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//
// File: test_aacode.cpp
// Created by: Olivier Langella
// Created on: 29/4/2015
//
/*******************************************************************************
* Copyright (c) 2025 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/catch2-only-tests [AaCode] -s
// ./tests/catch2-only-tests [AaStringCodec] -s
#include <catch2/catch_test_macros.hpp>
#include <catch2/catch_approx.hpp>
#include <catch2/matchers/catch_matchers_vector.hpp>
#include <QDebug>
#include <QString>
#include <pappsomspp/core/amino_acid/aacode.h>
#include <pappsomspp/core/amino_acid/aastringcodec.h>
#include <pappsomspp/core/amino_acid/aastringcodemassmatching.h>
#include <iostream>
#include <pappsomspp/core/obo/filterobopsimodtermlabel.h>
#include <pappsomspp/core/obo/filterobopsimodsink.h>
#include <pappsomspp/core/obo/filterobopsimodtermdiffmono.h>
#include <pappsomspp/core/exception/exceptionnotfound.h>
#include <pappsomspp/core/exception/exceptionoutofrange.h>
#include <pappsomspp/core/obo/filterobopsimodmap.h>
#include <pappsomspp/core/exception/exceptionnotpossible.h>
using namespace pappso;
using namespace std;
TEST_CASE("Amino Acid code test suite.", "[AaCode]")
{
// Set the debugging message formatting pattern.
qSetMessagePattern(QString("%{file}@%{line}, %{function}(): %{message}"));
SECTION("..:: AA code init ::..", "[AaCode]")
{
AaCode aa_code;
REQUIRE(aa_code.getAa('C').getMass() == Catch::Approx(103.0091849597));
REQUIRE(aa_code.getAaCode('C') == 7);
REQUIRE(aa_code.getAa((uint8_t)6).getMass() < aa_code.getAa((uint8_t)7).getMass());
aa_code.addAaModification('C', AaModification::getInstance("MOD:00397"));
REQUIRE(aa_code.getAaCode('M') == 13);
REQUIRE(aa_code.getAaCode('A') == 2);
REQUIRE(aa_code.getAaCode('I') == 7);
REQUIRE(aa_code.getAa('C').getMass() == Catch::Approx(160.0306486807));
REQUIRE(aa_code.getAaCode('C') == 17);
REQUIRE(aa_code.getAa((uint8_t)16).getMass() < aa_code.getAa((uint8_t)17).getMass());
REQUIRE(aa_code.getAa((uint8_t)17).getMass() < aa_code.getAa((uint8_t)18).getMass());
REQUIRE(aa_code.getAa((uint8_t)1).getLetter() == 'G');
REQUIRE(aa_code.getAa((uint8_t)19).getLetter() == 'W');
REQUIRE_THROWS_AS(aa_code.getAa((uint8_t)20).getMass(), ExceptionOutOfRange);
}
SECTION("..:: AA code init search by mass::..", "[AaCode]")
{
AaCode aa_code;
uint8_t aa =
aa_code.getAaCodeByMass(103.0091849597, pappso::PrecisionFactory::getDaltonInstance(0.01));
REQUIRE(aa == 7);
}
}
TEST_CASE("Amino Acid string codec test suite.", "[AaStringCodec]")
{
// Set the debugging message formatting pattern.
qSetMessagePattern(QString("%{file}@%{line}, %{function}(): %{message}"));
SECTION("..:: AA string codec init ::..", "[AaStringCodec]")
{
AaCode aa_code;
aa_code.addAaModification('C', AaModification::getInstance("MOD:00397"));
AaStringCodec codec(aa_code);
REQUIRE(codec.code("MAMI") == 61253);
std::uint64_t nbaa = aa_code.getSize() + 1;
REQUIRE(codec.code("SAM") == (aa_code.getAaCode('S') + aa_code.getAaCode('A') * (uint64_t)nbaa +
aa_code.getAaCode('M') * (uint64_t)nbaa * (uint64_t)nbaa));
REQUIRE(codec.codeLlc("SAM") == 873);
REQUIRE(codec.decode(873).toStdString() == "MSA");
REQUIRE(codec.getMass(873) == Catch::Approx(codec.getMass(5243)));
std::vector<CodeToMass> arr_codemass = codec.generateLlcCodeListByMaxPeptideSize(3);
REQUIRE(arr_codemass.size() == 1330);
std::sort(arr_codemass.begin(),
arr_codemass.end(),
[](const CodeToMass &a, const CodeToMass &b) { return a.mass < b.mass; });
REQUIRE(codec.decode(arr_codemass.at(0).code).toStdString() == "GGG");
REQUIRE(codec.decode(arr_codemass.back().code).toStdString() == "WWW");
arr_codemass = codec.generateLlcCodeListByMaxPeptideSize(4);
REQUIRE(arr_codemass.size() == 7315);
std::sort(arr_codemass.begin(),
arr_codemass.end(),
[](const CodeToMass &a, const CodeToMass &b) { return a.mass < b.mass; });
REQUIRE(codec.decode(arr_codemass.at(0).code).toStdString() == "GGGG");
REQUIRE(codec.decode(arr_codemass.back().code).toStdString() == "WWWW");
arr_codemass = codec.generateLlcCodeListByMaxPeptideSize(5);
REQUIRE(arr_codemass.size() == 33649);
std::sort(arr_codemass.begin(),
arr_codemass.end(),
[](const CodeToMass &a, const CodeToMass &b) { return a.mass < b.mass; });
REQUIRE(codec.decode(arr_codemass.at(0).code).toStdString() == "GGGGG");
REQUIRE(codec.decode(arr_codemass.back().code).toStdString() == "WWWWW");
qDebug() << std::numeric_limits<uint32_t>::max();
qDebug() << std::numeric_limits<uint64_t>::max();
REQUIRE(codec.getLimitMax(5) < std::numeric_limits<uint32_t>::max());
REQUIRE(codec.getLimitMax(6) < std::numeric_limits<uint32_t>::max());
REQUIRE(codec.getLimitMax(7) < std::numeric_limits<uint32_t>::max());
// amino acid code is safe on all platform using at maximum 7 amino acids
// some architectures ar ok with 8 (armel)
REQUIRE(codec.getLimitMax(5) == 3199999);
arr_codemass = codec.generateLlcCodeListUpToMaxPeptideSize(5);
std::sort(arr_codemass.begin(),
arr_codemass.end(),
[](const CodeToMass &a, const CodeToMass &b) { return a.mass < b.mass; });
REQUIRE(codec.decode(arr_codemass.at(0).code).toStdString() == "G");
REQUIRE(codec.decode(arr_codemass.back().code).toStdString() == "WWWWW");
REQUIRE(arr_codemass.size() == 42503);
}
SECTION("..:: AA string codec match :..", "[AaStringCodec]")
{
AaCode aa_code;
aa_code.addAaModification('C', AaModification::getInstance("MOD:00397"));
AaStringCodec codec(aa_code);
pappso::AaStringCodeMassMatching aaMatching(
aa_code, 7, pappso::PrecisionFactory::getDaltonInstance(0.25));
auto code_list = aaMatching.getAaCodeFromMass(800);
REQUIRE(code_list.size() == 19);
REQUIRE(codec.decode(code_list).join(" ").toStdString() ==
"CCCCC YCCDDS CCMMMS YCCMDA YCCMEG CCFMDS CCHDNN CCHDNGG CHEDDSG CHDDDTG "
"CHDDDSA CCHMDP WYCCM EDDDDNP QDDDDDP YCMDSSG YCCDTT YCCETS CCFMMA");
}
}
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