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//
// $Id$
//
//
// Original author: Darren Kessner <darren@proteowizard.org>
//
// Copyright 2008 Spielberg Family Center for Applied Proteomics
// Cedars-Sinai Medical Center, Los Angeles, California 90048
//
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
// You may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software
// distributed under the License is distributed on an "AS IS" BASIS,
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and
// limitations under the License.
//
#include "pwiz/data/msdata/MSDataFile.hpp"
#include "pwiz/data/msdata/examples.hpp"
#include "pwiz_tools/common/FullReaderList.hpp"
#include "pwiz/utility/misc/Std.hpp"
using namespace pwiz::data;
using namespace pwiz::msdata;
void writeTiny()
{
// create the MSData object in memory
MSData msd;
examples::initializeTiny(msd);
// write out mzML
string filename = "tiny.pwiz.mzML";
cout << "Writing file " << filename << endl;
MSDataFile::write(msd, filename);
// write out mzXML
filename = "tiny.pwiz.mzXML";
cout << "Writing file " << filename << endl;
MSDataFile::write(msd, filename, MSDataFile::Format_mzXML);
}
void writeSmall()
{
#ifdef PWIZ_READER_THERMO
const string& inputFile = "small.RAW";
try
{
FullReaderList readers;
MSDataFile msd(inputFile, &readers, true);
// msconvert defaults
MSDataFile::WriteConfig config;
config.binaryDataEncoderConfig.precision = BinaryDataEncoder::Precision_64;
config.binaryDataEncoderConfig.precisionOverrides[MS_m_z_array] = BinaryDataEncoder::Precision_64;
config.binaryDataEncoderConfig.precisionOverrides[MS_intensity_array] = BinaryDataEncoder::Precision_32;
// basic mzML conversion
string outputFile = "small.pwiz.mzML";
cout << "Writing file " << outputFile << endl;
msd.write(outputFile, config);
// with zlib compression, 32-bit encoding
config.binaryDataEncoderConfig.compression = BinaryDataEncoder::Compression_Zlib;
config.binaryDataEncoderConfig.precision
= config.binaryDataEncoderConfig.precisionOverrides[MS_m_z_array]
= config.binaryDataEncoderConfig.precisionOverrides[MS_intensity_array]
= BinaryDataEncoder::Precision_32;
outputFile = "small_zlib.pwiz.mzML";
cout << "Writing file " << outputFile << endl;
msd.write(outputFile, config);
// with MIAPE metadata added
examples::addMIAPEExampleMetadata(msd);
outputFile = "small_miape.pwiz.mzML";
cout << "Writing file " << outputFile << endl;
msd.write(outputFile, config);
}
catch (exception& e)
{
cerr << e.what() << endl;
cerr << "Error opening file " << inputFile << endl;
}
#endif
}
int main()
{
try
{
writeTiny();
writeSmall();
cout << "\nhttps://github.com/ProteoWizard\n"
<< "support@proteowizard.org\n";
return 0;
}
catch (exception& e)
{
cerr << e.what() << endl;
}
catch (...)
{
cerr << "Caught unknown exception.\n";
}
return 1;
}
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