From 04087dea54b85ecdfbae1b300382276a7b9a3c17 Mon Sep 17 00:00:00 2001 From: Dariusz Murakowski Date: Fri, 20 Mar 2015 14:26:11 -0400 Subject: [PATCH] ctags -a -R --- tags | 347 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 347 insertions(+) diff --git a/tags b/tags index a66f177..6a7cfa5 100644 --- a/tags +++ b/tags @@ -1,114 +1,461 @@ + session.vim /^noremap  h$/;" m + session.vim /^noremap  k$/;" m + session.vim /^noremap  l$/;" m + session.vim /^inoremap  u$/;" m + session.vim /^inoremap  u$/;" m !_TAG_FILE_FORMAT 2 /extended format; --format=1 will not append ;" to lines/ !_TAG_FILE_SORTED 1 /0=unsorted, 1=sorted, 2=foldcase/ !_TAG_PROGRAM_AUTHOR Darren Hiebert /dhiebert@users.sourceforge.net/ !_TAG_PROGRAM_NAME Exuberant Ctags // !_TAG_PROGRAM_URL http://ctags.sourceforge.net /official site/ !_TAG_PROGRAM_VERSION 5.8 // +0 session.vim /^normal! 0$/;" m +021l session.vim /^normal! 021l$/;" m + session.vim /^noremap j$/;" m +NetrwBrowseX session.vim /^nnoremap NetrwBrowseX :call netrw#NetrwBrowseX(expand(""),0)$/;" m AdjacencyList hamiltonian.h /^typedef std::vector > AdjacencyList;$/;" t +BuildIntersection main.cpp /^BuildIntersection(std::vector& v0,std::vector& v1)$/;" f +BuildIntersection1 main.cpp /^BuildIntersection1(std::vector& v0,std::vector& v1)$/;" f +CFLAGS Makefile /^CFLAGS = $(DBGFLAG) -Wall -Wextra -pedantic -Wno-unused-parameter$/;" m +CXX Makefile /^CXX = c++$/;" m +Cont sorted_vector.h /^ typedef typename std::vector Cont;$/;" t class:codeproject::sorted_vector Coupling hamiltonian.h /^typedef std::vector > 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 $/;" f class:codeproject::sorted_vector +ExecTests main.cpp /^void ExecTests(std::vector& v)$/;" 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 > 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;$/;" m class:RunParameters +Key snip.h /^typedef std::vector Key;$/;" 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$/;" f class:codeproject::sorted_vector +MC_H mc.h 2;" d +Main sorted_vector_doc.html /^ <\/a>$/;" a +MakeSTest main.cpp /^STest MakeSTest()$/;" f +MutatedSiteSequence hamiltonian.h /^typedef std::set MutatedSiteSequence;$/;" t +MutatedSiteSequence mc.h /^typedef std::set MutatedSiteSequence;$/;" t +Myt_ sorted_vector.h /^ typedef sorted_vector Myt_;$/;" t class:codeproject::sorted_vector +N pop_ss.h /^ unsigned int N; \/\/ Population size$/;" m class:Population N population.h /^ unsigned int N; \/\/ Population size$/;" m class:Population +POPULATION_H pop_ss.h 2;" d POPULATION_H population.h 2;" d +Paircc_ sorted_vector.h /^ typedef typename std::pair Paircc_;$/;" t class:codeproject::sorted_vector +Pairib_ sorted_vector.h /^ typedef typename std::pair Pairib_;$/;" t class:codeproject::sorted_vector +Pairii_ sorted_vector.h /^ typedef typename std::pair Pairii_;$/;" t class:codeproject::sorted_vector +PenaltyEACH ss.h /^ enum PenaltyTYPE { PenaltyEACH, PenaltyTOTAL };$/;" e enum:RunParameters_SS::PenaltyTYPE +PenaltyEACH wf.h /^ enum PenaltyTYPE { PenaltyEACH, PenaltyTOTAL };$/;" e enum:RunParameters::PenaltyTYPE +PenaltyTOTAL ss.h /^ enum PenaltyTYPE { PenaltyEACH, PenaltyTOTAL };$/;" e enum:RunParameters_SS::PenaltyTYPE +PenaltyTOTAL wf.h /^ enum PenaltyTYPE { PenaltyEACH, PenaltyTOTAL };$/;" e enum:RunParameters::PenaltyTYPE +PenaltyTYPE ss.h /^ enum PenaltyTYPE { PenaltyEACH, PenaltyTOTAL };$/;" g class:RunParameters_SS +PenaltyTYPE wf.h /^ enum PenaltyTYPE { PenaltyEACH, PenaltyTOTAL };$/;" g class:RunParameters +Population pop_ss.cpp /^Population::Population(const Hamiltonian &H, unsigned int N, double mu) {$/;" f class:Population +Population pop_ss.cpp /^Population::Population(const Hamiltonian &H, unsigned int N, double mu, const std::vector > &initPop, const std::vector &initFrac) {$/;" f class:Population +Population pop_ss.h /^class Population{$/;" c Population population.cpp /^Population::Population(const Hamiltonian &H, unsigned int N, double mu) {$/;" f class:Population Population population.cpp /^Population::Population(const Hamiltonian &H, unsigned 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/^ SimpTimer(const char* msg):m_msg(msg),m_start(clock()){}$/;" 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()$/;" f +TestMultiSet main.cpp /^void TestMultiSet(std::vector& v)$/;" f +TestSet main.cpp /^void TestSet(std::vector& v)$/;" f +TestSetOperations main.cpp /^void TestSetOperations(const std::vector& v0,$/;" f +TestSortedVector_AsMultiSet main.cpp /^void TestSortedVector_AsMultiSet(std::vector& v)$/;" f +TestSortedVector_AsSet main.cpp /^void TestSortedVector_AsSet(std::vector& v)$/;" f 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 > 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 &mutated_sites) {$/;" f class:Virus Virus virus.h /^class Virus {$/;" c +WF_H ss.h 2;" d WF_H wf.h 2;" d +Y session.vim /^nnoremap Y y\$$/;" m +[% session.vim /^vmap [% [%m'gv``$/;" m +]% session.vim /^vmap ]% ]%m'gv``$/;" m +_articleTop sorted_vector_doc.html /^ <\/a>$/;" a +a% session.vim /^vmap a% [%v]%$/;" 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$/;" m class:RunParameters +charmap seqTools.cpp /^typedef std::unordered_map charmap;$/;" 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{$/;" n +computeEnergy snip.cpp /^double computeEnergy(const Vector &J, const std::vector &config) {$/;" 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;$/;" t class:codeproject::sorted_vector +contains hamiltonian.cpp /^inline bool contains(const std::set &container, const T &value)$/;" f +contains hamiltonian.cpp /^inline bool contains(const std::vector &vec, const T &value)$/;" f +contains mc.cpp /^inline bool contains(const std::set &container, const T &value)$/;" f +contains mc.cpp /^inline bool contains(const std::vector &vec, const T &value)$/;" f +count sorted_vector.h /^ size_type count(const K& k) const$/;" 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)$/;" f +eMut mc.h /^ std::vector > eMut; \/\/ Sites that are mutant in the targeted epitope$/;" m class:RunParameters_MC +eMut ss.h /^ std::vector > eMut; \/\/ Sites that are mutant in the targeted epitope$/;" m class:RunParameters_SS +eMut wf.h /^ std::vector > eMut; \/\/ Sites that are mutant in the targeted epitope$/;" m class:RunParameters eMut wf.h /^ std::vector eMut; \/\/ Sites that are mutant in the targeted epitope$/;" m class:RunParameters +eWT mc.h /^ std::vector > eWT; \/\/ Sites that are consensus (WT) in the targeted epitope$/;" m class:RunParameters_MC +eWT ss.h /^ std::vector > eWT; \/\/ Sites that are consensus (WT) in the targeted epitope$/;" m class:RunParameters_SS +eWT wf.h /^ std::vector > eWT; \/\/ Sites that are consensus (WT) in the targeted epitope$/;" m class:RunParameters eWT wf.h /^ std::vector eWT; \/\/ Sites that are consensus (WT) in the targeted epitope$/;" m class:RunParameters +eend mc.h /^ int eend; \/\/ Epitope end position$/;" 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 &x) { EpitopeHamiltonian A((std::string&)""); return A.get_energy(x); }$/;" f +epitopeAllSites hamiltonian.h /^ MutatedSiteSequence epitopeAllSites; \/\/ all site indices belonging to an epitope (WT or mut ant)$/;" m class:EpitopeHamiltonian +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;$/;" m class:RunParameters +epitopeMut hamiltonian.h /^ std::vector > epitopeMut;$/;" m class:EpitopeHamiltonian epitopeMut hamiltonian.h /^ std::vector epitopeMut;$/;" m class:EpitopeHamiltonian +epitopeWT hamiltonian.h /^ std::vector > epitopeWT;$/;" m class:EpitopeHamiltonian epitopeWT hamiltonian.h /^ std::vector 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 +erase sorted_vector.h /^ iterator erase(iterator first, iterator beyond)$/;" f class:codeproject::sorted_vector +erase sorted_vector.h /^ iterator erase(iterator p) {return vec_.erase(p);}$/;" f class:codeproject::sorted_vector +erase sorted_vector.h /^ size_type erase(const K& key) $/;" f class:codeproject::sorted_vector +escape_variant pop_ss.cpp /^unsigned int Population::escape_variant(Hamiltonian &H, std::set &mutant) {$/;" f class:Population escape_variant population.cpp /^unsigned int Population::escape_variant(Hamiltonian &H, std::set &mutant) {$/;" f class:Population +escape_variant_all pop_ss.cpp /^unsigned int Population::escape_variant_all(Hamiltonian &H, std::set &mutant) {$/;" f class:Population +escape_variant_all population.cpp /^unsigned int Population::escape_variant_all(Hamiltonian &H, std::set &mutant) {$/;" f class:Population escaped hamiltonian.cpp /^bool EpitopeHamiltonian::escaped(const Virus &v) {$/;" f class:EpitopeHamiltonian +escaped hamiltonian.cpp /^bool EpitopeHamiltonian::escaped(const Virus &v, const std::vector &eWT, const std::vector &eMut) {$/;" f class:EpitopeHamiltonian escaped hamiltonian.cpp /^bool EpitopeHamiltonian::escaped(const std::set &mutated_sites) const {$/;" f class:EpitopeHamiltonian +escaped hamiltonian.cpp /^bool EpitopeHamiltonian::escaped(const std::set &mutated_sites, const std::vector &eWT, const std::vector &eMut) const {$/;" f class:EpitopeHamiltonian escaped hamiltonian.h /^ virtual bool escaped(const Virus &v) { return false; }$/;" f class:Hamiltonian escaped hamiltonian.h /^ virtual bool escaped(const std::set &mutated_sites) const { return false; }$/;" f class:Hamiltonian +escaped pop_ss.cpp /^bool Population::escaped(Hamiltonian &H) {$/;" 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 &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 &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 &mutated_sites) const {$/;" f class:EpitopeHamiltonian +get_energy hamiltonian.cpp /^double EpitopeHamiltonian::get_energy(const std::set &mutated_sites) const$/;" f class:EpitopeHamiltonian get_energy hamiltonian.cpp /^double Hamiltonian::get_energy(const std::set &mutated_sites) const {$/;" f class:Hamiltonian +gh session.vim /^map gh :exe 'normal '.(virtcol('.')\/2).'|'$/;" m +gl session.vim /^map gl :exe 'normal '.(virtcol('.') + (virtcol('$')-virtcol('.'))\/2).'|'$/;" m +glob test/make_tests.py /^import glob$/;" i +gm session.vim /^map gm :exe 'normal '.(virtcol('$')\/2).'|'$/;" m +gx session.vim /^nmap gx NetrwBrowseX$/;" 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 initFrac; \/\/ Initial population fraction$/;" m class:RunParameters_MC +initFrac ss.h /^ std::vector initFrac; \/\/ Initial population fraction$/;" m class:RunParameters_SS initFrac wf.h /^ std::vector initFrac; \/\/ Initial population fraction$/;" m class:RunParameters +initPop mc.h /^ std::vector > initPop; \/\/ Initial population sequences$/;" m class:RunParameters_MC +initPop ss.h /^ std::vector > initPop; \/\/ Initial population sequences$/;" m class:RunParameters_SS initPop wf.h /^ std::vector > initPop; \/\/ Initial population sequences$/;" m class:RunParameters +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 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$/;" m class:RunParameters +operator != sorted_vector.h /^ bool operator!=(const sorted_vector& x,$/;" 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& 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& 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_);$/;" f class:codeproject::sorted_vector +operator == sorted_vector.h /^ bool operator==(const sorted_vector& x,$/;" f namespace:codeproject +operator > sorted_vector.h /^ bool operator>(const sorted_vector& x,$/;" f namespace:codeproject +operator >= sorted_vector.h /^ bool operator>=(const sorted_vector& x,$/;" 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;$/;" m class:EpitopeHamiltonian +penalty hamiltonian.h /^ std::vector penalty;$/;" 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(":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() {$/;" f class:RunParameters set_epitope hamiltonian.cpp /^void EpitopeHamiltonian::set_epitope(const std::vector &eWT, const std::vector &eMut, double d) {$/;" f class:EpitopeHamiltonian set_temp hamiltonian.h /^ void set_temp(double x) { bh=x; bJ=x; }$/;" f class:Hamiltonian set_temp hamiltonian.h /^ void set_temp(double x, double y) { bh=x; bJ=y; }$/;" f class:Hamiltonian +sim_random_seed 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_map;$/;" t virus_map population.h /^typedef std::map virus_map;$/;" 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 -- 2.7.4