Package | Description |
---|---|
jebl.evolution.align |
Provides classes and interfaces for pairwise alignment of two sequences.
|
jebl.evolution.io | |
jebl.evolution.parsimony | |
jebl.evolution.trees |
Modifier and Type | Field and Description |
---|---|
Tree |
AlignmentTreeBuilderFactory.Result.tree |
Modifier and Type | Method and Description |
---|---|
Tree |
NewickImporter.importNextTree() |
Tree |
TreeImporter.importNextTree()
Import a single tree
|
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.
|
Modifier and Type | Method and Description |
---|---|
java.util.List<Tree> |
NewickImporter.importTrees() |
java.util.List<Tree> |
TreeImporter.importTrees()
Import all the trees
|
java.util.List<Tree> |
NexusImporter.importTrees()
Import all trees in the file from the current position.
|
java.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.
|
Modifier and Type | Method and Description |
---|---|
void |
NexusExporter.exportTree(Tree tree)
Export a single tree
|
void |
NewickExporter.exportTree(Tree tree)
Export a single tree
|
void |
PHYLIPExporter.exportTree(Tree tree) |
void |
TreeExporter.exportTree(Tree tree)
Export a single tree
|
Modifier and Type | Method and Description |
---|---|
void |
NexusExporter.exportTrees(java.util.Collection<? extends Tree> trees) |
void |
NewickExporter.exportTrees(java.util.Collection<? extends Tree> trees)
Export a collection of 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.exportTrees(java.util.Collection<? extends Tree> trees,
boolean writeTaxa) |
void |
NexusExporter.exportTreesWithTranslation(java.util.Collection<? extends Tree> trees,
java.util.Map<java.lang.String,java.lang.String> t) |
Modifier and Type | Method and 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.
|
Modifier and Type | Class and Description |
---|---|
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> |
Modifier and Type | Interface and Description |
---|---|
interface |
RootedTree
A tree with a root (node with maximum height).
|
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 |
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.
|
Modifier and Type | Method and Description |
---|---|
Tree |
TreeChangeEvent.getTree() |
Modifier and Type | Method and Description |
---|---|
java.util.List<Tree> |
MostProbableTopology.get(int max,
double threshold)
Get the most probable tree(s)
|
Modifier and Type | Method and 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 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.
|
Modifier and Type | Method and 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.
|
Constructor and 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 tree
|
SimpleTree(Tree tree)
Duplicate a tree.
|
TreeChangeEvent(Tree tree) |
Constructor and Description |
---|
MostProbableTopology(java.util.Collection<? extends Tree> trees) |
http://code.google.com/p/jebl2/