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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: Sandro Andreotti $
// $Authors: Sandro Andreotti $
// --------------------------------------------------------------------------
#include <OpenMS/CHEMISTRY/SvmTheoreticalSpectrumGeneratorTrainer.h>
#include <OpenMS/APPLICATIONS/TOPPBase.h>
#include <OpenMS/FORMAT/TextFile.h>
#include <OpenMS/FORMAT/MzMLFile.h>
#include <OpenMS/FORMAT/IdXMLFile.h>
#include <OpenMS/ANALYSIS/ID/IDMapper.h>
using namespace std;
using namespace OpenMS;
//-------------------------------------------------------------
//Doxygen docu
//-------------------------------------------------------------
//\link CHEMISTRY_SvmTheoreticalSpectrumGeneratorTrainer.
/**
@page UTILS_SvmTheoreticalSpectrumGeneratorTrainer SvmTheoreticalSpectrumGeneratorTrainer
@brief Trainer for SVM model as input for SvmTheoreticalSpectrumGenerator.
This application requires mzML file with ms2 spectra and annotations in an idXml file and trains a SVM model usable by
SvmTheoreticalSpectrumGenerator. Please refer to the documentation of the corresponding class @ref OpenMS::SvmTheoreticalSpectrumGeneratorTrainer
@note This tool is experimental!
<B>The command line parameters of this tool are:</B>
@verbinclude UTILS_SvmTheoreticalSpectrumGeneratorTrainer.cli
<B>INI file documentation of this tool:</B>
@htmlinclude UTILS_SvmTheoreticalSpectrumGeneratorTrainer.html
*/
// We do not want this class to show up in the docu:
/// @cond TOPPCLASSES
class SvmTheoreticalSpectrumGeneratorTrainerTOPP :
public TOPPBase
{
typedef SvmTheoreticalSpectrumGenerator::IonType IonType;
public:
SvmTheoreticalSpectrumGeneratorTrainerTOPP() :
TOPPBase("SvmTheoreticalSpectrumGeneratorTrainer", "Trainer for SVM models as input for SvmTheoreticalSpectrumGenerator", false)
{
}
protected:
void registerOptionsAndFlags_()
{
// I/O settings
registerInputFile_("in_spectra", "<file>", "", "Input Training Spectra in mzML", true);
setValidFormats_("in_spectra", StringList::create("mzML"));
registerInputFile_("in_identifications", "<file>", "", "Input file with corresponding sequences in idXML", true);
setValidFormats_("in_identifications", StringList::create("idXML"));
registerOutputFile_("model_output_file", "<file>", "",
"Name for output files. For each ion_type one file <filename>_residue_loss_charge.svm and one <filename>.info which has to be passed to the SvmTheoretical SpectrumGenerator", true);
//TODO: check how to handle file prefix properly for TOPPAS/KNIME/CTD
registerIntOption_("precursor_charge", "<Int>", 2, "Precursor charge state used for model training", false);
setMinInt_("precursor_charge", 1);
setMaxInt_("precursor_charge", 3);
registerFlag_("write_training_files", "No models are trained but input training files for libSVM command line tools are produced");
registerSubsection_("algorithm", "");
}
Param getSubsectionDefaults_(const String & /* section*/) const
{
Param tmp = SvmTheoreticalSpectrumGeneratorTrainer().getDefaults();
tmp.remove("write_training_files");
return tmp;
}
ExitCodes main_(int, const char **)
{
//-------------------------------------------------------------
// parameter handling
//-------------------------------------------------------------
String in_spectra = getStringOption_("in_spectra");
String in_identifications = getStringOption_("in_identifications");
String outfile = getStringOption_("model_output_file");
Int precursor_charge = getIntOption_("precursor_charge");
//-------------------------------------------------------------
// init SvmTheoreticalSpectrumGeneratorTrainer
//-------------------------------------------------------------
SvmTheoreticalSpectrumGeneratorTrainer trainer;
Param param = getParam_().copy("algorithm:", true);
String write_files = getFlag_("write_training_files") ? "true" : "false";
param.setValue("write_training_files", write_files);
trainer.setParameters(param);
//-------------------------------------------------------------
// loading input
//-------------------------------------------------------------
PeakMap map;
MzMLFile().load(in_spectra, map);
std::vector<PeptideIdentification> pep_ids;
std::vector<ProteinIdentification> prot_ids;
String tmp_str;
IdXMLFile().load(in_identifications, prot_ids, pep_ids, tmp_str);
IDMapper idmapper;
Param par;
par.setValue("rt_tolerance", 0.001);
par.setValue("mz_tolerance", 0.001);
idmapper.setParameters(par);
idmapper.annotate(map, pep_ids, prot_ids);
//generate vector of annotations
std::vector<AASequence> annotations;
PeakMap::iterator it;
for (it = map.begin(); it != map.end(); ++it)
{
annotations.push_back(it->getPeptideIdentifications()[0].getHits()[0].getSequence());
}
trainer.trainModel(map, annotations, outfile, precursor_charge);
return EXECUTION_OK;
}
};
int main(int argc, const char ** argv)
{
SvmTheoreticalSpectrumGeneratorTrainerTOPP tool;
return tool.main(argc, argv);
}
/// @endcond
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