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emzed.utils

NeighbourSearch

Grid-based neighbor lookup for small tolerance windows in numeric data.

find_matches(index, row)

Yield indices of rows that match row within the configured tolerances.

Parameters:

Name Type Description Default
index

index of the query row, which is excluded from the result.

 required
row

row vector to compare against the stored data.

 required

compute_spectra_alignments(spectra, mz_tolerance)

takes a list of spectra and groups peaks given mz_tolerance. it returns a list of lists. every inner list specifies the alignment of one input spectrum to its follower in the list. One assignment is a list of tuples, where the first entry is a peak index from the first list, the second entry is the index of a peak from the second spectrum.

For example:

if you run this method with a list or tuple of three spectra (s0, s1, s2) the
return values will be [align_0_to_1, align_1_to_2]

an alignment is a list [(i0, j0), (i1, j1),  ...]

so that s0.peaks[i0, :] is assigned to s1.peaks[j0, :] and so on.

mock_emzed_gui()

Temporarily inject a dummy emzed_gui module for tests.

temp_file_path()

Yield a temporary file path and clean up the file and directory afterwards.