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[WIP] Peak alignment#786

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RayMSMS wants to merge 65 commits intosmith-chem-wisc:mastersmith-chem-wisc/mzLib:masterfrom RayMSMS:PeakAlignmentRayMSMS/mzLib:PeakAlignmentCopy head branch name to clipboard

+1,719-262

Commits

Commits on Oct 23, 2023

• Predict Retention Time function added

  Alexander-Sol

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  4fe3343

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• breaking up mbr function, cont'd

  Alexander-Sol

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  742ac30

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Commits on Oct 31, 2023

• Decoy search is working

  Alexander-Sol

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Commits on Jan 30, 2024

• Merge branch 'master' into MbrRefactor

  Alexander-Sol

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  dc4493e

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• Removed decoy toggle from GetIsotopicEnvelopes

  Alexander-Sol

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  31ff285

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• About to start MbrScorer refactor

  Alexander-Sol

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  dda57b6

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• Refactor of MBR is working succesfully

  Alexander-Sol

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  ca9928a

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• Deleted unused code

  Alexander-Sol

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Commits on Jan 31, 2024

• got those decoys decoying naw mean

  Alexander-Sol

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  48239cc

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• refactore MBR to use concurrent dictionaries

  Alexander-Sol

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Commits on Feb 2, 2024

• Test method with output

  Alexander-Sol

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  1da0e13

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• Deleted unused fields and references to PearsonCorrelation in isotopicEnvelope class and CheckEnvelope method

  Alexander-Sol

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  03efb21

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• Deleted unused using statements in FlashLFQ engine

  Alexander-Sol

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  5eb2637

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• Commented + removed unused variables for PredicteRetentionTime method

  Alexander-Sol

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  1aeeb96

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• Added comments, removed unused using statements

  Alexander-Sol

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  112ae41

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• Merge branch 'master' into MbrRefactor

  Alexander-Sol

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  7703b75

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• Deleted unused variables

  Alexander-Sol

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  e3fe1e2

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• Merge branch 'MbrRefactor' of https://github.com/Alexander-Sol/mzLib into MbrRefactor

  Alexander-Sol

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  8993a25

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• fixed merge conflicts

  Alexander-Sol

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  7d9b6b1

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• Tests are still passing, but I'm about to break things

  Alexander-Sol

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  40d5f45

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• Edited scoring method

  Alexander-Sol

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  4f3fc9d

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Commits on Feb 6, 2024

• Umm, edited scoring, increased ppm tolerance, changed minimum rt width for variance and random rt transfers

  Alexander-Sol

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Commits on Feb 7, 2024

• Did some weird filtering of donor files that should probably be reverted

  Alexander-Sol

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  5d5c1ee

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Commits on Feb 12, 2024

• Peak Organism fix

  Alexander-Sol

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  4a9149c

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Commits on Feb 13, 2024

• fixed merge conflicts

  Alexander-Sol

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  d8a7a0c

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Commits on Feb 15, 2024

• Basically works, QValue still underestimates

  Alexander-Sol

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  61fac1c

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Commits on Feb 19, 2024

• Minor changes to peakfinding

  Alexander-Sol

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  363c457

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Commits on Feb 29, 2024

• MSMS double checking

  Alexander-Sol

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  c4720ba

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• Removed msms double checking

  Alexander-Sol

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Commits on Mar 1, 2024

• Add check for MBR/MSMS peak collision

  Alexander-Sol

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  e595cd4

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Commits on Mar 7, 2024

• Changed peak decoy selection method

  Alexander-Sol

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  c88e32e

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• Optional PeptidesForMbr argument added, not covered in previous commit messages. Not actually this commit

  Alexander-Sol

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  b6dbc8c

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• 5.3.2.4 - Changed randomRT selection method

  Alexander-Sol

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• 5.3.2.5 - Minimum rtWindowWidth = 30 seconds

  Alexander-Sol

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  6d96aa7

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• Actually updated nuget

  Alexander-Sol

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  8bb7cbe

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• 5.3.2.6 - Fixed decoy search. 2.4 and 2.5 are junk

  Alexander-Sol

  committed
  42e922c

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Commits on Mar 8, 2024

• Changed MBR RT prediction method

  Alexander-Sol

  committed
  12f3f34

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• Fixed bug in rtPrediction

  Alexander-Sol

  committed
  175e0a7

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Commits on Mar 9, 2024

• Changed decoy search method and fixed issues with decoy rt scoring

  Alexander-Sol

  committed
  bcf8d7c

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• small changes to double check procedure

  Alexander-Sol

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  768b921

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• Fixed merge conflicts

  Alexander-Sol

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  b324efe

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• Finished Merging in MbrFdr - mzLib 5341

  Alexander-Sol

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  9d13eb2

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• minor

  Alexander-Sol

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  b147e3b

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• Actually changed nuspec

  Alexander-Sol

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• Increased Rt Range

  Alexander-Sol

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  5ee1d21

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• Increased doublecheck count to 2500. mzLib 5343

  Alexander-Sol

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  7e32625

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• reduced window slightly. mzLib 5344

  Alexander-Sol

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  3ceb447

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Commits on Apr 18, 2024

• amended rt scoring distribution in mbr scorer

  Alexander-Sol

  committed
  1d5422f

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• Mostly deleted stuff that will be introduced in a different commit

  Alexander-Sol

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  5cbb1c5

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• Fixed all tests but one

  Alexander-Sol

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  c5249aa

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• Fixed final test

  Alexander-Sol

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  95f9281

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• minor

  Alexander-Sol

  committed
  e6294a9

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• fixed merge conflicts

  Alexander-Sol

  committed
  1fe4112

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Commits on Apr 23, 2024

• Merge branch 'master' into MbrPart1

  Alexander-Sol

  authored
  3d8a6e9

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• Increased number of anchor peptides

  Alexander-Sol

  committed
  afae344

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• Merge branch 'MbrPart1' of https://github.com/Alexander-Sol/mzLib into MbrPart1

  Alexander-Sol

  committed
  871c832

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• Changed anchors, updated test

  Alexander-Sol

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  6d44e98

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• nuspec revert

  Alexander-Sol

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  f08cba1

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Commits on Apr 24, 2024

• Addressed MRS comments, minor refactor so that scores are calculated in the ChromPeak class

  Alexander-Sol

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• Merge branch 'master' into MbrPart1

  Alexander-Sol

  committed
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• minor

  Alexander-Sol

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Commits on Jun 12, 2024

• first commit

  RayMSMS

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• example commit

  RayMSMS

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Commits on Jul 15, 2024

• update 7/15/2024

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Commits on Sep 24, 2024

• update the flashLFQ

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  RayMSMS

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