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//
// File: test_tims_dda.cpp
// Created by: Olivier Langella
// Created on: 6/9/2024
//
/*******************************************************************************
* 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 [dda] -s
#include <catch2/catch_test_macros.hpp>
#include <catch2/matchers/catch_matchers_vector.hpp>
#include "../common.h"
#include "tests-config.h"
#include <QDebug>
#include <QCoreApplication>
#include <pappsomspp/core/exception/exceptionnotfound.h>
#include <pappsomspp/core/exception/exceptionoutofrange.h>
TEST_CASE("test DDA file access.", "[dda]")
{
// Set the debugging message formatting pattern.
qSetMessagePattern(QString("%{file}@%{line}, %{function}(): %{message}"));
int argc(0);
char *argv[] = {};
QCoreApplication *app = new QCoreApplication(argc, argv);
SECTION("..:: test DIA file access ::..", "[dda]")
{
pappso::MsFileAccessor dda_accessor(
"/gorgone/pappso/jouy/raw/2024_timsTOF_Pro/20240826_30_Zuzana/8-30-2024_Gal_3_pool_9501.d",
"a1");
dda_accessor.setPreferredFileReaderType(Enums::MsDataFormat::brukerTims,
Enums::FileReaderType::tims_ms2);
pappso::MsRunReaderSPtr p_tims_reader =
dda_accessor.msRunReaderSPtr(dda_accessor.getMsRunIds().front());
REQUIRE(
p_tims_reader.get()->getOboPsiModTermInstrumentModelName().getAccession().toStdString() ==
"MS:1003005");
REQUIRE(p_tims_reader.get()->getOboPsiModTermInstrumentModelName().isA("MS:1003123"));
REQUIRE(p_tims_reader.get() != nullptr);
pappso::MsRunSimpleStatistics stats;
pappso::MsRunReadConfig config;
config.setNeedPeakList(false);
p_tims_reader.get()->readSpectrumCollection2(config, stats);
REQUIRE(stats.getMsLevelCount(1) == 98511);
REQUIRE(stats.getMsLevelCount(2) == 98511);
}
delete app;
}
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