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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_tools/common/FullReaderList.hpp"
#include "pwiz/utility/misc/Std.hpp"
using namespace pwiz::cv;
using namespace pwiz::msdata;
/*
This example program iterates through the spectra and chromatograms in a data file,
writing out the m/z-intensity and time-intensity pairs in a text column format.
# scanNumber msLevel m/z intensity
1 ms1 204.7591 0.00
1 ms1 204.7593 0.00
1 ms1 204.7596 1422.17
1 ms1 204.7598 3215.49
1 ms1 204.7601 3887.36
1 ms1 204.7604 2843.17
1 ms1 204.7606 582.91
1 ms1 204.7609 0.00
1 ms1 204.7611 0.00
# index id time intensity
0 TIC 30.9310 37.21
0 TIC 30.9392 95.23
0 TIC 30.9477 37.20
0 TIC 30.9558 99.50
1 SRM SIC 484.944,500.319 30.9310 34.29
1 SRM SIC 484.944,500.319 30.9477 33.29
1 SRM SIC 484.944,500.319 30.9643 29.88
1 SRM SIC 484.944,500.319 30.9809 24.00
[...]
*/
void cat(const char* filename)
{
// open the data file
FullReaderList readers; // for vendor Reader support
MSDataFile msd(filename, &readers);
// verify that we have a SpectrumList
if (!msd.run.spectrumListPtr.get() || !msd.run.spectrumListPtr->size())
{
if (!msd.run.chromatogramListPtr.get() || !msd.run.chromatogramListPtr->size())
throw runtime_error("[mscat] No spectra or chromatograms found.");
}
else
{
SpectrumList& spectrumList = *msd.run.spectrumListPtr;
// write header
const size_t columnWidth = 14;
cout << "#"
<< setw(columnWidth) << "scanNumber"
<< setw(columnWidth) << "msLevel"
<< setw(columnWidth) << "m/z"
<< setw(columnWidth) << "intensity" << endl;
// iterate through the spectra in the SpectrumList
for (size_t i=0, size=spectrumList.size(); i!=size; i++)
{
// retrieve the spectrum, with binary data
const bool getBinaryData = true;
SpectrumPtr spectrum = spectrumList.spectrum(i, getBinaryData);
// fill in MZIntensityPair vector for convenient access to binary data
vector<MZIntensityPair> pairs;
spectrum->getMZIntensityPairs(pairs);
// iterate through the m/z-intensity pairs
for (vector<MZIntensityPair>::const_iterator it=pairs.begin(), end=pairs.end(); it!=end; ++it)
{
cout << " "
<< setw(columnWidth) << id::value(spectrum->id, "scan")
<< setw(columnWidth) << "ms" + spectrum->cvParam(MS_ms_level).value
<< setw(columnWidth) << fixed << setprecision(4) << it->mz
<< setw(columnWidth) << fixed << setprecision(2) << it->intensity << endl;
}
}
}
if (msd.run.chromatogramListPtr.get() && msd.run.chromatogramListPtr->size())
{
ChromatogramList& chromatogramList = *msd.run.chromatogramListPtr;
// write header
const size_t columnWidth = 14;
cout << "#"
<< setw(columnWidth/2) << "index"
<< setw(columnWidth*2) << "id"
<< setw(columnWidth) << "time"
<< setw(columnWidth) << "intensity" << endl;
// iterate through the spectra in the chromatogramList
for (size_t i=0, size=chromatogramList.size(); i!=size; i++)
{
// retrieve the chromatogram, with binary data
const bool getBinaryData = true;
ChromatogramPtr chromatogram = chromatogramList.chromatogram(i, getBinaryData);
// fill in TimeIntensityPair vector for convenient access to binary data
vector<TimeIntensityPair> pairs;
chromatogram->getTimeIntensityPairs(pairs);
// iterate through the m/z-intensity pairs
for (vector<TimeIntensityPair>::const_iterator it=pairs.begin(), end=pairs.end(); it!=end; ++it)
{
cout << " "
<< setw(columnWidth/2) << chromatogram->index
<< setw(columnWidth*2) << chromatogram->id
<< setw(columnWidth) << fixed << setprecision(4) << it->time
<< setw(columnWidth) << fixed << setprecision(2) << it->intensity << endl;
}
}
}
}
int main(int argc, char* argv[])
{
try
{
if (argc != 2)
{
cout << "Usage: mscat filename\n"
<< "Write spectrum and chromatogram data as text to console.\n\n"
<< "https://github.com/ProteoWizard\n"
<< "support@proteowizard.org\n";
return 1;
}
const char* filename = argv[1];
cat(filename);
return 0;
}
catch (exception& e)
{
cerr << e.what() << endl;
}
catch (...)
{
cerr << "Caught unknown exception.\n";
}
return 1;
}
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