OpenMS
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This class provides Input/Output functionality for feature maps. More...
#include <OpenMS/FORMAT/FeatureXMLFile.h>
Constructors and Destructor | |
FeatureFileOptions | options_ |
Options that can be set. More... | |
FeatureXMLFile () | |
Default constructor. More... | |
~FeatureXMLFile () override | |
Destructor. More... | |
void | load (const String &filename, FeatureMap &feature_map) |
loads the file with name filename into map and calls updateRanges(). More... | |
Size | loadSize (const String &filename) |
void | store (const String &filename, const FeatureMap &feature_map) |
stores the map feature_map in file with name filename . More... | |
FeatureFileOptions & | getOptions () |
Mutable access to the options for loading/storing. More... | |
const FeatureFileOptions & | getOptions () const |
Non-mutable access to the options for loading/storing. More... | |
void | setOptions (const FeatureFileOptions &) |
setter for options for loading/storing More... | |
Additional Inherited Members | |
Public Types inherited from ProgressLogger | |
enum | LogType { CMD , GUI , NONE } |
Possible log types. 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 | setLogger (ProgressLoggerImpl *logger) |
Sets the logger to be used for progress logging. 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... | |
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) |
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_ |
This class provides Input/Output functionality for feature maps.
A documented schema for this format can be found at https://github.com/OpenMS/OpenMS/tree/develop/share/OpenMS/SCHEMAS
FeatureXMLFile | ( | ) |
Default constructor.
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override |
Destructor.
FeatureFileOptions& getOptions | ( | ) |
Mutable access to the options for loading/storing.
const FeatureFileOptions& getOptions | ( | ) | const |
Non-mutable access to the options for loading/storing.
void load | ( | const String & | filename, |
FeatureMap & | feature_map | ||
) |
loads the file with name filename
into map
and calls updateRanges().
Exception::FileNotFound | is thrown if the file could not be opened |
Exception::ParseError | is thrown if an error occurs during parsing |
void setOptions | ( | const FeatureFileOptions & | ) |
setter for options for loading/storing
void store | ( | const String & | filename, |
const FeatureMap & | feature_map | ||
) |
stores the map feature_map
in file with name filename
.
Exception::UnableToCreateFile | is thrown if the file could not be created |
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protected |
Options that can be set.