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//
// File: test_big_hyperscore.cpp
// Created by: Olivier Langella
// Created on: 19/3/2015
//
/*******************************************************************************
* 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 [bighyperscore] -s
#ifdef CATCH2_MAJOR_VERSION_2
#include <catch2/catch.hpp>
using namespace Catch;
#elif CATCH2_MAJOR_VERSION_3
#include <catch2/catch_all.hpp>
using namespace Catch;
using namespace Catch::Matchers;
#endif
#include <pappsomspp/core/mzrange.h>
#include <pappsomspp/core/peptide/peptidenaturalisotopelist.h>
#include <pappsomspp/core/peptide/peptidefragmentionlistbase.h>
#include <pappsomspp/core/massspectrum/massspectrum.h>
#include <pappsomspp/core/psm/xtandem/xtandemhyperscore.h>
#include <pappsomspp/core/pappsoexception.h>
#include <iostream>
#include <iomanip>
#include <cmath>
#include <set>
#include <QDebug>
#include <QString>
#include <QFileInfo>
#include "config.h"
#include "saxparsers/xtandemresultshandler.h"
using namespace pappso;
using namespace std;
// using namespace pwiz::msdata;
TEST_CASE("bighyperscore test suite.", "[bighyperscore]")
{
// Set the debugging message formatting pattern.
qSetMessagePattern(QString("%{file}@%{line}, %{function}(): %{message}"));
SECTION("..:: test bighyperscore ::..", "[bighyperscore]")
{
#if USEPAPPSOTREE == 1
// return 1;
std::cout
<< std::endl
<< "..:: test all identified peptides in an XML tandem result file ::.."
<< std::endl;
PrecisionPtr precision = PrecisionFactory::getDaltonInstance(0.02);
// bool refine_spectrum_synthesis = false;
QFileInfo fileinfo(
"/gorgone/pappso/formation/Janvier2014/TD/xml_tandem/"
"20120906_balliau_extract_1_A01_urnb-1.xml");
XtandemResultsHandler *parser = new XtandemResultsHandler(precision);
QXmlSimpleReader simplereader;
simplereader.setContentHandler(parser);
simplereader.setErrorHandler(parser);
qDebug() << "Read tandem XML result file '" << fileinfo.filePath() << "'";
QFile qfile(fileinfo.absoluteFilePath());
QXmlInputSource xmlInputSource(&qfile);
if(simplereader.parse(xmlInputSource))
{
}
else
{
qDebug() << parser->errorString();
// throw PappsoException(
// QObject::tr("error reading tandem XML result file :\n").append(
// parser->errorString()));
}
qfile.close();
#endif
// big hyperscore test :
// check every X!Tandem match in an XML result file
}
}
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