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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/CleavageAgent.hpp>
#include <libXpertMass/Sequence.hpp>
#include <libXpertMass/Monomer.hpp>
namespace MsXpS
{
namespace libXpertMassCore
{
TestUtils test_utils_cleavage_agent_1_letter("protein-1-letter", 1);
TestUtils test_utils_cleavage_agent_3_letters("protein-3-letters", 1);
ErrorList error_list_cleavage_agent;
SCENARIO(
"CleavageAgent objects can be constructed empty and then initialized "
"piecemeal -until they are valid",
"[CleavageAgent]")
{
test_utils_cleavage_agent_1_letter.initializeXpertmassLibrary();
PolChemDefCstSPtr pol_chem_def_csp =
test_utils_cleavage_agent_1_letter.msp_polChemDef;
GIVEN("A CleavageAgent constructed with no parameter at all")
{
CleavageAgent cleavage_agent;
REQUIRE_FALSE(cleavage_agent.isValid());
REQUIRE_FALSE(cleavage_agent.validate(error_list_cleavage_agent));
WHEN("The PolChemDef is set with the setter")
{
cleavage_agent.setPolchemDefCstSPtr(pol_chem_def_csp);
THEN(
"The CleavageAgent is still invalid and does not validate successfully")
{
REQUIRE(cleavage_agent.getPolchemDefCstSPtr() == pol_chem_def_csp);
REQUIRE_FALSE(cleavage_agent.isValid());
REQUIRE_FALSE(cleavage_agent.validate(error_list_cleavage_agent));
}
AND_WHEN("The name is set with the setter")
{
cleavage_agent.setName("Trypsin");
REQUIRE(cleavage_agent.getName().toStdString() == "Trypsin");
THEN(
"The CleavageAgent is still invalid and does not validate "
"successfully")
{
REQUIRE_FALSE(cleavage_agent.isValid());
REQUIRE_FALSE(cleavage_agent.validate(error_list_cleavage_agent));
}
AND_WHEN("The pattern is set")
{
cleavage_agent.setPattern("K/;-K/P;R/");
THEN(
"The CleavageAgent is fully initialized with proper CleavageMotif "
"objects (although no CleavageRule objects)")
{
QString expected_text = "Trypsin - K/;-K/P;R/ - 3 motifs - 0 rules";
REQUIRE(cleavage_agent.toString().toStdString() == expected_text.toStdString());
REQUIRE(cleavage_agent.isValid());
REQUIRE(cleavage_agent.validate(error_list_cleavage_agent));
REQUIRE(cleavage_agent.getMotifsCstRef().size() == 3);
REQUIRE(
cleavage_agent.getMotifsRef().at(0)->getMotif().toStdString() ==
"K");
REQUIRE(cleavage_agent.getMotifsCstRef()
.at(0)
->getMotif()
.toStdString() == "K");
REQUIRE(
cleavage_agent.getMotifsCstRef().at(0)->getCleavageAction() ==
Enums::CleavageAction::CLEAVE);
REQUIRE(cleavage_agent.getMotifsCstRef().at(0)->getOffset() == 1);
REQUIRE(cleavage_agent.getMotifsCstRef().at(0)->isValid());
REQUIRE(cleavage_agent.getMotifsCstRef().at(0)->validate(
error_list_cleavage_agent));
REQUIRE(cleavage_agent.getMotifsCstRef()
.at(1)
->getMotif()
.toStdString() == "KP");
REQUIRE(
cleavage_agent.getMotifsCstRef().at(1)->getCleavageAction() ==
Enums::CleavageAction::NO_CLEAVE);
REQUIRE(cleavage_agent.getMotifsCstRef().at(1)->getOffset() == 1);
REQUIRE(cleavage_agent.getMotifsCstRef().at(1)->isValid());
REQUIRE(cleavage_agent.getMotifsCstRef().at(1)->validate(
error_list_cleavage_agent));
REQUIRE(cleavage_agent.getMotifsCstRef()
.at(2)
->getMotif()
.toStdString() == "R");
REQUIRE(
cleavage_agent.getMotifsCstRef().at(2)->getCleavageAction() ==
Enums::CleavageAction::CLEAVE);
REQUIRE(cleavage_agent.getMotifsCstRef().at(2)->getOffset() == 1);
REQUIRE(cleavage_agent.getMotifsCstRef().at(2)->isValid());
REQUIRE(cleavage_agent.getMotifsCstRef().at(2)->validate(
error_list_cleavage_agent));
}
}
}
}
}
}
SCENARIO(
"CleavageAgent objects can be copy- or assignment-constructed and compared",
"[CleavageAgent]")
{
test_utils_cleavage_agent_1_letter.initializeXpertmassLibrary();
PolChemDefCstSPtr pol_chem_def_csp =
test_utils_cleavage_agent_1_letter.msp_polChemDef;
GIVEN("A CleavageAgent constructed with full parameters (with CleavageRules)")
{
CleavageAgent cleavage_agent(pol_chem_def_csp, "Trypsin", "K/;-K/P;R/");
CleavageRuleSPtr cleavage_rule_sp = std::make_shared<CleavageRule>(
pol_chem_def_csp, "Homoseryl", "A", "+CH3COOH", "M", "-CH2S+O");
cleavage_agent.getRulesRef().push_back(cleavage_rule_sp);
cleavage_rule_sp = std::make_shared<CleavageRule>(pol_chem_def_csp,
"Heteroseryl",
"C",
"+CH3COOH+CH3COOH",
"N",
"-CH2S+O-CH2S+O");
cleavage_agent.getRulesRef().push_back(cleavage_rule_sp);
THEN("The CleavageAgent is valid and validates successfully")
{
REQUIRE(cleavage_agent.isValid());
REQUIRE(cleavage_agent.validate(error_list_cleavage_agent));
REQUIRE(cleavage_agent.getMotifsCstRef().size() == 3);
REQUIRE(
cleavage_agent.getMotifsCstRef().at(0)->getMotif().toStdString() ==
"K");
REQUIRE(cleavage_agent.getMotifsCstRef().at(0)->getCleavageAction() ==
Enums::CleavageAction::CLEAVE);
REQUIRE(cleavage_agent.getMotifsCstRef().at(0)->getOffset() == 1);
REQUIRE(cleavage_agent.getMotifsCstRef().at(0)->isValid());
REQUIRE(cleavage_agent.getMotifsCstRef().at(0)->validate(
error_list_cleavage_agent));
REQUIRE(
cleavage_agent.getMotifsCstRef().at(1)->getMotif().toStdString() ==
"KP");
REQUIRE(cleavage_agent.getMotifsCstRef().at(1)->getCleavageAction() ==
Enums::CleavageAction::NO_CLEAVE);
REQUIRE(cleavage_agent.getMotifsCstRef().at(1)->getOffset() == 1);
REQUIRE(cleavage_agent.getMotifsCstRef().at(1)->isValid());
REQUIRE(cleavage_agent.getMotifsCstRef().at(1)->validate(
error_list_cleavage_agent));
REQUIRE(
cleavage_agent.getMotifsCstRef().at(2)->getMotif().toStdString() ==
"R");
REQUIRE(cleavage_agent.getMotifsCstRef().at(2)->getCleavageAction() ==
Enums::CleavageAction::CLEAVE);
REQUIRE(cleavage_agent.getMotifsCstRef().at(2)->getOffset() == 1);
REQUIRE(cleavage_agent.getMotifsCstRef().at(2)->isValid());
REQUIRE(cleavage_agent.getMotifsCstRef().at(2)->validate(
error_list_cleavage_agent));
REQUIRE(cleavage_agent.getRulesCstRef().size() == 2);
}
WHEN(
"Two other CleavageAgent are either copy-constructed or "
"assignment-copied")
{
CleavageAgent other_cleavage_agent(cleavage_agent);
CleavageAgent new_cleavage_agent;
new_cleavage_agent = other_cleavage_agent;
THEN("They are identical to the original one")
{
REQUIRE(new_cleavage_agent.isValid());
REQUIRE(new_cleavage_agent.validate(error_list_cleavage_agent));
REQUIRE(new_cleavage_agent.getMotifsCstRef().size() == 3);
REQUIRE(new_cleavage_agent.getMotifsCstRef()
.at(0)
->getMotif()
.toStdString() == "K");
REQUIRE(
new_cleavage_agent.getMotifsCstRef().at(0)->getCleavageAction() ==
Enums::CleavageAction::CLEAVE);
REQUIRE(new_cleavage_agent.getMotifsCstRef().at(0)->getOffset() == 1);
REQUIRE(new_cleavage_agent.getMotifsCstRef().at(0)->isValid());
REQUIRE(new_cleavage_agent.getMotifsCstRef().at(0)->validate(
error_list_cleavage_agent));
REQUIRE(new_cleavage_agent.getMotifsCstRef()
.at(1)
->getMotif()
.toStdString() == "KP");
REQUIRE(
new_cleavage_agent.getMotifsCstRef().at(1)->getCleavageAction() ==
Enums::CleavageAction::NO_CLEAVE);
REQUIRE(new_cleavage_agent.getMotifsCstRef().at(1)->getOffset() == 1);
REQUIRE(new_cleavage_agent.getMotifsCstRef().at(1)->isValid());
REQUIRE(new_cleavage_agent.getMotifsCstRef().at(1)->validate(
error_list_cleavage_agent));
REQUIRE(new_cleavage_agent.getMotifsCstRef()
.at(2)
->getMotif()
.toStdString() == "R");
REQUIRE(
new_cleavage_agent.getMotifsCstRef().at(2)->getCleavageAction() ==
Enums::CleavageAction::CLEAVE);
REQUIRE(new_cleavage_agent.getMotifsCstRef().at(2)->getOffset() == 1);
REQUIRE(new_cleavage_agent.getMotifsCstRef().at(2)->isValid());
REQUIRE(new_cleavage_agent.getMotifsCstRef().at(2)->validate(
error_list_cleavage_agent));
REQUIRE(new_cleavage_agent.getRulesCstRef().size() == 2);
}
THEN("The comparison operators return correct results")
{
REQUIRE(new_cleavage_agent == cleavage_agent);
REQUIRE_FALSE(new_cleavage_agent != cleavage_agent);
REQUIRE(new_cleavage_agent == new_cleavage_agent);
REQUIRE_FALSE(new_cleavage_agent != new_cleavage_agent);
}
AND_WHEN("One CleavageAgent's name is modified")
{
cleavage_agent.setName("OtherName");
THEN("The comparison operators return correct results")
{
REQUIRE_FALSE(new_cleavage_agent == cleavage_agent);
REQUIRE(new_cleavage_agent != cleavage_agent);
}
}
AND_WHEN("One CleavageAgent's motifs is removed")
{
cleavage_agent.setName("Trypsin");
cleavage_agent.getMotifsRef().erase(
cleavage_agent.getMotifsRef().begin());
THEN("The comparison operators return correct results")
{
REQUIRE_FALSE(new_cleavage_agent == cleavage_agent);
REQUIRE(new_cleavage_agent != cleavage_agent);
}
}
AND_WHEN("One CleavageAgent's motif is modified")
{
cleavage_agent = new_cleavage_agent;
REQUIRE(new_cleavage_agent == cleavage_agent);
cleavage_agent.getMotifsRef().front()->setMotif("M");
REQUIRE(
cleavage_agent.getMotifsRef().front()->getMotif().toStdString() ==
"M");
THEN(
"The two CleavageAgent instances are the same because the motif is a "
"vector of MonomerSPtr and the modification is done to the managed "
"object")
{
// The cleavage agents are still the same, because the
// Motif is actually MonomerSPtr which are shared.
REQUIRE(new_cleavage_agent == cleavage_agent);
REQUIRE_FALSE(new_cleavage_agent != cleavage_agent);
}
}
AND_WHEN("One CleavageAgent's cleavage rule is modified")
{
cleavage_agent = new_cleavage_agent;
REQUIRE(new_cleavage_agent == cleavage_agent);
cleavage_agent.getRulesRef().front()->setLeftCode("G");
REQUIRE(
cleavage_agent.getRulesRef().front()->getLeftCode().toStdString() ==
"G");
THEN(
"The two CleavageAgent instances are the same because the rules are "
"stored as a vector of CleavageRuleSPtr and the modification is done "
"to the managed object")
{
REQUIRE(new_cleavage_agent == cleavage_agent);
REQUIRE_FALSE(new_cleavage_agent != cleavage_agent);
}
}
AND_WHEN("One CleavageAgent's cleavage rule is removed")
{
cleavage_agent = new_cleavage_agent;
REQUIRE(new_cleavage_agent == cleavage_agent);
cleavage_agent.getRulesRef().erase(
cleavage_agent.getRulesRef().begin());
THEN("The two CleavageAgent instances are different")
{
REQUIRE_FALSE(new_cleavage_agent == cleavage_agent);
REQUIRE(new_cleavage_agent != cleavage_agent);
}
}
}
}
}
SCENARIO(
"CleavageAgent objects can be initialized from the polymer chemistry "
"definition",
"[CleavageAgent]")
{
PolChemDefCstSPtr pol_chem_def_csp =
test_utils_cleavage_agent_1_letter.msp_polChemDef;
WHEN("A CleavageAgent is initialized with name")
{
CleavageAgent cleavage_agent(pol_chem_def_csp, "Trypsin", "NOT_SET");
THEN("The matching CleavageAgent can be retrieved from PolChemDef")
{
CleavageAgentCstSPtr cleavage_agent_csp =
cleavage_agent.getFromPolChemDefByName();
REQUIRE(cleavage_agent_csp != nullptr);
REQUIRE(cleavage_agent_csp->getName().toStdString() == "Trypsin");
}
WHEN("A CleavageAgent is initialized with no name")
{
CleavageAgent cleavage_agent(pol_chem_def_csp, "", "NOT_SET");
THEN("The matching CleavageAgent can not be retrieved from PolChemDef")
{
CleavageAgentCstSPtr cleavage_agent_csp =
cleavage_agent.getFromPolChemDefByName();
REQUIRE(cleavage_agent_csp == nullptr);
}
}
WHEN("A CleavageAgent is initialized with proper name")
{
CleavageAgent cleavage_agent(pol_chem_def_csp, "Trypsin", "NOT_SET");
THEN("The matching CleavageAgent is not known to the PolChemDef")
{
REQUIRE(cleavage_agent.isKnownByNameInPolChemDef() ==
Enums::PolChemDefEntityStatus::ENTITY_KNOWN);
}
}
WHEN("A CleavageAgent is initialized with no name")
{
CleavageAgent cleavage_agent(pol_chem_def_csp, "", "NOT_SET");
THEN("The matching CleavageAgent is not known to the PolChemDef")
{
REQUIRE(cleavage_agent.isKnownByNameInPolChemDef() ==
Enums::PolChemDefEntityStatus::ENTITY_NOT_KNOWN);
}
}
}
}
SCENARIO(
"CleavageAgent objects can be initialized from a <cls> XML element and "
"can export themselves as <cla>",
"[CleavageAgent]")
{
PolChemDefCstSPtr pol_chem_def_csp =
test_utils_cleavage_agent_1_letter.msp_polChemDef;
// int cls_element_index = 0;
// int name_element_index = 1;
// int name_text_index = 2;
// int pattern_element_index = 3;
// int pattern_text_index = 4;
// int clr_element_index = 5;
// int clr_name_element_index = 6;
// int clr_name_text_index = 7;
// int le_mnm_code_element_index = 8;
// int le_mnm_code_text_index = 9;
// int le_formula_element_index = 10;
// int le_formula_text_index = 11;
// int re_mnm_code_element_index = 12;
// int re_mnm_code_text_index = 13;
// int re_formula_element_index = 14;
// int re_formula_text_index = 15;
// FAKE cls!
// <cls>
// <name>CyanogenBromide</name>
// <pattern>M/A</pattern>
// <clr>
// <le-mnm-code>M</le-mnm-code>
// <le-formula>-C1H2S1+O1</le-formula>
// <re-mnm-code>A</re-mnm-code>
// <re-formula>-CH3COOH</re-formula>
// </clr>
// </cls>
QStringList dom_strings{"cls", // 0
"name", // 1
"CyanogenBromide", // 2
"pattern", // 3
"M/A", // 4
"clr", // 5
"name", // 6
"Homoseryl", // 7
"le-mnm-code", // 8
"M", // 9
"le-formula", // 10
"-C1H2S1+O1", // 11
"re-mnm-code", // 12
"A", // 13
"re-formula", // 14
"-CH3COOH"}; // 15
QDomDocument document =
test_utils_cleavage_agent_1_letter.craftClsDomDocument(dom_strings);
QDomElement cleavage_agent_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);
// We need two versions: cls for version 1 and cla for version 2.
QString expected_cls_string =
"<cls><name>CyanogenBromide</name><pattern>M/A</"
"pattern><clr><name>Homoseryl</name><le-mnm-code>M</"
"le-mnm-code><le-formula>-C1H2S1+O1</le-formula><re-mnm-code>A</"
"re-mnm-code><re-formula>-CH3COOH</re-formula></clr></cls>";
expected_cls_string = Utils::unspacify(expected_cls_string);
QString expected_cla_string =
"<cla><name>CyanogenBromide</name><pattern>M/A</"
"pattern><clr><name>Homoseryl</name><le-mnm-code>M</"
"le-mnm-code><le-formula>-C1H2S1+O1</le-formula><re-mnm-code>A</"
"re-mnm-code><re-formula>-CH3COOH</re-formula></clr></cla>";
expected_cla_string = Utils::unspacify(expected_cla_string);
REQUIRE(document_string.toStdString() == expected_cls_string.toStdString());
WHEN("Creating a CleavageAgent only with PolChemDef")
{
CleavageAgent cleavage_agent(pol_chem_def_csp);
AND_WHEN("Initializing it with an XML <cls> element")
{
REQUIRE(cleavage_agent.renderXmlClsElement(cleavage_agent_element,
/*version*/ 1));
THEN("The initalized CleavageAgent is valid and validates successfully")
{
THEN("The CleavageAgent is valid and validates successfully")
{
REQUIRE(cleavage_agent.isValid());
REQUIRE(cleavage_agent.validate(error_list_cleavage_agent));
REQUIRE(cleavage_agent.getName().toStdString() == "CyanogenBromide");
REQUIRE(cleavage_agent.getPattern().toStdString() == "M/A");
REQUIRE(cleavage_agent.getMotifsCstRef().size() == 1);
REQUIRE(
cleavage_agent.getMotifsCstRef().at(0)->getMotif().toStdString() ==
"MA");
REQUIRE(cleavage_agent.getMotifsCstRef().at(0)->getCleavageAction() ==
Enums::CleavageAction::CLEAVE);
REQUIRE(cleavage_agent.getMotifsCstRef().at(0)->getOffset() == 1);
REQUIRE(cleavage_agent.getMotifsCstRef().at(0)->isValid());
REQUIRE(cleavage_agent.getMotifsCstRef().at(0)->validate(
error_list_cleavage_agent));
REQUIRE(cleavage_agent.getRulesCstRef().size() == 1);
REQUIRE(cleavage_agent.getCleavageRuleIndexByName("Homoseryl") == 0);
CleavageRuleCstSPtr cleavage_rule_csp =
cleavage_agent.getCleavageRuleCstSPtrByName("Homoseryl");
REQUIRE(cleavage_rule_csp != nullptr);
REQUIRE(cleavage_rule_csp->validate(error_list_cleavage_agent));
REQUIRE(cleavage_rule_csp->getName().toStdString() == "Homoseryl");
REQUIRE(cleavage_rule_csp->getLeftCode().toStdString() == "M");
REQUIRE(cleavage_rule_csp->getLeftFormula()
.getActionFormula()
.toStdString() == "-C1H2S1+O1");
REQUIRE(cleavage_rule_csp->getRightCode().toStdString() == "A");
REQUIRE(cleavage_rule_csp->getRightFormula()
.getActionFormula()
.toStdString() == "-CH3COOH");
CleavageRuleSPtr cleavage_rule_sp =
cleavage_agent.getCleavageRuleSPtrByName("Homoseryl");
REQUIRE(cleavage_rule_sp != nullptr);
REQUIRE(cleavage_rule_sp->validate(error_list_cleavage_agent));
REQUIRE(cleavage_rule_sp->getName().toStdString() == "Homoseryl");
REQUIRE(cleavage_rule_sp->getLeftCode().toStdString() == "M");
REQUIRE(cleavage_rule_sp->getLeftFormula()
.getActionFormula()
.toStdString() == "-C1H2S1+O1");
REQUIRE(cleavage_rule_sp->getRightCode().toStdString() == "A");
REQUIRE(cleavage_rule_sp->getRightFormula()
.getActionFormula()
.toStdString() == "-CH3COOH");
}
}
AND_WHEN("Exporting itself as a <cla> XML element")
{
QString xml_text = cleavage_agent.formatXmlClaElement(/*offset*/ 1);
xml_text = Utils::unspacify(xml_text);
THEN("The text must be identical to the expected XML <cla> string")
{
REQUIRE(xml_text.toStdString() == expected_cla_string.toStdString());
}
}
}
}
}
SCENARIO(
"CleavageAgent objects can be initialized from a <cla> XML element and "
"can "
"export themselves as such also",
"[CleavageAgent]")
{
PolChemDefCstSPtr pol_chem_def_csp =
test_utils_cleavage_agent_1_letter.msp_polChemDef;
// int cla_element_index = 0;
// int name_element_index = 1;
// int name_text_index = 2;
// int pattern_element_index = 3;
// int pattern_text_index = 4;
// int clr_element_index = 5;
// int clr_name_element_index = 6;
// int clr_name_text_index = 7;
// int le_mnm_code_element_index = 8;
// int le_mnm_code_text_index = 9;
// int le_formula_element_index = 10;
// int le_formula_text_index = 11;
// int re_mnm_code_element_index = 12;
// int re_mnm_code_text_index = 13;
// int re_formula_element_index = 14;
// int re_formula_text_index = 15;
// FAKE cla!
// <cla>
// <name>CyanogenBromide</name>
// <pattern>M/A</pattern>
// <clr>
// <le-mnm-code>M</le-mnm-code>
// <le-formula>-C1H2S1+O1</le-formula>
// <re-mnm-code>A</re-mnm-code>
// <re-formula>-CH3COOH</re-formula>
// </clr>
// </cla>
QStringList dom_strings{"cla", // 0
"name", // 1
"CyanogenBromide", // 2
"pattern", // 3
"M/A", // 4
"clr", // 5
"name", // 6
"Homoseryl", // 7
"le-mnm-code", // 8
"M", // 9
"le-formula", // 10
"-C1H2S1+O1", // 11
"re-mnm-code", // 12
"A", // 13
"re-formula", // 14
"-CH3COOH"}; // 15
QDomDocument document =
test_utils_cleavage_agent_1_letter.craftClaDomDocument(dom_strings);
QDomElement cleavage_agent_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_cla_string =
"<cla><name>CyanogenBromide</name><pattern>M/A</"
"pattern><clr><name>Homoseryl</name><le-mnm-code>M</"
"le-mnm-code><le-formula>-C1H2S1+O1</le-formula><re-mnm-code>A</"
"re-mnm-code><re-formula>-CH3COOH</re-formula></clr></cla>";
expected_cla_string = Utils::unspacify(expected_cla_string);
REQUIRE(document_string.toStdString() == expected_cla_string.toStdString());
WHEN("Creating a CleavageAgent only with PolChemDef")
{
CleavageAgent cleavage_agent(pol_chem_def_csp);
AND_WHEN("Initializing it with an XML <cls> element")
{
REQUIRE(cleavage_agent.renderXmlClaElement(cleavage_agent_element,
/*version*/ 1));
THEN("The initalized CleavageAgent is valid and validates successfully")
{
THEN("The CleavageAgent is valid and validates successfully")
{
REQUIRE(cleavage_agent.isValid());
REQUIRE(cleavage_agent.validate(error_list_cleavage_agent));
REQUIRE(cleavage_agent.getName().toStdString() == "CyanogenBromide");
REQUIRE(cleavage_agent.getPattern().toStdString() == "M/A");
REQUIRE(cleavage_agent.getMotifsCstRef().size() == 1);
REQUIRE(
cleavage_agent.getMotifsCstRef().at(0)->getMotif().toStdString() ==
"MA");
REQUIRE(cleavage_agent.getMotifsCstRef().at(0)->getCleavageAction() ==
Enums::CleavageAction::CLEAVE);
REQUIRE(cleavage_agent.getMotifsCstRef().at(0)->getOffset() == 1);
REQUIRE(cleavage_agent.getMotifsCstRef().at(0)->isValid());
REQUIRE(cleavage_agent.getMotifsCstRef().at(0)->validate(
error_list_cleavage_agent));
REQUIRE(cleavage_agent.getRulesCstRef().size() == 1);
CleavageRuleSPtr cleavage_rule_sp =
cleavage_agent.getCleavageRuleSPtrByName("Homoseryl");
REQUIRE(cleavage_rule_sp != nullptr);
REQUIRE(cleavage_rule_sp->validate(error_list_cleavage_agent));
REQUIRE(cleavage_rule_sp->getName().toStdString() == "Homoseryl");
REQUIRE(cleavage_rule_sp->getLeftCode().toStdString() == "M");
REQUIRE(cleavage_rule_sp->getLeftFormula()
.getActionFormula()
.toStdString() == "-C1H2S1+O1");
REQUIRE(cleavage_rule_sp->getRightCode().toStdString() == "A");
REQUIRE(cleavage_rule_sp->getRightFormula()
.getActionFormula()
.toStdString() == "-CH3COOH");
}
}
AND_WHEN("Exporting itself as a <cla> XML element")
{
QString xml_text = cleavage_agent.formatXmlClaElement(/*offset*/ 1);
xml_text = Utils::unspacify(xml_text);
THEN("The text must be identical to the expected XML <cla> string")
{
REQUIRE(xml_text.toStdString() == expected_cla_string.toStdString());
}
}
}
}
}
} // namespace libXpertMassCore
} // namespace MsXpS
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