void testToyExample()
{
vector< vector<Peak> > peaks = createToyPeaks();
PeakelGrower_Proximity::Config config;
config.mzTolerance = .1;
config.rtTolerance = 1.5;
PeakelGrower_Proximity peakelGrower(config);
PeakelField field;
peakelGrower.sowPeaks(field, peaks);
const double epsilon = .1;
unit_assert(field.size() == 4);
PeakelField::const_iterator it = field.begin();
unit_assert_equal((*it)->mz, 1000, epsilon);
unit_assert_equal((*it)->retentionTime, 0, epsilon);
++it;
unit_assert_equal((*it)->mz, 1000, epsilon);
unit_assert_equal((*it)->retentionTime, 3, epsilon);
++it;
unit_assert_equal((*it)->mz, 1001, epsilon);
unit_assert_equal((*it)->retentionTime, 1, epsilon);
++it;
unit_assert_equal((*it)->mz, 1002, epsilon);
unit_assert_equal((*it)->retentionTime, 0, epsilon);
}
void PeakelGrower_Proximity::sowPeak(PeakelField& peakelField, const Peak& peak) const
{
vector<PeakelPtr> candidates = peakelField.find(peak.mz, config_.mzTolerance,
RTMatches_Contains<Peakel>(peak.retentionTime, config_.rtTolerance));
if (candidates.empty())
insertNewPeakel(peakelField, peak);
else if (candidates.size() == 1)
updatePeakel(*candidates.front(), peak);
else
{
if (config_.log)
{
*config_.log << "[PeakelGrower_Proximity::sowPeak()] Warning: multiple candidate peakels.\n"
<< " peak: " << peak
<< " candidates: " << candidates.size() << endl;
for (vector<PeakelPtr>::const_iterator it=candidates.begin(); it!=candidates.end(); ++it)
*config_.log << **it << endl;
*config_.log << endl;
}
}
}
void testPeakelField()
{
if (os_) *os_ << "testPeakelField()\n";
PeakelPtr a(new Peakel(Peak(1.0, 1.0)));
PeakelPtr b(new Peakel(Peak(2.0, 1.0)));
PeakelPtr c(new Peakel(Peak(1.0, 2.0)));
PeakelField pf;
pf.insert(a);
pf.insert(b);
pf.insert(c);
if (os_) *os_ << pf << endl;
unit_assert(pf.size() == 3);
PeakelField::const_iterator it = pf.begin();
unit_assert(*it == a);
// note that std::set allows only const access
// however, we can modify **it
(*it)->peaks.push_back(Peak());
(*it)->peaks.clear();
++it;
unit_assert(*it == c);
++it;
unit_assert(*it == b);
// find()
if (os_) *os_ << "testPeakelField(): find()\n";
vector<PeakelPtr> v = pf.find(1.5, .6, RTMatches_Contains<Peakel>(1, .5));
if (os_)
{
*os_ << "find(): " << v.size() << endl;
for (vector<PeakelPtr>::const_iterator it=v.begin(); it!=v.end(); ++it)
*os_ << **it << endl;
}
unit_assert(v.size()==2 && v[0]==a && v[1]==b);
v = pf.find(1.5, .4, RTMatches_Contains<Peakel>(1, .5));
unit_assert(v.empty());
v = pf.find(2, .1, RTMatches_Contains<Peakel>(1, .1));
unit_assert(v.size()==1 && v[0]==b);
MZTolerance fiveppm(5, MZTolerance::PPM);
v = pf.find(1.000001, fiveppm, RTMatches_Contains<Peakel>(1, 10));
unit_assert(v.size()==2 && v[0]==a && v[1]==c);
v = pf.find(1.000006, fiveppm, RTMatches_Contains<Peakel>(1, 10));
unit_assert(v.empty());
// remove()
if (os_) *os_ << "testPeakelField(): remove()\n";
pf.remove(a);
unit_assert(pf.size() == 2);
it = pf.begin();
unit_assert(*it == c);
++it;
unit_assert(*it == b);
bool caught = false;
try {
pf.remove(a);
}
catch (exception& e) {
if (os_) *os_ << "Caught exception correctly: " << e.what() << endl;
caught = true;
}
unit_assert(caught);
pf.remove(b);
unit_assert(pf.size() == 1);
it = pf.begin();
unit_assert(*it == c);
pf.remove(c);
unit_assert(pf.empty());
if (os_) *os_ << endl;
}
