void Events::simulation() {
bool hasError = false;
while (lattice.coverage() < c::finalCoverage) {
execute();
//if (crossCheck()) {
// hasError = true;
//}
}
crossCheck(true);
std::cout << properties.showHead();
std::cout << properties.show();
if (hasError) {
std::cout << "Error encountered through simulation" << std::endl;
} else {
std::cout << "OK" << std::endl;
}
std::cout << "Diff barrier = " << E_d << std::endl;
countBounds();
std::cout << std::endl;
std::stringstream name;
name << "double" << E_d << ".pdb";
utils::saveFile(name.str(), lattice.gridToPdb());
//utils::loadInJMol(name.str());
}
//main ()
int main (int argc, char *argv[]) {
//Call syntax check
if (argc != 6) {
printf ("Usage: %s Fasta_filename Human_interactions Yeast_interactions Negative_interactions Output_CSV_filename\n", argv[0]);
exit (1);
}
//Main variables
fastaEntry *firFasta = NULL;
FILE *inFile, *fasFile, *outFile;
//File creation and checks
printf ("Opening initial files...\n");
createFile (&fasFile, argv[1], 'r');
createFile (&inFile, argv[2], 'r');
createFile (&outFile, argv[5], 'w');
fprintf (outFile, "Source,Protein,A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,Class\n");
//Build dynamic linked list of scaf data
printf ("Files found and created. Compiling fasta entries...\n");
createFastaEntry (&firFasta);
createFastaList (firFasta, fasFile);
fclose (fasFile);
//Find the entries from the Human interaction file
printf ("Compiled. Cross referencing with Human interaction profile...\n");
crossCheck (firFasta, 'H', 'I', inFile, outFile);
fclose (inFile);
//Find the entries from the Yeast interaction file
printf ("Cross referenced. Cross referencing with Yeast interaction profile...\n");
createFile (&inFile, argv[3], 'r');
crossCheck (firFasta, 'Y', 'I', inFile, outFile);
fclose (inFile);
//Find the entries from the Negative interaction file
printf ("Cross referenced. Cross referencing with Negative interaction profile...\n");
createFile (&inFile, argv[4], 'r');
crossCheck (firFasta, 'N', 'N', inFile, outFile);
fclose (inFile);
//Close everything
printf ("Cross referenced. Freeing memory and closing files...\n");
fclose (outFile);
freeFastaList (firFasta);
printf ("Done.\n");
return 0;
}
void hgLoadEranModules(char *database,
char *geneToModule, char *moduleToMotif, char *motifWeights,
char *motifPositions, char *genePositions)
/* hgLoadEranModules - Load regulatory modules from Eran Segal. */
{
struct sqlConnection *conn = sqlConnect(database);
struct hash *positionsHash = loadGenePositions(database, conn, genePositions);
struct hash *moduleAndMotifHash = loadModuleToMotif(conn, moduleToMotif, "esRegModuleToMotif");
struct hash *geneToModuleHash = loadGeneToModule(conn, geneToModule, "esRegGeneToModule");
struct hash *motifHash = loadMotifWeights(conn, motifWeights, "esRegMotif");
loadGeneToMotif(conn, motifPositions, "esRegGeneToMotif", geneToModuleHash, moduleAndMotifHash, motifHash, positionsHash, "esRegUpstreamRegion");
crossCheck(conn, "esRegMotif", "esRegGeneToModule", "esRegGeneToMotif", "esRegModuleToMotif");
}
simulationReturn Events::growthSimulation()
{
/*std::cout << std::endl;
for (int i = 0; i < 4; i++) {
std::cout << evolution._rates.getRate(0, i, 0);
}
for (int i = 0; i < 4; i++) {
std::cout << evolution._rates.getRate(i, 0, 0);
}
std::cin.ignore();*/
int position = c::A / 2 + c::w / 3;
//for (int n = 0; n < 6; n++) {
// adsorption(neigh::neigh(n,position), atomType::silicon);
//}
adsorption(position, atomType::silicon);
int nShows = 10;
double currTarget = _targetCoverage / 10;
while (_getCoverage() < _targetCoverage) {
if (_nEvents % 1000000 == 0) {
std::cout << _nEvents << "\t" << _getCoverage() << std::endl;
if (crossCheck(false) != 0) {
crossCheck();
std::cin.ignore();
}
}
if (_getCoverage() > currTarget) {
results.addGridState(grid._lattice);
results.addRow(getResultVector());
currTarget += _targetCoverage / 10;
}
execute();
}
crossCheck();
results.addGridState(grid._lattice);
results.addRow(getResultVector());
/*double relaxTime = 50.0;
double targetTime = evolution._masterTime + relaxTime;
evolution._rates.ads = 0.0;
evolution._rates.totalAds = 0.0;
while (evolution._masterTime < targetTime) {
if (_nEvents % 1000000 == 0) {
std::cout << _nEvents << "\t" << _getCoverage() << std::endl;
if (crossCheck(false) != 0) {
crossCheck();
std::cin.ignore();
}
}
execute();
}
crossCheck();
results.addGridState(grid._lattice);
results.addRow(getResultVector());*/
return simulationReturn::allright;
}
