void
MSCalibrateForm::setContents( const adcontrols::MSCalibrateMethod& m )
{
ui_locator accessor( ui );
boost::get< QSpinBox *>( accessor( ePolynomialDegree ) )->setValue( m.polynomialDegree() );
boost::get< QDoubleSpinBox *>( accessor( eMassTolerance ) )->setValue(m.massToleranceDa() );
boost::get< QDoubleSpinBox *>( accessor( eMinimumRA ) )->setValue( m.minimumRAPercent() );
boost::get< QDoubleSpinBox *>( accessor( eLowMass ) )->setValue( m.lowMass() );
boost::get< QDoubleSpinBox *>( accessor( eHighMass ) )->setValue( m.highMass() );
}
bool
DataprocHandler::doMSCalibration( adcontrols::MSCalibrateResult& res
, adcontrols::MassSpectrum& centroid
, const adcontrols::MSCalibrateMethod& m )
{
using adcontrols::MSProperty;
res.calibration( centroid.calibration() );
res.references( m.references() );
double tolerance = m.massToleranceDa();
double threshold = adcontrols::segments_helper::max_intensity( centroid ) * m.minimumRAPercent() / 100;
res.tolerance( tolerance );
res.threshold( threshold );
assign_masses assigner( tolerance, threshold );
adcontrols::MSAssignedMasses assignedMasses;
adcontrols::segment_wrapper< adcontrols::MassSpectrum > segments( centroid );
int n = 0;
for ( auto seg: segments )
assigner( assignedMasses, seg, res.references(), seg.mode(), n++ );
res.assignedMasses( assignedMasses ); // set peak assign result
// annotate each peak on spectrum
doAnnotateAssignedPeaks( centroid, assignedMasses );
mass_calibrator calibrator( assignedMasses, centroid.getMSProperty() );
adcontrols::MSCalibration calib;
if ( calibrator.polfit( calib, m.polynomialDegree() + 1 ) ) {
for ( auto it: assignedMasses ) {
double mass = calibrator.compute_mass( it.time(), it.mode(), calib );
it.mass( mass );
}
res.calibration( calib );
// res.assignedMasses( assignedMasses );
#if defined _DEBUG && 0
calibresult_validation( res, centroid, threshold );
#endif
return true;
}
return false;
}
void
MSCalibrationForm::getCalibrateMethod( adcontrols::MSCalibrateMethod& method ) const
{
QStandardItemModel& model = *pModel_;
method.polynomialDegree( ui->spinPolynomials->value() );
method.massToleranceDa( ui->spinMassTolerance->value() );
method.minimumRAPercent( ui->spinMinimumRA->value() );
method.lowMass( ui->spinLowMass->value() );
method.highMass( ui->spinHighMass->value() );
adcontrols::MSReferences references;
int nRows = model.rowCount();
for ( int row = 0; row < nRows; ++row ) {
adcontrols::MSReference reference;
reference.charge_count( model.index( row, c_charge ).data( Qt::EditRole ).toInt() );
// parse formula that contains adduct or lose followed by '+' or '-' sign
std::wstring text = model.index( row, c_formula ).data( Qt::EditRole ).toString().toStdWString();
if ( ! parse_formula( text, reference ) )
continue;
reference.exact_mass( model.index( row, c_exact_mass ).data( Qt::EditRole ).toDouble() );
reference.description( model.index( row, c_description ).data( Qt::EditRole ).toString().toStdWString().c_str() );
QVariant enable = model.index( row, c_enable ).data( Qt::EditRole );
reference.enable( enable.toBool() );
references << reference;
}
method.references( references );
}
void
MSReferenceTable::getContents( adcontrols::MSCalibrateMethod& m )
{
QStandardItemModel& model = *model_;
m.references().clear();
int nRows = model.rowCount();
for ( int row = 0; row < nRows; ++row ) {
std::pair< std::wstring, std::wstring > adducts;
std::wstring value = model.data( model.index( row, c_formula ), Qt::EditRole ).toString().toStdWString();
std::wstring formula = adcontrols::ChemicalFormula::splitFormula( adducts, value, false );
std::wstring adduct_string = adcontrols::ChemicalFormula::make_adduct_string( adducts );
double exactMass = model.data( model.index( row, c_exact_mass ), Qt::EditRole ).toDouble();
bool enable = model.data( model.index( row, c_enable ), Qt::CheckStateRole ).toBool();
int charge = model.data( model.index( row, c_charge ) ).toInt();
std::wstring description = model.data( model.index( row, c_description ) ).toString().toStdWString();
m.references() << adcontrols::MSReference( formula.c_str(), true, adduct_string.c_str(), enable, exactMass, charge, description.c_str() );
}
}
void
MSReferenceTable::setContents( const adcontrols::MSCalibrateMethod& m )
{
QStandardItemModel& model = *model_;
const adcontrols::MSReferences& references = m.references();
int nRows = static_cast<int>( references.size() );
if ( nRows < model.rowCount() )
model.removeRows( 0, model.rowCount() ); // make sure all clear
model.setRowCount( nRows + 1 ); // be sure last empty line
int row = 0;
for ( auto& ref: references )
addReference( ref, row++ );
resizeColumnsToContents();
resizeRowsToContents();
}
bool
DataprocHandler::doMSCalibration( adcontrols::MSCalibrateResult& res
, adcontrols::MassSpectrum& centroid
, const adcontrols::MSCalibrateMethod& m
, const adcontrols::MSAssignedMasses& assigned )
{
using adcontrols::MSProperty;
const double tolerance = m.massToleranceDa();
const double threshold = centroid.getMaxIntensity() * m.minimumRAPercent() / 100;
res.tolerance( tolerance ); // set tolerance in result
res.threshold( threshold ); // set threshold in result
std::map< size_t, size_t > mode_map;
for ( adcontrols::MSAssignedMasses::vector_type::const_iterator it = assigned.begin(); it != assigned.end(); ++it )
mode_map[ it->mode() ]++;
// std::map<size_t, size_t>::iterator itMax = std::max_element( mode_map.begin(), mode_map.end() );
// int mode = static_cast<int>(itMax->first);
mass_calibrator calibrator( assigned, centroid.getMSProperty() );
adcontrols::MSCalibration calib;
if ( ! calibrator.polfit( calib, m.polynomialDegree() + 1 ) )
return false;
res.references( m.references() );
res.calibration( calib );
centroid.setCalibration( calib, true ); // m/z assign based on manually determined peaks
// continue auto-assign
assign_masses assign( tolerance, threshold );
adcontrols::MSAssignedMasses assignedMasses;
adcontrols::segment_wrapper< adcontrols::MassSpectrum > segments( centroid );
for ( size_t n = 0; n < segments.size(); ++n ) {
assign( assignedMasses, segments[n], m.references(), 0, static_cast<int>(n) );
}
mass_calibrator calibrator2( assignedMasses, centroid.getMSProperty() );
if ( calibrator2.polfit( calib, m.polynomialDegree() + 1 ) ) {
for ( auto it: assignedMasses )
it.mass( calibrator2.compute_mass( it.time(), it.mode(), calib ) );
centroid.setCalibration( calib, true );
res.calibration( calib );
res.assignedMasses( assignedMasses );
return true;
}
return false;
}
void
MSCalibrationForm::setCalibrateMethod( const adcontrols::MSCalibrateMethod& method )
{
QStandardItemModel& model = *pModel_;
ui->spinPolynomials->setValue( method.polynomialDegree() );
ui->spinMassTolerance->setValue( method.massToleranceDa() );
ui->spinMinimumRA->setValue( method.minimumRAPercent() );
ui->spinLowMass->setValue( method.lowMass() );
ui->spinHighMass->setValue( method.highMass() );
const adcontrols::MSReferences& references = method.references();
int nRows = static_cast<int>( references.size() );
if ( nRows < model.rowCount() )
model.removeRows( 0, model.rowCount() ); // make sure all clear
model.setRowCount( nRows + 1 ); // be sure last empty line
int row = 0;
for ( auto& ref: references ) {
std::wstring formula = ref.display_formula();
model.setData( model.index( row, c_formula ), qtwrapper::qstring::copy( formula ) );
model.setData( model.index( row, c_exact_mass ), ref.exact_mass() );
model.setData( model.index( row, c_enable ), ref.enable() );
QStandardItem * chk = model.itemFromIndex( model.index( row, c_enable ) );
if ( chk ) {
chk->setFlags( Qt::ItemIsUserCheckable | Qt::ItemIsEnabled );
chk->setEditable( true );
model.setData( model.index( row, c_enable ), ref.enable() ? Qt::Checked : Qt::Unchecked, Qt::CheckStateRole );
}
model.setData( model.index( row, c_description ), qtwrapper::qstring::copy( ref.description() ) );
model.setData( model.index( row, c_charge ), ref.charge_count() );
++row;
}
}