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/*******************************************************************************
* Copyright (c) 2018 Olivier Langella <Olivier.Langella@u-psud.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@u-psud.fr> - initial API and
*implementation
******************************************************************************/
//./tests/catch2-only-tests [XICextractor] -s
#include <catch2/catch_test_macros.hpp>
#include <iostream>
#include <odsstream/odsdocreader.h>
#include <odsstream/odsdocwriter.h>
#include <pappsomspp/core/pappsoexception.h>
#include <pappsomspp/core/msfile/msfileaccessor.h>
#include <pappsomspp/core/xicextractor/msrunxicextractorfactory.h>
#include <pappsomspp/core/processing/uimonitor/uimonitortext.h>
#include <pappsomspp/core/processing/uimonitor/uimonitortext.h>
#include <QDebug>
#include <QElapsedTimer>
#include <QtCore>
#include <QFile>
#include "config.h"
// #include "common.h"
// make test ARGS="-V -I 19,19"
using namespace std;
TEST_CASE("XIC extractor test suite.", "[XICextractor]")
{
// Set the debugging message formatting pattern.
qSetMessagePattern(QString("%{file}@%{line}, %{function}(): %{message}"));
// QCoreApplication a(argc, argv);
SECTION("..:: Test XIC ::..", "[extract_1_A01]")
{
qDebug() << "init test XIC";
// QCoreApplication a(argc, argv);
qDebug() << "init test XIC extractor";
std::cout << std::endl << "..:: Test XIC ::.." << std::endl;
QElapsedTimer timer;
#if USEPAPPSOTREE == 1
pappso::MsFileAccessor file_access(
"/gorgone/pappso/data_extraction_pappso/mzXML/"
//"/home/langella/data1/mzxml/"
"20120906_balliau_extract_1_A01_urnb-1.mzXML",
"file");
pappso::MsRunReaderSPtr msrun = file_access.getMsRunReaderSPtrByRunId("", "runa1");
pappso::MsRunXicExtractorFactory::getInstance().setTmpDir("/tmp");
pappso::MzRange mass_range(600, pappso::PrecisionFactory::getPpmInstance(10));
pappso::XicCoordSPtr xic_coord = msrun.get()->newXicCoordSPtrFromSpectrumIndex(
3000, pappso::PrecisionFactory::getPpmInstance(10));
xic_coord.get()->mzRange = mass_range;
std::vector<pappso::XicCoordSPtr> xic_coord_list;
xic_coord_list.push_back(xic_coord.get()->initializeAndClone());
// MassRange mass_range_b(600.2, Precision::getPpmInstance(10));
pappso::MsRunXicExtractorInterfaceSp extractor_pwiz =
pappso::MsRunXicExtractorFactory::getInstance().buildMsRunXicExtractorSp(msrun);
extractor_pwiz->setXicExtractMethod(pappso::Enums::XicExtractMethod::max);
QTextStream outputStream(stdout, QIODevice::WriteOnly);
pappso::UiMonitorText monitor(outputStream);
extractor_pwiz.get()->extractXicCoordSPtrList(monitor, xic_coord_list);
pappso::XicCstSPtr xic_pwiz = xic_coord_list[0].get()->xicSptr;
std::cout << std::endl << "..:: XIC extractor pwiz is OK ::.." << std::endl;
std::cout << std::endl << "building XicExtractorDiskSp .." << std::endl;
timer.start();
pappso::MsRunXicExtractorFactory::getInstance().setMsRunXicExtractorFactoryType(
pappso::MsRunXicExtractorFactoryType::disk);
pappso::MsRunXicExtractorInterfaceSp extractor_disk =
pappso::MsRunXicExtractorFactory::getInstance().buildMsRunXicExtractorSp(msrun);
std::cout << std::endl
<< "XicExtractorDiskSp built " << timer.elapsed() / 1000 << " seconds" << std::endl;
xic_coord_list.clear();
xic_coord_list.push_back(xic_coord.get()->initializeAndClone());
extractor_disk.get()->extractXicCoordSPtrList(monitor, xic_coord_list);
pappso::XicCstSPtr xic_disk = xic_coord_list[0].get()->xicSptr;
REQUIRE(*xic_pwiz == *xic_disk);
std::cout << std::endl << "..:: XIC extractor on disk is OK ::.." << std::endl;
// return 0;
std::cout << std::endl << "building XicExtractorDiskBufferSp .." << std::endl;
timer.restart();
pappso::MsRunXicExtractorFactory::getInstance().setMsRunXicExtractorFactoryType(
pappso::MsRunXicExtractorFactoryType::diskbuffer);
pappso::MsRunXicExtractorInterfaceSp extractor_buffer =
pappso::MsRunXicExtractorFactory::getInstance().buildMsRunXicExtractorSp(msrun);
std::cout << std::endl
<< "XicExtractorDiskBufferSp built " << timer.elapsed() / 1000 << " seconds"
<< std::endl;
xic_coord_list.clear();
xic_coord_list.push_back(xic_coord.get()->initializeAndClone());
extractor_buffer.get()->extractXicCoordSPtrList(monitor, xic_coord_list);
pappso::XicCstSPtr xic_buffer = xic_coord_list[0].get()->xicSptr;
REQUIRE(*xic_pwiz == *xic_buffer);
std::cout << std::endl << "..:: XIC extractor buffered on disk is OK ::.." << std::endl;
#endif
}
}
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