java.io.Serializable
, IdGroup
, Report
, Units
, UnitsProvider
, Tree
public abstract static class Tree.TreeBase extends java.lang.Object implements Tree, Report, Units, java.io.Serializable
IdGroup.Utils
Tree.TreeBase
DAYS, EXPECTED_SUBSTITUTIONS, GENERATIONS, MONTHS, SAMPLE, SHORT_UNIT_NAMES, UNIT_NAMES, UNKNOWN, YEARS
Modifier | Constructor | Description |
---|---|---|
protected |
TreeBase() |
constructor
|
protected |
TreeBase(Node theRoot) |
constructor
|
protected |
TreeBase(Tree.TreeBase tree,
Node newRoot) |
clone constructor
|
Modifier and Type | Method | Description |
---|---|---|
void |
createNodeList() |
count and list external and internal nodes and
compute heights of each node
|
Node |
findNode(int num) |
return node with number num (as displayed in ASCII tree)
|
java.lang.Object |
getAttribute(Node node,
java.lang.String name) |
|
Node |
getExternalNode(int i) |
Returns the ith external node.
|
int |
getExternalNodeCount() |
Returns the number of external nodes.
|
int |
getIdCount() |
Returns the number of identifiers in this group
|
Identifier |
getIdentifier(int i) |
Returns the ith identifier.
|
Node |
getInternalNode(int i) |
Returns the ith internal node.
|
int |
getInternalNodeCount() |
Returns the number of internal nodes.
|
Node |
getRoot() |
Returns the root node of this tree.
|
int |
getUnits() |
Return the units that this tree is expressed in.
|
void |
report(java.io.PrintWriter out) |
print human readable report (e.g., on parameters and associated model)
|
void |
reroot(int num) |
make node with number num to root node
|
void |
reroot(Node node) |
make provided node the root node
|
void |
setAttribute(Node node,
java.lang.String name,
java.lang.Object value) |
Sets an named attribute for a given node.
|
void |
setIdentifier(int i,
Identifier id) |
Sets the ith identifier.
|
void |
setRoot(Node theRoot) |
Called by subclasses that can't give root at time of construction (of this class)
|
protected void |
setSetupLengthsAndHeights(boolean value) |
Set whether or not this class should call methods to adjust
either heights or lengths automatically
|
void |
setUnits(int units) |
Sets the units that this tree is expressed in.
|
java.lang.String |
toString() |
|
int |
whichIdNumber(java.lang.String s) |
returns the index of the identifier with the given name.
|
protected TreeBase(Node theRoot)
theRoot
- the node to base tree onprotected TreeBase()
protected TreeBase(Tree.TreeBase tree, Node newRoot)
public void setRoot(Node theRoot)
public final int getUnits()
getUnits
in interface Tree
getUnits
in interface UnitsProvider
public final void setUnits(int units)
public final int getExternalNodeCount()
getExternalNodeCount
in interface Tree
public final Node getExternalNode(int i)
getExternalNode
in interface Tree
public final int getInternalNodeCount()
getInternalNodeCount
in interface Tree
public final Node getInternalNode(int i)
getInternalNode
in interface Tree
public final Node getRoot()
public Node findNode(int num)
num
- number of nodepublic void createNodeList()
createNodeList
in interface Tree
protected void setSetupLengthsAndHeights(boolean value)
public java.lang.String toString()
toString
in class java.lang.Object
public void setAttribute(Node node, java.lang.String name, java.lang.Object value)
setAttribute
in interface Tree
node
- the node whose attribute is being set.name
- the name of the attribute.value
- the new value of the attribute.public java.lang.Object getAttribute(Node node, java.lang.String name)
getAttribute
in interface Tree
node
- the node being interrogated.name
- the name of the attribute of interest.public void reroot(int num)
num
- number of nodepublic void reroot(Node node)
node
- the node to make the root.public int getIdCount()
IdGroup
getIdCount
in interface IdGroup
public Identifier getIdentifier(int i)
IdGroup
getIdentifier
in interface IdGroup
public void setIdentifier(int i, Identifier id)
IdGroup
setIdentifier
in interface IdGroup
public int whichIdNumber(java.lang.String s)
IdGroup
whichIdNumber
in interface IdGroup