SwathWindowLoader Class Reference

#include <OpenMS/ANALYSIS/OPENSWATH/SwathWindowLoader.h>

Static Public Member Functions
static void	annotateSwathMapsFromFile (const std::string &filename, std::vector< OpenSwath::SwathMap > &swath_maps, bool do_sort, bool force)
	Overwrite the lower/upper precursor boundaries of swath_maps with the windows read from filename.
static void	readSwathWindows (const std::string &filename, std::vector< double > &swath_prec_lower, std::vector< double > &swath_prec_upper)

Detailed Description

@brief Reads a SWATH-window definition file and annotates SwathMaps with it.

The file format is tab- or space-delimited with two columns per row:

window_lower window_upper
400 425
425 450
...

The first line is treated as a header only if its first token cannot
be parsed as a number; otherwise the first line is read as data. The
reader does not require any specific header text and accepts files
without a header row.

@ingroup FileIO

Member Function Documentation

annotateSwathMapsFromFile()

static void annotateSwathMapsFromFile ( const std::string &  filename, std::vector< OpenSwath::SwathMap > &  swath_maps, bool  do_sort, bool  force  )

static

Overwrite the lower/upper precursor boundaries of swath_maps with the windows read from filename.

Walks swath_maps in order, skipping entries whose ms1 flag is set, and replaces each remaining entry's lower and upper with the corresponding row of the SWATH-window file. The number of non-MS1 entries in swath_maps must equal the number of rows in filename.

Note

The non-MS1 entries in swath_maps and the rows of the file are matched by position, so both must be in the same order (usually low-to-high m/z). When do_sort is true, swath_maps is sorted by its upper field before matching.

Parameters

[in]	filename	Path of the SWATH-window file.
[in,out]	swath_maps	SWATH maps to annotate; their lower / upper fields are overwritten in place (and the vector may be reordered when do_sort is true).
[in]	do_sort	If true, sort swath_maps by ascending upper before matching against the file.
[in]	force	If true, a file window that extends beyond the corresponding map's data boundaries is logged as an error and applied anyway; if false the same situation throws.

Exceptions

Exception::IllegalArgument	if the number of non-MS1 entries in swath_maps does not equal the number of rows in filename, or if a file window extends beyond the corresponding map's lower / upper and force is false.
Exception::InvalidValue	propagated from readSwathWindows when a row has lower >= upper.

readSwathWindows()

static void readSwathWindows ( const std::string &  filename, std::vector< double > &  swath_prec_lower, std::vector< double > &  swath_prec_upper  )

static

  @brief Read a SWATH-window definition file into two parallel vectors.

  The file format is two whitespace-separated columns
  (@c window_lower @c window_upper) per row:

window_lower window_upper
400 425
425 450
...

  A header row is detected automatically by trying to parse the first
  token of the first line as a number; if parsing fails, the line is
  treated as a header and skipped, otherwise the first line is read as
  data. No specific header text is required.

  @param[in]  filename         Path of the SWATH-window file. A
                               missing or unreadable file is not
                               reported as an exception; the output
                               vectors are left empty.
  @param[out] swath_prec_lower Lower boundary of each window, in file
                               order.
  @param[out] swath_prec_upper Upper boundary of each window, in file
                               order; same length as
                               @p swath_prec_lower.

  @throws Exception::InvalidValue if a row has @c lower >= @c upper.