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Packages that use RootedTree | |
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jebl.evolution.align | Provides classes and interfaces for pairwise alignment of two sequences. |
jebl.evolution.coalescent | |
jebl.evolution.treemetrics | |
jebl.evolution.trees | |
jebl.evolution.treesimulation |
Uses of RootedTree in jebl.evolution.align |
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Methods in jebl.evolution.align with parameters of type RootedTree | |
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Alignment |
BartonSternberg.doAlign(java.util.List<Sequence> seqs,
RootedTree guideTree,
ProgressListener progress)
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Alignment |
MultipleAligner.doAlign(java.util.List<Sequence> seqs,
RootedTree guideTree,
ProgressListener progress)
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Uses of RootedTree in jebl.evolution.coalescent |
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Constructors in jebl.evolution.coalescent with parameters of type RootedTree | |
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Coalescent(RootedTree tree,
DemographicFunction demographicFunction)
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Intervals(RootedTree tree)
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Uses of RootedTree in jebl.evolution.treemetrics |
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Methods in jebl.evolution.treemetrics with parameters of type RootedTree | |
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double |
CladeHeightMetric.getMetric(RootedTree tree1,
RootedTree tree2)
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double |
RootedTreeMetric.getMetric(RootedTree tree1,
RootedTree tree2)
calculates the metric between two rooted trees |
double |
RobinsonsFouldMetric.getMetric(RootedTree tree1,
RootedTree tree2)
|
double |
BilleraMetric.getMetric(RootedTree tree1,
RootedTree tree2)
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Uses of RootedTree in jebl.evolution.trees |
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Classes in jebl.evolution.trees that implement RootedTree | |
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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 |
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 RootedTree | |
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static RootedTree |
Utils.copyTree(RootedTree treeToCopy)
This method creates an unattached copy of the given rooted tree such that changes to the copied tree do not affect the original tree. |
RootedTree |
FilteredRootedTree.getSource()
|
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. |
Methods in jebl.evolution.trees with parameters of type RootedTree | |
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void |
CladeSystem.add(RootedTree tree)
adds all the clades in the tree |
void |
CalculateSplitRates.addTreeToDensityMap(jebl.evolution.trees.CalculateSplitRates.DensityMap densityMap,
RootedTree tree)
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static ConsensusTreeBuilder |
TreeBuilderFactory.buildRooted(RootedTree[] trees,
double supportThreshold,
TreeBuilderFactory.ConsensusMethod method)
|
static RootedTree |
Utils.copyTree(RootedTree treeToCopy)
This method creates an unattached copy of the given rooted tree such that changes to the copied tree do not affect the original tree. |
static java.util.Comparator<Node> |
Utils.createNodeDensityComparator(RootedTree tree)
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static java.util.Comparator<Node> |
Utils.createNodeDensityMinNodeHeightComparator(RootedTree tree)
|
Node |
SimpleRootedTree.createNodes(RootedTree tree,
Node node)
Clones the entire tree structure from the given RootedTree. |
static java.lang.String |
Utils.DEBUGsubTreeRep(RootedTree tree,
Node node)
|
static boolean |
RootedTreeUtils.equal(RootedTree tree1,
RootedTree tree2)
Compares 2 trees and returns true if they have the same topology. |
static Node |
RootedTreeUtils.getCommonAncestorNode(RootedTree tree,
java.util.Set<Node> tipNodes)
Gets the most recent common ancestor (MRCA) node of a set of tip nodes. |
static java.util.Set<Node> |
RootedTreeUtils.getDescendantTips(RootedTree tree,
Node node)
Gets a set of tip nodes descended from the given node. |
static int |
Utils.getExternalNodeCount(RootedTree tree,
Node node)
Return the number of external nodes under this node. |
static double |
RootedTreeUtils.getMaxTipHeight(RootedTree tree,
Node node)
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static double |
Utils.getMinNodeHeight(RootedTree tree,
Node node)
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static double |
RootedTreeUtils.getMinTipHeight(RootedTree tree,
Node node)
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static java.util.List<Node> |
Utils.getNodes(RootedTree tree,
Node node)
All nodes in subtree - parents before children (pre - order). |
static int |
RootedTreeUtils.getTipCount(RootedTree tree,
Node node)
Return the number of leaves under this node. |
static java.util.Set<Node> |
RootedTreeUtils.getTipsForTaxa(RootedTree tree,
java.util.Collection<Taxon> taxa)
Gets a set of external nodes that correspond to the given taxa. |
static boolean |
Utils.isBinary(RootedTree rootedTree)
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static boolean |
RootedTreeUtils.isBinary(RootedTree tree)
|
static boolean |
RootedTreeUtils.isMonophyletic(RootedTree tree,
java.util.Set<Node> tipNodes)
Performs the a monophyly test on a set of tip nodes. |
static boolean |
Utils.isUltrametric(RootedTree rootedTree)
|
static boolean |
RootedTreeUtils.isUltrametric(RootedTree tree,
double tolerance)
|
static Node |
Utils.leftNb(RootedTree tree,
Node node)
Left Neighbour of a tip (taxon). |
static int |
Utils.maxLevels(RootedTree tree)
|
static Node |
Utils.rightNb(RootedTree tree,
Node tipNode)
Right Neighbour of a tip (taxon). |
static double |
Utils.safeNodeHeight(RootedTree tree,
Node node)
|
static java.lang.String |
Utils.toNewick(RootedTree tree)
|
static java.lang.String |
Utils.toUniqueNewick(RootedTree tree)
Constructs a unique newick representation of a tree |
static java.lang.String |
Utils.toUniqueNewickByAttribute(RootedTree tree,
java.lang.String attribute)
Constructs a unique newick representation of a tree print only an attribute |
static java.lang.String |
RootedTreeUtils.uniqueNewick(RootedTree tree,
Node node)
Recursive function for constructing a newick tree representation in the given buffer. |
Constructors in jebl.evolution.trees with parameters of type RootedTree | |
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AttributedCladeSystem(java.lang.String name,
RootedTree tree)
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CladeSystem(RootedTree tree)
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CompactRootedTree(RootedTree t)
Do all the hard work. |
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FilteredRootedTree(RootedTree source)
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ReRootedTree(RootedTree source,
ReRootedTree.RootingType rootingType)
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RootedSubtree(RootedTree tree,
java.util.Set<Taxon> includedTaxa)
Make a copy of the given rooted tree |
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SimpleRootedTree(RootedTree tree)
Make a copy of the given rooted tree |
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SimpleRootedTree(RootedTree tree,
java.util.Map<Node,Node> nodeMapping)
Make a copy of the given rooted tree |
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SortedRootedTree(RootedTree source,
java.util.Comparator<Node> comparator)
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SortedRootedTree(RootedTree source,
SortedRootedTree.BranchOrdering branchOrdering)
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TransformedRootedTree(RootedTree source,
TransformedRootedTree.Transform transform)
|
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TreeBiPartitionInfo(RootedTree t,
java.util.List<Taxon> taxa)
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Uses of RootedTree in jebl.evolution.treesimulation |
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Methods in jebl.evolution.treesimulation that return RootedTree | |
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RootedTree |
TreeSimulator.simulate(IntervalGenerator intervalGenerator)
|
RootedTree |
TreeSimulator.simulate(IntervalGenerator intervalGenerator,
boolean medianHeights)
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