SIGRS
Class KDTreeNode

java.lang.Object
  SIGRS.KDTreeNode

public class KDTreeNode
extends java.lang.Object

SIGRS is a collection of routines used in searching for regions of contrasting composition (CCRs) in sequence files using a partial sum process. Significance of segments is evaluated using Karlin-Altschul statistics and specifically an extension by Karlin-Dembo allowing for nucleotides to have a Markov-dependence (see e.g. Karlin & Altschul (1993) and Karlin & Dembo (1992)

The routines are provided as is and no guarantee regarding stability etc. is given so use at your own risk!

See publication Larsson, P., Hinas, A., Ardell, D.H., Kirsebom, L.A., Virtanen, A. and Söderbom, F. De novo search for non-coding RNA genes in the AT-rich genome of Dictyostelium discoideum: performance of Markov-dependent genome feature scoring

Questions and comments can be directed to Pontus.Larsson@icm.uu.se

Constructor Summary

KDTreeNode(int label, Jama.Matrix value)

Method Summary

void	addChild(KDTreeNode child)
void	buildTree(int[] steps, int maxValue, KDTreeNode parent)
KDTreeNode	findNode(int lbl, java.util.Vector visited)
java.lang.Object[]	getChildren()
int	getLabel()
Jama.Matrix	getPath(int destination, int maxValue)
void	reset(java.util.Vector visited)
void	setChildren(java.lang.Object[] children)
void	setValue(Jama.Matrix value)
void	updateTree(int[] steps, Jama.Matrix[] q, int parent)

Methods inherited from class java.lang.Object

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

Constructor Detail

KDTreeNode

public KDTreeNode(int label,
                  Jama.Matrix value)

Method Detail

addChild

public void addChild(KDTreeNode child)

buildTree

public void buildTree(int[] steps,
                      int maxValue,
                      KDTreeNode parent)

findNode

public KDTreeNode findNode(int lbl,
                           java.util.Vector visited)

getLabel

public int getLabel()

getChildren

public java.lang.Object[] getChildren()

getPath

public Jama.Matrix getPath(int destination,
                           int maxValue)

reset

public void reset(java.util.Vector visited)

setChildren

public void setChildren(java.lang.Object[] children)

setValue

public void setValue(Jama.Matrix value)

updateTree

public void updateTree(int[] steps,
                       Jama.Matrix[] q,
                       int parent)