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OpenMS
2.4.0
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Go to the documentation of this file.
67 private std::vector<Peak1D>,
74 struct OPENMS_DLLAPI
RTLess :
public std::binary_function<MSSpectrum, MSSpectrum, bool>
100 typedef typename ContainerType::iterator
Iterator;
112 using ContainerType::operator[];
113 using ContainerType::begin;
114 using ContainerType::rbegin;
115 using ContainerType::end;
116 using ContainerType::rend;
117 using ContainerType::resize;
118 using ContainerType::size;
119 using ContainerType::push_back;
120 using ContainerType::emplace_back;
121 using ContainerType::pop_back;
122 using ContainerType::empty;
123 using ContainerType::front;
124 using ContainerType::back;
125 using ContainerType::reserve;
126 using ContainerType::insert;
127 using ContainerType::erase;
128 using ContainerType::swap;
130 using typename ContainerType::iterator;
131 using typename ContainerType::const_iterator;
132 using typename ContainerType::size_type;
133 using typename ContainerType::value_type;
134 using typename ContainerType::reference;
135 using typename ContainerType::const_reference;
136 using typename ContainerType::pointer;
137 using typename ContainerType::difference_type;
167 void updateRanges()
override;
172 double getRT()
const;
175 void setRT(
double rt);
185 double getDriftTime()
const;
190 void setDriftTime(
double dt);
197 UInt getMSLevel()
const;
200 void setMSLevel(
UInt ms_level);
203 const String& getName()
const;
206 void setName(
const String& name);
223 const FloatDataArrays& getFloatDataArrays()
const;
229 return float_data_arrays_;
233 void setFloatDataArrays(
const FloatDataArrays& fda);
236 const StringDataArrays& getStringDataArrays()
const;
239 StringDataArrays& getStringDataArrays();
242 void setStringDataArrays(
const StringDataArrays& sda);
245 const IntegerDataArrays& getIntegerDataArrays()
const;
248 IntegerDataArrays& getIntegerDataArrays();
251 void setIntegerDataArrays(
const IntegerDataArrays& ida);
261 void sortByIntensity(
bool reverse =
false);
268 void sortByPosition();
271 bool isSorted()
const;
287 Size findNearest(CoordinateType mz)
const;
300 Int findNearest(CoordinateType mz, CoordinateType tolerance)
const;
315 Int findNearest(CoordinateType mz, CoordinateType tolerance_left, CoordinateType tolerance_right)
const;
322 Iterator MZBegin(CoordinateType mz);
329 Iterator MZBegin(Iterator begin, CoordinateType mz, Iterator end);
336 Iterator MZEnd(CoordinateType mz);
343 Iterator MZEnd(Iterator begin, CoordinateType mz, Iterator end);
350 ConstIterator MZBegin(CoordinateType mz)
const;
357 ConstIterator MZBegin(ConstIterator begin, CoordinateType mz, ConstIterator end)
const;
364 ConstIterator MZEnd(CoordinateType mz)
const;
371 ConstIterator MZEnd(ConstIterator begin, CoordinateType mz, ConstIterator end)
const;
380 Iterator PosBegin(CoordinateType mz);
389 Iterator PosBegin(Iterator begin, CoordinateType mz, Iterator end);
398 ConstIterator PosBegin(CoordinateType mz)
const;
407 ConstIterator PosBegin(ConstIterator begin, CoordinateType mz, ConstIterator end)
const;
416 Iterator PosEnd(CoordinateType mz);
425 Iterator PosEnd(Iterator begin, CoordinateType mz, Iterator end);
434 ConstIterator PosEnd(CoordinateType mz)
const;
443 ConstIterator PosEnd(ConstIterator begin, CoordinateType mz, ConstIterator end)
const;
453 void clear(
bool clear_meta_data);
462 MSSpectrum& select(
const std::vector<Size>& indices);
490 os <<
"-- MSSPECTRUM BEGIN --" << std::endl;
493 os << static_cast<const SpectrumSettings&>(spec);
498 os << *it << std::endl;
501 os <<
"-- MSSPECTRUM END --" << std::endl;
Peak2D PeakType
Definition: MassTrace.h:47
Integer data array class.
Definition: DataArrays.h:51
PeakType::CoordinateType CoordinateType
Coordinate (m/z) type.
Definition: MSSpectrum.h:84
~MSSpectrum() override
Destructor.
Definition: MSSpectrum.h:148
Base class for TOPP applications.
Definition: TOPPBase.h:150
void store(const String &filename, const ConsensusMap &consensus_map)
Stores a consensus map to file.
Comparator for the retention time.
Definition: MSSpectrum.h:74
void simulate(SimTypes::MutableSimRandomNumberGeneratorPtr rnd_gen, SimTypes::SampleChannels &peptides)
General purpose function to simulate a mass spectrometry run.
This class serves for reading in and writing FASTA files.
Definition: FASTAFile.h:64
void store(const String &filename, const PeakMap &map) const
Stores a map in an MzML file.
Central class for simulation of mass spectrometry experiments.
Definition: MSSim.h:68
void setValue(const String &key, const DataValue &value, const String &description="", const StringList &tags=StringList())
Sets a value.
File adapter for MzML files.
Definition: MzMLFile.h:55
A more convenient string class.
Definition: String.h:57
const SimTypes::FeatureMapSim & getContaminants() const
Access the contaminants feature map of simulated features.
void setValidStrings(const String &key, const std::vector< String > &strings)
Sets the valid strings for the parameter key.
#define LOG_ERROR
Macro to be used if non-fatal error are reported (processing continues)
Definition: LogStream.h:446
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:149
std::vector< SimProtein > SampleProteins
Container for FASTAEntry & abundance information.
Definition: SimTypes.h:90
ConsensusMap & getLabelingConsensus()
Access the labeling consensus map of simulated features.
OpenMS::DataArrays::IntegerDataArray IntegerDataArray
Integer data array vector type.
Definition: MSSpectrum.h:94
boost::shared_ptr< SimRandomNumberGenerator > MutableSimRandomNumberGeneratorPtr
Definition: SimTypes.h:174
std::vector< StringDataArray > StringDataArrays
Definition: MSSpectrum.h:92
Wrapper class for random number generators used by the simulation classes.
Definition: SimTypes.h:118
bool operator!=(const MSSpectrum &rhs) const
Equality operator.
Definition: MSSpectrum.h:161
std::vector< SampleProteins > SampleChannels
Container for multiple channels of SampleProteins.
Definition: SimTypes.h:93
String name_
Name.
Definition: MSSpectrum.h:476
Exception indicating that an invalid parameter was handed over to an algorithm.
Definition: Exception.h:347
int Int
Signed integer type.
Definition: Types.h:102
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
Handles the management of a position and intensity range.
Definition: RangeManager.h:47
IntegerDataArrays integer_data_arrays_
Integer data arrays.
Definition: MSSpectrum.h:485
StringDataArrays string_data_arrays_
String data arrays.
Definition: MSSpectrum.h:482
double getClockTime() const
const SimTypes::MSSimExperiment & getPeakMap() const
Access the picked (centroided) experiment.
std::vector< IntegerDataArray > IntegerDataArrays
Definition: MSSpectrum.h:95
void setParameters(const Param ¶m)
Sets the parameters.
ConsensusMap & getChargeConsensus()
Access the charge consensus map of simulated features.
bool find(TFinder &finder, const Pattern< TNeedle, FuzzyAC > &me, PatternAuxData< TNeedle > &dh)
Definition: AhoCorasickAmbiguous.h:884
String data array class.
Definition: DataArrays.h:57
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:75
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:73
void store(const String &filename, const FeatureMap &feature_map)
stores the map feature_map in file with name filename.
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
StopWatch Class.
Definition: StopWatch.h:59
std::vector< FloatDataArray > FloatDataArrays
Definition: MSSpectrum.h:89
FloatDataArrays & getFloatDataArrays()
Returns a mutable reference to the float meta data arrays.
Definition: MSSpectrum.h:227
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
Plain data object holding sequence and abundance information on a single protein.
Definition: SimTypes.h:73
const ColumnHeaders & getColumnHeaders() const
Non-mutable access to the file descriptions.
void store(String filename, const std::vector< ProteinIdentification > &protein_ids, const std::vector< PeptideIdentification > &peptide_ids, const String &document_id="")
Stores the data in an idXML file.
double retention_time_
Retention time.
Definition: MSSpectrum.h:467
double drift_time_
Drift time.
Definition: MSSpectrum.h:470
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806
void setSectionDescription(const String &key, const String &description)
Sets a description for an existing section.
static void load(const String &filename, std::vector< FASTAEntry > &data)
loads a FASTA file given by 'filename' and stores the information in 'data'
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLFile.h:68
const SimTypes::FeatureMapSim & getSimulatedFeatures() const
Access the simulated features.
UInt ms_level_
MS level.
Definition: MSSpectrum.h:473
FloatDataArrays float_data_arrays_
Float data arrays.
Definition: MSSpectrum.h:479
Representation of 1D spectrum settings.
Definition: SpectrumSettings.h:63
Management and storage of parameters / INI files.
Definition: Param.h:74
std::vector< PeakType > ContainerType
Spectrum base type.
Definition: MSSpectrum.h:86
ContainerType::iterator Iterator
Mutable iterator.
Definition: MSSpectrum.h:101
OpenMS::DataArrays::StringDataArray StringDataArray
String data array vector type.
Definition: MSSpectrum.h:91
ContainerType::const_iterator ConstIterator
Non-mutable iterator.
Definition: MSSpectrum.h:103
ContainerType::reverse_iterator ReverseIterator
Mutable reverse iterator.
Definition: MSSpectrum.h:105
OpenMS::DataArrays::FloatDataArray FloatDataArray
Float data array vector type.
Definition: MSSpectrum.h:88
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
ContainerType::const_reverse_iterator ConstReverseIterator
Non-mutable reverse iterator.
Definition: MSSpectrum.h:107
Float data array class.
Definition: DataArrays.h:45
void insert(const String &prefix, const Param ¶m)
UInt64 getUniqueId() const
Non-mutable access to unique id - returns the unique id.
Definition: UniqueIdInterface.h:109
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!
void getIdentifications(std::vector< ProteinIdentification > &proteins, std::vector< PeptideIdentification > &peptides) const
Access the simulated identifications (proteins and peptides)
This class provides Input functionality for ConsensusMaps and Output functionality for alignments and...
Definition: ConsensusXMLFile.h:61
Used to load and store idXML files.
Definition: IdXMLFile.h:63
const SimTypes::MSSimExperiment & getExperiment() const
Access the simulated experiment.