35 #ifndef OPENMS_FORMAT_FILEHANDLER_H
36 #define OPENMS_FORMAT_FILEHANDLER_H
38 #include <OpenMS/config.h>
120 template <
class PeakType>
133 type = getType(filename);
155 f.
load(filename, exp);
165 f.
load(filename, exp);
175 f.
load(filename, exp);
184 f.
load(filename, exp);
193 f.
load(filename, exp);
202 f.
load(filename, exp);
250 template <
class PeakType>
254 switch (getTypeByFileName(filename))
261 f.
store(filename, exp);
274 f.
store(filename, exp2);
278 f.
store(filename, exp);
292 f.
store(filename, exp2);
296 f.
store(filename, exp);
306 f.
store(filename, exp);
324 template <
class FeatureType>
337 type = getType(filename);
383 #endif //OPENMS_FORMAT_FILEHANDLER_H
Type
Actual file types enum.
Definition: FileTypes.h:59
DTA2D File adapter.
Definition: DTA2DFile.h:64
msInspect file (.tsv)
Definition: FileTypes.h:87
PeakFileOptions options_
Definition: FileHandler.h:371
void load(const String &filename, MSSpectrum< PeakType > &spectrum)
Loads a spectrum from a XMass file.
Definition: XMassFile.h:84
void store(const String &filename, const MapType &map) const
Stores a map in a MzXML file.
Definition: MzXMLFile.h:101
A more convenient string class.
Definition: String.h:56
MS2 file (.ms2)
Definition: FileTypes.h:74
File adapter for MzXML 2.1 files.
Definition: MzXMLFile.h:52
void reset()
Resets all internal values.
Definition: MSExperiment.h:635
LogType
Possible log types.
Definition: ProgressLogger.h:66
void load(const String &filename, FeatureMapType &feature_map)
Loads a MsInspect file into a featureXML.
Definition: MsInspectFile.h:78
void load(const String &filename, MapType &map)
Loads a map from a MzXML file.
Definition: MzXMLFile.h:80
A container for features.
Definition: FeatureMap.h:111
static String path(const String &file)
Returns the path of the file (without the file name).
void setFileType(const String &file_type)
sets the file type
bool loadFeatures(const String &filename, FeatureMap< FeatureType > &map, FileTypes::Type force_type=FileTypes::UNKNOWN)
Loads a file into a FeatureMap.
Definition: FileHandler.h:325
File adapter for DTA files.
Definition: DTAFile.h:58
MzData file (.mzData)
Definition: FileTypes.h:64
Description of a file location, used to store the origin of (meta) data.
Definition: SourceFile.h:47
void resize(Size s)
Definition: MSExperiment.h:122
File not found exception.
Definition: Exception.h:524
File adapter for 'XMass Analysis (fid)' files.
Definition: XMassFile.h:66
File adapter for Kroenik (HardKloer sibling) files.
Definition: KroenikFile.h:67
void setChecksum(const String &checksum, ChecksumType type)
sets the file's checksum
Mascot input file adapter.
Definition: MascotGenericFile.h:64
specArray file (.peplist)
Definition: FileTypes.h:88
File adapter for SpecArray (.pepList) files.
Definition: SpecArrayFile.h:61
void load(const String &filename, FeatureMap<> &feature_map)
loads the file with name filename into map and calls updateRanges().
File adapter for MzML files.
Definition: MzMLFile.h:58
void load(const String &filename, SpectrumType &spectrum)
Loads a DTA file to a spectrum.
Definition: DTAFile.h:76
Unknown file extension.
Definition: FileTypes.h:61
File adapter for MzData files.
Definition: MzDataFile.h:51
No progress logging.
Definition: ProgressLogger.h:70
void load(const String &filename, MapType &exp)
Definition: MS2File.h:77
DTA file (.dta)
Definition: FileTypes.h:62
XMass Analysis file (fid)
Definition: FileTypes.h:86
kroenik file (.kroenik)
Definition: FileTypes.h:90
void load(const String &filename, MapType &map)
Loads a map from a MzML file.
Definition: MzMLFile.h:86
void store(const String &filename, const MapType &map) const
Stores a map in a MzML file.
Definition: MzMLFile.h:126
void store(const String &filename, const MapType &map) const
Stores a map in a DTA2D file.
Definition: DTA2DFile.h:268
void store(const String &filename, const MapType &map) const
Stores a map in a MzData file.
Definition: MzDataFile.h:102
void setNameOfFile(const String &name_of_file)
sets the file name
static String basename(const String &file)
Returns the basename of the file (without the path).
OpenMS feature file (.featureXML)
Definition: FileTypes.h:66
Representation of a mass spectrometry experiment.
Definition: MSExperiment.h:68
Secure Hash Algorithm-1.
Definition: SourceFile.h:55
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLFile.h:59
PeakFileOptions & getOptions()
Mutable access to the options for loading/storing.
PeakFileOptions & getOptions()
Mutable access to the options for loading/storing.
PeakFileOptions & getOptions()
Mutable access to the options for loading/storing.
void storeExperiment(const String &filename, const MSExperiment< PeakType > &exp, ProgressLogger::LogType log=ProgressLogger::NONE)
Stores an MSExperiment to a file.
Definition: FileHandler.h:251
bool loadExperiment(const String &filename, MSExperiment< PeakType > &exp, FileTypes::Type force_type=FileTypes::UNKNOWN, ProgressLogger::LogType log=ProgressLogger::NONE, const bool compute_hash=true)
Loads a file into an MSExperiment.
Definition: FileHandler.h:121
static String typeToMZML(Type type)
Returns the mzML name (TODO: switch to accession since they are more stable!)
DTA2D file (.dta2d)
Definition: FileTypes.h:63
void importExperimentalSettings(const String &filename, MSExperiment< PeakType > &exp)
Import settings from a XMass file.
Definition: XMassFile.h:182
void load(const String &filename, FeatureMapType &feature_map)
Loads a SpecArray file into a featureXML.
Definition: SpecArrayFile.h:78
Options for loading files containing peak data.
Definition: PeakFileOptions.h:47
File adapter for MsInspect files.
Definition: MsInspectFile.h:61
MS2 input file adapter.
Definition: MS2File.h:65
void load(const String &filename, MapType &exp)
loads a Mascot Generic File into a PeakMap
Definition: MascotGenericFile.h:90
void setPathToFile(const String &path_path_to_file)
sets the file path
PeakFileOptions & getOptions()
Mutable access to the options for loading/storing.
Mascot Generic Format (.mgf)
Definition: FileTypes.h:69
void load(const String &filename, FeatureMapType &feature_map)
Loads a Kroenik file into a featureXML.
Definition: KroenikFile.h:84
void load(const String &filename, MapType &map)
Loads a map from a MzData file.
Definition: MzDataFile.h:81
MzML file (.mzML)
Definition: FileTypes.h:73
Facilitates file handling by file type recognition.
Definition: FileHandler.h:73
void load(const String &filename, MapType &map)
Loads a map from a DTA2D file.
Definition: DTA2DFile.h:95
const std::vector< MSChromatogram< ChromatogramPeakType > > & getChromatograms() const
returns the chromatogram list
Definition: MSExperiment.h:768
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!
const std::vector< SourceFile > & getSourceFiles() const
returns a const reference to the source data file
MzXML file (.mzXML)
Definition: FileTypes.h:65