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... | |
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enum | { DIMENSION = 1 } |
typedef float | IntensityType |
Intensity type. More... | |
typedef DPosition< 1 > | PositionType |
Position type. More... | |
typedef double | 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... | |
double | getActivationEnergy () const |
returns the activation energy (in electronvolt) More... | |
void | setActivationEnergy (double activation_energy) |
sets the activation energy (in electronvolt) More... | |
double | getIsolationWindowLowerOffset () const |
Returns the lower offset from the target m/z. More... | |
void | setIsolationWindowLowerOffset (double bound) |
sets the lower offset from the target m/z More... | |
double | getIsolationWindowUpperOffset () const |
Returns the upper offset from the target m/z. More... | |
void | setIsolationWindowUpperOffset (double 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... | |
double | getUnchargedMass () const |
Returns the uncharged mass of the precursor, if charge is unknown, i.e. 0 best guess is its doubly charged. More... | |
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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... | |
void | consumeCVTerms (const Map< String, std::vector< CVTerm > > &cv_term_map) |
merges the given map into the member map, no duplicate checking 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... | |
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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... | |
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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 (PositionType a, IntensityType b) | |
construct with position and intensity More... | |
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_ |
double | activation_energy_ |
double | window_low_ |
double | window_up_ |
Int | charge_ |
std::vector< Int > | possible_charge_states_ |
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Map< String, std::vector< CVTerm > > | cv_terms_ |
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MetaInfo * | meta_ |
pointer to the MetaInfo object. 0 by default More... | |
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PositionType | position_ |
The data point position. More... | |
IntensityType | intensity_ |
The data point intensity. More... | |
Additional Inherited Members | |
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static MetaInfoRegistry & | metaRegistry () |
returns a reference to the MetaInfoRegistry More... | |
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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.
double 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 >::handleCVParam_(), 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().
double getIsolationWindowLowerOffset | ( | ) | const |
Returns the lower offset from the target m/z.
Referenced by MzMLHandler< MapType >::writePrecursor_(), and MzXMLHandler< MapType >::writeTo().
double 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 >::handleCVParam_(), and MzMLHandler< MapType >::writePrecursor_().
const std::vector<Int>& getPossibleChargeStates | ( | ) | const |
Non-mutable access to possible charge states.
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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.
void setActivationEnergy | ( | double | activation_energy | ) |
sets the activation energy (in electronvolt)
Referenced by MzMLHandler< MapType >::handleCVParam_().
void setActivationMethods | ( | const std::set< ActivationMethod > & | activation_methods | ) |
sets the activation methods
void setCharge | ( | Int | charge | ) |
Mutable access to the charge.
Referenced by MzMLHandler< MapType >::handleCVParam_(), DTAFile::load(), TOPPRNPxl::main_(), OfflinePrecursorIonSelection::makePrecursorSelectionForKnownLCMSMap(), and TOPPViewBase::showSpectrumGenerationDialog().
void setIsolationWindowLowerOffset | ( | double | bound | ) |
sets the lower offset from the target m/z
Referenced by MzMLHandler< MapType >::handleCVParam_(), ChromatogramExtractor::prepareSpectra_(), and ChromatogramExtractor::return_chromatogram().
void setIsolationWindowUpperOffset | ( | double | bound | ) |
sets the upper offset from the target m/z
Referenced by MzMLHandler< MapType >::handleCVParam_(), ChromatogramExtractor::prepareSpectra_(), and ChromatogramExtractor::return_chromatogram().
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 2.0.0 | Documentation generated on Tue Nov 1 2016 16:34:46 using doxygen 1.8.11 |