modele
Class Algorithms

java.lang.Object
  modele.Algorithms

Direct Known Subclasses:

AlgorithmsCT01, AlgorithmsCT02, AlgorithmsCT03

Deprecated. Implementation of STefan Engleen very specific with some tricks make results differents...

public class Algorithms
extends java.lang.Object

This class to get the different steps of P-DCFold algorithms.
INTERNAL NON JAVADOC COMMENTS MUST BE KEPT ! (for history and comprehension work on implementation) !! Especially deprecated and "Old" method of DCFold...

Since:

April 2008

Author:

Gabriel Chandesris (2008)

See Also:

OriginAlgorithmsStefan, OtherAlgorithmsStefan, AlgorithmsStefan

Field Summary

private SequenceListe	alignement Deprecated. The alignment submitted with all sequences.
private Sequence	cible Deprecated. Current selected sequence where to find Palindrome's, helix...
private static int	decalage Deprecated. Maximum gap's [FR : décalage], when checking conservation of Palindrome's.
private static double	delcrit Deprecated. Deletion criteria, originally D = 0.01 (percentage).
private static double	idecrit Deprecated. Identity percentage, originally I = 75.0 (percentage).
private static int	iteration Deprecated. Count number of iterations in compatibilityTreatment.
private static int	longBoucleMin Deprecated. Minimal length of loop.
private static int	longPalindMin Deprecated. Minimal length of palindrome / helix.
private static double	maxHomology Deprecated. Maximum homology rate for selection in SSCA.
private static double	minHomology Deprecated. Minimum homology rate for selection in SSCA.
static int	Ms Deprecated. Maximal number of alternate structure in Palindrome Search.
private static int	nbErreursMax Deprecated. Maximum possible errors in searching palindromes.
private static int	nbMaxSequences Deprecated. Maximum number of sequences for selection in SSCA.
private static int	nbMinSequences Deprecated. Minimum number of sequences for selection in SSCA.
private NoeudArbreExec	noeudCourant Deprecated. Current node of execution tree.
private static double	resolution Deprecated. Resolution for search of Palindrome in Sequence.

Constructor Summary

Algorithms(Sequence cible, SequenceListe alignement)
Deprecated. A constructor to launch searchAllStructuralPalindromes on elements.

Method Summary

static SequenceListe	algoSSCA(Sequence cible, SequenceListe homologues) Deprecated. SSCA algorithm.
static boolean	checkConservation(Palindrome current, SequenceListe alignement, int nbErreursMax) Deprecated. To check a Palindrome is present in a group of Sequence's.
static boolean	checkConservationOldVersion(Palindrome current, SequenceListe alignement, int nbErreursMax) Deprecated. Old and inacurate method
static PalindromeListe	commonPrediction(Sequence cible, SequenceListe[] listes) Deprecated. To search common structure prediction using P-DCFold with a cible Sequence and several list of homologuous Sequence's.
static PalindromeListeListe	compatibilityTreatment(PalindromeListe L) Deprecated. Here is a procedure Launcher This procedure to treat compatibility of found palindromes on each recursivity step, see searchStructuralPalindrome for launch.
static PalindromeListe	defaultPredictionOfStructure(Sequence cible, SequenceListe alignement, int numSelect) Deprecated. The default prediction of P-DCFold Software (Optimal Prediction).
SequenceListe	getAlignement() Deprecated. To get the group of aligned Sequence's.
Sequence	getCible() Deprecated. To get the cible Sequence.
static int	getDecalage() Deprecated.
static double	getDelcrit() Deprecated.
static double	getIdecrit() Deprecated.
protected static int	getIteration() Deprecated.
static int	getLongBoucleMin() Deprecated.
static int	getLongPalindMin() Deprecated.
static double	getMaxHomology() Deprecated.
static double	getMinHomology() Deprecated.
static int	getNbErreursMax() Deprecated.
static int	getNbMaxSequences() Deprecated.
static int	getNbMinSequences() Deprecated.
NoeudArbreExec	getNoeudCourant() Deprecated. Default node : result node (contain list of Palindrome's after exxecution).
static double	getResolution() Deprecated.
protected static void	iterationLessLess() Deprecated.
protected static void	iterationPlusPlus() Deprecated.
void	launchExecution() Deprecated. To launch searchAllStructuralPalindromes after constructor.
static Sequence	newSequenceDeduction(Sequence cible, PalindromeListe Lg) Deprecated. To get a new sequence without found palindromes in sequence.
static void	searchAllStructuralPalindromes(NoeudArbreExec Nd, Sequence cible, SequenceListe alignement, int decalage, int nbErreursMax) Deprecated. To search structural palindromes (helix) including pseudoknots.
static PalindromeListe	searchAnchorPoints(Alignement calcul, double Smin, SequenceListe alignement, int nbErreursMax, int longPalindMin, int longBoucleMin) Deprecated. Search procedure of structural palindromes with pairing matrix and new selection criteria.
static PalindromeListe	searchAnchorPoints(int debut, int fin, Alignement calcul, double Smin, SequenceListe alignement, int nbErreursMax, int longPalindMin, int longBoucleMin) Deprecated. M[i,j] too long...
static PalindromeListe	searchAnchorPoints(Sequence cible, Alignement calcul, double Lmin, SequenceListe alignement, int decalage, int nbErreursMax) Deprecated. Not the good prototype as algorithm is defined.
static void	searchStructuralPalindrome(NoeudArbreExec Nd, Sequence cible, int tailleCible, SequenceListe alignement, int decalage, int nbErreursMax) Deprecated. Searching structural palindromes in a selected sequence (cible), with comparison in a whole alignment of tests sequences.
static void	setDecalage(int decalage) Deprecated.
static void	setDelcrit(double delcrit) Deprecated. To set deletion criteria in SSCA to compute effects, if set under 0.000 : set to 0.00 ; if more than 100.0 : set to 1.00 (default value).
static void	setIdecrit(double idecrit) Deprecated. To set identity criteria in SSCA to compute effects, if set under 00.000 : set to 0.00 ; if more than 100.00 : set to 75.0 (default value).
protected static void	SetIterationZero() Deprecated.
static void	setLongBoucleMin(int longBoucleMin) Deprecated.
static void	setLongPalindMin(int longPalindMin) Deprecated.
static void	setMaxHomology(double maxHomology) Deprecated. To set the T=threshold of selection of strict maximal homology in SSCA, if set under 0.0 or minHomology : no changes ; if more than 100.0 : 100.0.
static void	setMinHomology(double minHomology) Deprecated. To set the threshold of selection of strict minimal homology in SSCA, if set under 0.0 : set to 0.0 ; if more than 100.0 or maxHomology : no changes.
static void	setNbErreursMax(int nbErreurMax) Deprecated.
static void	setNbMaxSequences(int nbMaxSequences) Deprecated. To set the maximal number of selection of sequences in SSCA.
static void	setNbMinSequences(int nbMinSequences) Deprecated. To set the minimal number of selection of sequences in SSCA.
static void	setResolution(double resolution) Deprecated.
static PalindromeListe	variableZonesTreatment(Sequence cible, int tailleCible, SequenceListe alignement, int decalage, int nbErreursMax) Deprecated. When no palindrome is found with searchAnchorPoints...

Methods inherited from class java.lang.Object

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

Field Detail

resolution

private static double resolution

Deprecated.

Resolution for search of Palindrome in Sequence.
Global Parameter of Algorithm (default = 0.05).

See Also:

compatibilityTreatment(PalindromeListe), variableZonesTreatment(modele.Sequence, int, modele.SequenceListe, int, int)

longPalindMin

private static int longPalindMin

Deprecated.

Minimal length of palindrome / helix.
Global Parameter of Algorithm (default = 3).

longBoucleMin

private static int longBoucleMin

Deprecated.

Minimal length of loop.
Global Parameter of Algorithm (default = 4).

nbErreursMax

private static int nbErreursMax

Deprecated.

Maximum possible errors in searching palindromes.
Global Parameter of Algorithm (default = 0).

decalage

private static int decalage

Deprecated.

Maximum gap's [FR : décalage], when checking conservation of Palindrome's.
Global Parameter of Algorithm (default = 0).

See Also:

checkConservation(Palindrome, SequenceListe, int)

minHomology

private static double minHomology

Deprecated.

Minimum homology rate for selection in SSCA.

See Also:

algoSSCA(Sequence, SequenceListe)

maxHomology

private static double maxHomology

Deprecated.

Maximum homology rate for selection in SSCA.

See Also:

algoSSCA(Sequence, SequenceListe)

nbMaxSequences

private static int nbMaxSequences

Deprecated.

Maximum number of sequences for selection in SSCA.

See Also:

algoSSCA(Sequence, SequenceListe)

nbMinSequences

private static int nbMinSequences

Deprecated.

Minimum number of sequences for selection in SSCA.

See Also:

algoSSCA(Sequence, SequenceListe)

Ms

public static final int Ms

Deprecated.

Maximal number of alternate structure in Palindrome Search. This to avoid an illimited search and crash the machine. (Can be change only in source code).

See Also:

searchStructuralPalindrome(NoeudArbreExec, Sequence, int, SequenceListe, int, int), compatibilityTreatment(PalindromeListe), Constant Field Values

iteration

private static int iteration

Deprecated.

Count number of iterations in compatibilityTreatment. In the way to avoid some "java heap space" problem on the java machine with very random sequences (seen on tests).

See Also:

compatibilityTreatment(PalindromeListe)

delcrit

private static double delcrit

Deprecated.

Deletion criteria, originally D = 0.01 (percentage).

See Also:

algoSSCA(Sequence, SequenceListe)

idecrit

private static double idecrit

Deprecated.

Identity percentage, originally I = 75.0 (percentage).

See Also:

algoSSCA(Sequence, SequenceListe)

cible

private Sequence cible

Deprecated.

Current selected sequence where to find Palindrome's, helix...

alignement

private SequenceListe alignement

Deprecated.

The alignment submitted with all sequences.

noeudCourant

private NoeudArbreExec noeudCourant

Deprecated.

Current node of execution tree.

Constructor Detail

Algorithms

public Algorithms(Sequence cible,
                  SequenceListe alignement)

Deprecated.

A constructor to launch searchAllStructuralPalindromes on elements.

Parameters:

cible - Sequence

alignement - Alignment group Sequence's.

See Also:

launchExecution()

Method Detail

getCible

public Sequence getCible()

Deprecated.

To get the cible Sequence.

Returns:

Sequence

See Also:

searchAllStructuralPalindromes(modele.NoeudArbreExec, modele.Sequence, modele.SequenceListe, int, int)

getAlignement

public SequenceListe getAlignement()

Deprecated.

To get the group of aligned Sequence's.

Returns:

SequenceListe

See Also:

searchAllStructuralPalindromes(modele.NoeudArbreExec, modele.Sequence, modele.SequenceListe, int, int)

getNoeudCourant

public NoeudArbreExec getNoeudCourant()

Deprecated.

Default node : result node (contain list of Palindrome's after exxecution).

Returns:

NoeudArbreExec

See Also:

searchAllStructuralPalindromes(modele.NoeudArbreExec, modele.Sequence, modele.SequenceListe, int, int), launchExecution()

launchExecution

public void launchExecution()

Deprecated.

To launch searchAllStructuralPalindromes after constructor.

See Also:

searchAllStructuralPalindromes(modele.NoeudArbreExec, modele.Sequence, modele.SequenceListe, int, int)

getResolution

public static double getResolution()

Deprecated.

getLongPalindMin

public static int getLongPalindMin()

Deprecated.

getLongBoucleMin

public static int getLongBoucleMin()

Deprecated.

getNbErreursMax

public static int getNbErreursMax()

Deprecated.

getDecalage

public static int getDecalage()

Deprecated.

setResolution

public static void setResolution(double resolution)

Deprecated.

setLongPalindMin

public static void setLongPalindMin(int longPalindMin)

Deprecated.

setLongBoucleMin

public static void setLongBoucleMin(int longBoucleMin)

Deprecated.

setNbErreursMax

public static void setNbErreursMax(int nbErreurMax)

Deprecated.

setDecalage

public static void setDecalage(int decalage)

Deprecated.

defaultPredictionOfStructure

public static PalindromeListe defaultPredictionOfStructure(Sequence cible,
                                                           SequenceListe alignement,
                                                           int numSelect)

Deprecated.

The default prediction of P-DCFold Software (Optimal Prediction). (figure 6.2 page 173 of thesis).
Should be main launch of P-DCFold.

Parameters:

cible - (S : sequence where making predictions of structure)

alignement - (A : group of whole tests alignment sequences)

numSelect - (number of sequences to select in A)

Returns:

PalindromeListe (Common Structure of helix).

See Also:

SequenceListe.combinationWithoutRepetition(int, int, SequenceListe)

commonPrediction

public static PalindromeListe commonPrediction(Sequence cible,
                                               SequenceListe[] listes)

Deprecated.

To search common structure prediction using P-DCFold with a cible Sequence and several list of homologuous Sequence's. (figure 6.1 in page 172 of thesis).
Algorithme Prediction_Commune
Should be considered as a Private method. (except for tests).

Parameters:

cible - Sequence (S : sequence where making predictions of structure)

listes - SequenceListe[] (J : table of SequenceListe).

Returns:

PalindromeListe (Common Structure of helix).

See Also:

Palindrome.equivalence(Palindrome, Palindrome), launchExecution(), searchAllStructuralPalindromes(modele.NoeudArbreExec, modele.Sequence, modele.SequenceListe, int, int)

searchAllStructuralPalindromes

public static void searchAllStructuralPalindromes(NoeudArbreExec Nd,
                                                  Sequence cible,
                                                  SequenceListe alignement,
                                                  int decalage,
                                                  int nbErreursMax)

Deprecated.

To search structural palindromes (helix) including pseudoknots. (figure 4.32 in page 101 of thesis).
Algorithme Recherche_Tous_Palindromes_Structurants
Should be considered as a Private method. (except for tests).

Parameters:

Nd - (Nd : Current node of execution tree, contain null on start)

cible - (S : sequence where making predictions of structure)

alignement - (A : group of whole tests alignment sequences)

decalage - (d : Maximum delay / gap in palindromes alignment)

nbErreursMax - (k : maximal number of errors)

See Also:

searchStructuralPalindrome(modele.NoeudArbreExec, modele.Sequence, int, modele.SequenceListe, int, int), newSequenceDeduction(Sequence, PalindromeListe), launchExecution()

newSequenceDeduction

public static Sequence newSequenceDeduction(Sequence cible,
                                            PalindromeListe Lg)

Deprecated.

To get a new sequence without found palindromes in sequence.
Algorithme Deduction_Nouvelle_Sequence
Should be considered as a Private method. (except for tests).

Parameters:

cible - (S : sequence where making predictions of structure)

Lg - (Lg : compatibles palindromes found)

Returns:

Sg : the new sequence deduced from S and removing palindromes.

See Also:

searchAllStructuralPalindromes(modele.NoeudArbreExec, modele.Sequence, modele.SequenceListe, int, int), Sequence.removeSubSequence(int, int)

searchStructuralPalindrome

public static void searchStructuralPalindrome(NoeudArbreExec Nd,
                                              Sequence cible,
                                              int tailleCible,
                                              SequenceListe alignement,
                                              int decalage,
                                              int nbErreursMax)

Deprecated.

Searching structural palindromes in a selected sequence (cible), with comparison in a whole alignment of tests sequences.
see thesis page 98 figure 4.30 Global Procedure
Algorithme Recherche_Palindrome_Structurant
Should be considered as a Private method. (except for tests).

Parameters:

Nd - (Nd : Current node of execution tree, contain null on start)

cible - (S : sequence where making predictions of structure)

tailleCible - (n : length of S)

alignement - (A : group of whole tests alignment sequences)

decalage - (d : Maximum delay / gap in palindromes alignment)

nbErreursMax - (k : maximal number of errors)

See Also:

searchAllStructuralPalindromes(modele.NoeudArbreExec, modele.Sequence, modele.SequenceListe, int, int), searchAnchorPoints(Alignement, double, SequenceListe, int, int, int), variableZonesTreatment(modele.Sequence, int, modele.SequenceListe, int, int), NoeudArbreExec.isTreeNotFull(int), Ms

searchAnchorPoints

public static PalindromeListe searchAnchorPoints(Sequence cible,
                                                 Alignement calcul,
                                                 double Lmin,
                                                 SequenceListe alignement,
                                                 int decalage,
                                                 int nbErreursMax)

Deprecated. Not the good prototype as algorithm is defined.

Search procedure of structural palindromes with pairing matrix and new selection criteria. . As prototype defined in figure 4.30 page 98 of thesis, but not as algorithm is defined (see the non deprecated method).

Parameters:

cible - Sequence.

calcul - (contain M : alignment score of the whole cible Sequence).

Lmin - (Smin : minimal score of palindrome).

alignement - (A : group of whole tests alignment sequences)

decalage - (d : Maximum delay / gap in palindromes alignment)

nbErreursMax - (k : maximal number of errors)

Returns:

Table of Palindrome's (PalindromeListe).

See Also:

DONE SERVLET remove this method ?? or keep it for "memory" ?? <= !!

searchAnchorPoints

public static PalindromeListe searchAnchorPoints(int debut,
                                                 int fin,
                                                 Alignement calcul,
                                                 double Smin,
                                                 SequenceListe alignement,
                                                 int nbErreursMax,
                                                 int longPalindMin,
                                                 int longBoucleMin)

Deprecated. M[i,j] too long...

Search procedure of structural palindromes with pairing matrix and new selection criteria.
see thesis page 90 figure 4.25
Algorithme Recherche_Point_Ancrage
Should be considered as a Private method. (except for tests).
searchANchorPoints and variableZoneTreament methods have been checked to take a little bit time (seen in tests) and are part of the limit of algorithms.

Parameters:

debut - d (beginning of sub-sequence)

fin - f (end of subsequence)

calcul - (contain M : alignment score of the whole cible Sequence)

Smin - (Smin : minimal score of palindrome)

alignement - (A : group of whole tests alignment sequences)

nbErreursMax - (k : maximal number of errors)

longPalindMin - (lpmin : minimal length of a palindrome)

longBoucleMin - (lbmin : minimal length of a loop)

Returns:

Table of Palindrome's (PalindromeListe).

See Also:

searchStructuralPalindrome(modele.NoeudArbreExec, modele.Sequence, int, modele.SequenceListe, int, int), checkConservation(modele.Palindrome, modele.SequenceListe, int), searchAnchorPoints(int, int, Alignement, double, SequenceListe, int, int, int)

searchAnchorPoints

public static PalindromeListe searchAnchorPoints(Alignement calcul,
                                                 double Smin,
                                                 SequenceListe alignement,
                                                 int nbErreursMax,
                                                 int longPalindMin,
                                                 int longBoucleMin)

Deprecated.

Search procedure of structural palindromes with pairing matrix and new selection criteria.
see thesis page 90 figure 4.25
Algorithme Recherche_Point_Ancrage
Should be considered as a Private method. (except for tests).
searchANchorPoints and variableZoneTreament methods have been checked to take a little bit time (seen in tests) and are part of the limit of algorithms.

Parameters:

calcul - (contain M : alignment score of the whole cible Sequence)

Smin - (Smin : minimal score of palindrome)

alignement - (A : group of whole tests alignment sequences)

nbErreursMax - (k : maximal number of errors)

longPalindMin - (lpmin : minimal length of a palindrome)

longBoucleMin - (lbmin : minimal length of a loop)

Returns:

Table of Palindrome's (PalindromeListe).

See Also:

searchStructuralPalindrome(modele.NoeudArbreExec, modele.Sequence, int, modele.SequenceListe, int, int), checkConservation(modele.Palindrome, modele.SequenceListe, int)

checkConservationOldVersion

public static boolean checkConservationOldVersion(Palindrome current,
                                                  SequenceListe alignement,
                                                  int nbErreursMax)

Deprecated. Old and inacurate method

To check a Palindrome is present in a group of Sequence's.
(Pages 83 and following of thesis).
Algorithme Verification_Conservation
Should be considered as a Private method. (except for tests).

1. First step in this method : selection of Palindrome's of same length : here are the cible Palindrome's
2. The second step of this procedure is made in SearchAnchorPoint procedure : thesis pages 85 to 90 and equations 4.7 to 4.12 : [selection and comparison (2 parts)]
   1. comparison part 1 : page 85 equations 4.7 and 4.8 : conservation
   2. comparison part 2 : page 86 equations 4.9 : relevance [pertinence]

Parameters:

current - (Pi : test Palindrome) palindrome to check

alignement - (A : group of whole tests alignment sequences)

nbErreursMax - (k : maximal number of errors)

Returns:

True if current present.

See Also:

searchAnchorPoints(modele.Sequence, modele.Alignement, double, modele.SequenceListe, int, int), Palindrome.computeNumbers(Palindrome)

checkConservation

public static boolean checkConservation(Palindrome current,
                                        SequenceListe alignement,
                                        int nbErreursMax)

Deprecated.

To check a Palindrome is present in a group of Sequence's.
(Pages 83 and following of thesis).
Algorithme Verification_Conservation
Should be considered as a Private method. (except for tests).

1. First step in this method : selection of Palindrome's of same length : here are the cible Palindrome's
2. The second step of this procedure is made in SearchAnchorPoint procedure : thesis pages 85 to 90 and equations 4.7 to 4.12 : [selection and comparison (2 parts)]
   1. comparison part 1 : page 85 equations 4.7 and 4.8 : conservation
   2. comparison part 2 : page 86 equations 4.9 : relevance [pertinence]

Parameters:

current - (Pi : test Palindrome)

alignement - (A : group of whole tests alignment sequences)

nbErreursMax - (k : maximal number of errors)

Returns:

True if current present.

See Also:

searchAnchorPoints(modele.Sequence, modele.Alignement, double, modele.SequenceListe, int, int), Palindrome.computeNumbers(Palindrome), decalage

variableZonesTreatment

public static PalindromeListe variableZonesTreatment(Sequence cible,
                                                     int tailleCible,
                                                     SequenceListe alignement,
                                                     int decalage,
                                                     int nbErreursMax)

Deprecated.

When no palindrome is found with searchAnchorPoints...
Searching sequences with lesser differences to compare with cible.
Not defined in thesis... see page 98 figure 4.30 line 9
This implementation is taken "as" the original implementation.
Algorithme Traitement_Zones_Variables
Should be considered as a Private method. (except for tests).
searchANchorPoints and variableZoneTreament methods have been checked to take a little bit time (seen in tests) and are part of the limit of algorithms.

Parameters:

cible - (S : sequence where making predictions of structure)

tailleCible - (n : length of the ALIGNMENT sequence)

alignement - (A : group of whole tests alignment sequences)

decalage - (d : Maximum delay / gap in palindromes alignment)

nbErreursMax - (k : maximal number of errors)

Returns:

(PalindromeListe) result

See Also:

searchStructuralPalindrome(modele.NoeudArbreExec, modele.Sequence, int, modele.SequenceListe, int, int), searchAnchorPoints(Alignement, double, SequenceListe, int, int, int), Alignement.Alignement(Sequence, Sequence, double, double)

compatibilityTreatment

public static PalindromeListeListe compatibilityTreatment(PalindromeListe L)

Deprecated.

Here is a procedure Launcher
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 (uised in 4.8 page 67 : DCFold)

Parameters:

L - PalindromeListe

Returns:

PalindromeListeListe

See Also:

searchStructuralPalindrome(modele.NoeudArbreExec, modele.Sequence, int, modele.SequenceListe, int, int), iteration, Ms, AlgorithmsCT01, AlgorithmsCT02

algoSSCA

public static SequenceListe algoSSCA(Sequence cible,
                                     SequenceListe homologues)

Deprecated.

SSCA algorithm.
see thesis pages 129 and following...

• Building model M with constraints.
• For each homologuous sequence of alignment :
  • Building substitution matrix between cible and current homologuous.
  • Scoring current homologuous with constraints of model and substitution matrix.
• Ranking of sequences with score.
• Selection of a number of sequences to predict cible structure.

Public method.

Parameters:

cible - Aim sequence (Sequence)

homologues - Alignment of homologuous sequences (SequenceListe)

Returns:

Selection of sequences to predict sequences (SequenceListe)

getMinHomology

public static double getMinHomology()

Deprecated.

getMaxHomology

public static double getMaxHomology()

Deprecated.

getNbMinSequences

public static int getNbMinSequences()

Deprecated.

getNbMaxSequences

public static int getNbMaxSequences()

Deprecated.

getDelcrit

public static double getDelcrit()

Deprecated.

getIdecrit

public static double getIdecrit()

Deprecated.

setMinHomology

public static void setMinHomology(double minHomology)

Deprecated.

To set the threshold of selection of strict minimal homology in SSCA, if set under 0.0 : set to 0.0 ; if more than 100.0 or maxHomology : no changes.

Parameters:

minHomology - (double)

See Also:

algoSSCA(Sequence, SequenceListe)

setMaxHomology

public static void setMaxHomology(double maxHomology)

Deprecated.

To set the T=threshold of selection of strict maximal homology in SSCA, if set under 0.0 or minHomology : no changes ; if more than 100.0 : 100.0.

Parameters:

maxHomology - (double)

See Also:

algoSSCA(Sequence, SequenceListe)

setNbMinSequences

public static void setNbMinSequences(int nbMinSequences)

Deprecated.

To set the minimal number of selection of sequences in SSCA. if set under 0 : set to 0. if more than nbMaxSequences : no changes.

Parameters:

nbMinSequences - (int)

See Also:

algoSSCA(Sequence, SequenceListe)

setNbMaxSequences

public static void setNbMaxSequences(int nbMaxSequences)

Deprecated.

To set the maximal number of selection of sequences in SSCA. if set under nbMinSequences : no changes.

Parameters:

nbMaxSequences - (int)

See Also:

algoSSCA(Sequence, SequenceListe)

setDelcrit

public static void setDelcrit(double delcrit)

Deprecated.

To set deletion criteria in SSCA to compute effects, if set under 0.000 : set to 0.00 ; if more than 100.0 : set to 1.00 (default value).

Parameters:

delcrit - (double)

See Also:

algoSSCA(Sequence, SequenceListe), delcrit

setIdecrit

public static void setIdecrit(double idecrit)

Deprecated.

To set identity criteria in SSCA to compute effects, if set under 00.000 : set to 0.00 ; if more than 100.00 : set to 75.0 (default value).

Parameters:

idecrit - (double)

See Also:

algoSSCA(Sequence, SequenceListe), idecrit

iterationPlusPlus

protected static void iterationPlusPlus()

Deprecated.

iterationLessLess

protected static void iterationLessLess()

Deprecated.

getIteration

protected static int getIteration()

Deprecated.

SetIterationZero

protected static void SetIterationZero()

Deprecated.