///////////////////////////////////////////////////////////////////////////////
// Run bimolecular folding calculations.
///////////////////////////////////////////////////////////////////////////////
void bifold::run() {
// Create a variable that handles errors.
int error = 0;
/*
* Use the constructor for HybridRNA that specifies two filenames and types.
* For both sequences, specify type = 2 (sequence file).
* isRNA identifies whether the strand is RNA (true) or DNA (false).
*
* After construction of the strand data structure, create the error checker
* which monitors for errors.
* Throughout, the error status of the calculation is checked with a variant
* of the isErrorStatus method, which returns 0 if no error occurred. The
* calculation proceeds as long as error = 0.
*/
cout << "Initializing nucleic acids..." << flush;
HybridRNA* strand =
new HybridRNA( seqFile1.c_str(), 2, seqFile2.c_str(), 2, isRNA );
ErrorChecker<HybridRNA>* checker = new ErrorChecker<HybridRNA>( strand );
error = checker->isErrorStatus();
if( error == 0 ) { cout << "done." << endl; }
/*
* Set the temperature using the SetTemperature method.
* Only set the temperature if a given temperature doesn't equal the default.
* If the temperature does need to be set, use the error checker's
* isErrorStatus method to check for errors.
*/
if( ( error == 0 ) && ( temperature != 310.15 ) ) {
// Show a message saying that the temperature is being set.
cout << "Setting temperature..." << flush;
// Set the temperature and check for errors.
int tempError = strand->SetTemperature( temperature );
error = checker->isErrorStatus( tempError );
// If no error occurred, print a message saying that temperature is set.
if( error == 0 ) { cout << "done." << endl; }
}
/*
* Set allowance or denial of intramolecular pairs using the
* SetForbidIntramolecular method.
* Since this method only sets a flag, error checking is not necessary.
*/
if( error == 0 ) {
strand->SetForbidIntramolecular( intramolecular );
}
/*
* Fold the hybrid strand using the FoldBimolecular method.
* If a save file name has been specified, the FoldBimolecular method also
* has the ability to write a folding save file.
* During calculation, monitor progress using the TProgressDialog class and
* the Start/StopProgress methods of the RNA class. Neither of these methods
* require any error checking.
* After the main calculation is complete, use the error checker's
* isErrorStatus method to check for errors in the main calculation.
*/
if( error == 0 ) {
// Show a message saying that the main calculation has started.
cout << "Folding two strands..." << endl;
// Create the progress monitor.
TProgressDialog* progress = new TProgressDialog();
strand->SetProgress( *progress );
// Fold the hybrid strand and check for errors.
int mainCalcError =
strand->FoldBimolecular( percent, maxStructures, windowSize,
saveFile.c_str(), maxLoop );
error = checker->isErrorStatus( mainCalcError );
// Delete the progress monitor.
strand->StopProgress();
delete progress;
// If no error occurred, print message that main calculation is done.
if( error == 0 ) { cout << "done." << endl; }
}
/*
* Write a CT output file using the WriteCt method.
* After writing is complete, use the error checker's isErrorStatus method to
* check for errors.
*/
if( error == 0 ) {
// Show a message saying that the CT file is being written.
cout << "Writing output ct file..." << flush;
// Write the CT file and check for errors.
int writeError = strand->WriteCt( ctFile.c_str() );
error = checker->isErrorStatus( writeError );
// If no errors occurred, show a CT file writing completion message.
if( error == 0 ) { cout << "done." << endl; }
}
// Delete the error checker and data structure.
delete checker;
delete strand;
// Print confirmation of run finishing.
if( error == 0 ) { cout << calcType << " complete." << endl; }
else { cerr << calcType << " complete with errors." << endl; }
}
///////////////////////////////////////////////////////////////////////////////
// Run calculations.
///////////////////////////////////////////////////////////////////////////////
void DuplexFold::run() {
// Create a variable that handles errors.
int error = 0;
/*
* Use the constructor for HybridRNA that specifies two filenames and types.
* For both sequences, specify type = 2 (sequence file).
* isRNA identifies whether the strand is RNA (true) or DNA (false).
*
* After construction of the strand data structure, create the error checker which monitors for errors.
* Throughout, the error status of the calculation is checked with a variant of the isErrorStatus method, which returns 0 if no error occurred.
* The calculation proceeds as long as error = 0.
*/
cout << "Initializing nucleic acids..." << flush;
HybridRNA* strand = new HybridRNA( seqFile1.c_str(), 2, seqFile2.c_str(), 2, isRNA );
ErrorChecker<HybridRNA>* checker = new ErrorChecker<HybridRNA>( strand );
error = checker->isErrorStatus();
if( error == 0 ) { cout << "done." << endl; }
/*
* Set the temperature using the SetTemperature method.
* Only set the temperature if a given temperature doesn't equal the default.
* If the temperature does need to be set, use the error checker's isErrorStatus method to check for errors.
*/
if( ( error == 0 ) && ( temperature != 310.15 ) ) {
// Show a message saying that the temperature is being set.
cout << "Setting temperature..." << flush;
// Set the temperature and check for errors.
int tempError = strand->SetTemperature( temperature );
error = checker->isErrorStatus( tempError );
// If no error occurred, print a message saying that temperature is set.
if( error == 0 ) { cout << "done." << endl; }
}
/*
* Fold the hybrid strand using the FoldDuplex method.
* After the main calculation is complete, use the error checker's isErrorStatus method to check for errors.
*/
if( error == 0 ) {
// Show a message saying that the main calculation has started.
cout << "Folding duplex..." << endl;
// Create the progress monitor.
TProgressDialog* progress = new TProgressDialog();
strand->SetProgress( *progress );
// Do the main calculation and check for errors.
int mainCalcError = strand->FoldDuplex( percent, maxStructures, windowSize, maxLoop );
error = checker->isErrorStatus( mainCalcError );
// Delete the progress monitor.
strand->StopProgress();
delete progress;
// If no error occurred, print message that main calculation is done.
if( error == 0 ) { cout << "done." << endl; }
}
/*
* Write a CT output file using the WriteCt method.
* After writing is complete, use the error checker's isErrorStatus method to check for errors.
*/
if( error == 0 ) {
// Show a message saying that the CT file is being written.
cout << "Writing output ct file..." << flush;
// Write the CT file and check for errors.
int writeError = strand->WriteCt( ctFile.c_str() );
error = checker->isErrorStatus( writeError );
// If no errors occurred, show a CT file writing completion message.
if( error == 0 ) { cout << "done." << endl; }
}
// Delete the error checker and data structure.
delete checker;
delete strand;
// Print confirmation of run finishing.
if( error == 0 ) { cout << calcType << " complete." << endl; }
else { cerr << calcType << " complete with errors." << endl; }
}
