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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: Clemens Groepl $
// $Authors: Clemens Groepl, Marc Sturm $
// --------------------------------------------------------------------------
#include <OpenMS/FORMAT/MzMLFile.h>
#include <OpenMS/FORMAT/FeatureXMLFile.h>
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/KERNEL/RangeUtils.h>
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinder_impl.h>
#include <OpenMS/APPLICATIONS/TOPPBase.h>
using namespace OpenMS;
using namespace std;
//-------------------------------------------------------------
//Doxygen docu
//-------------------------------------------------------------
/**
@page TOPP_FeatureFinderMRM FeatureFinderMRM
@brief The feature detection application for quantitation.
<CENTER>
<table>
<tr>
<td ALIGN = "center" BGCOLOR="#EBEBEB" ROWSPAN=1> pot. predecessor tools </td>
<td VALIGN="middle" ROWSPAN=3> \f$ \longrightarrow \f$ FeatureFinderMRM \f$ \longrightarrow \f$</td>
<td ALIGN = "center" BGCOLOR="#EBEBEB"> pot. successor tools </td>
</tr>
<tr>
<td VALIGN="middle" ALIGN = "center" ROWSPAN=2> </td>
<td VALIGN="middle" ALIGN = "center" ROWSPAN=1> @ref TOPP_FeatureLinkerUnlabeled @n (or another feature grouping tool) </td>
</tr>
<tr>
<td VALIGN="middle" ALIGN = "center" ROWSPAN=1> @ref TOPP_MapAlignerPoseClustering @n (or another alignment tool) </td>
</tr>
</table>
</CENTER>
This module identifies "features" in a LC/MS map. By feature, we understand a peptide in a MS sample that
reveals a characteristic isotope distribution. The algorithm
computes positions in rt and m/z dimension and a charge estimate
of each peptide.
How to find suitable parameters and details of the different algorithms implemented are described
in the @ref TOPP_example_featuredetection "TOPP tutorial".
Specialized tools are available for some experimental techniques: @ref TOPP_SILACAnalyzer, @ref TOPP_ITRAQAnalyzer.
<B>The command line parameters of this tool are:</B>
@verbinclude TOPP_FeatureFinderMRM.cli
<B>INI file documentation of this tool:</B>
@htmlinclude TOPP_FeatureFinderMRM.html
For the parameters of the algorithm section see the algorithms documentation: @n
@ref OpenMS::FeatureFinderAlgorithmMRM FeatureFinderAlgorithmMRM
*/
// We do not want this class to show up in the docu:
/// @cond TOPPCLASSES
class TOPPFeatureFinderMRM :
public TOPPBase
{
public:
TOPPFeatureFinderMRM() :
TOPPBase("FeatureFinderMRM", "Detects two-dimensional features in LC-MS data.")
{}
protected:
void registerOptionsAndFlags_()
{
registerInputFile_("in", "<file>", "", "input file");
setValidFormats_("in", StringList::create("mzML"));
registerOutputFile_("out", "<file>", "", "output file");
setValidFormats_("out", StringList::create("featureXML"));
addEmptyLine_();
registerSubsection_("algorithm", "Algorithm section");
}
Param getSubsectionDefaults_(const String & /*section*/) const
{
return FeatureFinder().getParameters(FeatureFinderAlgorithmMRM<Peak1D, Feature>::getProductName());
}
ExitCodes main_(int, const char **)
{
//input file names and types
String in = getStringOption_("in");
String out = getStringOption_("out");
Param feafi_param = getParam_().copy("algorithm:", true);
writeDebug_("Parameters passed to FeatureFinder", feafi_param, 3);
//setup of FeatureFinder
FeatureFinder ff;
ff.setLogType(log_type_);
//reading input data
PeakMap exp;
MzMLFile f;
f.setLogType(log_type_);
f.load(in, exp);
//no seeds supported
FeatureMap<> seeds;
//prevent loading of everything except MRM MS/MS spectra
//exp.getSpectra().erase(remove_if(exp.begin(), exp.end(), HasScanMode<PeakMap::SpectrumType>(InstrumentSettings::SRM, true)), exp.end());
// erase the spectra, we just need the chromatograms for the feature finder
exp.getSpectra().erase(exp.begin(), exp.end());
// A map for the resulting features
FeatureMap<> features;
// Apply the feature finder
ff.run(FeatureFinderAlgorithmMRM<Peak1D, Feature>::getProductName(), exp, features, feafi_param, seeds);
features.applyMemberFunction(&UniqueIdInterface::setUniqueId);
// DEBUG
if (debug_level_ > 10)
{
FeatureMap<>::Iterator it;
for (it = features.begin(); it != features.end(); ++it)
{
if (!it->isMetaEmpty())
{
vector<String> keys;
it->getKeys(keys);
LOG_INFO << "Feature " << it->getUniqueId() << endl;
for (Size i = 0; i < keys.size(); i++)
{
LOG_INFO << " " << keys[i] << " = " << it->getMetaValue(keys[i]) << endl;
}
}
}
}
//-------------------------------------------------------------
// writing files
//-------------------------------------------------------------
//annotate output with data processing info
addDataProcessing_(features, getProcessingInfo_(DataProcessing::QUANTITATION));
FeatureXMLFile map_file;
map_file.store(out, features);
return EXECUTION_OK;
}
};
int main(int argc, const char ** argv)
{
TOPPFeatureFinderMRM tool;
return tool.main(argc, argv);
}
/// @endcond
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