From: Dariusz Murakowski Date: Fri, 26 Jun 2015 20:20:04 +0000 (-0400) Subject: (minor) Don't build old Monte Carlo code. Print to stderr and throw exception. ctags... X-Git-Url: http://src.murakowski.org/?a=commitdiff_plain;h=059ef64ecf1aafddd375f249b2db7fd6c3deae32;p=VirEvoDyn.git (minor) Don't build old Monte Carlo code. Print to stderr and throw exception. ctags -a -R. --- diff --git a/Makefile b/Makefile index 18565ba..e352d7b 100644 --- a/Makefile +++ b/Makefile @@ -2,8 +2,8 @@ SRCS_WF = wf.cpp hamiltonian.cpp population.cpp virus.cpp EXECNAME_WF = wf -SRCS_MC = mc.cpp hamiltonian.cpp population.cpp virus.cpp -EXECNAME_MC = mc +#SRCS_MC = mc.cpp hamiltonian.cpp population.cpp virus.cpp +#EXECNAME_MC = mc SRCS_SS = ss.cpp ham_ss.cpp pop_ss.cpp reaction.cpp seqTools.cpp EXECNAME_SS = ss diff --git a/pop_ss.cpp b/pop_ss.cpp index 6ef8419..bebd37c 100644 --- a/pop_ss.cpp +++ b/pop_ss.cpp @@ -111,8 +111,10 @@ NTVirus::NTVirus(const PottsHamiltonian &H, const std::string &NT) , L_aa(this->L_nt/3) { //assert(this->L_aa == H.size); - if (this->L_aa != H.size) + if (this->L_aa != H.size) { + std::cerr << "ERROR in NTVirus constructor: mismatch between Hamiltonian size and sequence length." << std::endl; throw "mismatch between Hamiltonian size and sequence length."; + } config.resize(L_aa); H.coarse_grain(aa_seq,config); update_energy(H); diff --git a/tags b/tags index a1159c4..b9fc258 100644 --- a/tags +++ b/tags @@ -13,6 +13,8 @@ 021l session.vim /^normal! 021l$/;" m session.vim /^noremap j$/;" m NetrwBrowseX session.vim /^nnoremap NetrwBrowseX :call netrw#NetrwBrowseX(expand(""),0)$/;" m +AAKilling reaction.h /^enum class RxnType {Elementary, Virus, VirusDeath, Killing, CTLActivation, NTVirus, NTVirusDeath, AAKilling, CTLaaActivation, EscapeCounting, EscapeAACounting};$/;" m class:RxnType +AAKilling reaction.h /^enum class RxnType {Elementary, Virus, VirusDeath, Killing, CTLActivation, NTVirus, NTVirusDeath, AAKilling, CTLaaActivation};$/;" m class:RxnType AAKillingReaction reaction.h /^ AAKillingReaction() : Reaction() {}$/;" f class:AAKillingReaction AAKillingReaction reaction.h /^ AAKillingReaction(double k) : Reaction(k) {}$/;" f class:AAKillingReaction AAKillingReaction reaction.h /^class AAKillingReaction : public Reaction {$/;" c @@ -25,6 +27,8 @@ BuildIntersection main.cpp /^BuildIntersection(std::vector& v0,std::vector< BuildIntersection1 main.cpp /^BuildIntersection1(std::vector& v0,std::vector& v1)$/;" f CFLAGS Makefile /^CFLAGS = $(DBGFLAG) -Wall -Wextra -pedantic -Wno-unused-parameter$/;" m CFLAGS Makefile /^CFLAGS = -std=c++0x $(DBGFLAG) -Wall -Wextra -pedantic -Wno-unused-parameter$/;" m +CTLActivation reaction.h /^enum class RxnType {Elementary, Virus, VirusDeath, Killing, CTLActivation, NTVirus, NTVirusDeath, AAKilling, CTLaaActivation, EscapeCounting, EscapeAACounting};$/;" m class:RxnType +CTLActivation reaction.h /^enum class RxnType {Elementary, Virus, VirusDeath, Killing, CTLActivation, NTVirus, NTVirusDeath, AAKilling, CTLaaActivation};$/;" m class:RxnType CTLActivationReaction reaction.h /^ CTLActivationReaction() : Reaction() {}$/;" f class:CTLActivationReaction CTLActivationReaction reaction.h /^ CTLActivationReaction(double k) : Reaction(k) {}$/;" f class:CTLActivationReaction CTLActivationReaction reaction.h /^class CTLActivationReaction : public Reaction {$/;" c @@ -33,6 +37,7 @@ CTLSpecies pop_ss.h /^ CTLSpecies(long c) : Species(c), num_ep(0) {}$/;" f cl CTLSpecies pop_ss.h /^ CTLSpecies(std::string x) : Species(x), num_ep(0) {}$/;" f class:CTLSpecies CTLSpecies pop_ss.h /^ CTLSpecies(std::string x, long c) : Species(x,c), num_ep(0) {}$/;" f class:CTLSpecies CTLSpecies pop_ss.h /^class CTLSpecies : public Species {$/;" c +CTLaaActivation reaction.h /^enum class RxnType {Elementary, Virus, VirusDeath, Killing, CTLActivation, NTVirus, NTVirusDeath, AAKilling, CTLaaActivation, EscapeCounting, EscapeAACounting};$/;" m class:RxnType CTLaaActivationReaction reaction.h /^ CTLaaActivationReaction() : Reaction() {}$/;" f class:CTLaaActivationReaction CTLaaActivationReaction reaction.h /^ CTLaaActivationReaction(double k) : Reaction(k) {}$/;" f class:CTLaaActivationReaction CTLaaActivationReaction reaction.h /^class CTLaaActivationReaction : public Reaction {$/;" c @@ -55,6 +60,8 @@ EXECNAME_SS Makefile /^EXECNAME_SS = ss$/;" m EXECNAME_WF Makefile /^EXECNAME_WF = wf$/;" m Eavg pop_ss.h /^ double Eavg; \/\/ Average energy of the sequence population$/;" m class:Population Eavg population.h /^ double Eavg; \/\/ Average energy of the sequence population$/;" m class:Population +Elementary reaction.h /^enum class RxnType {Elementary, Virus, VirusDeath, Killing, CTLActivation, NTVirus, NTVirusDeath, AAKilling, CTLaaActivation, EscapeCounting, EscapeAACounting};$/;" m class:RxnType +Elementary reaction.h /^enum class RxnType {Elementary, Virus, VirusDeath, Killing, CTLActivation, NTVirus, NTVirusDeath, AAKilling, CTLaaActivation};$/;" m class:RxnType ElementaryReaction reaction.h /^ ElementaryReaction() : Reaction() {}$/;" f class:ElementaryReaction ElementaryReaction reaction.h /^ ElementaryReaction(double k) : Reaction(k) {}$/;" f class:ElementaryReaction ElementaryReaction reaction.h /^class ElementaryReaction : public Reaction {$/;" c @@ -62,6 +69,13 @@ EpitopeHamiltonian hamiltonian.cpp /^EpitopeHamiltonian::EpitopeHamiltonian(std: EpitopeHamiltonian hamiltonian.h /^class EpitopeHamiltonian : public Hamiltonian {$/;" c EpitopeRecognizer pop_ss.h /^class EpitopeRecognizer {$/;" c Eq_ sorted_vector.h /^ bool Eq_(const Myt_& x) const $/;" f class:codeproject::sorted_vector +EscapeAACountingReaction reaction.h /^ EscapeAACountingReaction() : Reaction() {}$/;" f class:EscapeAACountingReaction +EscapeAACountingReaction reaction.h /^ EscapeAACountingReaction(double k) : Reaction(k) {}$/;" f class:EscapeAACountingReaction +EscapeAACountingReaction reaction.h /^class EscapeAACountingReaction : public Reaction {$/;" c +EscapeCounting reaction.h /^enum class RxnType {Elementary, Virus, VirusDeath, Killing, CTLActivation, NTVirus, NTVirusDeath, AAKilling, CTLaaActivation, EscapeCounting, EscapeAACounting};$/;" m class:RxnType +EscapeCountingReaction reaction.h /^ EscapeCountingReaction() : Reaction() {}$/;" f class:EscapeCountingReaction +EscapeCountingReaction reaction.h /^ EscapeCountingReaction(double k) : Reaction(k) {}$/;" f class:EscapeCountingReaction +EscapeCountingReaction reaction.h /^class EscapeCountingReaction : public Reaction {$/;" c ExecTests main.cpp /^void ExecTests(std::vector& v)$/;" f Graph ham_ss.h /^ AdjacencyList Graph;$/;" m class:Hamiltonian Graph hamiltonian.h /^ AdjacencyList Graph;$/;" m class:Hamiltonian @@ -91,6 +105,8 @@ Key snip.h /^typedef std::vector Key;$/;" t KeyCompare_Geq_ sorted_vector.h /^ bool KeyCompare_Geq_(const K& ty0,const K& ty1)$/;" f class:codeproject::sorted_vector KeyCompare_Gt_ sorted_vector.h /^ bool KeyCompare_Gt_(const K& ty0,const K& ty1)$/;" f class:codeproject::sorted_vector KeyCompare_Leq_ sorted_vector.h /^ bool KeyCompare_Leq_(const K& ty0,const K& ty1)$/;" f class:codeproject::sorted_vector +Killing reaction.h /^enum class RxnType {Elementary, Virus, VirusDeath, Killing, CTLActivation, NTVirus, NTVirusDeath, AAKilling, CTLaaActivation, EscapeCounting, EscapeAACounting};$/;" m class:RxnType +Killing reaction.h /^enum class RxnType {Elementary, Virus, VirusDeath, Killing, CTLActivation, NTVirus, NTVirusDeath, AAKilling, CTLaaActivation};$/;" m class:RxnType KillingReaction reaction.h /^ KillingReaction() : Reaction() {}$/;" f class:KillingReaction KillingReaction reaction.h /^ KillingReaction(double k) : Reaction(k) {}$/;" f class:KillingReaction KillingReaction reaction.h /^class KillingReaction : public Reaction {$/;" c @@ -112,9 +128,16 @@ MutatedSiteSequence reaction.h /^typedef std::set MutatedSiteSeque Myt_ sorted_vector.h /^ typedef sorted_vector Myt_;$/;" t class:codeproject::sorted_vector N pop_ss.h /^ unsigned int N; \/\/ Population size$/;" m class:Population N population.h /^ unsigned int N; \/\/ Population size$/;" m class:Population +N population.h /^ unsigned int N; \/\/ Population size$/;" m class:Population +NTVirus pop_ss.cpp /^NTVirus::NTVirus()$/;" f class:NTVirus +NTVirus pop_ss.cpp /^NTVirus::NTVirus(const NTVirus &v)$/;" f class:NTVirus NTVirus pop_ss.cpp /^NTVirus::NTVirus(const PottsHamiltonian &H, const std::string &NT)$/;" f class:NTVirus NTVirus pop_ss.cpp /^NTVirus::NTVirus(const std::string &NT)$/;" f class:NTVirus NTVirus pop_ss.h /^class NTVirus {$/;" c +NTVirus reaction.h /^enum class RxnType {Elementary, Virus, VirusDeath, Killing, CTLActivation, NTVirus, NTVirusDeath, AAKilling, CTLaaActivation, EscapeCounting, EscapeAACounting};$/;" m class:RxnType +NTVirus reaction.h /^enum class RxnType {Elementary, Virus, VirusDeath, Killing, CTLActivation, NTVirus, NTVirusDeath, AAKilling, CTLaaActivation};$/;" m class:RxnType +NTVirusDeath reaction.h /^enum class RxnType {Elementary, Virus, VirusDeath, Killing, CTLActivation, NTVirus, NTVirusDeath, AAKilling, CTLaaActivation, EscapeCounting, EscapeAACounting};$/;" m class:RxnType +NTVirusDeath reaction.h /^enum class RxnType {Elementary, Virus, VirusDeath, Killing, CTLActivation, NTVirus, NTVirusDeath, AAKilling, CTLaaActivation};$/;" m class:RxnType NTVirusDeathReaction reaction.h /^ NTVirusDeathReaction() : Reaction() {}$/;" f class:NTVirusDeathReaction NTVirusDeathReaction reaction.h /^ NTVirusDeathReaction(double k) : Reaction(k) {}$/;" f class:NTVirusDeathReaction NTVirusDeathReaction reaction.h /^class NTVirusDeathReaction : public Reaction {$/;" c @@ -144,6 +167,7 @@ Population pop_ss.cpp /^Population::Population(const Hamiltonian &H, unsigned in Population pop_ss.h /^class Population{$/;" c Population population.cpp /^Population::Population(const Hamiltonian &H, unsigned int N, double mu) {$/;" 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 Population population.h /^class Population{$/;" c PottsHamiltonian ham_ss.cpp /^PottsHamiltonian::PottsHamiltonian(const std::string &couplingsFile, const std::string &seq2stateFile) : bh(1.0), bJ(1.0)$/;" f class:PottsHamiltonian PottsHamiltonian ham_ss.h /^ PottsHamiltonian() : bh(1.0), bJ(1.0) { }$/;" f class:PottsHamiltonian @@ -154,6 +178,7 @@ RC_fun reaction.cpp /^double RC_fun(double E)$/;" f REACTION_H reaction.h 2;" d Reaction reaction.h /^ Reaction() {}$/;" f class:Reaction Reaction reaction.h /^ Reaction(double k) : rate_constant(k) {}$/;" f class:Reaction +Reaction reaction.h /^ Reaction(double k) : rate_constant(k), affects() {}$/;" f class:Reaction Reaction reaction.h /^class Reaction {$/;" c RunParameters wf.h /^ RunParameters() {$/;" f class:RunParameters RunParameters wf.h /^class RunParameters {$/;" c @@ -161,6 +186,8 @@ RunParameters_MC mc.h /^ RunParameters_MC() {$/;" f class:RunParameters_MC RunParameters_MC mc.h /^class RunParameters_MC {$/;" c RunParameters_SS ss.h /^ RunParameters_SS() {$/;" f class:RunParameters_SS RunParameters_SS ss.h /^class RunParameters_SS {$/;" c +RxnType reaction.h /^enum class RxnType {Elementary, Virus, VirusDeath, Killing, CTLActivation, NTVirus, NTVirusDeath, AAKilling, CTLaaActivation, EscapeCounting, EscapeAACounting};$/;" c +RxnType reaction.h /^enum class RxnType {Elementary, Virus, VirusDeath, Killing, CTLActivation, NTVirus, NTVirusDeath, AAKilling, CTLaaActivation};$/;" c Rxn_parray ss.h /^typedef std::vector Rxn_parray;$/;" t SEQTOOLS_H seqTools.h 2;" d SGITest main.cpp /^int SGITest()$/;" f @@ -205,21 +232,31 @@ TwoSiteHamiltonian hamiltonian.h /^class TwoSiteHamiltonian : public Hamiltonian Unique_ sorted_vector.h /^ iterator Unique_()$/;" f class:codeproject::sorted_vector V reaction.h /^ NTVirusSpecies* V;$/;" m class:AAKillingReaction V reaction.h /^ NTVirusSpecies* V;$/;" m class:CTLaaActivationReaction +V reaction.h /^ NTVirusSpecies* V;$/;" m class:EscapeAACountingReaction V reaction.h /^ NTVirusSpecies* V;$/;" m class:NTVirusDeathReaction V reaction.h /^ NTVirusSpecies* V;$/;" m class:NTVirusReaction V reaction.h /^ VirusSpecies* V;$/;" m class:CTLActivationReaction +V reaction.h /^ VirusSpecies* V;$/;" m class:EscapeCountingReaction V reaction.h /^ VirusSpecies* V;$/;" m class:KillingReaction V reaction.h /^ VirusSpecies* V;$/;" m class:VirusDeathReaction V reaction.h /^ VirusSpecies* V;$/;" m class:VirusReaction VERSION_SORTED_VECTOR_ sorted_vector.h 25;" d VIRUS_H virus.h 2;" d Vector snip.h /^typedef std::vector > Vector;$/;" t +Virus pop_ss.cpp /^Virus::Virus()$/;" f class:Virus Virus pop_ss.cpp /^Virus::Virus(const Hamiltonian &H) {$/;" f class:Virus +Virus pop_ss.cpp /^Virus::Virus(const Hamiltonian &H)$/;" f class:Virus Virus pop_ss.cpp /^Virus::Virus(const Hamiltonian &H, const std::set &mutated_sites) {$/;" f class:Virus +Virus pop_ss.cpp /^Virus::Virus(const Hamiltonian &H, const std::set &mutated_sites_in)$/;" f class:Virus +Virus pop_ss.cpp /^Virus::Virus(const Virus &v)$/;" f class:Virus Virus pop_ss.h /^class Virus {$/;" c +Virus reaction.h /^enum class RxnType {Elementary, Virus, VirusDeath, Killing, CTLActivation, NTVirus, NTVirusDeath, AAKilling, CTLaaActivation, EscapeCounting, EscapeAACounting};$/;" m class:RxnType +Virus reaction.h /^enum class RxnType {Elementary, Virus, VirusDeath, Killing, CTLActivation, NTVirus, NTVirusDeath, AAKilling, CTLaaActivation};$/;" m class:RxnType Virus virus.cpp /^Virus::Virus(const Hamiltonian &H, double mu) {$/;" 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 +VirusDeath reaction.h /^enum class RxnType {Elementary, Virus, VirusDeath, Killing, CTLActivation, NTVirus, NTVirusDeath, AAKilling, CTLaaActivation, EscapeCounting, EscapeAACounting};$/;" m class:RxnType +VirusDeath reaction.h /^enum class RxnType {Elementary, Virus, VirusDeath, Killing, CTLActivation, NTVirus, NTVirusDeath, AAKilling, CTLaaActivation};$/;" m class:RxnType VirusDeathReaction reaction.h /^ VirusDeathReaction() : Reaction() {}$/;" f class:VirusDeathReaction VirusDeathReaction reaction.h /^ VirusDeathReaction(double k) : Reaction(k) {}$/;" f class:VirusDeathReaction VirusDeathReaction reaction.h /^class VirusDeathReaction : public Reaction {$/;" c @@ -247,6 +284,7 @@ aaseq2str pop_ss.cpp /^std::string aaseq2str(const std::vector &aa_seq)$/;" add_to_two_site_pop mc.cpp /^void add_to_two_site_pop(RunParameters_MC &r, bool s1, bool s2, double frac) {$/;" f add_to_two_site_pop ss.cpp /^void add_to_two_site_pop(RunParameters_SS &r, bool s1, bool s2, double frac) {$/;" f add_to_two_site_pop wf.cpp /^void add_to_two_site_pop(RunParameters &r, bool s1, bool s2, double frac) {$/;" f +affects reaction.h /^ std::vector affects; \/\/ reactions whose propensity must be updated when this one fires$/;" m class:Reaction affinity pop_ss.h /^ std::vector affinity;$/;" m class:CTLSpecies affinity pop_ss.h /^ std::vector affinity;$/;" m class:CTLaaSpecies ality sorted_vector_doc.html /^functionality (random access) in one container.<\/p>$/;" f @@ -372,6 +410,8 @@ directory mc.h /^ std::string directory; \/\/ Path to the directory wher directory ss.h /^ std::string directory; \/\/ Path to the directory where the inut file is located$/;" m class:RunParameters_SS directory wf.h /^ std::string directory; \/\/ Path to the directory where the inut file is located$/;" m class:RunParameters do_flip_or_not mc.cpp /^bool do_flip_or_not(const EpitopeHamiltonian &H, MutatedSiteSequence &seq, gsl_rng *r, unsigned &site)$/;" f +does_affect ss.cpp /^bool does_affect(Reaction *newrxn, Reaction *rxn)$/;" f +does_species_appear_in_reactants ss.cpp /^bool does_species_appear_in_reactants(Species *s, Reaction *rxn)$/;" f eMut mc.h /^ std::vector > eMut; \/\/ Sites that are mutant in the targeted epitope$/;" m class:RunParameters_MC eMut ss.h /^ std::vector > eMut; \/\/ Sites that are mutant in the targeted epitope$/;" m class:RunParameters_SS eMut wf.h /^ std::vector > eMut; \/\/ Sites that are mutant in the targeted epitope$/;" m class:RunParameters @@ -411,6 +451,8 @@ equal_range sorted_vector.h /^ Pairii_ equal_range(const K& k)$/;" f class:codep erase sorted_vector.h /^ iterator erase(iterator first, iterator beyond)$/;" f class:codeproject::sorted_vector erase sorted_vector.h /^ iterator erase(iterator p) {return vec_.erase(p);}$/;" f class:codeproject::sorted_vector erase sorted_vector.h /^ size_type erase(const K& key) $/;" f class:codeproject::sorted_vector +esc reaction.h /^ CTLSpecies* esc;$/;" m class:EscapeCountingReaction +esc reaction.h /^ CTLaaSpecies* esc;$/;" m class:EscapeAACountingReaction escape_variant pop_ss.cpp /^unsigned int Population::escape_variant(Hamiltonian &H, std::set &mutant) {$/;" f class:Population escape_variant population.cpp /^unsigned int Population::escape_variant(Hamiltonian &H, std::set &mutant) {$/;" f class:Population escape_variant_all pop_ss.cpp /^unsigned int Population::escape_variant_all(Hamiltonian &H, std::set &mutant) {$/;" f class:Population @@ -442,11 +484,14 @@ fire reaction.cpp /^void AAKillingReaction::fire()$/;" f class:AAKillingReaction fire reaction.cpp /^void CTLActivationReaction::fire()$/;" f class:CTLActivationReaction fire reaction.cpp /^void CTLaaActivationReaction::fire()$/;" f class:CTLaaActivationReaction fire reaction.cpp /^void ElementaryReaction::fire()$/;" f class:ElementaryReaction +fire reaction.cpp /^void EscapeAACountingReaction::fire()$/;" f class:EscapeAACountingReaction +fire reaction.cpp /^void EscapeCountingReaction::fire()$/;" f class:EscapeCountingReaction fire reaction.cpp /^void KillingReaction::fire()$/;" f class:KillingReaction fire reaction.cpp /^void NTVirusDeathReaction::fire()$/;" f class:NTVirusDeathReaction fire reaction.cpp /^void NTVirusReaction::fire()$/;" f class:NTVirusReaction fire reaction.cpp /^void VirusDeathReaction::fire()$/;" f class:VirusDeathReaction fire reaction.cpp /^void VirusReaction::fire()$/;" f class:VirusReaction +flushOften ss.h /^ bool flushOften; \/\/ flush output each line?$/;" m class:RunParameters_SS front sorted_vector.h /^ const_reference front() const {return vec_.front();}$/;" f class:codeproject::sorted_vector front sorted_vector.h /^ reference front() {return vec_.front();}$/;" f class:codeproject::sorted_vector g mc.h /^ unsigned int g; \/\/ Number of generations$/;" m class:RunParameters_MC @@ -465,6 +510,7 @@ get_energy ham_ss.cpp /^double PottsHamiltonian::get_energy(const PottsState &co get_energy hamiltonian.cpp /^double EpitopeHamiltonian::get_energy(const std::set &mutated_sites) const {$/;" f class:EpitopeHamiltonian 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 +get_rxn_type reaction.h /^inline RxnType get_rxn_type(const Reaction* const rxn)$/;" f gh session.vim /^map gh :exe 'normal '.(virtcol('.')\/2).'|'$/;" m gl session.vim /^map gl :exe 'normal '.(virtcol('.') + (virtcol('$')-virtcol('.'))\/2).'|'$/;" m glob test/make_tests.py /^import glob$/;" i @@ -515,6 +561,7 @@ insert sorted_vector.h /^ void insert(It first, It beyond)$/;" f class:codeproje insert sorted_vector.h /^ Pairib_ insert(const value_type& x)$/;" f class:codeproject::sorted_vector insert sorted_vector.h /^ iterator insert(iterator it, const value_type& x)\/\/it is the hint$/;" f class:codeproject::sorted_vector insert sorted_vector.h /^ void insert(const_iterator first, const_iterator beyond)$/;" f class:codeproject::sorted_vector +insertReferenceStates ham_ss.cpp /^unsigned PottsHamiltonian::insertReferenceStates()$/;" f class:PottsHamiltonian int2aa seqTools.cpp /^const int2str_map int2aa = {$/;" v int2str_map seqTools.h /^typedef std::unordered_map int2str_map;$/;" t is_unique main.cpp /^bool is_unique(It beg,It beyond,Pred pred)$/;" f @@ -523,6 +570,10 @@ key_comp sorted_vector.h /^ key_compare key_comp() const {return key_compare_; key_compare sorted_vector.h /^ typedef Pr key_compare;$/;" t class:codeproject::sorted_vector key_compare_ sorted_vector.h /^ key_compare key_compare_;$/;" m class:codeproject::sorted_vector key_type sorted_vector.h /^ typedef K key_type;$/;" t class:codeproject::sorted_vector +lastDeleted pop_ss.h /^ NTVirus lastDeleted;$/;" m class:NTVirusSpecies +lastDeleted pop_ss.h /^ Virus lastDeleted;$/;" m class:VirusSpecies +lastModified pop_ss.h /^ NTVirus_map::iterator lastModified;$/;" m class:NTVirusSpecies +lastModified pop_ss.h /^ virus_map::iterator lastModified;$/;" m class:VirusSpecies len pop_ss.h /^ size_t len;$/;" m class:AARecognizer lower_bound sorted_vector.h /^ const_iterator lower_bound(const K& k) const$/;" f class:codeproject::sorted_vector lower_bound sorted_vector.h /^ iterator lower_bound(const K& k)$/;" f class:codeproject::sorted_vector @@ -556,6 +607,7 @@ n mc.h /^ unsigned int n; \/\/ Population size$/;" m class:RunPar n ss.h /^ unsigned int n; \/\/ Population size$/;" m class:RunParameters_SS n wf.h /^ unsigned int n; \/\/ Population size$/;" m class:RunParameters name pop_ss.h /^ std::string name;$/;" m class:Species +name reaction.h /^ std::string name;$/;" m class:Reaction next_generation pop_ss.cpp /^void Population::next_generation(const Hamiltonian &H, gsl_rng* r, bool useRelative, bool useVerbose) {$/;" f class:Population next_generation population.cpp /^void Population::next_generation(const Hamiltonian &H, gsl_rng* r, bool useRelative, bool useVerbose) {$/;" f class:Population notEpitopeAllSites hamiltonian.h /^ MutatedSiteSequence notEpitopeAllSites; \/\/ all sites not involved in an epitope$/;" m class:EpitopeHamiltonian @@ -620,6 +672,8 @@ print_population_size pop_ss.cpp /^void Population::print_population_size() {$/; print_population_size population.cpp /^void Population::print_population_size() {$/;" f class:Population print_species_header ss.cpp /^void print_species_header(const Species_parray &print_spec)$/;" f print_species_traj ss.cpp /^void print_species_traj(double t, const Species_parray &print_spec, bool verbose)$/;" f +print_species_traj ss.cpp /^void print_species_traj(double t, long step, const Species_parray &print_spec, bool verbose)$/;" f +print_species_traj ss.cpp /^void print_species_traj(double t, long step, const Species_parray &print_spec, bool verbose, bool flushOften)$/;" f product_stoich reaction.h /^ std::vector product_stoich; \/\/ must be negative for reactants that are consumed!$/;" m class:ElementaryReaction products reaction.h /^ std::vector products; \/\/ effects of reaction$/;" m class:ElementaryReaction propensity reaction.h /^ double propensity;$/;" m class:Reaction @@ -642,14 +696,27 @@ rbegin sorted_vector.h /^ reverse_iterator rbegin() {return vec_.rbegin(); reactant_stoich reaction.h /^ std::vector reactant_stoich; \/\/ reaction order$/;" m class:ElementaryReaction reactants reaction.h /^ std::vector reactants; \/\/ anything that participates in reaction rate$/;" m class:ElementaryReaction recalc reaction.cpp /^double AAKillingReaction::recalc()$/;" f class:AAKillingReaction +recalc reaction.cpp /^double AAKillingReaction::recalc(Reaction *rxn_in)$/;" f class:AAKillingReaction recalc reaction.cpp /^double CTLActivationReaction::recalc()$/;" f class:CTLActivationReaction +recalc reaction.cpp /^double CTLActivationReaction::recalc(Reaction *rxn)$/;" f class:CTLActivationReaction recalc reaction.cpp /^double CTLaaActivationReaction::recalc()$/;" f class:CTLaaActivationReaction +recalc reaction.cpp /^double CTLaaActivationReaction::recalc(Reaction *rxn)$/;" f class:CTLaaActivationReaction recalc reaction.cpp /^double ElementaryReaction::recalc()$/;" f class:ElementaryReaction +recalc reaction.cpp /^double ElementaryReaction::recalc(Reaction *rxn)$/;" f class:ElementaryReaction +recalc reaction.cpp /^double EscapeAACountingReaction::recalc()$/;" f class:EscapeAACountingReaction +recalc reaction.cpp /^double EscapeAACountingReaction::recalc(Reaction *rxn_in)$/;" f class:EscapeAACountingReaction +recalc reaction.cpp /^double EscapeCountingReaction::recalc()$/;" f class:EscapeCountingReaction +recalc reaction.cpp /^double EscapeCountingReaction::recalc(Reaction *rxn_in)$/;" f class:EscapeCountingReaction recalc reaction.cpp /^double KillingReaction::recalc()$/;" f class:KillingReaction +recalc reaction.cpp /^double KillingReaction::recalc(Reaction *rxn_in)$/;" f class:KillingReaction recalc reaction.cpp /^double NTVirusDeathReaction::recalc()$/;" f class:NTVirusDeathReaction +recalc reaction.cpp /^double NTVirusDeathReaction::recalc(Reaction *rxn)$/;" f class:NTVirusDeathReaction recalc reaction.cpp /^double NTVirusReaction::recalc()$/;" f class:NTVirusReaction +recalc reaction.cpp /^double NTVirusReaction::recalc(Reaction *rxn)$/;" f class:NTVirusReaction recalc reaction.cpp /^double VirusDeathReaction::recalc()$/;" f class:VirusDeathReaction +recalc reaction.cpp /^double VirusDeathReaction::recalc(Reaction *rxn)$/;" f class:VirusDeathReaction recalc reaction.cpp /^double VirusReaction::recalc()$/;" f class:VirusReaction +recalc reaction.cpp /^double VirusReaction::recalc(Reaction *rxn)$/;" f class:VirusReaction recognized pop_ss.cpp /^double CTLSpecies::recognized(const MutatedSiteSequence &mutated_sites) const {$/;" f class:CTLSpecies recognized pop_ss.cpp /^double CTLSpecies::recognized(const Virus &v) const {$/;" f class:CTLSpecies recognized pop_ss.cpp /^double CTLaaSpecies::recognized(const NTVirus &v) const {$/;" f class:CTLaaSpecies @@ -695,6 +762,8 @@ sim_random_seed mc.cpp /^static unsigned sim_random_seed() {$/;" f file: sim_random_seed ss.cpp /^static unsigned sim_random_seed() {$/;" f file: sim_random_seed wf.cpp /^static unsigned sim_random_seed() {$/;" f file: simulate ss.cpp /^void simulate(Rxn_parray &reactions, Species_parray &species, double t_end, long max_steps, double sample_interval, const Species_parray &print_spec, bool verbose)$/;" f +simulate ss.cpp /^void simulate(Rxn_parray &reactions, Species_parray &species, double t_end, long max_steps, double sample_interval, unsigned step_sample_interval, const Species_parray &print_spec, bool verbose)$/;" f +simulate ss.cpp /^void simulate(Rxn_parray &reactions, Species_parray &species, double t_end, long max_steps, double sample_interval, unsigned step_sample_interval, const Species_parray &print_spec, bool verbose, bool flushOften)$/;" f sindex ham_ss.h /^inline int sindex(int i, int j, size_t qi, size_t qj) {$/;" f sindex snip.h /^inline int sindex(int i, int j, size_t qi, size_t qj) {$/;" f site pop_ss.h /^ std::vector site;$/;" m class:AARecognizer @@ -722,6 +791,7 @@ statefile mc.h /^ std::string statefile; \/\/ Input state file which con statefile ss.h /^ std::string statefile; \/\/ Input state file which contains initial population fractions$/;" m class:RunParameters_SS statefile wf.h /^ std::string statefile; \/\/ Input state file which contains initial population fractions$/;" m class:RunParameters std seqTools.h /^namespace std {$/;" n +step_sample_interval ss.h /^ unsigned step_sample_interval;$/;" m class:RunParameters_SS str2aa seqTools.cpp /^const str2aa_map str2aa = {$/;" v str2aa_map seqTools.h /^typedef std::unordered_map str2aa_map;$/;" t str2codon seqTools.cpp /^const str2codon_map str2codon = {$/;" v @@ -752,6 +822,8 @@ to_string_uint ss.cpp /^ to_string_uint(unsigned __val)$/;" f tostring mc.h /^inline std::string tostring (const T& t) {$/;" f tostring ss.h /^inline std::string tostring (const T& t) {$/;" f tostring wf.h /^inline std::string tostring (const T& t) {$/;" f +trackEscaped ss.h /^ bool trackEscaped; \/\/ Maintain counter to track number of escaped viruses?$/;" m class:RunParameters_SS +trackEscaped ss.h /^ bool trackEscaped;$/;" m class:RunParameters_SS trajectoryOutfile mc.h /^ std::string trajectoryOutfile;$/;" m class:RunParameters_MC trajectoryOutfile ss.h /^ std::string trajectoryOutfile;$/;" m class:RunParameters_SS trajectoryOutfile wf.h /^ std::string trajectoryOutfile;$/;" m class:RunParameters @@ -760,11 +832,13 @@ unsorted_find main.cpp /^FwIt unsorted_find(FwIt beg,FwIt beyond,Pred pred)$/;" update_energy pop_ss.cpp /^void NTVirus::update_energy(const PottsHamiltonian &H)$/;" f class:NTVirus update_energy pop_ss.cpp /^void Virus::update_energy(const Hamiltonian &H) {$/;" f class:Virus update_energy virus.cpp /^void Virus::update_energy(const Hamiltonian &H) {$/;" f class:Virus +update_rxn_dependents ss.cpp /^void update_rxn_dependents(Rxn_parray &reactions)$/;" f upper_bound sorted_vector.h /^ const_iterator upper_bound(const K& k) const$/;" f class:codeproject::sorted_vector upper_bound sorted_vector.h /^ iterator upper_bound(const K& k)$/;" f class:codeproject::sorted_vector usage mc.cpp /^void usage()$/;" f usage ss.cpp /^void usage()$/;" f usage wf.cpp /^void usage()$/;" f +usage_rates ss.cpp /^void usage_rates()$/;" f useEpitope mc.h /^ bool useEpitope; \/\/ Include selective pressure on an epitope $/;" m class:RunParameters_MC useEpitope ss.h /^ bool useEpitope; \/\/ Include selective pressure on an epitope $/;" m class:RunParameters_SS useEpitope ss.h /^ bool useEpitope; \/\/ Include selective pressure on an epitope$/;" m class:RunParameters_SS @@ -785,6 +859,7 @@ value_type sorted_vector.h /^ typedef typename Cont::value_type value_type;$/;" vec_ sorted_vector.h /^ Cont vec_;$/;" m class:codeproject::sorted_vector virus_map pop_ss.h /^typedef std::map virus_map;$/;" t virus_map population.h /^typedef std::map virus_map;$/;" t +vol ss.h /^ double vol;$/;" m class:RunParameters_SS write_mod mc.h /^ unsigned int write_mod; \/\/ Write state of the population every __ MC steps$/;" m class:RunParameters_MC write_mod ss.h /^ unsigned int write_mod; \/\/ Write state of the population every __ generations$/;" m class:RunParameters_SS write_mod wf.h /^ unsigned int write_mod; \/\/ Write state of the population every __ generations$/;" m class:RunParameters