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// File: test_timsxicextractor.cpp
// Created by: Olivier Langella
// Created on: 3/2/2021
//
/*******************************************************************************
* Copyright (c) 2021 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/>.
*
******************************************************************************/
// make test ARGS="-V -I 1,1"
// ./tests/pappsotree/catch2-only-pappsotree [TimsIonMobilityGrid] -a
#include <catch2/catch_test_macros.hpp>
#include <QDebug>
#include <pappsomspp/core/msrun/xiccoord/ionmobilitygrid.h>
#include "tests/tests-config.h"
#include "../common.h"
#include <time.h>
using namespace pappso;
TEST_CASE("test TimsIonMobilityGrid", "[TimsIonMobilityGrid]")
{
qSetMessagePattern(QString("%{file}@%{line}, %{function}(): %{message}"));
IonMobilityGrid ion_mobility_grid;
pappso::MsFileAccessor accessor(
"/gorgone/pappso/versions_logiciels_pappso/masschroq/donnees/"
"PXD010012_msfragger_timstof/"
"20180819_TIMS2_12-2_AnBr_SA_200ng_HeLa_50cm_120min_100ms_11CT_1_A1_01_"
"2767.d/analysis.tdf",
"a1");
accessor.setPreferredFileReaderType(Enums::MsDataFormat::brukerTims,
Enums::FileReaderType::tims_ms2);
pappso::MsRunReaderSPtr p_msreader =
accessor.msRunReaderSPtr(accessor.getMsRunIds().front());
REQUIRE(p_msreader != nullptr);
REQUIRE(accessor.getFileReaderType() == Enums::FileReaderType::tims_ms2);
pappso::MsFileAccessor accessor_a2(
"/gorgone/pappso/versions_logiciels_pappso/masschroq/donnees/"
"PXD010012_msfragger_timstof/"
"20180819_TIMS2_12-2_AnBr_SA_200ng_HeLa_50cm_120min_100ms_11CT_2_A1_01_"
"2768.d/analysis.tdf",
"a2");
accessor_a2.setPreferredFileReaderType(Enums::MsDataFormat::brukerTims,
Enums::FileReaderType::tims_ms2);
pappso::MsRunReaderSPtr p_msreader_a2 =
accessor_a2.msRunReaderSPtr(accessor_a2.getMsRunIds().front());
REQUIRE(p_msreader_a2 != nullptr);
REQUIRE(accessor_a2.getFileReaderType() == Enums::FileReaderType::tims_ms2);
auto msrunid_a1 = *p_msreader->getMsRunId().get();
auto msrunid_a2 = *p_msreader_a2->getMsRunId().get();
qInfo() << "store observed";
INFO("store observed");
auto a1 = p_msreader.get()->newXicCoordSPtrFromSpectrumIndex(
106171, pappso::PrecisionFactory::getPpmInstance(10));
auto a2 = p_msreader_a2.get()->newXicCoordSPtrFromSpectrumIndex(
106889, pappso::PrecisionFactory::getPpmInstance(10));
qInfo() << "first a1" << a1.get()->toString();
qInfo() << "first a2" << a2.get()->toString();
ion_mobility_grid.storeObservedIdentityBetween(
msrunid_a1, a1.get(), msrunid_a2, a2.get());
INFO("store observed pepa1e17369");
// pepa1e17369
// 20180819_TIMS2_12-2_AnBr_SA_200ng_HeLa_50cm_120min_100ms_11CT_1_A1_01_2767
// 261103 2586,61 650,346968967 ILDEIGADVQAR pepa1e17369
// 20180819_TIMS2_12-2_AnBr_SA_200ng_HeLa_50cm_120min_100ms_11CT_2_A1_01_2768
// 259019 2593,3 650,347328967 ILDEIGADVQAR
a1 = p_msreader.get()->newXicCoordSPtrFromSpectrumIndex(
261103, pappso::PrecisionFactory::getPpmInstance(10));
a2 = p_msreader_a2.get()->newXicCoordSPtrFromSpectrumIndex(
259019, pappso::PrecisionFactory::getPpmInstance(10));
qInfo() << "2 a1" << a1.get()->toString();
qInfo() << "2 a2" << a2.get()->toString();
ion_mobility_grid.storeObservedIdentityBetween(
msrunid_a1, a1.get(), msrunid_a2, a2.get());
INFO("store observed pepa1e31234");
// pepa1e31234
// 20180819_TIMS2_12-2_AnBr_SA_200ng_HeLa_50cm_120min_100ms_11CT_1_A1_01_2767
// 245667 2454,61 781,849418967 SNMEAQHNDLEFK
// pepa1e31234
// 20180819_TIMS2_12-2_AnBr_SA_200ng_HeLa_50cm_120min_100ms_11CT_2_A1_01_2768
// 243535 2460,95 781,849797967 SNMEAQHNDLEFK
a1 = p_msreader.get()->newXicCoordSPtrFromSpectrumIndex(
245667, pappso::PrecisionFactory::getPpmInstance(10));
a2 = p_msreader_a2.get()->newXicCoordSPtrFromSpectrumIndex(
243535, pappso::PrecisionFactory::getPpmInstance(10));
qInfo() << "3 a1" << a1.get()->toString();
qInfo() << "3 a2" << a2.get()->toString();
ion_mobility_grid.storeObservedIdentityBetween(
msrunid_a1, a1.get(), msrunid_a2, a2.get());
INFO("store observed pepb15b13");
// pepb15b13
// 20180819_TIMS2_12-2_AnBr_SA_200ng_HeLa_50cm_120min_100ms_11CT_1_A1_01_2767
// 249403 2486,14 699,856334967 DPEKPQLGMIDR pepb15b13
// 20180819_TIMS2_12-2_AnBr_SA_200ng_HeLa_50cm_120min_100ms_11CT_2_A1_01_2768
// 247155 2491,71 699,856816467 DPEKPQLGMIDR
ion_mobility_grid.storeObservedIdentityBetween(
msrunid_a1,
p_msreader.get()
->newXicCoordSPtrFromSpectrumIndex(
249403, pappso::PrecisionFactory::getPpmInstance(10))
.get(),
msrunid_a2,
p_msreader_a2.get()
->newXicCoordSPtrFromSpectrumIndex(
247155, pappso::PrecisionFactory::getPpmInstance(10))
.get());
INFO("store observed pepb54b12");
// pepb54b12
// 20180819_TIMS2_12-2_AnBr_SA_200ng_HeLa_50cm_120min_100ms_11CT_1_A1_01_2767
// 79843 1106,79 832,442628967 EAGTEVVK
// pepb54b12
// 20180819_TIMS2_12-2_AnBr_SA_200ng_HeLa_50cm_120min_100ms_11CT_2_A1_01_2768
// 79969 1104,68 832,440325967 EAGTEVVK
ion_mobility_grid.storeObservedIdentityBetween(
msrunid_a1,
p_msreader.get()
->newXicCoordSPtrFromSpectrumIndex(
79843, pappso::PrecisionFactory::getPpmInstance(10))
.get(),
msrunid_a2,
p_msreader_a2.get()
->newXicCoordSPtrFromSpectrumIndex(
79969, pappso::PrecisionFactory::getPpmInstance(10))
.get());
INFO("store observed pepb83a6");
// pepb83a6
// 20180819_TIMS2_12-2_AnBr_SA_200ng_HeLa_50cm_120min_100ms_11CT_1_A1_01_2767
// 289387 2830,6 610,302429967 AAYFGIYDTAK pepb83a6
// 20180819_TIMS2_12-2_AnBr_SA_200ng_HeLa_50cm_120min_100ms_11CT_2_A1_01_2768
// 286699 2828,24 610,303296967 AAYFGIYDTAK
ion_mobility_grid.storeObservedIdentityBetween(
msrunid_a1,
p_msreader.get()
->newXicCoordSPtrFromSpectrumIndex(
289387, pappso::PrecisionFactory::getPpmInstance(10))
.get(),
msrunid_a2,
p_msreader_a2.get()
->newXicCoordSPtrFromSpectrumIndex(
286699, pappso::PrecisionFactory::getPpmInstance(10))
.get());
auto map_diff = ion_mobility_grid.getMapDiferrencesStart();
for(auto itmap : map_diff)
{
qInfo() << (itmap.first);
for(auto list_diff : itmap.second)
{
qInfo() << (list_diff);
}
}
WARN("ion_mobility_grid.computeCorrections()");
ion_mobility_grid.computeCorrections();
auto map_delta = ion_mobility_grid.getMapCorrectionsStart();
REQUIRE(map_delta["a1a1-a2a1"] == -1);
// pepa1e31244
// 20180819_TIMS2_12-2_AnBr_SA_200ng_HeLa_50cm_120min_100ms_11CT_1_A1_01_2767
// 452469 4297,94 718,417257967 SNPDQPAVILLLR
// pepa1e31244
// 20180819_TIMS2_12-2_AnBr_SA_200ng_HeLa_50cm_120min_100ms_11CT_2_A1_01_2768
// 448731 4288,53 718,417001467 SNPDQPAVILLLR
auto target = p_msreader_a2.get()->newXicCoordSPtrFromSpectrumIndex(
448731, pappso::PrecisionFactory::getPpmInstance(10));
auto source = p_msreader.get()->newXicCoordSPtrFromSpectrumIndex(
452469, pappso::PrecisionFactory::getPpmInstance(10));
WARN("source");
REQUIRE(source->toString().toStdString() ==
"mz=mz=718.417 delta=0.00718417 : 718.41 < 718.417 < 718.424 "
"rt=4297.94 begin=532 end=557");
REQUIRE(source.get()
->getParam(XicCoordParam::TimsTofIonMobilityScanNumberStart)
.toInt() == 532);
WARN("target");
REQUIRE(target->toString().toStdString() ==
"mz=mz=718.417 delta=0.00718417 : 718.41 < 718.417 < 718.424 "
"rt=4288.53 begin=534 end=559");
auto result = ion_mobility_grid.translateXicCoordFromTo(
*source.get(), msrunid_a1, msrunid_a2);
REQUIRE(source.get()
->getParam(XicCoordParam::TimsTofIonMobilityScanNumberStart)
.toInt() == 532);
REQUIRE(result.get()
->getParam(XicCoordParam::TimsTofIonMobilityScanNumberStart)
.toInt() ==
(source.get()
->getParam(XicCoordParam::TimsTofIonMobilityScanNumberStart)
.toInt() -
1));
WARN("result");
REQUIRE(result->toString().toStdString() ==
"mz=mz=718.417 delta=0.00718417 : 718.41 < 718.417 < 718.424 "
"rt=4297.94 begin=531 end=556");
result = ion_mobility_grid.translateXicCoordFromTo(
*target.get(), msrunid_a2, msrunid_a1);
REQUIRE(target.get()
->getParam(XicCoordParam::TimsTofIonMobilityScanNumberStart)
.toInt() == 534);
REQUIRE(result.get()
->getParam(XicCoordParam::TimsTofIonMobilityScanNumberStart)
.toInt() ==
(target.get()
->getParam(XicCoordParam::TimsTofIonMobilityScanNumberStart)
.toInt() +
1));
WARN("result");
REQUIRE(result->toString().toStdString() ==
"mz=mz=718.417 delta=0.00718417 : 718.41 < 718.417 < 718.424 "
"rt=4288.53 begin=535 end=560");
}
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