Package | Description |
---|---|
jebl.evolution.graphs | |
jebl.evolution.trees |
Modifier and Type | Method | Description |
---|---|---|
Edge |
Graph.getEdge(Node node1,
Node node2) |
Returns the Edge that connects these two nodes
|
Modifier and Type | Method | Description |
---|---|---|
java.util.Set<Edge> |
Graph.getEdges() |
|
java.util.List<Edge> |
Graph.getEdges(Node node) |
Returns a list of edges connected to this node
|
Modifier and Type | Method | 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 | Class | Description |
---|---|---|
class |
BaseEdge |
Common implementation of Attributable interface used by Nodes.
|
Modifier and Type | Method | Description |
---|---|---|
Edge |
CompactRootedTree.getEdge(Node node1,
Node node2) |
|
Edge |
FilteredRootedTree.getEdge(Node node1,
Node node2) |
|
Edge |
MutableRootedTree.getEdge(Node node1,
Node node2) |
Returns the Edge that connects these two nodes
|
Edge |
RootedFromUnrooted.getEdge(Node node1,
Node node2) |
|
Edge |
RootedSubtree.getEdge(Node node1,
Node node2) |
Returns the Edge that connects these two nodes
|
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 |
CompactRootedTree.getParentEdge(Node node) |
|
Edge |
MutableRootedTree.getParentEdge(Node node) |
|
Edge |
RootedSubtree.getParentEdge(Node node) |
|
Edge |
SimpleRootedTree.getParentEdge(Node node) |
Modifier and Type | Method | Description |
---|---|---|
java.util.Set<Edge> |
CompactRootedTree.getEdges() |
|
java.util.List<Edge> |
CompactRootedTree.getEdges(Node node) |
|
java.util.Set<Edge> |
FilteredRootedTree.getEdges() |
|
java.util.List<Edge> |
FilteredRootedTree.getEdges(Node node) |
|
java.util.Set<Edge> |
MutableRootedTree.getEdges() |
|
java.util.List<Edge> |
MutableRootedTree.getEdges(Node node) |
Returns a list of edges connected to this node
|
java.util.Set<Edge> |
RootedFromUnrooted.getEdges() |
|
java.util.List<Edge> |
RootedFromUnrooted.getEdges(Node node) |
Returns a list of edges connected to this node
|
java.util.Set<Edge> |
RootedSubtree.getEdges() |
|
java.util.List<Edge> |
RootedSubtree.getEdges(Node node) |
Returns a list of edges connected to this node
|
java.util.Set<Edge> |
SimpleRootedTree.getEdges() |
|
java.util.List<Edge> |
SimpleRootedTree.getEdges(Node node) |
Returns a list of edges connected to this node
|
java.util.Set<Edge> |
SimpleTree.getEdges() |
|
java.util.List<Edge> |
SimpleTree.getEdges(Node node) |
Returns a list of edges connected to this node
|
java.util.Set<Edge> |
CompactRootedTree.getExternalEdges() |
|
java.util.Set<Edge> |
FilteredRootedTree.getExternalEdges() |
|
java.util.Set<Edge> |
MutableRootedTree.getExternalEdges() |
The set of external edges.
|
java.util.Set<Edge> |
RootedFromUnrooted.getExternalEdges() |
The set of external edges.
|
java.util.Set<Edge> |
RootedSubtree.getExternalEdges() |
The set of external edges.
|
java.util.Set<Edge> |
SimpleRootedTree.getExternalEdges() |
The set of external edges.
|
java.util.Set<Edge> |
SimpleTree.getExternalEdges() |
The set of external edges.
|
java.util.Set<Edge> |
Tree.getExternalEdges() |
|
java.util.Set<Edge> |
CompactRootedTree.getInternalEdges() |
|
java.util.Set<Edge> |
FilteredRootedTree.getInternalEdges() |
|
java.util.Set<Edge> |
MutableRootedTree.getInternalEdges() |
The set of internal edges.
|
java.util.Set<Edge> |
RootedFromUnrooted.getInternalEdges() |
The set of internal edges.
|
java.util.Set<Edge> |
RootedSubtree.getInternalEdges() |
The set of internal edges.
|
java.util.Set<Edge> |
SimpleRootedTree.getInternalEdges() |
The set of internal edges.
|
java.util.Set<Edge> |
SimpleTree.getInternalEdges() |
The set of internal edges.
|
java.util.Set<Edge> |
Tree.getInternalEdges() |
Modifier and Type | Method | Description |
---|---|---|
Node |
SimpleRootedTree.addNode(Edge edge) |
Adds a new node at the midpoint of the given edge
|
Node[] |
CompactRootedTree.getNodes(Edge edge) |
|
Node[] |
FilteredRootedTree.getNodes(Edge 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[] |
RootedSubtree.getNodes(Edge edge) |
Returns an array of 2 nodes which are the nodes at either end of the 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.
|
static void |
SplitUtils.getSplit(java.util.List<Taxon> taxa,
Tree tree,
Edge edge,
boolean[] split) |
get split for branch associated with internal node
|
boolean |
SimpleTree.isExternal(Edge edge) |
|
void |
SimpleTree.setEdgeLength(Edge edge,
double length) |
Change length of an existing edge.
|
http://code.google.com/p/jebl2/