OpenMS  3.0.0
FileTypes.h
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34 
35 #pragma once
36 
37 #include <OpenMS/config.h>
39 
40 #include <vector>
41 
42 namespace OpenMS
43 {
52  struct OPENMS_DLLAPI FileTypes
53  {
54 
56  enum Type
57  {
59  DTA,
66  MGF,
67  INI,
70  MZML,
72  MS2,
77  QCML,
78  MZQC,
81  MSP,
84  PNG,
86  TSV,
92  EDTA,
93  CSV,
94  TXT,
95  OBO,
96  HTML,
98  XSD,
99  PSQ,
100  MRM,
102  PQP,
103  MS,
104  OSW,
106  PIN,
113  RAW,
114  OMS,
115  EXE,
116  XML,
117  BZ2,
118  GZ,
119  SIZE_OF_TYPE
120  };
121 
123  static String typeToName(Type type);
124 
128  static String typeToDescription(Type type);
129 
132  static Type nameToType(const String& name);
133 
135  static String typeToMZML(Type type);
136  };
137 
138  enum class FilterLayout
139  {
140  COMPACT,
141  ONE_BY_ONE,
142  BOTH
143  };
149  class OPENMS_DLLAPI FileTypeList
150  {
151  public:
152  FileTypeList(const std::vector<FileTypes::Type>& types);
153 
155  bool contains(const FileTypes::Type& type) const;
156 
157  const std::vector<FileTypes::Type>& getTypes() const
158  {
159  return type_list_;
160  }
161 
166  String toFileDialogFilter(const FilterLayout style, bool add_all_filter) const;
167 
182  FileTypes::Type fromFileDialogFilter(const String& filter, const FileTypes::Type fallback = FileTypes::Type::UNKNOWN) const;
183 
184  private:
187  {
188  std::vector<String> items;
189  std::vector<FileTypes::Type> types;
190  };
194  FilterElements_ asFilterElements_(const FilterLayout style, bool add_all_filter) const;
195 
196  std::vector<FileTypes::Type> type_list_;
197  };
198 
199 } // namespace OpenMS
200 
OpenMS::Software
Description of the software used for processing.
Definition: Software.h:48
OpenMS::FileTypes::CACHEDMZML
CachedMzML file (.cachedmzML)
Definition: FileTypes.h:71
OpenMS::TransformationDescription::printSummary
void printSummary(std::ostream &os) const
Print summary statistics for the transformation.
OpenMS::FileTypes::IDXML
OpenMS identification format (.idXML)
Definition: FileTypes.h:64
OpenMS::FilterLayout::COMPACT
make a single item, e.g. 'all readable files (*.mzML *.mzXML);;'
ConsensusXMLFile.h
OpenMS::TOPPBase
Base class for TOPP applications.
Definition: TOPPBase.h:147
OpenMS::TransitionPQPFile
This class supports reading and writing of PQP files.
Definition: TransitionPQPFile.h:215
TargetedExperiment.h
OpenMS::ExperimentalSettings::getSourceFiles
const std::vector< SourceFile > & getSourceFiles() const
returns a const reference to the source data file
OpenMS::FileTypes::SQMASS
SqLite format for mass and chromatograms, see SqMassFile.
Definition: FileTypes.h:101
FileHandler.h
FileTypes.h
TextFile.h
OpenMS::Interfaces::SpectrumPtr
boost::shared_ptr< Spectrum > SpectrumPtr
Definition: openms/include/OpenMS/INTERFACES/DataStructures.h:236
OpenMS::Software::setName
void setName(const String &name)
Sets the name of the software.
OpenMS::TraMLFile::store
void store(const String &filename, const TargetedExperiment &id) const
Stores a map in a TraML file.
OpenMS::FileTypes::MZDATA
MzData file (.mzData)
Definition: FileTypes.h:61
OpenMS::Math::SummaryStatistics::mean
double mean
Definition: StatisticFunctions.h:698
OpenMS::MzDataFile
File adapter for MzData files.
Definition: MzDataFile.h:53
OpenMS::MapAlignmentTransformer::transformRetentionTimes
static void transformRetentionTimes(PeakMap &msexp, const TransformationDescription &trafo, bool store_original_rt=false)
Applies the given transformation to a peak map.
Size
OpenMS::writtenDigits
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
OpenMS::Math::SummaryStatistics::median
double median
Definition: StatisticFunctions.h:698
OpenMS::Internal::IndexedMzMLHandler::openFile
void openFile(const String &filename)
Open a file.
OpenMS::ChromatogramSettings::ChromatogramNames
static const char *const ChromatogramNames[SIZE_OF_CHROMATOGRAM_TYPE+1]
Names of chromatogram types corresponding to enum ChromatogramType.
Definition: ChromatogramSettings.h:82
OpenMS::FileTypes::GELML
GelML (HUPO PSI format) (.gelML)
Definition: FileTypes.h:79
VersionInfo.h
OpenMS::SysInfo::MemUsage
A convenience class to report either absolute or delta (between two timepoints) RAM usage.
Definition: SysInfo.h:83
OpenMS::ConsensusXMLFile::store
void store(const String &filename, const ConsensusMap &consensus_map)
Stores a consensus map to file.
OpenMS::toString
const std::string & toString(const DriftTimeUnit value)
OpenMS::FileTypes::PSQ
NCBI binary blast db.
Definition: FileTypes.h:99
OpenMS::Internal::IndexedMzMLHandler::getParsingSuccess
bool getParsingSuccess() const
Returns whether parsing was successful.
OpenMS::ExperimentalSettings::getInstrument
const Instrument & getInstrument() const
returns a const reference to the MS instrument description
OpenMS::SpectrumSettings::NamesOfSpectrumType
static const std::string NamesOfSpectrumType[SIZE_OF_SPECTRUMTYPE]
Names of spectrum types.
Definition: SpectrumSettings.h:78
TransitionTSVFile.h
OpenMS::MassAnalyzer::NamesOfAnalyzerType
static const std::string NamesOfAnalyzerType[SIZE_OF_ANALYZERTYPE]
Names of the analyzer types.
Definition: MassAnalyzer.h:72
OpenMS::ConsensusMap::updateRanges
void updateRanges() override
OpenMS::MSExperiment::getMSLevels
const std::vector< UInt > & getMSLevels() const
returns an array of MS levels
OpenMS::FASTAFile
This class serves for reading in and writing FASTA files If the protein/gene sequence contains unusua...
Definition: FASTAFile.h:60
OpenMS::FilterLayout::ONE_BY_ONE
list all types individually, e.g. 'mzML files (*.mzML);;mzXML files (*.mzXML);;'
OpenMS::MzMLFile::store
void store(const String &filename, const PeakMap &map) const
Stores a map in an MzML file.
OpenMS::FileTypes::MRM
SpectraST MRM List.
Definition: FileTypes.h:100
OpenMS::FileTypes::MZML
MzML file (.mzML)
Definition: FileTypes.h:70
OpenMS::FileTypes::MZXML
MzXML file (.mzXML)
Definition: FileTypes.h:62
OpenMS::InstrumentSettings::NamesOfScanMode
static const std::string NamesOfScanMode[SIZE_OF_SCANMODE]
Names of scan modes.
Definition: InstrumentSettings.h:73
OpenMS::Instrument::getName
const String & getName() const
returns the name of the instrument
OpenMS::FileTypes::PEPXML
TPP pepXML file (.pepXML)
Definition: FileTypes.h:73
OpenMS::Instrument::getMassAnalyzers
const std::vector< MassAnalyzer > & getMassAnalyzers() const
returns a const reference to the mass analyzer list
OpenMS::FileTypes::TOPPAS
OpenMS parameters file with workflow information (.toppas)
Definition: FileTypes.h:68
OpenMS::MzMLFile::isValid
bool isValid(const String &filename, std::ostream &os=std::cerr)
Checks if a file validates against the XML schema.
OpenMS::MzMLFile
File adapter for MzML files.
Definition: MzMLFile.h:57
OpenMS::String
A more convenient string class.
Definition: String.h:58
MzMLFile.h
OpenMS::PeakTypeEstimator::estimateType
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
OpenMS::DoubleList
std::vector< double > DoubleList
Vector of double precision real types.
Definition: ListUtils.h:62
Int
Feature.h
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
OpenMS::SpectrumSettings::getPrecursors
const std::vector< Precursor > & getPrecursors() const
returns a const reference to the precursors
OpenMS::FileTypes::CONSENSUSXML
OpenMS consensus map format (.consensusXML)
Definition: FileTypes.h:65
OpenMS::FileTypes::PARAMXML
internal format for writing and reading parameters (also used as part of CTD)
Definition: FileTypes.h:107
OpenMS::FileTypes::INI
OpenMS parameters file (.ini)
Definition: FileTypes.h:67
OpenMS::FileTypes::MZQUANTML
mzQuantML (HUPO PSI AnalysisXML followup format) (.mzq)
Definition: FileTypes.h:76
IdXMLFile.h
FeatureXMLFile.h
OpenMS::FileTypes::MSP
NIST spectra library file format (.msp)
Definition: FileTypes.h:81
OpenMS::FileTypes::JSON
JavaScript Object Notation file (.json)
Definition: FileTypes.h:112
OpenMS::FileTypeList::FilterElements_::types
std::vector< FileTypes::Type > types
Definition: FileTypes.h:189
OpenMS::Math::SummaryStatistics
Helper class to gather (and dump) some statistics from a e.g. vector<double>.
Definition: StatisticFunctions.h:672
OpenMS::TraMLFile::load
void load(const String &filename, TargetedExperiment &id)
Loads a map from a TraML file.
StatisticFunctions.h
OpenMS::FileTypes::TSV
any TSV file, for example msInspect file or OpenSWATH transition file (see TransitionTSVFile)
Definition: FileTypes.h:86
OpenMS::FileTypes::XSD
XSD schema format.
Definition: FileTypes.h:98
MapAlignmentTransformer.h
OpenMS::FileTypes::MZIDENTML
mzIdentML (HUPO PSI AnalysisXML followup format) (.mzid)
Definition: FileTypes.h:75
OpenMS::MzXMLFile
File adapter for MzXML 3.1 files.
Definition: MzXMLFile.h:52
OpenMS::SysInfo::MemUsage::delta
String delta(const String &event="delta")
OpenMS::MSExperiment::const_iterator
Base::const_iterator const_iterator
Definition: MSExperiment.h:118
OpenMS::operator<
bool operator<(const MultiplexDeltaMasses &dm1, const MultiplexDeltaMasses &dm2)
TransformationDescription.h
OpenMS::MSExperiment::getMaxRT
CoordinateType getMaxRT() const
returns the maximal retention time value
OpenMS::FileTypes::UNKNOWN
Unknown file extension.
Definition: FileTypes.h:58
OpenMS::FileTypes::FASTA
FASTA file (.fasta)
Definition: FileTypes.h:91
OpenMS::FASTAFile::FASTAEntry
FASTA entry type (identifier, description and sequence) The first String corresponds to the identifie...
Definition: FASTAFile.h:71
OpenMS::FileTypes::XMASS
XMass Analysis file (fid)
Definition: FileTypes.h:85
OpenMS::IonDetector::NamesOfType
static const std::string NamesOfType[SIZE_OF_TYPE]
Names of detector types.
Definition: IonDetector.h:78
OpenMS::FileTypes::SPLIB
SpectraST binary spectral library file (sptxt is the equivalent text-based format,...
Definition: FileTypes.h:108
OpenMS::FileTypes::KROENIK
kroenik file (.kroenik)
Definition: FileTypes.h:90
OpenMS::Software::setVersion
void setVersion(const String &version)
Sets the software version.
OpenMS::MSExperiment::size
Size size() const
Definition: MSExperiment.h:120
OpenMS::AASequence::getCTerminalModificationName
const String & getCTerminalModificationName() const
returns the name (ID) of the C-terminal modification, or an empty string if none is set
OpenMS::FileTypes::QCML
qcML (will undergo standardisation maybe) (.qcml)
Definition: FileTypes.h:77
OpenMS::Peak2D::CoordinateType
double CoordinateType
Coordinate type (of the position)
Definition: Peak2D.h:64
OpenMS::DataProcessing::NamesOfProcessingAction
static const std::string NamesOfProcessingAction[SIZE_OF_PROCESSINGACTION]
Names of inlet types.
Definition: DataProcessing.h:84
OpenMS::TransformationDescription::fitModel
void fitModel(const String &model_type, const Param &params=Param())
Fits a model to the data.
OpenMS::IdXMLFile::load
void load(const String &filename, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids)
Loads the identifications of an idXML file without identifier.
OpenMS::Internal::XMLFile::getVersion
const String & getVersion() const
return the version of the schema
OpenMS::ListUtils::concatenate
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
OpenMS::Interfaces::ChromatogramPtr
boost::shared_ptr< Chromatogram > ChromatogramPtr
Definition: openms/include/OpenMS/INTERFACES/DataStructures.h:156
OpenMS::Peak2D::MZ
Mass-to-charge dimension id (1 if used as a const int)
Definition: Peak2D.h:76
OpenMS::MSExperiment::reserve
void reserve(Size s)
Definition: MSExperiment.h:135
OpenMS::FileTypes::TXT
any text format, which has only loose definition of what it actually contains – thus it is usually ha...
Definition: FileTypes.h:94
OpenMS::MzIdentMLFile
File adapter for MzIdentML files.
Definition: MzIdentMLFile.h:67
OpenMS::MSSpectrum::getMSLevel
UInt getMSLevel() const
Returns the MS level.
OpenMS::FASTAFile::store
void store(const String &filename, const std::vector< FASTAEntry > &data) const
stores the data given by 'data' at the file 'filename'
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::FeatureMap::updateRanges
void updateRanges() override
OpenMS::String::number
static String number(double d, UInt n)
returns a string for d with exactly n decimal places
OpenMS::MSExperiment::addSpectrum
void addSpectrum(const MSSpectrum &spectrum)
adds a spectrum to the list
OpenMS::TraMLFile
File adapter for HUPO PSI TraML files.
Definition: TraMLFile.h:63
OpenMS::MSExperiment::getSize
UInt64 getSize() const
returns the total number of peaks
OpenMS::FileTypes::FEATUREXML
OpenMS feature file (.featureXML)
Definition: FileTypes.h:63
OpenMS::Math::SummaryStatistics::variance
double variance
Definition: StatisticFunctions.h:698
OpenMS::TransformationDescription::setDataPoints
void setDataPoints(const DataPoints &data)
Sets the data points.
OpenMS::FileTypes::OBO
Controlled Vocabulary format.
Definition: FileTypes.h:95
OpenMS::FileTypes::NOVOR
Novor custom parameter file.
Definition: FileTypes.h:109
OpenMS::DataValue
Class to hold strings, numeric values, lists of strings and lists of numeric values.
Definition: DataValue.h:58
OpenMS::MSExperiment::getChromatograms
const std::vector< MSChromatogram > & getChromatograms() const
returns the chromatogram list
OpenMS::Math::SummaryStatistics::max
T::value_type max
Definition: StatisticFunctions.h:699
TransformationXMLFile.h
FASTAFile.h
OpenMS::FileTypes::HTML
any HTML format
Definition: FileTypes.h:96
OpenMS::Peak2D::IntensityType
float IntensityType
Intensity type.
Definition: Peak2D.h:62
OpenMS::FileHandler
Facilitates file handling by file type recognition.
Definition: FileHandler.h:66
OpenMS::Precursor::NamesOfActivationMethodShort
static const std::string NamesOfActivationMethodShort[SIZE_OF_ACTIVATIONMETHOD]
Definition: Precursor.h:107
OpenMS::Internal::XMLFile::isValid
bool isValid(const String &filename, std::ostream &os)
Checks if a file validates against the XML schema.
MzXMLFile.h
OpenMS::FileTypes::PNG
Portable Network Graphics (.png)
Definition: FileTypes.h:84
OpenMS::FileHandler::loadExperiment
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.
OpenMS::FeatureXMLFile::load
void load(const String &filename, FeatureMap &feature_map)
loads the file with name filename into map and calls updateRanges().
FeatureMap.h
OpenMS::FileTypes::CSV
general comma separated files format (might also be tab or space separated!!!), data should be regula...
Definition: FileTypes.h:93
OpenMS::Internal::IndexedMzMLHandler::getNrChromatograms
size_t getNrChromatograms() const
Returns the number of chromatograms available.
OpenMS::FileTypes::Type
Type
Actual file types enum.
Definition: FileTypes.h:56
PeakTypeEstimator.h
MathFunctions.h
OpenMS::FileTypes::XQUESTXML
xQuest XML file format for protein-protein cross-link identifications (.xquest.xml)
Definition: FileTypes.h:110
OpenMS::BaseFeature::getCharge
const ChargeType & getCharge() const
Non-mutable access to charge state.
OpenMS::FileTypeList::FilterElements_::items
std::vector< String > items
Definition: FileTypes.h:188
OpenMS::FileTypes::MZQC
mzQC (HUPO PSI format) (.mzQC)
Definition: FileTypes.h:78
OpenMS::ConsensusFeature
A consensus feature spanning multiple LC-MS/MS experiments.
Definition: ConsensusFeature.h:69
OpenMS::TransformationDescription::getModelType
const String & getModelType() const
Gets the type of the fitted model.
OpenMS::FileTypes::MZTAB
mzTab file (.mzTab)
Definition: FileTypes.h:87
OpenMS::AASequence::size
Size size() const
returns the number of residues
OpenMS::MzMLFile::isSemanticallyValid
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.
OpenMS::FileHandler::getType
static FileTypes::Type getType(const String &filename)
Tries to determine the file type (by name or content)
OpenMS::Math::round
T round(T x)
Rounds the value.
Definition: MathFunctions.h:166
OpenMS::FileTypes::PIN
Percolator tab-delimited input (PSM level)
Definition: FileTypes.h:106
PepXMLFile.h
OpenMS::Math::SummaryStatistics::lowerq
double lowerq
Definition: StatisticFunctions.h:698
ms
Definition: MSNumpress.h:78
OpenMS::FileTypes::MS
SIRIUS file format (.ms)
Definition: FileTypes.h:103
OpenMS::FileTypeList::FilterElements_
hold filter items (for Qt dialogs) along with their OpenMS type
Definition: FileTypes.h:186
OpenMS::FileTypes::ANALYSISXML
analysisXML format
Definition: FileTypes.h:97
OpenMS::ChromatogramSettings::SELECTED_REACTION_MONITORING_CHROMATOGRAM
Definition: ChromatogramSettings.h:74
OpenMS::FileTypes::MASCOTXML
Mascot XML file format for peptide identifications (.xml)
Definition: FileTypes.h:83
OpenMS::FileTypes::PEPLIST
specArray file (.peplist)
Definition: FileTypes.h:88
OpenMS::Internal::IndexedMzMLHandler::getChromatogramById
OpenMS::Interfaces::ChromatogramPtr getChromatogramById(int id)
Retrieve the raw data for the chromatogram at position "id".
OpenMS::FileTypes::EDTA
enhanced comma separated files (RT, m/z, Intensity, [meta])
Definition: FileTypes.h:92
OpenMS::VersionInfo::getVersion
static String getVersion()
Return the version number of OpenMS.
OpenMS::MSExperiment::empty
bool empty() const
Definition: MSExperiment.h:130
OpenMS::FileTypes::OMSSAXML
OMSSA XML file format for peptide identifications (.xml)
Definition: FileTypes.h:82
OpenMS::TransitionPQPFile::convertPQPToTargetedExperiment
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)
OpenMS::FileTypeList::type_list_
std::vector< FileTypes::Type > type_list_
Definition: FileTypes.h:196
OpenMS::operator<<
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)
SysInfo.h
OpenMS::ConsensusMap
A container for consensus elements.
Definition: ConsensusMap.h:82
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
OpenMS::FeatureXMLFile::store
void store(const String &filename, const FeatureMap &feature_map)
stores the map feature_map in file with name filename.
OpenMS::ConsensusXMLFile::load
void load(const String &filename, ConsensusMap &map)
Loads a consensus map from file and calls updateRanges.
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::FileTypes::HARDKLOER
hardkloer file (.hardkloer)
Definition: FileTypes.h:89
OpenMS::FileTypes::DTA2D
DTA2D file (.dta2d)
Definition: FileTypes.h:60
OpenMS::MSSpectrum::getFloatDataArrays
const FloatDataArrays & getFloatDataArrays() const
Returns a const reference to the float meta data arrays.
OpenMS::TargetedExperiment::addSoftware
void addSoftware(const Software &software)
OpenMS::FileTypes::OSW
OpenSWATH OpenSWATH report (OSW) SQLite DB.
Definition: FileTypes.h:104
OpenMS::MzIdentMLFile::load
void load(const String &filename, std::vector< ProteinIdentification > &poid, std::vector< PeptideIdentification > &peid)
Loads the identifications from a MzIdentML file.
OpenMS::AASequence::getNTerminalModificationName
const String & getNTerminalModificationName() const
returns the name (ID) of the N-terminal modification, or an empty string if none is set
OpenMS::FileTypes::PROTXML
TPP protXML file (.protXML)
Definition: FileTypes.h:74
OpenMS::MSExperiment::addChromatogram
void addChromatogram(const MSChromatogram &chromatogram)
adds a chromatogram to the list
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:71
OpenMS::AASequence::hasCTerminalModification
bool hasCTerminalModification() const
predicate which is true if the peptide is C-term modified
OpenMS::TargetedExperiment::getSummary
SummaryStatistics getSummary() const
return summary stats about this TE.
OpenMS::Internal::IndexedMzMLHandler::getSpectrumById
OpenMS::Interfaces::SpectrumPtr getSpectrumById(int id)
Retrieve the raw data for the spectrum at position "id".
OpenMS::FeatureFileOptions::setLoadSubordinates
void setLoadSubordinates(bool sub)
OpenMS::TransformationXMLFile::load
void load(const String &filename, TransformationDescription &transformation, bool fit_model=true)
Loads the transformation from an TransformationXML file.
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:98
OpenMS::FileTypes::PQP
OpenSWATH Peptide Query Parameter (PQP) SQLite DB, see TransitionPQPFile.
Definition: FileTypes.h:102
OpenMS::FileTypes::MGF
Mascot Generic Format (.mgf)
Definition: FileTypes.h:66
OpenMS::TransformationXMLFile
Used to load and store TransformationXML files.
Definition: TransformationXMLFile.h:56
OpenMS::FileTypes::EXE
Executable (.exe)
Definition: FileTypes.h:115
OpenMS::Feature
An LC-MS feature.
Definition: Feature.h:70
OpenMS::FileTypes::SPECXML
xQuest XML file format for matched spectra for spectra visualization in the xQuest results manager (....
Definition: FileTypes.h:111
OpenMS::Math::mean
static double mean(IteratorType begin, IteratorType end)
Calculates the mean of a range of values.
Definition: StatisticFunctions.h:120
OpenMS::MzDataFile::isSemanticallyValid
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.
OpenMS::FileTypes::RAW
Thermo Raw File (.raw)
Definition: FileTypes.h:113
OpenMS::FASTAFile::load
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...
OpenMS::Exception::FileNotWritable
File not writable exception.
Definition: Exception.h:537
OpenMS::FileTypes::DTA
DTA file (.dta)
Definition: FileTypes.h:59
OpenMS::FeatureXMLFile
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLFile.h:62
float
OpenMS::OpenMS_Log_info
Logger::LogStream OpenMS_Log_info
Global static instance of a LogStream to capture messages classified as information....
OpenMS::FilterLayout::BOTH
combine COMPACT and ONE_BY_ONE
OpenMS::FileTypes::nameToType
static Type nameToType(const String &name)
OpenMS::MSChromatogram
The representation of a chromatogram.
Definition: MSChromatogram.h:53
OpenMS::FileTypes::GZ
any Gzipped file
Definition: FileTypes.h:118
OpenMS::FilterLayout
FilterLayout
Definition: FileTypes.h:138
String.h
OpenMS::MSExperiment::updateRanges
void updateRanges() override
OpenMS::Precursor::NamesOfActivationMethod
static const std::string NamesOfActivationMethod[SIZE_OF_ACTIVATIONMETHOD]
Names of activation methods.
Definition: Precursor.h:106
OpenMS::FileTypes::TRAML
TraML (HUPO PSI format) for transitions (.traML)
Definition: FileTypes.h:80
MzDataFile.h
OpenMS::Peak2D::RT
Retention time dimension id (0 if used as a const int)
Definition: Peak2D.h:75
OpenMS::TransformationXMLFile::store
void store(String filename, const TransformationDescription &transformation)
Stores the data in an TransformationXML file.
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:111
OpenMS::DataProcessing::FORMAT_CONVERSION
General file format conversion (if no other term applies)
Definition: DataProcessing.h:75
OpenMS::Internal::IndexedMzMLHandler::getNrSpectra
size_t getNrSpectra() const
Returns the number of spectra available.
OpenMS::AASequence::hasNTerminalModification
bool hasNTerminalModification() const
predicate which is true if the peptide is N-term modified
OpenMS::PepXMLFile
Used to load and store PepXML files.
Definition: PepXMLFile.h:63
OpenMS::FileTypes
Centralizes the file types recognized by FileHandler.
Definition: FileTypes.h:52
OpenMS::FileTypes::BZ2
any BZ2 compressed file
Definition: FileTypes.h:117
OpenMS::TargetedExperiment
A description of a targeted experiment containing precursor and production ions.
Definition: TargetedExperiment.h:64
OPENMS_LOG_INFO
#define OPENMS_LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:465
TransitionPQPFile.h
OpenMS::MSSpectrum::getIntegerDataArrays
const IntegerDataArrays & getIntegerDataArrays() const
Returns a const reference to the integer meta data arrays.
OpenMS::FeatureFileOptions::setLoadConvexHull
void setLoadConvexHull(bool convex)
OpenMS::Math::SummaryStatistics::upperq
double upperq
Definition: StatisticFunctions.h:698
OpenMS::BaseFeature::QualityType
float QualityType
Definition: BaseFeature.h:64
OpenMS::TransformationDescription::DataPoints
TransformationModel::DataPoints DataPoints
Vector of coordinate pairs.
Definition: TransformationDescription.h:97
OpenMS::FileTypeList::getTypes
const std::vector< FileTypes::Type > & getTypes() const
Definition: FileTypes.h:157
IndexedMzMLHandler.h
OpenMS::FileTypes::MS2
MS2 file (.ms2)
Definition: FileTypes.h:72
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
OpenMS::Precursor::ActivationMethod
ActivationMethod
Method of activation.
Definition: Precursor.h:84
OpenMS::Math::SummaryStatistics::count
size_t count
Definition: StatisticFunctions.h:700
TraMLFile.h
OpenMS::TransformationDescription
Generic description of a coordinate transformation.
Definition: TransformationDescription.h:62
OpenMS::FileTypes::XML
any XML format
Definition: FileTypes.h:116
OpenMS::Internal::ClassTest::infile
std::ifstream infile
Questionable file tested by TEST_FILE_EQUAL.
OpenMS::String::toFloat
float toFloat() const
Conversion to float.
MzIdentMLFile.h
OpenMS::FileTypes::TRANSFORMATIONXML
Transformation description file (.trafoXML)
Definition: FileTypes.h:69
OpenMS::FeatureXMLFile::getOptions
FeatureFileOptions & getOptions()
Mutable access to the options for loading/storing.
OpenMS::ProgressLogger::setLogType
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!
TOPPBase.h
OpenMS::Math::SummaryStatistics::min
T::value_type min
Definition: StatisticFunctions.h:699
OpenMS::ConsensusXMLFile
This class provides Input functionality for ConsensusMaps and Output functionality for alignments and...
Definition: ConsensusXMLFile.h:58
OpenMS::IdXMLFile
Used to load and store idXML files.
Definition: IdXMLFile.h:68
OpenMS::FileTypes::typeToName
static String typeToName(Type type)
Returns the name/extension of the type.
OpenMS::Internal::IndexedMzMLHandler
A low-level class to read an indexedmzML file.
Definition: IndexedMzMLHandler.h:79
OpenMS::MSExperiment::getMinRT
CoordinateType getMinRT() const
returns the minimal retention time value
OpenMS::FileTypes::OMS
OpenMS database file.
Definition: FileTypes.h:114
OpenMS::FileTypes::PSMS
Percolator tab-delimited output (PSM level)
Definition: FileTypes.h:105
OpenMS::ConsensusMap::ColumnHeaders
std::map< UInt64, ColumnHeader > ColumnHeaders
Definition: ConsensusMap.h:164
OpenMS::FileTypeList
holds a vector of known file types, e.g. as a way to specify supported input formats
Definition: FileTypes.h:149
OpenMS::IonSource::NamesOfIonizationMethod
static const std::string NamesOfIonizationMethod[SIZE_OF_IONIZATIONMETHOD]
Names of ionization methods.
Definition: IonSource.h:137
StringListUtils.h