From: Dariusz Murakowski Date: Tue, 28 Apr 2015 04:04:27 +0000 (-0400) Subject: ctags -a -R X-Git-Url: http://src.murakowski.org/?a=commitdiff_plain;h=050a72a880a5b4cc96b1e50e6dea508afe2b1a67;p=VirEvoDyn.git ctags -a -R --- diff --git a/tags b/tags index 6a7cfa5..a1159c4 100644 --- a/tags +++ b/tags @@ -13,32 +13,76 @@ 021l session.vim /^normal! 021l$/;" m session.vim /^noremap j$/;" m NetrwBrowseX session.vim /^nnoremap NetrwBrowseX :call netrw#NetrwBrowseX(expand(""),0)$/;" m +AAKillingReaction reaction.h /^ AAKillingReaction() : Reaction() {}$/;" f class:AAKillingReaction +AAKillingReaction reaction.h /^ AAKillingReaction(double k) : Reaction(k) {}$/;" f class:AAKillingReaction +AAKillingReaction reaction.h /^class AAKillingReaction : public Reaction {$/;" c +AARecognizer pop_ss.cpp /^AARecognizer::AARecognizer(const std::string &seq, const std::vector &s)$/;" f class:AARecognizer +AARecognizer pop_ss.cpp /^AARecognizer::AARecognizer(const std::string &seq, int start_index)$/;" f class:AARecognizer +AARecognizer pop_ss.h /^class AARecognizer {$/;" c +AdjacencyList ham_ss.h /^typedef std::vector > AdjacencyList;$/;" t AdjacencyList hamiltonian.h /^typedef std::vector > AdjacencyList;$/;" t BuildIntersection main.cpp /^BuildIntersection(std::vector& v0,std::vector& v1)$/;" f 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 +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 {$/;" c +CTLSpecies pop_ss.h /^ CTLSpecies() : Species(), num_ep(0) {}$/;" f class:CTLSpecies +CTLSpecies pop_ss.h /^ CTLSpecies(long c) : Species(c), num_ep(0) {}$/;" f class:CTLSpecies +CTLSpecies pop_ss.h /^ CTLSpecies(std::string x) : Species(x), num_ep(0) {}$/;" 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 +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 {$/;" c +CTLaaSpecies pop_ss.h /^ CTLaaSpecies() : Species(), num_ep(0) {}$/;" f class:CTLaaSpecies +CTLaaSpecies pop_ss.h /^ CTLaaSpecies(long c) : Species(c), num_ep(0) {}$/;" f class:CTLaaSpecies +CTLaaSpecies pop_ss.h /^ CTLaaSpecies(std::string x) : Species(x), num_ep(0) {}$/;" f class:CTLaaSpecies +CTLaaSpecies pop_ss.h /^ CTLaaSpecies(std::string x, long c) : Species(x,c), num_ep(0) {}$/;" f class:CTLaaSpecies +CTLaaSpecies pop_ss.h /^class CTLaaSpecies : public Species {$/;" c CXX Makefile /^CXX = c++$/;" m +CharVector seqTools.h /^typedef std::vector > CharVector;$/;" t Cont sorted_vector.h /^ typedef typename std::vector Cont;$/;" t class:codeproject::sorted_vector +Coupling ham_ss.h /^typedef std::vector > Coupling;$/;" t Coupling hamiltonian.h /^typedef std::vector > Coupling;$/;" t +DBGFLAG Makefile /^ DBGFLAG = -O3 -combine -DHAVE_INLINE$/;" m DBGFLAG Makefile /^ DBGFLAG = -O3 -combine$/;" m +DBGFLAG Makefile /^ DBGFLAG = -g -DDEBUG # -D_GLIBCXX_DEBUG$/;" m DBGFLAG Makefile /^ DBGFLAG = -g -DDEBUG$/;" m EXECNAME_MC Makefile /^EXECNAME_MC = mc$/;" m 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 +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 {$/;" c EpitopeHamiltonian hamiltonian.cpp /^EpitopeHamiltonian::EpitopeHamiltonian(std::string &FILENAME) {$/;" f class:EpitopeHamiltonian 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 $/;" f class:codeproject::sorted_vector ExecTests main.cpp /^void ExecTests(std::vector& v)$/;" f +Graph ham_ss.h /^ AdjacencyList Graph;$/;" m class:Hamiltonian Graph hamiltonian.h /^ AdjacencyList Graph;$/;" m class:Hamiltonian +H reaction.h /^ Hamiltonian H;$/;" m class:VirusDeathReaction +H reaction.h /^ Hamiltonian H;$/;" m class:VirusReaction +H reaction.h /^ PottsHamiltonian H;$/;" m class:NTVirusDeathReaction +H reaction.h /^ PottsHamiltonian H;$/;" m class:NTVirusReaction HAMILTONIAN_H hamiltonian.h 2;" d +HAM_SS_H ham_ss.h 2;" d +Hamiltonian ham_ss.cpp /^Hamiltonian::Hamiltonian(std::string &FILENAME) {$/;" f class:Hamiltonian +Hamiltonian ham_ss.h /^ Hamiltonian() { }$/;" f class:Hamiltonian +Hamiltonian ham_ss.h /^class Hamiltonian {$/;" c Hamiltonian hamiltonian.cpp /^Hamiltonian::Hamiltonian(std::string &FILENAME) {$/;" f class:Hamiltonian Hamiltonian hamiltonian.h /^ Hamiltonian() { }$/;" f class:Hamiltonian Hamiltonian hamiltonian.h /^class Hamiltonian {$/;" c INCLUDEDIR Makefile /^INCLUDEDIR = # -I\/usr\/local\/pkg\/gsl\/gsl-1.15\/include$/;" m InsertImpl_ sorted_vector.h /^ iterator InsertImpl_(iterator p,const value_type& x)$/;" f class:codeproject::sorted_vector +IntVector seqTools.h /^typedef std::vector > IntVector;$/;" t IntVector snip.h /^typedef std::vector > IntVector;$/;" t +J ham_ss.h /^ Coupling J;$/;" m class:Hamiltonian +J ham_ss.h /^ Coupling J;$/;" m class:PottsHamiltonian J hamiltonian.h /^ Coupling J;$/;" m class:Hamiltonian J12 mc.h /^ double J12;$/;" m class:RunParameters_MC J12 ss.h /^ double J12;$/;" m class:RunParameters_SS @@ -47,20 +91,45 @@ Key snip.h /^typedef std::vector Key;$/;" 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)$/;" f class:codeproject::sorted_vector +KillingReaction reaction.h /^ KillingReaction() : Reaction() {}$/;" f class:KillingReaction +KillingReaction reaction.h /^ KillingReaction(double k) : Reaction(k) {}$/;" f class:KillingReaction +KillingReaction reaction.h /^class KillingReaction : public Reaction {$/;" c +L pop_ss.h /^ unsigned int L;$/;" m class:Virus L virus.h /^ unsigned int L;$/;" m class:Virus LIBDIR Makefile /^LIBDIR = # -L\/usr\/local\/pkg\/gsl\/gsl-1.15\/lib$/;" m LIBS Makefile /^LIBS = -lgsl -lgslcblas -lm$/;" m +L_aa pop_ss.h /^ unsigned int L_aa;$/;" m class:NTVirus +L_nt pop_ss.h /^ unsigned int L_nt;$/;" m class:NTVirus Lt_ sorted_vector.h /^ bool Lt_(const Myt_& x) const$/;" f class:codeproject::sorted_vector MC_H mc.h 2;" d Main sorted_vector_doc.html /^ <\/a>$/;" a MakeSTest main.cpp /^STest MakeSTest()$/;" f +MutatedSiteSequence ham_ss.h /^typedef std::set MutatedSiteSequence;$/;" t MutatedSiteSequence hamiltonian.h /^typedef std::set MutatedSiteSequence;$/;" t MutatedSiteSequence mc.h /^typedef std::set MutatedSiteSequence;$/;" t +MutatedSiteSequence pop_ss.h /^typedef std::set MutatedSiteSequence;$/;" t +MutatedSiteSequence reaction.h /^typedef std::set MutatedSiteSequence;$/;" t 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$/;" m class:Population +NTVirus pop_ss.cpp /^NTVirus::NTVirus(const PottsHamiltonian &H, const std::string &NT)$/;" f class:NTVirus +NTVirus pop_ss.cpp /^NTVirus::NTVirus(const std::string &NT)$/;" f class:NTVirus +NTVirus pop_ss.h /^class NTVirus {$/;" c +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 {$/;" c +NTVirusReaction reaction.h /^ NTVirusReaction() : Reaction() {}$/;" f class:NTVirusReaction +NTVirusReaction reaction.h /^ NTVirusReaction(double k) : Reaction(k), mu(0) {}$/;" f class:NTVirusReaction +NTVirusReaction reaction.h /^class NTVirusReaction : public Reaction {$/;" c +NTVirusSpecies pop_ss.h /^ NTVirusSpecies() : Species() {}$/;" f class:NTVirusSpecies +NTVirusSpecies pop_ss.h /^ NTVirusSpecies(long c) : Species(c) {}$/;" f class:NTVirusSpecies +NTVirusSpecies pop_ss.h /^ NTVirusSpecies(std::string x) : Species(x) {}$/;" f class:NTVirusSpecies +NTVirusSpecies pop_ss.h /^ NTVirusSpecies(std::string x, long c) : Species(x,c) {}$/;" f class:NTVirusSpecies +NTVirusSpecies pop_ss.h /^class NTVirusSpecies : public Species {$/;" c +NTVirus_map pop_ss.h /^typedef std::map NTVirus_map;$/;" t POPULATION_H pop_ss.h 2;" d POPULATION_H population.h 2;" d +POP_SS_H pop_ss.h 2;" d Paircc_ sorted_vector.h /^ typedef typename std::pair Paircc_;$/;" t class:codeproject::sorted_vector Pairib_ sorted_vector.h /^ typedef typename std::pair Pairib_;$/;" t class:codeproject::sorted_vector Pairii_ sorted_vector.h /^ typedef typename std::pair Pairii_;$/;" t class:codeproject::sorted_vector @@ -76,22 +145,49 @@ Population pop_ss.h /^class Population{$/;" 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{$/;" c +PottsHamiltonian ham_ss.cpp /^PottsHamiltonian::PottsHamiltonian(const std::string &couplingsFile, const std::string &seq2stateFile) : bh(1.0), bJ(1.0)$/;" f class:PottsHamiltonian +PottsHamiltonian ham_ss.h /^ PottsHamiltonian() : bh(1.0), bJ(1.0) { }$/;" f class:PottsHamiltonian +PottsHamiltonian ham_ss.h /^class PottsHamiltonian {$/;" c +PottsState ham_ss.h /^typedef std::vector PottsState;$/;" t +PottsState pop_ss.h /^typedef std::vector PottsState;$/;" t +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) {}$/;" f class:Reaction +Reaction reaction.h /^class Reaction {$/;" c RunParameters wf.h /^ RunParameters() {$/;" f class:RunParameters RunParameters wf.h /^class RunParameters {$/;" c 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 +Rxn_parray ss.h /^typedef std::vector Rxn_parray;$/;" t +SEQTOOLS_H seqTools.h 2;" d SGITest main.cpp /^int SGITest()$/;" f SNIP_H snip.h 2;" d SORTED_VECTOR_ sorted_vector.h 24;" d SRCS_MC Makefile /^SRCS_MC = mc.cpp hamiltonian.cpp population.cpp virus.cpp$/;" m +SRCS_SS Makefile /^SRCS_SS = ss.cpp ham_ss.cpp pop_ss.cpp reaction.cpp seqTools.cpp$/;" m SRCS_SS Makefile /^SRCS_SS = ss.cpp hamiltonian.cpp population.cpp virus.cpp$/;" m SRCS_WF Makefile /^SRCS_WF = wf.cpp hamiltonian.cpp population.cpp virus.cpp$/;" m +SS_H ss.h 2;" d STest main.cpp /^struct STest{$/;" s file: SessionLoad session.vim /^let SessionLoad = 1$/;" v SimpTimer main.cpp /^ SimpTimer(const char* msg):m_msg(msg),m_start(clock()){}$/;" f class:SimpTimer SimpTimer main.cpp /^class SimpTimer{$/;" c file: +SimpleSpecies pop_ss.h /^ SimpleSpecies() : Species() {}$/;" f class:SimpleSpecies +SimpleSpecies pop_ss.h /^ SimpleSpecies(long c) : Species(c) {}$/;" f class:SimpleSpecies +SimpleSpecies pop_ss.h /^ SimpleSpecies(std::string x) : Species(x) {}$/;" f class:SimpleSpecies +SimpleSpecies pop_ss.h /^ SimpleSpecies(std::string x, long c) : Species(x,c) {}$/;" f class:SimpleSpecies +SimpleSpecies pop_ss.h /^class SimpleSpecies : public Species {$/;" c +Species pop_ss.h /^ Species() : count(0), name("") {}$/;" f class:Species +Species pop_ss.h /^ Species(long c) : count(c), name("") {}$/;" f class:Species +Species pop_ss.h /^ Species(std::string x) : count(0), name(x) {}$/;" f class:Species +Species pop_ss.h /^ Species(std::string x, long c) : count(c), name(x) {}$/;" f class:Species +Species pop_ss.h /^class Species {$/;" c +Species_parray ss.h /^typedef std::vector Species_parray;$/;" t +T reaction.h /^ CTLSpecies* T;$/;" m class:KillingReaction +T reaction.h /^ CTLaaSpecies* T;$/;" m class:AAKillingReaction Template test/make_tests.py /^from string import Template$/;" i TestAllSet main.cpp /^void TestAllSet()$/;" f TestMultiSet main.cpp /^void TestMultiSet(std::vector& v)$/;" f @@ -99,16 +195,42 @@ TestSet main.cpp /^void TestSet(std::vector& v)$/;" f TestSetOperations main.cpp /^void TestSetOperations(const std::vector& v0,$/;" f TestSortedVector_AsMultiSet main.cpp /^void TestSortedVector_AsMultiSet(std::vector& v)$/;" f TestSortedVector_AsSet main.cpp /^void TestSortedVector_AsSet(std::vector& v)$/;" f +Tfrom reaction.h /^ CTLSpecies* Tfrom;$/;" m class:CTLActivationReaction +Tfrom reaction.h /^ CTLaaSpecies* Tfrom;$/;" m class:CTLaaActivationReaction +Tto reaction.h /^ CTLSpecies* Tto;$/;" m class:CTLActivationReaction +Tto reaction.h /^ CTLaaSpecies* Tto;$/;" m class:CTLaaActivationReaction 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 {$/;" c Unique_ sorted_vector.h /^ iterator Unique_()$/;" 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;$/;" m class:NTVirusDeathReaction +V reaction.h /^ NTVirusSpecies* V;$/;" m class:NTVirusReaction +V reaction.h /^ VirusSpecies* V;$/;" m class:CTLActivationReaction +V reaction.h /^ VirusSpecies* V;$/;" 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;$/;" t +Virus pop_ss.cpp /^Virus::Virus(const Hamiltonian &H) {$/;" f class:Virus +Virus pop_ss.cpp /^Virus::Virus(const Hamiltonian &H, const std::set &mutated_sites) {$/;" f class:Virus +Virus pop_ss.h /^class Virus {$/;" c 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 {$/;" c +VirusDeathReaction reaction.h /^ VirusDeathReaction() : Reaction() {}$/;" f class:VirusDeathReaction +VirusDeathReaction reaction.h /^ VirusDeathReaction(double k) : Reaction(k) {}$/;" f class:VirusDeathReaction +VirusDeathReaction reaction.h /^class VirusDeathReaction : public Reaction {$/;" c +VirusReaction reaction.h /^ VirusReaction() : Reaction() {}$/;" f class:VirusReaction +VirusReaction reaction.h /^ VirusReaction(double k) : Reaction(k), mu(0) {}$/;" f class:VirusReaction +VirusReaction reaction.h /^class VirusReaction : public Reaction {$/;" c +VirusSpecies pop_ss.h /^ VirusSpecies() : Species() {}$/;" f class:VirusSpecies +VirusSpecies pop_ss.h /^ VirusSpecies(long c) : Species(c) {}$/;" f class:VirusSpecies +VirusSpecies pop_ss.h /^ VirusSpecies(std::string x) : Species(x) {}$/;" f class:VirusSpecies +VirusSpecies pop_ss.h /^ VirusSpecies(std::string x, long c) : Species(x,c) {}$/;" f class:VirusSpecies +VirusSpecies pop_ss.h /^class VirusSpecies : public Species {$/;" c WF_H ss.h 2;" d WF_H wf.h 2;" d Y session.vim /^nnoremap Y y\$$/;" m @@ -116,15 +238,26 @@ Y session.vim /^nnoremap Y y\$$/;" m ]% session.vim /^vmap ]% ]%m'gv``$/;" m _articleTop sorted_vector_doc.html /^ <\/a>$/;" a a% session.vim /^vmap a% [%v]%$/;" m +aa2int seqTools.cpp /^const str2int_map aa2int = {$/;" v +aa2state ham_ss.h /^ std::vector > aa2state;$/;" m class:PottsHamiltonian +aa2str seqTools.cpp /^const aa2str_map aa2str = {$/;" v +aa2str_map seqTools.h /^typedef std::unordered_map aa2str_map;$/;" t +aa_seq pop_ss.h /^ std::vector aa_seq;$/;" m class:NTVirus +aaseq2str pop_ss.cpp /^std::string aaseq2str(const std::vector &aa_seq)$/;" f add_to_two_site_pop mc.cpp /^void add_to_two_site_pop(RunParameters_MC &r, bool s1, bool s2, double frac) {$/;" 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 +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>$/;" f allocator_type sorted_vector.h /^ typedef typename Cont::allocator_type allocator_type;$/;" t class:codeproject::sorted_vector +allow_dynamic_cast pop_ss.h /^ virtual void allow_dynamic_cast() {}$/;" f class:Species assign sorted_vector.h /^ void assign(size_type n, const K& x = K())$/;" f class:codeproject::sorted_vector assign sorted_vector.h /^ void assign(const_iterator first, const_iterator beyond) $/;" f class:codeproject::sorted_vector at sorted_vector.h /^ const_reference at(size_type p) const {return vec_.at(p);}$/;" f class:codeproject::sorted_vector at sorted_vector.h /^ reference at(size_type p) {return vec_.at(p);}$/;" f class:codeproject::sorted_vector +bJ ham_ss.h /^ double bJ; \/\/ couplings "inverse temperature" multiplier$/;" m class:Hamiltonian +bJ ham_ss.h /^ double bJ; \/\/ couplings "inverse temperature" multiplier$/;" m class:PottsHamiltonian bJ hamiltonian.h /^ double bJ; \/\/ couplings "inverse temperature" multiplier$/;" m class:Hamiltonian bJ mc.h /^ double bJ; \/\/ Coupling "inverse temperature" multiplier$/;" m class:RunParameters_MC bJ ss.h /^ double bJ; \/\/ Coupling "inverse temperature" multiplier$/;" m class:RunParameters_SS @@ -133,6 +266,8 @@ back sorted_vector.h /^ const_reference back() const {return vec_.back();} back sorted_vector.h /^ reference back() {return vec_.back();}$/;" f class:codeproject::sorted_vector begin sorted_vector.h /^ const_iterator begin() const {return vec_.begin(); }$/;" f class:codeproject::sorted_vector begin sorted_vector.h /^ iterator begin() {return vec_.begin(); }$/;" f class:codeproject::sorted_vector +bh ham_ss.h /^ double bh; \/\/ fields "inverse temperature" multiplier$/;" m class:Hamiltonian +bh ham_ss.h /^ double bh; \/\/ fields "inverse temperature" multiplier$/;" m class:PottsHamiltonian bh hamiltonian.h /^ double bh; \/\/ fields "inverse temperature" multiplier$/;" m class:Hamiltonian bh mc.h /^ double bh; \/\/ Field "inverse temperature" multiplier$/;" m class:RunParameters_MC bh ss.h /^ double bh; \/\/ Field "inverse temperature" multiplier$/;" m class:RunParameters_SS @@ -140,7 +275,77 @@ bh wf.h /^ double bh; \/\/ Field "inverse temperature" multi charmap seqTools.cpp /^typedef std::unordered_map charmap;$/;" t file: checkTest test/runTests.sh /^checkTest () {$/;" f clear sorted_vector.h /^ void clear() {return vec_.clear();}$/;" f class:codeproject::sorted_vector +coarse_grain ham_ss.cpp /^void PottsHamiltonian::coarse_grain(const std::vector &aa_seq, PottsState &config) const$/;" f class:PottsHamiltonian +cod_AAA seqTools.h /^ cod_ATT,cod_ATC,cod_ATA,cod_ATG, cod_ACT,cod_ACC,cod_ACA,cod_ACG, cod_AAT,cod_AAC,cod_AAA,cod_AAG, cod_AGT,cod_AGC,cod_AGA,cod_AGG,$/;" e enum:codon +cod_AAC seqTools.h /^ cod_ATT,cod_ATC,cod_ATA,cod_ATG, cod_ACT,cod_ACC,cod_ACA,cod_ACG, cod_AAT,cod_AAC,cod_AAA,cod_AAG, cod_AGT,cod_AGC,cod_AGA,cod_AGG,$/;" e enum:codon +cod_AAG seqTools.h /^ cod_ATT,cod_ATC,cod_ATA,cod_ATG, cod_ACT,cod_ACC,cod_ACA,cod_ACG, cod_AAT,cod_AAC,cod_AAA,cod_AAG, cod_AGT,cod_AGC,cod_AGA,cod_AGG,$/;" e enum:codon +cod_AAT seqTools.h /^ cod_ATT,cod_ATC,cod_ATA,cod_ATG, cod_ACT,cod_ACC,cod_ACA,cod_ACG, cod_AAT,cod_AAC,cod_AAA,cod_AAG, cod_AGT,cod_AGC,cod_AGA,cod_AGG,$/;" e enum:codon +cod_ACA seqTools.h /^ cod_ATT,cod_ATC,cod_ATA,cod_ATG, cod_ACT,cod_ACC,cod_ACA,cod_ACG, cod_AAT,cod_AAC,cod_AAA,cod_AAG, cod_AGT,cod_AGC,cod_AGA,cod_AGG,$/;" e enum:codon +cod_ACC seqTools.h /^ cod_ATT,cod_ATC,cod_ATA,cod_ATG, cod_ACT,cod_ACC,cod_ACA,cod_ACG, cod_AAT,cod_AAC,cod_AAA,cod_AAG, cod_AGT,cod_AGC,cod_AGA,cod_AGG,$/;" e enum:codon +cod_ACG seqTools.h /^ cod_ATT,cod_ATC,cod_ATA,cod_ATG, cod_ACT,cod_ACC,cod_ACA,cod_ACG, cod_AAT,cod_AAC,cod_AAA,cod_AAG, cod_AGT,cod_AGC,cod_AGA,cod_AGG,$/;" e enum:codon +cod_ACT seqTools.h /^ cod_ATT,cod_ATC,cod_ATA,cod_ATG, cod_ACT,cod_ACC,cod_ACA,cod_ACG, cod_AAT,cod_AAC,cod_AAA,cod_AAG, cod_AGT,cod_AGC,cod_AGA,cod_AGG,$/;" e enum:codon +cod_AGA seqTools.h /^ cod_ATT,cod_ATC,cod_ATA,cod_ATG, cod_ACT,cod_ACC,cod_ACA,cod_ACG, cod_AAT,cod_AAC,cod_AAA,cod_AAG, cod_AGT,cod_AGC,cod_AGA,cod_AGG,$/;" e enum:codon +cod_AGC seqTools.h /^ cod_ATT,cod_ATC,cod_ATA,cod_ATG, cod_ACT,cod_ACC,cod_ACA,cod_ACG, cod_AAT,cod_AAC,cod_AAA,cod_AAG, cod_AGT,cod_AGC,cod_AGA,cod_AGG,$/;" e enum:codon +cod_AGG seqTools.h /^ cod_ATT,cod_ATC,cod_ATA,cod_ATG, cod_ACT,cod_ACC,cod_ACA,cod_ACG, cod_AAT,cod_AAC,cod_AAA,cod_AAG, cod_AGT,cod_AGC,cod_AGA,cod_AGG,$/;" e enum:codon +cod_AGT seqTools.h /^ cod_ATT,cod_ATC,cod_ATA,cod_ATG, cod_ACT,cod_ACC,cod_ACA,cod_ACG, cod_AAT,cod_AAC,cod_AAA,cod_AAG, cod_AGT,cod_AGC,cod_AGA,cod_AGG,$/;" e enum:codon +cod_ATA seqTools.h /^ cod_ATT,cod_ATC,cod_ATA,cod_ATG, cod_ACT,cod_ACC,cod_ACA,cod_ACG, cod_AAT,cod_AAC,cod_AAA,cod_AAG, cod_AGT,cod_AGC,cod_AGA,cod_AGG,$/;" e enum:codon +cod_ATC seqTools.h /^ cod_ATT,cod_ATC,cod_ATA,cod_ATG, cod_ACT,cod_ACC,cod_ACA,cod_ACG, cod_AAT,cod_AAC,cod_AAA,cod_AAG, cod_AGT,cod_AGC,cod_AGA,cod_AGG,$/;" e enum:codon +cod_ATG seqTools.h /^ cod_ATT,cod_ATC,cod_ATA,cod_ATG, cod_ACT,cod_ACC,cod_ACA,cod_ACG, cod_AAT,cod_AAC,cod_AAA,cod_AAG, cod_AGT,cod_AGC,cod_AGA,cod_AGG,$/;" e enum:codon +cod_ATT seqTools.h /^ cod_ATT,cod_ATC,cod_ATA,cod_ATG, cod_ACT,cod_ACC,cod_ACA,cod_ACG, cod_AAT,cod_AAC,cod_AAA,cod_AAG, cod_AGT,cod_AGC,cod_AGA,cod_AGG,$/;" e enum:codon +cod_CAA seqTools.h /^ cod_CTT,cod_CTC,cod_CTA,cod_CTG, cod_CCT,cod_CCC,cod_CCA,cod_CCG, cod_CAT,cod_CAC,cod_CAA,cod_CAG, cod_CGT,cod_CGC,cod_CGA,cod_CGG,$/;" e enum:codon +cod_CAC seqTools.h /^ cod_CTT,cod_CTC,cod_CTA,cod_CTG, cod_CCT,cod_CCC,cod_CCA,cod_CCG, cod_CAT,cod_CAC,cod_CAA,cod_CAG, cod_CGT,cod_CGC,cod_CGA,cod_CGG,$/;" e enum:codon +cod_CAG seqTools.h /^ cod_CTT,cod_CTC,cod_CTA,cod_CTG, cod_CCT,cod_CCC,cod_CCA,cod_CCG, cod_CAT,cod_CAC,cod_CAA,cod_CAG, cod_CGT,cod_CGC,cod_CGA,cod_CGG,$/;" e enum:codon +cod_CAT seqTools.h /^ cod_CTT,cod_CTC,cod_CTA,cod_CTG, cod_CCT,cod_CCC,cod_CCA,cod_CCG, cod_CAT,cod_CAC,cod_CAA,cod_CAG, cod_CGT,cod_CGC,cod_CGA,cod_CGG,$/;" e enum:codon +cod_CCA seqTools.h /^ cod_CTT,cod_CTC,cod_CTA,cod_CTG, cod_CCT,cod_CCC,cod_CCA,cod_CCG, cod_CAT,cod_CAC,cod_CAA,cod_CAG, cod_CGT,cod_CGC,cod_CGA,cod_CGG,$/;" e enum:codon +cod_CCC seqTools.h /^ cod_CTT,cod_CTC,cod_CTA,cod_CTG, cod_CCT,cod_CCC,cod_CCA,cod_CCG, cod_CAT,cod_CAC,cod_CAA,cod_CAG, cod_CGT,cod_CGC,cod_CGA,cod_CGG,$/;" e enum:codon +cod_CCG seqTools.h /^ cod_CTT,cod_CTC,cod_CTA,cod_CTG, cod_CCT,cod_CCC,cod_CCA,cod_CCG, cod_CAT,cod_CAC,cod_CAA,cod_CAG, cod_CGT,cod_CGC,cod_CGA,cod_CGG,$/;" e enum:codon +cod_CCT seqTools.h /^ cod_CTT,cod_CTC,cod_CTA,cod_CTG, cod_CCT,cod_CCC,cod_CCA,cod_CCG, cod_CAT,cod_CAC,cod_CAA,cod_CAG, cod_CGT,cod_CGC,cod_CGA,cod_CGG,$/;" e enum:codon +cod_CGA seqTools.h /^ cod_CTT,cod_CTC,cod_CTA,cod_CTG, cod_CCT,cod_CCC,cod_CCA,cod_CCG, cod_CAT,cod_CAC,cod_CAA,cod_CAG, cod_CGT,cod_CGC,cod_CGA,cod_CGG,$/;" e enum:codon +cod_CGC seqTools.h /^ cod_CTT,cod_CTC,cod_CTA,cod_CTG, cod_CCT,cod_CCC,cod_CCA,cod_CCG, cod_CAT,cod_CAC,cod_CAA,cod_CAG, cod_CGT,cod_CGC,cod_CGA,cod_CGG,$/;" e enum:codon +cod_CGG seqTools.h /^ cod_CTT,cod_CTC,cod_CTA,cod_CTG, cod_CCT,cod_CCC,cod_CCA,cod_CCG, cod_CAT,cod_CAC,cod_CAA,cod_CAG, cod_CGT,cod_CGC,cod_CGA,cod_CGG,$/;" e enum:codon +cod_CGT seqTools.h /^ cod_CTT,cod_CTC,cod_CTA,cod_CTG, cod_CCT,cod_CCC,cod_CCA,cod_CCG, cod_CAT,cod_CAC,cod_CAA,cod_CAG, cod_CGT,cod_CGC,cod_CGA,cod_CGG,$/;" e enum:codon +cod_CTA seqTools.h /^ cod_CTT,cod_CTC,cod_CTA,cod_CTG, cod_CCT,cod_CCC,cod_CCA,cod_CCG, cod_CAT,cod_CAC,cod_CAA,cod_CAG, cod_CGT,cod_CGC,cod_CGA,cod_CGG,$/;" e enum:codon +cod_CTC seqTools.h /^ cod_CTT,cod_CTC,cod_CTA,cod_CTG, cod_CCT,cod_CCC,cod_CCA,cod_CCG, cod_CAT,cod_CAC,cod_CAA,cod_CAG, cod_CGT,cod_CGC,cod_CGA,cod_CGG,$/;" e enum:codon +cod_CTG seqTools.h /^ cod_CTT,cod_CTC,cod_CTA,cod_CTG, cod_CCT,cod_CCC,cod_CCA,cod_CCG, cod_CAT,cod_CAC,cod_CAA,cod_CAG, cod_CGT,cod_CGC,cod_CGA,cod_CGG,$/;" e enum:codon +cod_CTT seqTools.h /^ cod_CTT,cod_CTC,cod_CTA,cod_CTG, cod_CCT,cod_CCC,cod_CCA,cod_CCG, cod_CAT,cod_CAC,cod_CAA,cod_CAG, cod_CGT,cod_CGC,cod_CGA,cod_CGG,$/;" e enum:codon +cod_GAA seqTools.h /^ cod_GTT,cod_GTC,cod_GTA,cod_GTG, cod_GCT,cod_GCC,cod_GCA,cod_GCG, cod_GAT,cod_GAC,cod_GAA,cod_GAG, cod_GGT,cod_GGC,cod_GGA,cod_GGG};$/;" e enum:codon +cod_GAC seqTools.h /^ cod_GTT,cod_GTC,cod_GTA,cod_GTG, cod_GCT,cod_GCC,cod_GCA,cod_GCG, cod_GAT,cod_GAC,cod_GAA,cod_GAG, cod_GGT,cod_GGC,cod_GGA,cod_GGG};$/;" e enum:codon +cod_GAG seqTools.h /^ cod_GTT,cod_GTC,cod_GTA,cod_GTG, cod_GCT,cod_GCC,cod_GCA,cod_GCG, cod_GAT,cod_GAC,cod_GAA,cod_GAG, cod_GGT,cod_GGC,cod_GGA,cod_GGG};$/;" e enum:codon +cod_GAT seqTools.h /^ cod_GTT,cod_GTC,cod_GTA,cod_GTG, cod_GCT,cod_GCC,cod_GCA,cod_GCG, cod_GAT,cod_GAC,cod_GAA,cod_GAG, cod_GGT,cod_GGC,cod_GGA,cod_GGG};$/;" e enum:codon +cod_GCA seqTools.h /^ cod_GTT,cod_GTC,cod_GTA,cod_GTG, cod_GCT,cod_GCC,cod_GCA,cod_GCG, cod_GAT,cod_GAC,cod_GAA,cod_GAG, cod_GGT,cod_GGC,cod_GGA,cod_GGG};$/;" e enum:codon +cod_GCC seqTools.h /^ cod_GTT,cod_GTC,cod_GTA,cod_GTG, cod_GCT,cod_GCC,cod_GCA,cod_GCG, cod_GAT,cod_GAC,cod_GAA,cod_GAG, cod_GGT,cod_GGC,cod_GGA,cod_GGG};$/;" e enum:codon +cod_GCG seqTools.h /^ cod_GTT,cod_GTC,cod_GTA,cod_GTG, cod_GCT,cod_GCC,cod_GCA,cod_GCG, cod_GAT,cod_GAC,cod_GAA,cod_GAG, cod_GGT,cod_GGC,cod_GGA,cod_GGG};$/;" e enum:codon +cod_GCT seqTools.h /^ cod_GTT,cod_GTC,cod_GTA,cod_GTG, cod_GCT,cod_GCC,cod_GCA,cod_GCG, cod_GAT,cod_GAC,cod_GAA,cod_GAG, cod_GGT,cod_GGC,cod_GGA,cod_GGG};$/;" e enum:codon +cod_GGA seqTools.h /^ cod_GTT,cod_GTC,cod_GTA,cod_GTG, cod_GCT,cod_GCC,cod_GCA,cod_GCG, cod_GAT,cod_GAC,cod_GAA,cod_GAG, cod_GGT,cod_GGC,cod_GGA,cod_GGG};$/;" e enum:codon +cod_GGC seqTools.h /^ cod_GTT,cod_GTC,cod_GTA,cod_GTG, cod_GCT,cod_GCC,cod_GCA,cod_GCG, cod_GAT,cod_GAC,cod_GAA,cod_GAG, cod_GGT,cod_GGC,cod_GGA,cod_GGG};$/;" e enum:codon +cod_GGG seqTools.h /^ cod_GTT,cod_GTC,cod_GTA,cod_GTG, cod_GCT,cod_GCC,cod_GCA,cod_GCG, cod_GAT,cod_GAC,cod_GAA,cod_GAG, cod_GGT,cod_GGC,cod_GGA,cod_GGG};$/;" e enum:codon +cod_GGT seqTools.h /^ cod_GTT,cod_GTC,cod_GTA,cod_GTG, cod_GCT,cod_GCC,cod_GCA,cod_GCG, cod_GAT,cod_GAC,cod_GAA,cod_GAG, cod_GGT,cod_GGC,cod_GGA,cod_GGG};$/;" e enum:codon +cod_GTA seqTools.h /^ cod_GTT,cod_GTC,cod_GTA,cod_GTG, cod_GCT,cod_GCC,cod_GCA,cod_GCG, cod_GAT,cod_GAC,cod_GAA,cod_GAG, cod_GGT,cod_GGC,cod_GGA,cod_GGG};$/;" e enum:codon +cod_GTC seqTools.h /^ cod_GTT,cod_GTC,cod_GTA,cod_GTG, cod_GCT,cod_GCC,cod_GCA,cod_GCG, cod_GAT,cod_GAC,cod_GAA,cod_GAG, cod_GGT,cod_GGC,cod_GGA,cod_GGG};$/;" e enum:codon +cod_GTG seqTools.h /^ cod_GTT,cod_GTC,cod_GTA,cod_GTG, cod_GCT,cod_GCC,cod_GCA,cod_GCG, cod_GAT,cod_GAC,cod_GAA,cod_GAG, cod_GGT,cod_GGC,cod_GGA,cod_GGG};$/;" e enum:codon +cod_GTT seqTools.h /^ cod_GTT,cod_GTC,cod_GTA,cod_GTG, cod_GCT,cod_GCC,cod_GCA,cod_GCG, cod_GAT,cod_GAC,cod_GAA,cod_GAG, cod_GGT,cod_GGC,cod_GGA,cod_GGG};$/;" e enum:codon +cod_TAA seqTools.h /^enum codon {cod_TTT,cod_TTC,cod_TTA,cod_TTG, cod_TCT,cod_TCC,cod_TCA,cod_TCG, cod_TAT,cod_TAC,cod_TAA,cod_TAG, cod_TGT,cod_TGC,cod_TGA,cod_TGG,$/;" e enum:codon +cod_TAC seqTools.h /^enum codon {cod_TTT,cod_TTC,cod_TTA,cod_TTG, cod_TCT,cod_TCC,cod_TCA,cod_TCG, cod_TAT,cod_TAC,cod_TAA,cod_TAG, cod_TGT,cod_TGC,cod_TGA,cod_TGG,$/;" e enum:codon +cod_TAG seqTools.h /^enum codon {cod_TTT,cod_TTC,cod_TTA,cod_TTG, cod_TCT,cod_TCC,cod_TCA,cod_TCG, cod_TAT,cod_TAC,cod_TAA,cod_TAG, cod_TGT,cod_TGC,cod_TGA,cod_TGG,$/;" e enum:codon +cod_TAT seqTools.h /^enum codon {cod_TTT,cod_TTC,cod_TTA,cod_TTG, cod_TCT,cod_TCC,cod_TCA,cod_TCG, cod_TAT,cod_TAC,cod_TAA,cod_TAG, cod_TGT,cod_TGC,cod_TGA,cod_TGG,$/;" e enum:codon +cod_TCA seqTools.h /^enum codon {cod_TTT,cod_TTC,cod_TTA,cod_TTG, cod_TCT,cod_TCC,cod_TCA,cod_TCG, cod_TAT,cod_TAC,cod_TAA,cod_TAG, cod_TGT,cod_TGC,cod_TGA,cod_TGG,$/;" e enum:codon +cod_TCC seqTools.h /^enum codon {cod_TTT,cod_TTC,cod_TTA,cod_TTG, cod_TCT,cod_TCC,cod_TCA,cod_TCG, cod_TAT,cod_TAC,cod_TAA,cod_TAG, cod_TGT,cod_TGC,cod_TGA,cod_TGG,$/;" e enum:codon +cod_TCG seqTools.h /^enum codon {cod_TTT,cod_TTC,cod_TTA,cod_TTG, cod_TCT,cod_TCC,cod_TCA,cod_TCG, cod_TAT,cod_TAC,cod_TAA,cod_TAG, cod_TGT,cod_TGC,cod_TGA,cod_TGG,$/;" e enum:codon +cod_TCT seqTools.h /^enum codon {cod_TTT,cod_TTC,cod_TTA,cod_TTG, cod_TCT,cod_TCC,cod_TCA,cod_TCG, cod_TAT,cod_TAC,cod_TAA,cod_TAG, cod_TGT,cod_TGC,cod_TGA,cod_TGG,$/;" e enum:codon +cod_TGA seqTools.h /^enum codon {cod_TTT,cod_TTC,cod_TTA,cod_TTG, cod_TCT,cod_TCC,cod_TCA,cod_TCG, cod_TAT,cod_TAC,cod_TAA,cod_TAG, cod_TGT,cod_TGC,cod_TGA,cod_TGG,$/;" e enum:codon +cod_TGC seqTools.h /^enum codon {cod_TTT,cod_TTC,cod_TTA,cod_TTG, cod_TCT,cod_TCC,cod_TCA,cod_TCG, cod_TAT,cod_TAC,cod_TAA,cod_TAG, cod_TGT,cod_TGC,cod_TGA,cod_TGG,$/;" e enum:codon +cod_TGG seqTools.h /^enum codon {cod_TTT,cod_TTC,cod_TTA,cod_TTG, cod_TCT,cod_TCC,cod_TCA,cod_TCG, cod_TAT,cod_TAC,cod_TAA,cod_TAG, cod_TGT,cod_TGC,cod_TGA,cod_TGG,$/;" e enum:codon +cod_TGT seqTools.h /^enum codon {cod_TTT,cod_TTC,cod_TTA,cod_TTG, cod_TCT,cod_TCC,cod_TCA,cod_TCG, cod_TAT,cod_TAC,cod_TAA,cod_TAG, cod_TGT,cod_TGC,cod_TGA,cod_TGG,$/;" e enum:codon +cod_TTA seqTools.h /^enum codon {cod_TTT,cod_TTC,cod_TTA,cod_TTG, cod_TCT,cod_TCC,cod_TCA,cod_TCG, cod_TAT,cod_TAC,cod_TAA,cod_TAG, cod_TGT,cod_TGC,cod_TGA,cod_TGG,$/;" e enum:codon +cod_TTC seqTools.h /^enum codon {cod_TTT,cod_TTC,cod_TTA,cod_TTG, cod_TCT,cod_TCC,cod_TCA,cod_TCG, cod_TAT,cod_TAC,cod_TAA,cod_TAG, cod_TGT,cod_TGC,cod_TGA,cod_TGG,$/;" e enum:codon +cod_TTG seqTools.h /^enum codon {cod_TTT,cod_TTC,cod_TTA,cod_TTG, cod_TCT,cod_TCC,cod_TCA,cod_TCG, cod_TAT,cod_TAC,cod_TAA,cod_TAG, cod_TGT,cod_TGC,cod_TGA,cod_TGG,$/;" e enum:codon +cod_TTT seqTools.h /^enum codon {cod_TTT,cod_TTC,cod_TTA,cod_TTG, cod_TCT,cod_TCC,cod_TCA,cod_TCG, cod_TAT,cod_TAC,cod_TAA,cod_TAG, cod_TGT,cod_TGC,cod_TGA,cod_TGG,$/;" e enum:codon codeproject sorted_vector.h /^namespace codeproject{$/;" n +codon seqTools.h /^enum codon {cod_TTT,cod_TTC,cod_TTA,cod_TTG, cod_TCT,cod_TCC,cod_TCA,cod_TCG, cod_TAT,cod_TAC,cod_TAA,cod_TAG, cod_TGT,cod_TGC,cod_TGA,cod_TGG,$/;" g +codon2aa seqTools.cpp /^const codon2aa_map codon2aa = {$/;" v +codon2aa_map seqTools.h /^typedef std::unordered_map codon2aa_map;$/;" t +codon2str seqTools.cpp /^const codon2str_map codon2str = {$/;" v +codon2str_map seqTools.h /^typedef std::unordered_map codon2str_map;$/;" t computeEnergy snip.cpp /^double computeEnergy(const Vector &J, const std::vector &config) {$/;" f compute_num_escaped pop_ss.cpp /^unsigned int Population::compute_num_escaped(Hamiltonian &H) {$/;" f class:Population compute_num_escaped population.cpp /^unsigned int Population::compute_num_escaped(Hamiltonian &H) {$/;" f class:Population @@ -148,6 +353,7 @@ compute_num_escaped_all pop_ss.cpp /^unsigned int Population::compute_num_escape compute_num_escaped_all population.cpp /^unsigned int Population::compute_num_escaped_all(Hamiltonian &H) {$/;" f class:Population compute_population_size pop_ss.cpp /^unsigned int Population::compute_population_size() {$/;" f class:Population compute_population_size population.cpp /^unsigned int Population::compute_population_size() {$/;" f class:Population +config pop_ss.h /^ PottsState config;$/;" m class:NTVirus const_iterator sorted_vector.h /^ typedef typename Cont::const_iterator const_iterator;$/;" t class:codeproject::sorted_vector const_reference sorted_vector.h /^ typedef typename Cont::const_reference const_reference;$/;" t class:codeproject::sorted_vector const_reverse_iterator sorted_vector.h /^ typedef typename Cont::const_reverse_iterator const_reverse_iterator;$/;" t class:codeproject::sorted_vector @@ -155,6 +361,7 @@ contains hamiltonian.cpp /^inline bool contains(const std::set &container, co contains hamiltonian.cpp /^inline bool contains(const std::vector &vec, const T &value)$/;" f contains mc.cpp /^inline bool contains(const std::set &container, const T &value)$/;" f contains mc.cpp /^inline bool contains(const std::vector &vec, const T &value)$/;" f +count pop_ss.h /^ long count;$/;" m class:Species count sorted_vector.h /^ size_type count(const K& k) const$/;" f class:codeproject::sorted_vector couplingsInfile mc.h /^ std::string couplingsInfile;$/;" m class:RunParameters_MC couplingsInfile ss.h /^ std::string couplingsInfile;$/;" m class:RunParameters_SS @@ -179,6 +386,8 @@ eend wf.h /^ int eend; \/\/ Epitope end position$/;" m clas empty sorted_vector.h /^ bool empty() const {return vec_.empty();}$/;" f class:codeproject::sorted_vector end sorted_vector.h /^ const_iterator end() const {return vec_.end();}$/;" f class:codeproject::sorted_vector end sorted_vector.h /^ iterator end() {return vec_.end();}$/;" f class:codeproject::sorted_vector +energy pop_ss.h /^ double energy;$/;" m class:NTVirus +energy pop_ss.h /^ double energy;$/;" m class:Virus energy virus.h /^ double energy;$/;" m class:Virus ensure_get_energy_false_instantiated hamiltonian.cpp /^double ensure_get_energy_false_instantiated(const std::set &x) { EpitopeHamiltonian A((std::string&)""); return A.get_energy(x); }$/;" f epitopeAllSites hamiltonian.h /^ MutatedSiteSequence epitopeAllSites; \/\/ all site indices belonging to an epitope (WT or mut ant)$/;" m class:EpitopeHamiltonian @@ -187,11 +396,16 @@ epitopeInfile ss.h /^ std::string epitopeInfile;$/;" m class:RunParameters_SS epitopeInfile wf.h /^ std::string epitopeInfile;$/;" m class:RunParameters epitopeMut hamiltonian.h /^ std::vector > epitopeMut;$/;" m class:EpitopeHamiltonian epitopeMut hamiltonian.h /^ std::vector epitopeMut;$/;" m class:EpitopeHamiltonian +epitopeMut pop_ss.h /^ std::vector epitopeMut; \/\/ sites with state=1 are recognized$/;" m class:EpitopeRecognizer epitopeWT hamiltonian.h /^ std::vector > epitopeWT;$/;" m class:EpitopeHamiltonian epitopeWT hamiltonian.h /^ std::vector epitopeWT;$/;" m class:EpitopeHamiltonian +epitopeWT pop_ss.h /^ std::vector epitopeWT; \/\/ sites with state=0 are recognized$/;" m class:EpitopeRecognizer epitopefile mc.h /^ std::string epitopefile; \/\/ Input file name for targeted epitopes$/;" m class:RunParameters_MC epitopefile ss.h /^ std::string epitopefile; \/\/ Input file name for targeted epitopes$/;" m class:RunParameters_SS epitopefile wf.h /^ std::string epitopefile; \/\/ Input file name for targeted epitopes$/;" m class:RunParameters +epitopefiles ss.h /^ std::vector epitopefiles;$/;" m class:RunParameters_SS +epitopes pop_ss.h /^ std::vector epitopes;$/;" m class:CTLaaSpecies +epitopes pop_ss.h /^ std::vector epitopes;$/;" m class:CTLSpecies equal_range sorted_vector.h /^ Paircc_ equal_range(const K& k) const$/;" f class:codeproject::sorted_vector equal_range sorted_vector.h /^ Pairii_ equal_range(const K& k)$/;" f class:codeproject::sorted_vector erase sorted_vector.h /^ iterator erase(iterator first, iterator beyond)$/;" f class:codeproject::sorted_vector @@ -207,6 +421,10 @@ escaped hamiltonian.cpp /^bool EpitopeHamiltonian::escaped(const std::set &mutated_sites, const std::vector &eWT, const std::vector &eMut) const {$/;" 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 pop_ss.cpp /^bool AARecognizer::escaped(const NTVirus &v) const {$/;" f class:AARecognizer +escaped pop_ss.cpp /^bool AARecognizer::escaped(const std::vector &aa_seq) const {$/;" f class:AARecognizer +escaped pop_ss.cpp /^bool EpitopeRecognizer::escaped(const MutatedSiteSequence &mutated_sites) const {$/;" f class:EpitopeRecognizer +escaped pop_ss.cpp /^bool EpitopeRecognizer::escaped(const Virus &v) const {$/;" f class:EpitopeRecognizer escaped pop_ss.cpp /^bool Population::escaped(Hamiltonian &H) {$/;" f class:Population escaped population.cpp /^bool Population::escaped(Hamiltonian &H) {$/;" f class:Population escaped_all hamiltonian.cpp /^bool EpitopeHamiltonian::escaped_all(const Virus &v) {$/;" f class:EpitopeHamiltonian @@ -220,6 +438,15 @@ estart ss.h /^ int estart; \/\/ Epitope start position$/;" m estart wf.h /^ int estart; \/\/ Epitope start position$/;" m class:RunParameters find sorted_vector.h /^ const_iterator find(const K& k) const$/;" f class:codeproject::sorted_vector find sorted_vector.h /^ iterator find(const K& k)$/;" f class:codeproject::sorted_vector +fire reaction.cpp /^void AAKillingReaction::fire()$/;" 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()$/;" f class:ElementaryReaction +fire reaction.cpp /^void KillingReaction::fire()$/;" 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 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$/;" m class:RunParameters_MC @@ -227,9 +454,14 @@ g ss.h /^ unsigned int g; \/\/ Number of generations$/;" m class: g wf.h /^ unsigned int g; \/\/ Number of generations$/;" m class:RunParameters generate_allsites_set hamiltonian.cpp /^void EpitopeHamiltonian::generate_allsites_set()$/;" f class:EpitopeHamiltonian getCorrelations snip.cpp /^void getCorrelations(FILE *input, Vector &p) {$/;" f +getCouplings ham_ss.cpp /^void PottsHamiltonian::getCouplings(const std::string &FILENAME)$/;" f class:PottsHamiltonian getCouplings snip.cpp /^void getCouplings(FILE *input, Vector &p) {$/;" f +getSeq2State ham_ss.cpp /^void PottsHamiltonian::getSeq2State(const std::string &FILENAME)$/;" f class:PottsHamiltonian +getSeq2State seqTools.cpp /^void getSeq2State(FILE *input, CharVector &p)$/;" f get_allocator sorted_vector.h /^ A get_allocator() const {return vec_.get_allocator();}$/;" f class:codeproject::sorted_vector get_container sorted_vector.h /^ Cont& get_container()$/;" f class:codeproject::sorted_vector +get_energy ham_ss.cpp /^double Hamiltonian::get_energy(const std::set &mutated_sites) const {$/;" f class:Hamiltonian +get_energy ham_ss.cpp /^double PottsHamiltonian::get_energy(const PottsState &config) const$/;" f class:PottsHamiltonian get_energy hamiltonian.cpp /^double EpitopeHamiltonian::get_energy(const std::set &mutated_sites) const {$/;" 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 @@ -244,16 +476,23 @@ h1 wf.h /^ double h1;$/;" m class:RunParameters h2 mc.h /^ double h2;$/;" m class:RunParameters_MC h2 ss.h /^ double h2;$/;" m class:RunParameters_SS h2 wf.h /^ double h2;$/;" m class:RunParameters +hash seqTools.h /^ template<> struct hash {$/;" s namespace:std +hash seqTools.h /^ template<> struct hash {$/;" s namespace:std +hash seqTools.h /^ template<> struct hash {$/;" s namespace:std id main.cpp /^ int id;$/;" m struct:STest file: importEpitope mc.cpp /^void importEpitope(RunParameters_MC &r) {$/;" f importEpitope ss.cpp /^void importEpitope(RunParameters_SS &r) {$/;" f +importEpitope ss.cpp /^void importEpitope(RunParameters_SS &r, Species_parray &species, Rxn_parray &reactions, VirusSpecies *V, Species_parray &print_spec)$/;" f importEpitope wf.cpp /^void importEpitope(RunParameters &r) {$/;" f +importEpitope_Potts ss.cpp /^void importEpitope_Potts(RunParameters_SS &r, Species_parray &species, Rxn_parray &reactions, NTVirusSpecies *V, Species_parray &print_spec)$/;" f importState mc.cpp /^void importState(RunParameters_MC &r) {$/;" f importState mc.h /^ bool importState; \/\/ If true, import state from a state file$/;" m class:RunParameters_MC importState ss.cpp /^void importState(RunParameters_SS &r) {$/;" f importState ss.h /^ bool importState; \/\/ If true, import state from a state file$/;" m class:RunParameters_SS importState wf.cpp /^void importState(RunParameters &r) {$/;" f importState wf.h /^ bool importState; \/\/ If true, import state from a state file$/;" m class:RunParameters +importState_Potts ss.cpp /^void importState_Potts(RunParameters_SS &r)$/;" f +index ham_ss.h /^inline int index(int i, int j, size_t length) {$/;" f index snip.h /^inline int index(int i, int j, size_t length) {$/;" f infile mc.h /^ std::string infile; \/\/ Input file from which couplings are to be read$/;" m class:RunParameters_MC infile ss.h /^ std::string infile; \/\/ Input file from which couplings are to be read$/;" m class:RunParameters_SS @@ -264,18 +503,27 @@ initFrac wf.h /^ std::vector initFrac; \/\/ Initial initPop mc.h /^ std::vector > initPop; \/\/ Initial population sequences$/;" m class:RunParameters_MC initPop ss.h /^ std::vector > initPop; \/\/ Initial population sequences$/;" m class:RunParameters_SS initPop wf.h /^ std::vector > initPop; \/\/ Initial population sequences$/;" m class:RunParameters +initPop_NT ss.h /^ std::vector initPop_NT;$/;" m class:RunParameters_SS initState mc.h /^ MutatedSiteSequence initState; \/\/ initial state of system$/;" m class:RunParameters_MC +init_CTL_numM ss.h /^ std::vector init_CTL_numM;$/;" m class:RunParameters_SS +init_CTL_numN ss.h /^ std::vector init_CTL_numN;$/;" m class:RunParameters_SS +init_CTL_numT ss.h /^ std::vector init_CTL_numT;$/;" m class:RunParameters_SS initial_sequence mc.cpp /^MutatedSiteSequence initial_sequence(const EpitopeHamiltonian &H, const MutatedSiteSequence &initState)$/;" f +initialize_Ising ss.cpp /^void initialize_Ising(RunParameters_SS &r, Species_parray &species, Rxn_parray &reactions, Species_parray &print_spec)$/;" f +initialize_Potts ss.cpp /^void initialize_Potts(RunParameters_SS &r, Species_parray &species, Rxn_parray &reactions, Species_parray &print_spec)$/;" f insert sorted_vector.h /^ void insert(It first, It beyond)$/;" f class:codeproject::sorted_vector 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)$/;" f class:codeproject::sorted_vector +int2aa seqTools.cpp /^const int2str_map int2aa = {$/;" 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 iterator sorted_vector.h /^ typedef typename Cont::iterator iterator;$/;" t class:codeproject::sorted_vector key_comp sorted_vector.h /^ key_compare key_comp() const {return key_compare_; }$/;" f class:codeproject::sorted_vector 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;$/;" t class:codeproject::sorted_vector +len pop_ss.h /^ size_t len;$/;" 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 ltstr main.cpp /^struct ltstr$/;" s file: @@ -285,37 +533,62 @@ m_stop main.cpp /^ time_t m_start, m_stop;$/;" m class:SimpTimer file: main main.cpp /^int main()$/;" f main mc.cpp /^int main(int argc, char *argv[]) {$/;" f main seqTools.cpp /^int main(int argc, char *argv[])$/;" f +main snip.cpp /^int main(int argc, char **argv)$/;" f main ss.cpp /^int main(int argc, char *argv[]) {$/;" f main test/make_tests.py /^def main():$/;" f main wf.cpp /^int main(int argc, char *argv[]) {$/;" f max_size sorted_vector.h /^ size_type max_size() const {return vec_.max_size();}$/;" f class:codeproject::sorted_vector +max_steps ss.h /^ long max_steps;$/;" m class:RunParameters_SS mu mc.h /^ double mu; \/\/ Mutation rate$/;" m class:RunParameters_MC mu pop_ss.h /^ double mu; \/\/ Mutation rate$/;" m class:Population mu population.h /^ double mu; \/\/ Mutation rate$/;" m class:Population +mu reaction.h /^ double mu;$/;" m class:NTVirusReaction +mu reaction.h /^ double mu;$/;" m class:VirusReaction mu ss.h /^ double mu; \/\/ Mutation rate$/;" m class:RunParameters_SS mu virus.h /^ double mu;$/;" 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 pop_ss.cpp /^void Population::mutate_population(const Hamiltonian &H, gsl_rng* r) {$/;" f class:Population mutate_population population.cpp /^void Population::mutate_population(const Hamiltonian &H, gsl_rng* r) {$/;" f class:Population +mutated_sites pop_ss.h /^ std::set mutated_sites;$/;" m class:Virus mutated_sites virus.h /^ std::set mutated_sites;$/;" m class:Virus n mc.h /^ unsigned int n; \/\/ Population size$/;" m class:RunParameters_MC n ss.h /^ unsigned int n; \/\/ Population size$/;" 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 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$/;" m class:EpitopeHamiltonian +nt seqTools.h /^enum nt {nt_T,nt_C,nt_A,nt_G};$/;" g +nt2str seqTools.cpp /^const nt2str_map nt2str = {$/;" v +nt2str_map seqTools.h /^typedef std::unordered_map nt2str_map;$/;" t +nt_A seqTools.h /^enum nt {nt_T,nt_C,nt_A,nt_G};$/;" e enum:nt +nt_C seqTools.h /^enum nt {nt_T,nt_C,nt_A,nt_G};$/;" e enum:nt +nt_G seqTools.h /^enum nt {nt_T,nt_C,nt_A,nt_G};$/;" e enum:nt +nt_T seqTools.h /^enum nt {nt_T,nt_C,nt_A,nt_G};$/;" e enum:nt +nt_seq pop_ss.h /^ std::string nt_seq;$/;" m class:NTVirus numEpitopes mc.h /^ unsigned int numEpitopes; \/\/ how many epitopes are targeted$/;" m class:RunParameters_MC numEpitopes ss.h /^ unsigned int numEpitopes; \/\/ how many epitopes are targeted$/;" m class:RunParameters_SS numEpitopes wf.h /^ unsigned int numEpitopes; \/\/ how many epitopes are targeted$/;" m class:RunParameters +num_CTL_clones ss.h /^ unsigned int num_CTL_clones;$/;" m class:RunParameters_SS +num_T_gen ss.h /^ unsigned int num_T_gen; \/\/ ND, number of effector cell generations (i.e. divisions)$/;" m class:RunParameters_SS +num_ep pop_ss.h /^ size_t num_ep;$/;" m class:CTLSpecies +num_ep pop_ss.h /^ size_t num_ep;$/;" m class:CTLaaSpecies num_runs mc.h /^ unsigned int num_runs; \/\/ Number of times to run the simulation for gathering overall statistics$/;" m class:RunParameters_MC num_runs ss.h /^ unsigned int num_runs; \/\/ Number of times to run the simulation for gathering overall statistics$/;" m class:RunParameters_SS num_runs wf.h /^ unsigned int num_runs; \/\/ Number of times to run the simulation for gathering overall statistics$/;" m class:RunParameters operator != sorted_vector.h /^ bool operator!=(const sorted_vector& x,$/;" f namespace:codeproject operator () main.cpp /^ bool operator()(const char* s1, const char* s2) const$/;" f struct:ltstr +operator () seqTools.h /^ inline size_t operator()(const aa &x) const { return static_cast(x); }$/;" f struct:std::hash +operator () seqTools.h /^ inline size_t operator()(const codon &x) const { return static_cast(x); }$/;" f struct:std::hash +operator () seqTools.h /^ inline size_t operator()(const nt &x) const { return static_cast(x); }$/;" f struct:std::hash operator < main.cpp /^bool operator<(const STest& t0,const STest& t1)$/;" f +operator < pop_ss.cpp /^bool operator<(const NTVirus& lhs, const NTVirus& rhs) {$/;" f +operator < pop_ss.cpp /^bool operator<(const Virus& lhs, const Virus& rhs) {$/;" f operator < sorted_vector.h /^ bool operator<(const sorted_vector& x,$/;" f namespace:codeproject operator < virus.cpp /^bool operator<(const Virus& lhs, const Virus& rhs) {$/;" f +operator << ss.h /^std::ostream& operator<<(std::ostream& os, MutatedSiteSequence s)$/;" f +operator << ss.h /^std::ostream& operator<<(std::ostream& os, std::vector s)$/;" f operator <= sorted_vector.h /^ bool operator<=(const sorted_vector& x,$/;" f namespace:codeproject operator = sorted_vector.h /^ Myt_& operator=(const Cont& x){vec_.operator=(x);$/;" f class:codeproject::sorted_vector operator = sorted_vector.h /^ Myt_& operator=(const Myt_& x) {vec_.operator=(x.vec_);$/;" f class:codeproject::sorted_vector @@ -337,19 +610,57 @@ penalty ss.h /^ double penalty; \/\/ Energy p penalty wf.h /^ double penalty; \/\/ Energy penalty if sequence contains the targeted epitope$/;" m class:RunParameters penaltyType ss.h /^ PenaltyTYPE penaltyType;$/;" m class:RunParameters_SS penaltyType wf.h /^ PenaltyTYPE penaltyType;$/;" m class:RunParameters +pop pop_ss.h /^ NTVirus_map pop;$/;" m class:NTVirusSpecies pop pop_ss.h /^ virus_map pop;$/;" m class:Population +pop pop_ss.h /^ virus_map pop;$/;" m class:VirusSpecies pop population.h /^ virus_map pop;$/;" m class:Population pop_back sorted_vector.h /^ void pop_back() {vec_.pop_back();}$/;" f class:codeproject::sorted_vector print_parameters virus.cpp /^void Virus::print_parameters() {$/;" f class:Virus print_population_size pop_ss.cpp /^void Population::print_population_size() {$/;" f class:Population 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)$/;" f +product_stoich reaction.h /^ std::vector product_stoich; \/\/ must be negative for reactants that are consumed!$/;" m class:ElementaryReaction +products reaction.h /^ std::vector products; \/\/ effects of reaction$/;" m class:ElementaryReaction +propensity reaction.h /^ double propensity;$/;" m class:Reaction +rate_a ss.h /^ double rate_a;$/;" m class:RunParameters_SS +rate_aprime ss.h /^ double rate_aprime;$/;" m class:RunParameters_SS +rate_b ss.h /^ double rate_b;$/;" m class:RunParameters_SS +rate_constant reaction.h /^ double rate_constant; \/\/ must manually ensure it includes division by statistical degeneracy factor (in case of reaction order >1 for any species)$/;" m class:Reaction +rate_d ss.h /^ double rate_d;$/;" m class:RunParameters_SS +rate_dprime ss.h /^ double rate_dprime;$/;" m class:RunParameters_SS +rate_e ss.h /^ double rate_e;$/;" m class:RunParameters_SS +rate_g ss.h /^ double rate_g;$/;" m class:RunParameters_SS +rate_h ss.h /^ double rate_h;$/;" m class:RunParameters_SS +rate_p ss.h /^ double rate_p;$/;" m class:RunParameters_SS +rate_r ss.h /^ double rate_r;$/;" m class:RunParameters_SS +rate_s ss.h /^ double rate_s;$/;" m class:RunParameters_SS +rate_u ss.h /^ double rate_u;$/;" m class:RunParameters_SS +rate_w ss.h /^ double rate_w;$/;" m class:RunParameters_SS rbegin sorted_vector.h /^ const_reverse_iterator rbegin() const $/;" f class:codeproject::sorted_vector rbegin sorted_vector.h /^ reverse_iterator rbegin() {return vec_.rbegin();}$/;" f class:codeproject::sorted_vector +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()$/;" f class:AAKillingReaction +recalc reaction.cpp /^double CTLActivationReaction::recalc()$/;" f class:CTLActivationReaction +recalc reaction.cpp /^double CTLaaActivationReaction::recalc()$/;" f class:CTLaaActivationReaction +recalc reaction.cpp /^double ElementaryReaction::recalc()$/;" f class:ElementaryReaction +recalc reaction.cpp /^double KillingReaction::recalc()$/;" f class:KillingReaction +recalc reaction.cpp /^double NTVirusDeathReaction::recalc()$/;" f class:NTVirusDeathReaction +recalc reaction.cpp /^double NTVirusReaction::recalc()$/;" f class:NTVirusReaction +recalc reaction.cpp /^double VirusDeathReaction::recalc()$/;" f class:VirusDeathReaction +recalc reaction.cpp /^double VirusReaction::recalc()$/;" f class:VirusReaction +recognized pop_ss.cpp /^double CTLSpecies::recognized(const MutatedSiteSequence &mutated_sites) const {$/;" 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 +recognized pop_ss.cpp /^double CTLaaSpecies::recognized(const std::vector &aa_seq) const {$/;" f class:CTLaaSpecies +ref pop_ss.h /^ std::vector ref;$/;" m class:AARecognizer reference sorted_vector.h /^ typedef typename Cont::reference reference;$/;" t class:codeproject::sorted_vector rend sorted_vector.h /^ const_reverse_iterator rend() const $/;" f class:codeproject::sorted_vector rend sorted_vector.h /^ reverse_iterator rend() {return vec_.rend();}$/;" f class:codeproject::sorted_vector reserve sorted_vector.h /^ void reserve(size_type n) {vec_.reserve(n);}$/;" f class:codeproject::sorted_vector reverse_iterator sorted_vector.h /^ typedef typename Cont::reverse_iterator reverse_iterator;$/;" t class:codeproject::sorted_vector +rnd ss.cpp /^gsl_rng *rnd; \/\/pointer to random number generator state$/;" v run mc.cpp /^void run(RunParameters_MC &r, unsigned seed) {$/;" f run ss.cpp /^void run(RunParameters_SS &r, unsigned seed) {$/;" f run wf.cpp /^void run(RunParameters &r) {$/;" f @@ -368,19 +679,31 @@ s:l session.vim /^let s:l = 55 - ((0 * winheight(0) + 13) \/ 26)$/;" v s:so_save session.vim /^let s:so_save = &so | let s:siso_save = &siso | set so=0 siso=0$/;" v s:sx session.vim /^let s:sx = expand(":p:r")."x.vim"$/;" v s:wipebuf session.vim /^ let s:wipebuf = bufnr('%')$/;" v +sample_interval ss.h /^ double sample_interval;$/;" m class:RunParameters_SS +seq2stateInfile ss.h /^ std::string seq2stateInfile;$/;" m class:RunParameters_SS setFiles mc.h /^ void setFiles() {$/;" f class:RunParameters_MC setFiles ss.h /^ void setFiles() {$/;" f class:RunParameters_SS 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 ham_ss.h /^ void set_temp(double x) { bh=x; bJ=x; }$/;" f class:Hamiltonian +set_temp ham_ss.h /^ void set_temp(double x) { bh=x; bJ=x; }$/;" f class:PottsHamiltonian +set_temp ham_ss.h /^ void set_temp(double x, double y) { bh=x; bJ=y; }$/;" f class:Hamiltonian +set_temp ham_ss.h /^ void set_temp(double x, double y) { bh=x; bJ=y; }$/;" f class:PottsHamiltonian 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 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 +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;$/;" m class:AARecognizer +size ham_ss.h /^ int size;$/;" m class:Hamiltonian +size ham_ss.h /^ unsigned int size; \/\/ amino acid length$/;" m class:PottsHamiltonian size hamiltonian.h /^ int size;$/;" m class:Hamiltonian size sorted_vector.h /^ size_type size() const {return vec_.size();}$/;" f class:codeproject::sorted_vector size_type sorted_vector.h /^ typedef typename Cont::size_type size_type;$/;" t class:codeproject::sorted_vector +sizetolength ham_ss.h /^inline int sizetolength(size_t size) {$/;" f sizetolength snip.h /^inline int sizetolength(size_t size) {$/;" f sort sorted_vector.h /^ void sort()\/\/restore sorted order after low level access $/;" f class:codeproject::sorted_vector sorted_vector sorted_vector.h /^ class sorted_vector {$/;" c namespace:codeproject @@ -388,13 +711,24 @@ sorted_vector sorted_vector.h /^ explicit sorted_vector(const Pr& pred = Pr(),co sorted_vector sorted_vector.h /^ sorted_vector(It first, It beyond, $/;" f class:codeproject::sorted_vector sorted_vector sorted_vector.h /^ sorted_vector(const Myt_& x)$/;" f class:codeproject::sorted_vector sorted_vector sorted_vector.h /^ sorted_vector(const_iterator first, const_iterator beyond, $/;" f class:codeproject::sorted_vector +split ss.h /^inline std::vector &split(const std::string &s, char delim, std::vector &elems) {$/;" f +split ss.h /^inline std::vector split(const std::string &s, char delim) {$/;" f stable_sort sorted_vector.h /^ void stable_sort()\/\/restore sorted order after low level access $/;" f class:codeproject::sorted_vector +state2aa ham_ss.h /^ std::vector > state2aa;$/;" m class:PottsHamiltonian stateInfile mc.h /^ std::string stateInfile;$/;" m class:RunParameters_MC stateInfile ss.h /^ std::string stateInfile;$/;" m class:RunParameters_SS stateInfile wf.h /^ std::string stateInfile;$/;" m class:RunParameters statefile mc.h /^ std::string statefile; \/\/ Input state file which contains initial population fractions$/;" m class:RunParameters_MC 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 {$/;" n +str2aa seqTools.cpp /^const str2aa_map str2aa = {$/;" v +str2aa_map seqTools.h /^typedef std::unordered_map str2aa_map;$/;" t +str2codon seqTools.cpp /^const str2codon_map str2codon = {$/;" v +str2codon_map seqTools.h /^typedef std::unordered_map str2codon_map;$/;" t +str2int_map seqTools.h /^typedef std::unordered_map str2int_map;$/;" t +str2nt seqTools.cpp /^const str2nt_map str2nt = {$/;" v +str2nt_map seqTools.h /^typedef std::unordered_map str2nt_map;$/;" t strtodouble mc.h /^inline double strtodouble(const std::string &s) {$/;" f strtodouble ss.h /^inline double strtodouble(const std::string &s) {$/;" f strtodouble wf.h /^inline double strtodouble(const std::string &s) {$/;" f @@ -403,6 +737,7 @@ strtoint ss.h /^inline int strtoint(const std::string &s) {$/;" f strtoint wf.h /^inline int strtoint(const std::string &s) {$/;" f strtouint mc.h /^inline int strtouint(const std::string &s) {$/;" f strtouint ss.h /^inline int strtouint(const std::string &s) {$/;" f +strtouint ss.h /^inline unsigned int strtouint(const std::string &s) {$/;" f strtouint wf.h /^inline int strtouint(const std::string &s) {$/;" f supplementaryOutfile mc.h /^ std::string supplementaryOutfile;$/;" m class:RunParameters_MC supplementaryOutfile ss.h /^ std::string supplementaryOutfile;$/;" m class:RunParameters_SS @@ -412,13 +747,18 @@ survival virus.cpp /^double Virus::survival(double Eavg) const {$/;" f class:Vir swap sorted_vector.h /^ friend void swap(Myt_& x, Myt_& Y_)$/;" f class:codeproject::sorted_vector swap sorted_vector.h /^ void swap(Myt_& x)$/;" f class:codeproject::sorted_vector sys test/make_tests.py /^import sys$/;" i +t_end ss.h /^ double t_end;$/;" m class:RunParameters_SS +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 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;$/;" m class:RunParameters +translate_nt_seq pop_ss.cpp /^std::vector translate_nt_seq(const std::string &nt_seq)$/;" f unsorted_find main.cpp /^FwIt unsorted_find(FwIt beg,FwIt beyond,Pred pred)$/;" f +update_energy pop_ss.cpp /^void NTVirus::update_energy(const PottsHamiltonian &H)$/;" 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 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 @@ -427,7 +767,9 @@ usage ss.cpp /^void usage()$/;" f usage wf.cpp /^void usage()$/;" 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 useEpitope wf.h /^ bool useEpitope; \/\/ Include selective pressure on an epitope $/;" m class:RunParameters +usePotts ss.h /^ bool usePotts;$/;" m class:RunParameters_SS useRelative mc.h /^ bool useRelative; \/\/ If true, use relative energy for survival probability$/;" m class:RunParameters_MC useRelative ss.h /^ bool useRelative; \/\/ If true, use relative energy for survival probability$/;" m class:RunParameters_SS useRelative wf.h /^ bool useRelative; \/\/ If true, use relative energy for survival probability$/;" m class:RunParameters @@ -453,6 +795,7 @@ write_population population.cpp /^void Population::write_population(std::string write_two_site_population pop_ss.cpp /^void Population::write_two_site_population(FILE *output, const Hamiltonian &H, unsigned int generation) {$/;" f class:Population write_two_site_population population.cpp /^void Population::write_two_site_population(FILE *output, const Hamiltonian &H, unsigned int generation) {$/;" f class:Population zt session.vim /^normal! zt$/;" m +~Hamiltonian ham_ss.h /^ virtual ~Hamiltonian() { }$/;" f class:Hamiltonian ~Hamiltonian hamiltonian.h /^ virtual ~Hamiltonian() { }$/;" f class:Hamiltonian ~RunParameters wf.h /^ ~RunParameters() {}$/;" f class:RunParameters ~RunParameters_MC mc.h /^ ~RunParameters_MC() {}$/;" f class:RunParameters_MC