A basic LC-MS feature. More...
#include <OpenMS/KERNEL/BaseFeature.h>
Classes | |
struct | QualityLess |
Compare by quality. More... | |
Public Member Functions | |
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... | |
Constructors and Destructor | |
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... | |
Quality methods | |
QualityType | getQuality () const |
Non-mutable access to the overall quality. More... | |
void | setQuality (QualityType q) |
Set the overall quality. More... | |
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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... | |
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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... | |
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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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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 | |
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... | |
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PositionType | position_ |
The data point position. More... | |
IntensityType | intensity_ |
The data point intensity. More... | |
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MetaInfo * | meta_ |
pointer to the MetaInfo object. 0 by default More... | |
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UInt64 | unique_id_ |
the unique id More... | |
Type definitions | |
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... | |
static const std::string | NamesOfAnnotationState [SIZE_OF_ANNOTATIONSTATE] |
Additional Inherited Members | |
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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... | |
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enum | { INVALID = 0 } |
This is the invalid unique id (cast it to a UInt64 if you like) More... | |
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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... | |
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static MetaInfoRegistry & | metaRegistry () |
retuns a reference to the MetaInfoRegistry More... | |
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static bool | isValid (UInt64 unique_id) |
Returns true if the unique_id is valid, false otherwise. More... | |
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void | createIfNotExists_ () |
creates the MetaInfo object if it does not exist More... | |
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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 basic LC-MS feature.
This class represents a "minimal" feature, defined by a position in RT and m/z, intensity, charge, quality, and annotated peptides. Most classes dealing with features will use the subclasses Feature or ConsensusFeature directly. However, algorithms that rely on very general characteristics of features can use this class to provide a unified solution for both "normal" features and consensus features.
typedef Int ChargeType |
Type of charge values.
typedef Real QualityType |
Type of quality values.
enum AnnotationState |
BaseFeature | ( | ) |
Default constructor.
BaseFeature | ( | const BaseFeature & | feature | ) |
Copy constructor.
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explicit |
Constructor from raw data point.
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explicit |
Constructor from raw data point with meta information.
~BaseFeature | ( | ) |
Destructor.
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
const ChargeType& getCharge | ( | ) | const |
Non-mutable access to charge state.
Referenced by IDMapper::annotate(), ModelFitter< PeakType, FeatureType >::fit(), KroenikFile::load(), FeatureFinderAlgorithmSimplest< PeakType, FeatureType >::run(), FeatureFinderAlgorithmSimple< PeakType, FeatureType >::run(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run().
const std::vector<PeptideIdentification>& getPeptideIdentifications | ( | ) | const |
returns a const reference to the PeptideIdentification vector
Referenced by IDMapper::annotate().
std::vector<PeptideIdentification>& getPeptideIdentifications | ( | ) |
returns a mutable reference to the PeptideIdentification vector
QualityType getQuality | ( | ) | const |
Non-mutable access to the overall quality.
Referenced by BaseFeature::QualityLess::operator()().
WidthType getWidth | ( | ) | const |
Non-mutable access to the features width (full width at half max, FWHM)
bool operator!= | ( | const BaseFeature & | rhs | ) | const |
Unequality operator.
BaseFeature& operator= | ( | const BaseFeature & | rhs | ) |
Assignment operator.
bool operator== | ( | const BaseFeature & | rhs | ) | const |
Equality operator.
void setCharge | ( | const ChargeType & | ch | ) |
void setPeptideIdentifications | ( | const std::vector< PeptideIdentification > & | peptides | ) |
sets the PeptideIdentification vector
void setQuality | ( | QualityType | q | ) |
Set the overall quality.
void setWidth | ( | WidthType | fwhm | ) |
Set the width of the feature (FWHM)
Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run().
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protected |
Charge of the peptide represented by this feature. The default value is 0, which represents an unknown charge state.
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static |
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protected |
Peptide PeptideIdentifications belonging to the feature.
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protected |
Overall quality measure of the feature.
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protected |
Width (FWHM) for the feature. The default value is 0.0, a feature finding algorithm can compute this form the model.
OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:31 using doxygen 1.8.5 |