IonizeRule Class

Member Function Documentation

IonizeRule::IonizeRule()

Constructs an IonizeRule initialized as an empty object.

IonizeRule::IonizeRule(const IonizeRule &other)

Constructs an IonizeRule as a copy of other.

int IonizeRule::charge() const

Returns the charge.

See also setCharge().

QString *IonizeRule::formatXmlIonizeRuleElement(int offset, const QString &indent = QString(" "))

Formats a string suitable to use as an XML element.

Formats a string suitable to be used as an XML element in a polymer chemistry definition file. The typical ionization rule element that is generated in this function looks like this:

The DTD says this: <!ELEMENT ionizerule(formula,charge,level)>

A typical ionization rule element looks like this:

<ionizerule>
~~<formula>+H</formula>
~~<charge>1</charge>
~~<level>1</level>
</ionizerule>

offset times the indent string must be used as a lead in the formatting of elements.

Returns a dynamically allocated string that needs to be freed after use.

See also renderXmlIonizeRuleElement(const QDomElement &element).

QString IonizeRule::formula() const

Returns the formula.

bool IonizeRule::isValid() const

Returns true if this IonizeRule is valid, false otherwise.

See also validate().

int IonizeRule::level() const

Returns the ionization level.

See also setLevel().

bool IonizeRule::renderXmlIonizeRuleElement(const QDomElement &element)

Renders the ionization rule XML element.

The XML element is parsed and the data extracted from the XML data are set to this IonizeRule instance.

The DTD says this: <!ELEMENT ionizerule(formula,charge,level)>

A typical ionization rule element looks like this:

<ionizerule>
<formula>+H</formula>
<charge>1</charge>
<level>1</level>
</ionizerule>

Note that this IonizeRule is not valid, as it has not been validated by calling validate(). The caller is reponsible for checking the validity of the IonizeRule prior use.

Returns true if the parsing is successful, false otherwise.

See also formatXmlIonizeRuleElement(int offset, const QString &indent).

void IonizeRule::setCharge(int value)

Sets the charge to value.

An IonizeRule with a(charge <= 0) is invalid by definition. If so, the m_isValid member is set to false.

See also charge().

void IonizeRule::setLevel(int value)

Sets the ionzation level to value.

An IonizeRule might have an ionization level == 0 but not level < 0, as this means that the analyte is not ionized at all. If (level < 0), then the m_isValid member is set to false.

See also level().

[override virtual] QString IonizeRule::toString() const

Reimplements: Formula::toString() const.

Returns a string holding a textual representation of the member data.

[override virtual] bool IonizeRule::validate(IsotopicDataCstSPtr isotopic_data_csp)

Reimplements: Formula::validate(IsotopicDataCstSPtr isotopic_data_csp).

Validates this IonizeRule against the isotopic_data_csp.

An IonizeRule is valid if it generates a new m/z ratio after ionization (or deionization if (m_level == 0) of the analyte that is different than the previous one and if its Formula validates successfully. This means that the following should be true:

• The Formula should be valid (that is, should contain at least one atom (use a 0-weighing atom if necessary, like Nul from the polymer chemistry definitions shipped with the software);
• The charge should > 0;
• The level should >= 0;

If these three tests do not fail, the IonizeRule is considered valid and the m_isValid boolean value is set to true; false otherwise.

Returns true if validation succeeds, false otherwise.

See also Formula::validate().

bool IonizeRule::operator!=(const IonizeRule &other) const

Returns true if this IonizeRule is different than other, false otherwise.

IonizeRule &IonizeRule::operator=(const IonizeRule &other)

Assigns other to this IonizeRule. Returns a reference to this ionization rule.

bool IonizeRule::operator==(const IonizeRule &other) const

Returns true if this IonizeRule is identical to other, false otherwise.