Cleaver Class

Member Function Documentation

Cleaver::Cleaver()

Constructs an entirely empty Cleaver instance.

Cleaver::Cleaver(MsXpS::libXpertMassCore::PolymerCstQSPtr polymer_cqsp, MsXpS::libXpertMassCore::PolChemDefCstSPtr pol_chem_def_csp, const MsXpS::libXpertMassCore::CleavageConfig &cleavage_config, const MsXpS::libXpertMassCore::CalcOptions &calc_options, const MsXpS::libXpertMassCore::Ionizer &ionizer)

Constructs a Cleaver instance with a number of parameters.

• polymer_cqsp The Polymer instance to be cleaved.
• pol_chem_def_csp The PolChemDef (polymer chemistry definition) that is the context in which the Polymer exists.
• cleavage_config The CleavageConfig instance that configures the cleavage.
• calc_options The CalcOptions instance that configures the mass and formula calculations.
• ionizer The Ionizer instance that drives the ionization of the Oligomer instances generated by the cleavage.

If polymer_cqsp or pol_chem_def_csp is nullptr, that is a fatal error.

Cleaver::Cleaver(const MsXpS::libXpertMassCore::Cleaver &other)

Constructs Cleaver instance as a copy of other.

If polymer_cqsp or pol_chem_def_csp is nullptr, that is a fatal error.

[noexcept] Cleaver::~Cleaver()

Desstructs this Cleaver instance

bool Cleaver::accountCleavageRule(MsXpS::libXpertMassCore::CleavageRuleSPtr cleavage_rule_sp, MsXpS::libXpertMassCore::OligomerSPtr oligomer_sp)

Accounts into the oligomer_sp for the cleavage_rule_sp.

Returns true if the accounting succeeded, false otherwise.

int Cleaver::analyzeCrossLinkedOligomer(MsXpS::libXpertMassCore::OligomerSPtr oligomer_sp, MsXpS::libXpertMassCore::OligomerCollection &oligomers)

Pulls down all the Oligomer instances in oligomers that are found to be cross-linked to oligomer_sp.

Returns the count of IndexRange instances found in oligomer_sp, which is a reflection of the number of oligomers that are found to be cross-linked to it.

int Cleaver::analyzeCrossLinks(MsXpS::libXpertMassCore::OligomerCollection &oligomers)

Analyzes the CrossLink instances that might be involved in the Oligomer instances in the oligomers collection.

The Oligomers that are found cross-linked are set in oligomers and the size of this collection is returned.

bool Cleaver::cleave(bool reset = false)

Performs the actual cleavage, thus generating Oligomer instances that are added to the member OligomerCollection instance.

If reset is true, the member OligomerCollection is first cleared; otherwise the newly generated Oligomer instances are simply added to it.

Returns true upon success, false otherwise.

int Cleaver::cleavePartial(int partial_cleavage)

Performs a cleavage operation for partial cleavage partial_cleavage.

Returns -1 if an error occurred, the count of generated oligomers otherwise.

int Cleaver::fillCleavageIndices()

Fills-in all the index values that correspond to precise locations where the cleavage reactions must occur. These indices represent location in the member Polymer Sequence.

If the pattern only contains cleaving sites, all the indices are added to the member container of cleavage indices. If the pattern contains also no-cleaving sites (like with Trypsin's "-Lys/Pro" pattern), then the corresponding indices are set to the member container of no-cleavage indices.

Returns the sum of the two cleavage/no-cleavage containers sizes. Or 0 if not a single cleavage site was found in the Polymer Sequence.

int Cleaver::findCleavageMotif(MsXpS::libXpertMassCore::CleavageMotif &cleavage_motif, size_t index_start, std::size_t index_stop)

Returns an index at which the cleavage_motif CleavageMotif is found in the Polymer Sequence.

The search is started at index index_start and is stopped at index index_stop.

If cleavage_motif is not found, returns -1.

QString Cleaver::getCleaveAgentName() const

Returns the CleavageAgent name (from the member CleavageConfig instance's base class).

const MsXpS::libXpertMassCore::OligomerCollection &Cleaver::getOligomerCollectionCstRef() const

Returns a const reference to the member OligomerCollection instance.

MsXpS::libXpertMassCore::OligomerCollection &Cleaver::getOligomerCollectionRef()

Returns a reference to the member OligomerCollection instance.

int Cleaver::removeDuplicateCleavageIndices()

Removes the duplicate cleavage indices from the container of cleavage indices.

int Cleaver::resolveCleavageNoCleavage()

Removes form the container of cleavage indices all the indices that were found to be no-cleavage indices in the corresponding container.

Returns the size of the container of cleavage indices.

std::size_t Cleaver::transferOligomers(MsXpS::libXpertMassCore::OligomerCollection &source, MsXpS::libXpertMassCore::OligomerCollection &dest)

Transfers (using std::move()) all the Oligomer instances from source to dest.

After the transfer, the source Oligomer container is cleared since it contains only nullptr items.

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

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

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

Returns a reference to this Cleaver instance after initialization using other.

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

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