TimsFrame Class Reference

Public Member Functions
void	print () const
	Prints out to stdout a short summary of this frame.
size_t	data_size_bytes () const
	Return the size of back buffer needed to store raw TIMS data.
void	decompress (char *decompression_buffer=nullptr, ZSTD_DCtx *decomp_ctx=nullptr)
	Precalculates and memorizes all the information contained within this frame. More...
void	close ()
	Releases the storage taken by decompress() method, without destroying the frame. Will be called in destructor.
void	save_to_buffs (uint32_t *frame_ids, uint32_t *scan_ids, uint32_t *tofs, uint32_t *intensities, double *mzs, double *inv_ion_mobilities, double *retention_times, ZSTD_DCtx *decomp_ctx=nullptr)
	Retrieve the MS peak data held by the frame. More...
void	save_to_matrix_buffer (uint32_t *buf, ZSTD_DCtx *decomp_ctx=nullptr)
	This function is deprecated and intentionally undocumented; do not use.

Public Attributes
const uint32_t	id
	ID of the frame.
const uint32_t	num_scans
	Number of scans this frame contains.
const uint32_t	num_peaks
	Number of peaks this frame contains (summed across all scans)
const uint32_t	msms_type
	The MS/MS type of this frame.

Friends
class	TimsDataHandle
int	tims_sql_callback (void *out, int cols, char **row, char **colnames)

Member Function Documentation

decompress()

void TimsFrame::decompress	(	char *	decompression_buffer = nullptr,
		ZSTD_DCtx *	decomp_ctx = nullptr
	)

Precalculates and memorizes all the information contained within this frame.

This method extracts all the data associated with the frame and stores it in memory. Without it, the data (mz values, intensities, etc.) will be re-calculated every time they are accessed. After this method is called, they will be just retrieved from RAM.

This is a purely performance-enchancing method - it is recommended to call it if repeated access to the frame is necessary, before the access, and to call close() afterward.

Parameters

decompression_buffer	optional, a pre-allocated buffer which will be used for the decompression. If null, a pre-allocated buffer from parent TimsDataFrame will be used, making this method non-thread-safe. If TimsFrame is to be used in multithreaded context, a thread-local buffer must be passed here (or a mutex must be used). The buffer must be at least data_size_bytes() large.
decomp_ctx	optonal, a decompression buffer to be used by the method. If null, a ctx from parent handle will be used, possibly making this non-thread-safe. To ensure thread safety a thread-local context must be passed here.

save_to_buffs()

void TimsFrame::save_to_buffs	(	uint32_t *	frame_ids,
		uint32_t *	scan_ids,
		uint32_t *	tofs,
		uint32_t *	intensities,
		double *	mzs,
		double *	inv_ion_mobilities,
		double *	retention_times,
		ZSTD_DCtx *	decomp_ctx = nullptr
	)

Retrieve the MS peak data held by the frame.

The data is saved to the passed buffers - if some of this data is unnecessary, then nullptr may be passed as the corresponding pointer. The buffers are passed and returned by columns. Each row corresponds to one MS peak. Each buffer must be albe to hold at least this->num_peaks values.

Parameters

frame_ids	The repeated ID of this frame.
scan_ids	IDs of the scan a peak comes from.
tofs	Times of Flight of peaks.
intensities	Signal intensities of peaks.
mzs	M/Z ratios of peaks.
inv_ion_mobilities	Inverse ion mobilities (in seconds).
retention_times	Retention times (in seconds).

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The documentation for this class was generated from the following file:

• /home/mist/svn/git/opentims/opentims++/opentims.h