TEST_EQUAL(peak.getAtom(), &atom) RESULT CHECK(Peak1D::Peak1D(const Peak1D& peak)) Peak1D peak2(peak); TEST_REAL_EQUAL(peak2.getPosition(), 111.1) TEST_REAL_EQUAL(peak2.getWidth(), 222.2) TEST_REAL_EQUAL(peak2.getIntensity(), 333.3) TEST_EQUAL(peak2.getAtom(), &atom) RESULT CHECK(Peak1D::void operator = (const Peak1D& peak)) Peak1D peak2 = peak; TEST_REAL_EQUAL(peak2.getPosition(), 111.1) TEST_REAL_EQUAL(peak2.getWidth(), 222.2) TEST_REAL_EQUAL(peak2.getIntensity(), 333.3) TEST_EQUAL(peak2.getAtom(), &atom) RESULT CHECK(Peak1D::bool operator == (const Peak1D& peak) const ) Peak1D peak2 = peak; Peak1D peak3 = peak; TEST_EQUAL(peak2 == peak, true) TEST_EQUAL(peak2 == peak3, true) peak3.setWidth(0.0); TEST_EQUAL(peak2 == peak, true) TEST_EQUAL(peak2 == peak3, false) peak3.setWidth(peak2.getWidth()); TEST_EQUAL(peak2 == peak3, true) peak3.setIntensity(0.0); TEST_EQUAL(peak2 == peak3, false)
START_SECTION((PositionType const& getPosition() const)) TEST_REAL_SIMILAR(Peak1D().getPosition()[0], 0.0) END_SECTION START_SECTION((CoordinateType getMZ() const)) TEST_REAL_SIMILAR(Peak1D().getMZ(), 0.0) END_SECTION START_SECTION((CoordinateType getPos() const)) TEST_REAL_SIMILAR(Peak1D().getPos(), 0.0) END_SECTION START_SECTION((void setIntensity(IntensityType intensity))) Peak1D p; p.setIntensity(17.8f); TEST_REAL_SIMILAR(p.getIntensity(), 17.8) END_SECTION START_SECTION((void setPosition(PositionType const &position))) Peak1D::PositionType pos; pos[0] = 1.0; Peak1D p; p.setPosition(pos); TEST_REAL_SIMILAR(p.getPosition()[0], 1.0) END_SECTION START_SECTION((PositionType& getPosition())) Peak1D::PositionType pos; pos[0] = 1.0; Peak1D p; p.getPosition() = pos;
bool ShiftModel1D::finish()
{
if (!isValid())
{
return false;
}
if (!system_)
{
Log.info() << "No valid system found!" << std::endl;
return false;
}
// compute the shift model if necessary
if (compute_shifts_)
{
BALL::ShiftModel sm(parameters_.getFilename());
system_->apply(sm);
}
String element = "";
// Peter Bayer proposed as peak width
// for H 15Hz
// for N 10hz
// for C 5Hz
// peakwidth is meassured in ppm, since
// experiments were done in Hz, we convert the values
// according to the formular
//
// offset [Hz] = offset[ppm] * basic frequency
//
// for our prediction we assume a basic frequency of 700 MHz
float peakwidth = 0.0;
switch(type_)
{
case H:
case H_ON_BACKBONE:
element = "H";
//peakwidth = 0.02142; // Peter Bayers estimation
peakwidth = 0.0032; // this is the former BALL estimation
break;
case N:
case N_BACKBONE:
element = "N";
peakwidth = 0.01428;
break;
case C:
case C_BACKBONE:
element = "C";
peakwidth = 0.00714;
break;
}
int counter = 0;
if (element == "" )
return true;
for (BALL::ResidueIterator r_it = system_->beginResidue(); +r_it; ++r_it)
{
Atom* atom = NULL;
for (BALL::AtomIterator at_it = r_it->beginAtom(); +at_it; ++at_it)
{
if (hasType_(&(*at_it), type_))
{
counter++;
atom = &(*at_it);
// we have, get the shift
float shift = atom->getProperty(BALL::ShiftModule::PROPERTY__SHIFT).getFloat();
Peak1D peak;
float pos = shift;
peak.setPosition(pos);
peak.setWidth(peakwidth);
peak.setIntensity(peak.getIntensity()+1);
//setAtom();
peaks_.push_back(peak);
}
}
}
std::cout << "Number of considered atoms: "<< counter << std::endl;
return true;
}