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rernst
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Jul 18, 2025
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One minor comment, let me know if you would like to update the code.
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| while (segment_end < max_mz) { | ||
| if (segment_start < 100) { | ||
| mz_segments <- c(mz_segments, segment_start) | ||
| segment_start <- segment_start + 5 | ||
| segment_end <- segment_end + 5 | ||
| } else { | ||
| mz_segments <- c(mz_segments, segment_start) | ||
| segment_start <- segment_start + 10 | ||
| segment_end <- segment_end + 10 | ||
| } | ||
| } |
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To separate some logic (prepare for tests and easier to maintain) I would write this like:
while (segment_end < max_mz) {
if (segment_start < 100) {
segment_size = 5
} else {
segment_size = 10
}
mz_segments <- c(mz_segments, segment_start)
segment_start <- segment_start + segment_size
segment_end <- segment_end + segment_size
}
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Good suggestion; I implemented the modification.
rernst
approved these changes
Sep 30, 2025
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HMDB database (including adducts and isotopes) is divided into parts to enable parallel processing. In the old setup, each part contained 20000 lines; in the new set-up, each part contains a certain mass range. For m/z < 100, smaller ranges are used because of the higher abundance of peaks at lower masses.
There are no modifications in the DIMS repo necessary for this change.