#1 - Update Mzlib to 1.0.547 (Omics Update) #2334
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…into mzlibUpdate
Codecov ReportAttention:
Additional details and impacted files@@ Coverage Diff @@
## master #2334 +/- ##
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- Coverage 92.68% 92.65% -0.03%
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Files 136 137 +1
Lines 21302 21274 -28
Branches 2924 2928 +4
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- Hits 19744 19712 -32
+ Misses 1086 1083 -3
- Partials 472 479 +7
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nbollis
commented
Jan 19, 2024
| @@ -258,9 +260,19 @@ private void AddInteriorTerminalModsToPrecursorIndex(List<int>[] precursorIndex, | |||
| foreach (KeyValuePair<int, List<Modification>> relevantDatabaseMod in databaseAnnotatedMods) | |||
| { | |||
| int fragmentNumber = relevantDatabaseMod.Key; | |||
| Product fragmentAtIndex = fragmentMasses.Where(x => x.FragmentNumber == fragmentNumber).FirstOrDefault(); | |||
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In the previous version, default Proudct would produce an a1 product with a mass of 0.0
nbollis
changed the title
Alexander-Sol
approved these changes
Jan 30, 2024
elaboy
approved these changes
Feb 11, 2024
trishorts
reviewed
Feb 12, 2024
| @@ -162,7 +163,7 @@ public static List<MatchedFragmentIon> MatchFragmentIons(Ms2ScanWithSpecificMass | |||
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| if (commonParameters.ProductMassTolerance.Within(scan.TheScan.MassSpectrum.XArray[closestMzIndex], theoreticalFragmentMz)) | |||
| { | |||
| matchedFragmentIons.Add(new MatchedFragmentIon(ref product, theoreticalFragmentMz, scan.TheScan.MassSpectrum.YArray[closestMzIndex], 1)); | |||
| matchedFragmentIons.Add(new MatchedFragmentIon(product, theoreticalFragmentMz, scan.TheScan.MassSpectrum.YArray[closestMzIndex], 1)); | |||
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explain the elimination of the ref keyword
trishorts
approved these changes
Feb 12, 2024
* reverted filtering method for psms passed to FlashLFQ * refactor glycospsmwriter and split from xlwriter * fix unit tests * rename N and O glyco test classes * refactor is patially working * files written to correct directory * now with glyco protein parsimony and writing all quantified proteins * nglycoBugged * n glyco output is correct now i think * yo * fix unit tests * fix more unit tests * dont need glyco stuff in writexl anymore * n glyco individual file unit test --------- Co-authored-by: Alex <AlexSolivais@gmail.com> Co-authored-by: MICHAEL SHORTREED <mrshortreed@wisc.edu>
nbollis
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nbollis
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A vast majority of the files changed is just changing using statements at the top. The rest are noted below
IndexingEngine.cs
-- Default product no longer exists, instread changed to code to check for null
Tweaked TomlConfig to ignore new fields in DigestionParams, enabling old toml's to be read in and written
Changed many property names to match new Interfaces
MatchedFragmentIon constructor changed to exclude the ref on first parameter. This change was made due to the Product class changing from a struct, which is passed by value, to a class, which is automatically passed by reference.