libXpertMassCore and libXpertMassGui Developer Documentation

libXpertMassCore Namespace

MsXpS::libXpertMassCore

Contains the libXpertMassCore documentation. More...

Header: #include <libXpertMassCore>

Namespaces

namespace Enums

Classes

class CalcOptions
class ChemicalGroup
class ChemicalGroupProp
class ChemicalGroupRule
class CleavageAgent
class CleavageConfig
class CleavageMotif
class CleavageRule
class Cleaver
class CrossLink
class CrossLinkedRegion
class CrossLinker
class DoubleProp
class Formula
class FragmentationConfig
class FragmentationPathway
class FragmentationRule
class Fragmenter
class IndexRange
class IndexRangeCollection
class IntProp
class Ionizer
class Isotope
class IsotopicClusterGenerator
class IsotopicClusterShaper
class IsotopicData
class IsotopicDataBaseHandler
class IsotopicDataLibraryHandler
class IsotopicDataManualConfigHandler
class IsotopicDataUserConfigHandler
class MassCollection
class MassDataCborBaseHandler
class MassDataCborMassSpectrumHandler
class MassDataClient
class MassDataServer
class MassPeakShaper
class MassPeakShaperConfig
class Modif
class Monomer
class MonomerDictionary
class NoDeletePointerProp
class Oligomer
class OligomerCollection
class OligomerPair
class PkaPhPi
class PkaPhPiDataParser
class PolChemDef
class PolChemDefSpec
class Polymer
class Prop
class PropListHolder
class Sequence
class StringProp
class Utils

Types

CleavageAgentCstSPtr
CleavageAgentSPtr
CrossLinkCstSPtr
CrossLinkCstWPtr
CrossLinkSPtr
CrossLinkWPtr
ErrorList
FormulaChargePair
IsotopeCstQSPtr
enum class IsotopeFields { NAME, SYMBOL, MASS, PROBABILITY }
IsotopeListCstIterator
IsotopeListCstIteratorPair
IsotopeListIterator
IsotopeQSPtr
IsotopicClusterChargePair
IsotopicClusterGeneratorCstSPtr
IsotopicClusterGeneratorSPtr
IsotopicDataCstSPtr
IsotopicDataLibraryHandlerCstSPtr
IsotopicDataLibraryHandlerSPtr
IsotopicDataManualConfigHandlerCstSPtr
IsotopicDataManualConfigHandlerSPtr
IsotopicDataSPtr
enum class IsotopicDataType { NOT_SET, LIBRARY_CONFIG, USER_CONFIG, MANUAL_CONFIG }
MassPeakShaperSPtr
MonomerCstRPtr
MonomerCstSPtr
MonomerCstUPtr
MonomerCstWPtr
MonomerRPtr
MonomerSPtr
MonomerUPtr
MonomerWPtr
OligomerCollectionCstSPtr
OligomerCollectionSPtr
OligomerCstSPtr
OligomerPairCstSPtr
OligomerPairSPtr
OligomerSPtr
PolymerCstQSPtr
PolymerSPtr
SymbolCountMap
UuidCrossLinkCstWPtrPair
UuidCrossLinkWPtrPair
UuidMonomerCstWPtrPair

Variables

int ATOM_DEC_PLACES
std::map<MsXpS::libXpertMassCore::Enums::CleavageAction, QString> CleavageActionMap
int FWHM_PEAK_SPAN_FACTOR
int OLIGOMER_DEC_PLACES
int PKA_PH_PI_DEC_PLACES
int POLYMER_DEC_PLACES
const int POL_CHEM_DEF_FILE_FORMAT_VERSION
const int POL_SEQ_FILE_FORMAT_VERSION
std::map<MsXpS::libXpertMassCore::Enums::CapType, QString> capTypeMap
std::map<MsXpS::libXpertMassCore::Enums::ChemicalEntity, QString> chemicalEntityMap
std::map<MsXpS::libXpertMassCore::Enums::ChemicalGroupFate, QString> chemicalGroupFateMap
std::map<MsXpS::libXpertMassCore::Enums::ChemicalGroupTrapped, QString> chemicalGroupTrappedMap
std::map<MsXpS::libXpertMassCore::Enums::CrossLinkEncompassed, QString> crossLinkEncompassedMap
std::map<MsXpS::libXpertMassCore::Enums::FragEnd, QString> fragEndMap
std::map<MsXpS::libXpertMassCore::Enums::IonizationOutcome, QString> ionizationOutcomeMap
std::map<MsXpS::libXpertMassCore::Enums::LocationType, QString> locationTypeMap
std::map<MsXpS::libXpertMassCore::Enums::MassDataType, QString> massDataTypeMap
std::map<MsXpS::libXpertMassCore::Enums::MassPeakShapeType, QString> massPeakShapeTypeMap
std::map<MsXpS::libXpertMassCore::Enums::MassPeakWidthLogic, QString> massPeakWidthLogicMap
std::map<MsXpS::libXpertMassCore::Enums::MassToleranceType, QString> massToleranceTypeMap
std::map<MsXpS::libXpertMassCore::Enums::MassType, QString> massTypeMap
std::map<MsXpS::libXpertMassCore::Enums::PolymerEnd, QString> polymerEndMap
std::map<MsXpS::libXpertMassCore::Enums::SelectionType, QString> selectionTypeMap

Detailed Description

Namespaces

namespace libXpertMassCore::Enums

Classes

class CalcOptions

The CalcOptions class provides the specifications that configure the way masses are calculated for Oligomers, Polymers and product ions. More...

class ChemicalGroup

The ChemicalGroup class provides a model for specifying the acido-basic behaviour of a chemical group of either a Monomer object or of a Modif object. More...

class ChemicalGroupProp

The ChemicalGroupProp class provides a Prop instance of which the member data points to a dynamically allocated ChemicalGroup instance. More...

class ChemicalGroupRule

The ChemicalGroupRule class provides a model for refining the acido-basic behaviour of a chemical group of either a Monomer object or of a Modif object. More...

class CleavageAgent

The CleavageAgent class provides a model for specifying aqueous cleavage specifications (patterns) of Polymer Sequences. More...

class CleavageConfig

The CleavageConfig class derives from CleavageAgent to provide a model for specifying aqueous cleavage specifications (patterns) of Polymer Sequences along with instructions on the way the cleavage must occur. More...

class CleavageMotif

The CleavageMotif class provides a model for specifying aqueous cleavage motfis of Polymer Sequences. More...

class CleavageRule

The CleavageRule class provides a model for specifying aqueous cleavage rules for refining cleavage agent specifications (CleavageAgent) of Polymer Sequences. More...

class Cleaver

The Cleaver class provides a model for performing aqueous cleavage reactions involving CleavageAgent objects and Polymer Sequences. More...

class CrossLink

The CrossLink class provides abstractions to work with a cross-link entity between Monomer instances. More...

class CrossLinkedRegion

The CrossLinkedRegion class provides abstractions to work with cross-links and detect the region of oligomers that are linked together. More...

class CrossLinker

The CrossLinker class provides abstractions to define the chemical basis of a cross-linking reaction. More...

class DoubleProp

The DoubleProp class is the specialized class for properties that hold data in the form of double values. More...

class Formula

The Formula class provides sophisticated abstractions to work with formulas. More...

class FragmentationConfig

The FragmentationConfig class derives from FragmentationPathway and adds functionality to configure the way the fragmentation occurs in the Oligomer Sequence. More...

class FragmentationPathway

The FragmentationPathway class provides a model for specifying gas phase fragmentation pathways of Oligomer Sequences. More...

class FragmentationRule

The FragmentationRule class provides a model for specifying gas phase fragmentation rules for refining fragmentation pathway specifications (FragmentationPathway) of Oligomer Sequences. More...

class Fragmenter

The Fragmenter class provides a model for performing gas phase fragmentation reactions involving FragmentationPathway objects and Polymer Sequences. More...

class IndexRange

The IndexRange class provides a range of indices that delimit a region of interest in a Polymer's Sequence instance. More...

class IndexRangeCollection

The IndexRangeCollection class provides a collection of IndexRange instances that enable delimiting Sequence regions of interest in a given Polymer instance. More...

class IntProp

The IntProp class is the specialized class for properties that hold data in the form of integer values. More...

class Ionizer

The Ionizer class provides abstractions to ionize analytes. More...

class Isotope

The Isotope class models an isotope. More...

class IsotopicClusterGenerator

The IsotopicClusterGenerator class provides the features needed to model isotopic clusters starting from (elemental-composition, charge) pairs. More...

class IsotopicClusterShaper

The IsotopicClusterShaper class provides the features needed to shape sets of (peak centroid m/z, intensity) pairs associated to a given charge into a mass spectral pappso;:Trace. More...

class IsotopicData

The IsotopicData class provides a collection of Isotopes and associated methods to access them in various ways. More...

class IsotopicDataBaseHandler

The IsotopicDataBaseHandler class features basic handling of IsotopicData. More...

class IsotopicDataLibraryHandler

The IsotopicDataLibraryHandler class handles IsotopicData from the IsoSpec element data tables directly from the library's data. These are the reference, pristine, unmodified, isotopic data. More...

class IsotopicDataManualConfigHandler

The IsotopicDataManualConfigHandler class handles a peculiar kind of IsotopicData that cannot be handled with the other handlers. More...

class IsotopicDataUserConfigHandler

The IsotopicDataUserConfigHandler class handles user-defined IsotopicData. More...

class MassCollection

The MassCollection class provides a container for masses (as double values) and for text representing thoses values. More...

class MassDataCborBaseHandler

The MassDataCborBaseHandler class provides features to handle mass spectrometric data using the CBOR (Concise Binary Object Representation) container streaming classes. More...

class MassDataCborMassSpectrumHandler

The MassDataCborMassSpectrumHandler class provides features to handle mass spectrum data using the CBOR (Concise Binary Object Representation) container streaming classes. More...

class MassDataClient

The MassDataClient class provides a network client. More...

class MassDataServer

The MassDataServer class provides a network server. More...

class MassPeakShaper

The MassPeakShaper class provides the features needed to shape a mass peak. More...

class MassPeakShaperConfig

The MassPeakShaperConfig class provides the features required to configure the shaping of a mass peak centroid into a Gaussian or a Lorentzian fully profiled shape. More...

class Modif

The Modif class provides abstractions to work with chemical modifications. More...

class Monomer

The Monomer class provides abstractions to work with monomers. More...

class MonomerDictionary

The MonomerDictionary class provides a Monomer code dictionary allowing the user to automatically translate Monomer codes from x-letter codes to y-letter codes. For example, a monomer dictionary file can define how to translate 3-letter monomer codes to 1-letter codes. This is typically useful when working on Protein Database (PDB) file. More...

class NoDeletePointerProp

The NoDeletePointerProp class provides a pointer property. More...

class Oligomer

The Oligomer class provides abstractions to work with an oligomer molecule (peptide or oligonucleotide, for example). More...

class OligomerCollection

The OligomerCollection class provides abstractions to work with Oligomer instances that have been produced in specific contexts, like Polymer cleavages or Oligomer fragmentations. More...

class OligomerPair

The OligomerPair class provides abstractions to work with a pair of Oligomer instances. More...

class PkaPhPi

The PkaPhPi class provides a model for specifying the acido-basic properties of a chemical entity. More...

class PkaPhPiDataParser

The PkaPhPiDataParser class provides a file reader for the pKa, pH, pI data XML file. More...

class PolChemDef

The PolChemDef class provides a complete set of chemical entities fully qualifying a polymer chemistry definition, like Proteins, Saccharides or Nucleic acids. More...

class PolChemDefSpec

The PolChemDefSpec class provides metadata for accessing a given polymer chemistry definition's data on disk. More...

class Polymer

The Polymer class provides abstractions to work with a polymer molecule (protein or saccharide , for example). More...

class Prop

The Prop class is the abstract base class for a number of specialized properties. More...

class PropListHolder

The PropListHolder class is the base class for a number of classes that need storing Prop instances. More...

class Sequence

The Sequence class provides abstractions to work with a simple sequence of Monomers. More...

class StringProp

The StringProp class is the specialized class for properties that hold data in the form of string objects. More...

class Utils

The Utils class provides a number of utilitary features that may be of use anywhere in the XpertMass source code tree. More...

Type Documentation

[alias] CleavageAgentCstSPtr

Synonym for std::shared_ptr<const CleavageAgent>.

[alias] CleavageAgentSPtr

Synonym for std::shared_ptr<CleavageAgent>.

CrossLinkCstSPtr

Synonym for std::shared_ptr<const CrossLink>.

CrossLinkCstWPtr

Synonym for std::weak_ptr<const CrossLink>.

CrossLinkSPtr

Synonym for std::shared_ptr<CrossLink>.

CrossLinkWPtr

Synonym for std::weak_ptr<CrossLink>.

ErrorList

Synonym for std::vector<QString> ErrorList.

[alias] libXpertMassCore::FormulaChargePair

Alias for std::pair<QString, int>.

IsotopeCstQSPtr

Synonym for std::shared_ptr<const Isotope>.

enum class libXpertMassCore::IsotopeFields

This enum type documents the various member data in Isotope.

The values assigned to the various enum members are used to specify the columsn in the GUI table view. They are also used to access substrings in the proper order in the overloaded initialize() function.

ConstantValueDescription
MsXpS::libXpertMassCore::IsotopeFields::NAME0Indicates Isotope::m_name.
MsXpS::libXpertMassCore::IsotopeFields::SYMBOL1Indicates the Isotope::m_symbol.
MsXpS::libXpertMassCore::IsotopeFields::MASS2Indicates the Isotope::m_mass.
MsXpS::libXpertMassCore::IsotopeFields::PROBABILITY3Indicates the Isotope::m_probability.

[alias] libXpertMassCore::IsotopeListCstIterator

Alias for QList<IsotopeQSPtr>::const_iterator.

[alias] libXpertMassCore::IsotopeListCstIteratorPair

Alias for std::pair<IsotopeListCstIterator, IsotopeListCstIterator>.

[alias] libXpertMassCore::IsotopeListIterator

Alias for QList<IsotopeQSPtr>::iterator.

IsotopeQSPtr

Synonym for std::shared_ptr<Isotope>.

[alias] libXpertMassCore::IsotopicClusterChargePair

Alias for std::pair<pappso::TraceCstSPtr, int>.

IsotopicClusterGeneratorCstSPtr

Synonym for std::shared_ptr<const IsotopicClusterGenerator>.

IsotopicClusterGeneratorSPtr

Synonym for std::shared_ptr<IsotopicClusterGenerator>.

IsotopicDataCstSPtr

Synonym for std::shared_ptr<const IsotopicData>.

IsotopicDataLibraryHandlerCstSPtr

Synonym for std::shared_ptr<const IsotopicDataLibraryHandler>.

IsotopicDataLibraryHandlerSPtr

Synonym for std::shared_ptr<IsotopicDataLibraryHandler>.

IsotopicDataManualConfigHandlerCstSPtr

Synonym for std::shared_ptr<const IsotopicDataManualConfigHandler>.

IsotopicDataManualConfigHandlerSPtr

Synonym for std::shared_ptr<IsotopicDataManualConfigHandler>.

IsotopicDataSPtr

Synonym for std::shared_ptr<IsotopicData>.

enum class libXpertMassCore::IsotopicDataType

This enum specifies the type of isotopic data.

ConstantValueDescription
MsXpS::libXpertMassCore::IsotopicDataType::NOT_SET0: Not configured. .
MsXpS::libXpertMassCore::IsotopicDataType::LIBRARY_CONFIG1: The isotopic data are loaded intact from the IsoSpec library data and are considered pristine natural abundance data. .
MsXpS::libXpertMassCore::IsotopicDataType::USER_CONFIG2: The isotopic data are in the same format as for LIBRARY_CONFIG but might have been modified by the user to configure new abundances. .
MsXpS::libXpertMassCore::IsotopicDataType::MANUAL_CONFIG3: The isotopic data are in a specific format, different than the two above, that actually crafts the isotopes starting from scratch.

MassPeakShaperSPtr

Synonym for std::shared_ptr<MassPeakShaper>.

MonomerCstRPtr

Synonym for const Monomer *.

[alias] MonomerCstSPtr

Synonym for std::shared_ptr<const Monomer>.

MonomerCstUPtr

Synonym for std::unique_ptr<const Monomer>.

MonomerCstWPtr

Synonym for std::weak_ptr<const Monomer>.

MonomerRPtr

Synonym for Monomer *.

[alias] MonomerSPtr

Synonym for std::shared_ptr<Monomer>.

MonomerUPtr

Synonym for std::unique_ptr<Monomer>.

MonomerWPtr

Synonym for std::weak_ptr<Monomer>.

OligomerCollectionCstSPtr

Synonym for std::shared_ptr<const OligomerCollection>.

OligomerCollectionSPtr

Synonym for std::shared_ptr<OligomerCollection>.

OligomerCstSPtr

Synonym for std::shared_ptr<const Oligomer>.

OligomerPairCstSPtr

Synonym for std::shared_ptr<const OligomerPair>.

OligomerPairSPtr

Synonym for std::shared_ptr<OligomerPair>.

OligomerSPtr

Synonym for std::shared_ptr<Oligomer>.

PolymerCstQSPtr

Synonym for std::shared_ptr<const Polymer>.

PolymerSPtr

Synonym for std::shared_ptr<Polymer>.

[alias] libXpertMassCore::SymbolCountMap

Alias for to std::map<QString, int>.

[alias] UuidCrossLinkCstWPtrPair

Synonym for std::pair<QString, CrossLinkCstWPtr>.

[alias] UuidCrossLinkWPtrPair

Synonym for std::pair<QString, CrossLinkWPtr>.

These pairs are used to store a unique identifier (Uuid) string related to a std::shared_ptr<CrossLink> type. This kind of pair is used in a container in the Polymer class. The fact that the std::shared_ptr is converted to a std::weak_ptr is interesting because the item in the pair will not increase the reference count.

[alias] UuidMonomerCstWPtrPair

Synonym for std::pair<QString, MonomerCstWPtr> items.

These pairs are used to store a unique identifier (Uuid) string related to a std::shared_ptr<const Monomer> type. This kind of pair is used in a container in the CrossLink class. The fact that the std::shared_ptr is converted to a std::weak_ptr is interesting because the item in the pair will not increase the reference count.

Variable Documentation

int libXpertMassCore::ATOM_DEC_PLACES

Number of decimal places after the decimal symbol for atom masses.

std::map<MsXpS::libXpertMassCore::Enums::CleavageAction, QString> libXpertMassCore::CleavageActionMap

Map relating each CleavageAction member to a corresponding textual representation.

int libXpertMassCore::FWHM_PEAK_SPAN_FACTOR

This variable holds the compounding factor to account for when shaping the sides of the peak.

The shape of the peak needs to reflect a real mass peak. In particular, the shape of the peak has to return, on each one of both sides, to the baseline, thus mimicking the baseline for a m/z distance equivalent to FWHM_PEAK_SPAN_FACTOR times the FWHM m/z range from left to right. That means that the simulated peak region at the left hand side of the centroid value will span (FWHM_PEAK_SPAN_FACTOR/2) times the FWHM and the same one right. Empirically, a good FWHM_PEAK_SPAN_FACTOR is 4, meaning that the left half of the peak (that is centered on the centroid) will have a size corresponding to two times the FHWM, and the same for the right half of the peak.

This is best exemplified as follows:

                    Centroid value
                     ^
                     |
[ m/z - (2 * FWHM) <-|-> m/z + (2 * FWHM) ]
<----- width of the whole peak shape ----->

int libXpertMassCore::OLIGOMER_DEC_PLACES

Number of decimal places after the decimal symbol for oligomer masses.

int libXpertMassCore::PKA_PH_PI_DEC_PLACES

Number of decimal places after the decimal symbol for pH/pKa values.

int libXpertMassCore::POLYMER_DEC_PLACES

Number of decimal places after the decimal symbol for polymer masses.

const int libXpertMassCore::POL_CHEM_DEF_FILE_FORMAT_VERSION

This variable holds the latest version of the format of the file containing the polymer chemistry definition.

Brought to 1 30 january 2023 for massXpert2 Brought to 2 10 november 2024 for massXpert2

const int libXpertMassCore::POL_SEQ_FILE_FORMAT_VERSION

Version number of the polymer sequence file format.

std::map<MsXpS::libXpertMassCore::Enums::CapType, QString> libXpertMassCore::capTypeMap

Map relating each CapType member to a corresponding textual representation.

std::map<MsXpS::libXpertMassCore::Enums::ChemicalEntity, QString> libXpertMassCore::chemicalEntityMap

Map relating each ChemicalEntity member to a corresponding textual representation.

std::map<MsXpS::libXpertMassCore::Enums::ChemicalGroupFate, QString> libXpertMassCore::chemicalGroupFateMap

Map relating each ChemicalGroupFate member to a corresponding textual representation.

std::map<MsXpS::libXpertMassCore::Enums::ChemicalGroupTrapped, QString> libXpertMassCore::chemicalGroupTrappedMap

Map relating each ChemicalGroupTrapped member to a corresponding textual representation.

std::map<MsXpS::libXpertMassCore::Enums::CrossLinkEncompassed, QString> libXpertMassCore::crossLinkEncompassedMap

Map relating each CrossLinkEncompassed member to a corresponding textual representation.

std::map<MsXpS::libXpertMassCore::Enums::FragEnd, QString> libXpertMassCore::fragEndMap

Map relating each FragEnd member to a corresponding textual representation.

std::map<MsXpS::libXpertMassCore::Enums::IonizationOutcome, QString> libXpertMassCore::ionizationOutcomeMap

Map relating each IonizationOutcome member to a corresponding textual representation.

std::map<MsXpS::libXpertMassCore::Enums::LocationType, QString> libXpertMassCore::locationTypeMap

Map relating each LocationType member to a corresponding textual representation.

std::map<MsXpS::libXpertMassCore::Enums::MassDataType, QString> libXpertMassCore::massDataTypeMap

Map relating each MassDataType member to a corresponding textual representation.

std::map<MsXpS::libXpertMassCore::Enums::MassPeakShapeType, QString> libXpertMassCore::massPeakShapeTypeMap

Map relating each MassPeakShapeType member to a corresponding textual representation.

std::map<MsXpS::libXpertMassCore::Enums::MassPeakWidthLogic, QString> libXpertMassCore::massPeakWidthLogicMap

Map relating each MassPeakWidthLogic member to a corresponding textual representation.

std::map<MsXpS::libXpertMassCore::Enums::MassToleranceType, QString> libXpertMassCore::massToleranceTypeMap

Map relating each MassToleranceType member to a corresponding textual representation.

std::map<MsXpS::libXpertMassCore::Enums::MassType, QString> libXpertMassCore::massTypeMap

Map relating each MassType member to a corresponding textual representation.

std::map<MsXpS::libXpertMassCore::Enums::PolymerEnd, QString> libXpertMassCore::polymerEndMap

Map relating each PolymerEnd member to a corresponding textual representation.

std::map<MsXpS::libXpertMassCore::Enums::SelectionType, QString> libXpertMassCore::selectionTypeMap

Map relating each SelectionType member to a corresponding textual representation.