org.forester.sdi

Class DistanceCalculator

java.lang.Object

org.forester.sdi.DistanceCalculator

public class DistanceCalculator
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field and Description
static double	DEFAULT

Constructor Summary

Constructors

Constructor and Description
DistanceCalculator() Default constructor.
DistanceCalculator(Phylogeny t) Constructor.
DistanceCalculator(Phylogeny t, java.util.Vector<PhylogenyNode> ext_nodes) Constructor.

Method Summary

Methods

Modifier and Type	Method and Description
double	getDistanceToLCA(java.lang.String seq_name) Calculates the distance of the PhylogenyNode with seq name seq_name to the LCA of ext_nodes, which has been set either with constructor DistanceCalculator(Phylogeny,Vector) or method setTreeAndExtNodes(Phylogeny,Vector).
double	getDistanceToNode(PhylogenyNode outer, PhylogenyNode inner) Calculates the distance of PhylogenyNode outer to PhylogenyNode inner.
double	getDistanceToNode(java.lang.String seq_name, PhylogenyNode inner) Calculates the distance of the PhylogenyNode with seq name seq_name to PhylogenyNode inner.
double	getDistanceToRoot(PhylogenyNode n) Calculates the distance of PhylogenyNode n to the root of Phylogeny t which has been set either with a constructor, setTree(Phylogeny), or setTreeAndExtNodes(Phylogeny,Vector).
double	getDistanceToRoot(java.lang.String seq_name) Calculates the distance of the PhylogenyNode with seq name seq_name to the root of Phylogeny t, which has been set either with a constructor, setTree(Phylogeny), or setTreeAndExtNodes(Phylogeny,Vector).
double	getMean() Returns the mean distance.
int	getN() Returns the sum of all Nodes used to calculate the mean.
double	getStandardDeviation() Returns the standard deviation.
double	getVariance() Returns the variance.
static void	main(java.lang.String[] args)
void	setTree(Phylogeny t) Sets the rooted Phylogeny t for which the mean distance to the root and its variance and standard deviation are calculated.
void	setTreeAndExtNodes(Phylogeny t, java.util.ArrayList<PhylogenyNode> ext_nodes) Sets the rooted Phylogeny t and the external Nodes ext_nodes for which the mean distance to their lowest common ancestor and its variance and standard deviation are calculated.
void	setTreeAndExtNodes(Phylogeny t, java.util.Vector<PhylogenyNode> ext_nodes) Sets the rooted Phylogeny t and the external Nodes ext_nodes for which the mean distance to their lowest common ancestor and its variance and standard deviation are calculated.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

DEFAULT

public static final double DEFAULT

See Also:

Constant Field Values

Constructor Detail

DistanceCalculator

public DistanceCalculator()

Default constructor. (Last modified: 11/30/00)

DistanceCalculator

public DistanceCalculator(Phylogeny t)

Constructor. Sets the rooted Phylogeny t for which the mean distance to the root and its variance and standard deviation are calculated. (Last modified: 12/01/00)

Parameters:

t - the rooted Phylogeny for which the mean distance to the root and its variance and standard deviation are calculated

DistanceCalculator

public DistanceCalculator(Phylogeny t,
                  java.util.Vector<PhylogenyNode> ext_nodes)

Constructor. Sets the rooted Phylogeny t and the external Nodes ext_nodes for which the mean distance to their lowest common ancestor and its variance and standard deviation are calculated. (Last modified: 12/01/00)

Parameters:

t - the rooted Phylogeny containing Nodes in Vector ext_nodes

ext_nodes - a Vector of Nodes of t, the mean distance to their lowest common ancestor and its variance and standard deviation are calculated

Method Detail

getDistanceToLCA

public double getDistanceToLCA(java.lang.String seq_name)

Calculates the distance of the PhylogenyNode with seq name seq_name to the LCA of ext_nodes, which has been set either with constructor DistanceCalculator(Phylogeny,Vector) or method setTreeAndExtNodes(Phylogeny,Vector). Throws an exception if no PhylogenyNode with seq name_seq name is found or if seq_name is not unique. (Last modified: 12/03/00)

Parameters:

seq_name - the seq name for the PhylogenyNode for which the distance to the LCA is to be calculated

Returns:

distance of PhylogenyNode with seq name seq_name to the LCA of Nodes in ext_nodes

See Also:

DistanceCalculator(Phylogeny,Vector), setTreeAndExtNodes(Phylogeny,Vector), setTreeAndExtNodes(Phylogeny,ArrayList)

getDistanceToNode

public double getDistanceToNode(PhylogenyNode outer,
                       PhylogenyNode inner)

Calculates the distance of PhylogenyNode outer to PhylogenyNode inner. PhylogenyNode inner must be closer to the root than PhylogenyNode outer and on the same "path". (Last modified: 12/01/00)

Parameters:

outer - a PhylogenyNode

inner - a PhylogenyNode closer to the root than outer

Returns:

distance of PhylogenyNode outer to PhylogenyNode inner

getDistanceToNode

public double getDistanceToNode(java.lang.String seq_name,
                       PhylogenyNode inner)

Calculates the distance of the PhylogenyNode with seq name seq_name to PhylogenyNode inner. PhylogenyNode inner must be closer to the root than the PhylogenyNode with seq name seq_name and on the same "path". Throws an exception if no PhylogenyNode with seq name_seq name is found or if seq_name is not unique. (Last modified: 12/01/00)

Parameters:

seq_name - the seq name of a PhylogenyNode further from the root than PhylogenyNode inner

inner - a PhylogenyNode

Returns:

distance of PhylogenyNode with seq name seq_nam to PhylogenyNode inner

getDistanceToRoot

public double getDistanceToRoot(PhylogenyNode n)

Calculates the distance of PhylogenyNode n to the root of Phylogeny t which has been set either with a constructor, setTree(Phylogeny), or setTreeAndExtNodes(Phylogeny,Vector). (Last modified: 12/01/00)

Parameters:

n - the PhylogenyNode for which the distance to the root is to be calculated

Returns:

distance of PhylogenyNode n to the root

See Also:

DistanceCalculator(Phylogeny), DistanceCalculator(Phylogeny,Vector), setTree(Phylogeny), setTreeAndExtNodes(Phylogeny,Vector)

getDistanceToRoot

public double getDistanceToRoot(java.lang.String seq_name)

Calculates the distance of the PhylogenyNode with seq name seq_name to the root of Phylogeny t, which has been set either with a constructor, setTree(Phylogeny), or setTreeAndExtNodes(Phylogeny,Vector). Throws an exception if no PhylogenyNode with seq name_seq name is found or if seq_name is not unique. (Last modified: 12/01/00)

Parameters:

seq_name - the seq name for the PhylogenyNode for which the distance to the root is to be calculated

Returns:

distance of PhylogenyNode with seq name seq_name to the root

See Also:

DistanceCalculator(Phylogeny), DistanceCalculator(Phylogeny,Vector), setTree(Phylogeny), setTreeAndExtNodes(Phylogeny,Vector), setTreeAndExtNodes(Phylogeny,ArrayList)

getMean

public double getMean()

Returns the mean distance. If constructor DistanceCalculator(Phylogeny) or method setTree(Phylogeny) have been used, it is the mean of the distances from the root to all external Nodes. If constructor DistanceCalculator(Phylogeny,Vector) or method setTreeAndExtNodes(Phylogeny,Vector) have been used, it is the mean of the distances from the external nodes ext_nodes to their lowest common ancestor. (Last modified: 11/30/00)

Returns:

mean distance

See Also:

DistanceCalculator(Phylogeny), DistanceCalculator(Phylogeny,Vector), setTree(Phylogeny), setTreeAndExtNodes(Phylogeny,Vector), setTreeAndExtNodes(Phylogeny,ArrayList)

getN

public int getN()

Returns the sum of all Nodes used to calculate the mean. (Last modified: 12/01/00)

Returns:

n

getStandardDeviation

public double getStandardDeviation()

Returns the standard deviation. If constructor DistanceCalculator(Phylogeny) or method setTree(Phylogeny) have been used, it is the standard deviation of the distances from the root to all external Nodes. If constructor DistanceCalculator(Phylogeny,Vector) or method setTreeAndExtNodes(Phylogeny,Vector) have been used, it is the standard deviation of the distances from the external nodes ext_nodes to their lowest common ancestor. (Last modified: 11/30/00)

Returns:

standard deviation

See Also:

DistanceCalculator(Phylogeny), DistanceCalculator(Phylogeny,Vector), setTree(Phylogeny), setTreeAndExtNodes(Phylogeny,Vector), setTreeAndExtNodes(Phylogeny,ArrayList)

getVariance

public double getVariance()

Returns the variance. ( 1/(N - 1) * Sum((x-mean)^2) ) If constructor DistanceCalculator(Phylogeny) or method setTree(Phylogeny) have been used, it is the variance of the distances from the root to all external Nodes. If constructor DistanceCalculator(Phylogeny,Vector) or method setTreeAndExtNodes(Phylogeny,Vector) have been used, it is the variance of the distances from the external nodes ext_nodes to their lowest common ancestor. (Last modified: 11/30/00)

Returns:

variance

See Also:

DistanceCalculator(Phylogeny), DistanceCalculator(Phylogeny,Vector), setTree(Phylogeny), setTreeAndExtNodes(Phylogeny,Vector), setTreeAndExtNodes(Phylogeny,ArrayList)

setTree

public void setTree(Phylogeny t)

Sets the rooted Phylogeny t for which the mean distance to the root and its variance and standard deviation are calculated. (Last modified: 12/01/00)

Parameters:

t - the rooted Phylogeny for which the mean distance to the root and its variance and standard deviation are calculated

setTreeAndExtNodes

public void setTreeAndExtNodes(Phylogeny t,
                      java.util.ArrayList<PhylogenyNode> ext_nodes)

Sets the rooted Phylogeny t and the external Nodes ext_nodes for which the mean distance to their lowest common ancestor and its variance and standard deviation are calculated. (Last modified: 12/03/00)

Parameters:

t - the rooted Phylogeny containing Nodes in Vector ext_nodes

ext_nodes - a ArrayList of Nodes of t, the mean distance to their lowest common ancestor and its variance and standard deviation are calculated

setTreeAndExtNodes

public void setTreeAndExtNodes(Phylogeny t,
                      java.util.Vector<PhylogenyNode> ext_nodes)

Sets the rooted Phylogeny t and the external Nodes ext_nodes for which the mean distance to their lowest common ancestor and its variance and standard deviation are calculated. (Last modified: 12/03/00)

Parameters:

t - the rooted Phylogeny containing Nodes in Vector ext_nodes

ext_nodes - a Vector of Nodes of t, the mean distance to their lowest common ancestor and its variance and standard deviation are calculated

main

public static void main(java.lang.String[] args)