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OpenMS
2.5.0
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37 #include <OpenMS/config.h>
121 static String typeToName(Type type);
124 static String typeToMZML(Type type);
127 static Type nameToType(
const String& name);
137 static std::map<Type, String> initializeMap_();
140 static std::map<Type, String> initializeMZMLMap_();
const String & getVersion() const
return the version of the schema
OpenMS::Interfaces::SpectrumPtr getSpectrumById(int id)
Retrieve the raw data for the spectrum at position "id".
File adapter for MzXML 3.1 files.
Definition: MzXMLFile.h:52
FeatureFileOptions & getOptions()
Mutable access to the options for loading/storing.
static String number(double d, UInt n)
returns a string for d with exactly n decimal places
OpenSWATH OpenSWATH report (OSW) SQLite DB.
Definition: FileTypes.h:106
const std::vector< DataProcessing > & getDataProcessing() const
returns a const reference to the description of the applied data processing
void load(const String &filename, TransformationDescription &transformation, bool fit_model=true)
Loads the transformation from an TransformationXML file.
void setLoadSubordinates(bool sub)
void store(const String &filename, const ConsensusMap &consensus_map)
Stores a consensus map to file.
void store(const String &filename, const TargetedExperiment &id) const
Stores a map in a TraML file.
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLFile.h:68
void updateRanges() override
Updates minimum and maximum position/intensity.
OpenSWATH Peptide Query Parameter (PQP) SQLite DB, see TransitionPQPFile.
Definition: FileTypes.h:104
ConsensusMap & appendColumns(const ConsensusMap &rhs)
Add consensus map entries as new columns.
bool has(const Key &key) const
Test whether the map contains the given key.
Definition: Map.h:108
void fitModel(const String &model_type, const Param ¶ms=Param())
Fits a model to the data.
static const std::string NamesOfScanMode[SIZE_OF_SCANMODE]
Names of scan modes.
Definition: InstrumentSettings.h:73
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS identification format (.idXML)
Definition: FileTypes.h:66
OpenMS consensus map format (.consensusXML)
Definition: FileTypes.h:67
Portable Network Graphics (.png)
Definition: FileTypes.h:85
SpectraST MRM List.
Definition: FileTypes.h:102
T::value_type min
Definition: StatisticFunctions.h:687
void load(const String &filename, std::vector< ProteinIdentification > &poid, std::vector< PeptideIdentification > &peid)
Loads the identifications from a MzIdentML file.
CachedMzML file (.cachedmzML)
Definition: FileTypes.h:73
void addSoftware(const Software &software)
NCBI binary blast db.
Definition: FileTypes.h:101
ExitCodes
Exit codes.
Definition: TOPPBase.h:149
enhanced comma separated files (RT, m/z, Intensity, [meta])
Definition: FileTypes.h:93
void setLoadConvexHull(bool convex)
any HTML format
Definition: FileTypes.h:97
static void load(const String &filename, std::vector< FASTAEntry > &data)
loads a FASTA file given by 'filename' and stores the information in 'data'
static const std::string NamesOfProcessingAction[SIZE_OF_PROCESSINGACTION]
Names of inlet types.
Definition: DataProcessing.h:83
String toString(const T &i)
fallback template for general purpose using Boost::Karma; more specializations below
Definition: StringUtils.h:85
T::value_type max
Definition: StatisticFunctions.h:687
A convenience class to report either absolute or delta (between two timepoints) RAM usage.
Definition: SysInfo.h:83
analysisXML format
Definition: FileTypes.h:99
Novor custom parameter file.
Definition: FileTypes.h:111
const std::vector< MSChromatogram > & getChromatograms() const
returns the chromatogram list
qcML (will undergo standardisation maybe) (.qcml)
Definition: FileTypes.h:79
bool hasCTerminalModification() const
predicate which is true if the peptide is C-term modified
A low-level class to read an indexedmzML file.
Definition: IndexedMzMLHandler.h:78
void load(const String &filename, FeatureMap &feature_map)
loads the file with name filename into map and calls updateRanges().
boost::shared_ptr< Spectrum > SpectrumPtr
Definition: openms/include/OpenMS/INTERFACES/DataStructures.h:236
Size size() const
Definition: MSExperiment.h:127
void store(const String &filename, const FeatureMap &feature_map)
stores the map feature_map in file with name filename.
mzIdentML (HUPO PSI AnalysisXML followup format) (.mzid)
Definition: FileTypes.h:77
float QualityType
Type of quality values.
Definition: BaseFeature.h:63
static const std::map< Type, String > name_of_MZMLtypes_
Maps the FileType::Type to the preferred mzML CV name.
Definition: FileTypes.h:134
const std::vector< SourceFile > & getSourceFiles() const
returns a const reference to the source data file
void load(const String &filename, TargetedExperiment &id)
Loads a map from a TraML file.
double CoordinateType
Coordinate type (of the position)
Definition: Peak2D.h:64
Generic description of a coordinate transformation.
Definition: TransformationDescription.h:61
void load(const String &filename, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids)
Loads the identifications of an idXML file without identifier.
size_t getNrSpectra() const
Returns the number of spectra available.
DTA2D file (.dta2d)
Definition: FileTypes.h:62
any TSV file, for example msInspect file or OpenSWATH transition file (see TransitionTSVFile)
Definition: FileTypes.h:87
UInt64 getSize() const
returns the total number of peaks
any text format, which has only loose definition of what it actually contains – thus it is usually ha...
Definition: FileTypes.h:95
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:50
const PositionType & getMin() const
Returns the minimum position.
Definition: RangeManager.h:111
A container for features.
Definition: FeatureMap.h:95
Description of the software used for processing.
Definition: Software.h:48
double mean
Definition: StatisticFunctions.h:686
Executable (.exe)
Definition: FileTypes.h:116
static const std::string NamesOfType[SIZE_OF_TYPE]
Names of detector types.
Definition: IonDetector.h:78
bool isValid(const String &filename, std::ostream &os=std::cerr)
Checks if a file validates against the XML schema.
File adapter for MzIdentML files.
Definition: MzIdentMLFile.h:67
MzML file (.mzML)
Definition: FileTypes.h:72
Base::const_iterator const_iterator
Definition: MSExperiment.h:125
void updateRanges() override
Updates minimum and maximum position/intensity.
static SpectrumSettings::SpectrumType estimateType(const PeakConstIterator &begin, const PeakConstIterator &end)
Estimates the peak type of the peaks in the iterator range based on intensity characteristics of up t...
Definition: PeakTypeEstimator.h:69
static String typeToName(Type type)
Returns the name/extension of the type.
static const std::string NamesOfActivationMethodShort[SIZE_OF_ACTIVATIONMETHOD]
Definition: Precursor.h:95
void updateRanges() override
Updates minimum and maximum position/intensity.
Iterator begin()
Definition: MSExperiment.h:157
size_t getNrChromatograms() const
Returns the number of chromatograms available.
static const std::map< Type, String > name_of_types_
Maps the FileType::Type to the preferred extension.
Definition: FileTypes.h:131
bool isSemanticallyValid(const String &filename, StringList &errors, StringList &warnings)
Checks if a file is valid with respect to the mapping file and the controlled vocabulary.
Base class for TOPP applications.
Definition: TOPPBase.h:144
boost::shared_ptr< Chromatogram > ChromatogramPtr
Definition: openms/include/OpenMS/INTERFACES/DataStructures.h:156
double variance
Definition: StatisticFunctions.h:686
static void transformRetentionTimes(PeakMap &msexp, const TransformationDescription &trafo, bool store_original_rt=false)
Applies the given transformation to a peak map.
MzXML file (.mzXML)
Definition: FileTypes.h:64
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
This class provides Input functionality for ConsensusMaps and Output functionality for alignments and...
Definition: ConsensusXMLFile.h:61
mzTab file (.mzTab)
Definition: FileTypes.h:88
const std::vector< UInt > & getMSLevels() const
returns an array of MS levels
File adapter for HUPO PSI TraML files.
Definition: TraMLFile.h:63
String delta(const String &event="delta")
Controlled Vocabulary format.
Definition: FileTypes.h:96
specArray file (.peplist)
Definition: FileTypes.h:89
std::ifstream infile
Questionable file tested by TEST_FILE_EQUAL.
Centralizes the file types recognized by FileHandler.
Definition: FileTypes.h:53
FASTA file (.fasta)
Definition: FileTypes.h:92
Mascot Generic Format (.mgf)
Definition: FileTypes.h:68
any XML format
Definition: FileTypes.h:98
void setVersion(const String &version)
Sets the software version.
Iterator end()
Definition: MSExperiment.h:167
Unknown file extension.
Definition: FileTypes.h:60
kroenik file (.kroenik)
Definition: FileTypes.h:91
mzQuantML (HUPO PSI AnalysisXML followup format) (.mzq)
Definition: FileTypes.h:78
static const std::string NamesOfIonizationMethod[SIZE_OF_IONIZATIONMETHOD]
Names of ionization methods.
Definition: IonSource.h:137
OpenMS parameters file with workflow information (.toppas)
Definition: FileTypes.h:70
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!
XSD schema format.
Definition: FileTypes.h:100
T round(T x)
Rounds the value.
Definition: MathFunctions.h:138
TransformationModel::DataPoints DataPoints
Vector of coordinate pairs.
Definition: TransformationDescription.h:103
Representation of a peptide/protein sequence.
Definition: AASequence.h:113
static void store(const String &filename, const std::vector< FASTAEntry > &data)
stores the data given by 'data' at the file 'filename'
hardkloer file (.hardkloer)
Definition: FileTypes.h:90
constexpr Int writtenDigits(const FloatingPointType &=FloatingPointType())
Number of digits commonly used for writing a floating point type (a.k.a. precision)....
Definition: Types.h:294
NIST spectra library file format (.msp)
Definition: FileTypes.h:82
TPP pepXML file (.pepXML)
Definition: FileTypes.h:75
Used to load and store PepXML files.
Definition: PepXMLFile.h:62
const ColumnHeaders & getColumnHeaders() const
Non-mutable access to the file descriptions.
A container for consensus elements.
Definition: ConsensusMap.h:79
const String & getIdentifier() const
retrieve document identifier (e.g. an LSID)
SIRIUS file format (.ms)
Definition: FileTypes.h:105
GelML (HUPO PSI format) (.gelML)
Definition: FileTypes.h:80
xQuest XML file format for protein-protein cross-link identifications (.xquest.xml)
Definition: FileTypes.h:112
Size size() const
returns the number of residues
Helper class to gather (and dump) some statistics from a e.g. vector<double>.
Definition: StatisticFunctions.h:657
static FileTypes::Type getType(const String &filename)
Tries to determine the file type (by name or content)
static const std::string NamesOfActivationMethod[SIZE_OF_ACTIVATIONMETHOD]
Names of activation methods.
Definition: Precursor.h:94
void reserve(Size s)
Definition: MSExperiment.h:142
void setName(const String &name)
Sets the name of the software.
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
Logger::LogStream OpenMS_Log_info
Global static instance of a LogStream to capture messages classified as information....
DTA file (.dta)
Definition: FileTypes.h:61
static const std::string NamesOfSpectrumType[SIZE_OF_SPECTRUMTYPE]
Names of spectrum types.
Definition: SpectrumSettings.h:78
FASTA entry type (identifier, description and sequence)
Definition: FASTAFile.h:76
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)
void store(const String &filename, const PeakMap &map) const
Stores a map in an MzML file.
OpenMS feature file (.featureXML)
Definition: FileTypes.h:65
void load(const String &filename, ConsensusMap &map)
Loads a consensus map from file and calls updateRanges.
static const std::string NamesOfAnalyzerType[SIZE_OF_ANALYZERTYPE]
Names of the analyzer types.
Definition: MassAnalyzer.h:72
void openFile(String filename)
Open a file.
Type
Actual file types enum.
Definition: FileTypes.h:58
Percolator tab-delimited input (PSM level)
Definition: FileTypes.h:108
Used to load and store idXML files.
Definition: IdXMLFile.h:63
OMSSA XML file format for peptide identifications (.xml)
Definition: FileTypes.h:83
File adapter for MzML files.
Definition: MzMLFile.h:55
TraML (HUPO PSI format) for transitions (.traML)
Definition: FileTypes.h:81
bool loadExperiment(const String &filename, MSExperiment &exp, FileTypes::Type force_type=FileTypes::UNKNOWN, ProgressLogger::LogType log=ProgressLogger::NONE, const bool rewrite_source_file=true, const bool compute_hash=true)
Loads a file into an MSExperiment.
const String & getNTerminalModificationName() const
returns the name (ID) of the N-terminal modification, or an empty string if none is set
size_t count
Definition: StatisticFunctions.h:688
MS2 file (.ms2)
Definition: FileTypes.h:74
MzData file (.mzData)
Definition: FileTypes.h:63
A more convenient string class.
Definition: String.h:58
Mascot XML file format for peptide identifications (.xml)
Definition: FileTypes.h:84
General file format conversion (if no other term applies)
Definition: DataProcessing.h:75
Class to hold strings, numeric values, lists of strings and lists of numeric values.
Definition: DataValue.h:56
OpenMS::Interfaces::ChromatogramPtr getChromatogramById(int id)
Retrieve the raw data for the chromatogram at position "id".
general comma separated files format (might also be tab or space separated!!!), data should be regula...
Definition: FileTypes.h:94
Thermo Raw File (.raw)
Definition: FileTypes.h:115
static double mean(IteratorType begin, IteratorType end)
Calculates the mean of a range of values.
Definition: StatisticFunctions.h:133
void addChromatogram(const MSChromatogram &chromatogram)
adds a chromatogram to the list
XMass Analysis file (fid)
Definition: FileTypes.h:86
float toFloat() const
Conversion to float.
void addSpectrum(const MSSpectrum &spectrum)
adds a spectrum to the list
double lowerq
Definition: StatisticFunctions.h:686
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
bool empty() const
Definition: MSExperiment.h:137
bool hasNTerminalModification() const
predicate which is true if the peptide is N-term modified
ConsensusMap & appendRows(const ConsensusMap &rhs)
Add consensus map entries as new rows.
std::vector< double > DoubleList
Vector of double precision real types.
Definition: ListUtils.h:62
Retention time dimension id (0 if used as a const int)
Definition: Peak2D.h:75
static String getVersion()
Return the version number of OpenMS.
OpenMS parameters file (.ini)
Definition: FileTypes.h:69
static const char *const ChromatogramNames[SIZE_OF_CHROMATOGRAM_TYPE+1]
Names of chromatogram types corresponding to enum ChromatogramType.
Definition: ChromatogramSettings.h:82
Transformation description file (.trafoXML)
Definition: FileTypes.h:71
const PositionType & getMax() const
Returns the maximum position.
Definition: RangeManager.h:117
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
bool isValid(const String &filename, std::ostream &os)
Checks if a file validates against the XML schema.
File adapter for MzData files.
Definition: MzDataFile.h:53
void printSummary(std::ostream &os=std::cout) const
Print summary statistics for the transformation.
double upperq
Definition: StatisticFunctions.h:686
Used to load and store TransformationXML files.
Definition: TransformationXMLFile.h:56
Base::const_iterator ConstIterator
Definition: Map.h:81
Facilitates file handling by file type recognition.
Definition: FileHandler.h:62
double median
Definition: StatisticFunctions.h:686
Base::iterator iterator
Definition: MSExperiment.h:124
std::map< UInt64, ColumnHeader > ColumnHeaders
Definition: ConsensusMap.h:158
Mass-to-charge dimension id (1 if used as a const int)
Definition: Peak2D.h:76
This class serves for reading in and writing FASTA files.
Definition: FASTAFile.h:64
static Type nameToType(const String &name)
Converts a file type name into a Type.
bool getParsingSuccess() const
Returns whether parsing was successful.
float IntensityType
Intensity type.
Definition: Peak2D.h:62
void store(String filename, const TransformationDescription &transformation)
Stores the data in an TransformationXML file.
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
A description of a targeted experiment containing precursor and production ions.
Definition: TargetedExperiment.h:64
internal format for writing and reading parameters (also used as part of CTD)
Definition: FileTypes.h:109
JavaScript Object Notation file (.json)
Definition: FileTypes.h:114
SqLite format for mass and chromatograms, see SqMassFile.
Definition: FileTypes.h:103
Percolator tab-delimited output (PSM level)
Definition: FileTypes.h:107
xQuest XML file format for matched spectra for spectra visualization in the xQuest results manager (....
Definition: FileTypes.h:113
void setDataPoints(const DataPoints &data)
Sets the data points.
const String & getModelType() const
Gets the type of the fitted model.
Definition: ChromatogramSettings.h:74
bool isSemanticallyValid(const String &filename, StringList &errors, StringList &warnings)
Checks if a file is valid with respect to the mapping file and the controlled vocabulary.
SpectraST binary spectral library file (sptxt is the equivalent text-based format,...
Definition: FileTypes.h:110
const String & getCTerminalModificationName() const
returns the name (ID) of the C-terminal modification, or an empty string if none is set
TPP protXML file (.protXML)
Definition: FileTypes.h:76