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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 $
// $Authors: Chris Bielow $
// --------------------------------------------------------------------------
#include <OpenMS/CONCEPT/ClassTest.h>
///////////////////////////
#include <OpenMS/DATASTRUCTURES/Compomer.h>
#include <OpenMS/DATASTRUCTURES/Adduct.h>
#include <OpenMS/CHEMISTRY/EmpiricalFormula.h>
using namespace OpenMS;
using namespace std;
START_TEST(Compomer, "$Id: Compomer_test.C 10915 2013-04-04 20:14:57Z aiche $")
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
Compomer* ptr = 0;
Compomer* nullPointer = 0;
START_SECTION(Compomer())
{
ptr = new Compomer();
TEST_NOT_EQUAL(ptr, nullPointer)
}
END_SECTION
START_SECTION(~Compomer())
{
delete ptr;
}
END_SECTION
START_SECTION((Compomer(Int net_charge, DoubleReal mass, DoubleReal log_p)))
{
Compomer c(34, 45.32f, 12.34f);
TEST_EQUAL(c.getNetCharge(), 34);
TEST_REAL_SIMILAR(c.getMass(), 45.32);
TEST_REAL_SIMILAR(c.getLogP(), 12.34);
}
END_SECTION
START_SECTION((Compomer(const Compomer& p) ))
{
Compomer c(34, 45.32f, 12.34f);
Adduct a1(123, 3, 123.456f, "S", -0.3453f, 0);
Adduct b1(3, -2, 1.456f, "H", -0.13f, 0);
c.setID(434);
c.add(a1, Compomer::RIGHT);
c.add(b1, Compomer::LEFT);
Compomer c2(c);
TEST_EQUAL(c2.getNetCharge(), c.getNetCharge());
TEST_REAL_SIMILAR(c2.getMass(), c.getMass());
TEST_EQUAL(c2.getPositiveCharges(), c.getPositiveCharges());
TEST_EQUAL(c2.getNegativeCharges(), c.getNegativeCharges());
TEST_REAL_SIMILAR(c2.getLogP(), c.getLogP());
TEST_EQUAL(c2.getID(), c.getID());
}
END_SECTION
START_SECTION((Compomer& operator=(const Compomer &source)))
{
Compomer c(34, 45.32f, 12.34f);
Adduct a1(123, 3, 123.456f, "S", -0.3453f, 0);
Adduct b1(3, -2, 1.456f, "H", -0.13f, 0);
c.setID(434);
c.add(a1, Compomer::RIGHT);
c.add(b1, Compomer::LEFT);
Compomer c2 = c;
TEST_EQUAL(c2.getNetCharge(), c.getNetCharge());
TEST_REAL_SIMILAR(c2.getMass(), c.getMass());
TEST_EQUAL(c2.getPositiveCharges(), c.getPositiveCharges());
TEST_EQUAL(c2.getNegativeCharges(), c.getNegativeCharges());
TEST_REAL_SIMILAR(c2.getLogP(), c.getLogP());
TEST_EQUAL(c2.getID(), c.getID());
}
END_SECTION
START_SECTION([EXTRA] friend OPENMS_DLLAPI bool operator==(const Compomer& a, const Compomer& b))
{
Compomer c(34, 45.32f, 12.34f);
Adduct a1(123, 3, 123.456f, "S", -0.3453f, 0);
Adduct b1(3, -2, 1.456f, "H", -0.13f, 0);
c.setID(434);
c.add(a1, Compomer::RIGHT);
Compomer c2(c);
TEST_EQUAL(c==c2, true);
c.setID(2);
TEST_EQUAL(c==c2, false);
}
END_SECTION
START_SECTION((void add(const Adduct &a, UInt side)))
{
//Adduct(Int charge, Int amount, DoubleReal singleMass, String formula, DoubleReal log_prob
Adduct a1(123, 43, 123.456f, "S", -0.3453f, 0);
Adduct a2(123, 3, 123.456f, "S", -0.3453f, 0);
Adduct b1(3, -2, 1.456f, "H", -0.13f, 0);
Compomer c;
c.add(a1, Compomer::RIGHT);
//PRECISION(0.0001);
TEST_EQUAL(c.getNetCharge(), 123*43);
TEST_REAL_SIMILAR(c.getMass(), 123.456*43);
TEST_REAL_SIMILAR(c.getLogP(), -0.3453*43);
TEST_EQUAL(c.getPositiveCharges(), 123*43);
TEST_EQUAL(c.getNegativeCharges(), 0);
c.add(a2, Compomer::RIGHT);
TEST_EQUAL(c.getNetCharge(), 123*46);
TEST_REAL_SIMILAR(c.getMass(), 123.456*46);
TEST_REAL_SIMILAR(c.getLogP(), -0.3453*46);
TEST_EQUAL(c.getPositiveCharges(), 123*46);
TEST_EQUAL(c.getNegativeCharges(), 0);
c.add(b1, Compomer::RIGHT);
TEST_EQUAL(c.getNetCharge(), 123*46+ 3*(-2));
TEST_REAL_SIMILAR(c.getMass(), 123.456*46 - 2*1.456);
TEST_REAL_SIMILAR(c.getLogP(), -0.3453*46 -0.13*2);
TEST_EQUAL(c.getPositiveCharges(), 123*46);
TEST_EQUAL(c.getNegativeCharges(), 6);
}
END_SECTION
START_SECTION(bool isConflicting(const Compomer &cmp, UInt side_this, UInt side_other) const)
{
EmpiricalFormula ef("H");
Adduct default_adduct(1, 1, ef.getMonoWeight(), ef.getString(), log(0.7f), 0);
{
Adduct a1(1, 1, 1.007f, "H1", -0.13f, 0);
Adduct a2(1, 2, 123.456f, "NH4", -0.3453f, 0);
Compomer c,d;
c.add(a1, Compomer::RIGHT);
d.add(a1, Compomer::RIGHT);
TEST_EQUAL(c.isConflicting(d,Compomer::RIGHT,Compomer::RIGHT), false);
TEST_EQUAL(c.isConflicting(d,Compomer::LEFT,Compomer::RIGHT), true);
TEST_EQUAL(c.isConflicting(d,Compomer::RIGHT,Compomer::LEFT), true);
// this should not change the result
c.add(a1, Compomer::RIGHT);
d.add(a1, Compomer::RIGHT);
TEST_EQUAL(c.isConflicting(d,Compomer::RIGHT,Compomer::RIGHT), false);
TEST_EQUAL(c.isConflicting(d,Compomer::LEFT,Compomer::RIGHT), true);
TEST_EQUAL(c.isConflicting(d,Compomer::RIGHT,Compomer::LEFT), true);
// this neither
c.add(a2, Compomer::LEFT);
TEST_EQUAL(c.isConflicting(d,Compomer::RIGHT,Compomer::RIGHT), false);
TEST_EQUAL(c.isConflicting(d,Compomer::LEFT,Compomer::RIGHT), true);
TEST_EQUAL(c.isConflicting(d,Compomer::RIGHT,Compomer::LEFT), true);
}
{
Adduct a1(1, -2, 123.456f, "NH4", -0.3453f, 0);
Adduct a2(1, 1, 1.007f, "H1", -0.13f, 0);
Adduct b1(1, 2, 1.007f, "H1", -0.13f, 0);
Compomer c,d;
c.add(a1, Compomer::RIGHT);
c.add(a2, Compomer::RIGHT);
d.add(b1, Compomer::RIGHT);
TEST_EQUAL(c.isConflicting(d,Compomer::RIGHT,Compomer::RIGHT), true);
TEST_EQUAL(c.isConflicting(d,Compomer::RIGHT,Compomer::LEFT), true);
TEST_EQUAL(c.isConflicting(d,Compomer::LEFT,Compomer::RIGHT), true);
TEST_EQUAL(c.isConflicting(d,Compomer::LEFT,Compomer::LEFT), false);
}
{
Adduct a1(1, 3, 123.456f, "NH4", -0.3453f, 0);
Adduct a2(1, 3, 1.007f, "H1", -0.13f, 0);
Compomer c,d;
c.add(a1, Compomer::RIGHT);
d.add(a1, Compomer::LEFT);
TEST_EQUAL(c.isConflicting(d,Compomer::RIGHT,Compomer::LEFT), false);
TEST_EQUAL(c.isConflicting(d,Compomer::RIGHT,Compomer::RIGHT), true);
TEST_EQUAL(c.isConflicting(d,Compomer::LEFT,Compomer::RIGHT), false);
TEST_EQUAL(c.isConflicting(d,Compomer::LEFT,Compomer::LEFT), true);
c.add(a1, Compomer::LEFT);
c.add(a2, Compomer::RIGHT);
d.add(a1, Compomer::LEFT);
d.add(a2, Compomer::RIGHT);
// C D
//a1 a1a2 ; a1a1 a2
TEST_EQUAL(c.isConflicting(d,Compomer::RIGHT,Compomer::LEFT), true);
TEST_EQUAL(c.isConflicting(d,Compomer::RIGHT,Compomer::RIGHT), true);
TEST_EQUAL(c.isConflicting(d,Compomer::LEFT,Compomer::RIGHT), true);
TEST_EQUAL(c.isConflicting(d,Compomer::LEFT,Compomer::LEFT), true);
c.add(a1, Compomer::RIGHT);
d.add(a2, Compomer::LEFT);
d.add(a1, Compomer::RIGHT);
d.add(a1, Compomer::RIGHT);
// C D
//a1 a1a2a1 ; a1a1a2 a2a1a1
TEST_EQUAL(c.isConflicting(d,Compomer::RIGHT,Compomer::LEFT), false);
TEST_EQUAL(c.isConflicting(d,Compomer::RIGHT,Compomer::RIGHT), false);
TEST_EQUAL(c.isConflicting(d,Compomer::LEFT,Compomer::RIGHT), true);
TEST_EQUAL(c.isConflicting(d,Compomer::LEFT,Compomer::LEFT), true);
}
}
END_SECTION
START_SECTION((void setID(const Size &id)))
{
NOT_TESTABLE //well.. tested below...
}
END_SECTION
START_SECTION((const Size& getID() const))
{
Compomer c;
c.setID(123);
TEST_EQUAL(c.getID(), 123)
}
END_SECTION
START_SECTION((const Int& getNetCharge() const))
{
Compomer c(-123,1.23,-0.12);
TEST_EQUAL(c.getNetCharge(), -123)
}
END_SECTION
START_SECTION((const DoubleReal& getMass() const))
{
Compomer c(1,-123.12, 0.23);
TEST_REAL_SIMILAR(c.getMass(), -123.12)
}
END_SECTION
START_SECTION((const Int& getPositiveCharges() const))
{
Compomer c;
Adduct a1(3, -2, 123.456f, "NH4", -0.3453f, 0);
Adduct a2(6, 1, 1.007f, "H1", -0.13f, 0);
c.add(a1, Compomer::RIGHT);
c.add(a2, Compomer::RIGHT);
TEST_EQUAL(c.getPositiveCharges(), 6)
}
END_SECTION
START_SECTION((const Int& getNegativeCharges() const))
{
Compomer c;
Adduct a1(3, -2, 123.456f, "NH4", -0.3453f, 0);
Adduct a2(6, 1, 1.007f, "H1", -0.13f, 0);
c.add(a1, Compomer::RIGHT);
c.add(a2, Compomer::RIGHT);
TEST_EQUAL(c.getNegativeCharges(), 6)
}
END_SECTION
START_SECTION((const DoubleReal& getLogP() const))
{
Compomer c(1,1,-123.12);
TEST_REAL_SIMILAR(c.getLogP(), -123.12)
}
END_SECTION
START_SECTION((const DoubleReal& getRTShift() const))
{
Compomer c(1,1,-123.12);
Adduct a(123, 43, 123.456f, "S", -0.3453, -10.12);
c.add(a,0);
TEST_REAL_SIMILAR(c.getRTShift(), 435.16)
}
END_SECTION
START_SECTION((StringList getLabels(const UInt side) const))
{
Compomer c(1,1,-123.12);
TEST_EQUAL(c.getLabels(0).size(), 0)
Adduct a(123, 43, 123.456f, "S", -0.3453, -10.12, "testlabel");
c.add(a,0);
TEST_EQUAL(c.getLabels(0).size(), 1)
TEST_EQUAL(c.getLabels(1).size(), 0)
}
END_SECTION
START_SECTION((String getAdductsAsString() const))
{
Adduct a1(1, 2, 123.456f, "NH4", -0.3453f, 0);
Adduct a2(1, -1, 1.007f, "H1", -0.13f, 0);
Compomer c;
c.add(a1, Compomer::RIGHT);
c.add(a2, Compomer::RIGHT);
TEST_EQUAL(c.getAdductsAsString(), "() --> (H-1H8N2)");
c.add(a1, Compomer::LEFT);
TEST_EQUAL(c.getAdductsAsString(), "(H8N2) --> (H-1H8N2)");
}
END_SECTION
START_SECTION((String getAdductsAsString(UInt side) const))
{
Adduct a1(1, 2, 123.456f, "NH4", -0.3453f, 0);
Adduct a2(1, -1, 1.007f, "H1", -0.13f, 0);
Compomer c;
c.add(a1, Compomer::RIGHT);
c.add(a2, Compomer::RIGHT);
TEST_EQUAL(c.getAdductsAsString(Compomer::LEFT), "");
TEST_EQUAL(c.getAdductsAsString(Compomer::RIGHT), "H-1H8N2");
c.add(a1, Compomer::LEFT);
TEST_EQUAL(c.getAdductsAsString(Compomer::LEFT), "H8N2");
TEST_EQUAL(c.getAdductsAsString(Compomer::RIGHT), "H-1H8N2");
}
END_SECTION
START_SECTION((const CompomerComponents& getComponent() const))
{
Adduct a1(1, 2, 123.456f, "NH4", -0.3453f, 0);
Adduct a2(1, -1, 1.007f, "H1", -0.13f, 0);
Compomer c;
Compomer::CompomerComponents comp(2);
TEST_EQUAL(c.getComponent()==comp, true);
c.add(a1, Compomer::RIGHT);
c.add(a2, Compomer::RIGHT);
c.add(a1, Compomer::LEFT);
comp[Compomer::RIGHT][a1.getFormula()] = a1;
comp[Compomer::RIGHT][a2.getFormula()] = a2;
comp[Compomer::LEFT][a1.getFormula()] = a1;
TEST_EQUAL(c.getComponent()==comp, true);
}
END_SECTION
START_SECTION((Compomer removeAdduct(const Adduct& a) const))
{
Adduct a1(1, 2, 123.456f, "NH4", -0.3453f, 0);
Adduct a2(1, -1, 1.007f, "H1", -0.13f, 0);
Compomer c;
c.add(a1, Compomer::RIGHT);
c.add(a2, Compomer::RIGHT);
c.add(a1, Compomer::LEFT);
Compomer tmp = c.removeAdduct(a1);
TEST_EQUAL(tmp.getAdductsAsString(), "() --> (H-1)");
}
END_SECTION
START_SECTION((Compomer removeAdduct(const Adduct& a, const UInt side) const))
{
Adduct a1(1, 2, 123.456f, "NH4", -0.3453f, 0);
Adduct a2(1, -1, 1.007f, "H1", -0.13f, 0);
Compomer c;
c.add(a1, Compomer::RIGHT);
c.add(a2, Compomer::RIGHT);
c.add(a1, Compomer::LEFT);
Compomer tmp = c.removeAdduct(a1, Compomer::RIGHT);
TEST_EQUAL(tmp.getAdductsAsString(), "(H8N2) --> (H-1)");
tmp = c.removeAdduct(a1, Compomer::LEFT);
TEST_EQUAL(tmp.getAdductsAsString(), "() --> (H-1H8N2)");
}
END_SECTION
START_SECTION((void add(const CompomerSide& add_side, UInt side)))
{
Adduct a1(1, 2, 123.456f, "NH4", -0.3453f, 0);
Adduct a2(1, -1, 1.007f, "H1", -0.13f, 0);
Compomer c;
c.add(a1, Compomer::RIGHT);
c.add(a2, Compomer::RIGHT);
c.add(a1, Compomer::LEFT);
TEST_EQUAL(c.getAdductsAsString(), "(H8N2) --> (H-1H8N2)");
Compomer tmp = c;
tmp.add(c.getComponent()[Compomer::RIGHT], Compomer::RIGHT);
TEST_EQUAL(tmp.getAdductsAsString(), "(H8N2) --> (H-2H16N4)");
tmp.add(c.getComponent()[Compomer::RIGHT], Compomer::LEFT);
TEST_EQUAL(tmp.getAdductsAsString(), "(H-1H16N4) --> (H-2H16N4)");
}
END_SECTION
START_SECTION((bool isSingleAdduct(Adduct &a, const UInt side) const))
Adduct a1(1, 2, 123.456f, "NH4", -0.3453f, 0);
Adduct a2(1, -1, 1.007f, "H1", -0.13f, 0);
Compomer c;
c.add(a1, Compomer::RIGHT);
c.add(a2, Compomer::RIGHT);
c.add(a1, Compomer::LEFT);
TEST_EQUAL(c.isSingleAdduct(a1,Compomer::LEFT), true);
TEST_EQUAL(c.isSingleAdduct(a2,Compomer::LEFT), false);
TEST_EQUAL(c.isSingleAdduct(a1,Compomer::RIGHT), false);
TEST_EQUAL(c.isSingleAdduct(a2,Compomer::RIGHT), false);
END_SECTION
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
END_TEST
|
