MsXpS::libXpertMassCore::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 with a number of parameters.

• pol_chem_def_csp: initializes mcsp_polChemDef, the Polymer chemistry definition.
• name: initializes m_name.
• left_code: initializes m_leftCode, the Monomer code at the left of the cleavage site.
• left_formula: initializes m_leftFormula, the Formula to be applied onto the left monomer code.
• right_code: initializes m_rightCode, the Monomer code at the right of the cleavage site.
• right_formula: initializes m_rightFormula, the Formula to be applied onto the right monomer code.

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

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 m_isValid is set to the result of that validation.

[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.

A typical element reads like this:

<clr>
<name>Homoseryl</name>
<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 the formatted string.

See also renderXmlClrElement().

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 mcsp_polChemDef PolChemDef member.

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, the member data are updated from the parsed element entities and validated along the process, thus essentially initializing this instance.

A typical element reads like this:

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

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

See also formatXmlClrElement().

void CleavageRule::setLeftCode(const QString &code)

Sets the left code.

This is the code of the Monomer that sits left of the cleavage site. Upon the actual cleavage, this Monomer will be the right-end (Enums::PolymerEnd::RIGHT) Monomer of the left Oligomer.

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

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

Sets the m_leftFormula member to formula.

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

void CleavageRule::setName(const QString &name)

Sets the name to name.

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

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 m_isValid is set to the result of that validation.

void CleavageRule::setRightCode(const QString &code)

Sets the right code.

This is the code of the Monomer that sits right of the cleavage site. Upon the actual cleavage, this Monomer will be the left-end (Enums::PolymerEnd::LEFT) Monomer of the right Oligomer.

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

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

Sets the m_rightFormula member to formula.

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

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

Returns true if validation of this CleavageRule instance was successful, false otherwise.

The validation process encompasses the following steps:

• The member mcsp_polChemDef cannot be nullptr.
• The member m_name name cannot be empty;
• If the member m_leftCode left monomer code is not empty, it must be known to the polymer chemistry definition. In that case, if the member m_leftFormula 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.

If errors are encountered and error_list_p is not nullptr, these errors are stored in that ErrorList.

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

Returns true if this instance and other are different.

Returns the negated value of operator==().

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

Assigns other to this CleavageRule instance.

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

Returns a reference to this CleavageRule instance.

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

Returns true if this instance and other are identical.

See also operator!=().