rapgreen

Class TreeScoring

java.lang.Object

rapgreen.TreeScoring

public class TreeScoring
extends java.lang.Object

Tree scoring class.

This class contains several tools to compute gene to gene scores in an annotated phylogenetic tree.

Field Summary

Fields

Modifier and Type	Field and Description
double[][]	distance Distance between two genes
boolean[][]	fitchOrthology Strict orthology relationship
static double	iDupWeight
static double	lengthThreshold
static double	lengthWeight
int[][]	nbIntersectionDuplications Number of taxonomic intersection duplications between two genes
int[][]	nbSpeciations Number of spectiations between two genes
int[][]	nbTopologicalDuplications Number of topological incongruence duplications between two genes
int[][]	nbUltraParalogy Number of ultraparalogy relationship under this node
java.lang.StringBuffer	phyloXMLBuffer PhyloXML relationship buffer
static double	specWeight
static double	tDupWeight Global scoring attributs
Tree	tree The reference tree
boolean[][]	ultraParalogy Ultraparalogy relationship
static double	uParaWeight

Constructor Summary

Constructors

Constructor and Description
TreeScoring(Tree tree) Generic constructor

Method Summary

Methods

Modifier and Type	Method and Description
void	computeScores() Compute scores for every pair of genes, and stock it
void	writeScores(java.io.File file) Write in a CSV file every scores

Methods inherited from class java.lang.Object

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

Field Detail

tree

public Tree tree

The reference tree

distance

public double[][] distance

Distance between two genes

nbTopologicalDuplications

public int[][] nbTopologicalDuplications

Number of topological incongruence duplications between two genes

nbIntersectionDuplications

public int[][] nbIntersectionDuplications

Number of taxonomic intersection duplications between two genes

nbSpeciations

public int[][] nbSpeciations

Number of spectiations between two genes

fitchOrthology

public boolean[][] fitchOrthology

Strict orthology relationship

ultraParalogy

public boolean[][] ultraParalogy

Ultraparalogy relationship

nbUltraParalogy

public int[][] nbUltraParalogy

Number of ultraparalogy relationship under this node

phyloXMLBuffer

public java.lang.StringBuffer phyloXMLBuffer

PhyloXML relationship buffer

tDupWeight

public static double tDupWeight

Global scoring attributs

iDupWeight

public static double iDupWeight

specWeight

public static double specWeight

uParaWeight

public static double uParaWeight

lengthWeight

public static double lengthWeight

lengthThreshold

public static double lengthThreshold

Constructor Detail

TreeScoring

public TreeScoring(Tree tree)

Generic constructor

Parameters:

tree - The tree to score

Method Detail

computeScores

public void computeScores()

Compute scores for every pair of genes, and stock it

writeScores

public void writeScores(java.io.File file)

Write in a CSV file every scores

Parameters:

file - Destination file