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/* BEGIN software license
*
* MsXpertSuite - mass spectrometry software suite
* -----------------------------------------------
* Copyright(C) 2009,...,2024 Filippo Rusconi
*
* http://www.msxpertsuite.org
*
* This file is part of the MsXpertSuite project.
*
* The MsXpertSuite project is the successor of the massXpert project. This
* project now includes various independent modules:
*
* - massXpert, model polymer chemistries and simulate mass spectrometric data;
* - mineXpert, a powerful TIC chromatogram/mass spectrum viewer/miner;
*
* This program 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.
*
* This program 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 this program. If not, see <http://www.gnu.org/licenses/>.
*
* END software license
*/
/////////////////////// Stdlib includes
/////////////////////// Qt includes
#include <QDebug>
#include <QString>
#include <QStringList>
#include <QDomDocument>
/////////////////////// libXpertMassCore includes
#include <libXpertMass/Isotope.hpp>
#include <libXpertMass/PolChemDef.hpp>
/////////////////////// Local includes
#include "tests-config.h"
#pragma once
namespace MsXpS
{
namespace libXpertMassCore
{
class DECLSPEC TestUtils
{
public:
TestUtils();
TestUtils(const QString &pol_chem_def_name, int version);
virtual ~TestUtils();
QString m_testsInputDataDir = QString(TESTS_INPUT_DIR);
QString m_testsOutputDataDir = QString(TESTS_OUTPUT_DIR);
QString m_testsInputPolChemDefsDir =
QString("%1/polymer-chemistry-definitions").arg(m_testsInputDataDir);
QString m_testsOutputPolChemDefsDir =
QString("%1/polymer-chemistry-definitions").arg(m_testsOutputDataDir);
QString m_testsInputPolSeqsDir =
QString("%1/polymer-sequences").arg(m_testsInputDataDir);
QString m_testsOutputPolSeqsDir =
QString("%1/polymer-sequences").arg(m_testsOutputDataDir);
QString m_polChemDefDirName;
QString m_polChemDefFileBaseName;
QString m_polChemDefName;
PolChemDefSpec m_polChemDefSpec;
PolChemDefSPtr msp_polChemDef = nullptr;
QString xml_format_indent_string = " ";
Isotope m_isotopeC12 =
Isotope("carbon",
"C",
12.0,
0.989211941850466902614869013632414862513542175292968750000000);
IsotopeQSPtr msp_isotopeC12 = std::make_shared<Isotope>(m_isotopeC12);
Isotope m_isotopeC13 =
Isotope("carbon",
"C",
13.0033548352,
0.010788058149533083507343178553128382191061973571777343750000);
IsotopeQSPtr msp_isotopeC13 = std::make_shared<Isotope>(m_isotopeC13);
Isotope m_isotopeN14 =
Isotope("nitrogen",
"N",
14.0030740042,
0.996358014567941707717579902237048372626304626464843750000000);
IsotopeQSPtr msp_isotopeN14 = std::make_shared<Isotope>(m_isotopeN14);
Isotope m_isotopeN15 =
Isotope("nitrogen",
"N",
15.0001088994,
0.003641985432058271465738386041266494430601596832275390625000);
IsotopeQSPtr msp_isotopeN15 = std::make_shared<Isotope>(m_isotopeN15);
std::size_t m_isotopeCount = 0;
QString m_acetylationFormulaString = "-H2O+CH3COOH";
QString m_tryptophanFormulaString = "C11H10N2O1";
// 157 residues
QString m_telokinAsMonomerText1Letter =
"MAMISGMSGRKASGSSPTSPINADKVENEDAFLEEVAEEKPHVKPYFTKTILDMEVVEGSAARFDCKIEGYPDP"
"EVMWYKDDQPVKESRHFQIDYDEEGNCSLTISEVCGDDDAKYTCKAVNSLGEATCTAELLVETMGKEGEGEGEG"
"EEDEEEEEE";
QString m_telokinNtermPeptideAsMonomerText1Letter =
"MAMISGMSGRKASGSSPTSPINADKV";
int m_telokinSequenceMonomerCount = 157;
// 157 residues, 7 spaces
QString m_telokinAsMonomerText1LetterWithSpaces =
"MAMISGMSGRKASGSSP TSPINADK "
"VENEDAFLEEVAEEKPHVKPYFTKTILDMEVVEGSAARFDCKIEGYPDP"
"EVMWYKDDQPVKESRHFQIDYDEEGNCSL TISEVCGDD DAKYTCKAVNSLG "
"EATCTA\nELLVETMGKEGEGEGEG"
"EEDE\tEEEEE";
// 157 residues
QString m_telokinAsMonomerText3Letters =
"MetAlaMetIleSerGlyMetSerGlyArgLysAlaSerGlySerSerProThrSerProIleAsnAlaAspLy"
"sValGluAsnGluAspAlaPheLeuGluGluValAlaGluGluLysProHisValLysProTyrPheThrLysT"
"hrIleLeuAspMetGluValValGluGlySerAlaAlaArgPheAspCysLysIleGluGlyTyrProAspPro"
"GluValMetTrpTyrLysAspAspGlnProValLysGluSerArgHisPheGlnIleAspTyrAspGluGluGl"
"yAsnCysSerLeuThrIleSerGluValCysGlyAspAspAspAlaLysTyrThrCysLysAlaValAsnSerL"
"euGlyGluAlaThrCysThrAlaGluLeuLeuValGluThrMetGlyLysGluGlyGluGlyGluGlyGluGly"
"GluGluAspGluGluGluGluGluGlu";
QString m_glucoseFormulaString = QString("C6H12O6");
QString m_saccharoseFormulaString = QString("C12H22O11");
QString m_formulaTitle = "MA dipeptide";
QString m_actionFormulaStringMetAlaDipeptidyl =
QString("+C5H11N1O2S1-H2O+C3H7N1O2-H2O");
QString m_actionFormulaStringMetAlaDipeptidylSpaces =
QString("+C5 H11 N1\nO2S1-H2O+C3 H7 N1 O2 - H2O");
// See the constructor
QString m_actionFormulaStringMetAlaDipeptidylTitled;
QString m_naturalIsotopicDataFileName = "light-c-n.dat";
QString m_manualUserIsotopicDataFileName =
"one-C14-radioactive-on-glucose-manual-config.dat";
static void initializeXpertmassLibrary();
PolChemDefSPtr initializePolChemDef(const QString &pol_chem_def_name,
int version);
QDomDocument craftFormulaDomDocument(const QStringList &dom_strings);
QDomDocument craftIonizeruleDomDocument(const QStringList &dom_strings);
QDomDocument craftMdfDomDocument(const QStringList &dom_strings);
QDomDocument craftMnmDomDocument(const QStringList &dom_strings);
QDomDocument craftMonomerDomDocument(const QStringList &dom_strings);
QDomDocument craftClkDomDocument(const QStringList &dom_strings);
QDomDocument craftClrDomDocument(const QStringList &dom_strings);
QDomDocument craftClsDomDocument(const QStringList &dom_strings);
QDomDocument craftClaDomDocument(const QStringList &dom_strings);
QDomDocument craftFgrDomDocument(const QStringList &dom_strings);
QDomDocument craftFgsDomDocument(const QStringList &dom_strings);
};
} // namespace libXpertMassCore
} // namespace MsXpS
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