Oligomer Class

Member Function Documentation

Oligomer::Oligomer(Polymer *polymer, const QString &name, const QString &description, bool modified, const Ponderable &ponderable, const IonizeRule &ionizeRule, const CalcOptions &calcOptions, bool isIonized, int startIndex, int endIndex)

Constructs an oligomer.

The Oligomer instance is constructed with these arguments:

polymer: The polymer instance that encloses this Oligomer. Used to intialize the member m_polymer and the Ionizable base class' polymer chemistry definition

name: The name of this Oligomer, used to intialize the Ionizable base class

description: The description of this Oligomer (m_description)

modified: Tells if the Oligomer is modified

ponderable: Used to initialize the Ionizable base class

ionizeRule: Used to initialize the Ionizable base class

calcOptions: Used to initialize the m_calcOptions member

isIonized: Tells if this Oligomer instance is ionized

startIndex: The oligomer's start index coordinate in the enclosing Polymer

endIndex: The oligomer's end index coordinate in the enclosing Polymer

Oligomer::Oligomer(PolChemDefCstSPtr pol_chem_def_csp, const QString &name, const QString &description, bool modified, const Ponderable &ponderable, const IonizeRule &ionizeRule, const CalcOptions &calcOptions, bool isIonized, int startIndex, int endIndex)

Constructs an oligomer.

The Oligomer instance is constructed with these arguments:

pol_chem_def_csp: The polymer chemistry definition used to initialize the Ionizable base class

name: The name of this Oligomer, used to intialize the Ionizable base class

description: The description of this Oligomer (m_description)

modified: Tells if the Oligomer is modified

ponderable: Used to initialize the Ionizable base class

ionizeRule: Used to initialize the Ionizable base class

calcOptions: Used to initialize the m_calcOptions member

isIonized: Tells if this Oligomer instance is ionized

startIndex: The oligomer's start index coordinate in the enclosing Polymer

endIndex: The oligomer's end index coordinate in the enclosing Polymer

Oligomer::Oligomer(Polymer *polymer, const QString &name, const QString &description, bool modified = false, const Ponderable &ponderable = Ponderable(), int startIndex = -1, int endIndex = -1, const CalcOptions &calcOptions = CalcOptions())

Constructs an oligomer.

The Oligomer instance is constructed with these arguments:

polymer: The polymer instance that encloses this Oligomer. Used to intialize the member m_polymer and the Ionizable base class' polymer

name: The name of this Oligomer, used to intialize the Ionizable base class

description: The description of this Oligomer (m_description)

modified: Tells if the Oligomer is modified

ponderable: Used to initialize the Ionizable base class

calcOptions: Used to initialize the m_calcOptions member

startIndex: The oligomer's start index coordinate in the enclosing Polymer

endIndex: The oligomer's end index coordinate in the enclosing Polymer

Oligomer::Oligomer(PolChemDefCstSPtr pol_chem_def_csp, const QString &name, const QString &description, bool modified = false, const Ponderable &ponderable = Ponderable(), const CalcOptions &calcOptions = CalcOptions(), int startIndex = -1, int endIndex = -1)

Constructs an oligomer.

The Oligomer instance is constructed with these arguments:

pol_chem_def_csp: The polymer chemistry definition used to initialize the Ionizable base class

name: The name of this Oligomer, used to intialize the Ionizable base class

description: The description of this Oligomer (m_description)

modified: Tells if the Oligomer is modified

ponderable: Used to initialize the Ionizable base class

calcOptions: Used to initialize the m_calcOptions member

startIndex: The oligomer's start index coordinate in the enclosing Polymer

endIndex: The oligomer's end index coordinate in the enclosing Polymer

Oligomer::Oligomer(const Ionizable &ionizable, const CalcOptions &calcOptions = CalcOptions(), int startIndex = -1, int endIndex = -1)

Constructs an oligomer.

The Oligomer instance is constructed with these arguments:

ionizable: Used to initialize the Ionizable base class

calcOptions: Used to initialize the m_calcOptions member

startIndex: The oligomer's start index coordinate in the enclosing Polymer

endIndex: The oligomer's end index coordinate in the enclosing Polymer

Oligomer::Oligomer(Polymer *polymer, const QString &name, const QString &description, bool modified = false, double mono = 0, double avg = 0, int startIndex = -1, int endIndex = -1, const CalcOptions &calcOptions = CalcOptions())

Constructs an oligomer.

The Oligomer instance is constructed with these arguments:

polymer: Use to initialize the member mp_polymer and also to initialize the Ionizable base class (by using its polymer chemistry definition member).

name: The name of this Oligomer, used to intialize the Ionizable base class

description: The description of this Oligomer (m_description)

modified: Tells if the Oligomer is modified

mono and avg: Used to initialize the Ionizable::Ponderable base class

calcOptions: Used to initialize the m_calcOptions member

startIndex: The oligomer's start index coordinate in the enclosing Polymer

endIndex: The oligomer's end index coordinate in the enclosing Polymer

Oligomer::Oligomer(PolChemDefCstSPtr pol_chem_def_csp, const QString &name, const QString &description, bool modified = false, const CalcOptions &calcOptions = CalcOptions(), double mono = 0, double avg = 0, int startIndex = -1, int endIndex = -1)

Constructs an oligomer.

The Oligomer instance is constructed with these arguments:

pol_chem_def_csp: The polymer chemistry definition used to initialize the Ionizable base class

name: The name of this Oligomer, used to intialize the Ionizable base class

description: The description of this Oligomer (m_description)

modified: Tells if the Oligomer is modified

calcOptions: Used to initialize the m_calcOptions member

mono and avg: Used to initialize the Ionizable::Ponderable base class

startIndex: The oligomer's start index coordinate in the enclosing Polymer

endIndex: The oligomer's end index coordinate in the enclosing Polymer

Oligomer::Oligomer(const Oligomer &other)

Constructs the Oligomer as a copy of other.

[virtual noexcept] Oligomer::~Oligomer()

Destructs this Oligomer.

bool Oligomer::addCrossLink(CrossLink *cross_link)

Add the cross_link CrossLink to this Oligomer's list of CrossLinks

Returns true if the cross-link was added succesfully, or false if cross_link was already in the list.

int Oligomer::appendCoordinates(CoordinateList *list)

Add to the member CoordinateList all the Coordinates instances found in list.

The added Coordinates instances are copies of the instances found in list.

Returns the count of added Coordinates instances allocated on the heap.

const Monomer &Oligomer::atLeftEnd() const

Returns the Monomer in the enclosing Polymer that is located at the start index of this oligomer.

See also atRightEnd() and startIndex().

const Monomer &Oligomer::atRightEnd() const

Returns the Monomer in the enclosing Polymer that is located at the end index of this oligomer.

See also atLeftEnd() and endIndex().

const CalcOptions &Oligomer::calcOptions() const

Returns the calculation options.

See also setCalcOptions().

[override virtual] bool Oligomer::calculateMasses()

Reimplements: Ionizable::calculateMasses().

Calculates the monoisotopic and average masses.

The calculation is performed by computing the mono and avg masses of the sequence stretch as described by the start and end indices in the polymer sequence. Default calculation options are used.

Returns true if calculations were successful, false otherwise.

[virtual] bool Oligomer::calculateMasses(const CalcOptions *calc_options, const IonizeRule *ionize_rule = 0)

Calculates the monoisotopic and average masses.

The calculation is performed by computing the mono and avg masses of the sequence stretch as described by the start and end indices in the polymer sequence. The calculations are configured by calc_options and the ionization is defined in ionize_rule.

Returns true if calculations were successful, false otherwise.

QList<CrossLink *> *Oligomer::crossLinkList()

Returns the member crossLinkList.

QString Oligomer::description() const

Returns the description.

See also setDescription().

[virtual] QString Oligomer::elementalComposition()

Returns the elemental composition of this Oligomer instance.

[virtual] QString Oligomer::elementalComposition(const CalcOptions &calc_options, const IonizeRule &ionize_rule)

Returns the elemental composition of this Oligomer instance.

The computation of the elemental composition is performed as configured in calc_options and using the ionization described in ionize_rule.

bool Oligomer::encompasses(int index) const

Returns true if this Oligomer spans at least one region of the enclosing polymer that contains a Monomer at index, false otherwise.

bool Oligomer::encompasses(const Monomer *monomer) const

Returns true if this Oligomer spans at least one region of the enclosing polymer that contains the Monomer monomer, false otherwise.

The search is performed by comparing pointers, thus the Monomer to be search is monomer.

int Oligomer::endIndex() const

Returns the end index.

The end index that is returned is the end index of the first Coordinates instance of the CoordinateList member.

See also setEndIndex().

IonizeRule &Oligomer::ionizeRule()

Returns a reference to the IonizeRule member.

See also setIonizeRule().

[virtual] bool Oligomer::isModified(bool deep = true)

Returns the chemical modification status of this Oligomer.

If deep is true, the enclosing Polymer must exist (m_polymer cannot be nullptr) because each monomer of the Polymer is probed for a potential modification. This function returns true as soon as such a modified monomer is encountered.

If deep is false, the value of m_isModified is returned.

See also m_isModified and Monomer::isModified().

[override virtual] int Oligomer::makeMonomerText()

Reimplements: Sequence::makeMonomerText().

Calculates the sequence of this Oligomer and sets it to the Sequence base class member m_monomerText.

Returns the size of m_monomerText. If m_polymer is nullptr, return 0.

See also Sequence.

const Monomer *Oligomer::monomerAt(int index) const

Return the Monomer that is located in the enclosing Polymer at index.

QString *Oligomer::monomerText()

Returns a string with the sequence of this Oligomer.

If mp_polymer is non-nullptr, the sequence is calculated by looking into the Polymer using member Coordinates.

If mp_polymer is nullptr and if Sequence::m_monomerText is not empty, that is returned.

If mp_polymer is nullptr and if Sequence::m_monomerText is emtpy, then the sequence is crafted by looking into Sequence::m_monomerList.

See also makeMonomerText().

const Polymer *Oligomer::polymer() const

Returns the polymer.

void Oligomer::setCalcOptions(const CalcOptions &calc_options)

Set the calculation options to calc_options.

See also m_calcOptions.

void Oligomer::setDescription(const QString &description)

Set the description to description.

See also description().

void Oligomer::setEndIndex(int value)

Sets the end index to value.

The value is used to construct a Coordinates instance that is allocated on the heap and added to member CoordinateList if that list is empty. If the CoordinateList is not empty, then the value is set to the first Coordinates instance in that list.

See also endIndex().

void Oligomer::setIonizeRule(IonizeRule &ionize_rule)

Set the IonizeRule member to ionize_rule.

See also MsXpS::libXpertMass::Ionizable::m_ionizeRule.

void Oligomer::setModified(bool modified = true)

Set the m_isModified status of this Oligomer to modified.

See also isModified().

void Oligomer::setStartEndIndices(int value1, int value2)

Sets the start and end indices to value1 and value2 respectively.

The values are used to construct a Coordinates instance that is allocated on the heap and added to member CoordinateList if that list is empty. If the CoordinateList is not empty, then the values are set to the first Coordinates instance in that list.

See also setStartIndex() and setEndIndex().

void Oligomer::setStartIndex(int value)

Sets the start index to value.

The value is used to construct a Coordinates instance that is allocated on the heap and added to member CoordinateList if that list is empty. If the CoordinateList is not empty, then the value is set to the first Coordinates instance in that list.

See also startIndex().

int Oligomer::size()

Returns the size of this Oligomer.

The size is computed by adding the length of all the regions of the enclosing Polymer as documented in the Coordinates instances in the member coordinateList.

int Oligomer::startIndex() const

Returns the start index, or -1 if no Coordinates instance is found in the CoordinateList member.

The start index that is returned is the start index of the first Coordinates instance of the CoordinateList member.

See also setStartIndex().

void Oligomer::updateCalcOptions()

Updates the member calculation options with this Oligomer's CoordinateList.

The data in m_calcOptions that need updating are the CoordinateList elements.