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Viewing changes to source/TEST/MapAlignmentAlgorithmSpectrumAlignment_test.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/TEST/MapAlignmentAlgorithmSpectrumAlignment_test.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: Erhan Kenar $
 
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// $Authors: Vipul Patel $
 
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// --------------------------------------------------------------------------
 
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#include <OpenMS/CONCEPT/ClassTest.h>
 
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#include <OpenMS/ANALYSIS/MAPMATCHING/MapAlignmentAlgorithmSpectrumAlignment.h>
 
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using namespace std;
 
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using namespace OpenMS;
 
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/////////////////////////////////////////////////////////////
 
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START_TEST(MapAlignmentAlgorithmSpectrumAlignment, "$Id: MapAlignmentAlgorithmSpectrumAlignment_test.C 8788 2011-09-10 20:44:01Z hendrikweisser $")
 
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/////////////////////////////////////////////////////////////
 
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/////////////////////////////////////////////////////////////
 
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MapAlignmentAlgorithmSpectrumAlignment* ptr = 0;
 
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MapAlignmentAlgorithmSpectrumAlignment* nullPointer = 0;
 
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MapAlignmentAlgorithm* base_nullPointer = 0;
 
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START_SECTION((MapAlignmentAlgorithmSpectrumAlignment()))
 
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        ptr = new MapAlignmentAlgorithmSpectrumAlignment();
 
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        TEST_NOT_EQUAL(ptr, nullPointer)
 
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END_SECTION
 
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START_SECTION((virtual ~MapAlignmentAlgorithmSpectrumAlignment()))
 
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        delete ptr;
 
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END_SECTION
 
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START_SECTION((static MapAlignmentAlgorithm* create()))
 
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  TEST_NOT_EQUAL(MapAlignmentAlgorithmSpectrumAlignment::create(),base_nullPointer)
 
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END_SECTION
 
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START_SECTION((static String getProductName()))
 
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        TEST_EQUAL(MapAlignmentAlgorithmSpectrumAlignment::getProductName(), "spectrum_alignment")
 
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END_SECTION
 
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START_SECTION((virtual void alignPeakMaps(std::vector< MSExperiment<> > &, std::vector< TransformationDescription > &)))
 
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{
 
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  MapAlignmentAlgorithmSpectrumAlignment ma;
 
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  std::vector< MSExperiment<> > maps;
 
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        PeakMap map1;
 
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        PeakMap map2;   
 
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        for (UInt i= 0; i< 15; ++i)
 
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        {
 
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                for (UInt j =1 ; j < 5; ++j)
 
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                {
 
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                        PeakSpectrum spectrum;
 
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                        spectrum.setRT(i);
 
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                        spectrum.setMSLevel(j);
 
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                        for (Real mz=500.0; mz<=900; mz+=100.0)
 
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                    { 
 
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                                Peak1D peak;
 
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                                peak.setMZ(mz+i);
 
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                                peak.setIntensity(mz+i);
 
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                                spectrum.push_back(peak);  
 
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                    }
 
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                    map1.push_back(spectrum);
 
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                }
 
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        }
 
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        for (UInt i= 0; i< 15; ++i)
 
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                {
 
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                        for (UInt j =1 ; j < 5; ++j)
 
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                        {
 
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                                PeakSpectrum spectrum;
 
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                                spectrum.setRT(i*1.2+200);
 
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                                spectrum.setMSLevel(j);
 
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                                for (Real mz=500.0; mz<=900; mz+=100.0)
 
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                            { 
 
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                                        Peak1D peak;
 
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                                        peak.setMZ(mz+i);
 
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                                        peak.setIntensity(mz+i);
 
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                                        spectrum.push_back(peak);  
 
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                            }
 
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                            map2.push_back(spectrum);
 
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                        }
 
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                }
 
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        maps.push_back(map1);
 
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        maps.push_back(map2);
 
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        std::vector<TransformationDescription> transformations;
 
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  ma.alignPeakMaps(maps, transformations);
 
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        String model_type = "interpolated";
 
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        Param params;
 
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        params.setValue("interpolation_type", "cspline");
 
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        ma.fitModel(model_type, params, transformations);
 
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        ma.transformPeakMaps(maps, transformations);
 
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        maps[0].updateRanges(-1);
 
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        maps[1].updateRanges(-1);
 
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  for (Size i=0; i< maps[0].size(); ++i)
 
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  {
 
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                if((maps[0])[i].getMSLevel() <2)
 
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                {
 
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                        TEST_REAL_SIMILAR(maps[0][i].getRT(), maps[1][i].getRT());
 
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                }
 
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  }
 
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}
 
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END_SECTION
 
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START_SECTION([EXTRA] void alignFeatureMaps(std::vector< FeatureMap<> >&))
 
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  MapAlignmentAlgorithmSpectrumAlignment ma;
 
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  std::vector< FeatureMap<> > maps;
 
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        std::vector<TransformationDescription> transformations;
 
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  TEST_EXCEPTION(Exception::NotImplemented, ma.alignFeatureMaps(maps,transformations));
 
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END_SECTION
 
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/////////////////////////////////////////////////////////////
 
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/////////////////////////////////////////////////////////////
 
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END_TEST
 
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