modele
Class ConvertedProfil

java.lang.Object
  modele.ConvertedProfil

public class ConvertedProfil
extends java.lang.Object

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

Since:

August 28, 2008

Author:

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

Field Summary

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

Constructor Summary

ConvertedProfil()
Deprecated. [not used]

ConvertedProfil(Sequence target, Sequence[] tableauSequences)
Constrcutor with given target sequence and table of test sequences.

Method Summary

void	change_adn(Sequence 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)
Sequence	quel_adn()
double[][]	quel_profil()
Sequence[]	quels_adns_tests()
void	remplir(Palindrome[] 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

target

private Sequence target

Target sequence ?

tableauSequences

private Sequence[] tableauSequences

Homologuous / test sequences ?

numerosequence

private int numerosequence

Sequence which will be compared to others.

Constructor Detail

ConvertedProfil

public ConvertedProfil()

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()

ConvertedProfil

public ConvertedProfil(Sequence target,
                       Sequence[] tableauSequences)

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

Parameters:

target - (Sequence)

tableauSequences - (Sequence[])

See Also:

initialisation(), OtherAlgoStefanConverter.algoSSCA(Sequence, SequenceListe), OtherAlgoStefanConverter.algoSSCA(Sequence, SequenceListe, int, int, double, double, boolean)

Method Detail

quel_profil

public double[][] quel_profil()

quel_adn

public Sequence quel_adn()

quels_adns_tests

public Sequence[] quels_adns_tests()

pourcentage

public double pourcentage(int i,
                          int j)

change_adn

public void change_adn(Sequence 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:

ConvertedProfil(), ConvertedProfil(Sequence, Sequence[]), remplir(Palindrome[], int)

remplir

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

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

Parameters:

tabpal - (Palindrome)

numerosequence - (int) number of sequence

See Also:

OtherAlgoStefanConverter.algoSSCA(Sequence, SequenceListe), OtherAlgoStefanConverter.algoSSCA(Sequence, SequenceListe, int, int, double, double, boolean)

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object