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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/FragmentationConfig.hpp>
namespace MsXpS
{
namespace libXpertMassCore
{
TestUtils test_utils_fragmentation_config_1_letter("protein-1-letter", 1);
TestUtils test_utils_fragmentation_config_3_letters("protein-3-letters", 1);
ErrorList error_list_fragmentation_config;
SCENARIO("FragmentationConfig objects can be constructed in various ways",
"[FragmentationConfig]")
{
test_utils_fragmentation_config_1_letter.initializeXpertmassLibrary();
PolChemDefCstSPtr pol_chem_def_csp =
test_utils_fragmentation_config_1_letter.msp_polChemDef;
WHEN(
"Constructing of a FragmentationConfig instances with or without explicit "
"FragmentationPathway object use")
{
FragmentationConfig fragmentation_config_1(pol_chem_def_csp,
"a",
"-C1O1",
Enums::FragEnd::LE,
"frag_a_comment",
/*sequence_embedded*/ true);
fragmentation_config_1.setStartIndex(0);
fragmentation_config_1.setStopIndex(120);
fragmentation_config_1.setStartIonizeLevel(1);
fragmentation_config_1.setStopIonizeLevel(3);
FragmentationPathway fragmentation_pathway(
pol_chem_def_csp, "a", "-C1O1", Enums::FragEnd::LE, "frag_a_comment");
// Trick to test the setIonizeLevels() function.
FragmentationConfig fragmentation_config_2(
fragmentation_pathway, 5, 8, /*sequence_embedded*/ true);
fragmentation_config_2.setStartIndex(0);
fragmentation_config_2.setStopIndex(120);
fragmentation_config_2.setIonizeLevels(1, 3);
fragmentation_config_1.addFormula(Formula("-H2O"));
fragmentation_config_1.addFormula(Formula("-NH3"));
fragmentation_config_2.addFormula(Formula("-H2O"));
fragmentation_config_2.addFormula(Formula("-NH3"));
THEN("All the member data are set correctly for both instances")
{
REQUIRE(fragmentation_config_1.getPolchemDefCstSPtr() ==
pol_chem_def_csp);
REQUIRE(fragmentation_config_1.getName().toStdString() == "a");
REQUIRE(fragmentation_config_1.getFormulaCstRef()
.getActionFormula()
.toStdString() == "-C1O1");
REQUIRE(fragmentation_config_1.getFormulaRef()
.getActionFormula()
.toStdString() == "-C1O1");
REQUIRE(fragmentation_config_1.getFragEnd() == Enums::FragEnd::LE);
REQUIRE(fragmentation_config_1.getComment().toStdString() ==
"frag_a_comment");
REQUIRE(fragmentation_config_1.getRulesCstRef().size() == 0);
REQUIRE(fragmentation_config_1.getRulesRef().size() == 0);
REQUIRE(fragmentation_config_1.getStartIonizeLevel() == 1);
REQUIRE(fragmentation_config_1.getStopIonizeLevel() == 3);
REQUIRE(fragmentation_config_1.isSequenceEmbedded() == true);
REQUIRE(fragmentation_config_1.getFormulasRef().size() == 2);
REQUIRE(fragmentation_config_1.getFormulasCstRef().size() == 2);
REQUIRE(fragmentation_config_1.getFormulasCstRef()
.front()
.getActionFormula()
.toStdString() == "-H2O");
REQUIRE(fragmentation_config_1.getFormulasCstRef()
.back()
.getActionFormula()
.toStdString() == "-NH3");
REQUIRE(fragmentation_config_2.getPolchemDefCstSPtr() ==
pol_chem_def_csp);
REQUIRE(fragmentation_config_2.getName().toStdString() == "a");
REQUIRE(fragmentation_config_2.getFormulaCstRef()
.getActionFormula()
.toStdString() == "-C1O1");
REQUIRE(fragmentation_config_2.getFormulaRef()
.getActionFormula()
.toStdString() == "-C1O1");
REQUIRE(fragmentation_config_2.getFragEnd() == Enums::FragEnd::LE);
REQUIRE(fragmentation_config_2.getComment().toStdString() ==
"frag_a_comment");
REQUIRE(fragmentation_config_2.getRulesCstRef().size() == 0);
REQUIRE(fragmentation_config_2.getRulesRef().size() == 0);
REQUIRE(fragmentation_config_2.getStartIonizeLevel() == 1);
REQUIRE(fragmentation_config_2.getStopIonizeLevel() == 3);
REQUIRE(fragmentation_config_2.isSequenceEmbedded() == true);
REQUIRE(fragmentation_config_2.getFormulasRef().size() == 2);
REQUIRE(fragmentation_config_2.getFormulasCstRef().size() == 2);
REQUIRE(fragmentation_config_2.getFormulasCstRef()
.front()
.getActionFormula()
.toStdString() == "-H2O");
REQUIRE(fragmentation_config_2.getFormulasCstRef()
.back()
.getActionFormula()
.toStdString() == "-NH3");
AND_WHEN("The copy constructor or the assignment operator are used")
{
FragmentationConfig another_fragmentation_config(
fragmentation_config_1);
FragmentationConfig other_fragmentation_config(
pol_chem_def_csp, "NOT_SET", "NOT_SET");
other_fragmentation_config = another_fragmentation_config;
THEN("All the FragmentationConfig need to be identical")
{
REQUIRE(other_fragmentation_config.getPolchemDefCstSPtr() ==
pol_chem_def_csp);
REQUIRE(other_fragmentation_config.getName().toStdString() == "a");
REQUIRE(other_fragmentation_config.getFormulaCstRef()
.getActionFormula()
.toStdString() == "-C1O1");
REQUIRE(other_fragmentation_config.getFormulaRef()
.getActionFormula()
.toStdString() == "-C1O1");
REQUIRE(other_fragmentation_config.getFragEnd() == Enums::FragEnd::LE);
REQUIRE(other_fragmentation_config.getComment().toStdString() ==
"frag_a_comment");
REQUIRE(other_fragmentation_config.getRulesCstRef().size() == 0);
REQUIRE(other_fragmentation_config.getRulesRef().size() == 0);
REQUIRE(other_fragmentation_config.getStartIonizeLevel() == 1);
REQUIRE(other_fragmentation_config.getStopIonizeLevel() == 3);
REQUIRE(other_fragmentation_config.isSequenceEmbedded() == true);
REQUIRE(other_fragmentation_config.getFormulasRef().size() == 2);
REQUIRE(other_fragmentation_config.getFormulasCstRef().size() == 2);
REQUIRE(other_fragmentation_config.getFormulasCstRef()
.front()
.getActionFormula()
.toStdString() == "-H2O");
REQUIRE(other_fragmentation_config.getFormulasCstRef()
.back()
.getActionFormula()
.toStdString() == "-NH3");
AND_WHEN("The FragmentationConfig outputs itself as a string")
{
QString text = other_fragmentation_config.toString();
text = text.remove(QRegularExpression("\\s"));
QString expected_text = QString("FragmentationConfig:\nFragmentation pathway:\nName: a - Formula: -C1O1 - Frag end: LE - Monomer contribution: 0\nisValid: true\n\nIndices [0-120] -- ionization levels [1-3].\nFormulas:\n-H2O -\n-NH3 -\n");
expected_text = expected_text.remove(QRegularExpression("\\s"));
THEN("The string matches the expected string.")
{
REQUIRE(text.toStdString() == expected_text.toStdString());
}
}
}
}
}
}
}
} // namespace libXpertMassCore
} // namespace MsXpS
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