modele
Class Palindrome

java.lang.Object
  modele.Palindrome

Direct Known Subclasses:

PalindromeCible, PalindromeTest

public class Palindrome
extends java.lang.Object

This class define object which are part of sequences found in auto reverse alignment and cearching structure with positive score.
Old name of this class : Palindrome1 and fusion of Palindrome1cible and Palindrome1test
Some protected methods : use in inheritant classe(s), following indications of aim of these old classe(s).

Author:

Stéfan Engelen (2006), Gabriel Chandesris (2008)

Field Summary

private int[]	carac_max Cible : Maximum characteristics ?
private int[]	carac_min Cible : Minimum characteristics ?
private int	conservationInSequences Cible : Number of conservation in sequences"
private int	count For counting each time Palindrome / Helix is present.
private boolean	indeci "Cible : Undecided" (default is false).
private double	longMut Second rate of selection.
private int	longueur Palindrome length.
private int	longueur1 Test : Length of complementary reverse 5' repetition.
private int	longueur2 Test : Length of complementary reverse 3' repetition.
private Sequence	mainSequence Use when checking Conservation and relevance of palindrome.
private int	nombre_palindromes Cible : Number of represented palindromes.
private int	nombreErreur Nomber of errors.
private int	nombreMutationDouble Nombres de Mutations Doubles (compensatoires).
private int	nombreMutationSimple Nombres de Mutations Simples (consistantes).
private double	pertinence Palindrome relevance [FR : pertinence].
private double	poid Palindrome weight.
private int	positionDebut Position of the Palindrome on sequence (begin and end).
private int	positionFin Position of the Palindrome on sequence (begin and end).
private double	pourcentage_conservation Cible : Conservation rate / percentage (default is 1).
private int	realLength Cible : "Real length"
private double	score Palindrome score (S or M[i,j]).
private double	taux Rate of selection.
private int	typeCritere Cible : criterion type (default is TAUX_MUT == 3)

Constructor Summary

Palindrome(int debut, int fin, int longueur)
Short constructor with beginning, end and length of Palindrome.

Palindrome(int debut, int fin, int longueur, double score)
The complete constructor of an Palindrome Object.

Palindrome(int debut, int fin, int longueur, int typeCritere)
The complete constructor of a cible Palindrome.

Palindrome(int debut, int fin, int longueur, int longueur2, boolean diff)
The complete constructor of a test Palindrome.

Method Summary

void	change_position_debut(int pos)
void	change_position_fin(int pos)
void	changer_carac_max(int quelle_carac, int nv_carac)
void	changer_carac_min(int quelle_carac, int nv_carac)
void	changer_conservation(int conservation)
void	changer_indeci(boolean b)
void	changer_longueur_Reelle(int longueur)
void	changer_longueur(int longueur)
void	changer_nb_pal(int nv)
void	changer_pourcentage_conservation(double nv)
boolean	chevauchant(Palindrome p) Deprecated. see also chevauchant(Palindrome, Palindrome) and equivalence(Palindrome, Palindrome)
static boolean	chevauchant(Palindrome pal1, Palindrome pal2) Cible : "Following methods sorted by use order in ADN1 Class". (17) "to know if two palindrome are crossed together"
static Palindrome[]	choisir_meilleur(int nb, Palindrome[] tabpal) Deprecated. [unused] Calling method ADN1cible.verifier_Conservation(Palindrome1cible, Palindrome1test, double, double, int, ADN1test[]) is not maintained in OtherAlgorithmsStefan...
void	computeNumbers(Palindrome current) This procedure to compute compensatory and single mutations number, and errors number between a test Palindrome (current instance) and a cible Palindrome.
Palindrome	copie() Cible : To get a clone of the current instance of PalindromeCible.
void	countPlusPlus()
boolean	equals(Palindrome toCompare) To know if instance of the class and an other are the same.
static boolean	equivalence(Palindrome helix1, Palindrome helix2) To know if two helix are equivalent : (helix1 in helix2) or (helix2 in helix1).
static boolean	est_Compatible(Palindrome pal1, Palindrome pal2) Cible : "Following methods sorted by use order in ADN1 Class". (5) "To know if two palindromes are compatibles" After reading the code, not sure that fully correct...
boolean	est_indeci()
int	getCount()
double	getLongMut()
int	getNombreErreur()
int	getNombreMutationDouble()
int	getNombreMutationSimple()
double	getPertinence()
double	getPoid()
int	getPositionDebut()
int	getPositionFin()
double	getScore()
Sequence	getSequence()
double	getTaux()
boolean	inclu_dans(Palindrome p) Cible : "Following methods sorted by use order in ADN1 Class". (16) "this method to know if current instance is included in argument with common pairwise "
boolean	isCompatible(Palindrome with)
boolean	isCompatibleWith(Palindrome other) Deprecated. not exact... (see tests)
boolean	isScore(int score) To check if current Palindrome has a given score.
boolean	isSelected(int Lmin) Deprecated. DCFold => PDCFold
boolean	isSelectedCible(double Lmin, double Stest, boolean conservation) For selection of Palindrome cible, if conservation is true : equation 4.11, else 4.12.
boolean	isSelectedTest(double Lmin) For selection of Palindrome test.
int	length() Length of the current instance of Palindrome.
void	nbErreursPlusPlus()
void	nbMutDoublePlusPlus()
void	nbMutSimplePlusPlus()
int	nombre_sequence_conserve()
double	quel_critere()
int	quel_nb_pal()
double	quel_pourcentage_conservation()
int	quel_type_critere()
int	quelle_carac_max(int i)
int	quelle_carac_min(int i)
int	quelle_longueur_reelle()
int	quelle_longueur1()
int	quelle_longueur2()
int	quelle_position_debut()
int	quelle_position_fin()
int	rechercher_approx(java.util.Vector tabPal) Deprecated. see also PalindromeListe.rechercher_approx(Palindrome) and PalindromeListe.whichPositionApprox(Palindrome)
int	rechercher(java.util.Vector tabPal) Deprecated. see also PalindromeListe.rechercher(Palindrome) and PalindromeListe.whichPosition(Palindrome)
static boolean	rssh(Palindrome helix1, Palindrome helix2) To know if on two helix (Palindrome here), the second is included into the first.
void	setCountZero()
protected void	setLength(int length)
void	setLongMut(double longMut)
void	setNombreErreur(int nombreErreur)
void	setNombreMutationDouble(int nombreMutationDouble)
void	setNombreMutationSimple(int nombreMutationSimple)
void	setPertinence(double pertinence)
void	setPoid(double poid)
protected void	setPositionDebut(int positionDebut)
protected void	setPositionFin(int positionFin)
void	setScore(double score)
void	setSequence(Sequence mainSequence)
void	setTaux(double taux)

Methods inherited from class java.lang.Object

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

Field Detail

longueur

private int longueur

Palindrome length.

positionDebut

private int positionDebut

Position of the Palindrome on sequence (begin and end).

positionFin

private int positionFin

Position of the Palindrome on sequence (begin and end).

nombreMutationDouble

private int nombreMutationDouble

Nombres de Mutations Doubles (compensatoires).

nombreMutationSimple

private int nombreMutationSimple

Nombres de Mutations Simples (consistantes).

nombreErreur

private int nombreErreur

Nomber of errors.

score

private double score

Palindrome score (S or M[i,j]).

poid

private double poid

Palindrome weight.
Pcible = M[i][j]/(2*longueur) and >= Lmin and althought LongMut*Pcible >= 2*Lmin
thesis page 82 equations 4.4, 4.5 and 4.6
Ptest = Score/2*Lmin
thesis page 85 equations 4.7 and 4.8

See Also:

longMut, Palindrome(int, int, int), Palindrome(int, int, int, double), isSelectedTest(double), isSelectedCible(double, double, boolean)

pertinence

private double pertinence

Palindrome relevance [FR : pertinence].
(this.longMut*this.poid*Stest)
LongMut = N + L (>= 2*Lmin)
thesis page 87 equation 4.10

See Also:

isSelectedCible(double, double, boolean)

taux

private double taux

Rate of selection.
N = 2*Ncomp + Ncons - Nerr
Taux = N/L ; Taux >= 1
see thesis page 86 equation 4.9 :

See Also:

isSelectedCible(double, double, boolean)

longMut

private double longMut

Second rate of selection.

See Also:

pertinence, isSelectedCible(double, double, boolean)

mainSequence

private Sequence mainSequence

Use when checking Conservation and relevance of palindrome.

See Also:

Alignement.recoverPalindromes()

count

private int count

For counting each time Palindrome / Helix is present.

See Also:

Algorithms.commonPrediction(Sequence, SequenceListe[])

realLength

private int realLength

Cible : "Real length"

carac_max

private int[] carac_max

Cible : Maximum characteristics ?

carac_min

private int[] carac_min

Cible : Minimum characteristics ?

nombre_palindromes

private int nombre_palindromes

Cible : Number of represented palindromes.

conservationInSequences

private int conservationInSequences

Cible : Number of conservation in sequences"

indeci

private boolean indeci

"Cible : Undecided" (default is false).

pourcentage_conservation

private double pourcentage_conservation

Cible : Conservation rate / percentage (default is 1).

typeCritere

private int typeCritere

Cible : criterion type (default is TAUX_MUT == 3)

longueur1

private int longueur1

Test : Length of complementary reverse 5' repetition.

longueur2

private int longueur2

Test : Length of complementary reverse 3' repetition.

Constructor Detail

Palindrome

public Palindrome(int debut,
                  int fin,
                  int longueur)

Short constructor with beginning, end and length of Palindrome.
Sometimes for cible Palindrome.

Parameters:

debut - (int) begin

fin - (int) end

longueur - (int) length

See Also:

setPoid(double)

Palindrome

public Palindrome(int debut,
                  int fin,
                  int longueur,
                  double score)

The complete constructor of an Palindrome Object. (begin,end,length,score). And proceed weight.

Parameters:

debut - (int) begin

fin - (int) end

longueur - (int) length

score - (double) ( == Alignement#matrice[i][j])

See Also:

Alignement.recoverPalindromes()

Palindrome

public Palindrome(int debut,
                  int fin,
                  int longueur,
                  int typeCritere)

The complete constructor of a cible Palindrome. (begin,end,length,criterion type).

Parameters:

debut - (int) begin

fin - (int) end

longueur - (int) length

typeCritere - (int) criterion type

See Also:

Alignement.recoverPalindromes()

Palindrome

public Palindrome(int debut,
                  int fin,
                  int longueur,
                  int longueur2,
                  boolean diff)

The complete constructor of a test Palindrome. (begin,end,length,length2).

Parameters:

debut - (int) begin

fin - (int) end

longueur - (int) length

longueur2 - (int) length2

diff - (boolean) [not used, just to make difference with Palindrome(int, int, int, int)]

See Also:

Alignement.recoverPalindromes()

Method Detail

length

public int length()

Length of the current instance of Palindrome.

Returns:

int

getPositionDebut

public int getPositionDebut()

getPositionFin

public int getPositionFin()

getNombreMutationSimple

public int getNombreMutationSimple()

getNombreMutationDouble

public int getNombreMutationDouble()

getNombreErreur

public int getNombreErreur()

getPoid

public double getPoid()

getPertinence

public double getPertinence()

getTaux

public double getTaux()

setTaux

public void setTaux(double taux)

getLongMut

public double getLongMut()

setLongMut

public void setLongMut(double longMut)

setPositionDebut

protected void setPositionDebut(int positionDebut)

setPositionFin

protected void setPositionFin(int positionFin)

setLength

protected void setLength(int length)

setNombreMutationSimple

public void setNombreMutationSimple(int nombreMutationSimple)

setNombreMutationDouble

public void setNombreMutationDouble(int nombreMutationDouble)

setNombreErreur

public void setNombreErreur(int nombreErreur)

setPoid

public void setPoid(double poid)

setPertinence

public void setPertinence(double pertinence)

getSequence

public Sequence getSequence()

setSequence

public void setSequence(Sequence mainSequence)

getScore

public double getScore()

setScore

public void setScore(double score)

nbMutDoublePlusPlus

public void nbMutDoublePlusPlus()

nbMutSimplePlusPlus

public void nbMutSimplePlusPlus()

nbErreursPlusPlus

public void nbErreursPlusPlus()

isSelected

public boolean isSelected(int Lmin)

Deprecated. DCFold => PDCFold

Covariation criteria.
[DCFold]see thesis page 61 equations 4.2 and 4.3
[DCFold]see thesis page 82 equations 4.5 then 4.6 and explanation

Parameters:

Lmin - The value to compare with (int).

Returns:

boolean

isSelectedTest

public boolean isSelectedTest(double Lmin)

For selection of Palindrome test.

Parameters:

Lmin - The value to Compute with (double)

Returns:

boolean

See Also:

Algorithms.checkConservation(Palindrome, SequenceListe, int)

isSelectedCible

public boolean isSelectedCible(double Lmin,
                               double Stest,
                               boolean conservation)

For selection of Palindrome cible, if conservation is true : equation 4.11, else 4.12.

Parameters:

Lmin - (double) The value to compare with

Stest - (int) Score Average of tests palindromes

conservation - (boolean)

Returns:

boolean

See Also:

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

isScore

public boolean isScore(int score)

To check if current Palindrome has a given score.

Parameters:

score - The score to test (int).

Returns:

boolean

isCompatibleWith

public boolean isCompatibleWith(Palindrome other)

Deprecated. not exact... (see tests)

Procedure to know if two palindromes are compatible or not.

Parameters:

other - PalindromeCible

See Also:

Algorithms.compatibilityTreatment(modele.PalindromeListe), isCompatible(Palindrome)

isCompatible

public boolean isCompatible(Palindrome with)

computeNumbers

public void computeNumbers(Palindrome current)

This procedure to compute compensatory and single mutations number, and errors number between a test Palindrome (current instance) and a cible Palindrome.

Parameters:

current - One Palindrome of cible Sequence.

See Also:

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

getCount

public int getCount()

setCountZero

public void setCountZero()

countPlusPlus

public void countPlusPlus()

equals

public boolean equals(Palindrome toCompare)

To know if instance of the class and an other are the same.

Parameters:

toCompare - An other Palindrome.

Returns:

boolean

rssh

public static boolean rssh(Palindrome helix1,
                           Palindrome helix2)

To know if on two helix (Palindrome here), the second is included into the first. (test if helix2 is in helix1).
(see thesis page 171 definition 21)

Parameters:

helix1 - First Palindrome

helix2 - Second Palindrome

Returns:

boolean

See Also:

Algorithms.commonPrediction(Sequence, SequenceListe[]).

equivalence

public static boolean equivalence(Palindrome helix1,
                                  Palindrome helix2)

To know if two helix are equivalent : (helix1 in helix2) or (helix2 in helix1).

Parameters:

helix1 - Palindrome

helix2 - Palindrome

Returns:

boolean

See Also:

Algorithms.commonPrediction(Sequence, SequenceListe[])., rssh(Palindrome, Palindrome)

quelle_position_debut

public int quelle_position_debut()

quelle_position_fin

public int quelle_position_fin()

quelle_longueur_reelle

public int quelle_longueur_reelle()

quel_pourcentage_conservation

public double quel_pourcentage_conservation()

est_indeci

public boolean est_indeci()

quelle_carac_max

public int quelle_carac_max(int i)

quelle_carac_min

public int quelle_carac_min(int i)

quel_nb_pal

public int quel_nb_pal()

quel_type_critere

public int quel_type_critere()

quel_critere

public double quel_critere()

change_position_debut

public void change_position_debut(int pos)

change_position_fin

public void change_position_fin(int pos)

changer_longueur

public void changer_longueur(int longueur)

changer_longueur_Reelle

public void changer_longueur_Reelle(int longueur)

changer_pourcentage_conservation

public void changer_pourcentage_conservation(double nv)

changer_indeci

public void changer_indeci(boolean b)

changer_carac_max

public void changer_carac_max(int quelle_carac,
                              int nv_carac)

changer_carac_min

public void changer_carac_min(int quelle_carac,
                              int nv_carac)

changer_nb_pal

public void changer_nb_pal(int nv)

est_Compatible

public static boolean est_Compatible(Palindrome pal1,
                                     Palindrome pal2)

Cible : "Following methods sorted by use order in ADN1 Class". (5)
"To know if two palindromes are compatibles"
After reading the code, not sure that fully correct...

Parameters:

pal1 - (Palindrome1cible)

pal2 - (Palindrome1cible)

Returns:

(boolean) compatible or not

See Also:

OtherAlgorithmsStefan.incompatibilite_plusieurs_choix(PalindromeListeListe, int, int, int, double, boolean, int), OtherAlgorithmsStefan.incompatibilite_un_choix(Palindrome[], int, int), AlgorithmsStefan.incompatibilite_plusieurs_choix(PalindromeListeListe, int, int, int, double, boolean, int), AlgorithmsStefan.incompatibilite_un_choix(Palindrome[], int, int), isCompatible(Palindrome)

inclu_dans

public boolean inclu_dans(Palindrome p)

Cible : "Following methods sorted by use order in ADN1 Class". (16)
"this method to know if current instance is included in argument with common pairwise "

Parameters:

p - (Palindrome)

Returns:

(boolean)

See Also:

PalindromeListe.rechercher_approx(Palindrome), OtherAlgorithmsStefan.incompatibilite_plusieurs_choix(PalindromeListeListe, int, int, int, double, boolean, int), OtherAlgorithmsStefan.incompatibilite_un_choix(Palindrome[], int, int), OtherAlgorithmsStefan.palindromes_communs(Palindrome[], Palindrome[], boolean), XXX ??deprecated?? see also {@linkplain Palindrome#rssh(Palindrome, Palindrome)}

chevauchant

public boolean chevauchant(Palindrome p)

Deprecated. see also chevauchant(Palindrome, Palindrome) and equivalence(Palindrome, Palindrome)

Cible : "Following methods sorted by use order in ADN1 Class". (17)
"to know if two palindrome are crossed together"

Parameters:

p - (Palindrome)

Returns:

(boolean)

See Also:

AlgorithmsStefan.resultat_commun(PalindromeListeListe)

chevauchant

public static boolean chevauchant(Palindrome pal1,
                                  Palindrome pal2)

Cible : "Following methods sorted by use order in ADN1 Class". (17)
"to know if two palindrome are crossed together"

Parameters:

pal1 - (Palindrome)

pal2 - (Palindrome)

Returns:

(boolean)

See Also:

OtherAlgorithmsStefan.resultat_commun(PalindromeListeListe), AlgorithmsStefan.resultat_commun(PalindromeListeListe), equivalence(Palindrome, Palindrome)

rechercher

public int rechercher(java.util.Vector tabPal)

Deprecated. see also PalindromeListe.rechercher(Palindrome) and PalindromeListe.whichPosition(Palindrome)

Cible : "Following methods sorted by use order in ADN1 Class". (14)
"to find a palindrome in a Vector of palindromes"

Parameters:

tabPal - (Vector)

Returns:

(int) position

See Also:

OtherAlgorithmsStefan.resultat_commun(PalindromeListeListe), AlgorithmsStefan.resultat_commun(PalindromeListeListe)

rechercher_approx

public int rechercher_approx(java.util.Vector tabPal)

Deprecated. see also PalindromeListe.rechercher_approx(Palindrome) and PalindromeListe.whichPositionApprox(Palindrome)

Cible : "Following methods sorted by use order in ADN1 Class". (15)
"to find an approximate palindrome in a vector of palindromes."

Parameters:

tabPal - (Vector)

Returns:

(int) position

See Also:

OtherAlgorithmsStefan.resultat_commun(PalindromeListeListe), AlgorithmsStefan.resultat_commun(PalindromeListeListe)

copie

public Palindrome copie()

Cible : To get a clone of the current instance of PalindromeCible.

Returns:

(Palindrome1cible)

See Also:

OtherAlgorithmsStefan.computing(SequenceListe[], Sequence, boolean, boolean), AlgorithmsStefan.computing(SequenceListe[], Sequence, boolean, boolean)

changer_conservation

public void changer_conservation(int conservation)

nombre_sequence_conserve

public int nombre_sequence_conserve()

quelle_longueur1

public int quelle_longueur1()

quelle_longueur2

public int quelle_longueur2()

choisir_meilleur

public static Palindrome[] choisir_meilleur(int nb,
                                            Palindrome[] tabpal)

Deprecated. [unused] Calling method ADN1cible.verifier_Conservation(Palindrome1cible, Palindrome1test, double, double, int, ADN1test[]) is not maintained in OtherAlgorithmsStefan...

Test : "This method choose the best _nb_ test palindromes"

Parameters:

nb - (int) number of palindrome to choose

tabpal - (Palindromes1test[])

Returns:

(Palindrome1tets[])

See Also:

ADN1cible.verifier_Conservation(Palindrome1cible, Palindrome1test, double, double, int, ADN1test[])