///////////////////////////////////////////////////////////////////////////////
// Run calculations.
///////////////////////////////////////////////////////////////////////////////
void EnergyPlot::run() {
/*
* Make sure the dot plot data can be accessed.
*/
// Print a message that says the dot plot data file is being checked.
cout << "Checking dot plot input file..." << flush;
// Initialize the dot plot handler and an error string.
DotPlotHandler* plotHandler = 0;
string error = "";
// Create the RNA strand that holds the dot plot data.
RNA* strand = new RNA( inputFile.c_str(), 4 );
ErrorChecker<RNA>* checker = new ErrorChecker<RNA>( strand );
error = checker->returnError();
if( error == "" ) { cout << "done." << endl; }
/*
* Prepare the dot plot data.
*/
if( error == "" ) {
// Print a message saying that the dot plot data is being prepared.
cout << "Preparing dot plot data..." << flush;
// Build the dot plot handler using the strand's sequence length.
int length = strand->GetSequenceLength();
plotHandler = new DotPlotHandler( descriptionSettings.getDescription(inputFile, true), length );
// Add all possible dots to the dot plot.
for( int i = 1; i <= length; i++ ) {
for( int j = i; j <= length; j++ ) {
double energy = strand->GetPairEnergy( i, j );
if( energy > 0.0 ) { energy = numeric_limits<double>::infinity(); }
else {
stringstream stream( stringstream::in | stringstream::out );
stream << fixed << setprecision( 1 ) << energy;
stream >> energy;
}
plotHandler->addDotValue( i, j, energy );
}
}
// Print a message saying that the dot plot data has been prepared.
cout << "done." << endl;
}
