CleavageRule Class

Member Function Documentation

CleavageRule::CleavageRule(MsXpS::libXpertMassCore::PolChemDefCstSPtr pol_chem_def_csp)

Constructs a CleavageRule instance with pol_chem_def_csp as the polymer chemistry definition.

The validiy status (m_isValid) of this install will be set to false.

CleavageRule::CleavageRule(MsXpS::libXpertMassCore::PolChemDefCstSPtr pol_chem_def_csp, const QString &name, const QString &left_code, const QString &left_formula, const QString &right_code, const QString &right_formula)

Constructs a CleavageRule instance

• pol_chem_def_csp: Polymer chemistry definition.
• name: the name.
• left_code: The Monomer code at the left of the cleavage site.
• left_formula: .The Formula to be applied onto the left monomer code.
• right_code: .The Monomer code at the right of the cleavage site.
• right_formula: .The Formula to be applied onto the right monomer code.

After setting the member data, the instance is validated and the result is set to m_isValid.

CleavageRule::CleavageRule(const MsXpS::libXpertMassCore::CleavageRule &other)

Constructs a CleavageRule instance as a copy of other.

After setting the member data, the instance is validated and the result is set to m_isValid.

[noexcept] CleavageRule::~CleavageRule()

Destructs this CleavageRule instance

QString CleavageRule::formatXmlClrElement(int offset, const QString &indent = Utils::xmlIndentationToken)

Formats a string representing this CleavageRule instance suitable to use as an XML element.

The typical cleavage rule element that is generated in this function looks like this:

<clr>
<re-mnm-code>M</re-mnm-code>
<re-formula>-CH2S+O</re-formula>
</clr>

The formatting of the XML element takes into account offset and indent by prepending the string with offset * indent character substring.

indent defaults to two spaces.

Returns a string.

const QString &CleavageRule::getLeftCode() const

Returns the left code.

const MsXpS::libXpertMassCore::Formula &CleavageRule::getLeftFormula() const

Returns the left formula.

const QString &CleavageRule::getName() const

Returns the name.

MsXpS::libXpertMassCore::PolChemDefCstSPtr CleavageRule::getPolchemDefCstSPtr() const

Returns the PolChemDef.

const QString &CleavageRule::getRightCode() const

Returns the right code.

const MsXpS::libXpertMassCore::Formula &CleavageRule::getRightFormula() const

Returns the right formula.

bool CleavageRule::isValid() const

Returns the validity status of this CleavageRule.

bool CleavageRule::renderXmlClrElement(const QDomElement &element, int version)

Parses the CleavageRule XML element using a versioned function.

Upon parsing of the element, its data are validated and set to this CleavageRule instance, thus essentially initializing it.

Returns true if parsing and validation were successful, false otherwise.

void CleavageRule::setLeftCode(const QString &code)

Sets the left code.

After setting the member data, the instance is validated and the result is set to m_isValid.

void CleavageRule::setLeftFormula(const MsXpS::libXpertMassCore::Formula &formula)

Sets the left formula.

After setting the member data, the instance is validated and the result is set to m_isValid.

void CleavageRule::setName(const QString &name)

Sets the name to name.

After setting the member data, the instance is validated and the result is set to m_isValid.

void CleavageRule::setPolchemDefCstSPtr(MsXpS::libXpertMassCore::PolChemDefCstSPtr pol_chem_def_csp)

Sets the PolChemDef to pol_chem_def_csp.

After setting the member data, the instance is validated and the result is set to m_isValid.

void CleavageRule::setRightCode(const QString &code)

Sets the right code.

After setting the member data, the instance is validated and the result is set to m_isValid.

void CleavageRule::setRightFormula(const MsXpS::libXpertMassCore::Formula &formula)

Sets the right formula.

After setting the member data, the instance is validated and the result is set to m_isValid.

bool CleavageRule::validate(MsXpS::libXpertMassCore::ErrorList *error_list_p) const

Validates this CleavageRule instance and stores error messages to error_list_p.

Validation entails the following:

• The member PolChemDef cannot be nullptr;
• The member name cannot be empty;
• If the left monomer code is not empty, it must be known to the polymer chemistry definition. In that case, if the left formula is not empty, it needs to validate successfully.
• The same logic is applied to the monomer at the right hand side of the cleavage site.

Sets m_isValid to true if the validation is successful, false otherwise. Returns m_isValid.

bool CleavageRule::operator!=(const MsXpS::libXpertMassCore::CleavageRule &other) const

Returns true if this and other are different.

MsXpS::libXpertMassCore::CleavageRule &CleavageRule::operator=(const MsXpS::libXpertMassCore::CleavageRule &other)

Assigns to other to this CleavageRule instance.

After setting the member data, the instance is validated and the result is set to m_isValid.

Returns a reference to this CleavageRule instance.

bool CleavageRule::operator==(const MsXpS::libXpertMassCore::CleavageRule &other) const

Returns true if this and other are identical.