APTFileIO.h File Reference

#include "common/basics.h"

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Enumerations
enum	posErrors {   POS_ALLOC_FAIL =1, POS_OPEN_FAIL, POS_EMPTY_FAIL, POS_SIZE_MODULUS_ERR,   POS_READ_FAIL, POS_NAN_LOAD_ERROR, POS_INF_LOAD_ERROR, POS_ABORT_FAIL,   POS_ERR_FINAL }
	Errors that can be encountered when openning pos files. More...

Functions
unsigned int	GenericLoadFloatFile (unsigned int inputnumcols, unsigned int outputnumcols, const unsigned int index[], vector< IonHit > &posIons, const char *posFile, unsigned int &progress, ATOMIC_BOOL &wantAbort)
	Load a pos file directly into a single ion list. More...
unsigned int	LimitLoadPosFile (unsigned int inputnumcols, unsigned int outputnumcols, const unsigned int index[], vector< IonHit > &posIons, const char *posFile, size_t limitCount, unsigned int &progress, ATOMIC_BOOL &wantAbort, bool strongRandom)
unsigned int	limitLoadTextFile (unsigned int numColsTotal, vector< vector< float > > &data, const char *posFile, const char *deliminator, const size_t limitCount, unsigned int &progress, ATOMIC_BOOL &wantAbort, bool strongRandom)
unsigned int	loadTapsimBinFile (const char *filename, unsigned int &progress, ATOMIC_BOOL &wantAbort, vector< IonHit > &posions)
unsigned int	LoadATOFile (const char *fileName, vector< IonHit > &ions, unsigned int &progressm, ATOMIC_BOOL &wantAbort, unsigned int forceEndian=0)

Variables
const char *	POS_ERR_STRINGS []
const char *	ION_TEXT_ERR_STRINGS []
const char *	LAWATAP_ATO_ERR_STRINGS []
const char *	TEXT_LOAD_ERR_STRINGS []
const char *	TAPSIM_ERR_STRINGS []

Enumeration Type Documentation

posErrors

enum posErrors

Errors that can be encountered when openning pos files.

Enumerator
POS_ALLOC_FAIL
POS_OPEN_FAIL
POS_EMPTY_FAIL
POS_SIZE_MODULUS_ERR
POS_READ_FAIL
POS_NAN_LOAD_ERROR
POS_INF_LOAD_ERROR
POS_ABORT_FAIL
POS_ERR_FINAL

Function Documentation

GenericLoadFloatFile()

unsigned int GenericLoadFloatFile	(	unsigned int	inputnumcols,
		unsigned int	outputnumcols,
		const unsigned int	index[],
		vector< IonHit > &	posIons,
		const char *	posFile,
		unsigned int &	progress,
		ATOMIC_BOOL &	wantAbort
	)

Load a pos file directly into a single ion list.

Pos files are fixed record size files, with data stored as 4byte big endian floating point. (IEEE 574?). Data is stored as x,y,z,mass/charge. Load a pos file into a T of IonHits

References ASSERT, IonHit::DATA_SIZE, IonHit::hasInf(), IonHit::hasNaN(), POS_ABORT_FAIL, POS_ALLOC_FAIL, POS_EMPTY_FAIL, POS_INF_LOAD_ERROR, POS_NAN_LOAD_ERROR, POS_OPEN_FAIL, POS_READ_FAIL, POS_SIZE_MODULUS_ERR, PROGRESS_REDUCE, and IonHit::setHit().

Referenced by LimitLoadPosFile(), ExternalProgramFilter::refresh(), DataLoadFilter::refresh(), and SpatialAnalysisFilter::refresh().

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LimitLoadPosFile()

unsigned int LimitLoadPosFile	(	unsigned int	inputnumcols,
		unsigned int	outputnumcols,
		const unsigned int	index[],
		vector< IonHit > &	posIons,
		const char *	posFile,
		size_t	limitCount,
		unsigned int &	progress,
		ATOMIC_BOOL &	wantAbort,
		bool	strongRandom
	)

References ASSERT, ATOMIC_BOOL, GenericLoadFloatFile(), getFilesize(), RandNumGen::initTimer(), LimitLoadPosFile(), POS_ABORT_FAIL, POS_ALLOC_FAIL, POS_EMPTY_FAIL, POS_INF_LOAD_ERROR, POS_NAN_LOAD_ERROR, POS_OPEN_FAIL, POS_READ_FAIL, POS_SIZE_MODULUS_ERR, PROGRESS_REDUCE, and randomDigitSelection().

Referenced by LimitLoadPosFile(), and DataLoadFilter::refresh().

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limitLoadTextFile()

unsigned int limitLoadTextFile	(	unsigned int	numColsTotal,
		vector< vector< float > > &	data,
		const char *	posFile,
		const char *	deliminator,
		const size_t	limitCount,
		unsigned int &	progress,
		ATOMIC_BOOL &	wantAbort,
		bool	strongRandom
	)

References ASSERT, RandNumGen::initTimer(), loadTextData(), POS_ABORT_FAIL, randomDigitSelection(), splitStrsRef(), stream_cast(), stripZeroEntries(), TEXT_ERR_ALLOC_FAIL, TEXT_ERR_FORMAT, TEXT_ERR_ONLY_HEADER, TEXT_ERR_OPEN, TEXT_ERR_READ_CONTENTS, and TEXT_ERR_REOPEN.

Referenced by DataLoadFilter::refresh().

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LoadATOFile()

unsigned int LoadATOFile	(	const char *	fileName,
		vector< IonHit > &	ions,
		unsigned int &	progressm,
		ATOMIC_BOOL &	wantAbort,
		unsigned int	forceEndian = 0
	)

References ASSERT, floatSwapBytes(), RandNumGen::initTimer(), LAWATAP_ATO_EMPTY_FAIL, LAWATAP_ATO_MEM_ERR, LAWATAP_ATO_OPEN_FAIL, LAWATAP_ATO_SIZE_ERR, LAWATAP_ATO_VERSIONCHECK_ERR, and randomDigitSelection().

Referenced by loadTapsimBinFile(), and DataLoadFilter::refresh().

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loadTapsimBinFile()

unsigned int loadTapsimBinFile	(	const char *	filename,
		unsigned int &	progress,
		ATOMIC_BOOL &	wantAbort,
		vector< IonHit > &	posions
	)

References ASSERT, ATOMIC_BOOL, floatSwapBytes(), genRandomFilename(), LoadATOFile(), IonHit::makePosData(), rmFile(), IonHit::setMassToCharge(), IonHit::setPos(), shortSwapBytes(), splitStrsRef(), stream_cast(), TAPSIM_ERR_ABORTED, TAPSIM_ERR_FILE_FORMAT_FAIL, TAPSIM_ERR_FILE_OPEN_FAIL, TEST, and WARN.

Referenced by DataLoadFilter::refresh().

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Variable Documentation

ION_TEXT_ERR_STRINGS

const char* ION_TEXT_ERR_STRINGS[]

LAWATAP_ATO_ERR_STRINGS

const char* LAWATAP_ATO_ERR_STRINGS[]

Referenced by DataLoadFilter::refresh().

POS_ERR_STRINGS

const char* POS_ERR_STRINGS[]

Referenced by DataLoadFilter::refresh().

TAPSIM_ERR_STRINGS

const char* TAPSIM_ERR_STRINGS[]

Referenced by DataLoadFilter::refresh().

TEXT_LOAD_ERR_STRINGS

const char* TEXT_LOAD_ERR_STRINGS[]

Referenced by DataLoadFilter::refresh().