(minor) Don't build old Monte Carlo code. Print to stderr and throw exception. ctags...

diff --git a/Makefile b/Makefile
index 18565ba..e352d7b 100644 (file)
--- a/Makefile
+++ b/Makefile
@@ -2,8 +2,8 @@
 SRCS_WF = wf.cpp hamiltonian.cpp population.cpp virus.cpp
 EXECNAME_WF = wf
 
-SRCS_MC = mc.cpp hamiltonian.cpp population.cpp virus.cpp
-EXECNAME_MC = mc
+#SRCS_MC = mc.cpp hamiltonian.cpp population.cpp virus.cpp
+#EXECNAME_MC = mc
 
 SRCS_SS = ss.cpp ham_ss.cpp pop_ss.cpp reaction.cpp seqTools.cpp
 EXECNAME_SS = ss

diff --git a/pop_ss.cpp b/pop_ss.cpp
index 6ef8419..bebd37c 100644 (file)
--- a/pop_ss.cpp
+++ b/pop_ss.cpp
@@ -111,8 +111,10 @@ NTVirus::NTVirus(const PottsHamiltonian &H, const std::string &NT)
 , L_aa(this->L_nt/3)
 {
     //assert(this->L_aa == H.size);
-    if (this->L_aa != H.size)
+    if (this->L_aa != H.size) {
+        std::cerr << "ERROR in NTVirus constructor: mismatch between Hamiltonian size and sequence length." << std::endl;
         throw "mismatch between Hamiltonian size and sequence length.";
+    }
     config.resize(L_aa);
     H.coarse_grain(aa_seq,config);
     update_energy(H);

diff --git a/tags b/tags
index a1159c4..b9fc258 100644 (file)
--- a/tags
+++ b/tags
@@ -13,6 +13,8 @@
 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$/;"      m
+AAKilling      reaction.h      /^enum class RxnType {Elementary, Virus, VirusDeath, Killing, CTLActivation, NTVirus, NTVirusDeath, AAKilling, CTLaaActivation, EscapeCounting, EscapeAACounting};$/;"  m       class:RxnType
+AAKilling      reaction.h      /^enum class RxnType {Elementary, Virus, VirusDeath, Killing, CTLActivation, NTVirus, NTVirusDeath, AAKilling, CTLaaActivation};$/;"    m       class:RxnType
 AAKillingReaction      reaction.h      /^    AAKillingReaction() : Reaction() {}$/;"   f       class:AAKillingReaction
 AAKillingReaction      reaction.h      /^    AAKillingReaction(double k) : Reaction(k) {}$/;"  f       class:AAKillingReaction
 AAKillingReaction      reaction.h      /^class AAKillingReaction : public Reaction {$/;"       c
@@ -25,6 +27,8 @@ BuildIntersection     main.cpp        /^BuildIntersection(std::vector<int>& v0,std::vector<
 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
+CTLActivation  reaction.h      /^enum class RxnType {Elementary, Virus, VirusDeath, Killing, CTLActivation, NTVirus, NTVirusDeath, AAKilling, CTLaaActivation, EscapeCounting, EscapeAACounting};$/;"  m       class:RxnType
+CTLActivation  reaction.h      /^enum class RxnType {Elementary, Virus, VirusDeath, Killing, CTLActivation, NTVirus, NTVirusDeath, AAKilling, CTLaaActivation};$/;"    m       class:RxnType
 CTLActivationReaction  reaction.h      /^    CTLActivationReaction() : Reaction() {}$/;"       f       class:CTLActivationReaction
 CTLActivationReaction  reaction.h      /^    CTLActivationReaction(double k) : Reaction(k) {}$/;"      f       class:CTLActivationReaction
 CTLActivationReaction  reaction.h      /^class CTLActivationReaction : public Reaction {$/;"   c
@@ -33,6 +37,7 @@ CTLSpecies    pop_ss.h        /^    CTLSpecies(long c) : Species(c), num_ep(0) {}$/;" f       cl
 CTLSpecies     pop_ss.h        /^    CTLSpecies(std::string x) : Species(x), num_ep(0) {}$/;"  f       class:CTLSpecies
 CTLSpecies     pop_ss.h        /^    CTLSpecies(std::string x, long c) : Species(x,c), num_ep(0) {}$/;"        f       class:CTLSpecies
 CTLSpecies     pop_ss.h        /^class CTLSpecies : public Species {$/;"       c
+CTLaaActivation        reaction.h      /^enum class RxnType {Elementary, Virus, VirusDeath, Killing, CTLActivation, NTVirus, NTVirusDeath, AAKilling, CTLaaActivation, EscapeCounting, EscapeAACounting};$/;"  m       class:RxnType
 CTLaaActivationReaction        reaction.h      /^    CTLaaActivationReaction() : Reaction() {}$/;"     f       class:CTLaaActivationReaction
 CTLaaActivationReaction        reaction.h      /^    CTLaaActivationReaction(double k) : Reaction(k) {}$/;"    f       class:CTLaaActivationReaction
 CTLaaActivationReaction        reaction.h      /^class CTLaaActivationReaction : public Reaction {$/;" c
@@ -55,6 +60,8 @@ EXECNAME_SS   Makefile        /^EXECNAME_SS = ss$/;"  m
 EXECNAME_WF    Makefile        /^EXECNAME_WF = wf$/;"  m
 Eavg   pop_ss.h        /^    double Eavg;    \/\/ Average energy of the sequence population$/;"        m       class:Population
 Eavg   population.h    /^    double Eavg;    \/\/ Average energy of the sequence population$/;"        m       class:Population
+Elementary     reaction.h      /^enum class RxnType {Elementary, Virus, VirusDeath, Killing, CTLActivation, NTVirus, NTVirusDeath, AAKilling, CTLaaActivation, EscapeCounting, EscapeAACounting};$/;"  m       class:RxnType
+Elementary     reaction.h      /^enum class RxnType {Elementary, Virus, VirusDeath, Killing, CTLActivation, NTVirus, NTVirusDeath, AAKilling, CTLaaActivation};$/;"    m       class:RxnType
 ElementaryReaction     reaction.h      /^    ElementaryReaction() : Reaction() {}$/;"  f       class:ElementaryReaction
 ElementaryReaction     reaction.h      /^    ElementaryReaction(double k) : Reaction(k) {}$/;" f       class:ElementaryReaction
 ElementaryReaction     reaction.h      /^class ElementaryReaction : public Reaction {$/;"      c
@@ -62,6 +69,13 @@ EpitopeHamiltonian   hamiltonian.cpp /^EpitopeHamiltonian::EpitopeHamiltonian(std:
 EpitopeHamiltonian     hamiltonian.h   /^class EpitopeHamiltonian : public Hamiltonian {$/;"   c
 EpitopeRecognizer      pop_ss.h        /^class EpitopeRecognizer {$/;" c
 Eq_    sorted_vector.h /^    bool Eq_(const Myt_& x) const      $/;"   f       class:codeproject::sorted_vector
+EscapeAACountingReaction       reaction.h      /^    EscapeAACountingReaction() : Reaction() {}$/;"    f       class:EscapeAACountingReaction
+EscapeAACountingReaction       reaction.h      /^    EscapeAACountingReaction(double k) : Reaction(k) {}$/;"   f       class:EscapeAACountingReaction
+EscapeAACountingReaction       reaction.h      /^class EscapeAACountingReaction : public Reaction {$/;"        c
+EscapeCounting reaction.h      /^enum class RxnType {Elementary, Virus, VirusDeath, Killing, CTLActivation, NTVirus, NTVirusDeath, AAKilling, CTLaaActivation, EscapeCounting, EscapeAACounting};$/;"  m       class:RxnType
+EscapeCountingReaction reaction.h      /^    EscapeCountingReaction() : Reaction() {}$/;"      f       class:EscapeCountingReaction
+EscapeCountingReaction reaction.h      /^    EscapeCountingReaction(double k) : Reaction(k) {}$/;"     f       class:EscapeCountingReaction
+EscapeCountingReaction reaction.h      /^class EscapeCountingReaction : public Reaction {$/;"  c
 ExecTests      main.cpp        /^void ExecTests(std::vector<T>& v)$/;" f
 Graph  ham_ss.h        /^    AdjacencyList Graph;$/;"  m       class:Hamiltonian
 Graph  hamiltonian.h   /^    AdjacencyList Graph;$/;"  m       class:Hamiltonian
@@ -91,6 +105,8 @@ Key  snip.h  /^typedef std::vector<unsigned long> Key;$/;"   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)$/;"       f       class:codeproject::sorted_vector
+Killing        reaction.h      /^enum class RxnType {Elementary, Virus, VirusDeath, Killing, CTLActivation, NTVirus, NTVirusDeath, AAKilling, CTLaaActivation, EscapeCounting, EscapeAACounting};$/;"  m       class:RxnType
+Killing        reaction.h      /^enum class RxnType {Elementary, Virus, VirusDeath, Killing, CTLActivation, NTVirus, NTVirusDeath, AAKilling, CTLaaActivation};$/;"    m       class:RxnType
 KillingReaction        reaction.h      /^    KillingReaction() : Reaction() {}$/;"     f       class:KillingReaction
 KillingReaction        reaction.h      /^    KillingReaction(double k) : Reaction(k) {}$/;"    f       class:KillingReaction
 KillingReaction        reaction.h      /^class KillingReaction : public Reaction {$/;" c
@@ -112,9 +128,16 @@ MutatedSiteSequence        reaction.h      /^typedef std::set<unsigned int> MutatedSiteSeque
 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$/;"        m       class:Population
+N      population.h    /^    unsigned int N; \/\/ Population size$/;"  m       class:Population
+NTVirus        pop_ss.cpp      /^NTVirus::NTVirus()$/;"        f       class:NTVirus
+NTVirus        pop_ss.cpp      /^NTVirus::NTVirus(const NTVirus &v)$/;"        f       class:NTVirus
 NTVirus        pop_ss.cpp      /^NTVirus::NTVirus(const PottsHamiltonian &H, const std::string &NT)$/;"        f       class:NTVirus
 NTVirus        pop_ss.cpp      /^NTVirus::NTVirus(const std::string &NT)$/;"   f       class:NTVirus
 NTVirus        pop_ss.h        /^class NTVirus {$/;"   c
+NTVirus        reaction.h      /^enum class RxnType {Elementary, Virus, VirusDeath, Killing, CTLActivation, NTVirus, NTVirusDeath, AAKilling, CTLaaActivation, EscapeCounting, EscapeAACounting};$/;"  m       class:RxnType
+NTVirus        reaction.h      /^enum class RxnType {Elementary, Virus, VirusDeath, Killing, CTLActivation, NTVirus, NTVirusDeath, AAKilling, CTLaaActivation};$/;"    m       class:RxnType
+NTVirusDeath   reaction.h      /^enum class RxnType {Elementary, Virus, VirusDeath, Killing, CTLActivation, NTVirus, NTVirusDeath, AAKilling, CTLaaActivation, EscapeCounting, EscapeAACounting};$/;"  m       class:RxnType
+NTVirusDeath   reaction.h      /^enum class RxnType {Elementary, Virus, VirusDeath, Killing, CTLActivation, NTVirus, NTVirusDeath, AAKilling, CTLaaActivation};$/;"    m       class:RxnType
 NTVirusDeathReaction   reaction.h      /^    NTVirusDeathReaction() : Reaction() {}$/;"        f       class:NTVirusDeathReaction
 NTVirusDeathReaction   reaction.h      /^    NTVirusDeathReaction(double k) : Reaction(k) {}$/;"       f       class:NTVirusDeathReaction
 NTVirusDeathReaction   reaction.h      /^class NTVirusDeathReaction : public Reaction {$/;"    c
@@ -144,6 +167,7 @@ Population  pop_ss.cpp      /^Population::Population(const Hamiltonian &H, unsigned in
 Population     pop_ss.h        /^class Population{$/;" c
 Population     population.cpp  /^Population::Population(const Hamiltonian &H, unsigned int N, double mu) {$/;" f       class:Population
 Population     population.cpp  /^Population::Population(const Hamiltonian &H, unsigned int N, double mu, const std::vector<std::set<unsigned int> > &initPop, const std::vector<double> &initFrac) {$/;"       f       class:Population
+Population     population.h    /^class Population {$/;"        c
 Population     population.h    /^class Population{$/;" c
 PottsHamiltonian       ham_ss.cpp      /^PottsHamiltonian::PottsHamiltonian(const std::string &couplingsFile, const std::string &seq2stateFile) : bh(1.0), bJ(1.0)$/;" f       class:PottsHamiltonian
 PottsHamiltonian       ham_ss.h        /^    PottsHamiltonian() : bh(1.0), bJ(1.0) { }$/;"     f       class:PottsHamiltonian
@@ -154,6 +178,7 @@ RC_fun      reaction.cpp    /^double RC_fun(double E)$/;"   f
 REACTION_H     reaction.h      2;"     d
 Reaction       reaction.h      /^    Reaction() {}$/;" f       class:Reaction
 Reaction       reaction.h      /^    Reaction(double k) : rate_constant(k) {}$/;"      f       class:Reaction
+Reaction       reaction.h      /^    Reaction(double k) : rate_constant(k), affects() {}$/;"   f       class:Reaction
 Reaction       reaction.h      /^class Reaction {$/;"  c
 RunParameters  wf.h    /^    RunParameters() {$/;"     f       class:RunParameters
 RunParameters  wf.h    /^class RunParameters {$/;"     c
@@ -161,6 +186,8 @@ RunParameters_MC    mc.h    /^    RunParameters_MC() {$/;"  f       class:RunParameters_MC
 RunParameters_MC       mc.h    /^class RunParameters_MC {$/;"  c
 RunParameters_SS       ss.h    /^    RunParameters_SS() {$/;"  f       class:RunParameters_SS
 RunParameters_SS       ss.h    /^class RunParameters_SS {$/;"  c
+RxnType        reaction.h      /^enum class RxnType {Elementary, Virus, VirusDeath, Killing, CTLActivation, NTVirus, NTVirusDeath, AAKilling, CTLaaActivation, EscapeCounting, EscapeAACounting};$/;"  c
+RxnType        reaction.h      /^enum class RxnType {Elementary, Virus, VirusDeath, Killing, CTLActivation, NTVirus, NTVirusDeath, AAKilling, CTLaaActivation};$/;"    c
 Rxn_parray     ss.h    /^typedef std::vector<Reaction*> Rxn_parray;$/;"        t
 SEQTOOLS_H     seqTools.h      2;"     d
 SGITest        main.cpp        /^int SGITest()$/;"     f
@@ -205,21 +232,31 @@ TwoSiteHamiltonian        hamiltonian.h   /^class TwoSiteHamiltonian : public Hamiltonian
 Unique_        sorted_vector.h /^    iterator Unique_()$/;"    f       class:codeproject::sorted_vector
 V      reaction.h      /^    NTVirusSpecies* V;$/;"    m       class:AAKillingReaction
 V      reaction.h      /^    NTVirusSpecies* V;$/;"    m       class:CTLaaActivationReaction
+V      reaction.h      /^    NTVirusSpecies* V;$/;"    m       class:EscapeAACountingReaction
 V      reaction.h      /^    NTVirusSpecies* V;$/;"    m       class:NTVirusDeathReaction
 V      reaction.h      /^    NTVirusSpecies* V;$/;"    m       class:NTVirusReaction
 V      reaction.h      /^    VirusSpecies* V;$/;"      m       class:CTLActivationReaction
+V      reaction.h      /^    VirusSpecies* V;$/;"      m       class:EscapeCountingReaction
 V      reaction.h      /^    VirusSpecies* V;$/;"      m       class:KillingReaction
 V      reaction.h      /^    VirusSpecies* V;$/;"      m       class:VirusDeathReaction
 V      reaction.h      /^    VirusSpecies* V;$/;"      m       class:VirusReaction
 VERSION_SORTED_VECTOR_ sorted_vector.h 25;"    d
 VIRUS_H        virus.h 2;"     d
 Vector snip.h  /^typedef std::vector<std::vector<double> > Vector;$/;" t
+Virus  pop_ss.cpp      /^Virus::Virus()$/;"    f       class:Virus
 Virus  pop_ss.cpp      /^Virus::Virus(const Hamiltonian &H) {$/;"      f       class:Virus
+Virus  pop_ss.cpp      /^Virus::Virus(const Hamiltonian &H)$/;"        f       class:Virus
 Virus  pop_ss.cpp      /^Virus::Virus(const Hamiltonian &H, const std::set<unsigned int> &mutated_sites) {$/;" f       class:Virus
+Virus  pop_ss.cpp      /^Virus::Virus(const Hamiltonian &H, const std::set<unsigned int> &mutated_sites_in)$/;"        f       class:Virus
+Virus  pop_ss.cpp      /^Virus::Virus(const Virus &v)$/;"      f       class:Virus
 Virus  pop_ss.h        /^class Virus {$/;"     c
+Virus  reaction.h      /^enum class RxnType {Elementary, Virus, VirusDeath, Killing, CTLActivation, NTVirus, NTVirusDeath, AAKilling, CTLaaActivation, EscapeCounting, EscapeAACounting};$/;"  m       class:RxnType
+Virus  reaction.h      /^enum class RxnType {Elementary, Virus, VirusDeath, Killing, CTLActivation, NTVirus, NTVirusDeath, AAKilling, CTLaaActivation};$/;"    m       class:RxnType
 Virus  virus.cpp       /^Virus::Virus(const Hamiltonian &H, double mu) {$/;"   f       class:Virus
 Virus  virus.cpp       /^Virus::Virus(const Hamiltonian &H, double mu, const std::set<unsigned int> &mutated_sites) {$/;"      f       class:Virus
 Virus  virus.h /^class Virus {$/;"     c
+VirusDeath     reaction.h      /^enum class RxnType {Elementary, Virus, VirusDeath, Killing, CTLActivation, NTVirus, NTVirusDeath, AAKilling, CTLaaActivation, EscapeCounting, EscapeAACounting};$/;"  m       class:RxnType
+VirusDeath     reaction.h      /^enum class RxnType {Elementary, Virus, VirusDeath, Killing, CTLActivation, NTVirus, NTVirusDeath, AAKilling, CTLaaActivation};$/;"    m       class:RxnType
 VirusDeathReaction     reaction.h      /^    VirusDeathReaction() : Reaction() {}$/;"  f       class:VirusDeathReaction
 VirusDeathReaction     reaction.h      /^    VirusDeathReaction(double k) : Reaction(k) {}$/;" f       class:VirusDeathReaction
 VirusDeathReaction     reaction.h      /^class VirusDeathReaction : public Reaction {$/;"      c
@@ -247,6 +284,7 @@ aaseq2str   pop_ss.cpp      /^std::string aaseq2str(const std::vector<aa> &aa_seq)$/;"
 add_to_two_site_pop    mc.cpp  /^void add_to_two_site_pop(RunParameters_MC &r, bool s1, bool s2, double frac) {$/;"    f
 add_to_two_site_pop    ss.cpp  /^void add_to_two_site_pop(RunParameters_SS &r, bool s1, bool s2, double frac) {$/;"    f
 add_to_two_site_pop    wf.cpp  /^void add_to_two_site_pop(RunParameters &r, bool s1, bool s2, double frac) {$/;"       f
+affects        reaction.h      /^    std::vector<Reaction*> affects; \/\/ reactions whose propensity must be updated when this one fires$/;"   m       class:Reaction
 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>$/;"      f
@@ -372,6 +410,8 @@ directory   mc.h    /^    std::string directory;      \/\/ Path to the directory wher
 directory      ss.h    /^    std::string directory;      \/\/ Path to the directory where the inut file is located$/;" m       class:RunParameters_SS
 directory      wf.h    /^    std::string directory;      \/\/ Path to the directory where the inut file is located$/;" m       class:RunParameters
 do_flip_or_not mc.cpp  /^bool do_flip_or_not(const EpitopeHamiltonian &H, MutatedSiteSequence &seq, gsl_rng *r, unsigned &site)$/;"    f
+does_affect    ss.cpp  /^bool does_affect(Reaction *newrxn, Reaction *rxn)$/;" f
+does_species_appear_in_reactants       ss.cpp  /^bool does_species_appear_in_reactants(Species *s, Reaction *rxn)$/;"  f
 eMut   mc.h    /^    std::vector<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$/;"       m       class:RunParameters
@@ -411,6 +451,8 @@ equal_range sorted_vector.h /^      Pairii_ equal_range(const K& k)$/;"     f       class:codep
 erase  sorted_vector.h /^      iterator erase(iterator first, iterator beyond)$/;"     f       class:codeproject::sorted_vector
 erase  sorted_vector.h /^    iterator erase(iterator p)          {return vec_.erase(p);}$/;"   f       class:codeproject::sorted_vector
 erase  sorted_vector.h /^    size_type erase(const K& key)     $/;"    f       class:codeproject::sorted_vector
+esc    reaction.h      /^    CTLSpecies* esc;$/;"      m       class:EscapeCountingReaction
+esc    reaction.h      /^    CTLaaSpecies* esc;$/;"    m       class:EscapeAACountingReaction
 escape_variant pop_ss.cpp      /^unsigned int Population::escape_variant(Hamiltonian &H, std::set<unsigned int> &mutant) {$/;" 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
@@ -442,11 +484,14 @@ fire      reaction.cpp    /^void AAKillingReaction::fire()$/;"    f       class:AAKillingReaction
 fire   reaction.cpp    /^void CTLActivationReaction::fire()$/;"        f       class:CTLActivationReaction
 fire   reaction.cpp    /^void CTLaaActivationReaction::fire()$/;"      f       class:CTLaaActivationReaction
 fire   reaction.cpp    /^void ElementaryReaction::fire()$/;"   f       class:ElementaryReaction
+fire   reaction.cpp    /^void EscapeAACountingReaction::fire()$/;"     f       class:EscapeAACountingReaction
+fire   reaction.cpp    /^void EscapeCountingReaction::fire()$/;"       f       class:EscapeCountingReaction
 fire   reaction.cpp    /^void KillingReaction::fire()$/;"      f       class:KillingReaction
 fire   reaction.cpp    /^void NTVirusDeathReaction::fire()$/;" f       class:NTVirusDeathReaction
 fire   reaction.cpp    /^void NTVirusReaction::fire()$/;"      f       class:NTVirusReaction
 fire   reaction.cpp    /^void VirusDeathReaction::fire()$/;"   f       class:VirusDeathReaction
 fire   reaction.cpp    /^void VirusReaction::fire()$/;"        f       class:VirusReaction
+flushOften     ss.h    /^    bool flushOften;            \/\/ flush output each line?$/;"      m       class:RunParameters_SS
 front  sorted_vector.h /^      const_reference front() const                           {return vec_.front();}$/;"      f       class:codeproject::sorted_vector
 front  sorted_vector.h /^    reference front()                                                 {return vec_.front();}$/;"      f       class:codeproject::sorted_vector
 g      mc.h    /^    unsigned int g;             \/\/ Number of generations$/;"        m       class:RunParameters_MC
@@ -465,6 +510,7 @@ get_energy  ham_ss.cpp      /^double PottsHamiltonian::get_energy(const PottsState &co
 get_energy     hamiltonian.cpp /^double EpitopeHamiltonian::get_energy(const std::set<unsigned int> &mutated_sites) const {$/;"        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
+get_rxn_type   reaction.h      /^inline RxnType get_rxn_type(const Reaction* const rxn)$/;"    f
 gh     session.vim     /^map <silent> gh :exe 'normal '.(virtcol('.')\/2).'\16|'\16$/;"    m
 gl     session.vim     /^map <silent> gl :exe 'normal '.(virtcol('.') + (virtcol('$')-virtcol('.'))\/2).'\16|'\16$/;"      m
 glob   test/make_tests.py      /^import glob$/;"       i
@@ -515,6 +561,7 @@ insert      sorted_vector.h /^      void insert(It first, It beyond)$/;"    f       class:codeproje
 insert sorted_vector.h /^   Pairib_ insert(const value_type& x)$/;"    f       class:codeproject::sorted_vector
 insert sorted_vector.h /^   iterator insert(iterator it, const value_type& x)\/\/it is the hint$/;"    f       class:codeproject::sorted_vector
 insert sorted_vector.h /^   void insert(const_iterator first, const_iterator beyond)$/;"       f       class:codeproject::sorted_vector
+insertReferenceStates  ham_ss.cpp      /^unsigned PottsHamiltonian::insertReferenceStates()$/;"        f       class:PottsHamiltonian
 int2aa seqTools.cpp    /^const int2str_map int2aa = {$/;"      v
 int2str_map    seqTools.h      /^typedef std::unordered_map<int,char> int2str_map;$/;" t
 is_unique      main.cpp        /^bool is_unique(It beg,It beyond,Pred pred)$/;"        f
@@ -523,6 +570,10 @@ key_comp   sorted_vector.h /^      key_compare key_comp() const                    {return key_compare_;
 key_compare    sorted_vector.h /^    typedef Pr                                                key_compare;$/;"        t       class:codeproject::sorted_vector
 key_compare_   sorted_vector.h /^    key_compare         key_compare_;$/;"     m       class:codeproject::sorted_vector
 key_type       sorted_vector.h /^    typedef K                                         key_type;$/;"   t       class:codeproject::sorted_vector
+lastDeleted    pop_ss.h        /^    NTVirus lastDeleted;$/;"  m       class:NTVirusSpecies
+lastDeleted    pop_ss.h        /^    Virus lastDeleted;$/;"    m       class:VirusSpecies
+lastModified   pop_ss.h        /^    NTVirus_map::iterator lastModified;$/;"   m       class:NTVirusSpecies
+lastModified   pop_ss.h        /^    virus_map::iterator lastModified;$/;"     m       class:VirusSpecies
 len    pop_ss.h        /^    size_t len;$/;"   m       class:AARecognizer
 lower_bound    sorted_vector.h /^      const_iterator lower_bound(const K& k) const$/;"        f       class:codeproject::sorted_vector
 lower_bound    sorted_vector.h /^      iterator lower_bound(const K& k)$/;"    f       class:codeproject::sorted_vector
@@ -556,6 +607,7 @@ n   mc.h    /^    unsigned int n;             \/\/ Population size$/;"      m       class:RunPar
 n      ss.h    /^    unsigned int n;             \/\/ Population size$/;"      m       class:RunParameters_SS
 n      wf.h    /^    unsigned int n;             \/\/ Population size$/;"      m       class:RunParameters
 name   pop_ss.h        /^    std::string name;$/;"     m       class:Species
+name   reaction.h      /^    std::string name;$/;"     m       class:Reaction
 next_generation        pop_ss.cpp      /^void Population::next_generation(const Hamiltonian &H, gsl_rng* r, bool useRelative, bool useVerbose) {$/;"   f       class:Population
 next_generation        population.cpp  /^void Population::next_generation(const Hamiltonian &H, gsl_rng* r, bool useRelative, bool useVerbose) {$/;"   f       class:Population
 notEpitopeAllSites     hamiltonian.h   /^    MutatedSiteSequence notEpitopeAllSites; \/\/ all sites not involved in an epitope$/;"     m       class:EpitopeHamiltonian
@@ -620,6 +672,8 @@ print_population_size       pop_ss.cpp      /^void Population::print_population_size() {$/;
 print_population_size  population.cpp  /^void Population::print_population_size() {$/;"        f       class:Population
 print_species_header   ss.cpp  /^void print_species_header(const Species_parray &print_spec)$/;"       f
 print_species_traj     ss.cpp  /^void print_species_traj(double t, const Species_parray &print_spec, bool verbose)$/;" f
+print_species_traj     ss.cpp  /^void print_species_traj(double t, long step, const Species_parray &print_spec, bool verbose)$/;"      f
+print_species_traj     ss.cpp  /^void print_species_traj(double t, long step, const Species_parray &print_spec, bool verbose, bool flushOften)$/;"     f
 product_stoich reaction.h      /^    std::vector<int> product_stoich;  \/\/ must be negative for reactants that are consumed!$/;"      m       class:ElementaryReaction
 products       reaction.h      /^    std::vector<Species*> products;  \/\/ effects of reaction$/;"     m       class:ElementaryReaction
 propensity     reaction.h      /^    double propensity;$/;"    m       class:Reaction
@@ -642,14 +696,27 @@ rbegin    sorted_vector.h /^    reverse_iterator  rbegin()                                {return vec_.rbegin();
 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()$/;"        f       class:AAKillingReaction
+recalc reaction.cpp    /^double AAKillingReaction::recalc(Reaction *rxn_in)$/;"        f       class:AAKillingReaction
 recalc reaction.cpp    /^double CTLActivationReaction::recalc()$/;"    f       class:CTLActivationReaction
+recalc reaction.cpp    /^double CTLActivationReaction::recalc(Reaction *rxn)$/;"       f       class:CTLActivationReaction
 recalc reaction.cpp    /^double CTLaaActivationReaction::recalc()$/;"  f       class:CTLaaActivationReaction
+recalc reaction.cpp    /^double CTLaaActivationReaction::recalc(Reaction *rxn)$/;"     f       class:CTLaaActivationReaction
 recalc reaction.cpp    /^double ElementaryReaction::recalc()$/;"       f       class:ElementaryReaction
+recalc reaction.cpp    /^double ElementaryReaction::recalc(Reaction *rxn)$/;"  f       class:ElementaryReaction
+recalc reaction.cpp    /^double EscapeAACountingReaction::recalc()$/;" f       class:EscapeAACountingReaction
+recalc reaction.cpp    /^double EscapeAACountingReaction::recalc(Reaction *rxn_in)$/;" f       class:EscapeAACountingReaction
+recalc reaction.cpp    /^double EscapeCountingReaction::recalc()$/;"   f       class:EscapeCountingReaction
+recalc reaction.cpp    /^double EscapeCountingReaction::recalc(Reaction *rxn_in)$/;"   f       class:EscapeCountingReaction
 recalc reaction.cpp    /^double KillingReaction::recalc()$/;"  f       class:KillingReaction
+recalc reaction.cpp    /^double KillingReaction::recalc(Reaction *rxn_in)$/;"  f       class:KillingReaction
 recalc reaction.cpp    /^double NTVirusDeathReaction::recalc()$/;"     f       class:NTVirusDeathReaction
+recalc reaction.cpp    /^double NTVirusDeathReaction::recalc(Reaction *rxn)$/;"        f       class:NTVirusDeathReaction
 recalc reaction.cpp    /^double NTVirusReaction::recalc()$/;"  f       class:NTVirusReaction
+recalc reaction.cpp    /^double NTVirusReaction::recalc(Reaction *rxn)$/;"     f       class:NTVirusReaction
 recalc reaction.cpp    /^double VirusDeathReaction::recalc()$/;"       f       class:VirusDeathReaction
+recalc reaction.cpp    /^double VirusDeathReaction::recalc(Reaction *rxn)$/;"  f       class:VirusDeathReaction
 recalc reaction.cpp    /^double VirusReaction::recalc()$/;"    f       class:VirusReaction
+recalc reaction.cpp    /^double VirusReaction::recalc(Reaction *rxn)$/;"       f       class:VirusReaction
 recognized     pop_ss.cpp      /^double CTLSpecies::recognized(const MutatedSiteSequence &mutated_sites) const {$/;"   f       class:CTLSpecies
 recognized     pop_ss.cpp      /^double CTLSpecies::recognized(const Virus &v) const {$/;"     f       class:CTLSpecies
 recognized     pop_ss.cpp      /^double CTLaaSpecies::recognized(const NTVirus &v) const {$/;" f       class:CTLaaSpecies
@@ -695,6 +762,8 @@ sim_random_seed     mc.cpp  /^static unsigned sim_random_seed() {$/;"       f       file:
 sim_random_seed        ss.cpp  /^static unsigned sim_random_seed() {$/;"       f       file:
 sim_random_seed        wf.cpp  /^static unsigned sim_random_seed() {$/;"       f       file:
 simulate       ss.cpp  /^void simulate(Rxn_parray &reactions, Species_parray &species, double t_end, long max_steps, double sample_interval, const Species_parray &print_spec, bool verbose)$/;"       f
+simulate       ss.cpp  /^void simulate(Rxn_parray &reactions, Species_parray &species, double t_end, long max_steps, double sample_interval, unsigned step_sample_interval, const Species_parray &print_spec, bool verbose)$/;"        f
+simulate       ss.cpp  /^void simulate(Rxn_parray &reactions, Species_parray &species, double t_end, long max_steps, double sample_interval, unsigned step_sample_interval, const Species_parray &print_spec, bool verbose, bool flushOften)$/;"       f
 sindex ham_ss.h        /^inline int sindex(int i, int j, size_t qi, size_t qj) {$/;"   f
 sindex snip.h  /^inline int sindex(int i, int j, size_t qi, size_t qj) {$/;"   f
 site   pop_ss.h        /^    std::vector<unsigned> site;$/;"   m       class:AARecognizer
@@ -722,6 +791,7 @@ statefile   mc.h    /^    std::string statefile;      \/\/ Input state file which con
 statefile      ss.h    /^    std::string statefile;      \/\/ Input state file which contains initial population fractions$/;" m       class:RunParameters_SS
 statefile      wf.h    /^    std::string statefile;      \/\/ Input state file which contains initial population fractions$/;" m       class:RunParameters
 std    seqTools.h      /^namespace std {$/;"   n
+step_sample_interval   ss.h    /^    unsigned step_sample_interval;$/;"        m       class:RunParameters_SS
 str2aa seqTools.cpp    /^const str2aa_map str2aa = {$/;"       v
 str2aa_map     seqTools.h      /^typedef std::unordered_map<char,aa> str2aa_map;$/;"   t
 str2codon      seqTools.cpp    /^const str2codon_map str2codon = {$/;" v
@@ -752,6 +822,8 @@ to_string_uint      ss.cpp  /^  to_string_uint(unsigned __val)$/;"  f
 tostring       mc.h    /^inline std::string tostring (const T& t) {$/;"        f
 tostring       ss.h    /^inline std::string tostring (const T& t) {$/;"        f
 tostring       wf.h    /^inline std::string tostring (const T& t) {$/;"        f
+trackEscaped   ss.h    /^    bool trackEscaped;          \/\/ Maintain counter to track number of escaped viruses?$/;" m       class:RunParameters_SS
+trackEscaped   ss.h    /^    bool trackEscaped;$/;"    m       class:RunParameters_SS
 trajectoryOutfile      mc.h    /^    std::string trajectoryOutfile;$/;"        m       class:RunParameters_MC
 trajectoryOutfile      ss.h    /^    std::string trajectoryOutfile;$/;"        m       class:RunParameters_SS
 trajectoryOutfile      wf.h    /^    std::string trajectoryOutfile;$/;"        m       class:RunParameters
@@ -760,11 +832,13 @@ unsorted_find     main.cpp        /^FwIt unsorted_find(FwIt beg,FwIt beyond,Pred pred)$/;"
 update_energy  pop_ss.cpp      /^void NTVirus::update_energy(const PottsHamiltonian &H)$/;"    f       class:NTVirus
 update_energy  pop_ss.cpp      /^void Virus::update_energy(const Hamiltonian &H) {$/;" f       class:Virus
 update_energy  virus.cpp       /^void Virus::update_energy(const Hamiltonian &H) {$/;" f       class:Virus
+update_rxn_dependents  ss.cpp  /^void update_rxn_dependents(Rxn_parray &reactions)$/;" f
 upper_bound    sorted_vector.h /^      const_iterator upper_bound(const K& k) const$/;"        f       class:codeproject::sorted_vector
 upper_bound    sorted_vector.h /^      iterator upper_bound(const K& k)$/;"    f       class:codeproject::sorted_vector
 usage  mc.cpp  /^void usage()$/;"      f
 usage  ss.cpp  /^void usage()$/;"      f
 usage  wf.cpp  /^void usage()$/;"      f
+usage_rates    ss.cpp  /^void usage_rates()$/;"        f
 useEpitope     mc.h    /^    bool useEpitope;            \/\/ Include selective pressure on an epitope $/;"    m       class:RunParameters_MC
 useEpitope     ss.h    /^    bool useEpitope;            \/\/ Include selective pressure on an epitope $/;"    m       class:RunParameters_SS
 useEpitope     ss.h    /^    bool useEpitope;            \/\/ Include selective pressure on an epitope$/;"     m       class:RunParameters_SS
@@ -785,6 +859,7 @@ value_type  sorted_vector.h /^      typedef typename Cont::value_type               value_type;$/;"
 vec_   sorted_vector.h /^    Cont                vec_;$/;"     m       class:codeproject::sorted_vector
 virus_map      pop_ss.h        /^typedef std::map<Virus, unsigned int> virus_map;$/;"  t
 virus_map      population.h    /^typedef std::map<Virus, unsigned int> virus_map;$/;"  t
+vol    ss.h    /^    double vol;$/;"   m       class:RunParameters_SS
 write_mod      mc.h    /^    unsigned int write_mod;     \/\/ Write state of the population every __ MC steps$/;"      m       class:RunParameters_MC
 write_mod      ss.h    /^    unsigned int write_mod;     \/\/ Write state of the population every __ generations$/;"   m       class:RunParameters_SS
 write_mod      wf.h    /^    unsigned int write_mod;     \/\/ Write state of the population every __ generations$/;"   m       class:RunParameters