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OpenMS
2.5.0
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122 elements_(alphabet.elements_)
132 return elements_.size();
144 return elements_[index];
157 void setElement(
const name_type & name, mass_type mass,
bool forced =
false);
165 bool erase(
const name_type & name);
175 const element_type & getElement(
const name_type & name)
const;
183 const name_type & getName(size_type index)
const;
194 mass_type getMass(
const name_type & name)
const;
203 mass_type getMass(size_type index)
const;
211 masses_type getMasses(size_type isotope_index = 0)
const;
218 masses_type getAverageMasses()
const;
227 bool hasName(
const name_type & name)
const;
250 elements_.push_back(element);
266 virtual void sortByNames();
274 virtual void sortByValues();
286 virtual void load(
const std::string & fname);
336 OPENMS_DLLAPI std::ostream &
operator<<(std::ostream & os,
const IMSAlphabet & alphabet);
A gradient of multiple colors and arbitrary distances between colors.
Definition: MultiGradient.h:67
mass_container::const_iterator const_mass_iterator
Definition: IMSAlphabet.h:97
void push_back(const name_type &name, mass_type value)
Definition: IMSAlphabet.h:238
Base class for TOPP applications.
Definition: TOPPBase.h:144
void resize(size_type i, size_type j, value_type value=value_type())
Definition: Matrix.h:243
IMSElement element_type
Definition: IMSAlphabet.h:85
CoordinateType minX() const
Accessor for min_ coordinate minimum.
Definition: DIntervalBase.h:243
mass_container::iterator mass_iterator
Definition: IMSAlphabet.h:96
Base::iterator Iterator
Definition: FeatureMap.h:139
std::vector< mass_type > masses_type
Definition: IMSAlphabet.h:98
std::vector< mass_type > mass_container
Definition: IMSAlphabet.h:95
name_container::const_iterator const_name_iterator
Definition: IMSAlphabet.h:94
File adapter for MzML files.
Definition: MzMLFile.h:55
name_container::iterator name_iterator
Definition: IMSAlphabet.h:93
A more convenient string class.
Definition: String.h:58
Iterator begin()
Definition: MSExperiment.h:157
String & trim()
removes whitespaces (space, tab, line feed, carriage return) at the beginning and the end of the stri...
std::string name_type
Type of element's name.
Definition: IMSElement.h:62
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
container::iterator iterator
Definition: IMSAlphabet.h:90
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
static bool contains(const std::vector< T > &container, const E &elem)
Checks whether the element elem is contained in the given container.
Definition: ListUtils.h:146
static void toUpper(StringList &sl)
Transforms all strings contained in the passed StringList to upper case.
IMSAlphabet()
Definition: IMSAlphabet.h:103
element_type::mass_type mass_type
Definition: IMSAlphabet.h:86
static MultiGradient getDefaultGradientLinearIntensityMode()
Returns the default gradient for linear intensity mode.
Holds an indexed list of bio-chemical elements.
Definition: IMSAlphabet.h:81
std::pair< Size, Size > sizePair() const
Definition: Matrix.h:269
CoordinateType minY() const
Accessor for max_ coordinate minimum.
Definition: DIntervalBase.h:249
CoordinateType getMaxRT() const
returns the maximal retention time value
const_reference getValue(size_type const i, size_type const j) const
Definition: Matrix.h:165
IMSAlphabet(const IMSAlphabet &alphabet)
Definition: IMSAlphabet.h:121
container::const_iterator const_iterator
Definition: IMSAlphabet.h:91
Size size() const
Definition: MSExperiment.h:127
ConstIterator getPrecursorSpectrum(ConstIterator iterator) const
Returns the precursor spectrum of the scan pointed to by iterator.
Provides access to bilinearly interpolated values (and derivatives) from discrete data points....
Definition: BilinearInterpolation.h:72
std::vector< element_type > container
Definition: IMSAlphabet.h:88
A 2-dimensional hull representation in [counter]clockwise direction - depending on axis labelling.
Definition: ConvexHull2D.h:72
Predicate that determines if a spectrum's precursor is within a certain m/z range.
Definition: RangeUtils.h:394
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
std::vector< SpectrumType >::iterator Iterator
Mutable iterator.
Definition: MSExperiment.h:111
void push_back(const element_type &element)
Definition: IMSAlphabet.h:248
CoordinateType getMaxMZ() const
returns the maximal m/z value
const element_type & getElement(size_type index) const
Definition: IMSAlphabet.h:142
void load(const String &filename, PeakMap &map)
Loads a map from a MzML file. Spectra and chromatograms are sorted by default (this can be disabled u...
void load(const String &filename, FeatureMap &feature_map)
loads the file with name filename into map and calls updateRanges().
ContainerType & getData()
Returns the internal random access container storing the data.
Definition: BilinearInterpolation.h:510
void setMapping_1(KeyType const &scale, KeyType const &inside_low, KeyType const &outside_low)
Specifies the mapping from "outside" to "inside" coordinates by the following data:
Definition: BilinearInterpolation.h:713
QString toQString() const
Conversion to Qt QString.
Math namespace.
Definition: BilinearInterpolation.h:42
void addValue(KeyType arg_pos_0, KeyType arg_pos_1, ValueType arg_value)
Performs bilinear resampling. The arg_value is split up and added to the data points around arg_pos....
Definition: BilinearInterpolation.h:316
String & toUpper()
Converts the string to uppercase.
std::vector< name_type > name_container
Definition: IMSAlphabet.h:92
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
CoordinateType maxY() const
Accessor for max_ coordinate maximum.
Definition: DIntervalBase.h:261
#define OPENMS_LOG_ERROR
Macro to be used if non-fatal error are reported (processing continues)
Definition: LogStream.h:455
A container for features.
Definition: FeatureMap.h:95
size_type size() const
Definition: IMSAlphabet.h:130
Represents a chemical atom with name and isotope distribution.
Definition: IMSElement.h:58
bool operator()(const element_type &el1, const element_type &el2) const
Definition: IMSAlphabet.h:320
void setRTRange(const DRange< 1 > &range)
restricts the range of RT values for peaks to load
Iterator end()
Definition: MSExperiment.h:167
const std::vector< MSSpectrum > & getSpectra() const
returns the spectrum list
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLFile.h:68
void clear()
Definition: IMSAlphabet.h:256
Private class-functor to sort out elements in mass ascending order.
Definition: IMSAlphabet.h:317
DBoundingBox< 2 > getBoundingBox() const
returns the bounding box of the feature hull points
void updateRanges() override
Updates minimum and maximum position/intensity.
CoordinateType maxX() const
Accessor for min_ coordinate maximum.
Definition: DIntervalBase.h:255
std::ostream & operator<<(std::ostream &os, const IMSAlphabet &alphabet)
mass_type getMass(size_type index=0) const
Definition: IMSElement.h:172
void setMZRange(const DRange< 1 > &range)
restricts the range of MZ values for peaks to load
std::vector< SpectrumType >::const_iterator ConstIterator
Non-mutable iterator.
Definition: MSExperiment.h:113
static MultiGradient getDefaultGradientLogarithmicIntensityMode()
Returns the default gradient for logarithmic intensity mode.
void setMSLevels(const std::vector< Int > &levels)
sets the desired MS levels for peaks to load
Element could not be found exception.
Definition: Exception.h:662
void fromString(const std::string &gradient)
Sets the gradient by string representation.
String suffix(SizeType length) const
returns the suffix of length length
container elements_
Definition: IMSAlphabet.h:312
CoordinateType getMinMZ() const
returns the minimal m/z value
container::size_type size_type
Definition: IMSAlphabet.h:89
IMSAlphabet(const container &elements)
Definition: IMSAlphabet.h:111
PeakFileOptions & getOptions()
Mutable access to the options for loading/storing.
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!
element_type::name_type name_type
Definition: IMSAlphabet.h:87
virtual ~IMSAlphabet()
Definition: IMSAlphabet.h:306
CoordinateType getMinRT() const
returns the minimal retention time value
void setMapping_0(KeyType const &scale, KeyType const &inside_low, KeyType const &outside_low)
Specifies the mapping from "outside" to "inside" coordinates by the following data:
Definition: BilinearInterpolation.h:670
QColor interpolatedColorAt(double position) const
Returns the color as position.