Public Member Functions
	TimsDataHandle (const std::string &tims_data_dir)
	Open TimsTOF dataset. More...

	~TimsDataHandle ()
	Close and deallocate the TimsTOF data handle (destructor).

TimsFrame &	get_frame (uint32_t frame_no)
	Access a single frame by its ID.

const std::unordered_map< uint32_t, TimsFrame > &	get_frame_descs ()
	Access a dictionary containing all the frames from this dataset, keyed by ID.

size_t	no_peaks_total () const
	Returns the total number of MS peaks in this handle.

size_t	no_peaks_in_frames (const uint32_t indexes[], size_t no_indexes)
	Count the peaks in a subset of frames. More...

size_t	no_peaks_in_frames (const std::vector< uint32_t > &indexes)
	Count the peaks in a subset of frames. More...

size_t	no_peaks_in_slice (uint32_t start, uint32_t end, uint32_t step)
	Count the peaks in a subset of frames, selected by a slice. More...

uint32_t	min_frame_id () const
	Access the lowest id of a valid frame from this dataset.

uint32_t	max_frame_id () const
	Access the highest id of a valid frame from this dataset.

bool	has_frame (uint32_t frame_id) const
	Check whether a frame with provided ID exists in the dataset.

void	extract_frames (const uint32_t indexes, size_t no_indexes, uint32_t result)
	This function is deprecated, and left deliberately undocumented; do not use.

void	extract_frames (const std::vector< uint32_t > &indexes, uint32_t *result)
	This function is deprecated, and left deliberately undocumented; do not use.

void	extract_frames_slice (uint32_t start, uint32_t end, uint32_t step, uint32_t *result)
	This function is deprecated, and left deliberately undocumented; do not use.

void	extract_frames (const uint32_t indexes, size_t no_indexes, uint32_t frame_ids, uint32_t scan_ids, uint32_t tofs, uint32_t intensities, double mzs, double inv_ion_mobilities, double retention_times)
	This function is deprecated, and left deliberately undocumented; do not use.

void	extract_frames (const std::vector< uint32_t > &indexes, uint32_t frame_ids, uint32_t scan_ids, uint32_t tofs, uint32_t intensities, double mzs, double inv_ion_mobilities, double *retention_times)
	Extract a subset of frames, selected by indexes, filling provided buffers with MS peak data. More...

void	extract_frames_slice (uint32_t start, uint32_t end, uint32_t step, uint32_t frame_ids, uint32_t scan_ids, uint32_t tofs, uint32_t intensities, double mzs, double inv_ion_mobilities, double *retention_times)
	Extract a subset of frames, selected by a slice, filling provided buffers with MS peak data. More...

void	allocate_buffers ()

void	ensure_buffers_allocated ()

void	free_buffers ()

size_t	max_peaks_in_frame ()
	Return the maximal number of peaks in the biggest frame in this dataset.

size_t	expose_frame (size_t frame_id)
	Expermental API - use discouraged.

const std::unique_ptr< uint32_t[]> &	scan_ids_buffer ()
	Expermental API - use discouraged.

const std::unique_ptr< uint32_t[]> &	tofs_buffer ()
	Expermental API - use discouraged.

const std::unique_ptr< uint32_t[]> &	intensities_buffer ()
	Expermental API - use discouraged.

Friends
class	BrukerTof2MzConverter

class	BrukerScan2InvIonMobilityConverter

class	TimsFrame

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

Constructor & Destructor Documentation

◆ TimsDataHandle()

TimsDataHandle::TimsDataHandle ( const std::string & tims_data_dir )

Open TimsTOF dataset.

Open a TimsTOF dataset (read-only access supported). Return a handle using which Tims data may be retrieved.

Parameters

Path	to the dataset (typically a *.d directory, containing a analysis.tdf and analysis.tdf_bin files).

Member Function Documentation

◆ extract_frames()

void TimsDataHandle::extract_frames	(	const std::vector< uint32_t > &	indexes,
		uint32_t *	frame_ids,
		uint32_t *	scan_ids,
		uint32_t *	tofs,
		uint32_t *	intensities,
		double *	mzs,
		double *	inv_ion_mobilities,
		double *	retention_times
	)

inline

Extract a subset of frames, selected by indexes, filling provided buffers with MS peak data.

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 able to hold at least no_peaks_in_frames(indexes) values.

Parameters

indexes	Set of indexes of frames for which data is to be obtained.
frame_ids	The IDs of frames containing the associated peaks.
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).

◆ extract_frames_slice()

void TimsDataHandle::extract_frames_slice	(	uint32_t	start,
		uint32_t	end,
		uint32_t	step,
		uint32_t *	frame_ids,
		uint32_t *	scan_ids,
		uint32_t *	tofs,
		uint32_t *	intensities,
		double *	mzs,
		double *	inv_ion_mobilities,
		double *	retention_times
	)

Extract a subset of frames, selected by a slice, filling provided buffers with MS peak data.

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 able to hold at least no_peaks_in_slice(start, stop, end) values.

IDs of the returned frames come from start:stop:step slice.

Parameters

indexes	Start of the slice.
end	End of the slice.
step	Step of the slice.
frame_ids	The IDs of frames containing the associated peaks.
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).

◆ no_peaks_in_frames() [1/2]

size_t TimsDataHandle::no_peaks_in_frames ( const std::vector< uint32_t > & indexes )

inline

Count the peaks in a subset of frames.

Returns the total number of peaks in the frames with given indexes.

Parameters

indexes Indexes of frames to count

◆ no_peaks_in_frames() [2/2]

size_t TimsDataHandle::no_peaks_in_frames	(	const uint32_t	indexes[],
		size_t	no_indexes
	)

Count the peaks in a subset of frames.

Returns the total number of peaks in the frames with given indexes.

Parameters

indexes	Indexes of frames to count
no_indexes	Number of indexes (and length of the indexes[] table).

◆ no_peaks_in_slice()

size_t TimsDataHandle::no_peaks_in_slice	(	uint32_t	start,
		uint32_t	end,
		uint32_t	step
	)

Count the peaks in a subset of frames, selected by a slice.

Returns the total number of peaks in frames with IDs contained in the start:stop:end slice

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

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

Public Member Functions

Friends

Constructor & Destructor Documentation

◆ TimsDataHandle()

Member Function Documentation

◆ extract_frames()

◆ extract_frames_slice()

◆ no_peaks_in_frames() [1/2]

◆ no_peaks_in_frames() [2/2]

◆ no_peaks_in_slice()