origincomment
Class Matrice_ALN

java.lang.Object
  origincomment.Matrice_ALN

public class Matrice_ALN
extends java.lang.Object

Alignment matrix...

Author:

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

See Also:

Case

Field Summary

private ADN1test	adncible Target sequence in format of test sequence.
private java.util.Vector	alignements Vector of alignments.
private int[]	courant A current tab of integers.
private static double	lmin Lmin / minimal length.
private Case[][]	matrice 2D table (default is null).
private static double[]	meilleurScore Best score matrix.
private int	nb_alignements Number of alignments.
private int	nb_alignements_trouves Number of alignments found.
private int[]	position3prime "bases postions of palindrome in test sequence" 3' side
private int[]	position5prime "bases postions of palindrome in test sequence" 5' side
private java.lang.String	seq3prime 3' sequence (default is empty ("")).
private java.lang.String	seq5prime 5' sequence (default is empty ("")).
private static int	taille3prime Length on 3' side.
private static int	taille5prime Length on 5' side.

Constructor Summary

Matrice_ALN(ADN1test seqcible, ADN1test seqtest, int debut5, int fin5, int debut3, int fin3, int nbaln, double lgmin)

Method Summary

private void	aligner() Local alignment (Smith and Waterman).
private static double[]	calcul_score(int[] quelAln, Matrice_ALN[] tabMat) Score computing ?
static void	change_meilleur_score(double[] nvscore, boolean forcage) To set the best scores.
private void	chercher_meilleur() Searching the best...
private static void	choisi_aln(int[] quelAln, Matrice_ALN[] tabMat, int etape) Alignment choice ?
private static void	choisi_seq(Matrice_ALN[] tabMat, int[] quelleSeq, int etape, int debut) Sequence choice ?
private void	initialiser() Initialization of scoring matrix with new Cases, height and width +1 more than sequences.
static double	meilleur_score(int i)
private boolean	meilleur() To get the best ??
static void	meilleure_combinaison(Matrice_ALN[] tabMat, int nbSeqTest, int typeRecherche) Best combination ?
int	quel_nombre_aln()
Case	quelle_case()
Case	quelle_case(int i, int j)
java.lang.String	quelle_seq_3prime()
java.lang.String	quelle_seq_5prime()
java.util.Vector	quels_alignements()
private void	recupere_alignement(Alignement align, int[] courant, int forcage) To gain the alignment ?
private int[]	score(char x, char y) Scoring a pairwise...
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

taille5prime

private static int taille5prime

Length on 5' side.

taille3prime

private static int taille3prime

Length on 3' side.

meilleurScore

private static double[] meilleurScore

Best score matrix. (default : {-100,-100,-100,-100,-100})
"{score,double mutation,error,relevance,single mutation}"
"{score,mutation double,erreur,pertinence,mutation simple}"

lmin

private static double lmin

Lmin / minimal length.

nb_alignements

private int nb_alignements

Number of alignments.

matrice

private Case[][] matrice

2D table (default is null).

courant

private int[] courant

A current tab of integers. (default has two columns).

seq5prime

private java.lang.String seq5prime

5' sequence (default is empty ("")).

seq3prime

private java.lang.String seq3prime

3' sequence (default is empty ("")).

position5prime

private int[] position5prime

"bases postions of palindrome in test sequence" 5' side

position3prime

private int[] position3prime

"bases postions of palindrome in test sequence" 3' side

alignements

private java.util.Vector alignements

Vector of alignments.

nb_alignements_trouves

private int nb_alignements_trouves

Number of alignments found.

adncible

private ADN1test adncible

Target sequence in format of test sequence.

Constructor Detail

Matrice_ALN

public Matrice_ALN(ADN1test seqcible,
                   ADN1test seqtest,
                   int debut5,
                   int fin5,
                   int debut3,
                   int fin3,
                   int nbaln,
                   double lgmin)

Parameters:

seqcible - (ADN1test) target sequence

seqtest - (ADN1test) test sequence

debut5 - (int) begining of palindrome

fin5 - (int) (begin+length-) of palindrome

debut3 - (int) end of palindrome

fin3 - (int) (end-length+1) of palindrome

nbaln - (int) number of alignment (1?)

lgmin - (double) lmin [unused]

See Also:

TestAln.main(String[]), ADN1cible.verifier_Conservation_Alignement(Palindrome1cible, Palindrome1test, double, ADN1test[]), initialiser(), aligner(), chercher_meilleur()

Method Detail

quelle_seq_5prime

public java.lang.String quelle_seq_5prime()

quelle_seq_3prime

public java.lang.String quelle_seq_3prime()

quelle_case

public Case quelle_case()

quelle_case

public Case quelle_case(int i,
                        int j)

quel_nombre_aln

public int quel_nombre_aln()

quels_alignements

public java.util.Vector quels_alignements()

meilleur_score

public static double meilleur_score(int i)

change_meilleur_score

public static void change_meilleur_score(double[] nvscore,
                                         boolean forcage)

To set the best scores.

Parameters:

nvscore - (double[])

forcage - (boolean) true to be sure to change, else check if first score is better to set.

See Also:

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

initialiser

private void initialiser()

Initialization of scoring matrix with new Cases, height and width +1 more than sequences.

See Also:

Matrice_ALN(ADN1test, ADN1test, int, int, int, int, int, double)

aligner

private void aligner()

Local alignment (Smith and Waterman).

See Also:

Matrice_ALN(ADN1test, ADN1test, int, int, int, int, int, double)

score

private int[] score(char x,
                    char y)

Scoring a pairwise...

Parameters:

x - (char)

y - (char)

Returns:

(int[]) 3 integers : {score, operation, normal score}

See Also:

aligner(), ADN1cible.score(char, char)

chercher_meilleur

private void chercher_meilleur()

Searching the best...

See Also:

Matrice_ALN(ADN1test, ADN1test, int, int, int, int, int, double), recupere_alignement(Alignement, int[], int), meilleur()

recupere_alignement

private void recupere_alignement(Alignement align,
                                 int[] courant,
                                 int forcage)

To gain the alignment ? Changes the alignment and mutations of current matrix instance.

Parameters:

align - (Alignement)

courant - (int[])

forcage - (int) operation

See Also:

chercher_meilleur()

meilleur

private boolean meilleur()

To get the best ??

Returns:

(boolean)

See Also:

chercher_meilleur()

meilleure_combinaison

public static void meilleure_combinaison(Matrice_ALN[] tabMat,
                                         int nbSeqTest,
                                         int typeRecherche)

Best combination ?

Parameters:

tabMat - (Matrice_ALN[])

nbSeqTest - (int)

typeRecherche - (typoeRecherche)

See Also:

ADN1cible.verifier_Conservation_Alignement(Palindrome1cible, Palindrome1test, double, ADN1test[])

choisi_aln

private static void choisi_aln(int[] quelAln,
                               Matrice_ALN[] tabMat,
                               int etape)

Alignment choice ?

Parameters:

quelAln - (int[])

tabMat - (Matrice_ALN[])

etape - (int) step

See Also:

meilleure_combinaison(Matrice_ALN[], int, int), choisi_seq(Matrice_ALN[], int[], int, int), change_meilleur_score(double[], boolean)

choisi_seq

private static void choisi_seq(Matrice_ALN[] tabMat,
                               int[] quelleSeq,
                               int etape,
                               int debut)

Sequence choice ?

Parameters:

tabMat - (Matrice_ALN[])

quelleSeq - (int[])

etape - (int) step

debut - (int) begin

See Also:

meilleure_combinaison(Matrice_ALN[], int, int)

calcul_score

private static double[] calcul_score(int[] quelAln,
                                     Matrice_ALN[] tabMat)

Score computing ?

Parameters:

quelAln - (int[])

tabMat - (Matrice_ALN[])

Returns:

(double[]) "{score,mutationDouble,erreur,pertinence,mutationSimple}"

See Also:

choisi_aln(int[], Matrice_ALN[], int)

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object