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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: $
// --------------------------------------------------------------------------
//
#include <OpenMS/CONCEPT/ClassTest.h>
///////////////////////////
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/SimpleExtender.h>
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinder_impl.h>
#include <OpenMS/CONCEPT/Exception.h>
#include <OpenMS/KERNEL/ComparatorUtils.h>
#include <OpenMS/DATASTRUCTURES/Param.h>
#include <OpenMS/FORMAT/MzDataFile.h>
///////////////////////////
START_TEST(SimpleExtender, "$Id: SimpleExtender_test.C 11338 2013-06-05 20:48:48Z hroest $")
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
using namespace OpenMS;
using namespace std;
typedef Peak1D PeakType;
typedef Feature FeatureType;
typedef SimpleExtender<PeakType,FeatureType> ExtenderType;
typedef FeatureFinderDefs::ChargedIndexSet ChargedIndexSet;
{
ExtenderType* ptr = 0;
ExtenderType* nullPointer = 0;
START_SECTION((SimpleExtender(const MSExperiment<PeakType>* map, FeatureMap<FeatureType>* features, FeatureFinder* ff)))
{
MSExperiment<PeakType> map;
FeatureMap<FeatureType> features;
FeatureFinder ff;
ptr = new ExtenderType(&map,&features,&ff);
TEST_EQUAL(ptr->getName(), "SimpleExtender")
TEST_NOT_EQUAL(ptr, nullPointer)
}
END_SECTION
START_SECTION((virtual ~SimpleExtender()))
delete ptr;
END_SECTION;
}
START_SECTION(void extend(const ChargedIndexSet &seed_region, ChargedIndexSet& result_region))
{
// this test checks the regions returned by SimpleExtender
// on one artificial data set and a picked (centroided) data set
// The test of the corresponding TOPP module performs further tests.
MSExperiment<PeakType> input;
FeatureMap<FeatureType> features;
FeatureFinder ff;
MSExperiment<PeakType>::SpectrumType spec;
spec.setRT(1);
DoubleReal mzs[] = {1, 2, 3, 4, 5};
DoubleReal its1[] = {1000, 1500,2000, 1500, 1000};
const UInt num = 5;
for (Size i=0; i < num; i++)
{
PeakType p;
p.setMZ(mzs[i]);
p.setIntensity(its1[i]);
spec.push_back(p);
}
input.addSpectrum(spec);
spec.clear(true);
spec.setRT(2);
DoubleReal its2[] = {1000, 1500, 2000, 1500, 1000};
for (Size i=0; i < num; i++)
{
PeakType p;
p.setMZ(mzs[i]);
p.setIntensity(its2[i]);
spec.push_back(p);
}
input.addSpectrum(spec);
spec.clear(true);
spec.setRT(3);
DoubleReal its3[] = {1000, 1500, 5000, 1500, 1000};
for (Size i=0; i < num; i++)
{
PeakType p;
p.setMZ(mzs[i]);
p.setIntensity(its3[i]);
spec.push_back(p);
}
input.addSpectrum(spec);
spec.clear(true);
spec.setRT(4);
// the last two data points should not be included (see param intensity_factor)
DoubleReal its4[] = {1000, 1500, 2000, 0.1, 0.1};
for (Size i=0; i < num; i++)
{
PeakType p;
p.setMZ(mzs[i]);
p.setIntensity(its4[i]);
spec.push_back(p);
}
input.addSpectrum(spec);
input.updateRanges();
ff.run("none", input, features, Param(), FeatureMap<>());
// first two points are already in some other feature region
// => check if points included in other features are ignored
ff.getPeakFlag(make_pair(0,0)) = FeatureFinderDefs::USED;
ff.getPeakFlag(make_pair(0,1)) = FeatureFinderDefs::USED;
ExtenderType extender(&input, &features, &ff);
ChargedIndexSet index_set;
index_set.insert( std::make_pair(2,2) ); // start extension with point of highest intensity
ChargedIndexSet region;
extender.extend(index_set,region);
// We have 20 points in total, 2 in another feature, 2 with too little
// intensity. Hence the region should be of size 16.
TEST_EQUAL(region.size(),16);
ChargedIndexSet::const_iterator citer = region.begin();
// first scan
TEST_EQUAL(extender.getPeakIntensity(*citer),2000.0);
TEST_EQUAL(extender.getPeakMz(*citer),3.0);
TEST_EQUAL(extender.getPeakRt(*citer),1.0);
++citer;
TEST_EQUAL(extender.getPeakIntensity(*citer),1500.0);
TEST_EQUAL(extender.getPeakMz(*citer),4.0);
TEST_EQUAL(extender.getPeakRt(*citer),1.0);
++citer;
TEST_EQUAL(extender.getPeakIntensity(*citer),1000.0);
TEST_EQUAL(extender.getPeakMz(*citer),5.0);
TEST_EQUAL(extender.getPeakRt(*citer),1.0);
// second scan
++citer;
TEST_EQUAL(extender.getPeakIntensity(*citer),1000.0);
TEST_EQUAL(extender.getPeakMz(*citer),1.0);
TEST_EQUAL(extender.getPeakRt(*citer),2.0);
++citer;
TEST_EQUAL(extender.getPeakIntensity(*citer),1500.0);
TEST_EQUAL(extender.getPeakMz(*citer),2.0);
TEST_EQUAL(extender.getPeakRt(*citer),2.0);
++citer;
TEST_EQUAL(extender.getPeakIntensity(*citer),2000.0);
TEST_EQUAL(extender.getPeakMz(*citer),3.0);
TEST_EQUAL(extender.getPeakRt(*citer),2.0);
++citer;
TEST_EQUAL(extender.getPeakIntensity(*citer),1500.0);
TEST_EQUAL(extender.getPeakMz(*citer),4.0);
TEST_EQUAL(extender.getPeakRt(*citer),2.0);
++citer;
TEST_EQUAL(extender.getPeakIntensity(*citer),1000.0);
TEST_EQUAL(extender.getPeakMz(*citer),5.0);
TEST_EQUAL(extender.getPeakRt(*citer),2.0);
// third scan
++citer;
TEST_EQUAL(extender.getPeakIntensity(*citer),1000.0);
TEST_EQUAL(extender.getPeakMz(*citer),1.0);
TEST_EQUAL(extender.getPeakRt(*citer),3.0);
++citer;
TEST_EQUAL(extender.getPeakIntensity(*citer),1500.0);
TEST_EQUAL(extender.getPeakMz(*citer),2.0);
TEST_EQUAL(extender.getPeakRt(*citer),3.0);
++citer;
TEST_EQUAL(extender.getPeakIntensity(*citer),5000.0);
TEST_EQUAL(extender.getPeakMz(*citer),3.0);
TEST_EQUAL(extender.getPeakRt(*citer),3.0);
++citer;
TEST_EQUAL(extender.getPeakIntensity(*citer),1500.0);
TEST_EQUAL(extender.getPeakMz(*citer),4.0);
TEST_EQUAL(extender.getPeakRt(*citer),3.0);
++citer;
TEST_EQUAL(extender.getPeakIntensity(*citer),1000.0);
TEST_EQUAL(extender.getPeakMz(*citer),5.0);
TEST_EQUAL(extender.getPeakRt(*citer),3.0);
// fourth scan
++citer;
TEST_EQUAL(extender.getPeakIntensity(*citer),1000.0);
TEST_EQUAL(extender.getPeakMz(*citer),1.0);
TEST_EQUAL(extender.getPeakRt(*citer),4.0);
++citer;
TEST_EQUAL(extender.getPeakIntensity(*citer),1500.0);
TEST_EQUAL(extender.getPeakMz(*citer),2.0);
TEST_EQUAL(extender.getPeakRt(*citer),4.0);
++citer;
TEST_EQUAL(extender.getPeakIntensity(*citer),2000.0);
TEST_EQUAL(extender.getPeakMz(*citer),3.0);
TEST_EQUAL(extender.getPeakRt(*citer),4.0);
// last two points have too little intensity
++ citer;
TEST_EQUAL(citer==region.end(),true)
}
END_SECTION
TOLERANCE_ABSOLUTE(0.01)
START_SECTION(([EXTRA] Extension on real-world data))
{
MSExperiment<PeakType> input;
FeatureMap<FeatureType> features;
FeatureFinder ff;
MzDataFile().load(OPENMS_GET_TEST_DATA_PATH("SimpleExtender_test.mzData"),input);
ExtenderType extender(&input, &features, &ff);
Param param;
param.setValue("intensity_factor",0.01);
extender.setParameters(param);
input.updateRanges();
ff.run("none", input, features, Param(), FeatureMap<>());
ChargedIndexSet set;
// SimpleExtender starts at maximum point
set.insert( std::make_pair(15,15) );
ChargedIndexSet region;
extender.extend(set,region);
ifstream infile( OPENMS_GET_TEST_DATA_PATH("SimpleExtender_region1"));
DoubleReal intensity, rt, mz;
ChargedIndexSet::const_iterator citer = region.begin();
while ( infile >> rt )
{
infile >> mz >> intensity;
TEST_NOT_EQUAL(citer == region.end(),true)
TEST_REAL_SIMILAR(extender.getPeakRt(*citer),rt)
TEST_REAL_SIMILAR(extender.getPeakMz(*citer),mz)
TEST_REAL_SIMILAR(extender.getPeakIntensity(*citer),intensity)
++citer;
}
infile.close();
TEST_EQUAL(citer == region.end(),true)
}
END_SECTION
TOLERANCE_ABSOLUTE(0.01)
START_SECTION(([EXTRA] Extension on picked data))
{
MSExperiment<PeakType> input;
FeatureMap<FeatureType> features;
FeatureFinder ff;
ExtenderType extender(&input, &features, &ff);
MzDataFile().load(OPENMS_GET_TEST_DATA_PATH("SimpleExtender_test2.mzData"),input);
input.updateRanges();
ff.run("none", input, features, Param(), FeatureMap<>());
ChargedIndexSet set;
// SimpleExtender starts at maximum point
set.insert( std::make_pair(2,42) );
ChargedIndexSet region;
extender.extend(set,region);
ifstream infile( OPENMS_GET_TEST_DATA_PATH("SimpleExtender_region2"));
DoubleReal intensity, rt, mz;
ChargedIndexSet::const_iterator citer = region.begin();
while ( infile >> rt )
{
infile >> mz >> intensity;
TEST_NOT_EQUAL(citer == region.end(),true)
TEST_REAL_SIMILAR(extender.getPeakRt(*citer),rt)
TEST_REAL_SIMILAR(extender.getPeakMz(*citer),mz)
{
TOLERANCE_ABSOLUTE(1000) // lower (absolute) precision for high intensities
TEST_REAL_SIMILAR(extender.getPeakIntensity(*citer),intensity)
}
++citer;
}
infile.close();
TEST_EQUAL(citer == region.end(),true)
}
END_SECTION
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
END_TEST
|
