A multi-chromatogram MRM feature. More...
#include <OpenMS/KERNEL/MRMFeature.h>
 
  
 | Public Types | |
| typedef std::vector< Feature > | FeatureListType | 
| Type definitions.  More... | |
| typedef std::map< String, double > | PGScoresType | 
| Peak group score type.  More... | |
|  Public Types inherited from Feature | |
| typedef QualityLess | OverallQualityLess | 
| Compare by quality.  More... | |
|  Public Types inherited from BaseFeature | |
| enum | AnnotationState { FEATURE_ID_NONE, FEATURE_ID_SINGLE, FEATURE_ID_MULTIPLE_SAME, FEATURE_ID_MULTIPLE_DIVERGENT, SIZE_OF_ANNOTATIONSTATE } | 
| state of identification, use getIDState() to query it  More... | |
| typedef Real | QualityType | 
| Type of quality values.  More... | |
| typedef Int | ChargeType | 
| Type of charge values.  More... | |
| typedef Real | WidthType | 
| Type of feature width/FWHM (RT)  More... | |
|  Public Types inherited from Peak2D | |
| typedef Real | IntensityType | 
| Intensity type.  More... | |
| typedef DoubleReal | CoordinateType | 
| Coordinate type (of the position)  More... | |
| typedef DPosition< 2 > | PositionType | 
| Position type.  More... | |
| enum | DimensionDescription { RT = 0, MZ = 1, DIMENSION = 2 } | 
| This enum maps the symbolic names of the dimensions to numbers.  More... | |
|  Public Types inherited from UniqueIdInterface | |
| enum | { INVALID = 0 } | 
| This is the invalid unique id (cast it to a UInt64 if you like)  More... | |
| Public Member Functions | |
| Constructors and Destructor | |
| MRMFeature () | |
| Default constructor.  More... | |
| MRMFeature (const MRMFeature &rhs) | |
| Copy constructor.  More... | |
| MRMFeature & | operator= (const MRMFeature &rhs) | 
| Assignment operator.  More... | |
| virtual | ~MRMFeature () | 
| Destructor.  More... | |
| Accessors | |
| const PGScoresType & | getScores () const | 
| get all peakgroup scores  More... | |
| double | getScore (const String &score_name) | 
| get a single peakgroup score  More... | |
| Feature & | getFeature (String key) | 
| get a specified feature  More... | |
| void | setScores (const PGScoresType &scores) | 
| set all peakgroup scores  More... | |
| void | addScore (const String &score_name, double score) | 
| set a single peakgroup score  More... | |
| void | addFeature (Feature &feature, const String &key) | 
| Adds an feature from a single chromatogram into the feature.  More... | |
| const std::vector< Feature > & | getFeatures () const | 
| void | getFeatureIDs (std::vector< String > &result) const | 
|  Public Member Functions inherited from Feature | |
| Feature & | operator= (const Feature &rhs) | 
| Assignment operator.  More... | |
| bool | operator== (const Feature &rhs) const | 
| Equality operator.  More... | |
| const std::vector< Feature > & | getSubordinates () const | 
| immutable access to subordinate features  More... | |
| std::vector< Feature > & | getSubordinates () | 
| mutable access to subordinate features  More... | |
| void | setSubordinates (const std::vector< Feature > &rhs) | 
| mutable access to subordinate features  More... | |
| template<typename Type > | |
| Size | applyMemberFunction (Size(Type::*member_function)()) | 
| Applies a member function of Type to the feature (including subordinates). The returned values are accumulated.  More... | |
| template<typename Type > | |
| Size | applyMemberFunction (Size(Type::*member_function)() const) const | 
| The "const" variant.  More... | |
| Feature () | |
| Default constructor.  More... | |
| Feature (const Feature &feature) | |
| Copy constructor.  More... | |
| ~Feature () | |
| Destructor.  More... | |
| const std::vector< ConvexHull2D > & | getConvexHulls () const | 
| Non-mutable access to the convex hulls.  More... | |
| std::vector< ConvexHull2D > & | getConvexHulls () | 
| Mutable access to the convex hulls of single mass traces.  More... | |
| void | setConvexHulls (const std::vector< ConvexHull2D > &hulls) | 
| Set the convex hulls of single mass traces.  More... | |
| ConvexHull2D & | getConvexHull () const | 
| Returns the overall convex hull of the feature (calculated from the convex hulls of the mass traces)  More... | |
| bool | encloses (DoubleReal rt, DoubleReal mz) const | 
| Returns if the mass trace convex hulls of the feature enclose the position specified by rtandmz.  More... | |
| QualityType | getOverallQuality () const | 
| Non-mutable access to the overall quality.  More... | |
| void | setOverallQuality (QualityType q) | 
| Set the overall quality.  More... | |
| QualityType | getQuality (Size index) const | 
| Non-mutable access to the quality in dimension c.  More... | |
| void | setQuality (Size index, QualityType q) | 
| Set the quality in dimension c.  More... | |
| const ModelDescription< 2 > & | getModelDescription () const | 
| Non-mutable access to the model description.  More... | |
| ModelDescription< 2 > & | getModelDescription () | 
| Mutable access to the model description.  More... | |
| void | setModelDescription (const ModelDescription< 2 > &q) | 
| Set the model description.  More... | |
|  Public Member Functions inherited from BaseFeature | |
| WidthType | getWidth () const | 
| Non-mutable access to the features width (full width at half max, FWHM)  More... | |
| void | setWidth (WidthType fwhm) | 
| Set the width of the feature (FWHM)  More... | |
| const ChargeType & | getCharge () const | 
| Non-mutable access to charge state.  More... | |
| void | setCharge (const ChargeType &ch) | 
| Set charge state.  More... | |
| BaseFeature & | operator= (const BaseFeature &rhs) | 
| Assignment operator.  More... | |
| bool | operator== (const BaseFeature &rhs) const | 
| Equality operator.  More... | |
| bool | operator!= (const BaseFeature &rhs) const | 
| Unequality operator.  More... | |
| const std::vector < PeptideIdentification > & | getPeptideIdentifications () const | 
| returns a const reference to the PeptideIdentification vector  More... | |
| std::vector < PeptideIdentification > & | getPeptideIdentifications () | 
| returns a mutable reference to the PeptideIdentification vector  More... | |
| void | setPeptideIdentifications (const std::vector< PeptideIdentification > &peptides) | 
| sets the PeptideIdentification vector  More... | |
| AnnotationState | getAnnotationState () const | 
| state of peptide identifications attached to this feature. If one ID has multiple hits, the output depends on the top-hit only  More... | |
| BaseFeature () | |
| Default constructor.  More... | |
| BaseFeature (const BaseFeature &feature) | |
| Copy constructor.  More... | |
| BaseFeature (const Peak2D &point) | |
| Constructor from raw data point.  More... | |
| BaseFeature (const RichPeak2D &point) | |
| Constructor from raw data point with meta information.  More... | |
| ~BaseFeature () | |
| Destructor.  More... | |
| QualityType | getQuality () const | 
| Non-mutable access to the overall quality.  More... | |
| void | setQuality (QualityType q) | 
| Set the overall quality.  More... | |
|  Public Member Functions inherited from RichPeak2D | |
| RichPeak2D () | |
| Default constructor.  More... | |
| RichPeak2D (const RichPeak2D &p) | |
| Copy constructor.  More... | |
| RichPeak2D (const Peak2D &p) | |
| Constructor from Peak2D.  More... | |
| ~RichPeak2D () | |
| Destructor.  More... | |
| RichPeak2D & | operator= (const RichPeak2D &rhs) | 
| Assignment operator.  More... | |
| RichPeak2D & | operator= (const Peak2D &rhs) | 
| Assignment operator.  More... | |
| bool | operator== (const RichPeak2D &rhs) const | 
| Equality operator.  More... | |
| bool | operator!= (const RichPeak2D &rhs) const | 
| Equality operator.  More... | |
|  Public Member Functions inherited from Peak2D | |
| Peak2D & | operator= (const Peak2D &rhs) | 
| Assignment operator.  More... | |
| bool | operator== (const Peak2D &rhs) const | 
| Equality operator.  More... | |
| bool | operator!= (const Peak2D &rhs) const | 
| Equality operator.  More... | |
| Peak2D () | |
| Peak2D (const Peak2D &p) | |
| Copy constructor.  More... | |
| ~Peak2D () | |
| Destructor.  More... | |
| IntensityType | getIntensity () const | 
| void | setIntensity (IntensityType intensity) | 
| Non-mutable access to the data point intensity (height)  More... | |
| PositionType const & | getPosition () const | 
| Non-mutable access to the position.  More... | |
| PositionType & | getPosition () | 
| Mutable access to the position.  More... | |
| void | setPosition (const PositionType &position) | 
| Mutable access to the position.  More... | |
| CoordinateType | getMZ () const | 
| Returns the m/z coordinate (index 1)  More... | |
| void | setMZ (CoordinateType coordinate) | 
| Mutable access to the m/z coordinate (index 1)  More... | |
| CoordinateType | getRT () const | 
| Returns the RT coordinate (index 0)  More... | |
| void | setRT (CoordinateType coordinate) | 
| Mutable access to the RT coordinate (index 0)  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 nameif it exists.  More... | |
| void | removeMetaValue (UInt index) | 
| Removes the DataValue corresponding to indexif 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 UniqueIdInterface | |
| UniqueIdInterface () | |
| Default constructor - the unique id will be invalid  More... | |
| UniqueIdInterface (const UniqueIdInterface &rhs) | |
| Copy constructor - copies the unique id.  More... | |
| UniqueIdInterface & | operator= (UniqueIdInterface const &rhs) | 
| Assignment operator - copies the unique id.  More... | |
| ~UniqueIdInterface () | |
| Destructor.  More... | |
| bool | operator== (UniqueIdInterface const &rhs) const | 
| Equality comparison operator - the unique ids must be equal (!)  More... | |
| UInt64 | getUniqueId () const | 
| Non-mutable access to unique id - returns the unique id.  More... | |
| Size | clearUniqueId () | 
| Clear the unique id. The new unique id will be invalid. Returns 1 if the unique id was changed, 0 otherwise.  More... | |
| void | swap (UniqueIdInterface &from) | 
| Size | hasValidUniqueId () const | 
| Returns whether the unique id is valid. Returns 1 if the unique id is valid, 0 otherwise.  More... | |
| Size | hasInvalidUniqueId () const | 
| Returns whether the unique id is invalid. Returns 1 if the unique id is invalid, 0 otherwise.  More... | |
| Size | setUniqueId () | 
| Assigns a new, valid unique id. Always returns 1.  More... | |
| Size | ensureUniqueId () | 
| Assigns a valid unique id, but only if the present one is invalid. Returns 1 if the unique id was changed, 0 otherwise.  More... | |
| void | setUniqueId (UInt64 rhs) | 
| Assigns the given unique id.  More... | |
| void | setUniqueId (const String &rhs) | 
| Mutable access to unique id.  More... | |
| Protected Attributes | |
| FeatureListType | features_ | 
| PGScoresType | pg_scores_ | 
| peak group scores  More... | |
| std::map< String, int > | feature_map_ | 
| map native ids to the features  More... | |
|  Protected Attributes inherited from Feature | |
| QualityType | qualities_ [2] | 
| Quality measures for each dimension.  More... | |
| ModelDescription< 2 > | model_desc_ | 
| Description of the theoretical model the feature was constructed with.  More... | |
| std::vector< ConvexHull2D > | convex_hulls_ | 
| Array of convex hulls (one for each mass trace)  More... | |
| bool | convex_hulls_modified_ | 
| Flag that indicates if the overall convex hull needs to be recomputed (i.e. mass trace convex hulls were modified)  More... | |
| ConvexHull2D | convex_hull_ | 
| Overall convex hull of the feature.  More... | |
| std::vector< Feature > | subordinates_ | 
| subordinate features (e.g. features that the ModelFitter discarded due to inferior quality)  More... | |
|  Protected Attributes inherited from BaseFeature | |
| QualityType | quality_ | 
| Overall quality measure of the feature.  More... | |
| ChargeType | charge_ | 
| Charge of the peptide represented by this feature. The default value is 0, which represents an unknown charge state.  More... | |
| WidthType | width_ | 
| Width (FWHM) for the feature. The default value is 0.0, a feature finding algorithm can compute this form the model.  More... | |
| std::vector < PeptideIdentification > | peptides_ | 
| Peptide PeptideIdentifications belonging to the feature.  More... | |
|  Protected Attributes inherited from Peak2D | |
| PositionType | position_ | 
| The data point position.  More... | |
| IntensityType | intensity_ | 
| The data point intensity.  More... | |
|  Protected Attributes inherited from MetaInfoInterface | |
| MetaInfo * | meta_ | 
| pointer to the MetaInfo object. 0 by default  More... | |
|  Protected Attributes inherited from UniqueIdInterface | |
| UInt64 | unique_id_ | 
| the unique id  More... | |
| Additional Inherited Members | |
|  Static Public Member Functions inherited from Peak2D | |
| static char const * | shortDimensionName (UInt const dim) | 
| Short name of the dimension (abbreviated form)  More... | |
| static char const * | shortDimensionNameRT () | 
| Short name of the dimension (abbreviated form)  More... | |
| static char const * | shortDimensionNameMZ () | 
| Short name of the dimension (abbreviated form)  More... | |
| static char const * | fullDimensionName (UInt const dim) | 
| Full name of the dimension (self-explanatory form)  More... | |
| static char const * | fullDimensionNameRT () | 
| Full name of the dimension (self-explanatory form)  More... | |
| static char const * | fullDimensionNameMZ () | 
| Full name of the dimension (self-explanatory form)  More... | |
| static char const * | shortDimensionUnit (UInt const dim) | 
| Unit of measurement (abbreviated form)  More... | |
| static char const * | shortDimensionUnitRT () | 
| Unit of measurement (abbreviated form)  More... | |
| static char const * | shortDimensionUnitMZ () | 
| Unit of measurement (abbreviated form)  More... | |
| static char const * | fullDimensionUnit (UInt const dim) | 
| Unit of measurement (self-explanatory form)  More... | |
| static char const * | fullDimensionUnitRT () | 
| Unit of measurement (self-explanatory form)  More... | |
| static char const * | fullDimensionUnitMZ () | 
| Unit of measurement (self-explanatory form)  More... | |
|  Static Public Member Functions inherited from MetaInfoInterface | |
| static MetaInfoRegistry & | metaRegistry () | 
| retuns a reference to the MetaInfoRegistry  More... | |
|  Static Public Member Functions inherited from UniqueIdInterface | |
| static bool | isValid (UInt64 unique_id) | 
| Returns true if the unique_id is valid, false otherwise.  More... | |
|  Static Public Attributes inherited from BaseFeature | |
| static const std::string | NamesOfAnnotationState [SIZE_OF_ANNOTATIONSTATE] | 
|  Protected Member Functions inherited from MetaInfoInterface | |
| void | createIfNotExists_ () | 
| creates the MetaInfo object if it does not exist  More... | |
|  Static Protected Attributes inherited from Peak2D | |
| static char const *const | dimension_name_short_ [DIMENSION] | 
| Short name of the dimension (abbreviated form)  More... | |
| static char const *const | dimension_name_full_ [DIMENSION] | 
| Full name of the dimension (self-explanatory form)  More... | |
| static char const *const | dimension_unit_short_ [DIMENSION] | 
| Unit of measurement (abbreviated form)  More... | |
| static char const *const | dimension_unit_full_ [DIMENSION] | 
| Unit of measurement (self-explanatory form)  More... | |
A multi-chromatogram MRM feature.
An MRM feature contains corresponding features in multiple chromatograms, it is thus a representation of a peak group. The individual features in each chromatogram are represented by OpenMS Features.
| typedef std::vector<Feature> FeatureListType | 
Type definitions.
Feature list type
| typedef std::map<String, double> PGScoresType | 
Peak group score type.
| MRMFeature | ( | ) | 
Default constructor.
| MRMFeature | ( | const MRMFeature & | rhs | ) | 
Copy constructor.
| 
 | virtual | 
Destructor.
Adds an feature from a single chromatogram into the feature.
Referenced by MRMTransitionGroupPicker::createMRMFeature().
set a single peakgroup score
Referenced by MRMFeatureFinderScoring::calculateSwathScores_().
get a specified feature
Referenced by EmgScoring::calcElutionFitScore().
| void getFeatureIDs | ( | std::vector< String > & | result | ) | const | 
| const std::vector<Feature>& getFeatures | ( | ) | const | 
| const PGScoresType& getScores | ( | ) | const | 
get all peakgroup scores
| MRMFeature& operator= | ( | const MRMFeature & | rhs | ) | 
Assignment operator.
| void setScores | ( | const PGScoresType & | scores | ) | 
set all peakgroup scores
| 
 | protected | 
map native ids to the features
| 
 | protected | 
| 
 | protected | 
peak group scores
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:32 using doxygen 1.8.5 |