From: Dariusz Murakowski <murakdar@mit.edu>
Date: Wed, 17 Jun 2015 17:29:18 +0000 (-0400)
Subject: Cosmetic changes to comments, format, and spacing.
X-Git-Url: http://src.murakowski.org/?a=commitdiff_plain;h=010fc9798fc67234636b774674e8a63a4b6cfd7f;p=VirEvoDyn.git

Cosmetic changes to comments, format, and spacing.
---

diff --git a/hamiltonian.cpp b/hamiltonian.cpp
index 71378f7..9768ac4 100644
--- a/hamiltonian.cpp
+++ b/hamiltonian.cpp
@@ -9,8 +9,7 @@
 #include "hamiltonian.h"
 
 
-//Constructor for loading couplings from John Barton's Ising Inversion code
-//Code for this function derived from John Barton's code
+// code for loading couplings adapted from John Barton via Tom Butler
 
 Hamiltonian::Hamiltonian(std::string &FILENAME) {
     
@@ -103,8 +102,7 @@ Hamiltonian::Hamiltonian(std::string &FILENAME) {
 }
 
 
-//Constructor for loading couplings from John Barton's Ising Inversion code
-//Code for this function derived from John Barton's code
+// code for loading couplings adapted from John Barton via Tom Butler
 
 EpitopeHamiltonian::EpitopeHamiltonian(std::string &FILENAME) {
     
@@ -201,14 +199,15 @@ double Hamiltonian::get_energy(const std::set<unsigned int> &mutated_sites) cons
     std::set<unsigned int>::iterator iter1;
     std::set<unsigned int>::iterator iter2;
     
-    for (iter1=mutated_sites.begin();iter1!=mutated_sites.end();++iter1) {
+    for (iter1=mutated_sites.begin(); iter1!=mutated_sites.end(); ++iter1) {
     
         efield -= J[*iter1][*iter1];
         
         iter2 = iter1;
         ++iter2;
         
-        for (;iter2!=mutated_sites.end();iter2++) ecoupling -= J[*iter1][*iter2];
+        for (; iter2!=mutated_sites.end(); iter2++)
+            ecoupling -= J[*iter1][*iter2];
          
     }
     
@@ -257,9 +256,9 @@ bool EpitopeHamiltonian::escaped(const Virus &v, const std::vector<unsigned int>
 
 bool EpitopeHamiltonian::escaped(const std::set<unsigned int> &mutated_sites, const std::vector<unsigned int> &eWT, const std::vector<unsigned int> &eMut) const {
 
-    bool escape=false;
+    bool escape = false;
     
-    for (unsigned i=0;i<eWT.size();i++) {
+    for (unsigned i=0; i<eWT.size(); i++) {
     
         if (mutated_sites.count(eWT[i])==1) { escape=true; break; }
         
@@ -267,7 +266,7 @@ bool EpitopeHamiltonian::escaped(const std::set<unsigned int> &mutated_sites, co
     
     if (!escape) {
     
-        for (unsigned i=0;i<eMut.size();i++) {
+        for (unsigned i=0; i<eMut.size(); i++) {
         
             if (mutated_sites.count(eMut[i])==0) { escape=true; break; }
             
@@ -321,14 +320,15 @@ double EpitopeHamiltonian::get_energy(const std::set<unsigned int> &mutated_site
     std::set<unsigned int>::iterator iter1;
     std::set<unsigned int>::iterator iter2;
     
-    for (iter1=mutated_sites.begin();iter1!=mutated_sites.end();++iter1) {
+    for (iter1=mutated_sites.begin(); iter1!=mutated_sites.end(); ++iter1) {
     
         efield -= J[*iter1][*iter1];
         
         iter2 = iter1;
         ++iter2;
         
-        for (;iter2!=mutated_sites.end();iter2++) ecoupling -= J[*iter1][*iter2];
+        for (; iter2!=mutated_sites.end(); iter2++)
+            ecoupling -= J[*iter1][*iter2];
          
     }
     
diff --git a/population.cpp b/population.cpp
index 6ea1166..701ac59 100644
--- a/population.cpp
+++ b/population.cpp
@@ -9,7 +9,7 @@
 #include "population.h"
 
 
-//Constructor that assembles a population of N viruses of wild type
+// constructor that assembles a population of N viruses of wild type
 
 Population::Population(const Hamiltonian &H, unsigned int N, double mu) {
     
@@ -24,11 +24,11 @@ Population::Population(const Hamiltonian &H, unsigned int N, double mu) {
 }
 
 
-//Constructor that assembles a population of N viruses given starting population fractions
+// constructor that assembles a population of N viruses given starting population fractions
 
 Population::Population(const Hamiltonian &H, unsigned int N, double mu, const std::vector<std::set<unsigned int> > &initPop, const std::vector<double> &initFrac) {
     
-    for (unsigned i=0;i<initPop.size();i++) {
+    for (unsigned i=0; i<initPop.size(); i++) {
     
         Virus V(H, mu, initPop[i]);
         pop[V] = (unsigned int) N * initFrac[i];
@@ -54,7 +54,7 @@ Population::Population(const Hamiltonian &H, unsigned int N, double mu, const st
 }
 
 
-//Step population forward a generation.
+// Step population forward a generation.
 
 void Population::next_generation(const Hamiltonian &H, gsl_rng* r, bool useRelative, bool useVerbose) {
     
@@ -66,7 +66,7 @@ void Population::next_generation(const Hamiltonian &H, gsl_rng* r, bool useRelat
     
     virus_map::iterator iter=pop.begin();
         
-    for(;iter!=pop.end();++iter){
+    for(; iter!=pop.end(); ++iter){
     
         if (useRelative) num_survive = gsl_ran_binomial(r,iter->first.survival(Eavg),iter->second);
         else             num_survive = gsl_ran_binomial(r,iter->first.survival(),iter->second);
@@ -76,7 +76,7 @@ void Population::next_generation(const Hamiltonian &H, gsl_rng* r, bool useRelat
         
         new_Eavg += iter->first.energy * num_survive;
         
-        // Report survival
+        // report survival
         
         if (useVerbose) {
             
@@ -93,7 +93,7 @@ void Population::next_generation(const Hamiltonian &H, gsl_rng* r, bool useRelat
     
     if (useVerbose) { std::cout << "checkpoint, " << "total_deaths = " << total_deaths << std::endl; }
     
-    //delete zero population strains
+    // delete zero population strains
     
     iter=pop.begin();
     
@@ -136,7 +136,7 @@ void Population::next_generation(const Hamiltonian &H, gsl_rng* r, bool useRelat
 }
 
 
-// Output population to file
+// Output population to file.
 
 void Population::write_population(std::string filename) {
 
@@ -167,7 +167,7 @@ void Population::write_population(std::string filename) {
 }
 
 
-// Output population to file
+// Output population to file.
 
 void Population::write_population(FILE *output, unsigned int generation) {
 
@@ -204,20 +204,21 @@ void Population::write_population(FILE *output, unsigned int generation) {
 }
 
 
-// Compute the total population size
+// Compute the total population size.
 
 unsigned int Population::compute_population_size() {
 
     unsigned int i=0;
   
-    for (virus_map::iterator iter=pop.begin(); iter!=pop.end(); ++iter) i+=iter->second;
+    for (virus_map::iterator iter=pop.begin(); iter!=pop.end(); ++iter)
+        i+=iter->second;
     
     return i;
     
 }
 
 
-// Print population size to standard out
+// Print population size to standard output.
 
 void Population::print_population_size() {
 
@@ -226,7 +227,7 @@ void Population::print_population_size() {
 }
 
 
-//Mutate every virus in the population
+// Mutate every virus in the population.
 
 void Population::mutate_population(const Hamiltonian &H, gsl_rng* r) {
     
@@ -256,20 +257,23 @@ void Population::mutate_population(const Hamiltonian &H, gsl_rng* r) {
 }
 
 
-// Compute the number of escaped viruses in the population
+// Compute the number of escaped viruses in the population.
 
 unsigned int Population::compute_num_escaped(Hamiltonian &H) {
 
     unsigned int i=0;
   
-    for (virus_map::iterator iter=pop.begin(); iter!=pop.end(); ++iter) { if (H.escaped(iter->first)) i+=iter->second; }
+    for (virus_map::iterator iter=pop.begin(); iter!=pop.end(); ++iter) {
+        if (H.escaped(iter->first))
+            i += iter->second;
+    }
     
     return i;
     
 }
 
 
-// Check whether most of the population has escaped from immune pressure
+// Check whether most of the population has escaped from immune pressure.
 
 bool Population::escaped(Hamiltonian &H) {
 
@@ -279,7 +283,7 @@ bool Population::escaped(Hamiltonian &H) {
 }
 
 
-// Compute the number of escaped viruses in the population
+// Compute the number of escaped viruses in the population.
 
 unsigned int Population::escape_variant(Hamiltonian &H, std::set<unsigned int> &mutant) {
 
@@ -289,8 +293,8 @@ unsigned int Population::escape_variant(Hamiltonian &H, std::set<unsigned int> &
     
         if (H.escaped(iter->first) && (iter->second)>i) {
         
-            i=iter->second;
-            mutant=iter->first.mutated_sites;
+            i = iter->second;
+            mutant = iter->first.mutated_sites;
             
         }
         
@@ -302,20 +306,23 @@ unsigned int Population::escape_variant(Hamiltonian &H, std::set<unsigned int> &
 
 
 
-// Compute the number of escaped viruses in the population
+// Compute the number of escaped viruses in the population.
 
 unsigned int Population::compute_num_escaped_all(Hamiltonian &H) {
 
     unsigned int i=0;
   
-    for (virus_map::iterator iter=pop.begin(); iter!=pop.end(); ++iter) { if (H.escaped_all(iter->first)) i+=iter->second; }
+    for (virus_map::iterator iter=pop.begin(); iter!=pop.end(); ++iter) {
+        if (H.escaped_all(iter->first))
+            i+=iter->second;
+    }
     
     return i;
     
 }
 
 
-// Check whether most of the population has escaped from *all* immune pressure
+// Check whether most of the population has escaped from *all* immune pressure.
 
 bool Population::escaped_all(Hamiltonian &H) {
 
@@ -325,7 +332,7 @@ bool Population::escaped_all(Hamiltonian &H) {
 }
 
 
-// Compute the number of escaped viruses in the population
+// Compute the number of escaped viruses in the population.
 
 unsigned int Population::escape_variant_all(Hamiltonian &H, std::set<unsigned int> &mutant) {
 
diff --git a/population.h b/population.h
index bf9c70a..b86a36a 100644
--- a/population.h
+++ b/population.h
@@ -12,7 +12,7 @@
 typedef std::map<Virus, unsigned int> virus_map;
 
 
-class Population{
+class Population {
     
 public:
     
diff --git a/virus.cpp b/virus.cpp
index 4dba473..c5124a9 100644
--- a/virus.cpp
+++ b/virus.cpp
@@ -8,31 +8,31 @@
 #include "virus.h"
 
 
-//Constuct a virus object of wildtype
+// Constuct a virus object of wildtype.
 
 Virus::Virus(const Hamiltonian &H, double mu) {
     
     this->mutated_sites.clear();
-    this->mu=mu;
-    L=H.size;
-    energy=0;
+    this->mu = mu;
+    L = H.size;
+    energy = 0;
 
 }
 
 
-//Construct a virus and compute its energy.
+// Construct a virus and compute its energy.
 
 Virus::Virus(const Hamiltonian &H, double mu, const std::set<unsigned int> &mutated_sites) {
     
     this->mutated_sites=mutated_sites;
-    this->mu=mu;
-    L=H.size;
+    this->mu = mu;
+    L = H.size;
     update_energy(H);
 
 }
 
 
-//Print key numerical parameters of the object to the terminal for diagnostics.
+// Print key numerical parameters of the object to the terminal for diagnostics.
 
 void Virus::print_parameters() {
     
@@ -42,16 +42,17 @@ void Virus::print_parameters() {
 }
 
 
-//Mutate the entire virus.  Takes a Hamiltonian object and a pointer
-//to an instance of a gsl_rng random number generator
+// Mutate the entire virus.  Takes a Hamiltonian object and a pointer
+// to an instance of a gsl_rng random number generator
 
 void Virus::mutate(const Hamiltonian &H, gsl_rng* r) {
     
-    unsigned int n=gsl_ran_binomial(r,mu,L);
+    unsigned int n = gsl_ran_binomial(r,mu,L);
     
-    while (n<1) n=gsl_ran_binomial(r,mu,L);
+    while (n<1)
+        n = gsl_ran_binomial(r,mu,L);
     
-    for (unsigned i=0;i<n;i++) {
+    for (unsigned i=0; i<n; i++) {
     
         unsigned int x=gsl_rng_uniform_int(r,H.size);
         
@@ -65,7 +66,7 @@ void Virus::mutate(const Hamiltonian &H, gsl_rng* r) {
 }
 
 
-//Computes the odds of survival
+// Computes the odds of survival.
 
 double Virus::survival() const {
 
@@ -75,7 +76,7 @@ double Virus::survival() const {
 }
 
 
-//Computes the odds of survival
+// Computes the odds of survival.
 
 double Virus::survival(double Eavg) const {
 
@@ -85,16 +86,18 @@ double Virus::survival(double Eavg) const {
 }
 
 
-//Update the energy of the virus object.  Takes as an argument the
-//Hamiltonian that determines the energy
+// 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);
+    energy = H.get_energy(mutated_sites);
     
 }
 
 
+// required by virus_map (std::map<Virus, unsigned int>) in Population
+
 bool operator<(const Virus& lhs, const Virus& rhs) {
     
     return lhs.mutated_sites < rhs.mutated_sites;
diff --git a/wf.cpp b/wf.cpp
index bd72472..567bd56 100644
--- a/wf.cpp
+++ b/wf.cpp
@@ -34,7 +34,7 @@ static unsigned sim_random_seed() {
 }
 
 
-// Run the program
+// Run the program.
 
 void run(RunParameters &r, unsigned seed) {
     
@@ -57,7 +57,7 @@ void run(RunParameters &r, unsigned seed) {
     fflush(stdout);
     
 
-    // Run (w/ targeted epitope)
+    // Run (with targeted epitope)
     
     if (r.useEpitope) {
     
@@ -144,7 +144,7 @@ void run(RunParameters &r, unsigned seed) {
     
     else {
 
-        for (unsigned int n=0;n<r.num_runs;n++) {
+        for (unsigned int n=0; n<r.num_runs; n++) {
         
             Hamiltonian H(r.couplingsInfile);
             H.set_temp(r.bh, r.bJ);
@@ -167,13 +167,14 @@ void run(RunParameters &r, unsigned seed) {
 
     gsl_rng_free(rnd);  //Free up memory from random number generator
 
-    fclose(popout);     // close file handles
+    // close file handles
+    fclose(popout);
     fclose(supout);
 
 }
 
 
-// Import initial state from a state file
+// Import initial state from a state file.
 
 void importState(RunParameters &r) {