| OpenMS 2.5.0

Public Member Functions | Protected Member Functions | Private Types | Private Attributes | List of all members
MzXMLFile Class Reference
Format » File IO

File adapter for MzXML 3.1 files. More...

`#include <OpenMS/FORMAT/MzXMLFile.h>`

Inheritance diagram for MzXMLFile:

## Public Member Functions

| MzXMLFile ()
| Default constructor. More...
| ~MzXMLFile () 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 MzXML file. More...
void | store (const String &filename, const MapType &map) const
| Stores a map in a MzXML file. More...
void | transform (const String &filename_in, Interfaces::IMSDataConsumer *consumer, bool skip_full_count=false)
| Transforms a map while loading using the supplied MSDataConsumer. More...
void | transform (const String &filename_in, Interfaces::IMSDataConsumer *consumer, MapType &map, bool skip_full_count=false)
| Transforms a map while loading using the supplied MSDataConsumer. 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...
| ~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 () const
| Ends the progress display. More...
void | nextProgress () const
| increment progress by 1 (according to range begin-end) More...

## Protected Member Functions

void | transformFirstPass_ (const String &filename_in, Interfaces::IMSDataConsumer *consumer, bool skip_full_count)
| Perform first pass through the file and retrieve the meta-data to initialize the consumer. 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)

## Private Types

typedef PeakMap | MapType

## Private Attributes

PeakFileOptions | options_

## Additional Inherited Members

Public Types inherited from ProgressLogger
enum | LogType { CMD, GUI, NONE }
| Possible log types. More...
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_

## Detailed Description

File adapter for MzXML 3.1 files.

## Member Typedef Documentation

## ◆ MapType

typedef PeakMap MapType

private

## Constructor & Destructor Documentation

## ◆ MzXMLFile()

MzXMLFile | ( |  | ) |

Default constructor.

## ◆ ~MzXMLFile()

~MzXMLFile | ( |  | ) |

override

Destructor.

## Member Function Documentation

## ◆ getOptions() [1/2]

PeakFileOptions& getOptions | ( |  | ) |

Mutable access to the options for loading/storing.

## ◆ getOptions() [2/2]

const PeakFileOptions& getOptions | ( |  | ) | const

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

## ◆ load()

void load | ( | const String & | filename,
|  | MapType & | map
| ) |  |

Loads a map from a MzXML file.

`map` has to be a MSExperiment or have the same interface.

Exceptions

  Exception::FileNotFound | is thrown if the file could not be opened
  Exception::ParseError | is thrown if an error occurs during parsing

## ◆ setOptions()

void setOptions | ( | const PeakFileOptions & |  | ) |

set options for loading/storing

## ◆ store()

void store | ( | const String & | filename,
|  | const MapType & | map
| ) |  | const

Stores a map in a MzXML file.

`map` has to be a MSExperiment or have the same interface.

Exceptions

  Exception::UnableToCreateFile | is thrown if the file could not be created

## ◆ transform() [1/2]

void transform | ( | const String & | filename_in,
|  | Interfaces::IMSDataConsumer * | consumer,
|  | bool | skip_full_count = `false`
| ) |  |

Transforms a map while loading using the supplied MSDataConsumer.

The result will not be stored directly but is available through the events triggered by the parser and caught by the provided IMSDataConsumer object.

This function should be used if processing and storage of the result can be performed directly in the provided IMSDataConsumer object.

Note
  Transformation can be speed up by setting skip_full_count which does not require a full first pass through the file to compute the correct number of spectra and chromatograms in the input file.

Parameters

  filename_in | Filename of input mzML file to transform
  consumer | Consumer class to operate on the input filename (implementing a transformation)
  skip_full_count | Whether to skip computing the correct number of spectra and chromatograms in the input file

## ◆ transform() [2/2]

void transform | ( | const String & | filename_in,
|  | Interfaces::IMSDataConsumer * | consumer,
|  | MapType & | map,
|  | bool | skip_full_count = `false`
| ) |  |

Transforms a map while loading using the supplied MSDataConsumer.

The result will be stored in the provided map.

This function should be used if a specific pre-processing should be applied to the data before storing them in a map (e.g. if data-reduction should be applied to the data before loading all data into memory).

Parameters

  filename_in | Filename of input mzXML file to transform
  consumer | Consumer class to operate on the input filename (implementing a transformation)
  map | Map to store the resulting spectra and chromatograms
  skip_full_count | Whether to skip computing the correct number of spectra and chromatograms in the input file

## ◆ transformFirstPass_()

void transformFirstPass_ | ( | const String & | filename_in,
|  | Interfaces::IMSDataConsumer * | consumer,
|  | bool | skip_full_count
| ) |  |

protected

Perform first pass through the file and retrieve the meta-data to initialize the consumer.

## Member Data Documentation

## ◆ options_

PeakFileOptions options_

private