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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: Marc Sturm, Clemens Groepl $
// --------------------------------------------------------------------------
#include <OpenMS/CONCEPT/ClassTest.h>
///////////////////////////
#include <OpenMS/ANALYSIS/MAPMATCHING/FeatureGroupingAlgorithm.h>
///////////////////////////
#include <OpenMS/ANALYSIS/MAPMATCHING/FeatureGroupingAlgorithmLabeled.h>
#include <OpenMS/ANALYSIS/MAPMATCHING/FeatureGroupingAlgorithmUnlabeled.h>
#include <OpenMS/ANALYSIS/MAPMATCHING/FeatureGroupingAlgorithmIdentification.h>
using namespace OpenMS;
using namespace std;
namespace OpenMS
{
class FGA
: public FeatureGroupingAlgorithm
{
public:
void group(const vector< FeatureMap<> >&, ConsensusMap& map)
{
map.getFileDescriptions()[0].filename = "bla";
map.getFileDescriptions()[0].size = 5;
}
};
}
START_TEST(FeatureGroupingAlgorithm, "$Id FeatureFinder_test.C 139 2006-07-14 10:08:39Z ole_st $")
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
FGA* ptr = 0;
FGA* nullPointer = 0;
START_SECTION((FeatureGroupingAlgorithm()))
ptr = new FGA();
TEST_NOT_EQUAL(ptr, nullPointer)
END_SECTION
START_SECTION((virtual ~FeatureGroupingAlgorithm()))
delete ptr;
END_SECTION
START_SECTION((virtual void group(const vector< FeatureMap<> > &maps, ConsensusMap &out)=0))
FGA fga;
vector< FeatureMap<> > in;
ConsensusMap map;
fga.group(in,map);
TEST_EQUAL(map.getFileDescriptions()[0].filename, "bla")
END_SECTION
START_SECTION((static void registerChildren()))
{
TEST_STRING_EQUAL(Factory<FeatureGroupingAlgorithm>::registeredProducts()[0],FeatureGroupingAlgorithmLabeled::getProductName());
TEST_STRING_EQUAL(Factory<FeatureGroupingAlgorithm>::registeredProducts()[1],FeatureGroupingAlgorithmUnlabeled::getProductName());
TEST_EQUAL(Factory<FeatureGroupingAlgorithm>::registeredProducts().size(), 3)
}
END_SECTION
START_SECTION((void transferSubelements(const vector<ConsensusMap>& maps, ConsensusMap& out) const))
{
vector<ConsensusMap> maps(2);
maps[0].getFileDescriptions()[0].filename = "file1";
maps[0].getFileDescriptions()[0].size = 1;
maps[0].getFileDescriptions()[1].filename = "file2";
maps[0].getFileDescriptions()[1].size = 1;
maps[1].getFileDescriptions()[0].filename = "file3";
maps[1].getFileDescriptions()[0].size = 1;
maps[1].getFileDescriptions()[1].filename = "file4";
maps[1].getFileDescriptions()[1].size = 1;
Feature feat1, feat2, feat3, feat4;
FeatureHandle handle1(0, feat1), handle2(1, feat2), handle3(0, feat3),
handle4(1, feat4);
maps[0].resize(1);
maps[0][0].insert(handle1);
maps[0][0].insert(handle2);
maps[0][0].setUniqueId(1);
maps[1].resize(1);
maps[1][0].insert(handle3);
maps[1][0].insert(handle4);
maps[1][0].setUniqueId(2);
ConsensusMap out;
FeatureHandle handle5(0, static_cast<BaseFeature>(maps[0][0]));
FeatureHandle handle6(1, static_cast<BaseFeature>(maps[1][0]));
out.resize(1);
out[0].insert(handle5);
out[0].insert(handle6);
// need an instance of FeatureGroupingAlgorithm:
String algo_name = Factory<FeatureGroupingAlgorithm>::registeredProducts()[0];
FeatureGroupingAlgorithm* algo = Factory<FeatureGroupingAlgorithm>::create(
algo_name);
algo->transferSubelements(maps, out);
TEST_EQUAL(out.getFileDescriptions().size(), 4);
TEST_EQUAL(out.getFileDescriptions()[0].filename, "file1");
TEST_EQUAL(out.getFileDescriptions()[3].filename, "file4");
TEST_EQUAL(out.size(), 1);
TEST_EQUAL(out[0].size(), 4);
ConsensusFeature::HandleSetType group = out[0].getFeatures();
ConsensusFeature::HandleSetType::const_iterator it = group.begin();
handle3.setMapIndex(2);
handle4.setMapIndex(3);
TEST_EQUAL(*it++ == handle1, true);
TEST_EQUAL(*it++ == handle2, true);
TEST_EQUAL(*it++ == handle3, true);
TEST_EQUAL(*it++ == handle4, true);
}
END_SECTION
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
END_TEST
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