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Packages that use Tree | |
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jebl.evolution.align | Provides classes and interfaces for pairwise alignment of two sequences. |
jebl.evolution.io | |
jebl.evolution.parsimony | |
jebl.evolution.trees |
Uses of Tree in jebl.evolution.align |
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Fields in jebl.evolution.align declared as Tree | |
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Tree |
AlignmentTreeBuilderFactory.Result.tree
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Uses of Tree in jebl.evolution.io |
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Methods in jebl.evolution.io that return Tree | |
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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 tree |
Tree |
NewickImporter.importNextTree()
|
Methods in jebl.evolution.io that return types with arguments of type Tree | |
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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 trees |
java.util.List<Tree> |
NewickImporter.importTrees()
|
java.util.Iterator<Tree> |
NexusImporter.iterator()
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java.util.Iterator<Tree> |
NewickImporter.iterator()
Returns an iterator over a set of elements of type T. |
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 | |
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void |
NewickExporter.exportTree(Tree tree)
Export a single tree |
void |
NexusExporter.exportTree(Tree tree)
Export a single tree |
void |
PHYLIPExporter.exportTree(Tree tree)
|
void |
TreeExporter.exportTree(Tree tree)
Export a single tree |
Method parameters in jebl.evolution.io with type arguments of type Tree | |
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void |
NewickExporter.exportTrees(java.util.Collection<? extends Tree> trees)
Export a collection of trees |
void |
NexusExporter.exportTrees(java.util.Collection<? extends Tree> trees)
|
void |
PHYLIPExporter.exportTrees(java.util.Collection<? extends Tree> trees)
|
void |
TreeExporter.exportTrees(java.util.Collection<? extends Tree> trees)
Export a collection of trees |
void |
NexusExporter.exportTreesWithTranslation(java.util.Collection<? extends Tree> trees,
java.util.Map<java.lang.String,java.lang.String> t)
|
Uses of Tree in jebl.evolution.parsimony |
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Methods in jebl.evolution.parsimony with parameters of type Tree | |
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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 |
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Classes in jebl.evolution.trees with type parameters of type Tree | |
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class |
ClusteringTreeBuilder<T extends Tree>
An abstract base class for clustering algorithms from pairwise distances |
class |
ConsensusTreeBuilder<T extends Tree>
A TreeBuilder 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 | |
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interface |
RootedTree
A tree with a root (node with maximum height). |
Classes in jebl.evolution.trees that implement Tree | |
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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 | |
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Tree |
TreeChangeEvent.getTree()
|
Methods in jebl.evolution.trees that return types with arguments of type Tree | |
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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 | |
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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 node |
static 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 point for any point on the tree x let D(x) = Max{distance between x and t : for all tips t} The "center" c is the point with the smallest distance, i.e. |
Method parameters in jebl.evolution.trees with type arguments of type Tree | |
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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 | |
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MutableRootedTree(Tree tree,
Node outGroup)
Construct a rooted tree from unrooted. |
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RootedFromUnrooted(Tree source,
Node root,
boolean intentUnrooted)
Root tree at some internal node. |
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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. |
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SimpleRootedTree(Tree tree,
Node ingroupNode,
Node outgroupNode,
double ingroupBranchLength)
Make a copy of the given unrooted tree |
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SimpleTree(Tree tree)
Duplicate a tree. |
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TreeChangeEvent(Tree tree)
|
Constructor parameters in jebl.evolution.trees with type arguments of type Tree | |
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MostProbableTopology(java.util.Collection<? extends Tree> trees)
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