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// --------------------------------------------------------------------------
// OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2013.
//
// This software is released under a three-clause BSD license:
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
// * Neither the name of any author or any participating institution
// may be used to endorse or promote products derived from this software
// without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: Mathias Walzer $
// $Authors: Mathias Walzer $
// --------------------------------------------------------------------------
#include <OpenMS/FORMAT/MzQuantMLFile.h>
#include <OpenMS/FORMAT/CVMappingFile.h>
#include <OpenMS/FORMAT/VALIDATORS/XMLValidator.h>
#include <OpenMS/FORMAT/HANDLERS/MzQuantMLHandler.h>
#include <OpenMS/SYSTEM/File.h>
#include <OpenMS/FORMAT/VALIDATORS/MzQuantMLValidator.h>
namespace OpenMS
{
MzQuantMLFile::MzQuantMLFile() :
XMLFile("/SCHEMAS/mzQuantML_1_0_0-rc2", "1.0.0")
{
}
MzQuantMLFile::~MzQuantMLFile()
{
}
void MzQuantMLFile::load(const String & filename, MSQuantifications & msq)
{
Internal::MzQuantMLHandler handler(msq, filename, schema_version_, *this);
parse_(filename, &handler);
}
void MzQuantMLFile::store(const String & filename, const MSQuantifications & cmsq) const
{
Internal::MzQuantMLHandler handler(cmsq, filename, schema_version_, *this);
save_(filename, &handler);
}
bool MzQuantMLFile::isSemanticallyValid(const String & filename, StringList & errors, StringList & warnings)
{
//load mapping
CVMappings mapping;
CVMappingFile().load(File::find("/MAPPING/mzQuantML-mapping_1.0.0-rc2-general.xml"), mapping);
//load cvs
ControlledVocabulary cv;
cv.loadFromOBO("MS", File::find("/CV/psi-ms.obo"));
cv.loadFromOBO("PATO", File::find("/CV/quality.obo"));
cv.loadFromOBO("UO", File::find("/CV/unit.obo"));
cv.loadFromOBO("BTO", File::find("/CV/brenda.obo"));
cv.loadFromOBO("GO", File::find("/CV/goslim_goa.obo"));
//validate TODO
Internal::MzQuantMLValidator v(mapping, cv);
bool result = v.validate(filename, errors, warnings);
return result;
}
} // namespace OpenMS
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