OpenMS  2.8.0
Public Member Functions | Static Public Member Functions | Private Attributes | List of all members
FileHandler Class Reference

Facilitates file handling by file type recognition. More...

#include <OpenMS/FORMAT/FileHandler.h>

Collaboration diagram for FileHandler:
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Public Member Functions

PeakFileOptionsgetOptions ()
 Mutable access to the options for loading/storing. More...
 
const PeakFileOptionsgetOptions () const
 Non-mutable access to the options for loading/storing. More...
 
void setOptions (const PeakFileOptions &)
 set options for loading/storing More...
 
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. More...
 
void storeExperiment (const String &filename, const MSExperiment &exp, ProgressLogger::LogType log=ProgressLogger::NONE)
 Stores an MSExperiment to a file. More...
 
bool loadFeatures (const String &filename, FeatureMap &map, FileTypes::Type force_type=FileTypes::UNKNOWN)
 Loads a file into a FeatureMap. More...
 
bool storeFeatures (const String &filename, const FeatureMap &map)
 Store a FeatureMap. More...
 
bool storeConsensusFeatures (const String &filename, const ConsensusMap &map)
 Store a ConsensFeatureMap. More...
 
bool loadConsensusFeatures (const String &filename, ConsensusMap &map)
 Loads a file into a ConsensMap. More...
 
bool loadIdentifications (const String &filename, std::vector< ProteinIdentification > additional_proteins, std::vector< PeptideIdentification > additional_peptides)
 
bool storeTransitions (const String &filename, const TargetedExperiment &library)
 Store transitions of a spectral library. More...
 

Static Public Member Functions

static FileTypes::Type getType (const String &filename)
 Tries to determine the file type (by name or content) More...
 
static FileTypes::Type getTypeByFileName (const String &filename)
 Determines the file type from a file name. More...
 
static bool hasValidExtension (const String &filename, const FileTypes::Type type)
 Check if filename has the extension type. More...
 
static String stripExtension (const String &filename)
 If filename contains an extension, it will be removed (including the '.'). Special extensions, known to OpenMS, e.g. '.mzML.gz' will be recognized as well. More...
 
static String swapExtension (const String &filename, const FileTypes::Type new_type)
 Tries to find and remove a known file extension, and append the new one. More...
 
static FileTypes::Type getConsistentOutputfileType (const String &output_filename, const String &requested_type)
 Useful function for TOPP tools which have an 'out_type' parameter and want to know what output format to write. This function makes sure that the type derived from output_filename and requested_type are consistent, i.e. are either identical or one of them is UNKNOWN. Upon conflict, an error message is printed and the UNKNOWN type is returned. More...
 
static FileTypes::Type getTypeByContent (const String &filename)
 Determines the file type of a file by parsing the first few lines. More...
 
static bool isSupported (FileTypes::Type type)
 Returns if the file type is supported in this build of the library. More...
 
static String computeFileHash (const String &filename)
 Computes a SHA-1 hash value for the content of the given file. More...
 

Private Attributes

PeakFileOptions options_
 

Detailed Description

Facilitates file handling by file type recognition.

This class provides file type recognition from the file name and from the file content.

It also offer a common interface to load MSExperiment data and allows querying for supported file types.

See also
FileTypes

Member Function Documentation

◆ computeFileHash()

static String computeFileHash ( const String filename)
static

Computes a SHA-1 hash value for the content of the given file.

Returns
The SHA-1 hash of the given file.

◆ getConsistentOutputfileType()

static FileTypes::Type getConsistentOutputfileType ( const String output_filename,
const String requested_type 
)
static

Useful function for TOPP tools which have an 'out_type' parameter and want to know what output format to write. This function makes sure that the type derived from output_filename and requested_type are consistent, i.e. are either identical or one of them is UNKNOWN. Upon conflict, an error message is printed and the UNKNOWN type is returned.

Parameters
output_filenameA full filename (with none, absolute or relative paths) whose type is determined using FileHandler::getTypeByFileName() internally
requested_typeA type as string, usually obtained from '-out_type', e.g. "FASTA" (case insensitive). The string can be empty (yields UNKNOWN for this type)
Returns
A consistent file type or UNKNOWN upon conflict

◆ getOptions() [1/2]

PeakFileOptions& getOptions ( )

Mutable access to the options for loading/storing.

Referenced by TOPPViewBase::metadataFileDialog().

◆ getOptions() [2/2]

const PeakFileOptions& getOptions ( ) const

Non-mutable access to the options for loading/storing.

◆ getType()

static FileTypes::Type getType ( const String filename)
static

Tries to determine the file type (by name or content)

First the type is determined from the file name. If this fails, the type is determined from the file content.

Exceptions
Exception::FileNotFoundis thrown if the file is not present

Referenced by TOPPViewBase::addDataFile(), and TOPPOpenSwathBase::performCalibration().

◆ getTypeByContent()

static FileTypes::Type getTypeByContent ( const String filename)
static

Determines the file type of a file by parsing the first few lines.

Exceptions
Exception::FileNotFoundis thrown if the file is not present

Referenced by InspectOutfile::getExperiment().

◆ getTypeByFileName()

static FileTypes::Type getTypeByFileName ( const String filename)
static

Determines the file type from a file name.

Referenced by TOPPOpenSwathBase::loadSwathFiles_().

◆ hasValidExtension()

static bool hasValidExtension ( const String filename,
const FileTypes::Type  type 
)
static

Check if filename has the extension type.

If the extension is not known (e.g. '.tmp') this is also allowed. However, if the extension is another one (neither type nor unknown), false is returned.

◆ isSupported()

static bool isSupported ( FileTypes::Type  type)
static

Returns if the file type is supported in this build of the library.

◆ loadConsensusFeatures()

bool loadConsensusFeatures ( const String filename,
ConsensusMap map 
)

Loads a file into a ConsensMap.

Parameters
filenamethe file name of the file to load.
mapThe ConsensMap to load the data into.
Returns
true if the file could be loaded, false otherwise
Exceptions
Exception::FileNotFoundis thrown if the file could not be opened
Exception::ParseErroris thrown if an error occurs during parsing

◆ 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.

Parameters
filenameThe file name of the file to load.
expThe experiment to load the data into.
force_typeForces 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).
logProgress logging mode
rewrite_source_fileSet'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_hashIf 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
Exceptions
Exception::FileNotFoundis thrown if the file could not be opened
Exception::ParseErroris thrown if an error occurs during parsing

Referenced by TOPPViewBase::addDataFile(), TOPPViewBase::fileChanged_(), InspectOutfile::getExperiment(), and TOPPViewBase::metadataFileDialog().

◆ loadFeatures()

bool loadFeatures ( const String filename,
FeatureMap map,
FileTypes::Type  force_type = FileTypes::UNKNOWN 
)

Loads a file into a FeatureMap.

Parameters
filenamethe file name of the file to load.
mapThe FeatureMap to load the data into.
force_typeForces 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
Exceptions
Exception::FileNotFoundis thrown if the file could not be opened
Exception::ParseErroris thrown if an error occurs during parsing

Referenced by TOPPViewBase::fileChanged_().

◆ loadIdentifications()

bool loadIdentifications ( const String filename,
std::vector< ProteinIdentification additional_proteins,
std::vector< PeptideIdentification additional_peptides 
)

◆ setOptions()

void setOptions ( const PeakFileOptions )

set options for loading/storing

◆ storeConsensusFeatures()

bool storeConsensusFeatures ( const String filename,
const ConsensusMap map 
)

Store a ConsensFeatureMap.

Parameters
filenamethe file name of the file to write.
mapThe ConsensusMap to store.
Returns
true if the file could be stored, false otherwise
Exceptions
Exception::UnableToCreateFileis thrown if the file could not be written

◆ storeExperiment()

void storeExperiment ( const String filename,
const MSExperiment exp,
ProgressLogger::LogType  log = ProgressLogger::NONE 
)

Stores an MSExperiment to a file.

The file type to store the data in is determined by the file name. Supported formats for storing are mzML, mzXML, mzData and DTA2D. If the file format cannot be determined from the file name, the mzML format is used.

Parameters
filenameThe name of the file to store the data in.
expThe experiment to store.
logProgress logging mode
Exceptions
Exception::UnableToCreateFileis thrown if the file could not be written

◆ storeFeatures()

bool storeFeatures ( const String filename,
const FeatureMap map 
)

Store a FeatureMap.

Parameters
filenamethe file name of the file to write.
mapThe FeatureMap to store.
Returns
true if the file could be stored, false otherwise
Exceptions
Exception::UnableToCreateFileis thrown if the file could not be written

◆ storeTransitions()

bool storeTransitions ( const String filename,
const TargetedExperiment library 
)

Store transitions of a spectral library.

Parameters
filenamethe file name of the file to write.
mapThe TargetedExperiment to store.
Returns
true if the file could be stored, false otherwise
Exceptions
Exception::UnableToCreateFileis thrown if the file could not be written

◆ stripExtension()

static String stripExtension ( const String filename)
static

If filename contains an extension, it will be removed (including the '.'). Special extensions, known to OpenMS, e.g. '.mzML.gz' will be recognized as well.

E.g. 'experiment.featureXML' becomes 'experiment' and 'c:\files\data.mzML.gz' becomes 'c:\files\data' If the extension is unknown, the everything in the basename of the file after the last '.' is removed. E.g. 'future.newEnding' becomes 'future' If the filename does not contain '.', but the path (if any) does, nothing is removed, e.g. '/my.dotted.dir/filename' is returned unchanged.

Referenced by TOPPViewBase::addDataFile().

◆ swapExtension()

static String swapExtension ( const String filename,
const FileTypes::Type  new_type 
)
static

Tries to find and remove a known file extension, and append the new one.

Internally calls 'stripExtension()' and adds the new suffix to the result. E.g. 'experiment.featureXML'+ FileTypes::TRAFOXML becomes 'experiment.trafoXML' and 'c:\files\data.mzML.gz' + FileTypes::FEATUREXML becomes 'c:\files\data.featureXML' If the existing extension is unknown, the everything after the last '.' is removed, e.g. 'exp.tmp'+FileTypes::IDXML becomes 'exp.idXML'

Referenced by TOPPViewBase::addDataFile().

Member Data Documentation

◆ options_

PeakFileOptions options_
private