021l session.vim /^normal! 021l$/;" m
<NL> session.vim /^noremap <NL> \16\17j$/;" m
<Plug>NetrwBrowseX session.vim /^nnoremap <silent> <Plug>NetrwBrowseX :call netrw#NetrwBrowseX(expand("\16<cWORD>"),0)\16$/;" m
+AAKillingReaction reaction.h /^ AAKillingReaction() : Reaction() {}$/;" 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<unsigned> &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 {$/;" c
+AdjacencyList ham_ss.h /^typedef std::vector<std::vector<int> > AdjacencyList;$/;" t
AdjacencyList hamiltonian.h /^typedef std::vector<std::vector<int> > AdjacencyList;$/;" t
BuildIntersection main.cpp /^BuildIntersection(std::vector<int>& v0,std::vector<int>& v1)$/;" f
BuildIntersection1 main.cpp /^BuildIntersection1(std::vector<int>& v0,std::vector<int>& 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++$/;" m
+CharVector seqTools.h /^typedef std::vector<std::vector<char> > CharVector;$/;" t
Cont sorted_vector.h /^ typedef typename std::vector<K,A> Cont;$/;" t class:codeproject::sorted_vector
+Coupling ham_ss.h /^typedef std::vector<std::vector<double> > Coupling;$/;" t
Coupling hamiltonian.h /^typedef std::vector<std::vector<double> > 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 $/;" f class:codeproject::sorted_vector
ExecTests main.cpp /^void ExecTests(std::vector<T>& v)$/;" 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<std::vector<int> > IntVector;$/;" t
IntVector snip.h /^typedef std::vector<std::vector<int> > IntVector;$/;" 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;$/;" m class:RunParameters_SS
KeyCompare_Geq_ sorted_vector.h /^ bool KeyCompare_Geq_(const K& ty0,const K& ty1)$/;" 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 name="Main"><\/a>$/;" a
MakeSTest main.cpp /^STest MakeSTest()$/;" f
+MutatedSiteSequence ham_ss.h /^typedef std::set<unsigned int> MutatedSiteSequence;$/;" t
MutatedSiteSequence hamiltonian.h /^typedef std::set<unsigned int> MutatedSiteSequence;$/;" t
MutatedSiteSequence mc.h /^typedef std::set<unsigned int> MutatedSiteSequence;$/;" t
+MutatedSiteSequence pop_ss.h /^typedef std::set<unsigned int> MutatedSiteSequence;$/;" t
+MutatedSiteSequence reaction.h /^typedef std::set<unsigned int> MutatedSiteSequence;$/;" t
Myt_ sorted_vector.h /^ typedef sorted_vector<K,bNoDuplicates,Pr,A> Myt_;$/;" 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, unsigned int> NTVirus_map;$/;" t
POPULATION_H pop_ss.h 2;" d
POPULATION_H population.h 2;" d
+POP_SS_H pop_ss.h 2;" d
Paircc_ sorted_vector.h /^ typedef typename std::pair<const_iterator, const_iterator> Paircc_;$/;" t class:codeproject::sorted_vector
Pairib_ sorted_vector.h /^ typedef typename std::pair<iterator, bool> Pairib_;$/;" t class:codeproject::sorted_vector
Pairii_ sorted_vector.h /^ typedef typename std::pair<iterator, iterator> Pairii_;$/;" t class:codeproject::sorted_vector
Population population.cpp /^Population::Population(const Hamiltonian &H, unsigned int N, double mu) {$/;" f class:Population
Population population.cpp /^Population::Population(const Hamiltonian &H, unsigned int N, double mu, const std::vector<std::set<unsigned int> > &initPop, const std::vector<double> &initFrac) {$/;" f class:Population
Population population.h /^class Population{$/;" c
+PottsHamiltonian ham_ss.cpp /^PottsHamiltonian::PottsHamiltonian(const std::string &couplingsFile, const std::string &seq2stateFile) : bh(1.0), bJ(1.0)$/;" 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<unsigned> PottsState;$/;" t
+PottsState pop_ss.h /^typedef std::vector<unsigned> PottsState;$/;" 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<Reaction*> 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*> 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()$/;" f
TestMultiSet main.cpp /^void TestMultiSet(std::vector<T>& v)$/;" f
TestSetOperations main.cpp /^void TestSetOperations(const std::vector<T>& v0,$/;" f
TestSortedVector_AsMultiSet main.cpp /^void TestSortedVector_AsMultiSet(std::vector<T>& v)$/;" f
TestSortedVector_AsSet main.cpp /^void TestSortedVector_AsSet(std::vector<T>& 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;$/;" m class:VirusReaction
VERSION_SORTED_VECTOR_ sorted_vector.h 25;" d
VIRUS_H virus.h 2;" d
Vector snip.h /^typedef std::vector<std::vector<double> > Vector;$/;" t
+Virus pop_ss.cpp /^Virus::Virus(const Hamiltonian &H) {$/;" f class:Virus
+Virus pop_ss.cpp /^Virus::Virus(const Hamiltonian &H, const std::set<unsigned int> &mutated_sites) {$/;" 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<unsigned int> &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
]% session.vim /^vmap ]% \16\e]%m'gv``$/;" m
_articleTop sorted_vector_doc.html /^ <a name="_articleTop" id="_articleTop"><\/a>$/;" a
a% session.vim /^vmap a% \16\e[%v]%$/;" m
+aa2int seqTools.cpp /^const str2int_map aa2int = {$/;" v
+aa2state ham_ss.h /^ std::vector<std::array<int,aa_END> > aa2state;$/;" m class:PottsHamiltonian
+aa2str seqTools.cpp /^const aa2str_map aa2str = {$/;" v
+aa2str_map seqTools.h /^typedef std::unordered_map<aa,char> aa2str_map;$/;" t
+aa_seq pop_ss.h /^ std::vector<aa> aa_seq;$/;" m class:NTVirus
+aaseq2str pop_ss.cpp /^std::string aaseq2str(const std::vector<aa> &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<double> affinity;$/;" m class:CTLSpecies
+affinity pop_ss.h /^ std::vector<double> affinity;$/;" 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
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
charmap seqTools.cpp /^typedef std::unordered_map<char,int> charmap;$/;" t file:
checkTest test/runTests.sh /^checkTest () {$/;" f
clear sorted_vector.h /^ void clear() {return vec_.clear();}$/;" f class:codeproject::sorted_vector
+coarse_grain ham_ss.cpp /^void PottsHamiltonian::coarse_grain(const std::vector<aa> &aa_seq, PottsState &config) const$/;" 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 = {$/;" v
+codon2aa_map seqTools.h /^typedef std::unordered_map<codon,aa> codon2aa_map;$/;" t
+codon2str seqTools.cpp /^const codon2str_map codon2str = {$/;" v
+codon2str_map seqTools.h /^typedef std::unordered_map<codon,std::string> codon2str_map;$/;" t
computeEnergy snip.cpp /^double computeEnergy(const Vector &J, const std::vector<int> &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) {$/;" f class:Population
compute_num_escaped_all population.cpp /^unsigned int Population::compute_num_escaped_all(Hamiltonian &H) {$/;" 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
contains hamiltonian.cpp /^inline bool contains(const std::vector<T> &vec, const T &value)$/;" f
contains mc.cpp /^inline bool contains(const std::set<T> &container, const T &value)$/;" f
contains mc.cpp /^inline bool contains(const std::vector<T> &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;$/;" m class:RunParameters_SS
empty sorted_vector.h /^ bool empty() const {return vec_.empty();}$/;" 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;$/;" m class:Virus
ensure_get_energy_false_instantiated hamiltonian.cpp /^double ensure_get_energy_false_instantiated(const std::set<unsigned int> &x) { EpitopeHamiltonian A((std::string&)""); return A.get_energy<false>(x); }$/;" f
epitopeAllSites hamiltonian.h /^ MutatedSiteSequence epitopeAllSites; \/\/ all site indices belonging to an epitope (WT or mut ant)$/;" m class:EpitopeHamiltonian
epitopeInfile wf.h /^ std::string epitopeInfile;$/;" m class:RunParameters
epitopeMut hamiltonian.h /^ std::vector<std::vector<unsigned int> > epitopeMut;$/;" m class:EpitopeHamiltonian
epitopeMut hamiltonian.h /^ std::vector<unsigned int> epitopeMut;$/;" m class:EpitopeHamiltonian
+epitopeMut pop_ss.h /^ std::vector<unsigned int> epitopeMut; \/\/ sites with state=1 are recognized$/;" m class:EpitopeRecognizer
epitopeWT hamiltonian.h /^ std::vector<std::vector<unsigned int> > epitopeWT;$/;" m class:EpitopeHamiltonian
epitopeWT hamiltonian.h /^ std::vector<unsigned int> epitopeWT;$/;" m class:EpitopeHamiltonian
+epitopeWT pop_ss.h /^ std::vector<unsigned int> epitopeWT; \/\/ sites with state=0 are recognized$/;" 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$/;" m class:RunParameters
+epitopefiles ss.h /^ std::vector<std::string> epitopefiles;$/;" m class:RunParameters_SS
+epitopes pop_ss.h /^ std::vector<AARecognizer> epitopes;$/;" m class:CTLaaSpecies
+epitopes pop_ss.h /^ std::vector<EpitopeRecognizer> epitopes;$/;" 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)$/;" f class:codeproject::sorted_vector
escaped hamiltonian.cpp /^bool EpitopeHamiltonian::escaped(const std::set<unsigned int> &mutated_sites, const std::vector<unsigned int> &eWT, const std::vector<unsigned int> &eMut) const {$/;" f class:EpitopeHamiltonian
escaped hamiltonian.h /^ virtual bool escaped(const Virus &v) { return false; }$/;" f class:Hamiltonian
escaped hamiltonian.h /^ virtual bool escaped(const std::set<unsigned int> &mutated_sites) const { return false; }$/;" f class:Hamiltonian
+escaped pop_ss.cpp /^bool AARecognizer::escaped(const NTVirus &v) const {$/;" f class:AARecognizer
+escaped pop_ss.cpp /^bool AARecognizer::escaped(const std::vector<aa> &aa_seq) const {$/;" 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) {$/;" f class:EpitopeHamiltonian
estart wf.h /^ int estart; \/\/ Epitope start position$/;" 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
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()$/;" f class:codeproject::sorted_vector
+get_energy ham_ss.cpp /^double Hamiltonian::get_energy(const std::set<unsigned int> &mutated_sites) const {$/;" f class:Hamiltonian
+get_energy ham_ss.cpp /^double PottsHamiltonian::get_energy(const PottsState &config) const$/;" f class:PottsHamiltonian
get_energy hamiltonian.cpp /^double EpitopeHamiltonian::get_energy(const std::set<unsigned int> &mutated_sites) const {$/;" f class:EpitopeHamiltonian
get_energy hamiltonian.cpp /^double EpitopeHamiltonian::get_energy(const std::set<unsigned int> &mutated_sites) const$/;" f class:EpitopeHamiltonian
get_energy hamiltonian.cpp /^double Hamiltonian::get_energy(const std::set<unsigned int> &mutated_sites) const {$/;" f class:Hamiltonian
h2 mc.h /^ double h2;$/;" m class:RunParameters_MC
h2 ss.h /^ double h2;$/;" m class:RunParameters_SS
h2 wf.h /^ double h2;$/;" m class:RunParameters
+hash seqTools.h /^ template<> struct hash<aa> {$/;" s namespace:std
+hash seqTools.h /^ template<> struct hash<codon> {$/;" s namespace:std
+hash seqTools.h /^ template<> struct hash<nt> {$/;" 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$/;" m class:RunParameters_SS
initPop mc.h /^ std::vector<std::set<unsigned int> > initPop; \/\/ Initial population sequences$/;" m class:RunParameters_MC
initPop ss.h /^ std::vector<std::set<unsigned int> > initPop; \/\/ Initial population sequences$/;" m class:RunParameters_SS
initPop wf.h /^ std::vector<std::set<unsigned int> > initPop; \/\/ Initial population sequences$/;" m class:RunParameters
+initPop_NT ss.h /^ std::vector<std::string> 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<long> init_CTL_numM;$/;" m class:RunParameters_SS
+init_CTL_numN ss.h /^ std::vector<long> init_CTL_numN;$/;" m class:RunParameters_SS
+init_CTL_numT ss.h /^ std::vector<long> 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 = {$/;" v
+int2str_map seqTools.h /^typedef std::unordered_map<int,char> int2str_map;$/;" 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:
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<unsigned int> mutated_sites;$/;" m class:Virus
mutated_sites virus.h /^ std::set<unsigned int> mutated_sites;$/;" 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 = {$/;" v
+nt2str_map seqTools.h /^typedef std::unordered_map<nt,char> nt2str_map;$/;" 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$/;" m class:RunParameters
operator != sorted_vector.h /^ bool operator!=(const sorted_vector<K, bNoDuplicates,Pr,A>& x,$/;" f namespace:codeproject
operator () main.cpp /^ bool operator()(const char* s1, const char* s2) const$/;" f struct:ltstr
+operator () seqTools.h /^ inline size_t operator()(const aa &x) const { return static_cast<int>(x); }$/;" f struct:std::hash
+operator () seqTools.h /^ inline size_t operator()(const codon &x) const { return static_cast<int>(x); }$/;" f struct:std::hash
+operator () seqTools.h /^ inline size_t operator()(const nt &x) const { return static_cast<int>(x); }$/;" 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) {$/;" f
operator < sorted_vector.h /^ bool operator<(const sorted_vector<K, bNoDuplicates,Pr,A>& x,$/;" 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<unsigned int> s)$/;" f
operator <= sorted_vector.h /^ bool operator<=(const sorted_vector<K, bNoDuplicates,Pr,A>& x,$/;" 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
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)$/;" f
+product_stoich reaction.h /^ std::vector<int> product_stoich; \/\/ must be negative for reactants that are consumed!$/;" m class:ElementaryReaction
+products reaction.h /^ std::vector<Species*> 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<int> reactant_stoich; \/\/ reaction order$/;" m class:ElementaryReaction
+reactants reaction.h /^ std::vector<Species*> reactants; \/\/ anything that participates in reaction rate$/;" 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> &aa_seq) const {$/;" f class:CTLaaSpecies
+ref pop_ss.h /^ std::vector<aa> ref;$/;" 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
s:so_save session.vim /^let s:so_save = &so | let s:siso_save = &siso | set so=0 siso=0$/;" v
s:sx session.vim /^let s:sx = expand("<sfile>:p:r")."x.vim"$/;" 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<unsigned int> &eWT, const std::vector<unsigned int> &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) {$/;" f
+site pop_ss.h /^ std::vector<unsigned> site;$/;" 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
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, $/;" f class:codeproject::sorted_vector
+split ss.h /^inline std::vector<std::string> &split(const std::string &s, char delim, std::vector<std::string> &elems) {$/;" f
+split ss.h /^inline std::vector<std::string> split(const std::string &s, char delim) {$/;" f
stable_sort sorted_vector.h /^ void stable_sort()\/\/restore sorted order after low level access $/;" f class:codeproject::sorted_vector
+state2aa ham_ss.h /^ std::vector<std::vector<aa> > state2aa;$/;" 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<char,aa> str2aa_map;$/;" t
+str2codon seqTools.cpp /^const str2codon_map str2codon = {$/;" v
+str2codon_map seqTools.h /^typedef std::unordered_map<std::string,codon> str2codon_map;$/;" t
+str2int_map seqTools.h /^typedef std::unordered_map<char,int> str2int_map;$/;" t
+str2nt seqTools.cpp /^const str2nt_map str2nt = {$/;" v
+str2nt_map seqTools.h /^typedef std::unordered_map<char,nt> str2nt_map;$/;" 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) {$/;" f
strtoint wf.h /^inline int strtoint(const std::string &s) {$/;" 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
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;$/;" m class:RunParameters
+translate_nt_seq pop_ss.cpp /^std::vector<aa> translate_nt_seq(const std::string &nt_seq)$/;" 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
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$/;" m class:RunParameters
write_two_site_population pop_ss.cpp /^void Population::write_two_site_population(FILE *output, const Hamiltonian &H, unsigned int generation) {$/;" 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
projects / VirEvoDyn.git / commitdiff