MSNumpressCoder Class Reference

Class to encode and decode data encoded with MSNumpress. More...

#include <OpenMS/FORMAT/MSNumpressCoder.h>

Classes
struct	NumpressConfig
	Configuration class for MSNumpress. More...

Public Types
enum	NumpressCompression {   NONE, LINEAR, PIC, SLOF,   SIZE_OF_NUMPRESSCOMPRESSION }

Public Member Functions
	MSNumpressCoder ()
	default constructor More...
virtual	~MSNumpressCoder ()
	Destructor. More...
void	encodeNP (const std::vector< double > &in, String &result, bool zlib_compression, const NumpressConfig &config)
	Encodes a vector of floating point numbers into a Base64 string using numpress. More...
void	encodeNP (const std::vector< float > &in, String &result, bool zlib_compression, const NumpressConfig &config)
	encodeNP from a float (convert first to double) More...
void	decodeNP (const String &in, std::vector< double > &out, bool zlib_compression, const NumpressConfig &config)
	Decodes a Base64 string to a vector of floating point numbers using numpress. More...
void	encodeNPRaw (const std::vector< double > &in, String &result, const NumpressConfig &config)
	Encode the vector in to the result string using numpress (unsafe) More...
void	decodeNPRaw (const std::string &in, std::vector< double > &out, const NumpressConfig &config)
	Decode the (not necessary null terminated) string in to the result vector out (unsafe) More...

Static Public Attributes
static const std::string	NamesOfNumpressCompression [SIZE_OF_NUMPRESSCOMPRESSION]
	Names of compression schemes. More...

Private Member Functions
void	decodeNPInternal_ (const unsigned char *in, size_t in_size, std::vector< double > &out, const NumpressConfig &config)

Private Attributes
Base64	base64coder_

Detailed Description

Class to encode and decode data encoded with MSNumpress.

MSNumpress supports three encoding schemata:

• Linear (MS:1002312, MS-Numpress linear prediction compression)
• Pic (MS:1002313, MS-Numpress positive integer compression)
• Slof (MS:1002314, MS-Numpress short logged float compression)

Member Enumeration Documentation

NumpressCompression

enum NumpressCompression

Enumerator
NONE
LINEAR
PIC
SLOF
SIZE_OF_NUMPRESSCOMPRESSION

Constructor & Destructor Documentation

MSNumpressCoder()

MSNumpressCoder ( )

inline

default constructor

~MSNumpressCoder()

virtual ~MSNumpressCoder ( )

inlinevirtual

Destructor.

Member Function Documentation

decodeNP()

void decodeNP	(	const String &	in,
		std::vector< double > &	out,
		bool	zlib_compression,
		const NumpressConfig &	config
	)

Decodes a Base64 string to a vector of floating point numbers using numpress.

This code is obtained from the proteowizard implementation ./pwiz/pwiz/data/msdata/BinaryDataEncoder.cpp (adapted by Hannes Roest).

This function will first decode the input base64 string (with optional zlib decompression after decoding) and then apply numpress decoding to the data.

Parameters

in	The base64 encoded string
out	The resulting vector of doubles
zlib_compression	Whether to apply zlib de-compression before numpress de-compression
config	The numpress configuration defining the compression strategy

Exceptions

throws

Exception::ConversionError if the string cannot be converted

decodeNPInternal_()

void decodeNPInternal_ ( const unsigned char *  in, size_t  in_size, std::vector< double > &  out, const NumpressConfig &  config  )

private

decodeNPRaw()

void decodeNPRaw	(	const std::string &	in,
		std::vector< double > &	out,
		const NumpressConfig &	config
	)

Decode the (not necessary null terminated) string in to the result vector out (unsafe)

Note

that the string in should *only* contain the data and _no_ extra null terminating byte (unless of course the last data byte is null)

This performs the raw numpress decoding on a raw byte array (not Base64 encoded). Therefore the input string is likely *unsafe* to handle and is basically a byte container.

Please use the safe versions above unless you only have the raw byte arrays.

Parameters

in	The base64 encoded string
out	The resulting vector of doubles
config	The numpress configuration defining the compression strategy

Exceptions

throws

Exception::ConversionError if the string cannot be converted

encodeNP() [1/2]

void encodeNP	(	const std::vector< double > &	in,
		String &	result,
		bool	zlib_compression,
		const NumpressConfig &	config
	)

Encodes a vector of floating point numbers into a Base64 string using numpress.

This code is obtained from the proteowizard implementation ./pwiz/pwiz/data/msdata/BinaryDataEncoder.cpp (adapted by Hannes Roest).

This function will first apply the numpress encoding to the data, then encode the result in base64 (with optional zlib compression before base64 encoding).

Note

In case of error, result string is empty

Parameters

in	The vector of floating point numbers to be encoded
result	The resulting string
zlib_compression	Whether to apply zlib compression after numpress compression
config	The numpress configuration defining the compression strategy

encodeNP() [2/2]

void encodeNP	(	const std::vector< float > &	in,
		String &	result,
		bool	zlib_compression,
		const NumpressConfig &	config
	)

encodeNP from a float (convert first to double)

encodeNPRaw()

void encodeNPRaw	(	const std::vector< double > &	in,
		String &	result,
		const NumpressConfig &	config
	)

Encode the vector in to the result string using numpress (unsafe)

Note

In case of error, result is given back unmodified

This performs the raw numpress encoding on a set of data and does no Base64 encoding on the result. Therefore the result string is likely *unsafe* to handle and is basically a byte container.

Please use the safe versions above unless you need access to the raw byte arrays.

Parameters

in	The vector of floating point numbers to be encoded
result	The resulting string
config	The numpress configuration defining the compression strategy

Member Data Documentation

base64coder_

Base64 base64coder_

private

NamesOfNumpressCompression

const std::string NamesOfNumpressCompression[SIZE_OF_NUMPRESSCOMPRESSION]

static

Names of compression schemes.