modele
Class SequenceCible

java.lang.Object
  modele.Sequence
      modele.SequenceCible

Deprecated. Transfered to Sequence

public class SequenceCible
extends Sequence

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

Since:

August, 29 2008

Author:

Gabriel Chandesris (2008)

See Also:

mettre_etoile(PalindromeCible[]), calcul_Taille(PalindromeCible), une_base(int), quelle_longueur()

Constructor Summary

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

Method Summary

int	calcul_Taille(PalindromeCible pal) Deprecated. COMPATIBLE PALINDROME SEARCH "This method to compute internal sequence length at step i
void	mettre_etoile(PalindromeCible[] structure) Deprecated. PSEUDOKNOTS SEARCH "This method to put stars (*) in found palindromes in aim to find pseudoknots"
int	quelle_longueur() Deprecated. To get the length of the sequence.
java.lang.String	toString(int debut, int fin) Deprecated. SOME SHOW FOR VIEW "To visualize considered sequence [current instance]"
Base	une_base(int position) Deprecated. To get a Base at a specific position.

Methods inherited from class modele.Sequence

calcul_Taille, change_score, clone, convertBasesToString, convertDecimale, equals, est_Une_Base, 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, quel_score, quelle_base, quelle_longueur_cible, quelle_longueur_test, removeSubSequence, setCombiGUGC, setEffetGC, setEffetGU, setEffetGUGC, setHomologie, setIndels, setIndeterminate, setNom, setNombreDecimale, setScore, setVariabilite

Methods inherited from class java.lang.Object

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

Constructor Detail

SequenceCible

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

Deprecated.

Method Detail

une_base

public Base une_base(int position)

Deprecated.

To get a Base at a specific position.
In the Base[] table (unaligned sequence : no gap).

Overrides:

une_base in class Sequence

Parameters:

position - (int)

Returns:

(Base)

See Also:

ADN1cible.une_base(int)

quelle_longueur

public int quelle_longueur()

Deprecated.

To get the length of the sequence.

Returns:

(int) length

See Also:

ADN1cible.quelle_longueur()

calcul_Taille

public int calcul_Taille(PalindromeCible pal)

Deprecated.

COMPATIBLE PALINDROME SEARCH
"This method to compute internal sequence length at step i. "

Parameters:

pal - (Palinrome1cible)

Returns:

(int)

See Also:

AlgorithmsStefan.diviser_regner(Palindrome[], Sequence, Sequence[], int, int, int, int, boolean, int), AlgorithmsStefan.recherche_Pseudonoeud(Sequence, Base[], Sequence[], boolean, int, int), OtherAlgorithmsStefan.diviser_regner(Palindrome[], Sequence, Sequence[], int, int, int, int, boolean, int), OtherAlgorithmsStefan.recherche_Pseudonoeud(Sequence, Base[], Sequence[], boolean, int, int), ADN1cible.calcul_Taille(origincomment.Palindrome1cible)

mettre_etoile

public void mettre_etoile(PalindromeCible[] structure)

Deprecated.

PSEUDOKNOTS SEARCH
"This method to put stars (*) in found palindromes in aim to find pseudoknots"

Parameters:

structure - (PalindromeCible[])

See Also:

AlgorithmsStefan.calcul_Resultat(Sequence, Sequence[], int, boolean, boolean), AlgorithmsStefan.recherche_Pseudonoeud(Sequence, Base[], Sequence[], boolean, int, int), OtherAlgorithmsStefan.calcul_Resultat(Sequence, Sequence[], int, boolean, boolean), OtherAlgorithmsStefan.recherche_Pseudonoeud(Sequence, Base[], Sequence[], boolean, int, int), Interface5.setInterface(ADN1cible, ADN1test[], int, int, int, int, int), ADN1cible.mettre_etoile(int), OriginAlgorithmsStefan.mettre_etoile(ADN1cible, int)

toString

public java.lang.String toString(int debut,
                                 int fin)

Deprecated.

SOME SHOW FOR VIEW
"To visualize considered sequence [current instance]"

Overrides:

toString in class Sequence

Parameters:

debut - (int) begin

fin - (int) end

Returns:

(String)

See Also:

ADN1cible.afficher_Caracteristique(), ADN1cible.toString(int, int), Interface12.setInterface(Profil, String, Palindrome1cible, int)