Package | Description |
---|---|
jebl.evolution.graphs | |
jebl.evolution.parsimony | |
jebl.evolution.trees |
Modifier and Type | Method and Description |
---|---|
Node[] |
Graph.getNodes(Edge edge)
Returns an array of 2 nodes which are the nodes at either end of the edge.
|
Modifier and Type | Method and Description |
---|---|
java.util.List<Node> |
Graph.getAdjacencies(Node node)
Returns a list of nodes connected to this node by an edge
|
java.util.Set<Node> |
Graph.getNodes() |
java.util.Set<Node> |
Graph.getNodes(int degree) |
Modifier and Type | Method and Description |
---|---|
java.util.List<Node> |
Graph.getAdjacencies(Node node)
Returns a list of nodes connected to this node by an edge
|
static int |
Graph.Utils.getDegree(Graph graph,
Node node) |
Edge |
Graph.getEdge(Node node1,
Node node2)
Returns the Edge that connects these two nodes
|
double |
Graph.getEdgeLength(Node node1,
Node node2)
Returns the length of the edge that connects these two nodes
|
java.util.List<Edge> |
Graph.getEdges(Node node)
Returns a list of edges connected to this node
|
Modifier and Type | Method and Description |
---|---|
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 |
BaseNode
Common implementation of Attributable interface used by Nodes.
|
Modifier and Type | Method and Description |
---|---|
Node |
SimpleRootedTree.addNode(Edge edge)
Adds a new node at the midpoint of the given edge
|
Node |
SimpleRootedTree.addNode(Node node)
Adds a new node at the midpoint of the edge connecting the given node to its parent.
|
Node |
SimpleRootedTree.createExternalNode(Taxon taxon)
Creates a new external node with the given taxon.
|
Node |
SimpleTree.createExternalNode(Taxon taxon)
Creates a new external node with the given taxon.
|
Node |
MutableRootedTree.createExternalNode(Taxon taxon)
Creates a new external node with the given taxon.
|
Node |
SimpleTree.createInternalNode(java.util.List<Node> adjacencies)
Once a SimpleTree has been created, the node stucture can be created by
calling createExternalNode and createInternalNode.
|
Node |
SimpleRootedTree.createNodes(RootedTree tree,
Node node)
Clones the entire tree structure from the given RootedTree.
|
Node |
SimpleRootedTree.createNodes(Tree tree,
Node parent,
Node child)
Clones the entire tree structure from the given (unrooted) Tree.
|
Node |
MutableRootedTree.detachChildren(Node node,
java.util.List<java.lang.Integer> split) |
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.
|
Node |
RootedSubtree.getNode(Taxon taxon) |
Node |
Tree.getNode(Taxon taxon) |
Node |
FilteredRootedTree.getNode(Taxon taxon) |
Node |
SimpleRootedTree.getNode(Taxon taxon) |
Node |
SimpleTree.getNode(Taxon taxon) |
Node |
MutableRootedTree.getNode(Taxon taxon) |
Node |
RootedFromUnrooted.getNode(Taxon taxon) |
Node |
CompactRootedTree.getNode(Taxon taxon) |
Node[] |
RootedSubtree.getNodes(Edge edge)
Returns an array of 2 nodes which are the nodes at either end of the edge.
|
Node[] |
FilteredRootedTree.getNodes(Edge edge) |
Node[] |
SimpleRootedTree.getNodes(Edge edge)
Returns an array of 2 nodes which are the nodes at either end of the edge.
|
Node[] |
SimpleTree.getNodes(Edge edge)
Returns an array of 2 nodes which are the nodes at either end of the edge.
|
Node[] |
MutableRootedTree.getNodes(Edge edge)
Returns an array of 2 nodes which are the nodes at either end of the edge.
|
Node[] |
RootedFromUnrooted.getNodes(Edge edge) |
Node[] |
CompactRootedTree.getNodes(Edge edge) |
Node |
RootedSubtree.getParent(Node node) |
Node |
FilteredRootedTree.getParent(Node node) |
Node |
RootedTree.getParent(Node node) |
Node |
SimpleRootedTree.getParent(Node node) |
Node |
MutableRootedTree.getParent(Node node) |
Node |
RootedFromUnrooted.getParent(Node node) |
Node |
CompactRootedTree.getParent(Node node) |
Node |
RootedSubtree.getRootNode()
The root of the tree has the largest node height of
all nodes in the tree.
|
Node |
FilteredRootedTree.getRootNode() |
Node |
RootedTree.getRootNode()
The root of the tree has the largest node height of
all nodes in the tree.
|
Node |
SimpleRootedTree.getRootNode()
The root of the tree has the largest node height of
all nodes in the tree.
|
Node |
MutableRootedTree.getRootNode()
The root of the tree has the largest node height of
all nodes in the tree.
|
Node |
RootedFromUnrooted.getRootNode() |
Node |
CompactRootedTree.getRootNode() |
static Node |
Utils.leftNb(RootedTree tree,
Node node)
Left Neighbour of a tip (taxon).
|
static Node |
Utils.rightNb(RootedTree tree,
Node tipNode)
Right Neighbour of a tip (taxon).
|
Modifier and Type | Method and Description |
---|---|
static java.util.Comparator<Node> |
Utils.createNodeDensityComparator(RootedTree tree) |
static java.util.Comparator<Node> |
Utils.createNodeDensityMinNodeHeightComparator(RootedTree tree) |
java.util.List<Node> |
RootedSubtree.getAdjacencies(Node node) |
java.util.List<Node> |
FilteredRootedTree.getAdjacencies(Node node) |
java.util.List<Node> |
SimpleRootedTree.getAdjacencies(Node node) |
java.util.List<Node> |
SimpleTree.getAdjacencies(Node node) |
java.util.List<Node> |
MutableRootedTree.getAdjacencies(Node node) |
java.util.List<Node> |
RootedFromUnrooted.getAdjacencies(Node node) |
java.util.List<Node> |
CompactRootedTree.getAdjacencies(Node node) |
java.util.List<Node> |
RootedSubtree.getChildren(Node node) |
java.util.List<Node> |
FilteredRootedTree.getChildren(Node node) |
java.util.List<Node> |
RootedTree.getChildren(Node node) |
java.util.List<Node> |
SimpleRootedTree.getChildren(Node node) |
java.util.List<Node> |
MutableRootedTree.getChildren(Node node) |
java.util.List<Node> |
SortedRootedTree.getChildren(Node node) |
java.util.List<Node> |
RootedFromUnrooted.getChildren(Node node) |
java.util.List<Node> |
CompactRootedTree.getChildren(Node node) |
static java.util.Set<Node> |
RootedTreeUtils.getDescendantTips(RootedTree tree,
Node node)
Gets a set of tip nodes descended from the given node.
|
java.util.Set<Node> |
RootedSubtree.getExternalNodes() |
java.util.Set<Node> |
Tree.getExternalNodes() |
java.util.Set<Node> |
FilteredRootedTree.getExternalNodes() |
java.util.Set<Node> |
SimpleRootedTree.getExternalNodes() |
java.util.Set<Node> |
SimpleTree.getExternalNodes() |
java.util.Set<Node> |
MutableRootedTree.getExternalNodes() |
java.util.Set<Node> |
RootedFromUnrooted.getExternalNodes() |
java.util.Set<Node> |
CompactRootedTree.getExternalNodes() |
java.util.Set<Node> |
RootedSubtree.getInternalNodes() |
java.util.Set<Node> |
Tree.getInternalNodes() |
java.util.Set<Node> |
FilteredRootedTree.getInternalNodes() |
java.util.Set<Node> |
SimpleRootedTree.getInternalNodes() |
java.util.Set<Node> |
SimpleTree.getInternalNodes() |
java.util.Set<Node> |
MutableRootedTree.getInternalNodes() |
java.util.Set<Node> |
RootedFromUnrooted.getInternalNodes() |
java.util.Set<Node> |
CompactRootedTree.getInternalNodes() |
java.util.Set<Node> |
RootedSubtree.getNodes() |
java.util.Set<Node> |
FilteredRootedTree.getNodes() |
java.util.Set<Node> |
SimpleRootedTree.getNodes() |
java.util.Set<Node> |
SimpleTree.getNodes() |
java.util.Set<Node> |
MutableRootedTree.getNodes() |
java.util.Set<Node> |
RootedFromUnrooted.getNodes() |
java.util.Set<Node> |
CompactRootedTree.getNodes() |
java.util.Set<Node> |
RootedSubtree.getNodes(int degree) |
java.util.Set<Node> |
FilteredRootedTree.getNodes(int degree) |
java.util.Set<Node> |
SimpleRootedTree.getNodes(int degree) |
java.util.Set<Node> |
SimpleTree.getNodes(int degree) |
java.util.Set<Node> |
MutableRootedTree.getNodes(int degree) |
java.util.Set<Node> |
RootedFromUnrooted.getNodes(int degree) |
java.util.Set<Node> |
CompactRootedTree.getNodes(int degree) |
static java.util.List<Node> |
Utils.getNodes(RootedTree tree,
Node node)
All nodes in subtree - parents before children (pre - order).
|
java.util.Set<Node> |
TreeSelectionChangeEvent.getSelectedNodes() |
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.
|
Modifier and Type | Method and Description |
---|---|
void |
MutableRootedTree.addChild(Node child,
Node parent)
Insert a child node.
|
void |
SimpleTree.addEdge(Node node1,
Node node2,
double length)
Add a new edge between two existing (non adjacent yet) nodes.
|
Node |
SimpleRootedTree.addNode(Node node)
Adds a new node at the midpoint of the edge connecting the given node to its parent.
|
Node |
SimpleRootedTree.createNodes(RootedTree tree,
Node node)
Clones the entire tree structure from the given RootedTree.
|
Node |
SimpleRootedTree.createNodes(Tree tree,
Node parent,
Node child)
Clones the entire tree structure from the given (unrooted) Tree.
|
static java.lang.String |
Utils.DEBUGsubTreeRep(RootedTree tree,
Node node) |
void |
SimpleRootedTree.deleteInternalNode(Node node)
Removes an internal node in this tree.
|
Node |
MutableRootedTree.detachChildren(Node node,
java.util.List<java.lang.Integer> split) |
java.util.List<Node> |
RootedSubtree.getAdjacencies(Node node) |
java.util.List<Node> |
FilteredRootedTree.getAdjacencies(Node node) |
java.util.List<Node> |
SimpleRootedTree.getAdjacencies(Node node) |
java.util.List<Node> |
SimpleTree.getAdjacencies(Node node) |
java.util.List<Node> |
MutableRootedTree.getAdjacencies(Node node) |
java.util.List<Node> |
RootedFromUnrooted.getAdjacencies(Node node) |
java.util.List<Node> |
CompactRootedTree.getAdjacencies(Node node) |
java.util.List<Node> |
RootedSubtree.getChildren(Node node) |
java.util.List<Node> |
FilteredRootedTree.getChildren(Node node) |
java.util.List<Node> |
RootedTree.getChildren(Node node) |
java.util.List<Node> |
SimpleRootedTree.getChildren(Node node) |
java.util.List<Node> |
MutableRootedTree.getChildren(Node node) |
java.util.List<Node> |
SortedRootedTree.getChildren(Node node) |
java.util.List<Node> |
RootedFromUnrooted.getChildren(Node node) |
java.util.List<Node> |
CompactRootedTree.getChildren(Node node) |
static java.util.Set<Node> |
RootedTreeUtils.getDescendantTips(RootedTree tree,
Node node)
Gets a set of tip nodes descended from the given node.
|
Edge |
RootedSubtree.getEdge(Node node1,
Node node2)
Returns the Edge that connects these two nodes
|
Edge |
FilteredRootedTree.getEdge(Node node1,
Node node2) |
Edge |
SimpleRootedTree.getEdge(Node node1,
Node node2)
Returns the Edge that connects these two nodes
|
Edge |
SimpleTree.getEdge(Node node1,
Node node2)
Returns the Edge that connects these two nodes
|
Edge |
MutableRootedTree.getEdge(Node node1,
Node node2)
Returns the Edge that connects these two nodes
|
Edge |
RootedFromUnrooted.getEdge(Node node1,
Node node2) |
Edge |
CompactRootedTree.getEdge(Node node1,
Node node2) |
double |
RootedSubtree.getEdgeLength(Node node1,
Node node2) |
double |
FilteredRootedTree.getEdgeLength(Node node1,
Node node2) |
double |
SimpleRootedTree.getEdgeLength(Node node1,
Node node2) |
double |
SimpleTree.getEdgeLength(Node node1,
Node node2) |
double |
MutableRootedTree.getEdgeLength(Node node1,
Node node2) |
double |
RootedFromUnrooted.getEdgeLength(Node node1,
Node node2) |
double |
CompactRootedTree.getEdgeLength(Node node1,
Node node2) |
java.util.List<Edge> |
RootedSubtree.getEdges(Node node)
Returns a list of edges connected to this node
|
java.util.List<Edge> |
FilteredRootedTree.getEdges(Node node) |
java.util.List<Edge> |
SimpleRootedTree.getEdges(Node node)
Returns a list of edges connected to this node
|
java.util.List<Edge> |
SimpleTree.getEdges(Node node)
Returns a list of edges connected to this node
|
java.util.List<Edge> |
MutableRootedTree.getEdges(Node node)
Returns a list of edges connected to this node
|
java.util.List<Edge> |
RootedFromUnrooted.getEdges(Node node)
Returns a list of edges connected to this node
|
java.util.List<Edge> |
CompactRootedTree.getEdges(Node node) |
static int |
Utils.getExternalNodeCount(RootedTree tree,
Node node)
Return the number of external nodes under this node.
|
double |
RootedSubtree.getHeight(Node node) |
double |
FilteredRootedTree.getHeight(Node node) |
double |
RootedTree.getHeight(Node node) |
double |
TransformedRootedTree.getHeight(Node node) |
double |
SimpleRootedTree.getHeight(Node node) |
double |
MutableRootedTree.getHeight(Node node) |
double |
RootedFromUnrooted.getHeight(Node node) |
double |
CompactRootedTree.getHeight(Node node) |
double |
RootedSubtree.getLength(Node node) |
double |
FilteredRootedTree.getLength(Node node) |
double |
RootedTree.getLength(Node node) |
double |
TransformedRootedTree.getLength(Node node) |
double |
SimpleRootedTree.getLength(Node node) |
double |
MutableRootedTree.getLength(Node node) |
double |
RootedFromUnrooted.getLength(Node node) |
double |
CompactRootedTree.getLength(Node 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).
|
Node |
RootedSubtree.getParent(Node node) |
Node |
FilteredRootedTree.getParent(Node node) |
Node |
RootedTree.getParent(Node node) |
Node |
SimpleRootedTree.getParent(Node node) |
Node |
MutableRootedTree.getParent(Node node) |
Node |
RootedFromUnrooted.getParent(Node node) |
Node |
CompactRootedTree.getParent(Node node) |
Edge |
RootedSubtree.getParentEdge(Node node) |
Edge |
SimpleRootedTree.getParentEdge(Node node) |
Edge |
MutableRootedTree.getParentEdge(Node node) |
Edge |
CompactRootedTree.getParentEdge(Node node) |
static double |
Utils.getPathLength(Tree tree,
Node node1,
Node node2) |
Taxon |
RootedSubtree.getTaxon(Node node) |
Taxon |
Tree.getTaxon(Node node) |
Taxon |
FilteredRootedTree.getTaxon(Node node) |
Taxon |
SimpleRootedTree.getTaxon(Node node) |
Taxon |
SimpleTree.getTaxon(Node node) |
Taxon |
MutableRootedTree.getTaxon(Node node) |
Taxon |
RootedFromUnrooted.getTaxon(Node node) |
Taxon |
CompactRootedTree.getTaxon(Node node) |
static int |
RootedTreeUtils.getTipCount(RootedTree tree,
Node node)
Return the number of leaves under this node.
|
boolean |
RootedSubtree.isExternal(Node node) |
boolean |
Tree.isExternal(Node node) |
boolean |
FilteredRootedTree.isExternal(Node node) |
boolean |
SimpleRootedTree.isExternal(Node node) |
boolean |
SimpleTree.isExternal(Node node) |
boolean |
MutableRootedTree.isExternal(Node node) |
boolean |
RootedFromUnrooted.isExternal(Node node) |
boolean |
CompactRootedTree.isExternal(Node node) |
boolean |
RootedSubtree.isRoot(Node node) |
boolean |
FilteredRootedTree.isRoot(Node node) |
boolean |
RootedTree.isRoot(Node node) |
boolean |
SimpleRootedTree.isRoot(Node node) |
boolean |
MutableRootedTree.isRoot(Node node) |
boolean |
RootedFromUnrooted.isRoot(Node node) |
boolean |
CompactRootedTree.isRoot(Node node) |
static Node |
Utils.leftNb(RootedTree tree,
Node node)
Left Neighbour of a tip (taxon).
|
void |
MutableRootedTree.refineNode(Node node,
int[] leftSet) |
void |
MutableRootedTree.removeChild(Node child,
Node parent)
Remove a child node.
|
void |
MutableRootedTree.removeInternalNode(Node node)
Remove internal node.
|
void |
MutableRootedTree.reRootWithOutgroup(Node outGroup,
java.util.Set<java.lang.String> attributeNames)
Re-root tree using an outgroup.
|
static Node |
Utils.rightNb(RootedTree tree,
Node tipNode)
Right Neighbour of a tip (taxon).
|
static double |
Utils.safeNodeHeight(RootedTree tree,
Node node) |
void |
SimpleTree.setEdgeLength(Node node1,
Node node2,
double length)
Set edge distance between two adjacent nodes.
|
void |
RootedSubtree.setHeight(Node node,
double height) |
void |
SimpleRootedTree.setHeight(Node node,
double height) |
void |
MutableRootedTree.setHeight(Node node,
double height) |
void |
RootedSubtree.setLength(Node node,
double length) |
void |
SimpleRootedTree.setLength(Node node,
double length) |
void |
MutableRootedTree.setLength(Node node,
double length) |
void |
MutableRootedTree.setRoot(Node root)
Set the root node.
|
void |
SimpleRootedTree.swapNodes(Node n,
int i0,
int i1) |
static java.lang.String |
RootedTreeUtils.uniqueNewick(RootedTree tree,
Node node)
Recursive function for constructing a newick tree representation in the given buffer.
|
Modifier and Type | Method and Description |
---|---|
jebl.evolution.trees.SimpleRootedTree.SimpleRootedNode |
SimpleRootedTree.createInternalNode(java.util.List<? extends Node> children)
Once a SimpleRootedTree has been created, the node stucture can be created by
calling createExternalNode and createInternalNode.
|
jebl.evolution.trees.MutableRootedTree.MutableRootedNode |
MutableRootedTree.createInternalNode(java.util.List<? extends Node> children)
Once a SimpleRootedTree has been created, the node stucture can be created by
calling createExternalNode and createInternalNode.
|
Node |
SimpleTree.createInternalNode(java.util.List<Node> adjacencies)
Once a SimpleTree has been created, the node stucture can be created by
calling createExternalNode and createInternalNode.
|
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 boolean |
RootedTreeUtils.isMonophyletic(RootedTree tree,
java.util.Set<Node> tipNodes)
Performs the a monophyly test on a set of tip nodes.
|
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
|
Constructor and Description |
---|
SimpleRootedTree(RootedTree tree,
java.util.Map<Node,Node> nodeMapping)
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) |
TreeSelectionChangeEvent(java.util.Set<Node> selectedNodes) |
http://code.google.com/p/jebl2/