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Viewing changes to source/APPLICATIONS/TOPP/SpectraFilterWindowMower.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/SpectraFilterWindowMower.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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// $Maintainer: Mathias Walzer$
 
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// $Authors: $
 
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// --------------------------------------------------------------------------
 
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#include <OpenMS/APPLICATIONS/TOPPBase.h>
 
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#include <OpenMS/FILTERING/TRANSFORMERS/WindowMower.h>
 
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#include <OpenMS/FORMAT/MzMLFile.h>
 
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#include <typeinfo>
 
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using namespace OpenMS;
 
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using namespace std;
 
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/**
 
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  @page TOPP_SpectraFilterWindowMower SpectraFilterWindowMower
 
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        @brief Filters the top Peaks in the given spectra according to a given schema/thresholdset
 
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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$ SpectraFilter \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_SpectraFilterWindowMower.cli
 
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        For the parameters of the algorithm section see the class documentation: @n
 
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                @ref OpenMS::WindowMower @n
 
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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 TOPPSpectraFilterWindowMower
 
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        : public TOPPBase
 
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{
 
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        public:
 
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    TOPPSpectraFilterWindowMower()
 
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      : TOPPBase("SpectraFilterWindowMower", "Applies thresholdfilter to peak spectra.")
 
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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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                        // register one section for each algorithm
 
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                        registerSubsection_("algorithm","Algorithm parameter subsection.");
 
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                }
 
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                Param getSubsectionDefaults_(const String& /*section*/) const
 
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                {
 
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                        return WindowMower().getParameters();
 
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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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                        //input/output files
 
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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<> exp;
 
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      MzMLFile f;
 
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      f.setLogType(log_type_);
 
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      f.load(in, exp);
 
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      //-------------------------------------------------------------
 
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      // if meta data arrays are present, remove them and warn
 
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      //-------------------------------------------------------------
 
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                        if (exp.clearMetaDataArrays())
 
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                        {
 
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                                writeLog_("Warning: Spectrum meta data arrays cannot be sorted. They are deleted.");
 
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                        }
 
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      //-------------------------------------------------------------
 
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      // filter
 
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      //-------------------------------------------------------------
 
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                        Param filter_param = getParam_().copy("algorithm:", true);
 
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                        writeDebug_("Used filter parameters", filter_param, 3);
 
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                        WindowMower filter;
 
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                        filter.setParameters(filter_param);
 
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                        filter.filterPeakMap(exp);
 
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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::FILTERING));
 
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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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/// @endcond
 
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int main( int argc, const char** argv )
 
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{
 
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  TOPPSpectraFilterWindowMower tool;
 
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        return tool.main(argc,argv);
 
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}
 
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