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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: Chris Bielow $
// --------------------------------------------------------------------------
#include <OpenMS/CONCEPT/ClassTest.h>
///////////////////////////
#include <OpenMS/ANALYSIS/DECHARGING/FeatureDeconvolution.h>
#include <OpenMS/KERNEL/FeatureMap.h>
#include <OpenMS/FORMAT/FeatureXMLFile.h>
#include <OpenMS/FORMAT/ConsensusXMLFile.h>
#include <OpenMS/CONCEPT/FuzzyStringComparator.h>
///////////////////////////
namespace OpenMS
{
class FeatureDeconvolutionTest
: public FeatureDeconvolution
{
public:
/// List of adducts used to explain mass differences
MassExplainer::AdductsType getPotentialAdducts()
{ return potential_adducts_;}
/// labeling table
Map<Size, String> getMapLabels()
{ return map_label_;}
/// labeling table inverse
Map<String, Size> getMapLabelInverse()
{ return map_label_inverse_;}
/// status of intensity filter for edges
bool isIntensityFilterEnabled()
{ return enable_intensity_filter_;}
/// status of charge discovery
CHARGEMODE getChargeMode()
{ return q_try_;}
};
}
using namespace OpenMS;
using namespace std;
START_TEST(FeatureDeconvolution, "$Id: FeatureDeconvolution_test.C 10915 2013-04-04 20:14:57Z aiche $")
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
FeatureDeconvolution* ptr = 0;
FeatureDeconvolution* nullPointer = 0;
START_SECTION(FeatureDeconvolution())
ptr = new FeatureDeconvolution();
TEST_NOT_EQUAL(ptr, nullPointer)
END_SECTION
START_SECTION(~FeatureDeconvolution())
delete ptr;
END_SECTION
START_SECTION([EXTRA](void updateMembers_()))
FeatureDeconvolutionTest fdt;
Param p;
p.setValue("charge_min", 11, "minimal possible charge");
p.setValue("charge_max", 13, "maximal possible charge");
p.setValue("retention_max_diff", 1.0, "maximum allowed RT difference between any two features if their relation shall be determined");
p.setValue("retention_max_diff_local", 2.0, "maxi");
p.setValue("potential_adducts", StringList::create("H+:0.7,Na+:0.1,(2)H4H-4:0.1:-2:heavy"), "Ad");
fdt.setParameters(p);
{
MassExplainer::AdductsType adducts = fdt.getPotentialAdducts();
Map<Size, String> map = fdt.getMapLabels();
Map<String, Size> map_i = fdt.getMapLabelInverse();
bool b_filter = fdt.isIntensityFilterEnabled();
FeatureDeconvolution::CHARGEMODE cm = fdt.getChargeMode();
TEST_EQUAL(adducts.size(), 3)
TEST_EQUAL(adducts[0].getFormula(), "H1");
TEST_EQUAL(adducts[0].getRTShift(), 0);
TEST_EQUAL(adducts[0].getCharge(), 1);
TEST_REAL_SIMILAR(adducts[0].getLogProb(), log(0.7));
TEST_EQUAL(adducts[1].getFormula(), "Na1");
TEST_EQUAL(adducts[1].getRTShift(), 0);
TEST_EQUAL(adducts[1].getCharge(), 1);
TEST_REAL_SIMILAR(adducts[1].getLogProb(), log(0.1));
TEST_EQUAL(adducts[2].getFormula(), "(2)H4H-4");
TEST_EQUAL(adducts[2].getRTShift(), -2);
TEST_EQUAL(adducts[2].getCharge(), 0);
TEST_REAL_SIMILAR(adducts[2].getLogProb(), log(0.1));
TEST_EQUAL(cm, FeatureDeconvolution::QFROMFEATURE)
TEST_EQUAL(map.size(), 2)
TEST_EQUAL(map_i.size(), 2)
TEST_EQUAL(map[0], "decharged features");
TEST_EQUAL(map_i["decharged features"], 0);
TEST_EQUAL(map[1], "heavy");
TEST_EQUAL(map_i["heavy"], 1);
TEST_EQUAL(b_filter, false)
Param p_internal = fdt.getParameters();
TEST_REAL_SIMILAR((DoubleReal) p_internal.getValue("retention_max_diff"), 1.0);
TEST_REAL_SIMILAR((DoubleReal) p_internal.getValue("retention_max_diff_local"), 1.0);
}
// second param set
p.setValue("charge_min", 11, "minimal possible charge");
p.setValue("charge_max", 13, "maximal possible charge");
p.setValue("q_try", "heuristic", "Try dif");
p.setValue("potential_adducts", StringList::create("H+:0.9,Na++:0.1"));
p.setValue("retention_max_diff", 1.0, "maximum ");
p.setValue("retention_max_diff_local", 1.0, "maxim");
p.setValue("intensity_filter", "true", "Enable");
p.setValue("default_map_label", "mylabel", "Label");
p.setValue("retention_max_diff", 2.0, "maximum allowed RT difference between any two features if their relation shall be determined");
p.setValue("retention_max_diff_local", 5.0, "maxi");
fdt.setParameters(p);
{
MassExplainer::AdductsType adducts = fdt.getPotentialAdducts();
Map<Size, String> map = fdt.getMapLabels();
Map<String, Size> map_i = fdt.getMapLabelInverse();
bool b_filter = fdt.isIntensityFilterEnabled();
FeatureDeconvolution::CHARGEMODE cm = fdt.getChargeMode();
TEST_EQUAL(adducts.size(), 2)
TEST_EQUAL(adducts[0].getFormula(), "H1");
TEST_EQUAL(adducts[0].getRTShift(), 0);
TEST_EQUAL(adducts[0].getCharge(), 1);
TEST_REAL_SIMILAR(adducts[0].getLogProb(), log(0.9));
TEST_EQUAL(adducts[1].getFormula(), "Na1");
TEST_EQUAL(adducts[1].getRTShift(), 0);
TEST_EQUAL(adducts[1].getCharge(), 2);
TEST_REAL_SIMILAR(adducts[1].getLogProb(), log(0.1));
TEST_EQUAL(cm, FeatureDeconvolution::QHEURISTIC)
TEST_EQUAL(map.size(), 1)
TEST_EQUAL(map_i.size(), 1)
TEST_EQUAL(map[0], "mylabel");
TEST_EQUAL(map_i["mylabel"], 0);
TEST_EQUAL(b_filter, true)
Param p_internal = fdt.getParameters();
TEST_REAL_SIMILAR((DoubleReal) p_internal.getValue("retention_max_diff"), 2.0);
TEST_REAL_SIMILAR((DoubleReal) p_internal.getValue("retention_max_diff_local"), 2.0);
}
END_SECTION
START_SECTION(FeatureDeconvolution(const FeatureDeconvolution &source))
FeatureDeconvolution fd;
Param p;
p.setValue("charge_min", 11, "minimal possible charge");
p.setValue("charge_max", 13, "maximal possible charge");
fd.setParameters(p);
FeatureDeconvolution fd2(fd);
FeatureDeconvolution fd_untouched;
TEST_EQUAL(fd2.getParameters(), fd.getParameters())
TEST_NOT_EQUAL(fd2.getParameters(), fd_untouched.getParameters())
END_SECTION
START_SECTION(FeatureDeconvolution& operator=(const FeatureDeconvolution &source))
FeatureDeconvolution fd;
Param p;
p.setValue("charge_min", 11, "minimal possible charge");
p.setValue("charge_max", 13, "maximal possible charge");
fd.setParameters(p);
FeatureDeconvolution fd2 = fd;
FeatureDeconvolution fd_untouched;
TEST_EQUAL(fd2.getParameters(), fd.getParameters())
TEST_NOT_EQUAL(fd2.getParameters(), fd_untouched.getParameters())
END_SECTION
START_SECTION(void compute(const FeatureMapType &fm_in, FeatureMapType &fm_out, ConsensusMap &cons_map, ConsensusMap &cons_map_p))
//_CrtSetDbgFlag(_CrtSetDbgFlag(0)|_CRTDBG_CHECK_ALWAYS_DF);
FeatureDeconvolution fd;
Param p;
p.setValue("potential_adducts", StringList::create("H+:0.7,Na+:0.1,(2)H4H-4:0.1:-2:heavy"), "Ad");
p.setValue("mass_max_diff", 0.1);
fd.setParameters(p);
FeatureMap<> fm_in, fm_out;
ConsensusMap cm, cm2;
FeatureXMLFile fl;
fl.load(OPENMS_GET_TEST_DATA_PATH("FeatureDeconvolution_easy_input.featureXML"), fm_in);
fd.compute(fm_in, fm_out, cm, cm2);
String out_file;
NEW_TMP_FILE(out_file)
ConsensusXMLFile c1;
c1.store(out_file,cm);
WHITELIST("xml-stylesheet");
// WHITELIST("xml-stylesheet,consensusElement id=");
// WHITELIST("xml-stylesheet,map id,consensusElement id=");
TEST_FILE_SIMILAR(out_file, OPENMS_GET_TEST_DATA_PATH("FeatureDeconvolution_easy_output.consensusXML"));
END_SECTION
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
END_TEST
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