origincomment
Class Profil

java.lang.Object
  origincomment.Profil

public class Profil
extends java.lang.Object

"A mutation profile is a 4*4 matrix" : in reality it is 4*7...

Author:

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

Field Summary

private ADN1cible	adn Target sequence ?
private ADN1test[]	adntest Homologuous / test sequences ?
private int	numerosequence Sequence which will be compared to others.
private double[][]	profil The matrix of profile

Constructor Summary

Profil()
Deprecated. [not used]

Profil(ADN1cible adn, ADN1test[] tabAdnTest)
Constrcutor with given target sequence and table of test sequences.

Method Summary

void	change_adn(ADN1cible nv)
void	change_case(double nv, int i, int j)
private void	initialisation() Initialise the current score matrix with all to 0.
double	pourcentage(int i, int j)
ADN1cible	quel_adn()
double[][]	quel_profil()
ADN1test[]	quels_adns_tests()
void	remplir(Palindrome1cible[] tabpal, int numerosequence) This procedure to make the profile will be not empty...
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

profil

private double[][] profil

The matrix of profile

adn

private ADN1cible adn

Target sequence ?

adntest

private ADN1test[] adntest

Homologuous / test sequences ?

numerosequence

private int numerosequence

Sequence which will be compared to others.

Constructor Detail

Profil

public Profil()

Deprecated. [not used]

Default constructor.
Initialize matrix 4*7 (and no content).
Sequences and table of sequences are null.
Number of sequence is -1.

See Also:

initialisation()

Profil

public Profil(ADN1cible adn,
              ADN1test[] tabAdnTest)

Constrcutor with given target sequence and table of test sequences.
Initialize matrix 4*7 (and no content).
Number of sequence is -1.

Parameters:

adn - (ADN1cible)

tabAdnTest - (ADN1test[])

See Also:

initialisation(), ADN1test.distance(ADN1cible, ADN1test, ADN1test[]), OriginAlgoStefanConverter.distance(ADN1cible, ADN1test, ADN1test[])

Method Detail

quel_profil

public double[][] quel_profil()

quel_adn

public ADN1cible quel_adn()

quels_adns_tests

public ADN1test[] quels_adns_tests()

pourcentage

public double pourcentage(int i,
                          int j)

change_adn

public void change_adn(ADN1cible nv)

change_case

public void change_case(double nv,
                        int i,
                        int j)

initialisation

private void initialisation()

Initialise the current score matrix with all to 0.

See Also:

Profil(), Profil(ADN1cible, ADN1test[]), remplir(Palindrome1cible[], int)

remplir

public void remplir(Palindrome1cible[] tabpal,
                    int numerosequence)

This procedure to make the profile will be not empty...

Parameters:

tabpal - (Palindrome1cible)

numerosequence - (int) number of sequence

See Also:

ADN1test.distance(ADN1cible, ADN1test, ADN1test[]), Interface12.setInterface(Profil, String, Palindrome1cible, int)

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object