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OpenMS
2.5.0
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42 #define OPENMS_CHEMISTRY_ELEMENT_NAME_DEFAULT "unknown"
43 #define OPENMS_CHEMISTRY_ELEMENT_SYMBOL_DEFAULT "??"
44 #define OPENMS_CHEMISTRY_ELEMENT_WEIGHT_DEFAULT 0.0
45 #define OPENMS_CHEMISTRY_ELEMENT_ATOMICNUMBER_DEFAULT 0
71 double average_weight,
82 void setAtomicNumber(
UInt atomic_number);
86 UInt getAtomicNumber()
const;
89 void setAverageWeight(
double weight);
92 double getAverageWeight()
const;
95 void setMonoWeight(
double weight);
98 double getMonoWeight()
const;
107 void setName(
const String & name);
110 const String & getName()
const;
113 void setSymbol(
const String & symbol);
116 const String & getSymbol()
const;
140 friend OPENMS_DLLAPI std::ostream &
operator<<(std::ostream & os,
const Element & element);
Base class for TOPP applications.
Definition: TOPPBase.h:144
ConstIterator end() const
Gives access to the underlying text buffer.
void addLine(const StringType &line)
Definition: TextFile.h:112
Forward iterator for an area of peaks in an experiment.
Definition: AreaIterator.h:57
double average_weight_
average weight over all isotopes
Definition: Element.h:154
Representation of an element.
Definition: Element.h:53
static String basename(const String &file)
Returns the basename of the file (without the path).
virtual double getSignalToNoise(const PeakIterator &data_point)
Definition: SignalToNoiseEstimator.h:128
void sortSpectra(bool sort_mz=true)
Sorts the data points by retention time.
ConstAreaIterator areaEndConst() const
Returns an non-mutable invalid area iterator marking the end of an area.
void store(const String &filename, const PeakMap &map) const
Stores a map in an MzML file.
void setMZ(CoordinateType mz)
Mutable access to m/z.
Definition: Peak1D.h:121
A 2-dimensional raw data point or peak.
Definition: Peak2D.h:54
void setValue(const String &key, const DataValue &value, const String &description="", const StringList &tags=StringList())
Sets a value.
File adapter for Enhanced DTA files.
Definition: EDTAFile.h:85
File adapter for MzML files.
Definition: MzMLFile.h:55
A more convenient string class.
Definition: String.h:58
Iterator begin()
Definition: MSExperiment.h:157
bool operator!=(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:824
String & trim()
removes whitespaces (space, tab, line feed, carriage return) at the beginning and the end of the stri...
void filter(MSSpectrum &spectrum)
Smoothes an MSSpectrum containing profile data.
Definition: GaussFilter.h:92
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
This class provides some basic file handling methods for text files.
Definition: TextFile.h:46
virtual void init(const PeakIterator &it_begin, const PeakIterator &it_end)
Set the start and endpoint of the raw data interval, for which signal to noise ratios will be estimat...
Definition: SignalToNoiseEstimator.h:109
void setChromatogramType(ChromatogramType type)
sets the chromatogram type
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
IntensityType getIntensity() const
Definition: Peak2D.h:166
void setIntensity(IntensityType intensity)
Mutable access to the data point intensity (height)
Definition: Peak1D.h:112
bool operator<(const MultiplexDeltaMasses &dm1, const MultiplexDeltaMasses &dm2)
UInt atomic_number_
atomic number of the element
Definition: Element.h:151
#define OPENMS_LOG_WARN
Macro if a warning, a piece of information which should be read by the user, should be logged.
Definition: LogStream.h:460
void setIntensity(IntensityType intensity)
Non-mutable access to the data point intensity (height)
Definition: Peak2D.h:172
Size size() const
Definition: MSExperiment.h:127
#define OPENMS_LOG_FATAL_ERROR
Macro to be used if fatal error are reported (processing stops)
Definition: LogStream.h:450
static String concatenate(const std::vector< T > &container, const String &glue="")
Concatenates all elements of the container and puts the glue string between elements.
Definition: ListUtils.h:193
void setIntensity(IntensityType intensity)
Mutable access to the data point intensity (height)
Definition: ChromatogramPeak.h:113
void setRT(CoordinateType coordinate)
Mutable access to the RT coordinate (index 0)
Definition: Peak2D.h:214
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
std::vector< SpectrumType >::iterator Iterator
Mutable iterator.
Definition: MSExperiment.h:111
This class implements a fast peak-picking algorithm best suited for high resolution MS data (FT-ICR-M...
Definition: PeakPickerHiRes.h:73
ConstAreaIterator areaBeginConst(CoordinateType min_rt, CoordinateType max_rt, CoordinateType min_mz, CoordinateType max_mz) const
Returns a non-mutable area iterator for area.
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, ConsensusMap &consensus_map)
Loads a EDTA file into a consensusXML.
A 1-dimensional raw data point or peak for chromatograms.
Definition: ChromatogramPeak.h:54
AreaIterator areaBegin(CoordinateType min_rt, CoordinateType max_rt, CoordinateType min_mz, CoordinateType max_mz)
Returns an area iterator for area.
String symbol_
symbol of the element
Definition: Element.h:148
A consensus feature spanning multiple LC-MS/MS experiments.
Definition: ConsensusFeature.h:69
#define OPENMS_LOG_DEBUG
Macro for general debugging information.
Definition: LogStream.h:470
void pick(const MSSpectrum &input, MSSpectrum &output) const
Applies the peak-picking algorithm to a single spectrum (MSSpectrum). The resulting picked peaks are ...
const MSChromatogram getTIC(float rt_bin_size=0) const
Compute Total Ion Count per MS1 spectrum and applies the resampling algorithm, if a bin size in RT se...
void setMZ(CoordinateType coordinate)
Mutable access to the m/z coordinate (index 1)
Definition: Peak2D.h:202
void setParameters(const Param ¶m)
Sets the parameters.
const Param & getParameters() const
Non-mutable access to the parameters.
bool empty() const
Definition: MSExperiment.h:137
A 1-dimensional raw data point or peak.
Definition: Peak1D.h:54
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)
A container for consensus elements.
Definition: ConsensusMap.h:79
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
CoordinateType getRT() const
Returns the RT coordinate (index 0)
Definition: Peak2D.h:208
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
AreaIterator areaEnd()
Returns an invalid area iterator marking the end of an area.
void setMZ(CoordinateType rt)
Alias for setRT()
Definition: ChromatogramPeak.h:146
void addChromatogram(const MSChromatogram &chromatogram)
adds a chromatogram to the list
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
ConstIterator begin() const
Gives access to the underlying text buffer.
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806
ptrdiff_t SignedSize
Signed Size type e.g. used as pointer difference.
Definition: Types.h:134
Definition: IsotopeDistribution.h:64
String substr(size_t pos=0, size_t n=npos) const
Wrapper for the STL substr() method. Returns a String object with its contents initialized to a subst...
void clear(bool clear_meta_data=true)
Clears all data and meta data.
Iterator end()
Definition: MSExperiment.h:167
double mono_weight_
mono isotopic weight of the most frequent isotope
Definition: Element.h:157
std::vector< ConsensusFeature >::iterator Iterator
Mutable iterator.
Definition: ConsensusMap.h:160
The representation of a chromatogram.
Definition: MSChromatogram.h:54
String name_
name of the element
Definition: Element.h:145
void store(const String &filename)
Writes the data to a file.
Management and storage of parameters / INI files.
Definition: Param.h:73
void concatenate(StringIterator first, StringIterator last, const String &glue="")
Concatenates all elements from first to last-1 and inserts glue between the elements.
Definition: String.h:466
Definition: ChromatogramSettings.h:71
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:50
CoordinateType getMZ() const
Returns the m/z coordinate (index 1)
Definition: Peak2D.h:196
#define OPENMS_LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:465
IsotopeDistribution isotopes_
distribution of the isotopes
Definition: Element.h:160
CoordinateType getRT() const
returns the retention time of the current scan
Definition: AreaIterator.h:198
ContainerType::const_iterator ConstIterator
Non-mutable iterator.
Definition: MSSpectrum.h:104
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
void load(const String &filename, bool trim_lines=false, Int first_n=-1, bool skip_empty_lines=false)
Loads data from a text file.
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!
This class represents a Gaussian lowpass-filter which works on uniform as well as on non-uniform prof...
Definition: GaussFilter.h:74
ConstIterator RTBegin(CoordinateType rt) const
Fast search for spectrum range begin.