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#include <iostream>
#include <iomanip>
#include <catch2/catch_test_macros.hpp>
#include <QDebug>
#include <pappsomspp/core/utils.h>
#include <pappsomspp/core/trace/datapoint.h>
#include <pappsomspp/core/trace/trace.h>
#include <pappsomspp/core/trace/maptrace.h>
#include <pappsomspp/core/massspectrum/massspectrum.h>
#include <pappsomspp/core/processing/combiners/massdatacombinerinterface.h>
#include <pappsomspp/core/processing/combiners/massspectrumpluscombiner.h>
#include <pappsomspp/core/processing/combiners/mzintegrationparams.h>
namespace pappso
{
TEST_CASE("Constructing MassSpectrumPlusCombiner objects.",
"[MassSpectrumPlusCombiner][constructors]")
{
SECTION("Construct a MassSpectrumPlusCombiner", "[MassSpectrumPlusCombiner]")
{
MassSpectrumPlusCombiner mass_spectrum_combiner1;
REQUIRE(mass_spectrum_combiner1.getDecimalPlaces() == -1);
int decimal_places = 3;
MassSpectrumPlusCombiner mass_spectrum_combiner2(decimal_places);
REQUIRE(mass_spectrum_combiner2.getDecimalPlaces() == decimal_places);
}
SECTION(
"Construct a MassSpectrumPlusCombiner from another "
"MassSpectrumPlusCombiner",
"[MassSpectrumPlusCombiner]")
{
int decimal_places = 3;
MassSpectrumPlusCombiner mass_spectrum_combiner(decimal_places);
MassSpectrumPlusCombiner mass_spectrum_combiner1(mass_spectrum_combiner);
REQUIRE(mass_spectrum_combiner1.getDecimalPlaces() == decimal_places);
// Test the handling of the bins.
// Create the bins
std::vector<double> bins{0.001, 0.002, 0.003, 0.004, 0.005};
MassSpectrumPlusCombiner mass_spectrum_combiner2(decimal_places);
mass_spectrum_combiner2.setBins(bins);
MassSpectrumPlusCombiner mass_spectrum_combiner3(mass_spectrum_combiner2);
REQUIRE(mass_spectrum_combiner3.getBins().size() == 5);
REQUIRE(mass_spectrum_combiner3.getBins().front() == 0.001);
REQUIRE(mass_spectrum_combiner3.getBins().back() == 0.005);
}
}
#if !defined(__i386__)
// This test unbelievable does not pass on i386...
TEST_CASE("Performing combinations with MassSpectrumPlusCombiner",
"[MassSpectrumPlusCombiner][combinations]")
{
SECTION("Combine two complementary MassSpectrum objects into a MapTrace.",
"[MassSpectrumPlusCombiner]")
{
// Create a MassSpectrum that looks like something real.
std::vector<DataPoint> data_point_vector;
// clang-format off
data_point_vector.push_back(DataPoint("610.02000 12963.5715942383"));
data_point_vector.push_back(DataPoint("610.07000 15639.6568298340"));
data_point_vector.push_back(DataPoint("610.12000 55999.7628784180"));
data_point_vector.push_back(DataPoint("610.17000 9335990.3578681946"));
data_point_vector.push_back(DataPoint("610.2200000 635674266.1611375809"));
data_point_vector.push_back(DataPoint("610.27000 54459.4762458801"));
data_point_vector.push_back(DataPoint("610.32000 205580.6580276489"));
data_point_vector.push_back(DataPoint("610.37000 84627.3196716309"));
data_point_vector.push_back(DataPoint("610.42000 51061.7636718750"));
data_point_vector.push_back(DataPoint("610.47000 0.0000000000"));
data_point_vector.push_back(DataPoint("610.52000 29848.3424072266"));
data_point_vector.push_back(DataPoint("610.57000 27266.8031616211"));
data_point_vector.push_back(DataPoint("610.62000 36922.3937377930"));
data_point_vector.push_back(DataPoint("610.67000 44082.4265441895"));
data_point_vector.push_back(DataPoint("610.72000 32580.1677703857"));
data_point_vector.push_back(DataPoint("610.77000 39453.8380126953"));
data_point_vector.push_back(DataPoint("610.82000 63698.7124328613"));
data_point_vector.push_back(DataPoint("610.87000 34406.7755126953"));
data_point_vector.push_back(DataPoint("610.92000 33385.7486267090"));
data_point_vector.push_back(DataPoint("610.97000 22105.9357604980"));
// clang-format on
REQUIRE(20 == data_point_vector.size());
MassSpectrum mass_spectrum1(data_point_vector);
REQUIRE(20 == mass_spectrum1.size());
data_point_vector.clear();
// Create another mass spectrum that is the "continuation" of the first one.
// clang-format off
data_point_vector.push_back(DataPoint("611.02000 12963.5715942383"));
data_point_vector.push_back(DataPoint("611.07000 15639.6568298340"));
data_point_vector.push_back(DataPoint("611.12000 55999.7628784180"));
data_point_vector.push_back(DataPoint("611.17000 9335990.3578681946"));
data_point_vector.push_back(DataPoint("611.2200000 635674266.1611375809"));
data_point_vector.push_back(DataPoint("611.27000 54459.4762458801"));
data_point_vector.push_back(DataPoint("611.32000 205580.6580276489"));
data_point_vector.push_back(DataPoint("611.37000 84627.3196716309"));
data_point_vector.push_back(DataPoint("611.42000 51061.7636718750"));
data_point_vector.push_back(DataPoint("611.47000 0.00000000"));
data_point_vector.push_back(DataPoint("611.52000 29848.3424072266"));
data_point_vector.push_back(DataPoint("611.57000 27266.8031616211"));
data_point_vector.push_back(DataPoint("611.62000 36922.3937377930"));
data_point_vector.push_back(DataPoint("611.67000 44082.4265441895"));
data_point_vector.push_back(DataPoint("611.72000 32580.1677703857"));
data_point_vector.push_back(DataPoint("611.77000 39453.8380126953"));
data_point_vector.push_back(DataPoint("611.82000 63698.7124328613"));
data_point_vector.push_back(DataPoint("611.87000 34406.7755126953"));
data_point_vector.push_back(DataPoint("611.92000 33385.7486267090"));
data_point_vector.push_back(DataPoint("611.97000 22105.9357604980"));
// clang-format on
REQUIRE(20 == data_point_vector.size());
MassSpectrum mass_spectrum2(data_point_vector);
REQUIRE(20 == mass_spectrum2.size());
// Prepare the bins on the basis of the spectrum.
int decimal_places = 5;
pappso::PrecisionPtr precision_p =
pappso::PrecisionFactory::getDaltonInstance(0.05);
bool binSizeDivisor = 6;
MzIntegrationParams mz_integration_params(610.02,
611.97,
MzIntegrationParams::BinningType::ARBITRARY,
precision_p,
binSizeDivisor,
decimal_places,
true);
// Check that it does not compute bins, since BinningType::NONE.
std::vector<double> bins = mz_integration_params.createBins();
// Creation of the same number of data points plus a last one bin.
REQUIRE(bins.size() == mass_spectrum1.size() + mass_spectrum2.size() + 1);
REQUIRE(bins[0] == 610.02000);
// The last bin matches the last DataPoint of the second spectrum + one bin
// size.
REQUIRE(bins.back() == 612.02000);
// Now compute the combination without binning.
MassSpectrumPlusCombiner mass_spectrum_combiner(decimal_places);
mass_spectrum_combiner.setBins(bins);
MapTrace map_trace;
mass_spectrum_combiner.combine(map_trace, mass_spectrum1);
// std::cout << std::setprecision(10)
//<< "First map item x: " << map_trace.begin()->first
//<< " y: " << map_trace.begin()->second << std::endl;
REQUIRE(map_trace.size() == 20);
REQUIRE(map_trace[610.02000] == 12963.5715942383);
REQUIRE(map_trace[610.27000] == 54459.4762458801);
REQUIRE(map_trace[610.97000] == 22105.9357604980);
// Now combine the second mass spectrum.
mass_spectrum_combiner.combine(map_trace, mass_spectrum2);
REQUIRE(map_trace.size() == 40);
REQUIRE(map_trace[610.02000] == 12963.5715942383);
REQUIRE(map_trace[610.27000] == 54459.4762458801);
REQUIRE(map_trace[610.97000] == 22105.9357604980);
}
SECTION("Combine two intermixed MassSpectrum objects into a MapTrace.",
"[MassSpectrumPlusCombiner]")
{
// Create a MassSpectrum that looks like something real.
std::vector<DataPoint> data_point_vector;
// clang-format off
data_point_vector.push_back(DataPoint("610.02000 12963.5715942383"));
data_point_vector.push_back(DataPoint("610.07000 15639.6568298340"));
data_point_vector.push_back(DataPoint("610.12000 55999.7628784180"));
data_point_vector.push_back(DataPoint("610.17000 9335990.3578681946"));
data_point_vector.push_back(DataPoint("610.2200000 635674266.1611375809"));
data_point_vector.push_back(DataPoint("610.27000 54459.4762458801"));
data_point_vector.push_back(DataPoint("610.32000 205580.6580276489"));
data_point_vector.push_back(DataPoint("610.37000 84627.3196716309"));
data_point_vector.push_back(DataPoint("610.42000 51061.7636718750"));
data_point_vector.push_back(DataPoint("610.47000 0.0000000000"));
data_point_vector.push_back(DataPoint("610.52000 29848.3424072266"));
data_point_vector.push_back(DataPoint("610.57000 27266.8031616211"));
data_point_vector.push_back(DataPoint("610.62000 36922.3937377930"));
data_point_vector.push_back(DataPoint("610.67000 44082.4265441895"));
data_point_vector.push_back(DataPoint("610.72000 32580.1677703857"));
data_point_vector.push_back(DataPoint("610.77000 39453.8380126953"));
data_point_vector.push_back(DataPoint("610.82000 63698.7124328613"));
data_point_vector.push_back(DataPoint("610.87000 34406.7755126953"));
data_point_vector.push_back(DataPoint("610.92000 33385.7486267090"));
data_point_vector.push_back(DataPoint("610.97000 22105.9357604980"));
// clang-format on
REQUIRE(20 == data_point_vector.size());
MassSpectrum mass_spectrum1(data_point_vector);
REQUIRE(20 == mass_spectrum1.size());
data_point_vector.clear();
// Create another mass spectrum that intermixes with the first one by adding
// 0.005 to the previous m/z values.
// clang-format off
data_point_vector.push_back(DataPoint("610.02500 12963.5715942383"));
data_point_vector.push_back(DataPoint("610.07500 15639.6568298340"));
data_point_vector.push_back(DataPoint("610.12500 55999.7628784180"));
data_point_vector.push_back(DataPoint("610.17500 9335990.3578681946"));
data_point_vector.push_back(DataPoint("610.2200000 635674266.1611375809"));
data_point_vector.push_back(DataPoint("610.27500 54459.4762458801"));
data_point_vector.push_back(DataPoint("610.32500 205580.6580276489"));
data_point_vector.push_back(DataPoint("610.37500 84627.3196716309"));
data_point_vector.push_back(DataPoint("610.42500 51061.7636718750"));
data_point_vector.push_back(DataPoint("610.47500 0.0000000000"));
data_point_vector.push_back(DataPoint("610.52500 29848.3424072266"));
data_point_vector.push_back(DataPoint("610.57500 27266.8031616211"));
data_point_vector.push_back(DataPoint("610.62500 36922.3937377930"));
data_point_vector.push_back(DataPoint("610.67500 44082.4265441895"));
data_point_vector.push_back(DataPoint("610.72500 32580.1677703857"));
data_point_vector.push_back(DataPoint("610.77500 39453.8380126953"));
data_point_vector.push_back(DataPoint("610.82500 63698.7124328613"));
data_point_vector.push_back(DataPoint("610.87500 34406.7755126953"));
data_point_vector.push_back(DataPoint("610.92500 33385.7486267090"));
data_point_vector.push_back(DataPoint("610.97500 22105.9357604980"));
// clang-format on
REQUIRE(20 == data_point_vector.size());
MassSpectrum mass_spectrum2(data_point_vector);
REQUIRE(20 == mass_spectrum2.size());
// Prepare the bins on the basis of the spectrum.
int decimal_places = 5;
pappso::PrecisionPtr precision_p =
pappso::PrecisionFactory::getDaltonInstance(0.05);
bool binSizeDivisor = 6;
MzIntegrationParams mz_integration_params(610.02,
610.975,
MzIntegrationParams::BinningType::ARBITRARY,
precision_p,
binSizeDivisor,
decimal_places,
true);
// Check that it does not compute bins, since BinningType::NONE.
std::vector<double> bins = mz_integration_params.createBins();
REQUIRE(bins.size() == 21);
REQUIRE(bins[0] == 610.02000);
REQUIRE(bins.back() == 610.97000 + 0.05);
MassSpectrumPlusCombiner mass_spectrum_combiner(decimal_places);
mass_spectrum_combiner.setBins(bins);
MapTrace map_trace;
mass_spectrum_combiner.combine(map_trace, mass_spectrum1);
REQUIRE(map_trace.size() == 20);
}
}
#endif
} // namespace pappso
|
