void Utils::writeCrashLog(std::string path)
{
string line;
ifstream myfile;
vector<string> cam;
myfile.open( getAssetPath(path).c_str(), ifstream::in);
int value = 0;
if (myfile.is_open())
{
while ( myfile.good() )
{
getline (myfile,line);
cam.push_back(line);
}
myfile.close();
value = ::atoi(cam[0].c_str());
}
value++;
ofstream myfile1 (getAssetPath(path).c_str());
if (myfile1.is_open())
{
myfile1 << value;
myfile.close();
}
}
void Make_log1(int frame_counter,std::vector <std::vector <int> > pos,int pos_counter){
std::ofstream fout("log1.txt",std::ios_base::app); //write
std::fstream myfile1("log1.txt",std::ios_base::in); //read
std::string read1;
int value;
bool has_non_absolute = false; //check if each centre has a non-absolute value, if not then put -1 into its position except the first frame
std::vector< std::vector<int> > log1_(2, std::vector<int>(10));
int log1_counter = 0;
int value1 = 0;
int value2 = 0;
for(int i = 0; i <= pos_counter - 1;i++){
log1_ = Calculate_dimens(pos[i][0],pos[i][1],pos[i][2],pos[i][3],log1_,log1_counter);
log1_counter += 2;
}
int kalimera = 5;
if(fout.is_open()){
if(frame_counter == 1){ //first frame
int i = 0;
while(i < log1_counter){
fout << log1_[1][i++];
fout << " ";
fout << log1_[1][i++];
fout << " ";
}
fout << "|";
fout << " ";
fout << "|";
fout << " ";
}
else{ //rest of the frames
int counter1 = 1;
int counter2 = 1;
int position1 = 0;
while(true){
myfile1 >> read1;
if(read1.compare("|") != 0 && counter2 == frame_counter - 1){ //in the absolute position values in one frame before the one that we are now
value = std::stoi(read1);
log1_[0][position1++] = value;
}
else if(read1.compare("|") == 0 && counter2 == frame_counter){ //if it is a bracket and we one frame before the one that we are now
break;
}
else if(read1.compare("|") == 0){ //we are not on the one frame before the last
if(counter1 > counter2){
counter2++;
}
else{
counter1++;
}
}
}
int i = 0;
if(log1_counter > 0){
while(i < log1_counter){ //put the new absolute values to txt
fout << log1_[1][i++];
fout << " ";
fout << log1_[1][i++];
fout << " ";
}
}
fout << "|";
fout << " ";
for(int i = 0;i < log1_counter;i++){ //find if two centres are closer than 5 pixel in x axis
for(int j = 0;j < position1;j++){
value1 = log1_[1][i];
value2 = log1_[0][j];
if(i % 2 == 0 || i == 0){ // if we are on a x-axis position
if(j % 2 == 0 || j == 0){
if(value1 > value2){ //check so that we don't have to check between positive and negative numbers
int temp = value1 - value2;
int bla = 5;
if(temp < 10){
fout << temp;
fout << " ";
has_non_absolute = true;
break;
}
}
else if(value1 < value2){
int temp = value2 - value1;
int bla = 5;
if(temp < 10){
fout << temp;
fout << " ";
has_non_absolute = true;
break;
}
}
else{
continue;
}
}
}
else if (i % 2 == 1){
if(j % 2 == 1){
if(value1 > value2){ //check so that we don't have to check between positive and negative numbers
int temp = value1 - value2;
if(temp < 10){
fout << temp;
fout << " ";
has_non_absolute = true;
break;
}
}
else if(value1 < value2){
int temp = value2 - value1;
int bla = 5;
if(temp < 10){
fout << temp;
fout << " ";
has_non_absolute = true;
break;
}
}
else{
continue;
}
}
}
}
if(has_non_absolute == false){ //if a centre has no non-absolute values then put -1 except first frame
fout << 0;
fout << " ";
}
else{
has_non_absolute = false;
}
value1 = 0;
value2 = 0;
}
fout << "|";
fout << " ";
}
}
}
void Simulation::setupFromFile(std::string centroid, std::string voronoi)
{
int vertexNumber = -1;
int faceNumber = -1;
bool vertex = false;
bool face = false;
std::string line;
int compteur = 0;
int skip = 2;
// Cellule correspondant en fait au bord
Cellule* border = new Cellule(0);
CELLULES[border->getID()] = border;
std::vector<std::string> tmp;
// On test déjà quelles cellules vont être gardés
ifstream myfile1(voronoi.c_str());
compteur = 0;
skip = 1;
tmp.clear();
//std::istringstream* iss;
std::set<int> goodCells;
if (myfile1.is_open())
{
while ( myfile1.good() )
{
for(int s = 0; s<=skip; s++) {
getline (myfile1,line);
}
compteur++;
if(compteur > nombreCellules) break;
if(compteur == 1 && !vertex) {
tmp.clear();
StringWorker::Split(line,tmp," ");
std::istringstream iss(tmp[0]);
// convertir en un int
iss >> vertexNumber;
compteur = 0;
vertex = true;
skip = vertexNumber;
} else {
if(vertex) {
skip = 0;
tmp.clear();
StringWorker::Split(line,tmp," ");
bool garde = true;
//std::cout<<line<<std::endl;
for(unsigned int i=0; i<tmp.size(); i++) {
int p;
std::istringstream iss(tmp[i]);
// convertir en un int
iss >> p;
//std::cout<<"pt : "<<p<<std::endl;
if(p == 0) {
garde = false;
break;
}
}
if(garde) {
//std::cout<<"garde "<<compteur<<std::endl;
goodCells.insert(compteur);
}
}
}
}
//Function to Read Sequences and Alignment from File and Initiliaze the Corresponding Sequences Object.
//The subtree argument is needed in order to delete all the "All-1" Columns from the OverallHomologies Matrix according to the specified subtree
void PairInitializer::InitSequences() {
ClearInputStream();
Seqs = new Sequences();
/** Read Bare Sequences and Sequence Ids **/
string line;
ifstream myfile (BareSequencesFile.c_str());
string filename = BareSequencesFile;
stringstream seqId;
stringstream seqText;
bool firstLine = true;
if (myfile.is_open()) {
while ( myfile.good() ) {
getline (myfile,line);
if (line.compare("")==0 || line.compare("\n")==0 || line.compare(" ")==0) continue; //skip empty lines
if (StartsWith(line, ">") || StartsWith(line,";")) {
if (!firstLine) {
Seqs->AddBareSequence(seqText.str());
Seqs->AddSequenceId(seqId.str());
seqId.str("");
seqText.str("");
}
seqId << line;
firstLine = false;
} else {
seqText << line;
}
}
Seqs->AddBareSequence(seqText.str());
Seqs->AddSequenceId(seqId.str());
} else cerr << " Unable to open file: "<<filename<<" for reading.";
myfile.close();
/** Read Alignment **/
string line1;
ifstream myfile1 (AlignedSequencesFile.c_str());
string filename1 = AlignedSequencesFile;
stringstream seqText1;
bool firstLine1 = true;
if (myfile1.is_open()) {
while ( myfile1.good() ) {
getline (myfile1,line1);
if (line1.compare("")==0 || line1.compare("\n")==0 || line1.compare(" ")==0) continue; //skip empty lines
if (StartsWith(line1, ">") || StartsWith(line1,";")) {
if (!firstLine1) {
Seqs->AddAlignedSequence(seqText1.str());
seqText1.str("");
}
firstLine1 = false;
} else {
seqText1 << line1;
}
}
Seqs->AddAlignedSequence(seqText1.str());
} else cerr << " Unable to open file: "<<filename1<<" for reading.";
myfile1.close();
Seqs->SetIndicesFromAlignment();
}
