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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/FragmentationRule.hpp>
#include <libXpertMass/Sequence.hpp>
#include <libXpertMass/Monomer.hpp>
namespace MsXpS
{
namespace libXpertMassCore
{
TestUtils test_utils_frag_rule_1_letter("protein-1-letter", 1);
TestUtils test_utils_frag_rule_3_letters("protein-3-letters", 1);
ErrorList error_list_frag_rule;
SCENARIO(
"FragmentationRule objects can be constructed fully qualified in one go",
"[FragmentationRule]")
{
test_utils_frag_rule_1_letter.initializeXpertmassLibrary();
PolChemDefCstSPtr pol_chem_def_csp =
test_utils_frag_rule_1_letter.msp_polChemDef;
WHEN("Constructing a FragmentationRule with all valid parameters")
{
FragmentationRule frag_rule(
pol_chem_def_csp, "a-fgr-2", "F", "D", "E", "thecomment", "+H100");
THEN("The FragmentationRule is valid and does validate successfully")
{
REQUIRE(frag_rule.isValid());
REQUIRE(frag_rule.validate(error_list_frag_rule));
}
AND_THEN("The FragmentationRule is valid and does validate successfully")
{
REQUIRE(frag_rule.getName().toStdString() == "a-fgr-2");
REQUIRE(frag_rule.getPrevCode().toStdString() == "F");
REQUIRE(frag_rule.getCurrCode().toStdString() == "D");
REQUIRE(frag_rule.getNextCode().toStdString() == "E");
REQUIRE(frag_rule.getFormulaCstRef().getActionFormula().toStdString() ==
"+H100");
REQUIRE(frag_rule.getComment().toStdString() == "thecomment");
}
}
}
SCENARIO(
"FragmentationRule objects can be constructed from a <fgr> XML element",
"[FragmentationRule]")
{
PolChemDefCstSPtr pol_chem_def_csp =
test_utils_frag_rule_1_letter.msp_polChemDef;
WHEN("Constructing a FragmentationRule with a valid XML element")
{
// Totally fake fgr !!!
// <fgr>
// <name>a-fgr-2</name>
// <formula>+H100</formula>
// <prev-mnm-code>F</prev-mnm-code>
// <curr-mnm-code>D</curr-mnm-code>
// <next-mnm-code>E</next-mnm-code>
// <comment>thecomment</comment>
// </fgr>
QStringList dom_strings{"fgr", // 0
"name",
"a-fgr-2",
"formula",
"+H100",
"prev-mnm-code",
"F",
"curr-mnm-code",
"D",
"next-mnm-code",
"E",
"comment",
"thecomment"};
QDomDocument document =
test_utils_frag_rule_1_letter.craftFgrDomDocument(dom_strings);
QDomElement frag_rule_element =
document.elementsByTagName(dom_strings[0]).item(0).toElement();
// Use indentation 1 to mimick what happens in XpertMass.
// qDebug().noquote() << "The document:\n'"
// << document.toString(/*indentation*/ 1) << "'";
// We need to remove all spaces from the strings to be able to compare
// them. There must be a bug somewhere because with the original output, at
// the screen everything seems correct, but test FAILED.
QString document_string = document.toString(/*indentation*/ 0);
document_string = Utils::unspacify(document_string);
QString expected_string =
"<fgr><name>a-fgr-2</name><formula>+H100</formula><prev-mnm-code>F</"
"prev-mnm-code><curr-mnm-code>D</curr-mnm-code><next-mnm-code>E</"
"next-mnm-code><comment>thecomment</comment></fgr>";
expected_string = Utils::unspacify(expected_string);
REQUIRE(document_string.toStdString() == expected_string.toStdString());
FragmentationRule frag_rule(pol_chem_def_csp, frag_rule_element, 1);
THEN("The FragmentationRule is valid and does validate successfully")
{
REQUIRE(frag_rule.isValid());
REQUIRE(frag_rule.validate(error_list_frag_rule));
}
AND_THEN("The FragmentationRule is valid and does validate successfully")
{
REQUIRE(frag_rule.getName().toStdString() == "a-fgr-2");
REQUIRE(frag_rule.getPrevCode().toStdString() == "F");
REQUIRE(frag_rule.getCurrCode().toStdString() == "D");
REQUIRE(frag_rule.getNextCode().toStdString() == "E");
REQUIRE(frag_rule.getFormulaCstRef().getActionFormula().toStdString() ==
"+H100");
REQUIRE(frag_rule.getComment().toStdString() == "thecomment");
}
}
}
SCENARIO(
"FragmentationRule objects can be constructed empty and then initialized "
"piecemeal "
"until they are valid",
"[FragmentationRule]")
{
PolChemDefCstSPtr pol_chem_def_csp =
test_utils_frag_rule_1_letter.msp_polChemDef;
WHEN("Constructing a FragmentationRule with no valid parameter")
{
FragmentationRule frag_rule;
THEN("The FragmentationRule is invalid and does not validate successfully")
{
REQUIRE_FALSE(frag_rule.isValid());
REQUIRE_FALSE(frag_rule.validate(error_list_frag_rule));
}
AND_WHEN(
"Setting PolChemDef, a name, correct prev/curr/next codes, formula and "
"comment")
{
frag_rule.setPolchemDefCstSPtr(pol_chem_def_csp);
frag_rule.setName("a-fgr-2");
frag_rule.setPrevCode("F");
frag_rule.setCurrCode("D");
frag_rule.setNextCode("E");
frag_rule.setFormula(Formula("+H100"));
frag_rule.setComment("thecomment");
THEN("The FragmentationRule is valid and does validate successfully")
{
REQUIRE(frag_rule.isValid());
REQUIRE(frag_rule.validate(error_list_frag_rule));
AND_THEN("All the members are set correctly")
{
REQUIRE(frag_rule.getName().toStdString() == "a-fgr-2");
REQUIRE(frag_rule.getPrevCode().toStdString() == "F");
REQUIRE(frag_rule.getCurrCode().toStdString() == "D");
REQUIRE(frag_rule.getNextCode().toStdString() == "E");
REQUIRE(
frag_rule.getFormulaCstRef().getActionFormula().toStdString() ==
"+H100");
REQUIRE(frag_rule.getComment().toStdString() == "thecomment");
}
}
}
}
}
SCENARIO(
"FragmentationRule objects can be initialized from an <fgr> XML element",
"[FragmentationRule]")
{
PolChemDefCstSPtr pol_chem_def_csp =
test_utils_frag_rule_1_letter.msp_polChemDef;
// Totally fake fgr !!!
// <fgr>
// <name>a-fgr-2</name>
// <formula>+H100</formula>
// <prev-mnm-code>F</prev-mnm-code>
// <curr-mnm-code>D</curr-mnm-code>
// <next-mnm-code>E</next-mnm-code>
// <comment>thecomment</comment>
// </fgr>
QStringList dom_strings{"fgr", // 0
"name",
"a-fgr-2",
"formula",
"+H100",
"prev-mnm-code",
"F",
"curr-mnm-code",
"D",
"next-mnm-code",
"E",
"comment",
"thecomment"};
QDomDocument document =
test_utils_frag_rule_1_letter.craftFgrDomDocument(dom_strings);
QDomElement frag_rule_element =
document.elementsByTagName(dom_strings[0]).item(0).toElement();
// Use indentation 1 to mimick what happens in XpertMass.
// qDebug().noquote() << "The document:\n'"
// << document.toString(/*indentation*/ 1) << "'";
// We need to remove all spaces from the strings to be able to compare
// them. There must be a bug somewhere because with the original output, at
// the screen everything seems correct, but test FAILED.
QString document_string = document.toString(/*indentation*/ 0);
document_string = Utils::unspacify(document_string);
QString expected_string =
"<fgr><name>a-fgr-2</name><formula>+H100</formula><prev-mnm-code>F</"
"prev-mnm-code><curr-mnm-code>D</curr-mnm-code><next-mnm-code>E</"
"next-mnm-code><comment>thecomment</comment></fgr>";
expected_string = Utils::unspacify(expected_string);
REQUIRE(document_string.toStdString() == expected_string.toStdString());
FragmentationRule frag_rule(pol_chem_def_csp, frag_rule_element, 1);
WHEN(
"A FragmentationRule instance is allocated entirely free of data (only the "
"polymer chemistry definition is provided to the constructor)")
{
FragmentationRule frag_rule(pol_chem_def_csp, "");
THEN("The FragmentationRule instance is not valid and cannot validate")
{
REQUIRE(frag_rule.getName().toStdString() == "");
REQUIRE_FALSE(frag_rule.isValid());
REQUIRE_FALSE(frag_rule.validate(error_list_frag_rule));
AND_WHEN(
"The FragmentationRule instance is asked to render in itself the <fgr> "
"XML "
"element")
{
REQUIRE(frag_rule.renderXmlFgrElement(frag_rule_element));
AND_THEN("All the members are set correctly")
{
REQUIRE(frag_rule.getName().toStdString() == "a-fgr-2");
REQUIRE(frag_rule.getPrevCode().toStdString() == "F");
REQUIRE(frag_rule.getCurrCode().toStdString() == "D");
REQUIRE(frag_rule.getNextCode().toStdString() == "E");
REQUIRE(
frag_rule.getFormulaCstRef().getActionFormula().toStdString() ==
"+H100");
REQUIRE(frag_rule.getComment().toStdString() == "thecomment");
}
}
}
}
}
SCENARIO(
"FragmentationRule objects can output themselves to a <fgr> XML element",
"[FragmentationRule]")
{
PolChemDefCstSPtr pol_chem_def_csp =
test_utils_frag_rule_1_letter.msp_polChemDef;
QString expected_string =
"<fgr><name>a-fgr-2</name><formula>+H100</formula><prev-mnm-code>F</"
"prev-mnm-code><curr-mnm-code>D</curr-mnm-code><next-mnm-code>E</"
"next-mnm-code><comment>thecomment</comment></fgr>";
expected_string = Utils::unspacify(expected_string);
GIVEN("Construction a FragmentationRule fully initialized")
{
FragmentationRule frag_rule(
pol_chem_def_csp, "a-fgr-2", "F", "D", "E", "thecomment", "+H100");
THEN("The FragmentationRule is valid and does validate successfully")
{
REQUIRE(frag_rule.isValid());
REQUIRE(frag_rule.validate(error_list_frag_rule));
REQUIRE(frag_rule.getName().toStdString() == "a-fgr-2");
REQUIRE(frag_rule.getPrevCode().toStdString() == "F");
REQUIRE(frag_rule.getCurrCode().toStdString() == "D");
REQUIRE(frag_rule.getNextCode().toStdString() == "E");
REQUIRE(frag_rule.getFormulaCstRef().getActionFormula().toStdString() ==
"+H100");
REQUIRE(frag_rule.getComment().toStdString() == "thecomment");
}
WHEN("The FragmentationRule is exported as a <fgr> XML element")
{
QString xml_text = frag_rule.formatXmlFgrElement(/*offset*/ 1);
xml_text = Utils::unspacify(xml_text);
THEN("The obtained text is as expected")
{
REQUIRE(xml_text.toStdString() == expected_string.toStdString());
}
}
}
}
SCENARIO(
"FragmentationRule objects can be constructed by copy constructor or by "
"assigment "
"and then compared",
"[FragmentationRule]")
{
test_utils_frag_rule_1_letter.initializeXpertmassLibrary();
PolChemDefCstSPtr pol_chem_def_csp =
test_utils_frag_rule_1_letter.msp_polChemDef;
GIVEN("Construction a FragmentationRule fully initialized")
{
FragmentationRule frag_rule(
pol_chem_def_csp, "a-fgr-2", "F", "D", "E", "thecomment", "+H100");
THEN("The FragmentationRule is valid and does validate successfully")
{
REQUIRE(frag_rule.isValid());
REQUIRE(frag_rule.validate(error_list_frag_rule));
REQUIRE(frag_rule.getName().toStdString() == "a-fgr-2");
REQUIRE(frag_rule.getPrevCode().toStdString() == "F");
REQUIRE(frag_rule.getCurrCode().toStdString() == "D");
REQUIRE(frag_rule.getNextCode().toStdString() == "E");
REQUIRE(frag_rule.getFormulaCstRef().getActionFormula().toStdString() ==
"+H100");
REQUIRE(frag_rule.getComment().toStdString() == "thecomment");
}
WHEN("A new FragmentationRule is instantiated by copy-construction")
{
FragmentationRule new_frag_rule(frag_rule);
THEN(
"The new FragmentationRule is valid and does validate successfully and "
"all "
"the members are set correctly")
{
REQUIRE(new_frag_rule.isValid());
REQUIRE(new_frag_rule.validate(error_list_frag_rule));
REQUIRE(new_frag_rule.getName().toStdString() == "a-fgr-2");
REQUIRE(new_frag_rule.getPrevCode().toStdString() == "F");
REQUIRE(new_frag_rule.getCurrCode().toStdString() == "D");
REQUIRE(new_frag_rule.getNextCode().toStdString() == "E");
REQUIRE(
new_frag_rule.getFormulaCstRef().getActionFormula().toStdString() ==
"+H100");
REQUIRE(new_frag_rule.getComment().toStdString() == "thecomment");
AND_THEN("The comparison operator do work properly")
{
REQUIRE(new_frag_rule == frag_rule);
REQUIRE_FALSE(new_frag_rule != frag_rule);
}
}
}
WHEN("A new FragmentationRule is instantiated by assignment")
{
FragmentationRule new_frag_rule;
new_frag_rule = frag_rule;
THEN(
"The new FragmentationRule is valid and does validate successfully and "
"all "
"the members are set correctly")
{
REQUIRE(new_frag_rule.isValid());
REQUIRE(new_frag_rule.validate(error_list_frag_rule));
REQUIRE(new_frag_rule.getName().toStdString() == "a-fgr-2");
REQUIRE(new_frag_rule.getPrevCode().toStdString() == "F");
REQUIRE(new_frag_rule.getCurrCode().toStdString() == "D");
REQUIRE(new_frag_rule.getNextCode().toStdString() == "E");
REQUIRE(
new_frag_rule.getFormulaCstRef().getActionFormula().toStdString() ==
"+H100");
REQUIRE(new_frag_rule.getComment().toStdString() == "thecomment");
AND_THEN("The comparison operator do work properly")
{
REQUIRE(new_frag_rule == frag_rule);
REQUIRE_FALSE(new_frag_rule != frag_rule);
}
}
}
}
}
} // namespace libXpertMassCore
} // namespace MsXpS
|
