IdGroup
, java.io.Serializable
, Units
, UnitsProvider
ParameterizedTree
ClockTree
, ClusterTree
, DemographicClockTree
, LogParameterizedTree
, MutationRateModelTree
, NeighborJoiningTree
, ParameterizedTree.ParameterizedTreeBase
, ReadTree
, SimpleTree
, SUPGMATree
, Tree.TreeBase
, UnconstrainedTree
, UPGMATree
public interface Tree extends IdGroup, Units, java.io.Serializable, UnitsProvider
Modifier and Type | Interface | Description |
---|---|---|
static class |
Tree.TreeBase |
IdGroup.Utils
DAYS, EXPECTED_SUBSTITUTIONS, GENERATIONS, MONTHS, SAMPLE, SHORT_UNIT_NAMES, UNIT_NAMES, UNKNOWN, YEARS
Modifier and Type | Method | Description |
---|---|---|
void |
createNodeList() |
This method is called to ensure that the calls to other methods
in this interface are valid.
|
java.lang.Object |
getAttribute(Node node,
java.lang.String name) |
|
Tree |
getCopy() |
|
Node |
getExternalNode(int i) |
|
int |
getExternalNodeCount() |
|
Node |
getInternalNode(int i) |
|
int |
getInternalNodeCount() |
|
Node |
getRoot() |
|
int |
getUnits() |
Gets the units that this tree's branch lengths and node
heights are expressed in.
|
void |
setAttribute(Node node,
java.lang.String name,
java.lang.Object value) |
Sets an named attribute for a given node.
|
void |
setRoot(Node root) |
This method constructs a tree from the given root node.
|
getIdCount, getIdentifier, setIdentifier, whichIdNumber
Node getRoot()
void setRoot(Node root)
root
- the root node of the tree to construct.int getExternalNodeCount()
int getInternalNodeCount()
Node getExternalNode(int i)
Node getInternalNode(int i)
void createNodeList()
int getUnits()
getUnits
in interface UnitsProvider
void setAttribute(Node node, java.lang.String name, java.lang.Object value)
node
- the node whose attribute is being set.name
- the name of the attribute.value
- the new value of the attribute.java.lang.Object getAttribute(Node node, java.lang.String name)
node
- the node being interrogated.name
- the name of the attribute of interest.Tree getCopy()