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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: $
// $Authors: Marc Sturm $
// --------------------------------------------------------------------------
#include <OpenMS/FORMAT/MzMLFile.h>
#include <OpenMS/APPLICATIONS/TOPPBase.h>
using namespace OpenMS;
using namespace std;
//-------------------------------------------------------------
//Doxygen docu
//-------------------------------------------------------------
/**
@page TOPP_MapNormalizer MapNormalizer
@brief Normalizes peak intensities to the percentage of the maximum intensity in the HPLC-MS map.
<center>
<table>
<tr>
<td ALIGN = "center" BGCOLOR="#EBEBEB"> pot. predecessor tools </td>
<td VALIGN="middle" ROWSPAN=2> \f$ \longrightarrow \f$ MapNormalizer \f$ \longrightarrow \f$</td>
<td ALIGN = "center" BGCOLOR="#EBEBEB"> pot. successor tools </td>
</tr>
<tr>
<td VALIGN="middle" ALIGN = "center" ROWSPAN=1> @ref TOPP_PeakPickerWavelet </td>
<td VALIGN="middle" ALIGN = "center" ROWSPAN=1> any tool operating on MS peak data @n (in mzML format)</td>
</tr>
</table>
</center>
<B>The command line parameters of this tool are:</B>
@verbinclude TOPP_MapNormalizer.cli
<B>INI file documentation of this tool:</B>
@htmlinclude TOPP_MapNormalizer.html
*/
// We do not want this class to show up in the docu:
/// @cond TOPPCLASSES
class TOPPMapNormalizer :
public TOPPBase
{
public:
TOPPMapNormalizer() :
TOPPBase("MapNormalizer", "Normalizes peak intensities in an MS run.")
{
}
protected:
void registerOptionsAndFlags_()
{
registerInputFile_("in", "<file>", "", "input file ");
setValidFormats_("in", StringList::create("mzML"));
registerOutputFile_("out", "<file>", "", "output file ");
setValidFormats_("out", StringList::create("mzML"));
}
ExitCodes main_(int, const char **)
{
//-------------------------------------------------------------
// parameter handling
//-------------------------------------------------------------
String in = getStringOption_("in");
String out = getStringOption_("out");
//-------------------------------------------------------------
// loading input
//-------------------------------------------------------------
MSExperiment<Peak1D> exp;
MzMLFile f;
f.load(in, exp);
//-------------------------------------------------------------
// calculations
//-------------------------------------------------------------
//determine maximum peak
exp.updateRanges();
DoubleReal max = exp.getMaxInt() / 100.0;
for (MSExperiment<Peak1D>::Iterator it = exp.begin(); it != exp.end(); ++it)
{
if (it->getMSLevel() < 2)
{
for (MSExperiment<Peak1D>::SpectrumType::Iterator it2 = it->begin(); it2 != it->end(); ++it2)
{
it2->setIntensity(it2->getIntensity() / max);
}
}
}
/// @todo add chromatogram support for normalization, e.g. for MRM stuff (Andreas)
/*
vector<MSChromatogram<> > chroms = exp.getChromatograms();
DoubleReal sum(0);
for (vector<MSChromatogram<> >::iterator it = chroms.begin(); it != chroms.end(); ++it)
{
for (MSChromatogram<>::Iterator it2 = it->begin(); it2 != it->end(); ++it2)
{
sum += it2->getIntensity();
}
}
for (vector<MSChromatogram<> >::iterator it = chroms.begin(); it != chroms.end(); ++it)
{
for (MSChromatogram<>::Iterator it2 = it->begin(); it2 != it->end(); ++it2)
{
it2->setIntensity(it2->getIntensity() / sum * 1000000.0);
}
}
exp.setChromatograms(chroms);
*/
//-------------------------------------------------------------
// writing output
//-------------------------------------------------------------
//annotate output with data processing info
addDataProcessing_(exp, getProcessingInfo_(DataProcessing::NORMALIZATION));
f.store(out, exp);
return EXECUTION_OK;
}
};
int main(int argc, const char ** argv)
{
TOPPMapNormalizer tool;
return tool.main(argc, argv);
}
/// @endcond
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