BioinfoFieldExtractor
Class PhylogenTree

java.lang.Object
  extended by BioinfoFieldExtractor.PhylogenTree

public class PhylogenTree
extends java.lang.Object

This is a generic class implementing a phylogenetic tree. It is used to construct clusters of similar messages for global alignment.

Author:
Serge Gorbunov

Constructor Summary
PhylogenTree()
           
 
Method Summary
 float getDistance()
          Returns the ditance score between the children
 java.util.ArrayList<java.lang.Integer> getGapsToBeInserted()
          Returns the array list of gaps
 int getHeight()
          Returns the height of the tree
 int getIndex()
          Returns the index
 boolean getIsLeaf()
          Check if the node is a leaf
 PhylogenTree getLeftChild()
          Returns the left child
 PhylogenTree getParent()
          Returns the parent node
 PhylogenTree getRightChild()
          Returns the right child
 java.util.ArrayList<java.lang.Integer> getValue()
          Returns the value
 void setDistance(float d)
          Sets the distance score between the children
 void setGapsToBoInserted(java.util.ArrayList<java.lang.Integer> g)
          Sets the gaps
 void setIndex(int i)
          Sets the index
 void setLeftChild(PhylogenTree l)
          Sets the left child
 void setParent(PhylogenTree p)
          Sets the parent
 void setRightChild(PhylogenTree r)
          Sets the right child
 void setValue(java.util.ArrayList<java.lang.Integer> newVal)
          Sets the value
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

PhylogenTree

public PhylogenTree()
Method Detail

getIsLeaf

public boolean getIsLeaf()
Check if the node is a leaf

Returns:
True if the node has no children, false otherwise

getHeight

public int getHeight()
Returns the height of the tree


getParent

public PhylogenTree getParent()
Returns the parent node


setParent

public void setParent(PhylogenTree p)
Sets the parent


getLeftChild

public PhylogenTree getLeftChild()
Returns the left child


setLeftChild

public void setLeftChild(PhylogenTree l)
Sets the left child


getRightChild

public PhylogenTree getRightChild()
Returns the right child


setRightChild

public void setRightChild(PhylogenTree r)
Sets the right child


setValue

public void setValue(java.util.ArrayList<java.lang.Integer> newVal)
Sets the value


getValue

public java.util.ArrayList<java.lang.Integer> getValue()
Returns the value


setIndex

public void setIndex(int i)
Sets the index


getIndex

public int getIndex()
Returns the index


setDistance

public void setDistance(float d)
Sets the distance score between the children


getDistance

public float getDistance()
Returns the ditance score between the children


setGapsToBoInserted

public void setGapsToBoInserted(java.util.ArrayList<java.lang.Integer> g)
Sets the gaps


getGapsToBeInserted

public java.util.ArrayList<java.lang.Integer> getGapsToBeInserted()
Returns the array list of gaps