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//
// File: test_isotope_with_spectrum.cpp
// Created by: Olivier Langella
// Created on: 13/3/2015
//
/*******************************************************************************
* Copyright (c) 2015 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
******************************************************************************/
// ./tests/catch2-only-tests [spectrumisotope] -s
#include <catch2/catch_test_macros.hpp>
#include <pappsomspp/core/mzrange.h>
#include <pappsomspp/core/peptide/peptidenaturalisotopelist.h>
#include <pappsomspp/core/peptide/peptidefragmentionlistbase.h>
#include <iostream>
#include <QDebug>
#include <QString>
#include "tests/tests-config.h"
#include "common.h"
using namespace pappso;
using namespace std;
TEST_CASE("Enums::Isotope with spectrum test suite.", "[spectrumisotope]")
{
// Set the debugging message formatting pattern.
qSetMessagePattern(QString("%{file}@%{line}, %{function}(): %{message}"));
SECTION("..:: MassSpectrum ::..", "[spectrumisotope]")
{
// 20120906_balliau_extract_1_A01_urnb-1
// http://pappso.inra.fr/protic/proticprod/angular/#/peptide_hits/947252
MassSpectrum spectrum = readMgf(
QString(CMAKE_SOURCE_DIR).append("/tests/data/peaklist_15046.mgf"));
std::cout << "spectrum size:" << spectrum.size() << std::endl;
Peptide peptide("AIADGSLLDLLR");
std::list<Enums::PeptideIon> cid_ion = PeptideFragmentIonListBase::getCIDionList();
PeptideFragmentIonListBase frag_cid(peptide.makePeptideSp(), cid_ion);
PeptideFragmentIonSp pep_frag_ion_sp =
frag_cid.getPeptideFragmentIonSp(Enums::PeptideIon::y, 8);
PeptideNaturalIsotopeList isotopeListFrag(pep_frag_ion_sp);
std::map<unsigned int, pappso_double> map_isotope_number =
isotopeListFrag.getIntensityRatioPerIsotopeNumber();
std::map<unsigned int, pappso_double> map_isotope_number2real(
map_isotope_number);
// iterate through the m/z-intensity pairs
// for (vector<MZIntensityPair>::const_iterator it=pairs.begin(),
// end=pairs.end(); it!=end; ++it)
for(auto peak : spectrum)
{
for(auto isotope : isotopeListFrag)
{
if(MzRange(isotope.get()->getMz(1),
PrecisionFactory::getPpmInstance(100))
.contains(peak.x))
{
std::cout << std::endl
<< isotope.get()->getIsotopeNumber() << "..:: "
<< isotope.get()->getFormula(1).toStdString()
<< " mz1=" << isotope.get()->getMz(1)
<< " ratio=" << isotope.get()->getIntensityRatio(1)
<< " ::.." << std::endl;
std::cout << " real mz=" << peak.x << " real intensity"
<< peak.y << std::endl;
}
}
}
map_isotope_number = isotopeListFrag.getIntensityRatioPerIsotopeNumber();
std::cout << "isotope levels" << std::endl;
for(unsigned int i = 0; i < map_isotope_number.size(); i++)
{
std::cout << "frag isotope " << i << " " << map_isotope_number[i]
<< std::endl;
}
/*
0..:: C39H70O11N11S0 C13(0) H2(0) O17(0) O18(0) N15(0) S34(0) mz1=886.536
ratio=0.599391 ::.. 7: real mz=886.535 real intensity75443.3 7: 7: 1..::
C39H70O11N11S0 C13(1) H2(0) O17(0) O18(0) N15(0) S34(0) mz1=887.539
ratio=0.261863 ::.. 7: real mz=887.538 real intensity41018.6 7: 7: 1..::
C39H70O11N11S0 C13(0) H2(1) O17(0) O18(0) N15(0) S34(0) mz1=887.542
ratio=0.00653545 ::.. 7: real mz=887.538 real intensity41018.6 7: 7: 1..::
C39H70O11N11S0 C13(0) H2(0) O17(0) O18(0) N15(1) S34(0) mz1=887.533
ratio=0.02424 ::.. 7: real mz=887.538 real intensity41018.6
*/
/*
0..:: C39H70O11N11S0 C13(0) H2(0) O17(0) O18(0) N15(0) S34(0) mz1=886.536
ratio=0.599391 ::.. 7: real mz=886.535 real intensity75443.3 7: 7: 1..::
C39H70O11N11S0 C13(1) H2(0) O17(0) O18(0) N15(0) S34(0) mz1=887.539
ratio=0.261863 ::.. 7: real mz=887.538 real intensity41018.6 7: 7: 1..::
C39H70O11N11S0 C13(0) H2(1) O17(0) O18(0) N15(0) S34(0) mz1=887.542
ratio=0.00653545 ::.. 7: real mz=887.538 real intensity41018.6 7: 7: 1..::
C39H70O11N11S0 C13(0) H2(0) O17(0) O18(0) N15(1) S34(0) mz1=887.533
ratio=0.02424 ::.. 7: real mz=887.538 real intensity41018.6
*/
// SUCCESS
}
}
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