Feature/DIMS_HMDBparts_bymz #77
Open
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
rernst
reviewed
Jul 18, 2025
Comment on lines
31
to
41
| 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 | ||
| } | ||
| } |
There was a problem hiding this comment.
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
}There was a problem hiding this comment.
Good suggestion; I implemented the modification.
rernst
approved these changes
Sep 30, 2025
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
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.