///////////////////////////////////////////////////////////////////////////////
// Run calculations.
///////////////////////////////////////////////////////////////////////////////
void refold::run() {
// Create a variable that handles errors.
int error = 0;
/*
* Use the constructor for RNA that specifies a filename.
* Specify type = 4 (folding save file).
* The save file handles the type of nucleic acid being folded, so it can be set as the default (RNA) in the constructor.
*
* 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;
RNA* strand = new RNA( saveFile.c_str(), 4 );
ErrorChecker<RNA>* checker = new ErrorChecker<RNA>( strand );
error = checker->isErrorStatus();
if( error == 0 ) { cout << "done." << endl; }
/*
* Set the window size, based on the length of the sequence given as input.
* Only do this if window size hasn't been set on the command line.
* Use method GetSequenceLength to get the length of the sequence.
* The window sizes in relation to the length are hardcoded values.
*/
if( windowSize == -1 && error == 0 ) {
int length = strand->GetSequenceLength();
windowSize =
( length > 1200 ) ? 20 :
( length > 800 ) ? 15 :
( length > 500 ) ? 11 :
( length > 300 ) ? 7 :
( length > 120 ) ? 5 :
( length > 50 ) ? 3 :
2;
}
/*
* Refold the regenerated strand using the ReFoldSingleStrand 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 << "Refolding nucleic acids..." << flush;
// Do the main calculation and check for errors.
int mainCalcError = strand->ReFoldSingleStrand( percent, maxStructures, windowSize );
error = checker->isErrorStatus( mainCalcError );
// If no error occurred, print a message saying that the 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 the suboptimal structure calculations.
///////////////////////////////////////////////////////////////////////////////
void AllSub::run() {
// Create a variable that handles errors.
int error = 0;
/*
* Use the constructor for RNA that specifies a filename.
* 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;
RNA* strand = new RNA( seqFile.c_str(), 2, isRNA );
ErrorChecker<RNA>* checker = new ErrorChecker<RNA>( strand );
error = checker->isErrorStatus();
if( error == 0 ) { cout << "done." << endl; }
/*
* Set the percent difference and the maximum absolute energy difference.
* Both differences are based on the length of the sequence, and their values
* in relation to the sequence length are hardcoded.
* Only set these values if they were not set on the command line. As one or
* the other of them may or may not be set, each one is checked individually.
*
* Get the length of the sequence using the GetSequenceLength method.
* Since this method only returns a length, error checking is not necessary.
*/
if( error == 0 ) {
// Get the sequence length to identify the hardcoded thresholds.
int length = strand->GetSequenceLength();
// Set the maximum percent difference, if applicable.
if( percent == -1 ) {
percent =
( length > 1200 ) ? 5 :
( length > 800 ) ? 8 :
( length > 500 ) ? 10 :
( length > 300 ) ? 15 :
( length > 120 ) ? 20 :
( length > 50 ) ? 25 :
50;
}
// Set the absolute energy difference, if applicable.
if( absolute == -1 ) {
absolute =
( length > 1200 ) ? 0.25 :
( length > 800 ) ? 0.5 :
( length > 500 ) ? 0.75 :
( length > 300 ) ? 1 :
( length > 120 ) ? 1.5 :
( length > 50 ) ? 3 :
10;
}
}
/*
* 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; }
}
/*
* Add constraints if a file has been given for their inclusion.
* Read in this constraints with method ReadConstraints.
* After constraints are read, use the error checker's isErrorStatus method
* to check for errors.
*/
if( error == 0 && constraintFile != "" ) {
// Show a message saying that constraints are being applied.
cout << "Applying constraints..." << flush;
// Apply constraints and check for errors.
int constraintError = strand->ReadConstraints( constraintFile.c_str() );
error = checker->isErrorStatus( constraintError );
// If no error occurred, print a message saying constraints were included.
if( error == 0 ) { cout << "done." << endl; }
}
/*
* Generate structures using the GenerateAllSuboptimalStructures method.
* 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.
*/
if( error == 0 ) {
// Show a message saying that the main calculation has started.
cout << "Generating suboptimal structures..." << endl;
// Create the progress monitor.
TProgressDialog* progress = new TProgressDialog();
strand->SetProgress( *progress );
// Generate the suboptimal structures and check for errors.
int mainCalcError =
strand->GenerateAllSuboptimalStructures( (float)percent, absolute );
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; }
}
