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Add precursor-mz match score #156

Merged
merged 28 commits into from
Nov 26, 2020
Merged

Add precursor-mz match score #156

merged 28 commits into from
Nov 26, 2020

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florian-huber
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@florian-huber florian-huber commented Nov 24, 2020 •
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  • fixed minor bug in add_parent_mass() : now finds precursor_mz from either pepmass or precursor_mz field.
  • added PrecursorMzMatch which is analog to ParentMassMatch (renamed here from ParentmassMatch).
  • include option to match based on relative ppm tolerance

@florian-huber florian-huber marked this pull request as ready for review November 25, 2020 14:00
@florian-huber florian-huber marked this pull request as draft November 25, 2020 14:12
@florian-huber florian-huber marked this pull request as ready for review November 25, 2020 15:01
sverhoeven
sverhoeven requested changes Nov 26, 2020
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The IntersectMz class uses capitailized Mz, but ParentmassMatch and PrecursormzMatch classes uses lower case mass/mz resp.. This seems inconsistent to me. Either rename to Intersectmz or rename to ParentMassMatch + PrecursorMzMatch.

matchms/similarity/PrecursormzMatch.py Outdated Show resolved Hide resolved
matchms/similarity/__init__.py Outdated Show resolved Hide resolved
matchms/similarity/PrecursormzMatch.py Outdated Show resolved Hide resolved
matchms/filtering/add_parent_mass.py Show resolved Hide resolved
@florian-huber
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The IntersectMz class uses capitailized Mz, but ParentmassMatch and PrecursormzMatch classes uses lower case mass/mz resp.. This seems inconsistent to me. Either rename to Intersectmz or rename to ParentMassMatch + PrecursorMzMatch.

Switched to ParentMassMatch and PrecursorMzMatch.

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sonarcloud bot commented Nov 26, 2020

Kudos, SonarCloud Quality Gate passed!

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 0 Code Smells

100.0% 100.0% Coverage
0.0% 0.0% Duplication

@florian-huber
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Thanks a lot for the review Stefan!

@florian-huber florian-huber merged commit 4c1350b into master Nov 26, 2020
@florian-huber florian-huber deleted the add_precursormz_match branch November 26, 2020 11:45
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@sverhoeven sverhoeven sverhoeven approved these changes

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