#include <stdio.h>
#include <stdlib.h>
#include <stdint.h>
#include <netinet/in.h>
#include <sys/stat.h>
#include "ramp_base64.h"
#include <string.h>
#include <string>
#include <ctype.h>

Classes
struct	RAMPFILE
struct	ScanHeaderStruct
struct	RunHeaderStruct
struct	InstrumentStruct
struct	ScanCacheStruct

Macros
#define	ramp_fread(buf, len, handle) fread(buf,1,len,(handle)->fileHandle)
#define	ramp_fgets(buf, len, handle) fgets(buf, len, (handle)->fileHandle)
#define	ramp_feof(handle) feof((handle)->fileHandle)
#define	ramp_fseek(a, b, c) fseeko((a)->fileHandle,b,c)
#define	ramp_ftell(a) ftello((a)->fileHandle)
#define	INSTRUMENT_LENGTH 2000
#define	SCANTYPE_LENGTH 32
#define	CHARGEARRAY_LENGTH 128

Typedefs
typedef FILE *	ramp_filehandle_t
typedef double	RAMPREAL
typedef off_t	ramp_fileoffset_t
typedef struct InstrumentStruct	InstrumentStruct

Enumerations
enum	e_contentType { mzInt = 0, mzRuler, mzOnly, intensityOnly }
enum	{ MASK_SCANS_TYPE = 0x0003, BIT_ORIGIN_SCANS = 0x0001, BIT_AVERAGE_SCANS = 0x0002, OPTION_AVERAGE_SCANS = BIT_AVERAGE_SCANS, OPTION_ORIGIN_SCANS = BIT_ORIGIN_SCANS, OPTION_ALL_SCANS = BIT_ORIGIN_SCANS \| BIT_AVERAGE_SCANS, DEFAULT_OPTION = OPTION_AVERAGE_SCANS }

Functions
RAMPFILE *	rampOpenFile (const char *filename)
void	rampCloseFile (RAMPFILE *pFI)
std::string	rampConstructInputFileName (const std::string &basename)
char *	rampConstructInputFileName (char buf, int buflen, const char basename)
char *	rampConstructInputPath (char buf, int inbuflen, const char dir_in, const char *basename)
int	rampValidateOrDeriveInputFilename (char inbuf, int inbuflen, char spectrumName)
char *	rampTrimBaseName (char *buf)
char *	rampValidFileType (const char *buf)
const char **	rampListSupportedFileTypes ()
int	rampSelfTest (char *filename)
ramp_fileoffset_t	getIndexOffset (RAMPFILE *pFI)
ramp_fileoffset_t *	readIndex (RAMPFILE pFI, ramp_fileoffset_t indexOffset, int iLastScan)
void	readHeader (RAMPFILE pFI, ramp_fileoffset_t lScanIndex, struct ScanHeaderStruct scanHeader)
int	readMsLevel (RAMPFILE *pFI, ramp_fileoffset_t lScanIndex)
double	readStartMz (RAMPFILE *pFI, ramp_fileoffset_t lScanIndex)
double	readEndMz (RAMPFILE *pFI, ramp_fileoffset_t lScanIndex)
int	readPeaksCount (RAMPFILE *pFI, ramp_fileoffset_t lScanIndex)
RAMPREAL *	readPeaks (RAMPFILE *pFI, ramp_fileoffset_t lScanIndex)
void	readRunHeader (RAMPFILE pFI, ramp_fileoffset_t pScanIndex, struct RunHeaderStruct *runHeader, int iLastScan)
void	readMSRun (RAMPFILE pFI, struct RunHeaderStruct runHeader)
InstrumentStruct *	getInstrumentStruct (RAMPFILE *pFI)
void	setRampOption (long option)
int	isScanAveraged (struct ScanHeaderStruct *scanHeader)
int	isScanMergedResult (struct ScanHeaderStruct *scanHeader)
void	getScanSpanRange (const struct ScanHeaderStruct scanHeader, int startScanNum, int *endScanNum)
struct ScanCacheStruct *	getScanCache (int size)
void	freeScanCache (struct ScanCacheStruct *cache)
void	clearScanCache (struct ScanCacheStruct *cache)
struct ScanHeaderStruct *	readHeaderCached (struct ScanCacheStruct cache, int seqNum, RAMPFILE pFI, ramp_fileoffset_t lScanIndex)
int	readMsLevelCached (struct ScanCacheStruct cache, int seqNum, RAMPFILE pFI, ramp_fileoffset_t lScanIndex)
const RAMPREAL *	readPeaksCached (struct ScanCacheStruct cache, int seqNum, RAMPFILE pFI, ramp_fileoffset_t lScanIndex)

Macro Definition Documentation

#define ramp_fread	(	buf,
		len,
		handle
	)	fread(buf,1,len,(handle)->fileHandle)

Definition at line 132 of file ramp.h.

#define ramp_fgets	(	buf,
		len,
		handle
	)	fgets(buf, len, (handle)->fileHandle)

Definition at line 133 of file ramp.h.

#define ramp_feof ( handle ) feof((handle)->fileHandle)

Definition at line 134 of file ramp.h.

#define ramp_fseek	(	a,
		b,
		c
	)	fseeko((a)->fileHandle,b,c)

Definition at line 141 of file ramp.h.

#define ramp_ftell ( a ) ftello((a)->fileHandle)

Definition at line 142 of file ramp.h.

#define INSTRUMENT_LENGTH 2000

Definition at line 152 of file ramp.h.

#define SCANTYPE_LENGTH 32

Definition at line 153 of file ramp.h.

#define CHARGEARRAY_LENGTH 128

Definition at line 154 of file ramp.h.

Typedef Documentation

typedef FILE* ramp_filehandle_t

Definition at line 79 of file ramp.h.

typedef double RAMPREAL

Definition at line 85 of file ramp.h.

typedef off_t ramp_fileoffset_t

Definition at line 140 of file ramp.h.

typedef struct InstrumentStruct InstrumentStruct

Enumeration Type Documentation

enum e_contentType

Enumerator:

mzInt
mzRuler
mzOnly
intensityOnly

Definition at line 91 of file ramp.h.

{ mzInt = 0 , mzRuler, mzOnly, intensityOnly } e_contentType;

anonymous enum

Enumerator:

MASK_SCANS_TYPE
BIT_ORIGIN_SCANS
BIT_AVERAGE_SCANS
OPTION_AVERAGE_SCANS
OPTION_ORIGIN_SCANS
OPTION_ALL_SCANS
DEFAULT_OPTION

Definition at line 270 of file ramp.h.

     {
  MASK_SCANS_TYPE = 0x0003,
  BIT_ORIGIN_SCANS = 0x0001,
  BIT_AVERAGE_SCANS = 0x0002,
  OPTION_AVERAGE_SCANS = BIT_AVERAGE_SCANS, // return scan including merged resultant scan
                                            // but exclude 'real' scan via peaksCount=0
  OPTION_ORIGIN_SCANS = BIT_ORIGIN_SCANS,   // return 'real' scan 
                                            // but exclude merged resultant scan via peaksCount=0
  OPTION_ALL_SCANS = BIT_ORIGIN_SCANS | BIT_AVERAGE_SCANS,
                                            // return 'real' scan + merged resultant scan
  DEFAULT_OPTION = OPTION_AVERAGE_SCANS
};

Function Documentation

RAMPFILE* rampOpenFile ( const char * filename )

void rampCloseFile ( RAMPFILE * pFI )

std::string rampConstructInputFileName ( const std::string & basename )

char* rampConstructInputFileName	(	char *	buf,
		int	buflen,
		const char *	basename
	)

char* rampConstructInputPath	(	char *	buf,
		int	inbuflen,
		const char *	dir_in,
		const char *	basename
	)

int rampValidateOrDeriveInputFilename	(	char *	inbuf,
		int	inbuflen,
		char *	spectrumName
	)

char* rampTrimBaseName ( char * buf )

char* rampValidFileType ( const char * buf )

const char** rampListSupportedFileTypes ( )

int rampSelfTest ( char * filename )

ramp_fileoffset_t getIndexOffset ( RAMPFILE * pFI )

ramp_fileoffset_t* readIndex	(	RAMPFILE *	pFI,
		ramp_fileoffset_t	indexOffset,
		int *	iLastScan
	)

void readHeader	(	RAMPFILE *	pFI,
		ramp_fileoffset_t	lScanIndex,
		struct ScanHeaderStruct *	scanHeader
	)

int readMsLevel	(	RAMPFILE *	pFI,
		ramp_fileoffset_t	lScanIndex
	)

double readStartMz	(	RAMPFILE *	pFI,
		ramp_fileoffset_t	lScanIndex
	)

double readEndMz	(	RAMPFILE *	pFI,
		ramp_fileoffset_t	lScanIndex
	)

int readPeaksCount	(	RAMPFILE *	pFI,
		ramp_fileoffset_t	lScanIndex
	)

RAMPREAL* readPeaks	(	RAMPFILE *	pFI,
		ramp_fileoffset_t	lScanIndex
	)

void readRunHeader	(	RAMPFILE *	pFI,
		ramp_fileoffset_t *	pScanIndex,
		struct RunHeaderStruct *	runHeader,
		int	iLastScan
	)

void readMSRun	(	RAMPFILE *	pFI,
		struct RunHeaderStruct *	runHeader
	)

InstrumentStruct* getInstrumentStruct ( RAMPFILE * pFI )

void setRampOption ( long option )

int isScanAveraged ( struct ScanHeaderStruct * scanHeader )

int isScanMergedResult ( struct ScanHeaderStruct * scanHeader )

void getScanSpanRange	(	const struct ScanHeaderStruct *	scanHeader,
		int *	startScanNum,
		int *	endScanNum
	)

struct ScanCacheStruct* getScanCache ( int size )

read

void freeScanCache ( struct ScanCacheStruct * cache )

void clearScanCache ( struct ScanCacheStruct * cache )

struct ScanHeaderStruct* readHeaderCached	(	struct ScanCacheStruct *	cache,
		int	seqNum,
		RAMPFILE *	pFI,
		ramp_fileoffset_t	lScanIndex
	)

read

int readMsLevelCached	(	struct ScanCacheStruct *	cache,
		int	seqNum,
		RAMPFILE *	pFI,
		ramp_fileoffset_t	lScanIndex
	)

const RAMPREAL* readPeaksCached	(	struct ScanCacheStruct *	cache,
		int	seqNum,
		RAMPFILE *	pFI,
		ramp_fileoffset_t	lScanIndex
	)

Classes

Macros

Typedefs

Enumerations

Functions

Macro Definition Documentation

Typedef Documentation

Enumeration Type Documentation

Function Documentation