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// ./tests/catch2-tests [section] -s
/////////////////////// Qt includes
#include <QDebug>
#include <QString>
#include <QStringList>
#include <QDir>
/////////////////////// IsoSpec
#include <IsoSpec++/isoSpec++.h>
#include <IsoSpec++/element_tables.h>
/////////////////////// Catch2 includes
#include <catch2/catch_test_macros.hpp>
#include <catch2/matchers/catch_matchers_floating_point.hpp>
/////////////////////// Local includes
#include "tests-config.h"
#include "TestUtils.hpp"
#include <libXpertMass/globals.hpp>
#include <libXpertMass/Polymer.hpp>
#include <libXpertMass/CrossLink.hpp>
#include <libXpertMass/CrossLinkedRegion.hpp>
namespace MsXpS
{
namespace libXpertMassCore
{
TestUtils test_utils_1_letter_cross_linked_region("protein-1-letter", 1);
ErrorList error_list_cross_linked_region;
SCENARIO("Construction of an empty CrossLinkedRegion", "[CrossLinkedRegion]")
{
CrossLinkedRegion cross_linked_region;
}
SCENARIO("Construction of a CrossLinkedRegion with indices",
"[CrossLinkedRegion]")
{
WHEN("Allocating a CrossLinkedRegion with indices")
{
CrossLinkedRegion cross_linked_region(100, 120);
THEN("The member data are set accordingly")
{
REQUIRE(cross_linked_region.getStartIndex() == 100);
REQUIRE(cross_linked_region.getStopIndex() == 120);
REQUIRE(cross_linked_region.getCrossLinksRef().size() == 0);
REQUIRE(cross_linked_region.getCrossLinksCstRef().size() == 0);
}
}
}
SCENARIO(
"Construction of an empty CrossLinkedRegion and setting indices with setters",
"[CrossLinkedRegion]")
{
WHEN("Allocating a CrossLinkedRegion with indices")
{
CrossLinkedRegion cross_linked_region;
cross_linked_region.setStartIndex(100);
cross_linked_region.setStopIndex(120);
THEN("The member data are set accordingly")
{
REQUIRE(cross_linked_region.getStartIndex() == 100);
REQUIRE(cross_linked_region.getStopIndex() == 120);
REQUIRE(cross_linked_region.getCrossLinksRef().size() == 0);
REQUIRE(cross_linked_region.getCrossLinksCstRef().size() == 0);
}
}
}
SCENARIO(
"Construction of an empty CrossLinkedRegion and adding CrossLink instances",
"[CrossLinkedRegion]")
{
GIVEN("CrossLink instances")
{
test_utils_1_letter_cross_linked_region.initializeXpertmassLibrary();
PolChemDefCstSPtr pol_chem_def_csp =
test_utils_1_letter_cross_linked_region.msp_polChemDef;
QString polymer_file_path =
QString("%1/polymer-sequences/%2")
.arg(TESTS_INPUT_DIR)
.arg("cyan-fluorescent-protein-no-cross-link.mxp");
PolymerSPtr polymer_sp = Polymer::createSPtr(pol_chem_def_csp);
REQUIRE(polymer_sp->renderXmlPolymerFile(polymer_file_path));
REQUIRE(polymer_sp->size() == 240);
CrossLinkSPtr cross_link_1_sp =
std::make_shared<CrossLink>(pol_chem_def_csp,
polymer_sp,
"CFP-chromophore",
"-H2OH2",
"This is a comment for cross-link 1");
CrossLinkSPtr cross_link_2_sp =
std::make_shared<CrossLink>(pol_chem_def_csp,
polymer_sp,
"CFP-chromophore",
"-H2OH2",
"This is a comment for cross-link 2");
CrossLinkSPtr cross_link_3_sp =
std::make_shared<CrossLink>(pol_chem_def_csp,
polymer_sp,
"CFP-chromophore",
"-H2OH2",
"This is a comment for cross-link 3");
std::vector<CrossLinkSPtr> cross_links;
cross_links.push_back(cross_link_2_sp);
cross_links.push_back(cross_link_3_sp);
AND_GIVEN("A CrossLinkedRegion allocated with indices")
{
CrossLinkedRegion cross_linked_region(100, 120);
THEN("The member data are set accordingly")
{
REQUIRE(cross_linked_region.getStartIndex() == 100);
REQUIRE(cross_linked_region.getStopIndex() == 120);
REQUIRE(cross_linked_region.getCrossLinksRef().size() == 0);
REQUIRE(cross_linked_region.getCrossLinksCstRef().size() == 0);
}
WHEN(
"New CrossLink instances are added, these are stored in the "
"CrossLinkedRegion")
{
cross_linked_region.appendCrossLink(cross_link_1_sp);
REQUIRE(cross_linked_region.getCrossLinksCstRef().size() == 1);
cross_linked_region.appendCrossLinks(cross_links);
REQUIRE(cross_linked_region.getCrossLinksCstRef().size() == 3);
AND_WHEN(
"CrossLink instances are remove, these disappear from the "
"CrossLinkedRegion")
{
cross_linked_region.removeCrossLink(cross_link_1_sp);
REQUIRE(cross_linked_region.getCrossLinksCstRef().size() == 2);
REQUIRE(cross_linked_region.getCrossLinksCstRef()
.front()
->getComment()
.toStdString() == "This is a comment for cross-link 2");
cross_linked_region.removeCrossLinkAt(0);
REQUIRE(cross_linked_region.getCrossLinksCstRef().size() == 1);
REQUIRE(cross_linked_region.getCrossLinksCstRef()
.front()
->getComment()
.toStdString() == "This is a comment for cross-link 3");
}
}
}
}
}
} // namespace libXpertMassCore
} // namespace MsXpS
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