Package | Description |
---|---|
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 |
Modifier and Type | Method and Description |
---|---|
Alignment |
MultipleAligner.doAlign(java.util.List<Sequence> seqs,
RootedTree guideTree,
ProgressListener progress) |
Alignment |
BartonSternberg.doAlign(java.util.List<Sequence> seqs,
RootedTree guideTree,
ProgressListener progress) |
Constructor and Description |
---|
Coalescent(RootedTree tree,
DemographicFunction demographicFunction) |
Intervals(RootedTree tree) |
Modifier and Type | Method and Description |
---|---|
double |
RobinsonsFouldMetric.getMetric(RootedTree tree1,
RootedTree tree2) |
double |
RootedTreeMetric.getMetric(RootedTree tree1,
RootedTree tree2)
calculates the metric between two rooted trees
|
double |
BilleraMetric.getMetric(RootedTree tree1,
RootedTree tree2) |
double |
CladeHeightMetric.getMetric(RootedTree tree1,
RootedTree tree2) |
Modifier and Type | Class and 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 |
SortedRootedTree |
class |
TransformedRootedTree
This RootedTree class wraps another RootedTree and transforms
the branch lengths and node heights using various functions.
|
Modifier and Type | Method and Description |
---|---|
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.
|
Modifier and Type | Method and Description |
---|---|
void |
CladeSystem.add(RootedTree tree)
adds all the clades in the tree
|
void |
CalculateSplitRates.addTreeToDensityMap(jebl.evolution.trees.CalculateSplitRates.DensityMap densityMap,
RootedTree tree) |
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) |
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) |
static double |
Utils.getMinNodeHeight(RootedTree tree,
Node node) |
static double |
RootedTreeUtils.getMinTipHeight(RootedTree tree,
Node node) |
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 |
RootedTreeUtils.isBinary(RootedTree tree) |
static boolean |
Utils.isBinary(RootedTree rootedTree) |
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.
|
Constructor and Description |
---|
AttributedCladeSystem(java.lang.String name,
RootedTree tree) |
CladeSystem(RootedTree tree) |
CompactRootedTree(RootedTree t)
Do all the hard work.
|
FilteredRootedTree(RootedTree source) |
ReRootedTree(RootedTree source,
ReRootedTree.RootingType rootingType) |
RootedSubtree(RootedTree tree,
java.util.Set<Taxon> includedTaxa)
Make a copy of the given rooted tree
|
SimpleRootedTree(RootedTree tree)
Make a copy of the given rooted tree
|
SimpleRootedTree(RootedTree tree,
java.util.Map<Node,Node> nodeMapping)
Make a copy of the given rooted tree
|
SortedRootedTree(RootedTree source,
java.util.Comparator<Node> comparator) |
SortedRootedTree(RootedTree source,
SortedRootedTree.BranchOrdering branchOrdering) |
TransformedRootedTree(RootedTree source,
TransformedRootedTree.Transform transform) |
TreeBiPartitionInfo(RootedTree t,
java.util.List<Taxon> taxa) |
Modifier and Type | Method and Description |
---|---|
RootedTree |
TreeSimulator.simulate(IntervalGenerator intervalGenerator) |
RootedTree |
TreeSimulator.simulate(IntervalGenerator intervalGenerator,
boolean medianHeights) |
http://code.google.com/p/jebl2/