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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: Andreas Bertsch $
// $Authors: Andreas Bertsch $
// --------------------------------------------------------------------------
#include <OpenMS/CONCEPT/ClassTest.h>
///////////////////////////
#include <OpenMS/CHEMISTRY/ModificationDefinitionsSet.h>
///////////////////////////
using namespace OpenMS;
using namespace std;
START_TEST(ModificationDefinitionsSet, "$Id: ModificationDefinitionsSet_test.C 10915 2013-04-04 20:14:57Z aiche $")
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
ModificationDefinitionsSet* ptr = 0;
ModificationDefinitionsSet* nullPointer = 0;
START_SECTION(ModificationDefinitionsSet())
{
ptr = new ModificationDefinitionsSet();
TEST_NOT_EQUAL(ptr, nullPointer)
}
END_SECTION
START_SECTION((ModificationDefinitionsSet(const ModificationDefinitionsSet &rhs)))
{
ModificationDefinitionsSet mod_set;
mod_set.setMaxModifications(2);
ModificationDefinition mod_def, mod_def2;
mod_def.setModification("Phospho (S)");
mod_def.setFixedModification(true);
mod_def2.setModification("Phospho (T)");
mod_def2.setFixedModification(false);
mod_def2.setMaxOccurences(10);
ModificationDefinitionsSet mod_set2(mod_set);
TEST_EQUAL(mod_set == mod_set2, true)
}
END_SECTION
START_SECTION((ModificationDefinitionsSet(const String &fixed_modifications, const String &variable_modifications="")))
{
ModificationDefinitionsSet mod_set("Phospho (S),Phospho (T),Phospho (Y)", "Carbamidomethyl (C)");
set<String> fixed_mods;
fixed_mods.insert("Phospho (S)");
fixed_mods.insert("Phospho (T)");
fixed_mods.insert("Phospho (Y)");
set<String> var_mods;
var_mods.insert("Carbamidomethyl (C)");
TEST_EQUAL(mod_set.getFixedModificationNames() == fixed_mods, true)
TEST_EQUAL(mod_set.getVariableModificationNames() == var_mods, true)
}
END_SECTION
START_SECTION((virtual ~ModificationDefinitionsSet()))
{
delete ptr;
}
END_SECTION
START_SECTION((void setMaxModifications(Size max_mod)))
{
ModificationDefinitionsSet mod_set;
mod_set.setMaxModifications(1);
TEST_EQUAL(mod_set.getMaxModifications(), 1)
mod_set.setMaxModifications(2);
TEST_EQUAL(mod_set.getMaxModifications(), 2)
}
END_SECTION
START_SECTION((Size getMaxModifications() const ))
{
// tested above
NOT_TESTABLE
}
END_SECTION
START_SECTION((Size getNumberOfModifications() const ))
{
ModificationDefinitionsSet mod_set("Phospho (S),Phospho (T),Phospho (Y)", "Carbamidomethyl (C)");
TEST_EQUAL(mod_set.getNumberOfModifications(), 4)
ModificationDefinitionsSet mod_set2("", "Carbamidomethyl (C)");
TEST_EQUAL(mod_set2.getNumberOfModifications(), 1)
ModificationDefinitionsSet mod_set3("Phospho (S)");
TEST_EQUAL(mod_set3.getNumberOfModifications(), 1)
}
END_SECTION
START_SECTION((Size getNumberOfFixedModifications() const ))
{
ModificationDefinitionsSet mod_set("Phospho (S),Phospho (T),Phospho (Y)", "Carbamidomethyl (C)");
TEST_EQUAL(mod_set.getNumberOfFixedModifications(), 3)
ModificationDefinitionsSet mod_set2("", "Carbamidomethyl (C)");
TEST_EQUAL(mod_set2.getNumberOfFixedModifications(), 0)
ModificationDefinitionsSet mod_set3("Phospho (S)");
TEST_EQUAL(mod_set3.getNumberOfFixedModifications(), 1)
}
END_SECTION
START_SECTION((Size getNumberOfVariableModifications() const ))
{
ModificationDefinitionsSet mod_set("Phospho (S),Phospho (T)", "Carbamidomethyl (C),Phospho (Y)");
TEST_EQUAL(mod_set.getNumberOfVariableModifications(), 2)
ModificationDefinitionsSet mod_set2("", "Carbamidomethyl (C)");
TEST_EQUAL(mod_set2.getNumberOfVariableModifications(), 1)
ModificationDefinitionsSet mod_set3("Phospho (S)");
TEST_EQUAL(mod_set3.getNumberOfVariableModifications(), 0)
}
END_SECTION
START_SECTION((void addModification(const ModificationDefinition& mod_def)))
{
ModificationDefinition mod_def;
mod_def.setModification("Phospho (Y)");
mod_def.setFixedModification(true);
ModificationDefinitionsSet mod_set;
mod_set.addModification(mod_def);
ModificationDefinitionsSet mod_set2;
TEST_EQUAL(mod_set != mod_set2, true)
TEST_EQUAL(mod_set.getNumberOfModifications(), 1)
TEST_EQUAL(mod_set.getNumberOfFixedModifications(), 1)
TEST_EQUAL(mod_set.getNumberOfVariableModifications(), 0)
ModificationDefinition mod_def3;
mod_def3.setModification("Phospho (T)");
mod_def3.setFixedModification(false);
ModificationDefinitionsSet mod_set3;
mod_set3.addModification(mod_def3);
mod_set3.addModification(mod_def);
TEST_EQUAL(mod_set3.getNumberOfModifications(), 2)
TEST_EQUAL(mod_set3.getNumberOfFixedModifications(), 1)
TEST_EQUAL(mod_set3.getNumberOfVariableModifications(), 1)
}
END_SECTION
START_SECTION((void setModifications(const std::set<ModificationDefinition>& mod_defs)))
{
ModificationDefinition mod_def1, mod_def2;
mod_def1.setModification("Phospho (T)");
mod_def1.setFixedModification(true);
mod_def2.setModification("Phospho (S)");
mod_def2.setFixedModification(false);
set<ModificationDefinition> mod_defs;
mod_defs.insert(mod_def1);
mod_defs.insert(mod_def2);
ModificationDefinitionsSet mod_set;
mod_set.setModifications(mod_defs);
TEST_EQUAL(mod_set.getNumberOfModifications(), 2)
TEST_EQUAL(mod_set.getNumberOfFixedModifications(), 1)
TEST_EQUAL(mod_set.getNumberOfVariableModifications(), 1)
}
END_SECTION
START_SECTION((void setModifications(const String& fixed_modifications, const String& variable_modifications)))
{
ModificationDefinitionsSet mod_set1("Phospho (S),Phospho (T),Phospho (Y)", "Carbamidomethyl (C)");
ModificationDefinitionsSet mod_set2;
mod_set2.setModifications("Phospho (S),Phospho (T),Phospho (Y)", "Carbamidomethyl (C)");
TEST_EQUAL(mod_set1.getFixedModificationNames() == mod_set2.getFixedModificationNames(), true)
TEST_EQUAL(mod_set1.getVariableModificationNames() == mod_set2.getVariableModificationNames(), true)
TEST_EQUAL(mod_set1.getModificationNames() == mod_set2.getModificationNames(), true)
TEST_EQUAL(mod_set1 == mod_set2, true)
mod_set1.setModifications("Phospho (S)", "Carbamidomethyl (C)");
TEST_EQUAL(mod_set1.getNumberOfModifications(), 2)
TEST_EQUAL(mod_set1.getNumberOfFixedModifications(), 1)
TEST_EQUAL(mod_set1.getNumberOfVariableModifications(), 1)
}
END_SECTION
START_SECTION((std::set<ModificationDefinition> getModifications() const ))
{
ModificationDefinitionsSet mod_set1("Phospho (S),Phospho (T),Phospho (Y)", "Carbamidomethyl (C)");
set<String> fixed_mods, var_mods;
fixed_mods.insert("Phospho (S)");
fixed_mods.insert("Phospho (T)");
fixed_mods.insert("Phospho (Y)");
var_mods.insert("Carbamidomethyl (C)");
set<ModificationDefinition> mod_defs = mod_set1.getModifications();
for (set<ModificationDefinition>::const_iterator it = mod_defs.begin(); it != mod_defs.end(); ++it)
{
if (it->isFixedModification())
{
TEST_EQUAL(fixed_mods.find(it->getModification()) != fixed_mods.end(), true)
}
else
{
TEST_EQUAL(var_mods.find(it->getModification()) != var_mods.end(), true)
}
}
}
END_SECTION
START_SECTION(const std::set<ModificationDefinition>& getFixedModifications() const)
ModificationDefinitionsSet mod_set1("Phospho (S),Phospho (T),Phospho (Y)", "Carbamidomethyl (C)");
set<String> fixed_mods;
fixed_mods.insert("Phospho (S)");
fixed_mods.insert("Phospho (T)");
fixed_mods.insert("Phospho (Y)");
set<ModificationDefinition> mod_defs = mod_set1.getFixedModifications();
TEST_EQUAL(mod_defs.size(), 3)
for (set<ModificationDefinition>::const_iterator it = mod_defs.begin(); it != mod_defs.end(); ++it)
{
TEST_EQUAL(it->isFixedModification(), true)
TEST_EQUAL(fixed_mods.find(it->getModification()) != fixed_mods.end(), true)
}
END_SECTION
START_SECTION(const std::set<ModificationDefinition>& getVariableModifications() const)
ModificationDefinitionsSet mod_set1("Phospho (S),Phospho (T),Phospho (Y)", "Carbamidomethyl (C),Phospho (S)");
set<String> mods;
mods.insert("Phospho (S)");
mods.insert("Carbamidomethyl (C)");
set<ModificationDefinition> mod_defs = mod_set1.getVariableModifications();
TEST_EQUAL(mod_defs.size(), 2)
for (set<ModificationDefinition>::const_iterator it = mod_defs.begin(); it != mod_defs.end(); ++it)
{
TEST_EQUAL(it->isFixedModification(), false)
TEST_EQUAL(mods.find(it->getModification()) != mods.end(), true)
}
END_SECTION
START_SECTION((std::set<String> getModificationNames() const ))
{
ModificationDefinitionsSet mod_set1("Phospho (S),Phospho (T),Phospho (Y)", "Carbamidomethyl (C)");
set<String> mods;
mods.insert("Phospho (S)");
mods.insert("Phospho (T)");
mods.insert("Phospho (Y)");
mods.insert("Carbamidomethyl (C)");
TEST_EQUAL(mod_set1.getModificationNames() == mods, true)
}
END_SECTION
START_SECTION((std::set<String> getFixedModificationNames() const ))
{
ModificationDefinitionsSet mod_set1("Phospho (S),Phospho (T),Phospho (Y)", "Carbamidomethyl (C)");
set<String> mods;
mods.insert("Phospho (S)");
mods.insert("Phospho (T)");
mods.insert("Phospho (Y)");
TEST_EQUAL(mod_set1.getFixedModificationNames() == mods, true)
}
END_SECTION
START_SECTION((std::set<String> getVariableModificationNames() const ))
{
ModificationDefinitionsSet mod_set1("Phospho (S),Phospho (T)", "Phospho (Y),Carbamidomethyl (C)");
set<String> mods;
mods.insert("Carbamidomethyl (C)");
mods.insert("Phospho (Y)");
TEST_EQUAL(mod_set1.getVariableModificationNames() == mods, true)
}
END_SECTION
START_SECTION((ModificationDefinitionsSet& operator=(const ModificationDefinitionsSet& element)))
{
ModificationDefinitionsSet mod_set1, mod_set2;
mod_set1.setModifications("Phospho (S),Phospho (T),Phospho (Y)", "");
TEST_EQUAL(mod_set1 == mod_set2, false)
mod_set2 = mod_set1;
TEST_EQUAL(mod_set1 == mod_set2, true)
mod_set1.setMaxModifications(3);
TEST_EQUAL(mod_set1 == mod_set2, false)
mod_set2 = mod_set1;
TEST_EQUAL(mod_set1 == mod_set2, true)
mod_set1.setModifications("Phospho (S),Phospho (T),Phospho (Y)", "Carbamidomethyl (C)");
TEST_EQUAL(mod_set1 == mod_set2, false)
mod_set2 = mod_set1;
TEST_EQUAL(mod_set1 == mod_set2, true)
}
END_SECTION
START_SECTION((bool operator==(const ModificationDefinitionsSet& rhs) const))
{
ModificationDefinitionsSet mod_set1, mod_set2;
mod_set1.setModifications("Phospho (S),Phospho (T),Phospho (Y)", "");
TEST_EQUAL(mod_set1 == mod_set2, false)
mod_set2 = mod_set1;
TEST_EQUAL(mod_set1 == mod_set2, true)
mod_set1.setMaxModifications(3);
TEST_EQUAL(mod_set1 == mod_set2, false)
mod_set2 = mod_set1;
TEST_EQUAL(mod_set1 == mod_set2, true)
mod_set1.setModifications("Phospho (S),Phospho (T),Phospho (Y)", "Carbamidomethyl (C)");
TEST_EQUAL(mod_set1 == mod_set2, false)
mod_set2 = mod_set1;
TEST_EQUAL(mod_set1 == mod_set2, true)
}
END_SECTION
START_SECTION((bool operator!=(const ModificationDefinitionsSet& rhs) const))
{
ModificationDefinitionsSet mod_set1, mod_set2;
mod_set1.setModifications("Phospho (S),Phospho (T),Phospho (Y)", "");
TEST_EQUAL(mod_set1 != mod_set2, true)
mod_set2 = mod_set1;
TEST_EQUAL(mod_set1 != mod_set2, false)
mod_set1.setMaxModifications(3);
TEST_EQUAL(mod_set1 != mod_set2, true)
mod_set2 = mod_set1;
TEST_EQUAL(mod_set1 != mod_set2, false)
mod_set1.setModifications("Phospho (S),Phospho (T),Phospho (Y)", "Carbamidomethyl (C)");
TEST_EQUAL(mod_set1 != mod_set2, true)
mod_set2 = mod_set1;
TEST_EQUAL(mod_set1 != mod_set2, false)
}
END_SECTION
START_SECTION((ModificationDefinitionsSet(const StringList &fixed_modifications, const StringList &variable_modifications=StringList::create(""))))
ModificationDefinitionsSet mod_set(StringList::create("Phospho (S),Phospho (T),Phospho (Y)"), StringList::create("Carbamidomethyl (C)"));
set<String> fixed_mods;
fixed_mods.insert("Phospho (S)");
fixed_mods.insert("Phospho (T)");
fixed_mods.insert("Phospho (Y)");
set<String> var_mods;
var_mods.insert("Carbamidomethyl (C)");
TEST_EQUAL(mod_set.getFixedModificationNames() == fixed_mods, true)
TEST_EQUAL(mod_set.getVariableModificationNames() == var_mods, true)
END_SECTION
START_SECTION((void setModifications(const StringList &fixed_modifications, const StringList &variable_modifications)))
ModificationDefinitionsSet mod_set;
mod_set.setModifications(StringList::create("Phospho (T)"), StringList::create("Phospho (S)"));
TEST_EQUAL(mod_set.getNumberOfModifications(), 2)
TEST_EQUAL(mod_set.getNumberOfFixedModifications(), 1)
TEST_EQUAL(mod_set.getNumberOfVariableModifications(), 1)
END_SECTION
START_SECTION((bool isCompatible(const AASequence &peptide) const))
ModificationDefinitionsSet mod_set(StringList::create("Carbamidomethyl (C)"), StringList::create("Phospho (S),Phospho (T),Phospho (Y)"));
AASequence pep1("CCTKPESER");
AASequence pep2("C(Carbamidomethyl)CTKPESER");
AASequence pep3("C(Carbamidomethyl)C(Carbamidomethyl)TKPESER");
AASequence pep4("C(Carbamidomethyl)C(Carbamidomethyl)T(Phospho)TKPESER");
AASequence pep5("(Acetyl)CCTKPESER");
AASequence pep6("(Acetyl)C(Carbamidomethyl)C(Carbamidomethyl)TKPES(Phospho)ER");
AASequence pep7("(Acetyl)C(Carbamidomethyl)C(Carbamidomethyl)T(Phospho)KPES(Phospho)ER");
TEST_EQUAL(mod_set.isCompatible(pep1), false);
TEST_EQUAL(mod_set.isCompatible(pep2), false);
TEST_EQUAL(mod_set.isCompatible(pep3), true);
TEST_EQUAL(mod_set.isCompatible(pep4), true);
TEST_EQUAL(mod_set.isCompatible(pep5), false);
TEST_EQUAL(mod_set.isCompatible(pep6), false);
TEST_EQUAL(mod_set.isCompatible(pep7), false);
END_SECTION
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
END_TEST
|
