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// ./tests/catch2-tests [section] -s
/////////////////////// Qt includes
#include <QDebug>
#include <QString>
#include <QDir>
/////////////////////// Catch2 includes
#include <catch2/catch_test_macros.hpp>
#include <catch2/matchers/catch_matchers_floating_point.hpp>
/////////////////////// Local includes
#include "TestUtils.hpp"
#include <libXpertMass/ChemicalGroup.hpp>
namespace MsXpS
{
namespace libXpertMassCore
{
TestUtils test_utils_chemical_group_rule_1_letter("protein-1-letter", 1);
ErrorList error_list_chemical_group_rule;
SCENARIO("ChemicalGroup object can be constructed empty", "[ChemicalGroup]")
{
WHEN("Constructing an empty ChemicalGroup")
{
ChemicalGroup chemical_group;
THEN("The object is invalid")
{
REQUIRE_FALSE(chemical_group.isValid());
}
AND_WHEN(
"Setting the name, the pKa, the charge bool, the Enums::ChemicalGroupTrapped")
{
chemical_group.setName("N-term NH2");
chemical_group.setPka(9.6);
chemical_group.setAcidCharged(true);
chemical_group.setPolRule(Enums::ChemicalGroupTrapped::LEFT);
THEN("The ChemicalGroup is valid.")
{
REQUIRE(chemical_group.isValid());
}
AND_WHEN("Constructing two fully initialized ChemicalGroupRule")
{
ChemicalGroupRule chemical_group_rule_1;
chemical_group_rule_1.setName("Acetylation");
chemical_group_rule_1.setEntity("LE_PLM_MODIF");
chemical_group_rule_1.setFate(Enums::ChemicalGroupFate::LOST);
ChemicalGroupRule chemical_group_rule_2;
chemical_group_rule_2.setName("Formylation");
chemical_group_rule_2.setEntity("LE_PLM_MODIF");
chemical_group_rule_2.setFate(Enums::ChemicalGroupFate::LOST);
AND_WHEN("Adding that rule to the chemical group")
{
chemical_group.getRulesRef().push_back(
std::make_shared<ChemicalGroupRule>(chemical_group_rule_1));
chemical_group.getRulesRef().push_back(
std::make_shared<ChemicalGroupRule>(chemical_group_rule_2));
REQUIRE(chemical_group.getRulesRef().size() == 2);
std::size_t index = 0;
THEN(
"The ChemicalGroupRule instances are findable in the "
"ChemicalGroup.")
{
REQUIRE(chemical_group.getRulesRef().size() == 2);
REQUIRE(chemical_group.getRulesCstRef().size() == 2);
ChemicalGroupRuleSPtr chemical_group_rule_1_sp =
chemical_group.getRulesCstRef().at(0);
REQUIRE(chemical_group_rule_1_sp != nullptr);
REQUIRE(chemical_group_rule_1_sp->getEntity().toStdString() ==
"LE_PLM_MODIF");
// Begin erroneous cases
REQUIRE(nullptr ==
chemical_group.findRuleByEntity("Not_existent", index));
std::size_t out_of_bounds_index = 10;
REQUIRE(nullptr == chemical_group.findRuleByEntity(
"LE_PLM_MODIF", out_of_bounds_index));
REQUIRE(nullptr ==
chemical_group.findRuleByName("Not_existent", index));
REQUIRE(nullptr == chemical_group.findRuleByName(
"Acetylation", out_of_bounds_index));
// End erroneous cases
chemical_group_rule_1_sp =
chemical_group.findRuleByEntity("LE_PLM_MODIF", index);
REQUIRE(chemical_group_rule_1_sp->getEntity().toStdString() ==
"LE_PLM_MODIF");
REQUIRE(index == 0);
chemical_group_rule_1_sp =
chemical_group.findRuleByName("Acetylation", index);
REQUIRE(chemical_group_rule_1_sp->getName().toStdString() ==
"Acetylation");
REQUIRE(index == 0);
chemical_group_rule_1_sp = chemical_group.findRuleByEntityAndName(
"LE_PLM_MODIF", "Acetylation", index);
REQUIRE(chemical_group_rule_1_sp->getEntity().toStdString() ==
"LE_PLM_MODIF");
REQUIRE(chemical_group_rule_1_sp->getName().toStdString() ==
"Acetylation");
REQUIRE(index == 0);
ChemicalGroupRuleSPtr chemical_group_rule_2_sp =
chemical_group.getRulesRef().at(1);
REQUIRE(chemical_group_rule_2_sp != nullptr);
REQUIRE(chemical_group_rule_2_sp->getEntity().toStdString() ==
"LE_PLM_MODIF");
index = 0;
chemical_group_rule_2_sp =
chemical_group.findRuleByEntity("LE_PLM_MODIF", index);
REQUIRE(chemical_group_rule_2_sp->getEntity().toStdString() ==
"LE_PLM_MODIF");
REQUIRE(index == 0);
index = 1;
chemical_group_rule_2_sp =
chemical_group.findRuleByEntity("LE_PLM_MODIF", index);
REQUIRE(chemical_group_rule_2_sp->getEntity().toStdString() ==
"LE_PLM_MODIF");
REQUIRE(index == 1);
index = 0;
chemical_group_rule_2_sp =
chemical_group.findRuleByName("Formylation", index);
REQUIRE(chemical_group_rule_2_sp->getName().toStdString() ==
"Formylation");
REQUIRE(index == 1);
index = 0;
chemical_group_rule_2_sp = chemical_group.findRuleByEntityAndName(
"LE_PLM_MODIF", "Formylation", index);
REQUIRE(chemical_group_rule_2_sp->getEntity().toStdString() ==
"LE_PLM_MODIF");
REQUIRE(chemical_group_rule_2_sp->getName().toStdString() ==
"Formylation");
REQUIRE(index == 1);
}
AND_WHEN(
"An new ChemicalGroup is allocated and initialized with "
"operator=() or allocated with the copy constructor")
{
ChemicalGroup other_chemical_group;
other_chemical_group = chemical_group;
ChemicalGroup another_chemical_group(other_chemical_group);
THEN("The new ChemicalGroup is identical to the first one.")
{
REQUIRE(another_chemical_group.isValid());
REQUIRE(another_chemical_group.getName().toStdString() ==
"N-term NH2");
REQUIRE_THAT(chemical_group.getPka(),
Catch::Matchers::WithinAbs(9.6, 0.0001));
REQUIRE(chemical_group.isAcidCharged());
REQUIRE(chemical_group.getPolRule() ==
Enums::ChemicalGroupTrapped::LEFT);
ChemicalGroupRuleSPtr chemical_group_rule_1_sp =
another_chemical_group.getRulesRef().at(0);
REQUIRE(chemical_group_rule_1_sp != nullptr);
REQUIRE(chemical_group_rule_1_sp->getEntity().toStdString() ==
"LE_PLM_MODIF");
chemical_group_rule_1_sp =
another_chemical_group.findRuleByEntity("LE_PLM_MODIF", index);
REQUIRE(chemical_group_rule_1_sp->getEntity().toStdString() ==
"LE_PLM_MODIF");
REQUIRE(index == 0);
chemical_group_rule_1_sp =
another_chemical_group.findRuleByName("Acetylation", index);
REQUIRE(chemical_group_rule_1_sp->getName().toStdString() ==
"Acetylation");
REQUIRE(index == 0);
chemical_group_rule_1_sp =
another_chemical_group.findRuleByEntityAndName(
"LE_PLM_MODIF", "Acetylation", index);
REQUIRE(chemical_group_rule_1_sp->getEntity().toStdString() ==
"LE_PLM_MODIF");
REQUIRE(chemical_group_rule_1_sp->getName().toStdString() ==
"Acetylation");
REQUIRE(index == 0);
ChemicalGroupRuleSPtr chemical_group_rule_2_sp =
another_chemical_group.getRulesRef().at(1);
REQUIRE(chemical_group_rule_2_sp != nullptr);
REQUIRE(chemical_group_rule_2_sp->getEntity().toStdString() ==
"LE_PLM_MODIF");
index = 0;
chemical_group_rule_2_sp =
another_chemical_group.findRuleByEntity("LE_PLM_MODIF", index);
REQUIRE(chemical_group_rule_2_sp->getEntity().toStdString() ==
"LE_PLM_MODIF");
REQUIRE(index == 0);
index = 1;
chemical_group_rule_2_sp =
another_chemical_group.findRuleByEntity("LE_PLM_MODIF", index);
REQUIRE(chemical_group_rule_2_sp->getEntity().toStdString() ==
"LE_PLM_MODIF");
REQUIRE(index == 1);
index = 0;
chemical_group_rule_2_sp =
another_chemical_group.findRuleByName("Formylation", index);
REQUIRE(chemical_group_rule_2_sp->getName().toStdString() ==
"Formylation");
REQUIRE(index == 1);
index = 0;
chemical_group_rule_2_sp =
another_chemical_group.findRuleByEntityAndName(
"LE_PLM_MODIF", "Formylation", index);
REQUIRE(chemical_group_rule_2_sp->getEntity().toStdString() ==
"LE_PLM_MODIF");
REQUIRE(chemical_group_rule_2_sp->getName().toStdString() ==
"Formylation");
REQUIRE(index == 1);
}
}
}
}
}
}
}
SCENARIO(
"ChemicalGroup objects can be created by reading a mnmchemgroup XML element",
"[ChemicalGroup]")
{
WHEN("Constructing an empty ChemicalGroup")
{
ChemicalGroup chemical_group;
AND_WHEN("Initializing it with a <mnmchemgroup> XML element")
{
// QString dom_string = "<mnmchemgroup><name>N-term
// NH2</name><pka>9.6</pka><acidcharged>TRUE</acidcharged><polrule>left_trapped</polrule><chemgrouprule><entity>LE_PLM_MODIF</entity><name>Acetylation</name><outcome>LOST</outcome></chemgrouprule></mnmchemgroup>";
QDomDocument document;
QDomElement mnmchemgroup_element = document.createElement("mnmchemgroup");
QDomElement name_element = document.createElement("name");
QDomText name_text = document.createTextNode("N-term NH2");
name_element.appendChild(name_text);
QDomElement pka_element = document.createElement("pka");
QDomText pka_text = document.createTextNode("9.6");
pka_element.appendChild(pka_text);
QDomElement acidcharged_element = document.createElement("acidcharged");
QDomText acidcharged_text = document.createTextNode("TRUE");
acidcharged_element.appendChild(acidcharged_text);
QDomElement polrule_element = document.createElement("polrule");
QDomText polrule_text = document.createTextNode("left_trapped");
polrule_element.appendChild(polrule_text);
QDomElement chemgrouprule_element =
document.createElement("chemgrouprule");
QDomElement entity_element = document.createElement("entity");
QDomText entity_text = document.createTextNode("LE_PLM_MODIF");
entity_element.appendChild(entity_text);
QDomElement rule_name_element = document.createElement("name");
QDomText rule_name_text = document.createTextNode("Acetylation");
rule_name_element.appendChild(rule_name_text);
QDomElement outcome_element = document.createElement("outcome");
QDomText outcome_text = document.createTextNode("LOST");
outcome_element.appendChild(outcome_text);
chemgrouprule_element.appendChild(entity_element);
chemgrouprule_element.appendChild(rule_name_element);
chemgrouprule_element.appendChild(outcome_element);
mnmchemgroup_element.appendChild(name_element);
mnmchemgroup_element.appendChild(pka_element);
mnmchemgroup_element.appendChild(acidcharged_element);
mnmchemgroup_element.appendChild(polrule_element);
mnmchemgroup_element.appendChild(chemgrouprule_element);
document.appendChild(mnmchemgroup_element);
REQUIRE(chemical_group.renderXmlMnmElement(mnmchemgroup_element));
THEN("The object is valid and the member data are set correctly")
{
REQUIRE(chemical_group.isValid());
REQUIRE(chemical_group.getName().toStdString() == "N-term NH2");
REQUIRE_THAT(chemical_group.getPka(),
Catch::Matchers::WithinAbs(9.6, 0.001));
REQUIRE(chemical_group.isAcidCharged());
REQUIRE(chemical_group.getPolRule() == Enums::ChemicalGroupTrapped::LEFT);
REQUIRE(
chemical_group.getRulesCstRef().front()->getName().toStdString() ==
"Acetylation");
REQUIRE(
chemical_group.getRulesCstRef().front()->getEntity().toStdString() ==
"LE_PLM_MODIF");
REQUIRE(chemical_group.getRulesCstRef().front()->getFate() ==
Enums::ChemicalGroupFate::LOST);
}
}
}
}
SCENARIO(
"ChemicalGroup objects can be created by reading a mdfchemgroup XML element",
"[ChemicalGroup]")
{
WHEN("Constructing an empty ChemicalGroup")
{
ChemicalGroup chemical_group;
AND_WHEN("Initializing it with a <mdfchemgroup> XML element")
{
// QString dom_string =
// "<mdfchemgroup><name>Phosphorylation</name><pka>1.2</pka><acidcharged>FALSE</acidcharged></mdfchemgroup>";
QDomDocument document;
QDomElement mdfchemgroup_element = document.createElement("mdfchemgroup");
QDomElement name_element = document.createElement("name");
QDomText name_text = document.createTextNode("Phosphorylation");
name_element.appendChild(name_text);
QDomElement pka_element = document.createElement("pka");
QDomText pka_text = document.createTextNode("1.2");
pka_element.appendChild(pka_text);
QDomElement acidcharged_element = document.createElement("acidcharged");
QDomText acidcharged_text = document.createTextNode("FALSE");
acidcharged_element.appendChild(acidcharged_text);
mdfchemgroup_element.appendChild(name_element);
mdfchemgroup_element.appendChild(pka_element);
mdfchemgroup_element.appendChild(acidcharged_element);
document.appendChild(mdfchemgroup_element);
REQUIRE(chemical_group.renderXmlMdfElement(mdfchemgroup_element));
THEN("The object is valid and the member data are set correctly")
{
REQUIRE(chemical_group.isValid());
REQUIRE(chemical_group.getName().toStdString() == "Phosphorylation");
REQUIRE_THAT(chemical_group.getPka(),
Catch::Matchers::WithinAbs(1.2, 0.001));
REQUIRE_FALSE(chemical_group.isAcidCharged());
}
}
}
}
} // namespace libXpertMassCore
} // namespace MsXpS
|
