From 4e6a91387833b95910f0b14f44e59edf237fd5a6 Mon Sep 17 00:00:00 2001 From: Dariusz Murakowski Date: Thu, 7 May 2015 17:06:25 -0400 Subject: [PATCH] Clean up extra debug printing. --- ss.cpp | 78 ++++++++++++++++++++++-------------------------------------------- 1 file changed, 26 insertions(+), 52 deletions(-) diff --git a/ss.cpp b/ss.cpp index 9705e55..3356b2e 100644 --- a/ss.cpp +++ b/ss.cpp @@ -49,32 +49,32 @@ bool does_species_appear_in_reactants(Species *s, Reaction *rxn) for (Species_parray::iterator t = dynamic_cast(rxn)->reactants.begin(), f = dynamic_cast(rxn)->reactants.end(); t != f; ++t) { - if (s == *t){std::cout << "elem: " << rxn->name << '\n'; return true;} + if (s == *t) { return true; } } break; case RxnType::Virus: - if (s == dynamic_cast(rxn)->V){std::cout << "virus: " << rxn->name << '\n'; return true;} + if (s == dynamic_cast(rxn)->V) { return true; } break; case RxnType::VirusDeath: - if (s == dynamic_cast(rxn)->V){std::cout << "vdeath: " << rxn->name << '\n'; return true;} + if (s == dynamic_cast(rxn)->V) { return true; } break; case RxnType::Killing: - if (s == dynamic_cast(rxn)->V || s == dynamic_cast(rxn)->T){std::cout << "killing: " << rxn->name << '\n'; return true;} + if (s == dynamic_cast(rxn)->V || s == dynamic_cast(rxn)->T) { return true; } break; case RxnType::CTLActivation: - if (s == dynamic_cast(rxn)->V || s == dynamic_cast(rxn)->Tfrom){std::cout << "ctlact: " << rxn->name << '\n'; return true;} + if (s == dynamic_cast(rxn)->V || s == dynamic_cast(rxn)->Tfrom) { return true; } // rxn->Tto is irrelevant to rate break; case RxnType::NTVirus: - if (s == dynamic_cast(rxn)->V){std::cout << "ntvirus: " << rxn->name << '\n'; return true;} + if (s == dynamic_cast(rxn)->V) { return true; } break; case RxnType::NTVirusDeath: - if (s == dynamic_cast(rxn)->V){std::cout << "ntvdeath: " << rxn->name << '\n'; return true;} + if (s == dynamic_cast(rxn)->V) { return true; } break; case RxnType::AAKilling: - if (s == dynamic_cast(rxn)->V || s == dynamic_cast(rxn)->T){std::cout << "aakilling: " << rxn->name << '\n'; return true;} + if (s == dynamic_cast(rxn)->V || s == dynamic_cast(rxn)->T) { return true; } break; case RxnType::CTLaaActivation: - if (s == dynamic_cast(rxn)->V || s == dynamic_cast(rxn)->Tfrom){std::cout << "ctlaaact: " << rxn->name << '\n'; return true;} + if (s == dynamic_cast(rxn)->V || s == dynamic_cast(rxn)->Tfrom) { return true; } // rxn->Tto is irrelevant to rate break; } @@ -99,90 +99,67 @@ bool does_affect(Reaction *newrxn, Reaction *rxn) for (Species_parray::iterator s = dynamic_cast(newrxn)->products.begin(), e = dynamic_cast(newrxn)->products.end(); s != e; ++s) { - std::cout << "newrxn = Elementary: " << newrxn->name << '\n'; affects |= does_species_appear_in_reactants(*s,rxn); + if (affects) { return true; } } break; } case RxnType::Virus: { - std::cout << "newrxn = Virus: " << newrxn->name << '\n'; Species *s = dynamic_cast(newrxn)->V; affects = does_species_appear_in_reactants(s,rxn); - return affects; break; } case RxnType::VirusDeath: { - std::cout << "newrxn = VirusDeath: " << newrxn->name << '\n'; Species *s = dynamic_cast(newrxn)->V; affects = does_species_appear_in_reactants(s,rxn); - return affects; break; } case RxnType::Killing: { - std::cout << "newrxn = Killing: " << newrxn->name << '\n'; Species *s = dynamic_cast(newrxn)->V; affects = does_species_appear_in_reactants(s,rxn); - return affects; - //Species *s2 = dynamic_cast(newrxn)->T; - //affects |= does_species_appear_in_reactants(s2,rxn); - //return affects; + // newrxn->T is irrelevant because it does not change when firing break; } case RxnType::CTLActivation: { - std::cout << "newrxn = CTLActivation: " << newrxn->name << '\n'; - Species *s; - //s = dynamic_cast(newrxn)->V; - //affects = does_species_appear_in_reactants(s,rxn); - //return affects; - s = dynamic_cast(newrxn)->Tfrom; + Species *s = dynamic_cast(newrxn)->Tfrom; affects = does_species_appear_in_reactants(s,rxn); - //return affects; + if (affects) { return affects; } s = dynamic_cast(newrxn)->Tto; affects |= does_species_appear_in_reactants(s,rxn); - return affects; + // newrxn->V is irrelevant because it does not change when firing break; } case RxnType::NTVirus: { - std::cout << "newrxn = NTVirus: " << newrxn->name << '\n'; Species *s = dynamic_cast(newrxn)->V; affects = does_species_appear_in_reactants(s,rxn); - return affects; break; } case RxnType::NTVirusDeath: { - std::cout << "newrxn = NTVirusDeath: " << newrxn->name << '\n'; Species *s = dynamic_cast(newrxn)->V; affects = does_species_appear_in_reactants(s,rxn); break; } case RxnType::AAKilling: { - std::cout << "newrxn = AAKilling: " << newrxn->name << '\n'; Species *s = dynamic_cast(newrxn)->V; affects = does_species_appear_in_reactants(s,rxn); - return affects; - //Species *s2 = dynamic_cast(newrxn)->T; - //affects = does_species_appear_in_reactants(s2,rxn); - //return affects; + // newrxn->T is irrelevant because it does not change when firing break; } case RxnType::CTLaaActivation: { - std::cout << "newrxn = CTLaaActivation: " << newrxn->name << '\n'; - //Species *s = dynamic_cast(newrxn)->V; - //affects = does_species_appear_in_reactants(s,rxn); - //return affects; - Species *s2 = dynamic_cast(newrxn)->Tfrom; - affects |= does_species_appear_in_reactants(s2,rxn); - s2 = dynamic_cast(newrxn)->Tto; - affects |= does_species_appear_in_reactants(s2,rxn); - return affects; + Species *s = dynamic_cast(newrxn)->Tfrom; + affects |= does_species_appear_in_reactants(s,rxn); + if (affects) { return affects; } + s = dynamic_cast(newrxn)->Tto; + affects |= does_species_appear_in_reactants(s,rxn); + // newrxn->V is irrelevant because it does not change when firing break; } @@ -197,7 +174,6 @@ bool does_affect(Reaction *newrxn, Reaction *rxn) // in order to update the existing Reaction objects' "affects" member void update_rxn_dependents(Rxn_parray &reactions) { - printf("----------\n"); Reaction *newrxn = reactions.back(); Rxn_parray::iterator rxn = reactions.begin(), @@ -205,11 +181,9 @@ void update_rxn_dependents(Rxn_parray &reactions) for (; rxn != end; ++rxn) { if (does_affect(newrxn,*rxn)) { // newrxn affects old? - printf("new affects old\n\n"); newrxn->affects.push_back(*rxn); } if (does_affect(*rxn,newrxn)) { // old reaction affects new? - printf("old affects new\n\n"); (*rxn)->affects.push_back(newrxn); } } @@ -369,7 +343,7 @@ void run(RunParameters_SS &r, unsigned seed) { void print_species_header(const Species_parray &print_spec) { - std::cout << "step\ttime"; + std::cout << "time"; for (Species_parray::const_iterator spec = print_spec.begin(), end = print_spec.end(); spec != end; ++spec) @@ -382,7 +356,7 @@ void print_species_header(const Species_parray &print_spec) void print_species_traj(double t, long step, const Species_parray &print_spec, bool verbose) { - std::cout << step << '\t' << t; + std::cout << t; for (Species_parray::const_iterator spec = print_spec.begin(), end = print_spec.end(); spec != end; ++spec) @@ -484,9 +458,9 @@ void simulate(Rxn_parray &reactions, Species_parray &species, double t_end, long oldA = (*rxn2)->propensity; (*rxn2)->recalc(); newA = (*rxn2)->propensity; - if (oldA == newA && newA != 0.0) { - std::cout << "SAME: " << (*rxn)->name << " affected " << (*rxn2)->name << " with propensity " << newA << '\n'; - } + //if (oldA == newA && newA != 0.0) { + // std::cout << "SAME: " << (*rxn)->name << " affected " << (*rxn2)->name << " with propensity " << newA << '\n'; + //} total_propensity = total_propensity - oldA + newA; } -- 2.7.4