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