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OpenMS
3.0.0
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37 #include <OpenMS/config.h>
123 static String typeToName(Type type);
128 static String typeToDescription(Type type);
132 static Type nameToType(
const String& name);
135 static String typeToMZML(Type type);
152 FileTypeList(
const std::vector<FileTypes::Type>& types);
157 const std::vector<FileTypes::Type>&
getTypes()
const
Description of the software used for processing.
Definition: Software.h:48
CachedMzML file (.cachedmzML)
Definition: FileTypes.h:71
OpenMS identification format (.idXML)
Definition: FileTypes.h:64
make a single item, e.g. 'all readable files (*.mzML *.mzXML);;'
Base class for TOPP applications.
Definition: TOPPBase.h:147
This class supports reading and writing of PQP files.
Definition: TransitionPQPFile.h:215
const std::vector< SourceFile > & getSourceFiles() const
returns a const reference to the source data file
SqLite format for mass and chromatograms, see SqMassFile.
Definition: FileTypes.h:101
boost::shared_ptr< Spectrum > SpectrumPtr
Definition: openms/include/OpenMS/INTERFACES/DataStructures.h:236
void setName(const String &name)
Sets the name of the software.
void store(const String &filename, const TargetedExperiment &id) const
Stores a map in a TraML file.
MzData file (.mzData)
Definition: FileTypes.h:61
double mean
Definition: StatisticFunctions.h:698
File adapter for MzData files.
Definition: MzDataFile.h:53
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
double median
Definition: StatisticFunctions.h:698
void openFile(const String &filename)
Open a file.
static const char *const ChromatogramNames[SIZE_OF_CHROMATOGRAM_TYPE+1]
Names of chromatogram types corresponding to enum ChromatogramType.
Definition: ChromatogramSettings.h:82
GelML (HUPO PSI format) (.gelML)
Definition: FileTypes.h:79
A convenience class to report either absolute or delta (between two timepoints) RAM usage.
Definition: SysInfo.h:83
void store(const String &filename, const ConsensusMap &consensus_map)
Stores a consensus map to file.
const std::string & toString(const DriftTimeUnit value)
NCBI binary blast db.
Definition: FileTypes.h:99
bool getParsingSuccess() const
Returns whether parsing was successful.
const Instrument & getInstrument() const
returns a const reference to the MS instrument description
static const std::string NamesOfSpectrumType[SIZE_OF_SPECTRUMTYPE]
Names of spectrum types.
Definition: SpectrumSettings.h:78
static const std::string NamesOfAnalyzerType[SIZE_OF_ANALYZERTYPE]
Names of the analyzer types.
Definition: MassAnalyzer.h:72
void updateRanges() override
const std::vector< UInt > & getMSLevels() const
returns an array of MS levels
This class serves for reading in and writing FASTA files If the protein/gene sequence contains unusua...
Definition: FASTAFile.h:60
list all types individually, e.g. 'mzML files (*.mzML);;mzXML files (*.mzXML);;'
void store(const String &filename, const PeakMap &map) const
Stores a map in an MzML file.
SpectraST MRM List.
Definition: FileTypes.h:100
MzML file (.mzML)
Definition: FileTypes.h:70
MzXML file (.mzXML)
Definition: FileTypes.h:62
static const std::string NamesOfScanMode[SIZE_OF_SCANMODE]
Names of scan modes.
Definition: InstrumentSettings.h:73
const String & getName() const
returns the name of the instrument
TPP pepXML file (.pepXML)
Definition: FileTypes.h:73
const std::vector< MassAnalyzer > & getMassAnalyzers() const
returns a const reference to the mass analyzer list
OpenMS parameters file with workflow information (.toppas)
Definition: FileTypes.h:68
bool isValid(const String &filename, std::ostream &os=std::cerr)
Checks if a file validates against the XML schema.
File adapter for MzML files.
Definition: MzMLFile.h:57
A more convenient string class.
Definition: String.h:58
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
std::vector< double > DoubleList
Vector of double precision real types.
Definition: ListUtils.h:62
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
const std::vector< Precursor > & getPrecursors() const
returns a const reference to the precursors
OpenMS consensus map format (.consensusXML)
Definition: FileTypes.h:65
internal format for writing and reading parameters (also used as part of CTD)
Definition: FileTypes.h:107
OpenMS parameters file (.ini)
Definition: FileTypes.h:67
mzQuantML (HUPO PSI AnalysisXML followup format) (.mzq)
Definition: FileTypes.h:76
NIST spectra library file format (.msp)
Definition: FileTypes.h:81
JavaScript Object Notation file (.json)
Definition: FileTypes.h:112
std::vector< FileTypes::Type > types
Definition: FileTypes.h:189
Helper class to gather (and dump) some statistics from a e.g. vector<double>.
Definition: StatisticFunctions.h:672
void load(const String &filename, TargetedExperiment &id)
Loads a map from a TraML file.
any TSV file, for example msInspect file or OpenSWATH transition file (see TransitionTSVFile)
Definition: FileTypes.h:86
XSD schema format.
Definition: FileTypes.h:98
mzIdentML (HUPO PSI AnalysisXML followup format) (.mzid)
Definition: FileTypes.h:75
File adapter for MzXML 3.1 files.
Definition: MzXMLFile.h:52
String delta(const String &event="delta")
Base::const_iterator const_iterator
Definition: MSExperiment.h:118
bool operator<(const MultiplexDeltaMasses &dm1, const MultiplexDeltaMasses &dm2)
CoordinateType getMaxRT() const
returns the maximal retention time value
Unknown file extension.
Definition: FileTypes.h:58
FASTA file (.fasta)
Definition: FileTypes.h:91
FASTA entry type (identifier, description and sequence) The first String corresponds to the identifie...
Definition: FASTAFile.h:71
XMass Analysis file (fid)
Definition: FileTypes.h:85
static const std::string NamesOfType[SIZE_OF_TYPE]
Names of detector types.
Definition: IonDetector.h:78
SpectraST binary spectral library file (sptxt is the equivalent text-based format,...
Definition: FileTypes.h:108
kroenik file (.kroenik)
Definition: FileTypes.h:90
void setVersion(const String &version)
Sets the software version.
Size size() const
Definition: MSExperiment.h:120
const String & getCTerminalModificationName() const
returns the name (ID) of the C-terminal modification, or an empty string if none is set
qcML (will undergo standardisation maybe) (.qcml)
Definition: FileTypes.h:77
double CoordinateType
Coordinate type (of the position)
Definition: Peak2D.h:64
static const std::string NamesOfProcessingAction[SIZE_OF_PROCESSINGACTION]
Names of inlet types.
Definition: DataProcessing.h:84
void load(const String &filename, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids)
Loads the identifications of an idXML file without identifier.
const String & getVersion() const
return the version of the schema
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:209
boost::shared_ptr< Chromatogram > ChromatogramPtr
Definition: openms/include/OpenMS/INTERFACES/DataStructures.h:156
Mass-to-charge dimension id (1 if used as a const int)
Definition: Peak2D.h:76
void reserve(Size s)
Definition: MSExperiment.h:135
any text format, which has only loose definition of what it actually contains – thus it is usually ha...
Definition: FileTypes.h:94
File adapter for MzIdentML files.
Definition: MzIdentMLFile.h:67
UInt getMSLevel() const
Returns the MS level.
void store(const String &filename, const std::vector< FASTAEntry > &data) const
stores the data given by 'data' at the file 'filename'
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
void updateRanges() override
static String number(double d, UInt n)
returns a string for d with exactly n decimal places
void addSpectrum(const MSSpectrum &spectrum)
adds a spectrum to the list
File adapter for HUPO PSI TraML files.
Definition: TraMLFile.h:63
UInt64 getSize() const
returns the total number of peaks
OpenMS feature file (.featureXML)
Definition: FileTypes.h:63
double variance
Definition: StatisticFunctions.h:698
Controlled Vocabulary format.
Definition: FileTypes.h:95
Novor custom parameter file.
Definition: FileTypes.h:109
Class to hold strings, numeric values, lists of strings and lists of numeric values.
Definition: DataValue.h:58
const std::vector< MSChromatogram > & getChromatograms() const
returns the chromatogram list
T::value_type max
Definition: StatisticFunctions.h:699
any HTML format
Definition: FileTypes.h:96
float IntensityType
Intensity type.
Definition: Peak2D.h:62
Facilitates file handling by file type recognition.
Definition: FileHandler.h:66
static const std::string NamesOfActivationMethodShort[SIZE_OF_ACTIVATIONMETHOD]
Definition: Precursor.h:107
bool isValid(const String &filename, std::ostream &os)
Checks if a file validates against the XML schema.
Portable Network Graphics (.png)
Definition: FileTypes.h:84
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.
void load(const String &filename, FeatureMap &feature_map)
loads the file with name filename into map and calls updateRanges().
general comma separated files format (might also be tab or space separated!!!), data should be regula...
Definition: FileTypes.h:93
size_t getNrChromatograms() const
Returns the number of chromatograms available.
Type
Actual file types enum.
Definition: FileTypes.h:56
xQuest XML file format for protein-protein cross-link identifications (.xquest.xml)
Definition: FileTypes.h:110
const ChargeType & getCharge() const
Non-mutable access to charge state.
std::vector< String > items
Definition: FileTypes.h:188
mzQC (HUPO PSI format) (.mzQC)
Definition: FileTypes.h:78
A consensus feature spanning multiple LC-MS/MS experiments.
Definition: ConsensusFeature.h:69
mzTab file (.mzTab)
Definition: FileTypes.h:87
Size size() const
returns the number of residues
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.
static FileTypes::Type getType(const String &filename)
Tries to determine the file type (by name or content)
T round(T x)
Rounds the value.
Definition: MathFunctions.h:166
Percolator tab-delimited input (PSM level)
Definition: FileTypes.h:106
double lowerq
Definition: StatisticFunctions.h:698
Definition: MSNumpress.h:78
SIRIUS file format (.ms)
Definition: FileTypes.h:103
hold filter items (for Qt dialogs) along with their OpenMS type
Definition: FileTypes.h:186
analysisXML format
Definition: FileTypes.h:97
Definition: ChromatogramSettings.h:74
Mascot XML file format for peptide identifications (.xml)
Definition: FileTypes.h:83
specArray file (.peplist)
Definition: FileTypes.h:88
OpenMS::Interfaces::ChromatogramPtr getChromatogramById(int id)
Retrieve the raw data for the chromatogram at position "id".
enhanced comma separated files (RT, m/z, Intensity, [meta])
Definition: FileTypes.h:92
static String getVersion()
Return the version number of OpenMS.
bool empty() const
Definition: MSExperiment.h:130
OMSSA XML file format for peptide identifications (.xml)
Definition: FileTypes.h:82
void convertPQPToTargetedExperiment(const char *filename, OpenMS::TargetedExperiment &targeted_exp, bool legacy_traml_id=false)
Read in a PQP file and construct a targeted experiment (TraML structure)
std::vector< FileTypes::Type > type_list_
Definition: FileTypes.h:196
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)
A container for consensus elements.
Definition: ConsensusMap.h:82
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
void store(const String &filename, const FeatureMap &feature_map)
stores the map feature_map in file with name filename.
void load(const String &filename, ConsensusMap &map)
Loads a consensus map from file and calls updateRanges.
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
hardkloer file (.hardkloer)
Definition: FileTypes.h:89
DTA2D file (.dta2d)
Definition: FileTypes.h:60
const FloatDataArrays & getFloatDataArrays() const
Returns a const reference to the float meta data arrays.
void addSoftware(const Software &software)
OpenSWATH OpenSWATH report (OSW) SQLite DB.
Definition: FileTypes.h:104
void load(const String &filename, std::vector< ProteinIdentification > &poid, std::vector< PeptideIdentification > &peid)
Loads the identifications from a MzIdentML file.
const String & getNTerminalModificationName() const
returns the name (ID) of the N-terminal modification, or an empty string if none is set
TPP protXML file (.protXML)
Definition: FileTypes.h:74
void addChromatogram(const MSChromatogram &chromatogram)
adds a chromatogram to the list
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:71
bool hasCTerminalModification() const
predicate which is true if the peptide is C-term modified
SummaryStatistics getSummary() const
return summary stats about this TE.
OpenMS::Interfaces::SpectrumPtr getSpectrumById(int id)
Retrieve the raw data for the spectrum at position "id".
void setLoadSubordinates(bool sub)
A container for features.
Definition: FeatureMap.h:98
OpenSWATH Peptide Query Parameter (PQP) SQLite DB, see TransitionPQPFile.
Definition: FileTypes.h:102
Mascot Generic Format (.mgf)
Definition: FileTypes.h:66
Executable (.exe)
Definition: FileTypes.h:115
An LC-MS feature.
Definition: Feature.h:70
xQuest XML file format for matched spectra for spectra visualization in the xQuest results manager (....
Definition: FileTypes.h:111
static double mean(IteratorType begin, IteratorType end)
Calculates the mean of a range of values.
Definition: StatisticFunctions.h:120
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.
Thermo Raw File (.raw)
Definition: FileTypes.h:113
void load(const String &filename, std::vector< FASTAEntry > &data) const
loads a FASTA file given by 'filename' and stores the information in 'data' This uses more RAM than r...
File not writable exception.
Definition: Exception.h:537
DTA file (.dta)
Definition: FileTypes.h:59
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLFile.h:62
Logger::LogStream OpenMS_Log_info
Global static instance of a LogStream to capture messages classified as information....
combine COMPACT and ONE_BY_ONE
static Type nameToType(const String &name)
The representation of a chromatogram.
Definition: MSChromatogram.h:53
any Gzipped file
Definition: FileTypes.h:118
FilterLayout
Definition: FileTypes.h:138
void updateRanges() override
static const std::string NamesOfActivationMethod[SIZE_OF_ACTIVATIONMETHOD]
Names of activation methods.
Definition: Precursor.h:106
TraML (HUPO PSI format) for transitions (.traML)
Definition: FileTypes.h:80
Retention time dimension id (0 if used as a const int)
Definition: Peak2D.h:75
Representation of a peptide/protein sequence.
Definition: AASequence.h:111
General file format conversion (if no other term applies)
Definition: DataProcessing.h:75
size_t getNrSpectra() const
Returns the number of spectra available.
bool hasNTerminalModification() const
predicate which is true if the peptide is N-term modified
Used to load and store PepXML files.
Definition: PepXMLFile.h:63
Centralizes the file types recognized by FileHandler.
Definition: FileTypes.h:52
any BZ2 compressed file
Definition: FileTypes.h:117
A description of a targeted experiment containing precursor and production ions.
Definition: TargetedExperiment.h:64
#define OPENMS_LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:465
const IntegerDataArrays & getIntegerDataArrays() const
Returns a const reference to the integer meta data arrays.
void setLoadConvexHull(bool convex)
double upperq
Definition: StatisticFunctions.h:698
float QualityType
Definition: BaseFeature.h:64
const std::vector< FileTypes::Type > & getTypes() const
Definition: FileTypes.h:157
MS2 file (.ms2)
Definition: FileTypes.h:72
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
ActivationMethod
Method of activation.
Definition: Precursor.h:84
size_t count
Definition: StatisticFunctions.h:700
any XML format
Definition: FileTypes.h:116
std::ifstream infile
Questionable file tested by TEST_FILE_EQUAL.
float toFloat() const
Conversion to float.
Transformation description file (.trafoXML)
Definition: FileTypes.h:69
FeatureFileOptions & 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!
T::value_type min
Definition: StatisticFunctions.h:699
This class provides Input functionality for ConsensusMaps and Output functionality for alignments and...
Definition: ConsensusXMLFile.h:58
Used to load and store idXML files.
Definition: IdXMLFile.h:68
static String typeToName(Type type)
Returns the name/extension of the type.
A low-level class to read an indexedmzML file.
Definition: IndexedMzMLHandler.h:79
CoordinateType getMinRT() const
returns the minimal retention time value
OpenMS database file.
Definition: FileTypes.h:114
Percolator tab-delimited output (PSM level)
Definition: FileTypes.h:105
std::map< UInt64, ColumnHeader > ColumnHeaders
Definition: ConsensusMap.h:164
holds a vector of known file types, e.g. as a way to specify supported input formats
Definition: FileTypes.h:149
static const std::string NamesOfIonizationMethod[SIZE_OF_IONIZATIONMETHOD]
Names of ionization methods.
Definition: IonSource.h:137