origincomment
Class Alignement

java.lang.Object
  origincomment.Alignement

public class Alignement
extends java.lang.Object

This class for alignment...

Author:

Stéfan Engelen (2006) for coding..., Gabriel Chandesris (2008) for comments and makeing the code readable.

See Also:

Matrice_ALN.chercher_meilleur()

Field Summary

private java.lang.String[]	alignement Alignment.
static int	AU AU is 1.
static int	CG CG is 4.
static int	CONSERVATION CONSERVATION is -3.
static int	ERREUR ERREUR is -1.
static int	GC GC is 3.
static int	GU GU is 5.
static int	MUTATION_SIMPLE MUTATION_SIMPLE (single mutation) is -2.
private int[][]	mutation3prime 3' mutation
private int[][]	mutation5prime 5' mutation
private int	nombre_match Macth number (default : 0).
private double	pertinence Relevance (deafult : 1.0).
static int	RIEN RIEN (nothing) is 0.
private int	taille3prime Length on 3' side.
private int	taille5prime Length on 5' side.
static int	UA UA is 2.
static int	UG UG is 6.

Constructor Summary

Alignement(int t5prime, int t3prime, java.lang.String[] aln)
Main constructor

Method Summary

void	ajoute_match(int match) Add 1 to nombre_match if more than 0.
double	calcul_pertinence() To get relevance without computing...
void	change_alignement_3_prime(java.lang.String nv)
void	change_alignement_5_prime(java.lang.String nv)
void	change_mutations_3_prime(int pos, int nvmut, int liaison5prime)
void	change_mutations_5_prime(int pos, int nvmut, int liaison3prime)
void	changer_pertinence(double nv)
Alignement	copie() To make a clone of the current instance of Alignment.
int	desequilibre_mutation_simple() To get number of mutation desequilibrium between 5' and 3'.
int	eccart_mutation_double() To get number of double mutations between 5' and 3'.
int	eccart_mutation_simple() To get number of single mutations between 5' and 3'.
int	nombre_mutation_simple_3prime() Single mutations number on side 3'.
int	nombre_mutation_simple_5prime() Single mutation number on side 5'.
java.lang.String	quel_alignement_3_prime()
java.lang.String	quel_alignement_5_prime()
static int	quel_match(char cinqprime, char troisprime) For two bases given, respond the alignment.
double	quelle_pertinence()
int[][]	quelles_mutations_3_prime()
int[]	quelles_mutations_3_prime(int lequel)
int[][]	quelles_mutations_5_prime()
int[]	quelles_mutations_5_prime(int lequel)
int	score() "Helix best mutate to stable pairwises
boolean	validation_nombre_conservation() Is the number of conservation correct ?
boolean	validation_nombre_mutation_double() Is the number of double mutations correct ?
boolean	validation_nombre_mutation_simple() Is the number of single mutations correct ?
boolean	validation() Validation, always true...

Methods inherited from class java.lang.Object

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

Field Detail

AU

public static final int AU

AU is 1.

See Also:

Constant Field Values

UA

public static final int UA

UA is 2.

See Also:

Constant Field Values

GC

public static final int GC

GC is 3.

See Also:

Constant Field Values

CG

public static final int CG

CG is 4.

See Also:

Constant Field Values

GU

public static final int GU

GU is 5.

See Also:

Constant Field Values

UG

public static final int UG

UG is 6.

See Also:

Constant Field Values

ERREUR

public static final int ERREUR

ERREUR is -1.

See Also:

Constant Field Values

MUTATION_SIMPLE

public static final int MUTATION_SIMPLE

MUTATION_SIMPLE (single mutation) is -2.

See Also:

Constant Field Values

CONSERVATION

public static final int CONSERVATION

CONSERVATION is -3.

See Also:

Constant Field Values

RIEN

public static final int RIEN

RIEN (nothing) is 0.

See Also:

Constant Field Values

alignement

private java.lang.String[] alignement

Alignment.

taille5prime

private int taille5prime

Length on 5' side.

taille3prime

private int taille3prime

Length on 3' side.

mutation5prime

private int[][] mutation5prime

5' mutation

mutation3prime

private int[][] mutation3prime

3' mutation

nombre_match

private int nombre_match

Macth number (default : 0).

pertinence

private double pertinence

Relevance (deafult : 1.0).

See Also:

Matrice_ALN.meilleur_score(int), Matrice_ALN.calcul_score(int[], Matrice_ALN[]), ADN1cible.verifier_Conservation_Alignement(Palindrome1cible, Palindrome1test, double, ADN1test[])

Constructor Detail

Alignement

public Alignement(int t5prime,
                  int t3prime,
                  java.lang.String[] aln)

Main constructor

Parameters:

t5prime - (int) first sequence length

t3prime - (int) second sequence length

aln - (String[]) alignment

Method Detail

quel_alignement_5_prime

public java.lang.String quel_alignement_5_prime()

quel_alignement_3_prime

public java.lang.String quel_alignement_3_prime()

quelles_mutations_5_prime

public int[][] quelles_mutations_5_prime()

quelles_mutations_3_prime

public int[][] quelles_mutations_3_prime()

quelles_mutations_5_prime

public int[] quelles_mutations_5_prime(int lequel)

quelles_mutations_3_prime

public int[] quelles_mutations_3_prime(int lequel)

quelle_pertinence

public double quelle_pertinence()

change_alignement_5_prime

public void change_alignement_5_prime(java.lang.String nv)

change_alignement_3_prime

public void change_alignement_3_prime(java.lang.String nv)

change_mutations_5_prime

public void change_mutations_5_prime(int pos,
                                     int nvmut,
                                     int liaison3prime)

change_mutations_3_prime

public void change_mutations_3_prime(int pos,
                                     int nvmut,
                                     int liaison5prime)

changer_pertinence

public void changer_pertinence(double nv)

ajoute_match

public void ajoute_match(int match)

Add 1 to nombre_match if more than 0.
To count matches.

Parameters:

match - (int) [unused]

calcul_pertinence

public double calcul_pertinence()

To get relevance without computing...

Returns:

(double) revelance.

eccart_mutation_double

public int eccart_mutation_double()

To get number of double mutations between 5' and 3'.
"Greater is bader..."

Returns:

(int)

eccart_mutation_simple

public int eccart_mutation_simple()

To get number of single mutations between 5' and 3'.
"Greater is bader..."

Returns:

(int)

desequilibre_mutation_simple

public int desequilibre_mutation_simple()

To get number of mutation desequilibrium between 5' and 3'.
"Greater is bader..."

Returns:

(int)

nombre_mutation_simple_5prime

public int nombre_mutation_simple_5prime()

Single mutation number on side 5'.

Returns:

(int)

nombre_mutation_simple_3prime

public int nombre_mutation_simple_3prime()

Single mutations number on side 3'.

Returns:

(int)

score

public int score()

"Helix best mutate to stable pairwises. "

Returns:

(int)

validation_nombre_mutation_double

public boolean validation_nombre_mutation_double()

Is the number of double mutations correct ?

Returns:

(boolean)

validation_nombre_mutation_simple

public boolean validation_nombre_mutation_simple()

Is the number of single mutations correct ?

Returns:

(boolean)

validation_nombre_conservation

public boolean validation_nombre_conservation()

Is the number of conservation correct ?

Returns:

(boolean)

quel_match

public static int quel_match(char cinqprime,
                             char troisprime)

For two bases given, respond the alignment.

Parameters:

cinqprime - (char)

troisprime - (char)

Returns:

(int)

See Also:

AU, UA, GC, CG, GU, UG, ERREUR

validation

public boolean validation()

Validation, always true...

Returns:

(boolean) true

See Also:

Matrice_ALN.recupere_alignement(Alignement, int[], int)

copie

public Alignement copie()

To make a clone of the current instance of Alignment.

Returns:

Alignement

See Also:

Matrice_ALN.recupere_alignement(Alignement, int[], int)