SIGRS
Class KDTreeStructure

java.lang.Object
  SIGRS.KDTreeStructure

public class KDTreeStructure
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

KDTreeStructure()

Method Summary

void	buildTree(int[] steps, int maxValue, KDTreeStructure other)
Jama.Matrix	getPath(int destination, int target, int maxValue)
KDTreeNode	getRoot()
void	reset(java.util.Vector visited)
void	setRoot(KDTreeNode rootNode)
void	updateTree(int[] labels, Jama.Matrix[] q)

Methods inherited from class java.lang.Object

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

Constructor Detail

KDTreeStructure

public KDTreeStructure()

Method Detail

buildTree

public void buildTree(int[] steps,
                      int maxValue,
                      KDTreeStructure other)

getPath

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

getRoot

public KDTreeNode getRoot()

reset

public void reset(java.util.Vector visited)

setRoot

public void setRoot(KDTreeNode rootNode)

updateTree

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