--- /dev/null
+!_TAG_FILE_FORMAT 2 /extended format; --format=1 will not append ;" to lines/
+!_TAG_FILE_SORTED 1 /0=unsorted, 1=sorted, 2=foldcase/
+!_TAG_PROGRAM_AUTHOR Darren Hiebert /dhiebert@users.sourceforge.net/
+!_TAG_PROGRAM_NAME Exuberant Ctags //
+!_TAG_PROGRAM_URL http://ctags.sourceforge.net /official site/
+!_TAG_PROGRAM_VERSION 5.8 //
+AdjacencyList hamiltonian.h /^typedef std::vector<std::vector<int> > AdjacencyList;$/;" t
+Coupling hamiltonian.h /^typedef std::vector<std::vector<double> > Coupling;$/;" t
+Eavg population.h /^ double Eavg; \/\/ Average energy of the sequence population$/;" m class:Population
+EpitopeHamiltonian hamiltonian.cpp /^EpitopeHamiltonian::EpitopeHamiltonian(std::string &FILENAME) {$/;" f class:EpitopeHamiltonian
+EpitopeHamiltonian hamiltonian.h /^class EpitopeHamiltonian : public Hamiltonian {$/;" c
+Graph hamiltonian.h /^ AdjacencyList Graph;$/;" m class:Hamiltonian
+HAMILTONIAN_H hamiltonian.h 2;" d
+Hamiltonian hamiltonian.cpp /^Hamiltonian::Hamiltonian(std::string &FILENAME) {$/;" f class:Hamiltonian
+Hamiltonian hamiltonian.h /^ Hamiltonian() { }$/;" f class:Hamiltonian
+Hamiltonian hamiltonian.h /^class Hamiltonian {$/;" c
+J hamiltonian.h /^ Coupling J;$/;" m class:Hamiltonian
+J12 wf.h /^ double J12;$/;" m class:RunParameters
+L virus.h /^ unsigned int L;$/;" m class:Virus
+N population.h /^ unsigned int N; \/\/ Population size$/;" m class:Population
+POPULATION_H population.h 2;" d
+Population population.cpp /^Population::Population(const Hamiltonian &H, unsigned int N, double mu) {$/;" f class:Population
+Population population.cpp /^Population::Population(const Hamiltonian &H, unsigned int N, double mu, const std::vector<std::set<unsigned int> > &initPop, const std::vector<double> &initFrac) {$/;" f class:Population
+Population population.h /^class Population{$/;" c
+RunParameters wf.h /^ RunParameters() {$/;" f class:RunParameters
+RunParameters wf.h /^class RunParameters {$/;" c
+TwoSiteHamiltonian hamiltonian.cpp /^TwoSiteHamiltonian::TwoSiteHamiltonian(double h1, double h2, double J12) {$/;" f class:TwoSiteHamiltonian
+TwoSiteHamiltonian hamiltonian.cpp /^TwoSiteHamiltonian::TwoSiteHamiltonian(std::string &FILENAME) {$/;" f class:TwoSiteHamiltonian
+TwoSiteHamiltonian hamiltonian.h /^class TwoSiteHamiltonian : public Hamiltonian {$/;" c
+VIRUS_H virus.h 2;" d
+Virus virus.cpp /^Virus::Virus(const Hamiltonian &H, double mu) {$/;" f class:Virus
+Virus virus.cpp /^Virus::Virus(const Hamiltonian &H, double mu, const std::set<unsigned int> &mutated_sites) {$/;" f class:Virus
+Virus virus.h /^class Virus {$/;" c
+WF_H wf.h 2;" d
+add_to_two_site_pop wf.cpp /^void add_to_two_site_pop(RunParameters &r, bool s1, bool s2, double frac) {$/;" f
+bJ hamiltonian.h /^ double bJ; \/\/ couplings "inverse temperature" multiplier$/;" m class:Hamiltonian
+bJ wf.h /^ double bJ; \/\/ Coupling "inverse temperature" multiplier$/;" m class:RunParameters
+bh hamiltonian.h /^ double bh; \/\/ fields "inverse temperature" multiplier$/;" m class:Hamiltonian
+bh wf.h /^ double bh; \/\/ Field "inverse temperature" multiplier$/;" m class:RunParameters
+compute_num_escaped population.cpp /^unsigned int Population::compute_num_escaped(Hamiltonian &H) {$/;" f class:Population
+compute_population_size population.cpp /^unsigned int Population::compute_population_size() {$/;" f class:Population
+couplingsInfile wf.h /^ std::string couplingsInfile;$/;" m class:RunParameters
+directory wf.h /^ std::string directory; \/\/ Path to the directory where the inut file is located$/;" m class:RunParameters
+eMut wf.h /^ std::vector<unsigned int> eMut; \/\/ Sites that are mutant in the targeted epitope$/;" m class:RunParameters
+eWT wf.h /^ std::vector<unsigned int> eWT; \/\/ Sites that are consensus (WT) in the targeted epitope$/;" m class:RunParameters
+eend wf.h /^ int eend; \/\/ Epitope end position$/;" m class:RunParameters
+energy virus.h /^ double energy;$/;" m class:Virus
+epitopeMut hamiltonian.h /^ std::vector<unsigned int> epitopeMut;$/;" m class:EpitopeHamiltonian
+epitopeWT hamiltonian.h /^ std::vector<unsigned int> epitopeWT;$/;" m class:EpitopeHamiltonian
+escape_variant population.cpp /^unsigned int Population::escape_variant(Hamiltonian &H, std::set<unsigned int> &mutant) {$/;" f class:Population
+escaped hamiltonian.cpp /^bool EpitopeHamiltonian::escaped(const Virus &v) {$/;" f class:EpitopeHamiltonian
+escaped hamiltonian.cpp /^bool EpitopeHamiltonian::escaped(const std::set<unsigned int> &mutated_sites) const {$/;" f class:EpitopeHamiltonian
+escaped hamiltonian.h /^ virtual bool escaped(const Virus &v) { return false; }$/;" f class:Hamiltonian
+escaped hamiltonian.h /^ virtual bool escaped(const std::set<unsigned int> &mutated_sites) const { return false; }$/;" f class:Hamiltonian
+escaped population.cpp /^bool Population::escaped(Hamiltonian &H) {$/;" f class:Population
+estart wf.h /^ int estart; \/\/ Epitope start position$/;" m class:RunParameters
+g wf.h /^ unsigned int g; \/\/ Number of generations$/;" m class:RunParameters
+get_energy hamiltonian.cpp /^double EpitopeHamiltonian::get_energy(const std::set<unsigned int> &mutated_sites) const {$/;" f class:EpitopeHamiltonian
+get_energy hamiltonian.cpp /^double Hamiltonian::get_energy(const std::set<unsigned int> &mutated_sites) const {$/;" f class:Hamiltonian
+h1 wf.h /^ double h1;$/;" m class:RunParameters
+h2 wf.h /^ double h2;$/;" m class:RunParameters
+importState wf.cpp /^void importState(RunParameters &r) {$/;" f
+importState wf.h /^ bool importState; \/\/ If true, import state from a state file$/;" m class:RunParameters
+infile wf.h /^ std::string infile; \/\/ Input file from which couplings are to be read$/;" m class:RunParameters
+initFrac wf.h /^ std::vector<double> initFrac; \/\/ Initial population fraction$/;" m class:RunParameters
+initPop wf.h /^ std::vector<std::set<unsigned int> > initPop; \/\/ Initial population sequences$/;" m class:RunParameters
+main wf.cpp /^int main(int argc, char *argv[]) {$/;" f
+mu population.h /^ double mu; \/\/ Mutation rate$/;" m class:Population
+mu virus.h /^ double mu;$/;" m class:Virus
+mu wf.h /^ double mu; \/\/ Mutation rate$/;" m class:RunParameters
+mutate virus.cpp /^void Virus::mutate(const Hamiltonian &H, gsl_rng* r) {$/;" f class:Virus
+mutate_population population.cpp /^void Population::mutate_population(const Hamiltonian &H, gsl_rng* r) {$/;" f class:Population
+mutated_sites virus.h /^ std::set<unsigned int> mutated_sites;$/;" m class:Virus
+n wf.h /^ unsigned int n; \/\/ Population size$/;" m class:RunParameters
+next_generation population.cpp /^void Population::next_generation(const Hamiltonian &H, gsl_rng* r, bool useRelative, bool useVerbose) {$/;" f class:Population
+num_runs wf.h /^ unsigned int num_runs; \/\/ Number of times to run the simulation for gathering overall statistics$/;" m class:RunParameters
+operator < virus.cpp /^bool operator<(const Virus& lhs, const Virus& rhs) {$/;" f
+outfile wf.h /^ std::string outfile; \/\/ Output file (prefix) where data is to be written$/;" m class:RunParameters
+p population.h /^ double p; \/\/ Probability that a sequence has one or more mutations$/;" m class:Population
+penalty hamiltonian.h /^ double penalty;$/;" m class:EpitopeHamiltonian
+penalty wf.h /^ double penalty; \/\/ Energy penalty if sequence contains the targeted epitope$/;" m class:RunParameters
+pop population.h /^ virus_map pop;$/;" m class:Population
+print_parameters virus.cpp /^void Virus::print_parameters() {$/;" f class:Virus
+print_population_size population.cpp /^void Population::print_population_size() {$/;" f class:Population
+run wf.cpp /^void run(RunParameters &r) {$/;" f
+runUntilEscape wf.h /^ bool runUntilEscape; \/\/ If true, run the simulation until the population escapes$/;" m class:RunParameters
+setFiles wf.h /^ void setFiles() {$/;" f class:RunParameters
+set_epitope hamiltonian.cpp /^void EpitopeHamiltonian::set_epitope(const std::vector<unsigned int> &eWT, const std::vector<unsigned int> &eMut, double d) {$/;" f class:EpitopeHamiltonian
+set_temp hamiltonian.h /^ void set_temp(double x) { bh=x; bJ=x; }$/;" f class:Hamiltonian
+set_temp hamiltonian.h /^ void set_temp(double x, double y) { bh=x; bJ=y; }$/;" f class:Hamiltonian
+sim_random_seed wf.cpp /^static unsigned sim_random_seed() {$/;" f file:
+size hamiltonian.h /^ int size;$/;" m class:Hamiltonian
+stateInfile wf.h /^ std::string stateInfile;$/;" m class:RunParameters
+statefile wf.h /^ std::string statefile; \/\/ Input state file which contains initial population fractions$/;" m class:RunParameters
+strtodouble wf.h /^inline double strtodouble(const std::string &s) {$/;" f
+strtoint wf.h /^inline int strtoint(const std::string &s) {$/;" f
+strtouint wf.h /^inline int strtouint(const std::string &s) {$/;" f
+supplementaryOutfile wf.h /^ std::string supplementaryOutfile;$/;" m class:RunParameters
+survival virus.cpp /^double Virus::survival() const {$/;" f class:Virus
+survival virus.cpp /^double Virus::survival(double Eavg) const {$/;" f class:Virus
+tostring wf.h /^inline std::string tostring (const T& t) {$/;" f
+trajectoryOutfile wf.h /^ std::string trajectoryOutfile;$/;" m class:RunParameters
+update_energy virus.cpp /^void Virus::update_energy(const Hamiltonian &H) {$/;" f class:Virus
+usage wf.cpp /^void usage()$/;" f
+useEpitope wf.h /^ bool useEpitope; \/\/ Include selective pressure on an epitope $/;" m class:RunParameters
+useRelative wf.h /^ bool useRelative; \/\/ If true, use relative energy for survival probability$/;" m class:RunParameters
+useTwoSite wf.h /^ bool useTwoSite; \/\/ If true, use two-site two-allele model$/;" m class:RunParameters
+useVerbose wf.h /^ bool useVerbose; \/\/ If true, print extra information while program is running$/;" m class:RunParameters
+virus_map population.h /^typedef std::map<Virus, unsigned int> virus_map;$/;" t
+write_population population.cpp /^void Population::write_population(FILE *output, unsigned int generation) {$/;" f class:Population
+write_population population.cpp /^void Population::write_population(std::string filename) {$/;" f class:Population
+write_two_site_population population.cpp /^void Population::write_two_site_population(FILE *output, const Hamiltonian &H, unsigned int generation) {$/;" f class:Population
+~Hamiltonian hamiltonian.h /^ virtual ~Hamiltonian() { }$/;" f class:Hamiltonian
+~RunParameters wf.h /^ ~RunParameters() {}$/;" f class:RunParameters
projects / VirEvoDyn.git / commitdiff