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Viewing changes to source/APPLICATIONS/TOPP/MapNormalizer.C

  • Committer: Package Import Robot
  • Author(s): Filippo Rusconi
  • Date: 2012-11-12 15:58:12 UTC
  • Revision ID: package-import@ubuntu.com-20121112155812-vr15wtg9b50cuesg
Tags: upstream-1.9.0
Import upstream version 1.9.0

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source/APPLICATIONS/TOPP/MapNormalizer.C
 
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// -*- mode: C++; tab-width: 2; -*-
 
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// vi: set ts=2:
 
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//
 
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// --------------------------------------------------------------------------
 
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//                   OpenMS Mass Spectrometry Framework
 
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// --------------------------------------------------------------------------
 
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//  Copyright (C) 2003-2011 -- Oliver Kohlbacher, Knut Reinert
 
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//
 
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//  This library is free software; you can redistribute it and/or
 
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//  modify it under the terms of the GNU Lesser General Public
 
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//  License as published by the Free Software Foundation; either
 
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//  version 2.1 of the License, or (at your option) any later version.
 
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//
 
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//  This library is distributed in the hope that it will be useful,
 
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//  but WITHOUT ANY WARRANTY; without even the implied warranty of
 
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//  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 
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//  Lesser General Public License for more details.
 
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//
 
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//  You should have received a copy of the GNU Lesser General Public
 
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//  License along with this library; if not, write to the Free Software
 
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//  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
 
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//
 
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// --------------------------------------------------------------------------
 
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// $Maintainer: $
 
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// $Authors: Marc Sturm $
 
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// --------------------------------------------------------------------------
 
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#include <OpenMS/FORMAT/MzMLFile.h>
 
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#include <OpenMS/APPLICATIONS/TOPPBase.h>
 
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using namespace OpenMS;
 
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using namespace std;
 
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//-------------------------------------------------------------
 
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//Doxygen docu
 
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//-------------------------------------------------------------
 
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/**
 
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        @page TOPP_MapNormalizer MapNormalizer
 
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        @brief Normalizes peak intensities to the percentage of the maximum intensity in the HPLC-MS map.
 
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<CENTER>
 
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        <table>
 
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                <tr>
 
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                        <td ALIGN = "center" BGCOLOR="#EBEBEB"> pot. predecessor tools </td>
 
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                        <td VALIGN="middle" ROWSPAN=2> \f$ \longrightarrow \f$ MapNormalizer \f$ \longrightarrow \f$</td>
 
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                        <td ALIGN = "center" BGCOLOR="#EBEBEB"> pot. successor tools </td>
 
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                </tr>
 
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                <tr>
 
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      <td VALIGN="middle" ALIGN = "center" ROWSPAN=1> @ref TOPP_PeakPickerWavelet </td>
 
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                        <td VALIGN="middle" ALIGN = "center" ROWSPAN=1> any tool operating on MS peak data @n (in mzML format)</td>
 
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                </tr>
 
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        </table>
 
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</CENTER>
 
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        <B>The command line parameters of this tool are:</B>
 
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        @verbinclude TOPP_MapNormalizer.cli
 
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*/
 
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// We do not want this class to show up in the docu:
 
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/// @cond TOPPCLASSES
 
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class TOPPMapNormalizer
 
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        : public TOPPBase
 
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{
 
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        public:
 
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                TOPPMapNormalizer()
 
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                        : TOPPBase("MapNormalizer","Normalizes peak intensities in an MS run.")
 
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                {
 
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                }
 
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        protected:
 
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                void registerOptionsAndFlags_()
 
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                {
 
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                        registerInputFile_("in","<file>","","input file ");
 
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                        setValidFormats_("in",StringList::create("mzML"));
 
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                        registerOutputFile_("out","<file>","","output file ");
 
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                setValidFormats_("out",StringList::create("mzML"));
 
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                }
 
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                ExitCodes main_(int , const char**)
 
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                {
 
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                        //-------------------------------------------------------------
 
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                        // parameter handling
 
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                        //-------------------------------------------------------------
 
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                        String in = getStringOption_("in");
 
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                        String out = getStringOption_("out");
 
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                        //-------------------------------------------------------------
 
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                        // loading input
 
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                        //-------------------------------------------------------------
 
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                        MSExperiment<Peak1D> exp;
 
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                        MzMLFile f;
 
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                        f.load(in,exp);
 
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                        //-------------------------------------------------------------
 
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                        // calculations
 
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                        //-------------------------------------------------------------
 
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                        //determine maximum peak
 
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                        exp.updateRanges();
 
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                        DoubleReal max = exp.getMaxInt() / 100.0;
 
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                        for (MSExperiment<Peak1D>::Iterator it = exp.begin(); it!= exp.end(); ++it)
 
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                        {
 
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                                if (it->getMSLevel() < 2)
 
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                                {
 
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                                        for (MSExperiment<Peak1D>::SpectrumType::Iterator it2 = it->begin(); it2!= it->end(); ++it2)
 
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                                        {
 
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                                                it2->setIntensity( it2->getIntensity() / max);
 
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                                        }
 
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                                }
 
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                        }
 
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                        /// @todo add chromatogram support for normalization, e.g. for MRM stuff (Andreas)
 
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                  /*
 
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                        vector<MSChromatogram<> > chroms = exp.getChromatograms();
 
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                        DoubleReal sum(0);
 
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      for (vector<MSChromatogram<> >::iterator it = chroms.begin(); it != chroms.end(); ++it)
 
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      {
 
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        for (MSChromatogram<>::Iterator it2 = it->begin(); it2 != it->end(); ++it2)
 
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        {
 
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                                        sum += it2->getIntensity();
 
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                                }
 
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                        }
 
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                        for (vector<MSChromatogram<> >::iterator it = chroms.begin(); it != chroms.end(); ++it)
 
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                        {
 
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                                for (MSChromatogram<>::Iterator it2 = it->begin(); it2 != it->end(); ++it2)
 
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                                {
 
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                                        it2->setIntensity(it2->getIntensity() / sum * 1000000.0);
 
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                                }
 
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                        }
 
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                        exp.setChromatograms(chroms);
 
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                  */
 
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                        //-------------------------------------------------------------
 
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                        // writing output
 
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                        //-------------------------------------------------------------
 
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                        //annotate output with data processing info
 
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                        addDataProcessing_(exp, getProcessingInfo_(DataProcessing::NORMALIZATION));
 
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                        f.store(out,exp);
 
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                        return EXECUTION_OK;
 
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                }
 
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};
 
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int main( int argc, const char** argv )
 
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{
 
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        TOPPMapNormalizer tool;
 
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        return tool.main(argc,argv);
 
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}
 
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/// @endcond