OpenMS
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File adapter for MzData files. More...
#include <OpenMS/FORMAT/MzDataFile.h>
Public Member Functions | |
MzDataFile () | |
Default constructor. More... | |
~MzDataFile () override | |
Destructor. More... | |
PeakFileOptions & | getOptions () |
Mutable access to the options for loading/storing. More... | |
const PeakFileOptions & | getOptions () const |
Non-mutable access to the options for loading/storing. More... | |
void | setOptions (const PeakFileOptions &) |
set options for loading/storing More... | |
void | load (const String &filename, MapType &map) |
Loads a map from a MzData file. More... | |
void | store (const String &filename, const MapType &map) const |
Stores a map in a MzData file. More... | |
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. More... | |
Public Member Functions inherited from XMLFile | |
XMLFile () | |
Default constructor. More... | |
XMLFile (const String &schema_location, const String &version) | |
Constructor that sets the schema location. More... | |
virtual | ~XMLFile () |
Destructor. More... | |
bool | isValid (const String &filename, std::ostream &os) |
Checks if a file validates against the XML schema. More... | |
const String & | getVersion () const |
return the version of the schema More... | |
Public Member Functions inherited from ProgressLogger | |
ProgressLogger () | |
Constructor. More... | |
virtual | ~ProgressLogger () |
Destructor. More... | |
ProgressLogger (const ProgressLogger &other) | |
Copy constructor. More... | |
ProgressLogger & | operator= (const ProgressLogger &other) |
Assignment Operator. More... | |
void | setLogType (LogType type) const |
Sets the progress log that should be used. The default type is NONE! More... | |
LogType | getLogType () const |
Returns the type of progress log being used. More... | |
void | startProgress (SignedSize begin, SignedSize end, const String &label) const |
Initializes the progress display. More... | |
void | setProgress (SignedSize value) const |
Sets the current progress. More... | |
void | endProgress (UInt64 bytes_processed=0) const |
void | nextProgress () const |
increment progress by 1 (according to range begin-end) More... | |
Private Types | |
typedef PeakMap | MapType |
Private Attributes | |
PeakFileOptions | options_ |
Options for loading / storing. More... | |
Additional Inherited Members | |
Public Types inherited from ProgressLogger | |
enum | LogType { CMD , GUI , NONE } |
Possible log types. More... | |
Protected Member Functions inherited from XMLFile | |
void | parse_ (const String &filename, XMLHandler *handler) |
Parses the XML file given by filename using the handler given by handler . More... | |
void | parseBuffer_ (const std::string &buffer, XMLHandler *handler) |
Parses the in-memory buffer given by buffer using the handler given by handler . More... | |
void | save_ (const String &filename, XMLHandler *handler) const |
Stores the contents of the XML handler given by handler in the file given by filename . More... | |
void | enforceEncoding_ (const String &encoding) |
Static Protected Member Functions inherited from ProgressLogger | |
static String | logTypeToFactoryName_ (LogType type) |
Return the name of the factory product used for this log type. More... | |
Protected Attributes inherited from XMLFile | |
String | schema_location_ |
XML schema file location. More... | |
String | schema_version_ |
Version string. More... | |
String | enforced_encoding_ |
Encoding string that replaces the encoding (system dependent or specified in the XML). Disabled if empty. Used as a workaround for XTandem output xml. More... | |
Protected Attributes inherited from ProgressLogger | |
LogType | type_ |
time_t | last_invoke_ |
ProgressLoggerImpl * | current_logger_ |
Static Protected Attributes inherited from ProgressLogger | |
static int | recursion_depth_ |
File adapter for MzData files.
MzDataFile | ( | ) |
Default constructor.
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override |
Destructor.
PeakFileOptions& getOptions | ( | ) |
Mutable access to the options for loading/storing.
const PeakFileOptions& getOptions | ( | ) | const |
Non-mutable access to the options for loading/storing.
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.
filename | File name of the file to be checked. |
errors | Errors during the validation are returned in this output parameter. |
warnings | Warnings during the validation are returned in this output parameter. |
Exception::FileNotFound | is thrown if the file could not be opened |
Loads a map from a MzData file.
map
has to be a MSExperiment or have the same interface.
Exception::FileNotFound | is thrown if the file could not be opened |
Exception::ParseError | is thrown if an error occurs during parsing |
void setOptions | ( | const PeakFileOptions & | ) |
set options for loading/storing
Stores a map in a MzData file.
map
has to be a MSExperiment or have the same interface.
Exception::UnableToCreateFile | is thrown if the file could not be created |
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private |
Options for loading / storing.