jprotein.tree.tools
Class Tree
java.lang.Object
jprotein.tree.tools.Tree
public class Tree
- extends java.lang.Object
Field Summary |
static int |
LEFT
|
static int |
RIGHT
|
Constructor Summary |
Tree()
|
Method Summary |
Leaf |
getLeaf(SimpleNode node,
int direction)
|
Leaf |
getLeaf(SimpleNode root,
Sequence alignment)
|
java.util.Vector |
getNodeDistance(SimpleNode root,
double distance)
|
java.util.Vector |
getNodePartition(SimpleNode root,
double maxDistance)
|
double |
getPathDistance(SimpleNode root,
PathIndex pathIndex)
|
PathIndex |
getPathIndex(SimpleNode root,
Leaf leaf)
|
java.util.Vector |
getTrace(java.util.Vector partition)
|
java.util.Vector |
getTraceAnalysis(SimpleNode root)
|
double |
getVertice(SimpleNode node,
int direction)
|
void |
moveRoot(SimpleNode root,
PathIndex pathIndex,
double distance)
|
int |
opposite(int direction)
|
void |
rootMidTree(SimpleNode root,
Leaf leaf1,
Leaf leaf2)
|
void |
setLeaf(SimpleNode node,
int direction,
Leaf leaf)
|
void |
setVertice(SimpleNode node,
int direction,
double distance)
|
void |
shiftRoot(SimpleNode root,
int direction1,
int direction2)
|
void |
translateRoot(SimpleNode root,
int direction,
double distance)
|
Methods inherited from class java.lang.Object |
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
LEFT
public static final int LEFT
- See Also:
- Constant Field Values
RIGHT
public static final int RIGHT
- See Also:
- Constant Field Values
Tree
public Tree()
getLeaf
public Leaf getLeaf(SimpleNode root,
Sequence alignment)
getPathIndex
public PathIndex getPathIndex(SimpleNode root,
Leaf leaf)
getPathDistance
public double getPathDistance(SimpleNode root,
PathIndex pathIndex)
setLeaf
public void setLeaf(SimpleNode node,
int direction,
Leaf leaf)
getLeaf
public Leaf getLeaf(SimpleNode node,
int direction)
setVertice
public void setVertice(SimpleNode node,
int direction,
double distance)
getVertice
public double getVertice(SimpleNode node,
int direction)
rootMidTree
public void rootMidTree(SimpleNode root,
Leaf leaf1,
Leaf leaf2)
moveRoot
public void moveRoot(SimpleNode root,
PathIndex pathIndex,
double distance)
translateRoot
public void translateRoot(SimpleNode root,
int direction,
double distance)
shiftRoot
public void shiftRoot(SimpleNode root,
int direction1,
int direction2)
opposite
public int opposite(int direction)
getNodeDistance
public java.util.Vector getNodeDistance(SimpleNode root,
double distance)
getNodePartition
public java.util.Vector getNodePartition(SimpleNode root,
double maxDistance)
getTraceAnalysis
public java.util.Vector getTraceAnalysis(SimpleNode root)
getTrace
public java.util.Vector getTrace(java.util.Vector partition)