modele
Class SequenceTest

java.lang.Object
  modele.Sequence
      modele.SequenceTest

Deprecated. Transfered to Sequence

public class SequenceTest
extends Sequence

Extension of class Sequence, useful for conversion of Stefan Engelen's implementation of algorithms.
Aim is to have an equivalent Sequence "aligned" : translation interface (Interface Design Pattern).

Since:

August, 29 2008

Author:

Gabriel Chandesris (2008)

See Also:

quelle_base(int), quelle_longueur(), est_Une_Base(char)

Field Summary

private double[]

score Deprecated. Tab of scores of current sequence of length 7.

Constructor Summary

SequenceTest(java.lang.String nom, java.lang.String sequence)
Deprecated.

Method Summary

void	change_score(double[] sc) Deprecated. To change current score of test sequence.
boolean	est_Une_Base(char base) Deprecated. Replace by use of Base.isBaseOrGap(char)...
double[]	quel_score() Deprecated. TEST SEQUENCE
char	quelle_base(int pos) Deprecated. To get a Base at a specific position.
int	quelle_longueur() Deprecated. Length of aligned sequence (gap's included).

Methods inherited from class modele.Sequence

calcul_Taille, clone, convertBasesToString, convertDecimale, equals, externalSequence, getBase, getBaseAt, getBaseChar, getBaseIn, getBasePos, getCarbonCopy, getCombiGUGC, getEffetGC, getEffetGU, getEffetGUGC, getHomologie, getIndels, getIndeterminate, getNom, getNombreDecimale, getScore, getSequence, getSequenceBase, getSequenceBaseToString, getSequenceChar, getSequenceCharToString, getSequenceToString, getSubSequence, getVariabilite, internalSequence, length, lengthAlign, limitDecimale, mettre_etoile, pourcentageBases, quelle_longueur_cible, quelle_longueur_test, removeSubSequence, setCombiGUGC, setEffetGC, setEffetGU, setEffetGUGC, setHomologie, setIndels, setIndeterminate, setNom, setNombreDecimale, setScore, setVariabilite, toString, une_base

Methods inherited from class java.lang.Object

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

Field Detail

score

private double[] score

Deprecated.

Tab of scores of current sequence of length 7.

Constructor Detail

SequenceTest

public SequenceTest(java.lang.String nom,
                    java.lang.String sequence)

Deprecated.

Method Detail

quelle_base

public char quelle_base(int pos)

Deprecated.

To get a Base at a specific position.
In the char[] table (aligned sequence : can be gap).

Overrides:

quelle_base in class Sequence

Parameters:

pos - (int)

Returns:

(Base)

See Also:

ADN1test.quelle_base(int)

quelle_longueur

public int quelle_longueur()

Deprecated.

Length of aligned sequence (gap's included).

Returns:

(int)

See Also:

ADN1test.quelle_longueur()

est_Une_Base

public boolean est_Une_Base(char base)

Deprecated. Replace by use of Base.isBaseOrGap(char)...

"Method which test if read character is a base in aligned sequences"

Overrides:

est_Une_Base in class Sequence

Parameters:

base - (char)

Returns:

(boolean) true if base or '-'

See Also:

ADN1test.est_Une_Base(char)

quel_score

public double[] quel_score()

Deprecated.

Description copied from class: Sequence

TEST SEQUENCE

Overrides:

quel_score in class Sequence

Returns:

(double[7])

change_score

public void change_score(double[] sc)

Deprecated.

To change current score of test sequence.

Overrides:

change_score in class Sequence

Parameters:

sc - (double[7])