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Resolve Compiler Warnings for the SIST 1.0.0 Release #37

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Merged
harryswift01 merged 3 commits into from
Aug 13, 2026
Merged

Resolve Compiler Warnings for the SIST 1.0.0 Release #37

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bee88d4
fix: avoid uninitialised window bounds in constructors
harryswift01 Aug 13, 2026
125f3f4
fix: validate cruciform energy records
harryswift01 Aug 13, 2026
e28665b
fix: address misleading indentation warnings
harryswift01 Aug 13, 2026
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4 changes: 2 additions & 2 deletions trans_compete/SIDD_3R.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -126,8 +126,8 @@ bool SIDD_3R::Search_Low3RE()
}
}
}

if (results)
if (results)
cout << "Number of three-run states = " << count << endl;
StatesInThreeRuns = (long)count;
ZsumB += sum_3RB;
Expand Down
4 changes: 2 additions & 2 deletions trans_compete/SIDD_4R.cpp
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Expand Up @@ -70,8 +70,8 @@ bool SIDD_4R::Search_Low4RE()
if(Lst_OBE[n1][t1].begin()->get_energy() + min_RE[t2] + min_RE[t3]+ min_RE[t4] + minGres >= max_E)
continue;
for(int n2 = n1; n2 <= (window_size - n1)/3 ; n2++){
if (n1==n2 && t1==1 && t2==0)
continue;
if (n1==n2 && t1==1 && t2==0)
continue;
if(Lst_OBE[n1][t1].begin()->get_energy() + Lst_OBE[n2][t2].begin()->get_energy()+ min_RE[t3] + min_RE[t4] + minGres >= max_E)
continue;
for(int n3 = n2; n3 <= (window_size - n1 - n2)/2; n3++){
Expand Down
37 changes: 19 additions & 18 deletions trans_compete/SIDD_Base.cpp
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Expand Up @@ -32,7 +32,7 @@ SIDD_Base::SIDD_Base()
en_cruciforms = 0;
for (int t=0; t<=Ns; t++) {
profile[t] = 0;
for(int m = MinWindowSize; m <= MaxWindowSize; m++) {
for(int m = 0; m <= MaxInitialWindowSize; m++) {
promatrix[m][t] = 0;
}
}
Expand Down Expand Up @@ -246,8 +246,8 @@ double SIDD_Base::prepare_sequence(std::string sequence) {
void SIDD_Base::prepare_cruciforms() {
string str1 = cr_string;
size_t found1 = 0;
int IR[2];
double energy;
int IR[2] = {0, 0};
double energy = 0.0;
int pos1 = 0;
int pos2 = 0;
string str2;
Expand Down Expand Up @@ -276,15 +276,16 @@ void SIDD_Base::prepare_cruciforms() {
if(found2!=string::npos) {
str3 = str2.substr(pos2,found2-pos2);
pos2 = int(found2)+1;
if (i==2)
energy=atof(str3.c_str());
else
if (i == 2)
energy = atof(str3.c_str());
else if (i < 2)
IR[i] = atoi(str3.c_str());
i++;
}
}
if (IR[1] <= MaxWindowSize)
en_cruciforms[IR[0]-1][IR[1]] = energy;
if (i == 3 && IR[0] > 0 && IR[0] <= length_seq &&
IR[1] > 0 && IR[1] <= MaxWindowSize)
en_cruciforms[IR[0]-1][IR[1]] = energy;
pos1 = int(found1)+1;
}
}
Expand Down Expand Up @@ -835,11 +836,11 @@ void SIDD_Base::calc_profile()
// V: The following lines is just a search of the maximum Gx for each transition, to substitute the Infinite.
maxGx = profile[1][0].get_ave_Gx();
for(int t=0; t<=Ns; t++) {
for(int j = 1; j < length_seq; j++){
if(maxGx < profile[t][j].get_ave_Gx()){
maxGx = profile[t][j].get_ave_Gx(); // find max Gx
}
}
for(int j = 1; j < length_seq; j++){
if(maxGx < profile[t][j].get_ave_Gx()){
maxGx = profile[t][j].get_ave_Gx(); // find max Gx
}
}
}
// V: This is for the substitution.
for(int t=0; t<=Ns; t++) {
Expand All @@ -859,11 +860,11 @@ void SIDD_Base::sum_open()
sumn[t]+=profile[t][i].get_px();
}
}
if (results) {
cout << "N_Melting = " << sumn[0] << endl;
cout << "N_Z = " << sumn[1] << endl;
cout << "N_Cruciform = " << sumn[2] << endl;
}
if (results) {
cout << "N_Melting = " << sumn[0] << endl;
cout << "N_Z = " << sumn[1] << endl;
cout << "N_Cruciform = " << sumn[2] << endl;
}
}

void SIDD_Base::get_column_header() {
Expand Down
6 changes: 3 additions & 3 deletions trans_compete/qsidd.cpp
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Expand Up @@ -161,13 +161,13 @@ int main(int argc, char* argv[])
cerr << "sidd.initializer failed" << endl;
exit(1);
}
if (sidd.get_Flag_PEA()) sidd.assign_pea(energy);
if (sidd.get_Flag_PEA()) sidd.assign_pea(energy);

if (threshold < 9)
cout << "WARNING: threshold is too small, results may be inaccurate"<< endl;
if (threshold > 15)
if (threshold > 15)
cout << "WARNING: threshold is too high, execution time may be very long"<< endl;
if (stress_level > 0.15 || stress_level < -0.15)
if (stress_level > 0.15 || stress_level < -0.15)
cout << "WARNING: superhelical density is outside of physiological range"<< endl;
if (temperature < 220 || temperature > 320)
cout << "WARNING: temperature is outside of physiological range"<< endl;
Expand Down
2 changes: 1 addition & 1 deletion trans_three/SIDD_1R.cpp
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Expand Up @@ -90,7 +90,7 @@ bool SIDD_1R::Search_Low1RE()

ZsumB = sum_1RB + closed;
ZsumG = sum_1RG+alpha*alpha*K/2*closed;
if (write_profile && results)
if (write_profile && results)
cout << "Number of one-run states = " << count << endl;
return flag_minE1;
}
Expand Down
4 changes: 2 additions & 2 deletions trans_three/SIDD_2R.cpp
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Expand Up @@ -97,8 +97,8 @@ bool SIDD_2R::Search_Low2RE()
StatesInTwoRuns = count;
ZsumB += sum_2RB;
ZsumG +=sum_2RG;

if (results)
if (results)
cout << "Number of two-run states = " << count << endl;
return flag_minE2;
}
Expand Down
2 changes: 1 addition & 1 deletion trans_three/SIDD_3R.cpp
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Expand Up @@ -100,7 +100,7 @@ bool SIDD_3R::Search_Low3RE()
}
}
}
if (results)
if (results)
cout << "Number of three-run states = " << count << endl;
StatesInThreeRuns = (long)count;
ZsumB += sum_3RB;
Expand Down
41 changes: 21 additions & 20 deletions trans_three/SIDD_Base.cpp
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Expand Up @@ -32,7 +32,7 @@ SIDD_Base::SIDD_Base()
plasmid_seq = 0;
en_cruciforms = 0;
profile = 0;
for(int m = MinWindowSize; m <= MaxWindowSize; m++)
for(int m = 0; m <= MaxInitialWindowSize; m++)
promatrix[m] = 0;
R = 8.314/(4.2*1000.0); // gas constant
C = 3.6; // stiffness constant
Expand Down Expand Up @@ -240,8 +240,8 @@ double SIDD_Base::prepare_sequence(std::string sequence) {
void SIDD_Base::prepare_cruciforms() {
string str1 = cr_string;
size_t found1 = 0;
int IR[2];
double energy;
int IR[2] = {0, 0};
double energy = 0.0;
int pos1 = 0;
int pos2 = 0;
string str2;
Expand All @@ -267,15 +267,16 @@ void SIDD_Base::prepare_cruciforms() {
if(found2!=string::npos) {
str3 = str2.substr(pos2,found2-pos2);
pos2 = int(found2)+1;
if (i==2)
energy=atof(str3.c_str());
else
if (i == 2)
energy = atof(str3.c_str());
else if (i < 2)
IR[i] = atoi(str3.c_str());
i++;
}
}
if (IR[1] <= MaxWindowSize)
en_cruciforms[IR[0]-1][IR[1]] = energy;
if (i == 3 && IR[0] > 0 && IR[0] <= length_seq &&
IR[1] > 0 && IR[1] <= MaxWindowSize)
en_cruciforms[IR[0]-1][IR[1]] = energy;
pos1 = int(found1)+1;
}
}
Expand Down Expand Up @@ -836,17 +837,17 @@ void SIDD_Base::calc_profile()

void SIDD_Base::sum_open()
{
double sumn=0.0;
for(int i = 0; i < length_seq; i++)
sumn+=profile[i].get_px();
if (results) {
if (EnergyType == Z_DNA)
cout << "Number of Z-DNA bases = " << sumn << endl;
else if (EnergyType == Cruciform)
cout << "Number of cruciform bases = " << sumn << endl;
else
cout << "Number of melted bases = " << sumn << endl;
}
double sumn=0.0;
for(int i = 0; i < length_seq; i++)
sumn+=profile[i].get_px();
if (results) {
if (EnergyType == Z_DNA)
cout << "Number of Z-DNA bases = " << sumn << endl;
else if (EnergyType == Cruciform)
cout << "Number of cruciform bases = " << sumn << endl;
else
cout << "Number of melted bases = " << sumn << endl;
}
}

void SIDD_Base::get_column_header()
Expand Down Expand Up @@ -955,7 +956,7 @@ void SIDD_Base::show_parameter()
cout << "Energetics: Melting - nearest neighbor energetics\n";
else if (EnergyType == Z_DNA)
cout << "Transition: Z-DNA\n";
else if (EnergyType == Cruciform)
else if (EnergyType == Cruciform)
cout << "Transition: Cruciform\n";
if(MoleculeType == Circular)
cout << "Molecule type: circular DNA\n";
Expand Down
8 changes: 4 additions & 4 deletions trans_three/qsidd.cpp
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Expand Up @@ -160,18 +160,18 @@ int main(int argc, char* argv[])
}
sidd.set_Flag_PEA(energy);
}
if (!sidd.initializer(dnasequence.str().c_str(),length)) {
if (!sidd.initializer(dnasequence.str().c_str(),length)) {
cerr << "sidd.initializer failed" << endl;
exit(1);
exit(1);
}
if (sidd.get_Flag_PEA()) sidd.assign_pea(energy);

if (threshold < 9)
cout << "WARNING: threshold is too small, results may be inaccurate"<< endl;
if (threshold > 15)
cout << "WARNING: threshold is too high, execution time may be very long"<< endl;
if (stress_level > 0.15 || stress_level < -0.15)
if (stress_level > 0.15 || stress_level < -0.15)
cout << "WARNING: superhelical density is outside of physiological range"<< endl;
if (temperature < 220 || temperature > 320)
cout << "WARNING: temperature is outside of physiological range"<< endl;
Expand Down