection of treesvoid
NexusExporter. exportTrees(java.util.Collection<? extends Tree> trees)
void
NexusExporter. exportTrees(java.util.Collection<? extends Tree> trees, boolean writeTaxa)
void
PHYLIPExporter. exportTrees(java.util.Collection<? extends Tree> trees)
void
TreeExporter. exportTrees(java.util.Collection<? extends Tree> trees)
Export a collection of treesvoid
NexusExporter. exportTreesWithTranslation(java.util.Collection<? extends Tree> trees, java.util.Map<java.lang.String,java.lang.String> translationMap)
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Uses of Tree in jebl.evolution.parsimony
Methods in jebl.evolution.parsimony with parameters of type Tree Modifier and Type Method Description double
FitchParsimony. getScore(Tree tree)
double
ParsimonyCriterion. getScore(Tree tree)
Calculates the minimum number of steps for the parsimony reconstruction for the given tree.double[]
FitchParsimony. getSiteScores(Tree tree)
Calculates the minimum number of siteScores for the parsimony reconstruction of a a set of character patterns on a tree.double[]
ParsimonyCriterion. getSiteScores(Tree tree)
Calculates the minimum number of steps for the parsimony reconstruction for the given tree.State[]
FitchParsimony. getStates(Tree tree, Node node)
Returns the reconstructed character states for a given node in the tree.State[]
ParsimonyCriterion. getStates(Tree tree, Node node)
Returns the reconstructed character states for a given node in the tree. -
Uses of Tree in jebl.evolution.trees
Classes in jebl.evolution.trees with type parameters of type Tree Modifier and Type Class Description class
ClusteringTreeBuilder<T extends Tree>
An abstract base class for clustering algorithms from pairwise distancesclass
ConsensusTreeBuilder<T extends Tree>
ATreeBuilder
that builds a consensus tree for a set of trees on identical leaf sets.interface
TreeBuilder<T extends Tree>
Subinterfaces of Tree in jebl.evolution.trees Modifier and Type Interface Description interface
RootedTree
A tree with a root (node with maximum height).Classes in jebl.evolution.trees that implement Tree Modifier and Type Class Description class
CompactRootedTree
A memory efficient rooted tree.class
FilteredRootedTree
class
MutableRootedTree
A simple rooted tree providing some ability to manipulate the tree.class
ReRootedTree
class
RootedFromUnrooted
Root an unrooted tree.class
RootedSubtree
A simple, immutable rooted tree implementation that is a subtree of an existing tree subtending a specified set of taxa..class
SimpleRootedTree
A simple, and initially immutable rooted tree implementation.class
SimpleTree
A basic implementation on an unrooted tree.class
SortedRootedTree
class
TransformedRootedTree
This RootedTree class wraps another RootedTree and transforms the branch lengths and node heights using various functions.Methods in jebl.evolution.trees that return Tree Modifier and Type Method Description Tree
TreeChangeEvent. getTree()
Methods in jebl.evolution.trees that return types with arguments of type Tree Modifier and Type Method Description java.util.List<Tree>
MostProbableTopology. get(int max, double threshold)
Get the most probable tree(s)Methods in jebl.evolution.trees with parameters of type Tree Modifier and Type Method Description static java.lang.String
Utils. asText(Tree tree)
static java.lang.String[]
Utils. asText(Tree tree, int widthGuide)
static ConsensusTreeBuilder
TreeBuilderFactory. buildRooted(Tree[] trees, double supportThreshold, TreeBuilderFactory.ConsensusMethod method)
convenience method.static ConsensusTreeBuilder
TreeBuilderFactory. buildUnRooted(Tree[] trees, Taxon outGroup, double supportThreshold, TreeBuilderFactory.ConsensusMethod method)
Node
SimpleRootedTree. createNodes(Tree tree, Node parent, Node child)
Clones the entire tree structure from the given (unrooted) Tree.static double
Utils. getPathLength(Tree tree, Node node1, Node node2)
static void
SplitUtils. getSplit(java.util.List<Taxon> taxa, Tree tree, Edge edge, boolean[] split)
get split for branch associated with internal nodestatic SplitSystem
SplitUtils. getSplits(java.util.List<Taxon> taxa, Tree tree)
creates a split system from a tree (using a pre-specified order of sequences)static SplitSystem
SplitUtils. getSplits(Tree tree)
creates a split system from a tree (using tree-induced order of sequences)static RootedTree
Utils. rootTheTree(Tree tree)
Return a rooted tree from any tree.static RootedTree
Utils. rootTreeAtCenter(Tree tree)
Root any tree by locating the "center" of tree and adding a new root node at that pointMethod parameters in jebl.evolution.trees with type arguments of type Tree Modifier and Type Method Description static void
Utils. assertAllTreesHaveTheSameTaxa(java.util.List<? extends Tree> trees)
Checks whether all of the trees passed in have the same taxa sets (ignoring order of taxa), and throws an IllegalArgumentException if this is not the case.Constructors in jebl.evolution.trees with parameters of type Tree Constructor Description MutableRootedTree(Tree tree, Node outGroup)
Construct a rooted tree from unrooted.RootedFromUnrooted(Tree source, Node root, boolean intentUnrooted)
Root tree at some internal node.RootedFromUnrooted(Tree source, Node left, Node right, double fromLeft)
Root source by creating a new internal node whose children are (the adjacent) left and right.SimpleRootedTree(Tree tree, Node ingroupNode, Node outgroupNode, double ingroupBranchLength)
Make a copy of the given unrooted treeSimpleTree(Tree tree)
Duplicate a tree.TreeChangeEvent(Tree tree)
Constructor parameters in jebl.evolution.trees with type arguments of type Tree Constructor Description MostProbableTopology(java.util.Collection<? extends Tree> trees)
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