IndexedMzMLFileLoader Class Reference

A class to load an indexedmzML file. More...

#include <OpenMS/FORMAT/IndexedMzMLFileLoader.h>

Collaboration diagram for IndexedMzMLFileLoader:

Public Member Functions
	IndexedMzMLFileLoader ()
	Constructor.
	~IndexedMzMLFileLoader ()
	Destructor.
PeakFileOptions &	getOptions ()
	Mutable access to the options for loading/storing.
const PeakFileOptions &	getOptions () const
	Non-mutable access to the options for loading/storing.
void	setOptions (const PeakFileOptions &)
	set options for loading/storing
bool	load (const std::string &filename, OnDiscPeakMap &exp)
	Load a file.
void	store (const std::string &filename, OnDiscPeakMap &exp)
	Store a file from an on-disc data-structure.
void	store (const std::string &filename, PeakMap &exp)
	Store a file from an in-memory data-structure.

Private Attributes
PeakFileOptions	options_
	Options for storing.

Detailed Description

A class to load an indexedmzML file.

Providing the same interface as the other classes such as MzMLFile, MzXMLFile etc. to load and store a file. Reading a file from disk will load the file into a OnDiscMSExperiment while the class can write to disk both, a MSExperiment and a OnDiscMSExperiment.

Constructor & Destructor Documentation

IndexedMzMLFileLoader()

IndexedMzMLFileLoader

(

)

Constructor.

~IndexedMzMLFileLoader()

~IndexedMzMLFileLoader

(

)

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()

bool load	(	const std::string &	filename,
		OnDiscPeakMap &	exp
	)

Load a file.

Tries to parse the file, success needs to be checked with the return value.

Note

The return value only distinguishes a successfully parsed indexed mzML from a file that exists but is not a valid/indexed mzML (in which case false is returned and exp is left empty/invalid). It does not signal every error: a missing or unreadable file still throws Exception::FileNotFound / Exception::FileNotReadable / Exception::IOException, and a corrupt indexListOffset throws Exception::ConversionError (both raised while reading the index footer, before any value is returned). This differs from the sibling file classes (MzMLFile, MzDataFile, MzXMLFile) whose load() returns void and reports all failures via exceptions.

Parameters

[out]	filename	Filename determines where the file is located
[out]	exp	Object which will contain the data after the call

Returns

Indicates whether parsing was successful (if it is false, the file exists but most likely was not an mzML or not indexed); the return value must be checked.

Exceptions

Exception::FileNotFound	if filename does not exist.
Exception::FileNotReadable	if filename cannot be read.
Exception::ConversionError	if the index footer (indexListOffset) is corrupt.

setOptions()

void setOptions

(

const PeakFileOptions &

)

set options for loading/storing

store() [1/2]

void store	(	const std::string &	filename,
		OnDiscPeakMap &	exp
	)

Store a file from an on-disc data-structure.

Parameters

[out]	filename	Filename determines where the file will be stored
[out]	exp	MS data to be stored

store() [2/2]

void store	(	const std::string &	filename,
		PeakMap &	exp
	)

Store a file from an in-memory data-structure.

Parameters

[in]	filename	Filename determines where the file will be stored
[out]	exp	MS data to be stored

Member Data Documentation

options_

PeakFileOptions options_

private

Options for storing.