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//
// File: test_rawmasslist.cpp
// Created by: Olivier Langella
// Created on: 19/07/2016
//
/*******************************************************************************
* Copyright (c) 2016 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
******************************************************************************/
// make test ARGS="-V -I 12,12"
// ./tests/catch2-only-tests [rawmasslist] -s
#include <catch2/catch_test_macros.hpp>
#include <catch2/matchers/catch_matchers_vector.hpp>
#include <iostream>
#include <pappsomspp/core/peptide/peptiderawfragmentmasses.h>
#include <pappsomspp/core/peptide/peptidefragmentionlistbase.h>
#include <pappsomspp/core/mzrange.h>
#include <pappsomspp/core/peptide/peptideproformaparser.h>
#include <list>
#include <QDebug>
#include <QString>
using namespace pappso;
using namespace std;
TEST_CASE("..:: Raw mass list ::..", "[rawmasslist]")
{
// Set the debugging message formatting pattern.
qSetMessagePattern(QString("%{file}@%{line}, %{function}(): %{message}"));
SECTION("..:: Raw mass list ::..", "[rawmasslist]")
{
std::cout << std::endl << "..:: Raw mass list ::.." << std::endl;
PeptideSp peptide_sp(Peptide("SAMPLER").makePeptideSp());
std::list<Enums::PeptideIon> ion_type_list;
ion_type_list.push_back(Enums::PeptideIon::y);
PeptideFragmentIonListBase fragmentIonList(peptide_sp, ion_type_list);
auto ion_list = fragmentIonList.getPeptideFragmentIonSp(Enums::PeptideIon::y);
PeptideRawFragmentMasses calc_mass_list(*peptide_sp.get(), RawFragmentationMode::full);
std::vector<pappso_double> mass_list_from_raw;
calc_mass_list.pushBackIonMasses(mass_list_from_raw, Enums::PeptideIon::y);
std::vector<pappso_double> mass_list_from_fragment;
for(auto current_fragment : ion_list)
{
mass_list_from_fragment.push_back(current_fragment.get()->getMass());
}
REQUIRE(Catch::Approx(mass_list_from_fragment[0]) == 174.1116757097);
// REQUIRE_THAT(mass_list_from_fragment, Catch::Matchers::UnorderedEquals(mass_list_from_raw));
REQUIRE_THAT(mass_list_from_fragment, Catch::Matchers::Approx(mass_list_from_raw));
std::vector<pappso_double> mz_list_from_raw;
calc_mass_list.pushBackIonMz(mz_list_from_raw, Enums::PeptideIon::y, 1);
std::vector<pappso_double> mz_list_from_fragment;
for(auto current_fragment : ion_list)
{
mz_list_from_fragment.push_back(current_fragment.get()->getMz(1));
}
REQUIRE_THAT(mz_list_from_fragment, Catch::Matchers::Approx(mz_list_from_raw));
PeptideRawFragmentMasses calc_mass_list_proline(*peptide_sp.get(),
RawFragmentationMode::proline_effect);
}
SECTION("..:: Raw mass list Proforma ::..", "[rawmasslist2]")
{
std::cout << std::endl << "..:: Raw mass list ::.." << std::endl;
PeptideSp peptide_sp =
PeptideProFormaParser::parseString("[Acetyl]-M[MOD:00719]QNDAGEFVDLYVPR");
std::list<Enums::PeptideIon> ion_type_list;
ion_type_list.push_back(Enums::PeptideIon::b);
PeptideFragmentIonListBase fragmentIonList(peptide_sp, ion_type_list);
auto ion_list = fragmentIonList.getPeptideFragmentIonSp(Enums::PeptideIon::b);
PeptideRawFragmentMasses calc_mass_list(*peptide_sp.get(), RawFragmentationMode::full);
std::vector<pappso_double> mass_list_from_raw;
calc_mass_list.pushBackIonMasses(mass_list_from_raw, Enums::PeptideIon::b);
std::vector<pappso_double> mass_list_from_fragment;
for(auto current_fragment : ion_list)
{
mass_list_from_fragment.push_back(current_fragment.get()->getMass());
}
REQUIRE(Catch::Approx(mass_list_from_fragment[0]) == 189.0459643922);
// REQUIRE_THAT(mass_list_from_fragment, Catch::Matchers::UnorderedEquals(mass_list_from_raw));
REQUIRE_THAT(mass_list_from_fragment, Catch::Matchers::Approx(mass_list_from_raw));
std::vector<pappso_double> mz_list_from_raw;
calc_mass_list.pushBackIonMz(mz_list_from_raw, Enums::PeptideIon::b, 1);
std::vector<pappso_double> mz_list_from_fragment;
for(auto current_fragment : ion_list)
{
mz_list_from_fragment.push_back(current_fragment.get()->getMz(1));
}
REQUIRE_THAT(mz_list_from_fragment, Catch::Matchers::Approx(mz_list_from_raw));
PeptideRawFragmentMasses calc_mass_list_proline(*peptide_sp.get(),
RawFragmentationMode::proline_effect);
}
SECTION("..:: Raw mass list Proforma no acetyl ::..", "[rawmasslist3]")
{
std::cout << std::endl << "..:: Raw mass list ::.." << std::endl;
PeptideSp peptide_sp = PeptideProFormaParser::parseString("M[MOD:00719]QNDAGEFVDLYVPR");
std::list<Enums::PeptideIon> ion_type_list;
ion_type_list.push_back(Enums::PeptideIon::b);
PeptideFragmentIonListBase fragmentIonList(peptide_sp, ion_type_list);
auto ion_list = fragmentIonList.getPeptideFragmentIonSp(Enums::PeptideIon::b);
PeptideRawFragmentMasses calc_mass_list(*peptide_sp.get(), RawFragmentationMode::full);
std::vector<pappso_double> mass_list_from_raw;
calc_mass_list.pushBackIonMasses(mass_list_from_raw, Enums::PeptideIon::b);
std::vector<pappso_double> mass_list_from_fragment;
for(auto current_fragment : ion_list)
{
mass_list_from_fragment.push_back(current_fragment.get()->getMass());
}
REQUIRE(Catch::Approx(mass_list_from_fragment[0]) == 147.0353997082);
// REQUIRE_THAT(mass_list_from_fragment, Catch::Matchers::UnorderedEquals(mass_list_from_raw));
REQUIRE_THAT(mass_list_from_fragment, Catch::Matchers::Approx(mass_list_from_raw));
std::vector<pappso_double> mz_list_from_raw;
calc_mass_list.pushBackIonMz(mz_list_from_raw, Enums::PeptideIon::b, 1);
std::vector<pappso_double> mz_list_from_fragment;
for(auto current_fragment : ion_list)
{
mz_list_from_fragment.push_back(current_fragment.get()->getMz(1));
}
REQUIRE_THAT(mz_list_from_fragment, Catch::Matchers::Approx(mz_list_from_raw));
PeptideRawFragmentMasses calc_mass_list_proline(*peptide_sp.get(),
RawFragmentationMode::proline_effect);
}
}
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