jprotein.tree.tools
Class Tree

java.lang.Object
  extended by 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
 

Field Detail

LEFT

public static final int LEFT
See Also:
Constant Field Values

RIGHT

public static final int RIGHT
See Also:
Constant Field Values
Constructor Detail

Tree

public Tree()
Method Detail

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)