mutation.h

/*  
 * Authors: Joanna Masel, Alex Lancaster, Kun Xiong
 * Copyright (c) 2018 Arizona Board of Regents on behalf of the University of Arizona
 
 * This file is part of network-evolution-simulator.
 * network-evolution-simulator is free software: you can redistribute it and/or modify
 * it under the terms of the GNU Affero General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 * network-evolution-simulator 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 Affero General Public License for more details.
 * You should have received a copy of the GNU Affero General Public License
 * along with network-evolution-simulator. If not, see <https://www.gnu.org/licenses/>.
 */

#ifndef MUTATION_H
#define MUTATION_H

#include "RngStream.h"
#include "netsim.h"

#define SIMPLE_SUBSTITUTION 1

/*mutation rate*/
extern float DUPLICATION;   
extern float SILENCING;  

/*mutation effect*/
extern float miu_ACT_TO_INT_RATE;
extern float miu_protein_syn_rate;
extern float miu_Kd;


/*Wrapper of mutation functions*/
void mutate(Genotype *, RngStream, Mutation *);

/*Calculate mutation flux for each type of mutation, and pick one based the flux*/
void draw_mutation(Genotype *, char *, RngStream);

/*single nucleotide mutation in cisreg-sequence*/
void mut_substitution(Genotype *, Mutation *, RngStream);

/*delete a gene and its cisreg_sequence*/
void mut_whole_gene_deletion(Genotype *,Mutation *, RngStream);

/*duplicate a gene and its cisreg_sequence*/
void mut_duplication(Genotype *,Mutation *, RngStream);

/*mutate the concensus binding sequence of a TF*/
void mut_binding_sequence(Genotype *,Mutation *, RngStream);

/*mutate r_mRNA_deg, r_protein_deg, r_transl, r_ACT_to_INT, min_N_activator_to_transc*/
void mut_kinetic_constant(Genotype *, Mutation *, RngStream);

/*mutate locus_length*/
void mut_locus_length(Genotype *, Mutation *, RngStream);

/*mutate Kd of a TF*/
void mut_Kd(Genotype *, Mutation *, RngStream);

/*activator to repressor or the reverse*/
void mut_identity(Genotype *, Mutation *, RngStream);

/* Below are functions used to replay mutations*/
void reproduce_mutate(Genotype *, Mutation *);

void reproduce_substitution(Genotype *, Mutation *);

void reproduce_whole_gene_deletion(Genotype *,Mutation *);

void reproduce_gene_duplication(Genotype *,Mutation *);

void reproduce_mut_binding_sequence(Genotype *,Mutation *);

void reproduce_mut_kinetic_constant(Genotype *, Mutation *);

void reproduce_mut_identity(Genotype *, Mutation *);

void reproduce_mut_Kd(Genotype *, Mutation *);

void reproduce_mut_locus_length(Genotype *, Mutation *);
#endif /* MUTATION_H */