Uses of Class
modele.Base

Packages that use Base

modele	Model for objet representation and computing P-DCFold Algorithms.
tests	First part of tests : the simpliest classes of the model.

Uses of Base in modele

Fields in modele declared as Base

private Base[]

Sequence.sequenceBase Base tabled/ formatted sequence without gap's/ indel's.

Methods in modele that return Base

Base	Sequence.getBase(int position) To get the Base at position [position] in the table of Base's.
Base[]	Sequence.getSequenceBase()
Base[]	Sequence.getSubSequence(int debut, int fin) To get a subsequence of the sequence (not of the alignment), start from 0 (positions debut AND fin are included).
Base	SequenceCible.une_base(int position) Deprecated. To get a Base at a specific position.
Base	Sequence.une_base(int position) To get a Base at a specific position.

Methods in modele with parameters of type Base

static java.lang.String	Sequence.convertBasesToString(Base[] subsequence) To get a String from a Base[] (maybe useful after getting a subsequence).
boolean	Base.equals(Base toCompare) To know if instance of the class and an other are the same.
static boolean	Base.matchBases(Base x, Base y) To know if two Base's can go together.
static boolean	Base.matchBasesGap(Base x, Base y) To know if two Base's can go together (including gap's).
private void	OriginAlgorithmsStefan.recherche_Pseudonoeud(ADN1cible target, Base[] sequencepseudonoeud, ADN1test[] tableauSequences, boolean plusieurs_resultats, int pos_struct, int nb_prediction) PSEUDOKNOTS SEARCH "This method for pseudoknots search : we launch search on each internal sequence of palindromes (form more external to more internal) as selection criteria decrease"
private void	OtherAlgorithmsStefan.recherche_Pseudonoeud(Sequence target, Base[] sequencepseudonoeud, Sequence[] tableauSequences, boolean plusieurs_resultats, int pos_struct, int nb_prediction) PSEUDOKNOTS SEARCH "This method for pseudoknots search : we launch search on each internal sequence of palindromes (form more external to more internal) as selection criteria decrease"
private void	AlgorithmsStefan.recherche_Pseudonoeud(Sequence target, Base[] sequencepseudonoeud, Sequence[] tableauSequences, boolean plusieurs_resultats, int pos_struct, int nb_prediction) PSEUDOKNOTS SEARCH "This method for pseudoknots search : we launch search on each internal sequence of palindromes (form more external to more internal) as selection criteria decrease"

Uses of Base in tests

Fields in tests declared as Base

private Base

TestBase.basetest A local instance of Base.