From: Dariusz Murakowski <murakdar@mit.edu>
Date: Tue, 21 Apr 2015 22:08:18 +0000 (-0400)
Subject: Remove mutation rate "mu" from Virus object; now exclusively in reaction.
X-Git-Url: http://src.murakowski.org/?a=commitdiff_plain;h=cd765f5de35139a68656663f0904c8523345b0c8;p=VirEvoDyn.git

Remove mutation rate "mu" from Virus object; now exclusively in reaction.
---

diff --git a/pop_ss.cpp b/pop_ss.cpp
index 0a3d5b0..5163e27 100644
--- a/pop_ss.cpp
+++ b/pop_ss.cpp
@@ -11,36 +11,21 @@
 
 
 //Constuct a virus object of wildtype
-
-Virus::Virus(const Hamiltonian &H, double mu) {
+Virus::Virus(const Hamiltonian &H) {
     this->mutated_sites.clear();
-    this->mu=mu;
     L=H.size;
     energy=0;
 }
 
-
 //Construct a virus and compute its energy.
-
-Virus::Virus(const Hamiltonian &H, double mu, const std::set<unsigned int> &mutated_sites) {
+Virus::Virus(const Hamiltonian &H, const std::set<unsigned int> &mutated_sites) {
     this->mutated_sites=mutated_sites;
-    this->mu=mu;
     L=H.size;
     update_energy(H);
 }
 
-
-//Print key numerical parameters of the object to the terminal for diagnostics.
-
-void Virus::print_parameters() {
-    std::cout << "mu = " << mu << std::endl;
-    std::cout << "energy = " << energy << std::endl;
-}
-
-
 //Update the energy of the virus object.  Takes as an argument the
 //Hamiltonian that determines the energy
-
 void Virus::update_energy(const Hamiltonian &H) {
     energy=H.get_energy(mutated_sites);
 }
diff --git a/pop_ss.h b/pop_ss.h
index 6bacf5e..26cf280 100644
--- a/pop_ss.h
+++ b/pop_ss.h
@@ -19,14 +19,11 @@ public:
     double energy;
     std::set<unsigned int> mutated_sites;
     
-    Virus(const Hamiltonian &H, double mu);
-    Virus(const Hamiltonian &H, double mu, const std::set<unsigned int> &mutated_sites);
-    
-    void print_parameters();
+    Virus(const Hamiltonian &H);
+    Virus(const Hamiltonian &H, const std::set<unsigned int> &mutated_sites);
     
 //private:
     
-    double mu;
     unsigned int L;
     
     void update_energy(const Hamiltonian &H);
diff --git a/reaction.cpp b/reaction.cpp
index 191fce1..e8a2e25 100644
--- a/reaction.cpp
+++ b/reaction.cpp
@@ -98,8 +98,7 @@ void VirusReaction::fire()
 
     // pick how many sites to mutate in the new virus
     // adapted from WF Virus::mutate()
-    //double mu = iter->first.mu;
-    Virus v(H,this->mu,iter->first.mutated_sites);
+    Virus v(H,iter->first.mutated_sites);
     unsigned int n = gsl_ran_binomial(rnd,mu,H.size);
     MutatedSiteSequence sites_to_mutate;
     while (sites_to_mutate.size() < n) {
diff --git a/ss.cpp b/ss.cpp
index 413e379..c4fecad 100644
--- a/ss.cpp
+++ b/ss.cpp
@@ -75,7 +75,7 @@ void run(RunParameters_SS &r, unsigned seed) {
     if (r.importState) {
         importState(r);      // <infile>.st
         for (size_t i=0; i<r.initPop.size(); i++) {
-            Virus V(H, r.mu, r.initPop[i]);
+            Virus V(H, r.initPop[i]);
             unsigned int N = (unsigned int) r.n * r.initFrac[i];
             s1->pop[V] = N;
             s1->count += N;
@@ -83,7 +83,7 @@ void run(RunParameters_SS &r, unsigned seed) {
     }
     else {
         s1->count = r.n;
-        s1->pop[Virus(H,r.mu)] = s1->count;   // default mu = 6.0e-5
+        s1->pop[Virus(H)] = s1->count;   // default mu = 6.0e-5
     }
 
     Species_parray print_spec;