Package | Description |
---|---|
jebl.evolution.graphs | |
jebl.evolution.trees |
Modifier and Type | Method and Description |
---|---|
Edge |
Graph.getEdge(Node node1,
Node node2)
Returns the Edge that connects these two nodes
|
Modifier and Type | Method and 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 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 | Class and Description |
---|---|
class |
BaseEdge
Common implementation of Attributable interface used by Nodes.
|
Modifier and Type | Method and Description |
---|---|
Edge |
MutableRootedTree.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 |
CompactRootedTree.getEdge(Node node1,
Node node2) |
Edge |
FilteredRootedTree.getEdge(Node node1,
Node node2) |
Edge |
RootedFromUnrooted.getEdge(Node node1,
Node node2) |
Edge |
RootedSubtree.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.getParentEdge(Node node) |
Edge |
SimpleRootedTree.getParentEdge(Node node) |
Edge |
CompactRootedTree.getParentEdge(Node node) |
Edge |
RootedSubtree.getParentEdge(Node node) |
Modifier and Type | Method and Description |
---|---|
java.util.Set<Edge> |
MutableRootedTree.getEdges() |
java.util.Set<Edge> |
SimpleRootedTree.getEdges() |
java.util.Set<Edge> |
CompactRootedTree.getEdges() |
java.util.Set<Edge> |
FilteredRootedTree.getEdges() |
java.util.Set<Edge> |
RootedFromUnrooted.getEdges() |
java.util.Set<Edge> |
RootedSubtree.getEdges() |
java.util.Set<Edge> |
SimpleTree.getEdges() |
java.util.List<Edge> |
MutableRootedTree.getEdges(Node node)
Returns a list of edges connected to this node
|
java.util.List<Edge> |
SimpleRootedTree.getEdges(Node node)
Returns a list of edges connected to this node
|
java.util.List<Edge> |
CompactRootedTree.getEdges(Node node) |
java.util.List<Edge> |
FilteredRootedTree.getEdges(Node node) |
java.util.List<Edge> |
RootedFromUnrooted.getEdges(Node node)
Returns a list of edges connected to this node
|
java.util.List<Edge> |
RootedSubtree.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.Set<Edge> |
MutableRootedTree.getExternalEdges()
The set of external edges.
|
java.util.Set<Edge> |
SimpleRootedTree.getExternalEdges()
The set of external edges.
|
java.util.Set<Edge> |
CompactRootedTree.getExternalEdges() |
java.util.Set<Edge> |
Tree.getExternalEdges() |
java.util.Set<Edge> |
FilteredRootedTree.getExternalEdges() |
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> |
SimpleTree.getExternalEdges()
The set of external edges.
|
java.util.Set<Edge> |
MutableRootedTree.getInternalEdges()
The set of internal edges.
|
java.util.Set<Edge> |
SimpleRootedTree.getInternalEdges()
The set of internal edges.
|
java.util.Set<Edge> |
CompactRootedTree.getInternalEdges() |
java.util.Set<Edge> |
Tree.getInternalEdges() |
java.util.Set<Edge> |
FilteredRootedTree.getInternalEdges() |
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> |
SimpleTree.getInternalEdges()
The set of internal edges.
|
Modifier and Type | Method and Description |
---|---|
Node |
SimpleRootedTree.addNode(Edge edge)
Adds a new node at the midpoint of the given edge
|
Node[] |
MutableRootedTree.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[] |
CompactRootedTree.getNodes(Edge edge) |
Node[] |
FilteredRootedTree.getNodes(Edge 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[] |
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/