modele
Class AlgorithmsCT01

java.lang.Object
  modele.Algorithms
      modele.AlgorithmsCT01

Deprecated. see also Algorithms

public class AlgorithmsCT01
extends Algorithms

This class to put procedures of compatibilityTreament made by Stefen Engelen and to test it. The procedures in french are the adaptation of (Stefan Engelen)'s implementation to the new model. The numbered and "origin" implementations are tests...

Since:

Stefan Engelen (2006), (Conversion to new model) Gabriel Chandesris (2008), July 2008

Author:

Gabriel Chandesris (2008)

See Also:

Algorithms.compatibilityTreatment(PalindromeListe), AlgorithmsCT02, AlgorithmsCT03

Field Summary

Fields inherited from class modele.Algorithms

Ms

Constructor Summary

AlgorithmsCT01(Sequence cible, SequenceListe alignement)
Deprecated. Do not instanciate this class.

Method Summary

static PalindromeListeListe	compatibilityTreamentCT01(PalindromeListe L) Deprecated. Polymorphism of procedure.
static PalindromeListeListe	compatibilityTreatment01(PalindromeListe L) Deprecated. Other is used (changesDCFold to P-DCFold)
static PalindromeListeListe	compatibilityTreatment02(PalindromeListe L) Deprecated. results of tests are not very good...
static PalindromeListeListe	compatibilityTreatment03(PalindromeListe L) Deprecated. ...
static PalindromeListeListe	compatibilityTreatment04(PalindromeListe L) Deprecated. July 2008
static PalindromeListeListe	compatibilityTreatment05(PalindromeListe Lbis) Deprecated.
static void	compatibilityTreatmentOrigin(PalindromeListe L, int posi, int posj, PalindromeListeListe E) Deprecated. July 2008
static void	incompatibilitePlusieursChoix(PalindromeListeListe listeTabPal, int posTab, int i, int j, double incertitude, boolean plusieursResultats, int nbPredictionMax) Deprecated. When more than one choice of palindromes are present.
static PalindromeListe	incompatibiliteUnChoix(PalindromeListe tabPalCibleTrier, int i, int j) Deprecated. When one choice is present for prediction.
static PalindromeListeListe	traitementIncompatibilite(PalindromeListe tabPalCible, boolean plusieursResultats, double incertitude, int nbPrediction, int nbPredictionMax) Deprecated. CompatibilityTreament...

Methods inherited from class modele.Algorithms

algoSSCA, checkConservation, checkConservationOldVersion, commonPrediction, compatibilityTreatment, defaultPredictionOfStructure, getAlignement, getCible, getDecalage, getDelcrit, getIdecrit, getIteration, getLongBoucleMin, getLongPalindMin, getMaxHomology, getMinHomology, getNbErreursMax, getNbMaxSequences, getNbMinSequences, getNoeudCourant, getResolution, iterationLessLess, iterationPlusPlus, launchExecution, newSequenceDeduction, searchAllStructuralPalindromes, searchAnchorPoints, searchAnchorPoints, searchAnchorPoints, searchStructuralPalindrome, setDecalage, setDelcrit, setIdecrit, SetIterationZero, setLongBoucleMin, setLongPalindMin, setMaxHomology, setMinHomology, setNbErreursMax, setNbMaxSequences, setNbMinSequences, setResolution, variableZonesTreatment

Methods inherited from class java.lang.Object

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

Constructor Detail

AlgorithmsCT01

public AlgorithmsCT01(Sequence cible,
                      SequenceListe alignement)

Deprecated. Do not instanciate this class.

Default Constructor.

Parameters:

cible - (Sequence)

alignement - (SequenceListe)

Method Detail

compatibilityTreamentCT01

public static PalindromeListeListe compatibilityTreamentCT01(PalindromeListe L)

Deprecated.

Polymorphism of procedure.

Parameters:

L - (PalindromeListe)

Returns:

PalindromeListeListe

traitementIncompatibilite

public static PalindromeListeListe traitementIncompatibilite(PalindromeListe tabPalCible,
                                                             boolean plusieursResultats,
                                                             double incertitude,
                                                             int nbPrediction,
                                                             int nbPredictionMax)

Deprecated.

CompatibilityTreament...

Parameters:

tabPalCible - (PalindromeListeListe)

plusieursResultats - (boolean)

incertitude - (double) resolution

nbPrediction - (int)

nbPredictionMax - (int) Algorithms.MS

Returns:

PalindromeListeListe

Since:

Stefan Engelen (2006), (Conversion to new model) Gabriel Chandesris (2008)

incompatibilitePlusieursChoix

public static void incompatibilitePlusieursChoix(PalindromeListeListe listeTabPal,
                                                 int posTab,
                                                 int i,
                                                 int j,
                                                 double incertitude,
                                                 boolean plusieursResultats,
                                                 int nbPredictionMax)

Deprecated.

When more than one choice of palindromes are present.
iteratif / recursif

Parameters:

listeTabPal - (PalindromeListeListe)

posTab - (int) ?? Position in list

i - (int) Current position in list

j - (int) Current analytic position in list

incertitude - (double) ?? unprecision / resolution

plusieursResultats - (boolean) Much results or not unused here ?

nbPredictionMax - (int) maximal number of strucutral prediction

Since:

Stefan Engelen (2006), (Conversion to new model) Gabriel Chandesris (2008) TODO SERVLET lire commentaires internes

incompatibiliteUnChoix

public static PalindromeListe incompatibiliteUnChoix(PalindromeListe tabPalCibleTrier,
                                                     int i,
                                                     int j)

Deprecated.

When one choice is present for prediction.

Parameters:

tabPalCibleTrier - (PalindromeListe)

i - (int) Current position in list

j - (int) Current analytic position in list

Returns:

PalindromeListe

Since:

Stefan Engelen (2006), (Conversion to new model) Gabriel Chandesris (2008) TODO SERVLET lire commentaires internes

compatibilityTreatment01

public static PalindromeListeListe compatibilityTreatment01(PalindromeListe L)

Deprecated. Other is used (changesDCFold to P-DCFold)

Procedure made from algorithm described in thesis of Stefan Engelen (2006).
see thesis page 94 figure 4.27

compatibilityTreatment02

public static PalindromeListeListe compatibilityTreatment02(PalindromeListe L)

Deprecated. results of tests are not very good...

Procedure re-made after reading implementation of Stefan Engelen (2006).

Parameters:

L - PalindromeListe

Returns:

PalindromeListeListe

compatibilityTreatment03

public static PalindromeListeListe compatibilityTreatment03(PalindromeListe L)

Deprecated. ...

Back to original idea ?

Parameters:

L - PalindromeListe

Returns:

PalindromeListeListe

compatibilityTreatment04

public static PalindromeListeListe compatibilityTreatment04(PalindromeListe L)

Deprecated. July 2008

Simpliest case we can do (without iteration).

Parameters:

L - PalindromeListe

Returns:

PalindromeListeListe

compatibilityTreatmentOrigin

public static void compatibilityTreatmentOrigin(PalindromeListe L,
                                                int posi,
                                                int posj,
                                                PalindromeListeListe E)

Deprecated. July 2008

This procedure to treat compatibility of found palindromes on each recursivity step, see searchStructuralPalindrome for launch.
Originally defined with more arguments (i-position, j-position and group of palindrome lists... but use with only a list of palindromes... It is originally returning a table of PalindromeListe !
Limit iteration of Algorithms put here (avoding some "java heap space" problems with high random sequences) !
Defined for DCFold but not for P-DCFold in thesis...
Algorithme Traitement_Compatibilite
Should be considered as a Private method. (except for tests).
see thesis page 94 figure 4.27

Parameters:

L - PalindromeListe

posi - (int) initially to 1

posj - (int) initially to 0

E - (PalindromeListeListe) (results) is modified !!

See Also:

Algorithms.searchStructuralPalindrome(modele.NoeudArbreExec, modele.Sequence, int, modele.SequenceListe, int, int), Algorithms.iteration, Algorithms.Ms

compatibilityTreatment05

public static PalindromeListeListe compatibilityTreatment05(PalindromeListe Lbis)

Deprecated.