FileHandler

class pyopenms.FileHandler

Bases: object

Cython implementation of _FileHandler

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1FileHandler.html

__init__()

Cython signature: void FileHandler()

Methods

__init__

Cython signature: void FileHandler()

computeFileHash

Cython signature: String computeFileHash(const String & filename)

getOptions

Cython signature: PeakFileOptions getOptions() Access to the options for loading/storing

getType

Cython signature: int getType(const String & filename)

getTypeByContent

Cython signature: FileType getTypeByContent(const String & filename)

getTypeByFileName

Cython signature: FileType getTypeByFileName(const String & filename)

hasValidExtension

Cython signature: bool hasValidExtension(const String & filename, FileType type_)

isSupported

Cython signature: bool isSupported(FileType type_)

loadExperiment

Cython signature: bool loadExperiment(String, MSExperiment &)

loadFeatures

Cython signature: bool loadFeatures(String, FeatureMap &)

setOptions

Cython signature: void setOptions(PeakFileOptions) Sets options for loading/storing

storeExperiment

Cython signature: void storeExperiment(String, MSExperiment)

stripExtension

Cython signature: String stripExtension(String file)

swapExtension

Cython signature: String swapExtension(String filename, FileType new_type)
computeFileHash()

Cython signature: String computeFileHash(const String & filename)

getOptions()

Cython signature: PeakFileOptions getOptions() Access to the options for loading/storing

getType()

Cython signature: int getType(const String & filename)

getTypeByContent()

Cython signature: FileType getTypeByContent(const String & filename)

getTypeByFileName()

Cython signature: FileType getTypeByFileName(const String & filename)

hasValidExtension()

Cython signature: bool hasValidExtension(const String & filename, FileType type_)

isSupported()

Cython signature: bool isSupported(FileType type_)

loadExperiment()

Cython signature: bool loadExperiment(String, MSExperiment &)

Parameters

  • filename – The file name of the file to load

  • exp – The experiment to load the data into

  • force_type – Forces to load the file with that file type. If no type is forced, it is determined from the extension (or from the content if that fails)

  • log – Progress logging mode

  • rewrite_source_file – Set’s the SourceFile name and path to the current file. Note that this looses the link to the primary MS run the file originated from

  • compute_hash – If source files are rewritten, this flag triggers a recomputation of hash values. A SHA1 string gets stored in the checksum member of SourceFile

Returns

true if the file could be loaded, false otherwise

Raises

Exception: FileNotFound is thrown if the file could not be opened

Raises

Exception: ParseError is thrown if an error occurs during parsing

Parameters

  • filename – The name of the file to store the data in

  • exp – The experiment to store

  • log – Progress logging mode

Raises

Exception: UnableToCreateFile is thrown if the file could not be written

Parameters

  • filename – The file name of the file to load

  • map – The FeatureMap to load the data into

  • force_type – Forces to load the file with that file type. If no type is forced, it is determined from the extension (or from the content if that fails)

Returns

true if the file could be loaded, false otherwise

Raises

Exception: FileNotFound is thrown if the file could not be opened

Raises

Exception: ParseError is thrown if an error occurs during parsing

loadFeatures()

Cython signature: bool loadFeatures(String, FeatureMap &)

Parameters

  • filename – The file name of the file to load

  • map – The FeatureMap to load the data into

  • force_type – Forces to load the file with that file type. If no type is forced, it is determined from the extension (or from the content if that fails)

Returns

true if the file could be loaded, false otherwise

Raises

Exception: FileNotFound is thrown if the file could not be opened

Raises

Exception: ParseError is thrown if an error occurs during parsing

setOptions()

Cython signature: void setOptions(PeakFileOptions) Sets options for loading/storing

storeExperiment()

Cython signature: void storeExperiment(String, MSExperiment)

Parameters

  • filename – The name of the file to store the data in

  • exp – The experiment to store

  • log – Progress logging mode

Raises

Exception: UnableToCreateFile is thrown if the file could not be written

Parameters

  • filename – The file name of the file to load

  • map – The FeatureMap to load the data into

  • force_type – Forces to load the file with that file type. If no type is forced, it is determined from the extension (or from the content if that fails)

Returns

true if the file could be loaded, false otherwise

Raises

Exception: FileNotFound is thrown if the file could not be opened

Raises

Exception: ParseError is thrown if an error occurs during parsing

stripExtension()

Cython signature: String stripExtension(String file)

swapExtension()

Cython signature: String swapExtension(String filename, FileType new_type)