cellule.hpp

/*
 * Copyright (C) 2005-2011 Hervé Rouault <rouault@lps.ens.fr>
 *
 * This file is part of Genherite.
 *
 * Genherite is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * Genherite is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with Genherite.  If not, see <http://www.gnu.org/licenses/>.
 */

#ifndef Cellule_H
#define Cellule_H

#include <iostream>

#include "composants.hpp"

extern int mode;

typedef vector < double >vd;
typedef vd::iterator ivd;

class Cellule {
  public:
    double score;
    double score_auxi;
    vector < Protein * >proteins;
    vector < Gene * >genes;
    vector < Promoter * >promoters;
    vector < Arn * >arns;
    vector < Reaction * >reactions;

    Cellule();
    ~Cellule();
    Protein *addprotein(double c = frand2(), double q = frand2());
    Protein *fusion(Protein * prot1, Protein * prot2);
    Reaction *adddimere(Protein * prot1, Protein * prot2, double c =
                        0.2 * frand2(), double q =
                        frand2(), double cdimerisation = frand2());
    Reaction *addreaction(Espece * react1, Espece * react2, Espece * prod1,
                          Espece * prod2, double c = frand2());
    Reaction *addrandreact();
    void phosphorylation(Protein * prot);
    void addphospho();
    Reaction *addrandactiv();
    Gene *addgene();
    Promoter *addpromotion(Gene * gene, Protein * prot, double e =
                           frand2() * 0.2, double t = frand2());
    void rmreaction(Reaction * r);
    bool rmrandprot();
    bool rmrandpromo();
    bool compprot(Protein & prot1, Protein & prot2);
    void evolution();
    bool evolution_modifq();
    bool evolution_ajout();
    void optievolution();
    void calculscore();
    double scorefunction(vector < double >fonction,
                         vector < double >resultatintegr);
    double calculscorebistable();
    double calculscoremultistable();
    double calculscoremultistable2();
    double calculscoreporte();
    double calculscoreoscill();
    double scorebioscill();
    Cellule *copycellule();
    void printgraph(ostream & out);
    void printinternpart(ostream & out);
    void printproperties(ostream & out);
    void printcellule(ostream & out);
    void printcelluleshort(ostream & out);
    void printcelluleintegr(ostream & out);
    void printintegration(ostream & out);
    //void printintegrationmultistable(ostream &out);
    void prtbioscill();
    bool addclivage();
    Cellule *optimisation();
    Protein *existe(Protein * prot);
    Protein *searchcopyprot(Protein * prot);
    void opticalculscore();
    /*double calculscoreporteinter(); */
    int especenum(Espece * pesp);
    string especestring(Espece * pesp);
    int reactionnum(Reaction * react);
    string reactionstring(Reaction * react);
    void printintegr(ostream & stre, double fint);
    void copygene(Gene * gene);
};

typedef vector < Cellule * >vcell;

typedef vcell::iterator ivcell;

void *calcsc_thr(void *cell);

#endif                          /* Cellule_H */