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/////////////////////// 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/CleavageConfig.hpp>
#include <libXpertMass/Sequence.hpp>
#include <libXpertMass/Monomer.hpp>
namespace MsXpS
{
namespace libXpertMassCore
{
TestUtils test_utils_cleavage_config_1_letter("protein-1-letter", 1);
TestUtils test_utils_cleavage_config_3_letters("protein-3-letters", 1);
ErrorList error_list_cleavage_config;
SCENARIO("Construction of a CleavageConfig object", "[CleavageConfig]")
{
test_utils_cleavage_config_1_letter.initializeXpertmassLibrary();
PolChemDefCstSPtr pol_chem_def_csp =
test_utils_cleavage_config_1_letter.msp_polChemDef;
WHEN("A CleavageConfig constructed with all params")
{
CleavageConfig cleavage_config(pol_chem_def_csp,
"Trypsin",
"K/;-K/P;R/",
0,
/*is_sequence_embedded*/ true);
cleavage_config.setStartIonizeLevel(1);
cleavage_config.setStopIonizeLevel(10);
THEN("All the members are set accordingly")
{
REQUIRE(cleavage_config.getPartials() == 0);
REQUIRE(cleavage_config.getStartIonizeLevel() == 1);
REQUIRE(cleavage_config.getStopIonizeLevel() == 10);
REQUIRE(cleavage_config.isSequenceEmbedded());
}
AND_WHEN("Some data members are modified")
{
cleavage_config.setPartials(1);
cleavage_config.setSequenceEmbedded(false);
THEN("The corresponding members are updated")
{
REQUIRE(cleavage_config.getPartials() == 1);
REQUIRE(cleavage_config.getStartIonizeLevel() == 1);
REQUIRE(cleavage_config.getStopIonizeLevel() == 10);
REQUIRE_FALSE(cleavage_config.isSequenceEmbedded());
}
AND_WHEN(
"Another CleavageConfig instance is created by copy-construction or "
"assignment")
{
CleavageConfig other_cleavage_config(cleavage_config);
CleavageConfig another_cleavage_config;
another_cleavage_config = other_cleavage_config;
THEN(
"The other CleavageConfig instances are identical to the initial one")
{
REQUIRE(another_cleavage_config.getPartials() == 1);
REQUIRE(another_cleavage_config.getStartIonizeLevel() == 1);
REQUIRE(another_cleavage_config.getStopIonizeLevel() == 10);
REQUIRE_FALSE(another_cleavage_config.isSequenceEmbedded());
}
}
}
}
}
SCENARIO("CleavageConfig objects can be compared with operators ==() and !=().",
"[CleavageConfig]")
{
test_utils_cleavage_config_1_letter.initializeXpertmassLibrary();
PolChemDefCstSPtr pol_chem_def_csp =
test_utils_cleavage_config_1_letter.msp_polChemDef;
WHEN("Two identical CleavageConfig objects are constructed with all params")
{
CleavageConfig cleavage_config_1(pol_chem_def_csp,
"Trypsin",
"K/;-K/P;R/",
0,
/*is_sequence_embedded*/ true);
cleavage_config_1.setStartIonizeLevel(1);
cleavage_config_1.setStopIonizeLevel(10);
CleavageConfig cleavage_config_2(pol_chem_def_csp,
"Trypsin",
"K/;-K/P;R/",
0,
/*is_sequence_embedded*/ true);
// Choose on purpose this variant :-)
cleavage_config_2.setIonizeLevels(1, 10);
THEN("All the members are set accordingly")
{
REQUIRE(cleavage_config_1.getName().toStdString() == "Trypsin");
REQUIRE(cleavage_config_1.getPattern().toStdString() == "K/;-K/P;R/");
REQUIRE(cleavage_config_1.isValid());
REQUIRE(cleavage_config_1.getPartials() == 0);
REQUIRE(cleavage_config_1.getStartIonizeLevel() == 1);
REQUIRE(cleavage_config_1.getStopIonizeLevel() == 10);
REQUIRE(cleavage_config_1.isSequenceEmbedded());
REQUIRE(cleavage_config_2.getName().toStdString() == "Trypsin");
REQUIRE(cleavage_config_2.getPattern().toStdString() == "K/;-K/P;R/");
REQUIRE(cleavage_config_2.isValid());
REQUIRE(cleavage_config_2.getPartials() == 0);
REQUIRE(cleavage_config_2.getStartIonizeLevel() == 1);
REQUIRE(cleavage_config_2.getStopIonizeLevel() == 10);
REQUIRE(cleavage_config_2.isSequenceEmbedded());
}
AND_THEN("The comparison operators return proper results")
{
REQUIRE(cleavage_config_1 == cleavage_config_2);
REQUIRE_FALSE(cleavage_config_1 != cleavage_config_2);
}
}
}
SCENARIO("CleavageConfig objects can be copy- or assignment- constructed",
"[CleavageConfig]")
{
test_utils_cleavage_config_1_letter.initializeXpertmassLibrary();
PolChemDefCstSPtr pol_chem_def_csp =
test_utils_cleavage_config_1_letter.msp_polChemDef;
WHEN("A CleavageConfig constructed with all params")
{
CleavageConfig cleavage_config(pol_chem_def_csp,
"Trypsin",
"K/;-K/P;R/",
0,
/*is_sequence_embedded*/ true);
cleavage_config.setStartIonizeLevel(1);
cleavage_config.setStopIonizeLevel(10);
THEN("All the members are set accordingly")
{
REQUIRE(cleavage_config.getPartials() == 0);
REQUIRE(cleavage_config.getStartIonizeLevel() == 1);
REQUIRE(cleavage_config.getStopIonizeLevel() == 10);
REQUIRE(cleavage_config.isSequenceEmbedded());
}
AND_WHEN("New CleavageConfig objects are instantiated")
{
CleavageConfig another_cleavage_config(cleavage_config);
CleavageConfig other_cleavage_config;
other_cleavage_config = another_cleavage_config;
THEN("The copies must be identical to the original object")
{
REQUIRE(other_cleavage_config.getPartials() == 0);
REQUIRE(other_cleavage_config.getStartIonizeLevel() == 1);
REQUIRE(other_cleavage_config.getStopIonizeLevel() == 10);
REQUIRE(other_cleavage_config.isSequenceEmbedded());
REQUIRE(other_cleavage_config == cleavage_config);
REQUIRE_FALSE(other_cleavage_config != cleavage_config);
}
}
}
}
SCENARIO("Construction of an empty CleavageConfig object", "[CleavageConfig]")
{
test_utils_cleavage_config_1_letter.initializeXpertmassLibrary();
PolChemDefCstSPtr pol_chem_def_csp =
test_utils_cleavage_config_1_letter.msp_polChemDef;
WHEN("An empty CleavageConfig constructed")
{
CleavageConfig cleavage_config;
AND_WHEN("A Cleavage agent is used to initialize it")
{
CleavageAgent cleavage_agent(pol_chem_def_csp, "Trypsin", "K/;-K/P;R/");
cleavage_config.setCleavageAgent(cleavage_agent);
AND_WHEN("The setter functions are used to configure the CleavageConfig")
{
cleavage_config.setPartials(0);
cleavage_config.setSequenceEmbedded(false);
cleavage_config.setStartIonizeLevel(1);
cleavage_config.setStopIonizeLevel(10);
THEN("The member data are correctly set")
{
REQUIRE(cleavage_config.getPartials() == 0);
REQUIRE(cleavage_config.getStartIonizeLevel() == 1);
REQUIRE(cleavage_config.getStopIonizeLevel() == 10);
REQUIRE_FALSE(cleavage_config.isSequenceEmbedded());
REQUIRE(static_cast<CleavageAgent>(cleavage_config) ==
cleavage_agent);
}
}
}
}
}
} // namespace libXpertMassCore
} // namespace MsXpS
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