// -------------------------------------------------------------------------- // 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: Andreas Bertsch $ // $Authors: Andreas Bertsch $ // -------------------------------------------------------------------------- // #include /////////////////////////// #include #include using namespace OpenMS; using namespace std; /////////////////////////// START_TEST(Residue, "$Id: ResidueModification_test.C 10915 2013-04-04 20:14:57Z aiche $") ///////////////////////////////////////////////////////////// // Modification tests ResidueModification* ptr = 0; ResidueModification* nullPointer = 0; START_SECTION(ResidueModification()) ptr = new ResidueModification(); TEST_NOT_EQUAL(ptr, nullPointer) END_SECTION START_SECTION(~ResidueModification()) delete ptr; END_SECTION ptr = new ResidueModification(); START_SECTION(ResidueModification(const ResidueModification& modification)) ResidueModification m(*ptr); TEST_EQUAL(m == *ptr, true) END_SECTION START_SECTION(ResidueModification& operator = (const ResidueModification& modification)) ResidueModification m; m = *ptr; TEST_EQUAL(m == *ptr, true) END_SECTION START_SECTION(void setId(const String &id)) ptr->setId("blubb_new_id"); TEST_STRING_EQUAL(ptr->getId(), "blubb_new_id") END_SECTION START_SECTION(const String& getId() const) NOT_TESTABLE END_SECTION START_SECTION(void setFullName(const String &full_name)) ptr->setFullName("blubb_new_full_name"); TEST_STRING_EQUAL(ptr->getFullName(), "blubb_new_full_name") END_SECTION START_SECTION(const String& getFullName() const) NOT_TESTABLE END_SECTION START_SECTION(void setName(const String &name)) ptr->setName("blubb_new_name"); TEST_STRING_EQUAL(ptr->getName(), "blubb_new_name") END_SECTION START_SECTION(const String& getName() const) NOT_TESTABLE END_SECTION START_SECTION((void setNeutralLossDiffFormula(const EmpiricalFormula& loss))) ptr->setNeutralLossDiffFormula(EmpiricalFormula("H2O2")); TEST_EQUAL(ptr->getNeutralLossDiffFormula() == EmpiricalFormula("H2O2"), true) END_SECTION START_SECTION(const EmpiricalFormula& getNeutralLossDiffFormula() const) NOT_TESTABLE END_SECTION START_SECTION(void setNeutralLossMonoMass(DoubleReal mono_mass)) ptr->setNeutralLossMonoMass(123.345678); TEST_REAL_SIMILAR(ptr->getNeutralLossMonoMass(), 123.345678); END_SECTION START_SECTION((DoubleReal getNeutralLossMonoMass() const)) NOT_TESTABLE END_SECTION START_SECTION((void setNeutralLossAverageMass(DoubleReal average_mass))) ptr->setNeutralLossAverageMass(23.345678); TEST_REAL_SIMILAR(ptr->getNeutralLossAverageMass(), 23.345678) END_SECTION START_SECTION(DoubleReal getNeutralLossAverageMass() const) NOT_TESTABLE END_SECTION START_SECTION((bool hasNeutralLoss() const)) TEST_EQUAL(ptr->hasNeutralLoss(), true) ResidueModification mod; TEST_EQUAL(mod.hasNeutralLoss(), false) mod.setNeutralLossDiffFormula(EmpiricalFormula("H2O")); TEST_EQUAL(mod.hasNeutralLoss(), true) END_SECTION START_SECTION((void setFullId(const String& full_id))) ptr->setFullId("blubb_new_fullid"); TEST_STRING_EQUAL(ptr->getFullId(), "blubb_new_fullid") END_SECTION START_SECTION((const String& getFullId() const)) NOT_TESTABLE END_SECTION START_SECTION((void setUniModAccession(const String &id))) ptr->setUniModAccession("blubb_new_UniModAccession"); TEST_STRING_EQUAL(ptr->getUniModAccession(), "blubb_new_UniModAccession") END_SECTION START_SECTION((const String& getUniModAccession() const)) NOT_TESTABLE END_SECTION START_SECTION((void setPSIMODAccession(const String& id))) ptr->setPSIMODAccession("blubb_new_PSIMODAccession"); TEST_STRING_EQUAL(ptr->getPSIMODAccession(), "blubb_new_PSIMODAccession") END_SECTION START_SECTION((const String& getPSIMODAccession() const)) NOT_TESTABLE END_SECTION START_SECTION(void setTermSpecificity(Term_Specificity term_spec)) ptr->setTermSpecificity(ResidueModification::ANYWHERE); TEST_EQUAL(ptr->getTermSpecificity(), ResidueModification::ANYWHERE) ptr->setTermSpecificity(ResidueModification::C_TERM); TEST_EQUAL(ptr->getTermSpecificity(), ResidueModification::C_TERM) ptr->setTermSpecificity(ResidueModification::N_TERM); TEST_EQUAL(ptr->getTermSpecificity(), ResidueModification::N_TERM) END_SECTION START_SECTION(void setTermSpecificity(const String &name)) ptr->setTermSpecificity("C-term"); TEST_EQUAL(ptr->getTermSpecificity(), ResidueModification::C_TERM) ptr->setTermSpecificity("N-term"); TEST_EQUAL(ptr->getTermSpecificity(), ResidueModification::N_TERM) ptr->setTermSpecificity("none"); TEST_EQUAL(ptr->getTermSpecificity(), ResidueModification::ANYWHERE) END_SECTION START_SECTION(Term_Specificity getTermSpecificity() const) NOT_TESTABLE END_SECTION START_SECTION(String getTermSpecificityName(Term_Specificity=NUMBER_OF_TERM_SPECIFICITY) const) ptr->setTermSpecificity(ResidueModification::C_TERM); TEST_STRING_EQUAL(ptr->getTermSpecificityName(), "C-term") ptr->setTermSpecificity(ResidueModification::N_TERM); TEST_STRING_EQUAL(ptr->getTermSpecificityName(), "N-term") ptr->setTermSpecificity(ResidueModification::ANYWHERE); TEST_STRING_EQUAL(ptr->getTermSpecificityName(), "none") TEST_STRING_EQUAL(ptr->getTermSpecificityName(ResidueModification::C_TERM), "C-term") TEST_STRING_EQUAL(ptr->getTermSpecificityName(ResidueModification::N_TERM), "N-term") TEST_STRING_EQUAL(ptr->getTermSpecificityName(ResidueModification::ANYWHERE), "none") END_SECTION START_SECTION(void setOrigin(const String &origin)) ptr->setOrigin("blubb_new_origin"); TEST_STRING_EQUAL(ptr->getOrigin(), "blubb_new_origin") END_SECTION START_SECTION(const String& getOrigin() const) NOT_TESTABLE END_SECTION START_SECTION(void setSourceClassification(Source_Classification classification)) ptr->setSourceClassification(ResidueModification::ARTIFACT); TEST_EQUAL(ptr->getSourceClassification(), ResidueModification::ARTIFACT) ptr->setSourceClassification(ResidueModification::NATURAL); TEST_EQUAL(ptr->getSourceClassification(), ResidueModification::NATURAL) ptr->setSourceClassification(ResidueModification::HYPOTHETICAL); TEST_EQUAL(ptr->getSourceClassification(), ResidueModification::HYPOTHETICAL) END_SECTION START_SECTION(void setSourceClassification(const String &classification)) ptr->setSourceClassification("Artifact"); TEST_EQUAL(ptr->getSourceClassification(), ResidueModification::ARTIFACT) ptr->setSourceClassification("Natural"); TEST_EQUAL(ptr->getSourceClassification(), ResidueModification::NATURAL) ptr->setSourceClassification("Hypothetical"); TEST_EQUAL(ptr->getSourceClassification(), ResidueModification::HYPOTHETICAL) END_SECTION START_SECTION(Source_Classification getSourceClassification() const) NOT_TESTABLE END_SECTION START_SECTION(String getSourceClassificationName(Source_Classification classification=NUMBER_OF_SOURCE_CLASSIFICATIONS) const) ptr->setSourceClassification(ResidueModification::ARTIFACT); TEST_STRING_EQUAL(ptr->getSourceClassificationName(), "Artefact") ptr->setSourceClassification(ResidueModification::NATURAL); TEST_STRING_EQUAL(ptr->getSourceClassificationName(), "Natural") ptr->setSourceClassification(ResidueModification::HYPOTHETICAL); TEST_STRING_EQUAL(ptr->getSourceClassificationName(), "Hypothetical") TEST_STRING_EQUAL(ptr->getSourceClassificationName(ResidueModification::ARTIFACT), "Artefact") TEST_STRING_EQUAL(ptr->getSourceClassificationName(ResidueModification::NATURAL), "Natural") TEST_STRING_EQUAL(ptr->getSourceClassificationName(ResidueModification::HYPOTHETICAL), "Hypothetical") END_SECTION START_SECTION(void setAverageMass(DoubleReal mass)) ptr->setAverageMass(2.0); TEST_REAL_SIMILAR(ptr->getAverageMass(), 2.0) END_SECTION START_SECTION(DoubleReal getAverageMass() const) NOT_TESTABLE END_SECTION START_SECTION(void setMonoMass(DoubleReal mass)) ptr->setMonoMass(3.0); TEST_REAL_SIMILAR(ptr->getMonoMass(), 3.0) END_SECTION START_SECTION(DoubleReal getMonoMass() const) NOT_TESTABLE END_SECTION START_SECTION(void setDiffAverageMass(DoubleReal mass)) ptr->setDiffAverageMass(4.0); TEST_REAL_SIMILAR(ptr->getDiffAverageMass(), 4.0) END_SECTION START_SECTION(DoubleReal getDiffAverageMass() const) NOT_TESTABLE END_SECTION START_SECTION(void setDiffMonoMass(DoubleReal mass)) ptr->setDiffMonoMass(5.0); TEST_REAL_SIMILAR(ptr->getDiffMonoMass(), 5.0) END_SECTION START_SECTION(DoubleReal getDiffMonoMass() const) NOT_TESTABLE END_SECTION START_SECTION(void setFormula(const String &composition)) ptr->setFormula("blubb_new_formula"); TEST_STRING_EQUAL(ptr->getFormula(), "blubb_new_formula") END_SECTION START_SECTION(const String& getFormula() const) NOT_TESTABLE END_SECTION START_SECTION(void setDiffFormula(const EmpiricalFormula& diff_formula)) EmpiricalFormula ef("C3H4S-3"); ptr->setDiffFormula(ef); TEST_EQUAL(ptr->getDiffFormula() == ef, true) END_SECTION START_SECTION(const EmpiricalFormula& getDiffFormula() const) NOT_TESTABLE END_SECTION START_SECTION(void setSynonyms(const std::set< String > &synonyms)) set synonyms; synonyms.insert("blubb_syn1"); synonyms.insert("blubb_syn2"); ptr->setSynonyms(synonyms); TEST_EQUAL(ptr->getSynonyms() == synonyms, true) END_SECTION START_SECTION(void addSynonym(const String &synonym)) ptr->addSynonym("blubb_syn3"); TEST_EQUAL(ptr->getSynonyms().size(), 3) END_SECTION START_SECTION(const std::set& getSynonyms() const) NOT_TESTABLE END_SECTION START_SECTION(bool operator==(const ResidueModification &modification) const) ResidueModification mod1, mod2; mod1.setId("Id"); TEST_EQUAL(mod1 == mod2, false) mod2.setId("Id"); TEST_EQUAL(mod1 == mod2, true) mod1.setFullName("FullName"); TEST_EQUAL(mod1 == mod2, false) mod2.setFullName("FullName"); TEST_EQUAL(mod1 == mod2, true) mod1.setName("Name"); TEST_EQUAL(mod1 == mod2, false) mod2.setName("Name"); TEST_EQUAL(mod1 == mod2, true) mod1.setTermSpecificity(ResidueModification::N_TERM); TEST_EQUAL(mod1 == mod2, false) mod2.setTermSpecificity(ResidueModification::N_TERM); TEST_EQUAL(mod1 == mod2, true) mod1.setOrigin("C"); TEST_EQUAL(mod1 == mod2, false) mod2.setOrigin("C"); TEST_EQUAL(mod1 == mod2, true) mod1.setSourceClassification(ResidueModification::NATURAL); TEST_EQUAL(mod1 == mod2, false) mod2.setSourceClassification(ResidueModification::NATURAL); TEST_EQUAL(mod1 == mod2, true) mod1.setAverageMass(0.123); TEST_EQUAL(mod1 == mod2, false) mod2.setAverageMass(0.123); TEST_EQUAL(mod1 == mod2, true) mod1.setMonoMass(1.23); TEST_EQUAL(mod1 == mod2, false) mod2.setMonoMass(1.23); TEST_EQUAL(mod1 == mod2, true) mod1.setDiffAverageMass(2.34); TEST_EQUAL(mod1 == mod2, false) mod2.setDiffAverageMass(2.34); TEST_EQUAL(mod1 == mod2, true) mod1.setDiffMonoMass(3.45); TEST_EQUAL(mod1 == mod2, false) mod2.setDiffMonoMass(3.45); TEST_EQUAL(mod1 == mod2, true) mod1.setFormula("C 3 H 4"); TEST_EQUAL(mod1 == mod2, false) mod2.setFormula("C 3 H 4"); TEST_EQUAL(mod1 == mod2, true) mod1.setDiffFormula(EmpiricalFormula("C0H-2N0O0")); TEST_EQUAL(mod1 == mod2, false) mod2.setDiffFormula(EmpiricalFormula("C0H-2N0O0")); TEST_EQUAL(mod1 == mod2, true) mod1.addSynonym("new_syn"); TEST_EQUAL(mod1 == mod2, false) mod2.addSynonym("new_syn"); TEST_EQUAL(mod1 == mod2, true) END_SECTION START_SECTION(bool operator!=(const ResidueModification &modification) const) ResidueModification mod1, mod2; mod1.setId("Id"); TEST_EQUAL(mod1 != mod2, true) mod2.setId("Id"); TEST_EQUAL(mod1 != mod2, false) mod1.setFullName("FullName"); TEST_EQUAL(mod1 != mod2, true) mod2.setFullName("FullName"); TEST_EQUAL(mod1 != mod2, false) mod1.setName("Name"); TEST_EQUAL(mod1 != mod2, true) mod2.setName("Name"); TEST_EQUAL(mod1 != mod2, false) mod1.setTermSpecificity(ResidueModification::N_TERM); TEST_EQUAL(mod1 != mod2, true) mod2.setTermSpecificity(ResidueModification::N_TERM); TEST_EQUAL(mod1 != mod2, false) mod1.setOrigin("C"); TEST_EQUAL(mod1 != mod2, true) mod2.setOrigin("C"); TEST_EQUAL(mod1 != mod2, false) mod1.setSourceClassification(ResidueModification::NATURAL); TEST_EQUAL(mod1 != mod2, true) mod2.setSourceClassification(ResidueModification::NATURAL); TEST_EQUAL(mod1 != mod2, false) mod1.setAverageMass(0.123); TEST_EQUAL(mod1 != mod2, true) mod2.setAverageMass(0.123); TEST_EQUAL(mod1 != mod2, false) mod1.setMonoMass(1.23); TEST_EQUAL(mod1 != mod2, true) mod2.setMonoMass(1.23); TEST_EQUAL(mod1 != mod2, false) mod1.setDiffAverageMass(2.34); TEST_EQUAL(mod1 != mod2, true) mod2.setDiffAverageMass(2.34); TEST_EQUAL(mod1 != mod2, false) mod1.setDiffMonoMass(3.45); TEST_EQUAL(mod1 != mod2, true) mod2.setDiffMonoMass(3.45); TEST_EQUAL(mod1 != mod2, false) mod1.setFormula("C 3 H 4"); TEST_EQUAL(mod1 != mod2, true) mod2.setFormula("C 3 H 4"); TEST_EQUAL(mod1 != mod2, false) mod1.setDiffFormula(EmpiricalFormula("C0H-2N0O0")); TEST_EQUAL(mod1 != mod2, true) mod2.setDiffFormula(EmpiricalFormula("C0H-2N0O0")); TEST_EQUAL(mod1 != mod2, false) mod1.addSynonym("new_syn"); TEST_EQUAL(mod1 != mod2, true) mod2.addSynonym("new_syn"); TEST_EQUAL(mod1 != mod2, false) END_SECTION END_TEST