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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, Andreas Bertsch $
// $Authors: Clemens Groepl, Andreas Bertsch $
// --------------------------------------------------------------------------
//
///////////////////////////
// This one is going to be tested.
#include <OpenMS/CHEMISTRY/IsotopeDistribution.h>
///////////////////////////
// More headers
#include <iostream>
#include <iterator>
#include <utility>
#include <OpenMS/CHEMISTRY/EmpiricalFormula.h>
#include <OpenMS/CONCEPT/ClassTest.h>
/////////////////////////////////////////////////////////////
START_TEST(IsotopeDistribution, "$Id: IsotopeDistribution_test.C 10915 2013-04-04 20:14:57Z aiche $")
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
using namespace OpenMS;
using namespace std;
IsotopeDistribution* nullPointer = 0;
START_SECTION(IsotopeDistribution())
IsotopeDistribution* ptr = 0;
ptr = new IsotopeDistribution();
Size max_isotope = ptr->getMaxIsotope();
TEST_EQUAL(max_isotope, 0)
TEST_NOT_EQUAL(ptr, nullPointer)
delete ptr;
END_SECTION
START_SECTION(IsotopeDistribution(Size max_isotope))
IsotopeDistribution* ptr = new IsotopeDistribution(117);
Size max_isotope = ptr->getMaxIsotope();
TEST_EQUAL(max_isotope, 117)
TEST_NOT_EQUAL(ptr, nullPointer)
delete ptr;
END_SECTION
IsotopeDistribution* iso = new IsotopeDistribution();
START_SECTION(IsotopeDistribution(const IsotopeDistribution& isotope_distribution))
IsotopeDistribution copy;
copy = *iso;
for (Size i = 0; i != copy.getContainer().size(); ++i)
{
TEST_EQUAL(copy.getContainer()[i].first, iso->getContainer()[i].first)
TEST_EQUAL(copy.getContainer()[i].second, iso->getContainer()[i].second)
}
TEST_EQUAL(copy.getMin(), iso->getMin())
TEST_EQUAL(copy.getMax(), iso->getMax())
TEST_EQUAL(copy.size(), iso->size())
TEST_EQUAL(copy.getMaxIsotope(), iso->getMaxIsotope())
END_SECTION
START_SECTION(~IsotopeDistribution())
IsotopeDistribution* ptr = new IsotopeDistribution(117);
delete ptr;
END_SECTION
START_SECTION(IsotopeDistribution& operator = (const IsotopeDistribution& isotope_distribution))
IsotopeDistribution copy;
copy = *iso;
for (Size i = 0; i != copy.getContainer().size(); ++i)
{
TEST_EQUAL(copy.getContainer()[i].first, iso->getContainer()[i].first)
TEST_EQUAL(copy.getContainer()[i].second, iso->getContainer()[i].second)
}
TEST_EQUAL(copy.getMin(), iso->getMin())
TEST_EQUAL(copy.getMax(), iso->getMax())
TEST_EQUAL(copy.size(), iso->size())
TEST_EQUAL(copy.getMaxIsotope(), iso->getMaxIsotope())
END_SECTION
START_SECTION(void setMaxIsotope(Size max_isotope))
IsotopeDistribution iso2;
iso2.estimateFromPeptideWeight(1234.2);
TEST_EQUAL(iso->getMaxIsotope(), 0)
TEST_EQUAL(iso2.getContainer().size(), 275)
iso->setMaxIsotope(117);
TEST_EQUAL(iso->getMaxIsotope(), 117)
END_SECTION
START_SECTION(Size getMaxIsotope() const)
NOT_TESTABLE
END_SECTION
START_SECTION(IsotopeDistribution operator + (const IsotopeDistribution& isotope_distribution) const)
IsotopeDistribution iso1(1), iso2(1);
IsotopeDistribution result = iso1 + iso2;
TEST_EQUAL(result.size(), 1)
IsotopeDistribution::ContainerType container = result.getContainer();
TEST_EQUAL(container[0].first, 0)
TEST_EQUAL(container[0].second, 1)
END_SECTION
START_SECTION(IsotopeDistribution& operator *= (Size factor))
EmpiricalFormula ef("C222N190O110");
IsotopeDistribution id = ef.getIsotopeDistribution(11);
IsotopeDistribution::ContainerType container;
container.push_back(make_pair<Size, double>(7084, 0.0349429));
container.push_back(make_pair<Size, double>(7085, 0.109888));
container.push_back(make_pair<Size, double>(7086, 0.180185));
container.push_back(make_pair<Size, double>(7087, 0.204395));
container.push_back(make_pair<Size, double>(7088, 0.179765));
container.push_back(make_pair<Size, double>(7089, 0.130358));
container.push_back(make_pair<Size, double>(7090, 0.0809864));
container.push_back(make_pair<Size, double>(7091, 0.0442441));
container.push_back(make_pair<Size, double>(7092, 0.0216593));
container.push_back(make_pair<Size, double>(7093, 0.00963707));
container.push_back(make_pair<Size, double>(7094, 0.0039406));
for (Size i = 0; i != id.size(); ++i)
{
TEST_EQUAL(id.getContainer()[i].first, container[i].first)
TEST_REAL_SIMILAR(id.getContainer()[i].second, container[i].second)
}
END_SECTION
START_SECTION(bool operator==(const IsotopeDistribution &isotope_distribution) const)
IsotopeDistribution iso1(1);
IsotopeDistribution iso2(2);
TEST_EQUAL(iso1 == iso2, false)
iso2.setMaxIsotope(1);
TEST_EQUAL(iso1 == iso2, true)
IsotopeDistribution iso3(EmpiricalFormula("C4").getIsotopeDistribution(11)),
iso4(EmpiricalFormula("C4").getIsotopeDistribution(11));
TEST_EQUAL(iso3 == iso4, true)
END_SECTION
START_SECTION(void set(const ContainerType &distribution))
IsotopeDistribution iso1(EmpiricalFormula("C4").getIsotopeDistribution(11)), iso2;
TEST_EQUAL(iso1 == iso2, false)
IsotopeDistribution::ContainerType container = iso1.getContainer();
iso2.set(container);
TEST_EQUAL(iso1.getContainer() == iso2.getContainer(), true)
iso2.setMaxIsotope(iso1.getMaxIsotope());
TEST_EQUAL(iso1 == iso2, true)
END_SECTION
START_SECTION(const ContainerType& getContainer() const)
NOT_TESTABLE
END_SECTION
START_SECTION(Size getMax() const)
IsotopeDistribution iso(EmpiricalFormula("H2").getIsotopeDistribution(11));
TEST_EQUAL(iso.getMax(), 6)
END_SECTION
START_SECTION(Size getMin() const)
IsotopeDistribution iso(EmpiricalFormula("H2").getIsotopeDistribution(11));
TEST_EQUAL(iso.getMin(), 2)
IsotopeDistribution iso2(EmpiricalFormula("C4").getIsotopeDistribution(11));
TEST_EQUAL(iso2.getMin(), 48)
END_SECTION
START_SECTION(Size size() const)
IsotopeDistribution iso1, iso2(EmpiricalFormula("C4").getIsotopeDistribution(11));
TEST_EQUAL(iso1.size(), 1)
TEST_EQUAL(iso2.size(), 5)
END_SECTION
START_SECTION(void clear())
IsotopeDistribution iso2(EmpiricalFormula("C4").getIsotopeDistribution(11));
TEST_EQUAL(iso2.size(), 5)
iso2.clear();
TEST_EQUAL(iso2.size(), 0)
END_SECTION
START_SECTION(void estimateFromPeptideWeight(double average_weight))
// hard to test as this is an rough estimate
IsotopeDistribution iso(3);
iso.estimateFromPeptideWeight(100.0);
iso.renormalize();
TEST_REAL_SIMILAR(iso.begin()->second, 0.95137)
iso.estimateFromPeptideWeight(1000.0);
TEST_REAL_SIMILAR(iso.begin()->second, 0.572779)
iso.estimateFromPeptideWeight(10000.0);
TEST_REAL_SIMILAR(iso.begin()->second, 0.00291426)
END_SECTION
START_SECTION(void trimRight(DoubleReal cutoff))
IsotopeDistribution iso(EmpiricalFormula("C160").getIsotopeDistribution(10));
TEST_NOT_EQUAL(iso.size(),3)
iso.trimRight(0.2);
TEST_EQUAL(iso.size(),3)
END_SECTION
START_SECTION(void trimLeft(DoubleReal cutoff))
IsotopeDistribution iso(EmpiricalFormula("C160").getIsotopeDistribution(10));
iso.trimRight(0.2);
iso.trimLeft(0.2);
TEST_EQUAL(iso.size(),2)
END_SECTION
START_SECTION(void renormalize())
IsotopeDistribution iso(EmpiricalFormula("C160").getIsotopeDistribution(10));
iso.trimRight(0.2);
iso.trimLeft(0.2);
iso.renormalize();
double sum = 0;
for (IsotopeDistribution::ConstIterator it = iso.begin(); it != iso.end(); ++it)
{
sum += it->second;
}
TEST_REAL_SIMILAR(sum, 1.0)
END_SECTION
START_SECTION(IsotopeDistribution& operator+=(const IsotopeDistribution &isotope_distribution))
IsotopeDistribution iso1(EmpiricalFormula("H1").getIsotopeDistribution(11)),
iso2(EmpiricalFormula("H2").getIsotopeDistribution(11));
TEST_EQUAL(iso1 == iso2, false)
iso1 += IsotopeDistribution(EmpiricalFormula("H1").getIsotopeDistribution(11));
TEST_EQUAL(iso1.size() == iso2.size(), true)
IsotopeDistribution::ConstIterator it1(iso1.begin()), it2(iso2.begin());
for (; it1 != iso1.end(); ++it1, ++it2)
{
TEST_EQUAL(it1->first, it2->first)
TEST_REAL_SIMILAR(it2->second, it2->second)
}
END_SECTION
START_SECTION(IsotopeDistribution operator *(Size factor) const)
IsotopeDistribution iso1(EmpiricalFormula("H1").getIsotopeDistribution(11)),
iso2(EmpiricalFormula("H5").getIsotopeDistribution(11));
TEST_EQUAL(iso1 == iso2, false)
IsotopeDistribution iso3 = iso1 * 5;
iso3.renormalize();
iso2.renormalize();
TEST_EQUAL(iso2.size(), iso3.size())
IsotopeDistribution::ConstIterator it1(iso2.begin()), it2(iso3.begin());
for (; it1 != iso2.end(); ++it1, ++it2)
{
TEST_EQUAL(it1->first, it2->first)
TEST_REAL_SIMILAR(it1->second, it2->second)
}
END_SECTION
START_SECTION(bool operator!=(const IsotopeDistribution &isotope_distribution) const)
IsotopeDistribution iso1(1);
IsotopeDistribution iso2(2);
TEST_EQUAL(iso1 != iso2, true)
iso2.setMaxIsotope(1);
TEST_EQUAL(iso1 != iso2, false)
IsotopeDistribution iso3(EmpiricalFormula("C4").getIsotopeDistribution(11)),
iso4(EmpiricalFormula("C4").getIsotopeDistribution(11));
TEST_EQUAL(iso3 != iso4, false)
END_SECTION
START_SECTION(Iterator begin())
NOT_TESTABLE
END_SECTION
START_SECTION(Iterator end())
NOT_TESTABLE
END_SECTION
START_SECTION(ConstIterator begin() const)
NOT_TESTABLE
END_SECTION
START_SECTION(ConstIterator end() const)
NOT_TESTABLE
END_SECTION
delete iso;
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
END_TEST
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