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//
// File: test_tims_dia.cpp
// Created by: Olivier Langella
// Created on: 7/6/2024
//
/*******************************************************************************
* Copyright (c) 2024 Olivier Langella
*<Olivier.Langella@universite-paris-saclay.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/>.
*
******************************************************************************/
// ./tests/pappsotree/catch2-only-pappsotree [diamicro] -s
#include <catch2/catch_test_macros.hpp>
#include <catch2/matchers/catch_matchers_vector.hpp>
#include <pappsomspp/core/msrun/private/timsmsrunreader.h>
#include "../common.h"
#include "tests-config.h"
#include <QDebug>
#include <QCoreApplication>
#include <pappsomspp/core/exception/exceptionnotfound.h>
#include <pappsomspp/core/exception/exceptionoutofrange.h>
#include <pappsomspp/core/vendors/tims/timsdiaslices.h>
TEST_CASE("test DIA file access.", "[diamicro]")
{
// Set the debugging message formatting pattern.
qSetMessagePattern(QString("%{file}@%{line}, %{function}(): %{message}"));
int argc(0);
char *argv[] = {};
QCoreApplication *app = new QCoreApplication(argc, argv);
pappso::MsFileAccessor dia_accessor(
"/gorgone/pappso/jouy/raw/2023_TimsTOF_Pro/20231214_Guillaume_DIA_DDA/"
"Short_Gradient_V2/ara1_8min_1500ng_DIA_short_gradientV2_1_1_7079.d",
"a1");
// report :
// /gorgone/pappso/moulon/users/Guillaume/TimsToF/Micro_DIA/DIANN_Method_3Rep/Short_GradientV2/8min/report.tsv'
dia_accessor.setPreferredFileReaderType(Enums::MsDataFormat::brukerTims,
Enums::FileReaderType::tims);
pappso::MsRunReaderSPtr p_tims_reader =
dia_accessor.msRunReaderSPtr(dia_accessor.getMsRunIds().front());
SECTION("..:: test DIA file access ::..", "[diamicro]")
{
pappso::TimsMsRunReader *p_msreader_tims =
dynamic_cast<pappso::TimsMsRunReader *>(p_tims_reader.get());
qDebug();
REQUIRE(p_msreader_tims->getTimsDataSPtr().get()->isDdaRun() == false);
REQUIRE(p_msreader_tims->getTimsDataSPtr().get()->isDiaRun() == true);
std::vector<double> rt_line = p_msreader_tims->getRetentionTimeLine();
REQUIRE((rt_line.back() / 60) == Catch::Approx(6.9968716));
pappso::TimsDiaSlices *dia_slices =
p_msreader_tims->getTimsDataSPtr().get()->getTimsDiaSlicesPtr();
REQUIRE(dia_slices->getMsMsWindowGroupList().size() == 7);
REQUIRE(dia_slices->getMsMsWindowGroupList().at(0)->size() == 3);
REQUIRE(dia_slices->getMsMsWindowGroupList().at(0)->at(0).IsolationWidth ==
Catch::Approx(25.0));
REQUIRE(dia_slices->getMsMsWindowGroupList().at(0)->at(0).ScanNumBegin == 458);
REQUIRE(dia_slices->getMsMsWindowGroupList().at(0)->at(0).ScanNumEnd == 650);
// 5565
// AAAEVLALQK
// mass 1012.59169531072
// mz 507.303
// rt 3,7727
pappso::QualifiedMassSpectrum qspectrum;
dia_slices->getMs2QualifiedSpectrumByGlobalSliceIndex(
p_msreader_tims->getMsRunId(), qspectrum, 5565, true);
REQUIRE(qspectrum.getRtInMinutes() == Catch::Approx(3.7727006667));
REQUIRE(qspectrum.getParameterValue(QualifiedMassSpectrumParameter::IsolationMz).toDouble() ==
Catch::Approx(852.8037150987));
REQUIRE(
qspectrum.getParameterValue(QualifiedMassSpectrumParameter::IsolationMzWidth).toDouble() ==
Catch::Approx(25.0));
dia_slices->getMs2QualifiedSpectrumByGlobalSliceIndex(
p_msreader_tims->getMsRunId(), qspectrum, 5566, true);
REQUIRE(qspectrum.getRtInMinutes() == Catch::Approx(3.7727006667));
REQUIRE(qspectrum.getParameterValue(QualifiedMassSpectrumParameter::IsolationMz).toDouble() ==
Catch::Approx(677.8037150987));
REQUIRE(
qspectrum.getParameterValue(QualifiedMassSpectrumParameter::IsolationMzWidth).toDouble() ==
Catch::Approx(25.0));
dia_slices->getMs2QualifiedSpectrumByGlobalSliceIndex(
p_msreader_tims->getMsRunId(), qspectrum, 5567, true);
REQUIRE(qspectrum.getRtInMinutes() == Catch::Approx(3.7727006667));
REQUIRE(qspectrum.getParameterValue(QualifiedMassSpectrumParameter::IsolationMz).toDouble() ==
Catch::Approx(502.8037150987));
REQUIRE(
qspectrum.getParameterValue(QualifiedMassSpectrumParameter::IsolationMzWidth).toDouble() ==
Catch::Approx(25.0));
}
}
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