From 55abfd3edf417a542bb4c8c62ba7e4fddf13deb7 Mon Sep 17 00:00:00 2001 From: Dariusz Murakowski Date: Fri, 20 Mar 2015 14:26:00 -0400 Subject: [PATCH] ctags --- tags | 114 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 114 insertions(+) create mode 100644 tags diff --git a/tags b/tags new file mode 100644 index 0000000..a66f177 --- /dev/null +++ b/tags @@ -0,0 +1,114 @@ +!_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 > AdjacencyList;$/;" t +Coupling hamiltonian.h /^typedef std::vector > Coupling;$/;" 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 > &initPop, const std::vector &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 &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$/;" m class:RunParameters +eMut wf.h /^ std::vector eMut; \/\/ Sites that are mutant in the targeted epitope$/;" m class:RunParameters +eWT wf.h /^ std::vector 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;$/;" m class:Virus +epitopeMut hamiltonian.h /^ std::vector epitopeMut;$/;" m class:EpitopeHamiltonian +epitopeWT hamiltonian.h /^ std::vector epitopeWT;$/;" m class:EpitopeHamiltonian +escape_variant population.cpp /^unsigned int Population::escape_variant(Hamiltonian &H, std::set &mutant) {$/;" f class:Population +escaped hamiltonian.cpp /^bool EpitopeHamiltonian::escaped(const Virus &v) {$/;" f class:EpitopeHamiltonian +escaped hamiltonian.cpp /^bool EpitopeHamiltonian::escaped(const std::set &mutated_sites) const {$/;" f class:EpitopeHamiltonian +escaped hamiltonian.h /^ virtual bool escaped(const Virus &v) { return false; }$/;" f class:Hamiltonian +escaped hamiltonian.h /^ virtual bool escaped(const std::set &mutated_sites) const { return false; }$/;" 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$/;" m class:RunParameters +get_energy hamiltonian.cpp /^double EpitopeHamiltonian::get_energy(const std::set &mutated_sites) const {$/;" f class:EpitopeHamiltonian +get_energy hamiltonian.cpp /^double Hamiltonian::get_energy(const std::set &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 initFrac; \/\/ Initial population fraction$/;" m class:RunParameters +initPop wf.h /^ std::vector > initPop; \/\/ Initial population sequences$/;" 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 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() {$/;" f class:RunParameters +set_epitope hamiltonian.cpp /^void EpitopeHamiltonian::set_epitope(const std::vector &eWT, const std::vector &eMut, double d) {$/;" 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_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 -- 2.7.4