MsXpS::libXpertMassCore::Averagine Class

Member Function Documentation

[explicit invokable] Averagine::Averagine(QObject *parent = nullptr)

Constructs a uninitialized Averagine instance.

m_isValid is inherently false.

[explicit invokable] Averagine::Averagine(MsXpS::libXpertMassCore::IsotopicDataCstSPtr isotopic_data_csp, QObject *parent = nullptr)

Constructs a Averagine instance setting the isotopic data to isotopic_data_csp and parentship to parent.

m_isValid is inherently false because the m_mono and m_avg masses cannot be computed without the formula.

[explicit invokable] Averagine::Averagine(const MsXpS::libXpertMassCore::Formula &formula, QObject *parent = nullptr)

Constructs a Averagine instance setting the formula to formula and parentship to parent.

m_isValid is inherently false because the m_mono and m_avg masses cannot be computed without the isotopic data.

[explicit invokable] Averagine::Averagine(const MsXpS::libXpertMassCore::Formula &formula, MsXpS::libXpertMassCore::IsotopicDataCstSPtr isotopic_data_csp, QObject *parent = nullptr)

Constructs an Averagine instance setting the formula to formula and the isotopic data to isotopic_data_csp. Parentship is established using parent.

m_isValid is set to the value returned by validate().

The m_mono and m_avg masses are updated by the call to validate().

See also validate().

[explicit invokable] Averagine::Averagine(const MsXpS::libXpertMassCore::Averagine &other, QObject *parent = nullptr)

Constructs a Averagine instance as a copy of other. Parentship is established with parent.

After the deep copy, validate() is not called.

[virtual noexcept] Averagine::~Averagine()

Destructs this Averagine object.

[invokable] double Averagine::averagineEquivalents(MsXpS::libXpertMassCore::Enums::MassType mass_type, double mass, bool &ok) const

Computes the averagine equivalents for mass_type mass and returns the result.

In a normal setting, mass_type is Enums::MassType::AVG because the idea is to model a monoisotopic mass on the basis of an average mass.

If an error occurs, ok is set to false.

For this function to work, the member m_mono mand m_avg cannot be naught (qFatal() is triggered).

[invokable] MsXpS::libXpertMassCore::Averagine *Averagine::clone(QObject *parent = nullptr)

Allocates a new Averagine instance with parent set to parent, assigns to it this instance and returns the allocated instance.

The new instance is initialized using this instance.

After the deep copy, validate() is not called.

See also initialize().

[static invokable] MsXpS::libXpertMassCore::Averagine *Averagine::clone(const MsXpS::libXpertMassCore::Averagine &other, QObject *parent = nullptr)

b*rief Returns a newly allocated Averagine instance initialized with other and with parent set to parent.

The copying is deep, that is, all the members of other are copied and validate() is not called.

See also Averagine::Averagine().

[invokable] QString Averagine::elementalComposition(MsXpS::libXpertMassCore::Enums::MassType mass_type, double mass, bool as_integer_indices, bool &ok) const

Computes the averagine equivalents for mass_type mass and determines the corresponding elemental composition formula that it returns.

If as_integer_indices is true, the returned elemental composition formula has integer atom indices.

In a normal setting, mass_type is Enums::MassType::AVG because the idea is to model a monoisotopic mass on the basis of an average mass.

If an error occurs, ok is set to false.

Calls averagineEquivalents().

For this function to work, the member m_mono mand m_avg cannot be naught.

See also averagineEquivalents().

[invokable] double Averagine::getAvgMass() const

Returns the average mass.

[invokable] const MsXpS::libXpertMassCore::Formula &Averagine::getFormula() const

Returns a const reference to the member formula.

This function alias is the getter for the Q_PROPERTY system.

[invokable] const MsXpS::libXpertMassCore::Formula &Averagine::getFormulaCstRef() const

Returns a const reference to the member formula.

[invokable] MsXpS::libXpertMassCore::Formula &Averagine::getFormulaRef()

Returns a reference to the member formula.

[invokable] const MsXpS::libXpertMassCore::IsotopicDataCstSPtr Averagine::getIsotopicData() const

Returns the isotopic data.

[invokable] double Averagine::getMonoMass() const

Returns the monoisotopic mass.

[invokable] MsXpS::libXpertMassCore::Averagine &Averagine::initialize(const MsXpS::libXpertMassCore::Averagine &other, QObject *parent = nullptr)

Assigns other to this instance, re-establishes parentship to parent and returns a reference to this instance.

After the deep copy, validate() is not called.

See also validate().

[invokable] bool Averagine::isValid() const

Returns m_isValid: true if this Averagine instance is valid, false otherwise.

[invokable] double Averagine::modelMonoMass(double mass, bool &ok) const

Computes the averagine equivalents for average mass mass and determines the corresponding elemental composition formula and finally returns the corresponding monoisotopic mass.

If an error occurs, ok is set to false.

Calls elementalComposition().

For this function to work, the member m_mono and m_avg cannot be naught.

See also elementalComposition().

[invokable] void Averagine::setFormula(const MsXpS::libXpertMassCore::Formula &formula)

Sets the member Formula to formula.

[invokable] void Averagine::setFormula(const QString &formula)

Sets the member Formula to formula.

[invokable] void Averagine::setIsotopicData(const MsXpS::libXpertMassCore::IsotopicDataCstSPtr isotopic_data_csp)

Sets the isotopic data to isotopic_data_csp.

[invokable] QString Averagine::toString() const

Crafts a string documenting this instance and returns it.

[invokable] bool Averagine::validate(MsXpS::libXpertMassCore::ErrorList *error_list_p)

Validates this instance and returns true if validation was successful, false otherwise.

Validation steps include checking that the isotopic data are correctly set, that the formula can validate against them and that the masses (mono and avg) of the averagine can be computed.

The errors, if any, are appended to error_list_p, that cannot be nullptr (qFatal()).

m_isValid is set to the result of the validation and is returned.

[invokable] bool Averagine::operator!=(const MsXpS::libXpertMassCore::Averagine &other) const

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

The comparison only accounts for the formula and the isotopic data.

[invokable] bool Averagine::operator==(const MsXpS::libXpertMassCore::Averagine &other) const

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

The comparison only accounts for the formula and the isotopic data.