core
Class Identifier

java.lang.Object
  core.Identifier

Direct Known Subclasses:

Bayes, Tree

public abstract class Identifier
extends java.lang.Object

Abstract class Identifier contains common methods for concrete implementations of identifications cores, like Tree or Bayes.

Version:

1.0

Author:

Oscar Flores

Field Summary

Configuration	cnf Configuration settings
Context	con Current context of execution
Matrix	mat Reference matrix
float	sum Mantains the sum of all probabilities

Constructor Summary

Identifier(Context con, Matrix mat, Configuration cnf)
Creates a new Identifier with no done tests

Method Summary

int	getBestTaxaIndex() Returns the index of the taxon with the higher relative probability
int	getBestTestIndex() Returns the key of the test with best value (all taxa vs. all others).
int	getBestTestIndex(Context con) Returns the key of the test with best value (all taxa vs. all others).
int	getBestTestIndex(int idTaxa) Returns the key of the test with best value (one taxon vs. all others).
int	getBestTestIndex(int idTaxa, Context con) Returns the key of the test with best value (one taxon vs. all others).
int[]	getTaxaIndex() Returns an ordered array (sorted from best to worse) with the index of all alive taxa (the ones which till this moment haven't been discarded)
int[]	getTestIndex() Returns an ordered array (sorted from best to worse) with the index of each missed test in order to choose the best one.
int[]	getTestIndex(Context con) Returns an ordered array (sorted from best to worse) with the index of each missed test in order to choose the best one.
int[]	getTestIndex(int idTaxa) Returns an ordered array (sorted from best to worse) with the index of each missed test in order to choose the best one.
int[]	getTestIndex(int idTaxa, Context con) Returns an ordered array (sorted from best to worse) with the index of each missed test in order to choose the best one.
protected boolean	isSeparator(int idTaxa1, int idTaxa2, int idTest) Returns true if a given pair of taxa are separated one from the other by the specified test
float	normTaxaProb(int idTaxa) Returns the relative probability beetween 0 to 1 of that given taxon is the unknown (wich probability has this taxon to be the unknown and not the other taxa)

Methods inherited from class java.lang.Object

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

Field Detail

cnf

public Configuration cnf

Configuration settings

con

public Context con

Current context of execution

mat

public final Matrix mat

Reference matrix

sum

public float sum

Mantains the sum of all probabilities

Constructor Detail

Identifier

public Identifier(Context con,
                  Matrix mat,
                  Configuration cnf)

Creates a new Identifier with no done tests

Parameters:

con - Context of the execution

mat - Reference matrix

Method Detail

getTaxaIndex

public int[] getTaxaIndex()

Returns an ordered array (sorted from best to worse) with the index of all alive taxa (the ones which till this moment haven't been discarded)

Returns:

Sorted array with alive taxon keys, or null if none

getBestTaxaIndex

public int getBestTaxaIndex()

Returns the index of the taxon with the higher relative probability

Returns:

Index of the best taxon

getTestIndex

public int[] getTestIndex()

Returns an ordered array (sorted from best to worse) with the index of each missed test in order to choose the best one. It uses "all taxa versus all other" comparison and only alive taxa are looked for

Returns:

Sorted array with remaining tests keys, or null if none

getTestIndex

public int[] getTestIndex(Context con)

Returns an ordered array (sorted from best to worse) with the index of each missed test in order to choose the best one. It uses "all taxa versus all other" comparison and only alive taxa are looked for This method use the given Context instead of the one from the Identifier. That could be usefull if we want to get the test for derivate Contexts

Parameters:

con - Reference Context

Returns:

Sorted array with remaining tests keys, or null if none

getTestIndex

public int[] getTestIndex(int idTaxa)

Returns an ordered array (sorted from best to worse) with the index of each missed test in order to choose the best one. It uses "one taxon versus all other" comparison and only alive taxa are looked for

Parameters:

idTaxa - Reference taxon key

Returns:

Sorted array with remaining tests keys, or null if none

getTestIndex

public int[] getTestIndex(int idTaxa,
                          Context con)

Returns an ordered array (sorted from best to worse) with the index of each missed test in order to choose the best one. It uses "one taxon versus all other" comparison and only alive taxa are looked for This method uses the given Context instead of the one from the Identifier. That could be usefull if we want to get the test for derivate Contexts

Parameters:

idTaxa - Reference taxon key

con - Reference Context

Returns:

Sorted array with remaining tests keys, or null if none

getBestTestIndex

public int getBestTestIndex()

Returns the key of the test with best value (all taxa vs. all others). This value is a function of the number of taxa that is separed and the sum of his probabilities.

Returns:

Key of the best test

getBestTestIndex

public int getBestTestIndex(Context con)

Returns the key of the test with best value (all taxa vs. all others). This value is a function of the number of taxa that is separed and the sum of his probabilities. This method uses the given Context instead of the one from the Identifier. That could be usefull if we want to get the test for derivate Contexts

Parameters:

con - Reference Context

Returns:

Key of the best test

getBestTestIndex

public int getBestTestIndex(int idTaxa)

Returns the key of the test with best value (one taxon vs. all others). This value is a function of the number of taxa that is separed and the sum of his probabilities.

Parameters:

idTaxa - Key of the reference taxons

Returns:

Key of the best test

getBestTestIndex

public int getBestTestIndex(int idTaxa,
                            Context con)

Returns the key of the test with best value (one taxon vs. all others). This value is a function of the number of taxa that is separed and the sum of his probabilities. This method uses the given Context instead of the one from the Identifier. That could be usefull if we want to get the test for derivate Contexts

Parameters:

idTaxa - Key of the reference taxons

con - Reference context

Returns:

Key of the best test

normTaxaProb

public float normTaxaProb(int idTaxa)

Returns the relative probability beetween 0 to 1 of that given taxon is the unknown (wich probability has this taxon to be the unknown and not the other taxa)

Parameters:

idTaxa - Key of reference taxon

Returns:

Normalized probability

isSeparator

protected boolean isSeparator(int idTaxa1,
                              int idTaxa2,
                              int idTest)

Returns true if a given pair of taxa are separated one from the other by the specified test

Parameters:

idTaxa1 - Identification of the first taxa

idTaxa2 - Identification of the second taxa

idTest - Identification of the test

Returns:

idTaxa1 is separated from idTaxa2 by the idTest on matrix mat?