+\16\b session.vim /^noremap \16\b \16\17h$/;" m
+\16\v session.vim /^noremap \16\v \16\17k$/;" m
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!_TAG_FILE_FORMAT 2 /extended format; --format=1 will not append ;" to lines/
!_TAG_FILE_SORTED 1 /0=unsorted, 1=sorted, 2=foldcase/
!_TAG_PROGRAM_AUTHOR Darren Hiebert /dhiebert@users.sourceforge.net/
!_TAG_PROGRAM_NAME Exuberant Ctags //
!_TAG_PROGRAM_URL http://ctags.sourceforge.net /official site/
!_TAG_PROGRAM_VERSION 5.8 //
+0 session.vim /^normal! 0$/;" m
+021l session.vim /^normal! 021l$/;" 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
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
+CXX Makefile /^CXX = c++$/;" m
+Cont sorted_vector.h /^ typedef typename std::vector<K,A> Cont;$/;" t class:codeproject::sorted_vector
Coupling hamiltonian.h /^typedef std::vector<std::vector<double> > Coupling;$/;" t
+DBGFLAG Makefile /^ DBGFLAG = -O3 -combine$/;" 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
EpitopeHamiltonian hamiltonian.cpp /^EpitopeHamiltonian::EpitopeHamiltonian(std::string &FILENAME) {$/;" f class:EpitopeHamiltonian
EpitopeHamiltonian hamiltonian.h /^class EpitopeHamiltonian : public Hamiltonian {$/;" 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 hamiltonian.h /^ AdjacencyList Graph;$/;" m class:Hamiltonian
HAMILTONIAN_H hamiltonian.h 2;" d
Hamiltonian hamiltonian.cpp /^Hamiltonian::Hamiltonian(std::string &FILENAME) {$/;" f class:Hamiltonian
Hamiltonian hamiltonian.h /^ Hamiltonian() { }$/;" f class:Hamiltonian
Hamiltonian hamiltonian.h /^class Hamiltonian {$/;" c
+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 snip.h /^typedef std::vector<std::vector<int> > IntVector;$/;" t
J hamiltonian.h /^ Coupling J;$/;" m class:Hamiltonian
+J12 mc.h /^ double J12;$/;" m class:RunParameters_MC
+J12 ss.h /^ double J12;$/;" m class:RunParameters_SS
J12 wf.h /^ double J12;$/;" m class:RunParameters
+Key snip.h /^typedef std::vector<unsigned long> Key;$/;" 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)$/;" f class:codeproject::sorted_vector
L virus.h /^ unsigned int L;$/;" m class:Virus
+LIBDIR Makefile /^LIBDIR = # -L\/usr\/local\/pkg\/gsl\/gsl-1.15\/lib$/;" m
+LIBS Makefile /^LIBS = -lgsl -lgslcblas -lm$/;" m
+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()$/;" f
+MutatedSiteSequence hamiltonian.h /^typedef std::set<unsigned int> MutatedSiteSequence;$/;" t
+MutatedSiteSequence mc.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
+POPULATION_H pop_ss.h 2;" d
POPULATION_H population.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_;$/;" t class:codeproject::sorted_vector
+PenaltyEACH ss.h /^ enum PenaltyTYPE { PenaltyEACH, PenaltyTOTAL };$/;" e enum:RunParameters_SS::PenaltyTYPE
+PenaltyEACH wf.h /^ enum PenaltyTYPE { PenaltyEACH, PenaltyTOTAL };$/;" e enum:RunParameters::PenaltyTYPE
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+PenaltyTYPE ss.h /^ enum PenaltyTYPE { PenaltyEACH, PenaltyTOTAL };$/;" g class:RunParameters_SS
+PenaltyTYPE wf.h /^ enum PenaltyTYPE { PenaltyEACH, PenaltyTOTAL };$/;" g class:RunParameters
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+Population pop_ss.cpp /^Population::Population(const Hamiltonian &H, unsigned int N, double mu, const std::vector<std::set<unsigned int> > &initPop, const std::vector<double> &initFrac) {$/;" f class:Population
+Population 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<std::set<unsigned int> > &initPop, const std::vector<double> &initFrac) {$/;" f class:Population
Population population.h /^class Population{$/;" c
RunParameters wf.h /^ RunParameters() {$/;" f class:RunParameters
RunParameters wf.h /^class RunParameters {$/;" c
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+RunParameters_SS ss.h /^class RunParameters_SS {$/;" c
+SGITest main.cpp /^int SGITest()$/;" 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$/;" m
+SRCS_SS Makefile /^SRCS_SS = ss.cpp hamiltonian.cpp population.cpp virus.cpp$/;" m
+SRCS_WF Makefile /^SRCS_WF = wf.cpp hamiltonian.cpp population.cpp virus.cpp$/;" m
+STest main.cpp /^struct STest{$/;" 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{$/;" c file:
+Template test/make_tests.py /^from string import Template$/;" i
+TestAllSet main.cpp /^void TestAllSet()$/;" f
+TestMultiSet main.cpp /^void TestMultiSet(std::vector<T>& v)$/;" f
+TestSet main.cpp /^void TestSet(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
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
+VERSION_SORTED_VECTOR_ sorted_vector.h 25;" d
VIRUS_H virus.h 2;" d
+Vector snip.h /^typedef std::vector<std::vector<double> > Vector;$/;" t
Virus virus.cpp /^Virus::Virus(const Hamiltonian &H, double mu) {$/;" f class:Virus
Virus virus.cpp /^Virus::Virus(const Hamiltonian &H, double mu, const std::set<unsigned int> &mutated_sites) {$/;" f class:Virus
Virus virus.h /^class Virus {$/;" c
+WF_H ss.h 2;" d
WF_H wf.h 2;" d
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+]% 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]%$/;" m
+add_to_two_site_pop mc.cpp /^void add_to_two_site_pop(RunParameters_MC &r, bool s1, bool s2, double frac) {$/;" 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
+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
+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);}$/;" f class:codeproject::sorted_vector
bJ hamiltonian.h /^ double bJ; \/\/ couplings "inverse temperature" multiplier$/;" 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
bJ wf.h /^ double bJ; \/\/ Coupling "inverse temperature" multiplier$/;" m class:RunParameters
+back sorted_vector.h /^ const_reference back() const {return vec_.back();}$/;" f class:codeproject::sorted_vector
+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(); }$/;" f class:codeproject::sorted_vector
bh hamiltonian.h /^ double bh; \/\/ fields "inverse temperature" multiplier$/;" 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
bh wf.h /^ double bh; \/\/ Field "inverse temperature" multiplier$/;" m class:RunParameters
+charmap seqTools.cpp /^typedef std::unordered_map<char,int> charmap;$/;" t file:
+checkTest test/runTests.sh /^checkTest () {$/;" f
+clear sorted_vector.h /^ void clear() {return vec_.clear();}$/;" f class:codeproject::sorted_vector
+codeproject sorted_vector.h /^namespace codeproject{$/;" n
+computeEnergy snip.cpp /^double computeEnergy(const Vector &J, const std::vector<int> &config) {$/;" 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 pop_ss.cpp /^unsigned int Population::compute_num_escaped_all(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
+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;$/;" t class:codeproject::sorted_vector
+contains hamiltonian.cpp /^inline bool contains(const std::set<T> &container, const T &value)$/;" f
+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)$/;" f
+count sorted_vector.h /^ size_type count(const K& k) const$/;" 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
couplingsInfile wf.h /^ std::string couplingsInfile;$/;" m class:RunParameters
+defrm sorted_vector_doc.html /^function defrm () { \/* thanks twitter *\/ document.write = ''; window.top.location = window.self.location; setTimeout(function() { document.body.innerHTML = ''; }, 0); window.self.onload = function(evt) { document.body.innerHTML = ''; }; }if (window.top !== window.self) { try { if (window.top.location.host) { \/* will throw *\/ } else { defrm(); \/* chrome *\/ } } catch (ex) { defrm(); \/* everyone else *\/ } }if (typeof(DemoUrl)!='undefined') document.write(unescape('%3Cme')+'ta http'+'-equiv="re'+'fresh" con'+'tent="1;url='+DemoUrl+unescape('"%3CE'));$/;" f
+difference_type sorted_vector.h /^ typedef typename Cont::difference_type difference_type;$/;" t class:codeproject::sorted_vector
+directory mc.h /^ std::string directory; \/\/ Path to the directory where the inut file is located$/;" m class:RunParameters_MC
+directory ss.h /^ std::string directory; \/\/ Path to the directory where the inut file is located$/;" m class:RunParameters_SS
directory wf.h /^ std::string directory; \/\/ Path to the directory where the inut file is located$/;" m class:RunParameters
+do_flip_or_not mc.cpp /^bool do_flip_or_not(const EpitopeHamiltonian &H, MutatedSiteSequence &seq, gsl_rng *r, unsigned &site)$/;" f
+eMut mc.h /^ std::vector<std::vector<unsigned int> > eMut; \/\/ Sites that are mutant in the targeted epitope$/;" m class:RunParameters_MC
+eMut ss.h /^ std::vector<std::vector<unsigned int> > eMut; \/\/ Sites that are mutant in the targeted epitope$/;" m class:RunParameters_SS
+eMut wf.h /^ std::vector<std::vector<unsigned int> > eMut; \/\/ Sites that are mutant in the targeted epitope$/;" m class:RunParameters
eMut wf.h /^ std::vector<unsigned int> eMut; \/\/ Sites that are mutant in the targeted epitope$/;" m class:RunParameters
+eWT mc.h /^ std::vector<std::vector<unsigned int> > eWT; \/\/ Sites that are consensus (WT) in the targeted epitope$/;" m class:RunParameters_MC
+eWT ss.h /^ std::vector<std::vector<unsigned int> > eWT; \/\/ Sites that are consensus (WT) in the targeted epitope$/;" m class:RunParameters_SS
+eWT wf.h /^ std::vector<std::vector<unsigned int> > eWT; \/\/ Sites that are consensus (WT) in the targeted epitope$/;" m class:RunParameters
eWT wf.h /^ std::vector<unsigned int> eWT; \/\/ Sites that are consensus (WT) in the targeted epitope$/;" m class:RunParameters
+eend mc.h /^ int eend; \/\/ Epitope end position$/;" m class:RunParameters_MC
+eend ss.h /^ int eend; \/\/ Epitope end position$/;" m class:RunParameters_SS
eend wf.h /^ int eend; \/\/ Epitope end position$/;" m class:RunParameters
+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();}$/;" f class:codeproject::sorted_vector
energy virus.h /^ double energy;$/;" 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 mc.h /^ std::string epitopeInfile;$/;" m class:RunParameters_MC
+epitopeInfile ss.h /^ std::string epitopeInfile;$/;" m class:RunParameters_SS
+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;$/;" m class:EpitopeHamiltonian
+epitopeWT hamiltonian.h /^ std::vector<std::vector<unsigned int> > epitopeWT;$/;" m class:EpitopeHamiltonian
epitopeWT hamiltonian.h /^ std::vector<unsigned int> epitopeWT;$/;" m class:EpitopeHamiltonian
+epitopefile mc.h /^ std::string epitopefile; \/\/ Input file name for targeted epitopes$/;" 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
+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
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+erase sorted_vector.h /^ iterator erase(iterator p) {return vec_.erase(p);}$/;" f class:codeproject::sorted_vector
+erase sorted_vector.h /^ size_type erase(const K& key) $/;" f class:codeproject::sorted_vector
+escape_variant pop_ss.cpp /^unsigned int Population::escape_variant(Hamiltonian &H, std::set<unsigned int> &mutant) {$/;" f class:Population
escape_variant population.cpp /^unsigned int Population::escape_variant(Hamiltonian &H, std::set<unsigned int> &mutant) {$/;" f class:Population
+escape_variant_all pop_ss.cpp /^unsigned int Population::escape_variant_all(Hamiltonian &H, std::set<unsigned int> &mutant) {$/;" f class:Population
+escape_variant_all population.cpp /^unsigned int Population::escape_variant_all(Hamiltonian &H, std::set<unsigned int> &mutant) {$/;" f class:Population
escaped hamiltonian.cpp /^bool EpitopeHamiltonian::escaped(const Virus &v) {$/;" f class:EpitopeHamiltonian
+escaped hamiltonian.cpp /^bool EpitopeHamiltonian::escaped(const Virus &v, const std::vector<unsigned int> &eWT, const std::vector<unsigned int> &eMut) {$/;" f class:EpitopeHamiltonian
escaped hamiltonian.cpp /^bool EpitopeHamiltonian::escaped(const std::set<unsigned int> &mutated_sites) const {$/;" f class:EpitopeHamiltonian
+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; }$/;" f class:Hamiltonian
+escaped pop_ss.cpp /^bool Population::escaped(Hamiltonian &H) {$/;" 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
+escaped_all hamiltonian.cpp /^bool EpitopeHamiltonian::escaped_all(const std::set<unsigned int> &mutated_sites) const {$/;" f class:EpitopeHamiltonian
+escaped_all hamiltonian.h /^ virtual bool escaped_all(const Virus &v) { return false; }$/;" f class:Hamiltonian
+escaped_all hamiltonian.h /^ virtual bool escaped_all(const std::set<unsigned int> &mutated_sites) const { return false; }$/;" f class:Hamiltonian
+escaped_all pop_ss.cpp /^bool Population::escaped_all(Hamiltonian &H) {$/;" f class:Population
+escaped_all population.cpp /^bool Population::escaped_all(Hamiltonian &H) {$/;" f class:Population
+estart mc.h /^ int estart; \/\/ Epitope start position$/;" m class:RunParameters_MC
+estart ss.h /^ int estart; \/\/ Epitope start position$/;" m class:RunParameters_SS
estart wf.h /^ int estart; \/\/ Epitope start position$/;" 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
+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$/;" m class:RunParameters_MC
+g ss.h /^ unsigned int g; \/\/ Number of generations$/;" m class:RunParameters_SS
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) {$/;" f
+getCouplings snip.cpp /^void getCouplings(FILE *input, Vector &p) {$/;" 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 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 {$/;" f class:Hamiltonian
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+gl session.vim /^map <silent> gl :exe 'normal '.(virtcol('.') + (virtcol('$')-virtcol('.'))\/2).'\16|'\16$/;" m
+glob test/make_tests.py /^import glob$/;" i
+gm session.vim /^map <silent> gm :exe 'normal '.(virtcol('$')\/2).'\16|'\16$/;" m
+gx session.vim /^nmap gx <Plug>NetrwBrowseX$/;" m
+h1 mc.h /^ double h1;$/;" m class:RunParameters_MC
+h1 ss.h /^ double h1;$/;" m class:RunParameters_SS
h1 wf.h /^ double h1;$/;" 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;$/;" m class:RunParameters
+id main.cpp /^ int id;$/;" m struct:STest file:
+importEpitope mc.cpp /^void importEpitope(RunParameters_MC &r) {$/;" f
+importEpitope ss.cpp /^void importEpitope(RunParameters_SS &r) {$/;" f
+importEpitope wf.cpp /^void importEpitope(RunParameters &r) {$/;" f
+importState mc.cpp /^void importState(RunParameters_MC &r) {$/;" 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$/;" m class:RunParameters
+index snip.h /^inline int index(int i, int j, size_t length) {$/;" 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
infile wf.h /^ std::string infile; \/\/ Input file from which couplings are to be read$/;" m class:RunParameters
+initFrac mc.h /^ std::vector<double> initFrac; \/\/ Initial population fraction$/;" m class:RunParameters_MC
+initFrac ss.h /^ std::vector<double> initFrac; \/\/ Initial population fraction$/;" m class:RunParameters_SS
initFrac wf.h /^ std::vector<double> initFrac; \/\/ Initial population fraction$/;" m class:RunParameters
+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$/;" m class:RunParameters
+initState mc.h /^ MutatedSiteSequence initState; \/\/ initial state of system$/;" m class:RunParameters_MC
+initial_sequence mc.cpp /^MutatedSiteSequence initial_sequence(const EpitopeHamiltonian &H, const MutatedSiteSequence &initState)$/;" f
+insert sorted_vector.h /^ void insert(It first, It beyond)$/;" 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)$/;" f class:codeproject::sorted_vector
+is_unique main.cpp /^bool is_unique(It beg,It beyond,Pred pred)$/;" 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;$/;" t class:codeproject::sorted_vector
+lower_bound sorted_vector.h /^ const_iterator lower_bound(const K& k) const$/;" 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:
+m_msg main.cpp /^ std::string m_msg;$/;" m class:SimpTimer file:
+m_start main.cpp /^ time_t m_start, m_stop;$/;" m class:SimpTimer file:
+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 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
+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$/;" m class:Population
+mu ss.h /^ double mu; \/\/ Mutation rate$/;" 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) {$/;" f class:Population
mutated_sites virus.h /^ std::set<unsigned int> mutated_sites;$/;" 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$/;" m class:RunParameters
+next_generation pop_ss.cpp /^void Population::next_generation(const Hamiltonian &H, gsl_rng* r, bool useRelative, bool useVerbose) {$/;" 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
+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$/;" m class:RunParameters
+num_runs mc.h /^ unsigned int num_runs; \/\/ Number of times to run the simulation for gathering overall statistics$/;" 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 < main.cpp /^bool operator<(const STest& t0,const STest& t1)$/;" f
+operator < sorted_vector.h /^ bool operator<(const sorted_vector<K, bNoDuplicates,Pr,A>& x,$/;" f namespace:codeproject
operator < virus.cpp /^bool operator<(const Virus& lhs, const Virus& rhs) {$/;" f
+operator <= sorted_vector.h /^ bool operator<=(const sorted_vector<K, bNoDuplicates,Pr,A>& x,$/;" 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
+operator == sorted_vector.h /^ bool operator==(const sorted_vector<K, bNoDuplicates,Pr,A>& x,$/;" f namespace:codeproject
+operator > sorted_vector.h /^ bool operator>(const sorted_vector<K, bNoDuplicates,Pr,A>& x,$/;" f namespace:codeproject
+operator >= sorted_vector.h /^ bool operator>=(const sorted_vector<K, bNoDuplicates,Pr,A>& x,$/;" f namespace:codeproject
+operator [] sorted_vector.h /^ const_reference operator[](size_type p) const$/;" f class:codeproject::sorted_vector
+operator [] sorted_vector.h /^ reference operator[](size_type p) {return vec_.operator[](p);}$/;" f class:codeproject::sorted_vector
+os test/make_tests.py /^import os$/;" i
+outfile mc.h /^ std::string outfile; \/\/ Output file (prefix) where data is to be written$/;" m class:RunParameters_MC
+outfile ss.h /^ std::string outfile; \/\/ Output file (prefix) where data is to be written$/;" m class:RunParameters_SS
outfile wf.h /^ std::string outfile; \/\/ Output file (prefix) where data is to be written$/;" m class:RunParameters
+p pop_ss.h /^ double p; \/\/ Probability that a sequence has one or more mutations$/;" m class:Population
p population.h /^ double p; \/\/ Probability that a sequence has one or more mutations$/;" m class:Population
penalty hamiltonian.h /^ double penalty;$/;" m class:EpitopeHamiltonian
+penalty hamiltonian.h /^ std::vector<double> penalty;$/;" m class:EpitopeHamiltonian
+penalty mc.h /^ double penalty; \/\/ Energy penalty if sequence contains the targeted epitope$/;" m class:RunParameters_MC
+penalty ss.h /^ double penalty; \/\/ Energy penalty if sequence contains the targeted epitope$/;" m class:RunParameters_SS
penalty wf.h /^ double penalty; \/\/ Energy penalty if sequence contains the targeted epitope$/;" m class:RunParameters
+penaltyType ss.h /^ PenaltyTYPE penaltyType;$/;" m class:RunParameters_SS
+penaltyType wf.h /^ PenaltyTYPE penaltyType;$/;" m class:RunParameters
+pop pop_ss.h /^ virus_map pop;$/;" m class:Population
pop population.h /^ virus_map pop;$/;" 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
+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
+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
+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) {$/;" f
+run wf.cpp /^void run(RunParameters &r, unsigned seed) {$/;" f
+runUntilEscape mc.h /^ bool runUntilEscape; \/\/ If true, run the simulation until the population escapes$/;" m class:RunParameters_MC
+runUntilEscape ss.h /^ bool runUntilEscape; \/\/ If true, run the simulation until the population escapes$/;" m class:RunParameters_SS
runUntilEscape wf.h /^ bool runUntilEscape; \/\/ If true, run the simulation until the population escapes$/;" m class:RunParameters
+runUntilEscape_all ss.h /^ bool runUntilEscape_all; \/\/ If true, run the simulation until the population escapes *all* immune pressure$/;" m class:RunParameters_SS
+runUntilEscape_all wf.h /^ bool runUntilEscape_all; \/\/ If true, run the simulation until the population escapes *all* immune pressure$/;" m class:RunParameters
+s main.cpp /^ std::string s;$/;" m struct:STest file:
+s:cpo_save session.vim /^let s:cpo_save=&cpo$/;" v
+s:l session.vim /^let s:l = 13 - ((0 * winheight(0) + 13) \/ 26)$/;" v
+s:l session.vim /^let s:l = 15 - ((0 * winheight(0) + 13) \/ 26)$/;" v
+s:l session.vim /^let s:l = 38 - ((12 * winheight(0) + 13) \/ 26)$/;" v
+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("<sfile>:p:r")."x.vim"$/;" v
+s:wipebuf session.vim /^ let s:wipebuf = bufnr('%')$/;" v
+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 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() {$/;" f file:
+sindex snip.h /^inline int sindex(int i, int j, size_t qi, size_t qj) {$/;" f
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;$/;" t class:codeproject::sorted_vector
+sizetolength snip.h /^inline int sizetolength(size_t size) {$/;" 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 /^ explicit sorted_vector(const Pr& pred = Pr(),const A& al = A())$/;" f class:codeproject::sorted_vector
+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
+stable_sort sorted_vector.h /^ void stable_sort()\/\/restore sorted order after low level access $/;" f class:codeproject::sorted_vector
+stateInfile mc.h /^ std::string stateInfile;$/;" 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$/;" m class:RunParameters
+strtodouble mc.h /^inline double strtodouble(const std::string &s) {$/;" f
+strtodouble ss.h /^inline double strtodouble(const std::string &s) {$/;" f
strtodouble wf.h /^inline double strtodouble(const std::string &s) {$/;" f
+strtoint mc.h /^inline int strtoint(const std::string &s) {$/;" f
+strtoint ss.h /^inline int strtoint(const std::string &s) {$/;" 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) {$/;" f
strtouint wf.h /^inline int strtouint(const std::string &s) {$/;" f
+supplementaryOutfile mc.h /^ std::string supplementaryOutfile;$/;" m class:RunParameters_MC
+supplementaryOutfile ss.h /^ std::string supplementaryOutfile;$/;" m class:RunParameters_SS
supplementaryOutfile wf.h /^ std::string supplementaryOutfile;$/;" m class:RunParameters
survival virus.cpp /^double Virus::survival() const {$/;" f class:Virus
survival virus.cpp /^double Virus::survival(double Eavg) const {$/;" f class:Virus
+swap sorted_vector.h /^ friend void swap(Myt_& x, Myt_& Y_)$/;" 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
+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
+unsorted_find main.cpp /^FwIt unsorted_find(FwIt beg,FwIt beyond,Pred pred)$/;" f
update_energy virus.cpp /^void Virus::update_energy(const Hamiltonian &H) {$/;" 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 mc.cpp /^void usage()$/;" f
+usage ss.cpp /^void usage()$/;" 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 wf.h /^ bool useEpitope; \/\/ Include selective pressure on an epitope $/;" m class:RunParameters
+useRelative mc.h /^ bool useRelative; \/\/ If true, use relative energy for survival probability$/;" 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
+useTwoSite mc.h /^ bool useTwoSite; \/\/ If true, use two-site two-allele model$/;" m class:RunParameters_MC
+useTwoSite ss.h /^ bool useTwoSite; \/\/ If true, use two-site two-allele model$/;" m class:RunParameters_SS
useTwoSite wf.h /^ bool useTwoSite; \/\/ If true, use two-site two-allele model$/;" m class:RunParameters
+useVerbose mc.h /^ bool useVerbose; \/\/ If true, print extra information while program is running$/;" m class:RunParameters_MC
+useVerbose ss.h /^ bool useVerbose; \/\/ If true, print extra information while program is running$/;" m class:RunParameters_SS
useVerbose wf.h /^ bool useVerbose; \/\/ If true, print extra information while program is running$/;" m class:RunParameters
+value_comp sorted_vector.h /^ value_compare value_comp() const {return (key_comp()); }$/;" f class:codeproject::sorted_vector
+value_compare sorted_vector.h /^ typedef Pr value_compare;$/;" t class:codeproject::sorted_vector
+value_type sorted_vector.h /^ typedef typename Cont::value_type value_type;$/;" t class:codeproject::sorted_vector
+vec_ sorted_vector.h /^ Cont vec_;$/;" m class:codeproject::sorted_vector
+virus_map pop_ss.h /^typedef std::map<Virus, unsigned int> virus_map;$/;" t
virus_map population.h /^typedef std::map<Virus, unsigned int> virus_map;$/;" t
+write_mod mc.h /^ unsigned int write_mod; \/\/ Write state of the population every __ MC steps$/;" m class:RunParameters_MC
+write_mod ss.h /^ unsigned int write_mod; \/\/ Write state of the population every __ generations$/;" m class:RunParameters_SS
+write_mod wf.h /^ unsigned int write_mod; \/\/ Write state of the population every __ generations$/;" m class:RunParameters
+write_population pop_ss.cpp /^void Population::write_population(FILE *output, unsigned int generation) {$/;" f class:Population
+write_population pop_ss.cpp /^void Population::write_population(std::string filename) {$/;" f class:Population
write_population population.cpp /^void Population::write_population(FILE *output, unsigned int generation) {$/;" f class:Population
write_population population.cpp /^void Population::write_population(std::string filename) {$/;" f class:Population
+write_two_site_population pop_ss.cpp /^void Population::write_two_site_population(FILE *output, const Hamiltonian &H, unsigned int generation) {$/;" 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 hamiltonian.h /^ virtual ~Hamiltonian() { }$/;" f class:Hamiltonian
~RunParameters wf.h /^ ~RunParameters() {}$/;" f class:RunParameters
+~RunParameters_MC mc.h /^ ~RunParameters_MC() {}$/;" f class:RunParameters_MC
+~RunParameters_SS ss.h /^ ~RunParameters_SS() {}$/;" f class:RunParameters_SS
+~SimpTimer main.cpp /^ ~SimpTimer()$/;" f class:SimpTimer
+~sorted_vector sorted_vector.h /^ ~sorted_vector() {}$/;" f class:codeproject::sorted_vector
projects / VirEvoDyn.git / commitdiff