Precursor meta information. More...
#include <OpenMS/METADATA/Precursor.h>
Public Types | |
| enum | ActivationMethod { CID, PSD, PD, SID, BIRD, ECD, IMD, SORI, HCID, LCID, PHD, ETD, PQD, SIZE_OF_ACTIVATIONMETHOD } |
| Method of activation. More... | |
Public Types inherited from Peak1D | |
| enum | { DIMENSION = 1 } |
| typedef Real | IntensityType |
| Intensity type. More... | |
| typedef DPosition< 1 > | PositionType |
| Position type. More... | |
| typedef DoubleReal | CoordinateType |
| Coordinate type. More... | |
Public Member Functions | |
| Precursor () | |
| Constructor. More... | |
| Precursor (const Precursor &source) | |
| Copy constructor. More... | |
| virtual | ~Precursor () |
| Destructor. More... | |
| Precursor & | operator= (const Precursor &source) |
| Assignment operator. More... | |
| bool | operator== (const Precursor &rhs) const |
| Equality operator. More... | |
| bool | operator!= (const Precursor &rhs) const |
| Equality operator. More... | |
| const std::set < ActivationMethod > & | getActivationMethods () const |
| returns a const reference to the activation methods More... | |
| std::set< ActivationMethod > & | getActivationMethods () |
| returns a mutable reference to the activation methods More... | |
| void | setActivationMethods (const std::set< ActivationMethod > &activation_methods) |
| sets the activation methods More... | |
| DoubleReal | getActivationEnergy () const |
| returns the activation energy (in electronvolt) More... | |
| void | setActivationEnergy (DoubleReal activation_energy) |
| sets the activation energy (in electronvolt) More... | |
| DoubleReal | getIsolationWindowLowerOffset () const |
| returns the lower offset from the target m/z More... | |
| void | setIsolationWindowLowerOffset (DoubleReal bound) |
| sets the lower offset from the target m/z More... | |
| DoubleReal | getIsolationWindowUpperOffset () const |
| returns the upper offset from the target m/z More... | |
| void | setIsolationWindowUpperOffset (DoubleReal bound) |
| sets the upper offset from the target m/z More... | |
| Int | getCharge () const |
| Non-mutable access to the charge. More... | |
| void | setCharge (Int charge) |
| Mutable access to the charge. More... | |
| std::vector< Int > & | getPossibleChargeStates () |
| Mutable access to possible charge states. More... | |
| const std::vector< Int > & | getPossibleChargeStates () const |
| Non-mutable access to possible charge states. More... | |
| void | setPossibleChargeStates (const std::vector< Int > &possible_charge_states) |
| Sets the possible charge states. More... | |
| DoubleReal | getUnchargedMass () const |
| Returns the uncharged mass of the precursor, if charge is unknown, i.e. 0 best guess is its doubly charged. More... | |
Public Member Functions inherited from CVTermList | |
| CVTermList () | |
| Defaults constructor. More... | |
| CVTermList (const CVTermList &rhs) | |
| Copy constructor. More... | |
| virtual | ~CVTermList () |
| Destructor. More... | |
| CVTermList & | operator= (const CVTermList &rhs) |
| Assignment operator. More... | |
| void | setCVTerms (const std::vector< CVTerm > &terms) |
| sets the CV terms More... | |
| void | replaceCVTerm (const CVTerm &cv_term) |
| replaces the specified CV term More... | |
| void | replaceCVTerms (const std::vector< CVTerm > &cv_terms, const String &accession) |
| replaces the specified CV terms using the given accession number More... | |
| void | replaceCVTerms (const Map< String, std::vector< CVTerm > > &cv_term_map) |
| replaces all cv terms with a map (can be obtained via getCVTerms) More... | |
| const Map< String, std::vector < CVTerm > > & | getCVTerms () const |
| returns the accession string of the term More... | |
| void | addCVTerm (const CVTerm &term) |
| adds a CV term More... | |
| bool | operator== (const CVTermList &cv_term_list) const |
| equality operator More... | |
| bool | operator!= (const CVTermList &cv_term_list) const |
| inequality operator More... | |
| bool | hasCVTerm (const String &accession) const |
| checks whether the term has a value More... | |
| bool | empty () const |
| return true if no terms are available More... | |
Public Member Functions inherited from MetaInfoInterface | |
| MetaInfoInterface () | |
| constructor More... | |
| MetaInfoInterface (const MetaInfoInterface &rhs) | |
| copy constructor More... | |
| ~MetaInfoInterface () | |
| destructor More... | |
| MetaInfoInterface & | operator= (const MetaInfoInterface &rhs) |
| assignment operator More... | |
| bool | operator== (const MetaInfoInterface &rhs) const |
| Equality operator. More... | |
| bool | operator!= (const MetaInfoInterface &rhs) const |
| Equality operator. More... | |
| const DataValue & | getMetaValue (const String &name) const |
| returns the value corresponding to a string More... | |
| const DataValue & | getMetaValue (UInt index) const |
| returns the value corresponding to an index More... | |
| bool | metaValueExists (const String &name) const |
| returns if this MetaInfo is set More... | |
| bool | metaValueExists (UInt index) const |
| returns if this MetaInfo is set More... | |
| void | setMetaValue (const String &name, const DataValue &value) |
| sets the DataValue corresponding to a name More... | |
| void | setMetaValue (UInt index, const DataValue &value) |
| sets the DataValue corresponding to an index More... | |
| void | removeMetaValue (const String &name) |
Removes the DataValue corresponding to name if it exists. More... | |
| void | removeMetaValue (UInt index) |
Removes the DataValue corresponding to index if it exists. More... | |
| void | getKeys (std::vector< String > &keys) const |
| fills the given vector with a list of all keys for which a value is set More... | |
| void | getKeys (std::vector< UInt > &keys) const |
| fills the given vector with a list of all keys for which a value is set More... | |
| bool | isMetaEmpty () const |
| returns if the MetaInfo is empty More... | |
| void | clearMetaInfo () |
| removes all meta values More... | |
Public Member Functions inherited from Peak1D | |
| Peak1D & | operator= (const Peak1D &rhs) |
| Assignment operator. More... | |
| bool | operator== (const Peak1D &rhs) const |
| Equality operator. More... | |
| bool | operator!= (const Peak1D &rhs) const |
| Equality operator. More... | |
| Peak1D () | |
| Peak1D (const Peak1D &p) | |
| Copy constructor. More... | |
| ~Peak1D () | |
| Destructor. More... | |
| IntensityType | getIntensity () const |
| void | setIntensity (IntensityType intensity) |
| Mutable access to the data point intensity (height) More... | |
| CoordinateType | getMZ () const |
| Non-mutable access to m/z. More... | |
| void | setMZ (CoordinateType mz) |
| Mutable access to m/z. More... | |
| CoordinateType | getPos () const |
| Alias for getMZ() More... | |
| void | setPos (CoordinateType pos) |
| Alias for setMZ() More... | |
| PositionType const & | getPosition () const |
| Non-mutable access to the position. More... | |
| PositionType & | getPosition () |
| Mutable access to the position. More... | |
| void | setPosition (PositionType const &position) |
| Mutable access to the position. More... | |
Static Public Attributes | |
| static const std::string | NamesOfActivationMethod [SIZE_OF_ACTIVATIONMETHOD] |
| Names of activation methods. More... | |
Protected Attributes | |
| std::set< ActivationMethod > | activation_methods_ |
| DoubleReal | activation_energy_ |
| DoubleReal | window_low_ |
| DoubleReal | window_up_ |
| Int | charge_ |
| std::vector< Int > | possible_charge_states_ |
Protected Attributes inherited from CVTermList | |
| Map< String, std::vector < CVTerm > > | cv_terms_ |
Protected Attributes inherited from MetaInfoInterface | |
| MetaInfo * | meta_ |
| pointer to the MetaInfo object. 0 by default More... | |
Protected Attributes inherited from Peak1D | |
| PositionType | position_ |
| The data point position. More... | |
| IntensityType | intensity_ |
| The data point intensity. More... | |
Additional Inherited Members | |
Static Public Member Functions inherited from MetaInfoInterface | |
| static MetaInfoRegistry & | metaRegistry () |
| retuns a reference to the MetaInfoRegistry More... | |
Protected Member Functions inherited from MetaInfoInterface | |
| void | createIfNotExists_ () |
| creates the MetaInfo object if it does not exist More... | |
Precursor meta information.
This class contains precursor information:
| enum ActivationMethod |
Method of activation.
| Precursor | ( | ) |
Constructor.
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virtual |
Destructor.
| DoubleReal getActivationEnergy | ( | ) | const |
returns the activation energy (in electronvolt)
Referenced by MzMLHandler< MapType >::writePrecursor_(), and MzDataHandler< MapType >::writeTo().
| const std::set<ActivationMethod>& getActivationMethods | ( | ) | const |
returns a const reference to the activation methods
Referenced by MzMLHandler< MapType >::writePrecursor_(), and MzDataHandler< MapType >::writeTo().
| std::set<ActivationMethod>& getActivationMethods | ( | ) |
returns a mutable reference to the activation methods
| Int getCharge | ( | ) | const |
Non-mutable access to the charge.
Referenced by DTAFile::store(), MzMLHandler< MapType >::writePrecursor_(), MzDataHandler< MapType >::writeTo(), and MzXMLHandler< MapType >::writeTo().
| DoubleReal getIsolationWindowLowerOffset | ( | ) | const |
returns the lower offset from the target m/z
Referenced by MzMLHandler< MapType >::writePrecursor_(), and MzXMLHandler< MapType >::writeTo().
| DoubleReal getIsolationWindowUpperOffset | ( | ) | const |
returns the upper offset from the target m/z
Referenced by MzMLHandler< MapType >::writePrecursor_(), and MzXMLHandler< MapType >::writeTo().
| std::vector<Int>& getPossibleChargeStates | ( | ) |
Mutable access to possible charge states.
Referenced by MzMLHandler< MapType >::writePrecursor_().
| const std::vector<Int>& getPossibleChargeStates | ( | ) | const |
Non-mutable access to possible charge states.
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inline |
Returns the uncharged mass of the precursor, if charge is unknown, i.e. 0 best guess is its doubly charged.
References OpenMS::Constants::c, and OpenMS::Constants::PROTON_MASS_U.
| bool operator!= | ( | const Precursor & | rhs | ) | const |
Equality operator.
| bool operator== | ( | const Precursor & | rhs | ) | const |
Equality operator.
| void setActivationEnergy | ( | DoubleReal | activation_energy | ) |
sets the activation energy (in electronvolt)
| void setActivationMethods | ( | const std::set< ActivationMethod > & | activation_methods | ) |
sets the activation methods
| void setCharge | ( | Int | charge | ) |
Mutable access to the charge.
Referenced by DTAFile::load(), TOPPRNPxl::main_(), OfflinePrecursorIonSelection::makePrecursorSelectionForKnownLCMSMap(), and TOPPViewBase::showSpectrumGenerationDialog().
| void setIsolationWindowLowerOffset | ( | DoubleReal | bound | ) |
sets the lower offset from the target m/z
Referenced by ChromatogramExtractor::prepareSpectra_().
| void setIsolationWindowUpperOffset | ( | DoubleReal | bound | ) |
sets the upper offset from the target m/z
Referenced by ChromatogramExtractor::prepareSpectra_().
| void setPossibleChargeStates | ( | const std::vector< Int > & | possible_charge_states | ) |
Sets the possible charge states.
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Names of activation methods.
Referenced by HasActivationMethod< SpectrumType >::operator()().
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| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:33 using doxygen 1.8.5 |