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//
// File: test_xtandem_spectrum.cpp
// Created by: Olivier Langella
// Created on: 13/3/2015
//
/*******************************************************************************
* Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
*
* This file is part of the PAPPSOms++ library.
*
* PAPPSOms++ is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* PAPPSOms++ is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with PAPPSOms++. If not, see <http://www.gnu.org/licenses/>.
*
* Contributors:
* Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
*implementation
******************************************************************************/
// ./tests/catch2-only-tests [xtandemspectrum] -s
#include <catch2/catch_test_macros.hpp>
#include <catch2/catch_approx.hpp>
#include <catch2/matchers/catch_matchers_vector.hpp>
#include <pappsomspp/core/mzrange.h>
#include <pappsomspp/core/peptide/peptidenaturalisotopelist.h>
#include <pappsomspp/core/peptide/peptidefragmentionlistbase.h>
#include <pappsomspp/core/massspectrum/massspectrum.h>
#include <pappsomspp/core/psm/xtandem/xtandemspectrumprocess.h>
#include <pappsomspp/core/processing/filters/filterpass.h>
#include <iostream>
#include <set>
#include <QDir>
#include <QDebug>
#include <QString>
#include "tests/tests-config.h"
#include "common.h"
using namespace pappso;
using namespace std;
// using namespace pwiz::msdata;
// make test ARGS="-V -I 16,16"
TEST_CASE("Xtandem spectrum test suite.", "[xtandemspectrum]")
{
// Set the debugging message formatting pattern.
qSetMessagePattern(QString("%{file}@%{line}, %{function}(): %{message}"));
SECTION("..:: readMgf ::..", "[xtandemspectrum]")
{
std::cout << std::endl
<< "..:: readMgf ::.." << QDir::currentPath().toStdString()
<< std::endl;
MassSpectrum spectrum = readMgf(
QString(CMAKE_SOURCE_DIR).append("/tests/data/peaklist_15046.mgf"));
std::cout << spectrum.toString().toStdString() << std::endl;
MassSpectrum spectrum_orig(spectrum);
REQUIRE(spectrum.equals(spectrum_orig,
PrecisionFactory::getDaltonInstance(0.00002)));
// spectrum =
// spectrum.applyCutOff(150).takeNmostIntense(100).applyDynamicRange(100).round();
MassSpectrum spectrum_b = readMgf(
QString(CMAKE_SOURCE_DIR).append("/tests/data/peaklist_15046.mgf"));
REQUIRE(spectrum == spectrum_b);
MassSpectrum spectrum_simple =
readMgf(QString(CMAKE_SOURCE_DIR)
.append("/tests/data/peaklist_15046_simple_xt.mgf"))
.massSpectrumFilter(MassSpectrumFilterGreatestItensities(7));
REQUIRE_FALSE(spectrum == spectrum_simple);
std::vector<double> expected_mass_list(
{157.133, 175.119, 185.128, 308.188, 401.287, 886.535, 1072.6});
REQUIRE_THAT(spectrum_simple.xValues(),
Catch::Matchers::Approx(expected_mass_list));
std::vector<double> expected_intensity_list(
{100.0, 30.0, 42.0, 33.0, 27.0, 19.0, 21.0});
REQUIRE_THAT(spectrum_simple.yValues(),
Catch::Matchers::Approx(expected_intensity_list));
// mh="1256.7213" z=2 AIADGSLLDLLR
Peptide peptide("AIADGSLLDLLR");
INFO("spectrum.removeParent");
XtandemSpectrumProcess xt_spectrum_process;
xt_spectrum_process.setExcludeParent(true);
xt_spectrum_process.setNmostIntense(7);
xt_spectrum_process.setDynamicRange(100);
xt_spectrum_process.setMinimumMz(150);
// MassRange neutral_loss_mass =
// xt_spectrum_process.getNeutralLossMassRange(peptide, 2);
// spectrum=
// spectrum.removeMassRange(neutral_loss_mass).applyCutOff(150).takeNmostIntense(7).applyDynamicRange(100).round();
spectrum = xt_spectrum_process.process(spectrum, 628.86414, 2);
FilterRoundY().filter(spectrum);
REQUIRE(peptide.makePeptideSp().get()->getMz(2) ==
Catch::Approx(628.8640771426));
spectrum.debugPrintValues();
spectrum_simple.debugPrintValues();
REQUIRE(spectrum.equals(spectrum_simple,
PrecisionFactory::getDaltonInstance(0.02)));
}
}
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