github.com/OpenMS/OpenMS commits | Ecosyste.ms: OpenCollective

Move intensity and rank calculation in all MI initialization to an outside function

780d619097d5c2180b363482c53d8455ce8a95bb authored almost 3 years ago by khue.nm <[email protected]>

Merge branch 'develop' of https://github.com/OpenMS/OpenMS into layer_refactor

6f408b3e2dbdcc42e0def9d8b97d06284727b30c authored almost 3 years ago by bielow <[email protected]>

use LayerBase to get everything running again...

59f83cae094527d42e48ad4944f6526548b17ac2 authored almost 3 years ago by bielow <[email protected]>

[INTERNAL] moved QtSql includes from OMSFile header to cpp file

63119ca61879f8db6a5d73b533f68522a564c40f authored almost 3 years ago by Hendrik Weisser <[email protected]>

Merge branch 'develop' of https://github.com/OpenMS/OpenMS into idfile-integration

4f339cc809391b9ecf7e6a4ee719c8e66b4dee18 authored almost 3 years ago by Hendrik Weisser <[email protected]>

apply clang-tidy modernize (#5670)

* add overwrite

* modernize raw literals

* modernize

* modernize-use-equals-delete,mode...

118387761a38222a84b557d3e891043bf6705214 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

adding mock layers for Peak, Chrom, Feature, Consensus, Ident

eb0f1b5cb9349b4d5cc7c2e51a6b7528b95bd701 authored almost 3 years ago by bielow <[email protected]>

A Chromatogram Data class (not populated yet)

55f6e74915663364a3aef9409a910ef0ea5ff3c8 authored almost 3 years ago by bielow <[email protected]>

simplify ctor

f0e034c23b5b15b9c73be8fae2ed8672851cfcc4 authored almost 3 years ago by bielow <[email protected]>

copy old LayerData and rename to LayerDataBase

ca9b2bc866ec3c05214c2d1906d70efb7340f919 authored almost 3 years ago by bielow <[email protected]>

Update .gitpod.Dockerfile

1b4fc7f55693e486dd777d6a390560298002c3b7 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

Merge branch 'develop' of https://github.com/cbielow/OpenMS into develop

560de0e162528f849e53ba902837a0ffad5b017f authored almost 3 years ago by bielow <[email protected]>

fix TOPPView checkbox state export (#5667)

3078952a87c60c84a409115e7b7977b0fee36499 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

Update TVToolDiscovery.cpp

e36d19d336003b79933749cb91f26cc2c4222c61 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

ffid annotate spectra file path already in algorithm (#5663)

* ffid annotate spectra file path already in algorithm

* Update FeatureFinderIdentificationAl...

af402dc88be99d59e5b9df67f7f03e9917e04f8f authored almost 3 years ago by Timo Sachsenberg <[email protected]>

add backlink to MS run in FFmetaboIdent (#5662)

* add backlink to MS run

* Update FeatureFinderAlgorithmMetaboIdent.cpp

* Update src/openm...

41a1538022f92c1af545fc8c269ee95d186c39f8 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

add python3-pip to use run-clang-tidy (#5664)

cf26d61e4e9ca935d5bede8d5b60202f2141b5b5 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

[FIX] add parameter to disable output of warnings in GaussFilter (#5661)

* [FIX] add parameter to disable output of warnings in GaussFilter

* Update GaussFilter.cpp

52bad9629676091081fdeed0cd73b73cb06e8786 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

FLASHIda log file read message updated

956362ac47d9f4cd9a099d428b3ff2745405eba5 authored almost 3 years ago by kyowonjeong <[email protected]>

Merge branch 'mrmscoring_test_micontrast' into swath_mimatrix

b64dddb933c4c658c8d8fc78b5048c19414fed14 authored almost 3 years ago by khue.nm <[email protected]>

[FIX] Decoding ontology in PeptideIdentification df conversion (#5659)

* fix tuple creation

* add pep evidence export

* update test

* add pep evidence concate...

7ae58db9e1e0718266379b4e12fabf30ce7c14d4 authored almost 3 years ago by axelwalter <[email protected]>

Removed ~ half of MIPrecursorCombinedMatrix calc

cd915eeeeb4af94a1b9d8fd4f50662c068b35c09 authored almost 3 years ago by khue.nm <[email protected]>

Merge branch 'swath4' of https://github.com/vmusch/openms into swath_mimatrix

2c484d804d2a2893dd30855bf5d194786cb17c8b authored almost 3 years ago by khue.nm <[email protected]>

Precompute rank for all MI matrix initialization

35261cbc0062a4b48572a0213aced527cca1abd6 authored almost 3 years ago by khue.nm <[email protected]>

Changed test for MIContrastMatrix to take 2 diff. ids vec

c9c9eca9cd39ded076c7b62ee750e539328a91ef authored almost 3 years ago by khue.nm <[email protected]>

Feature/pep evidences df (#5656)

* fix tuple creation

* add pep evidence export

* update test

* add pep evidence concate...

75dee2b1fabb6a2081276613bd9e0011dab9d0ab authored almost 3 years ago by axelwalter <[email protected]>

little fixes

5330cc681c59e4b8171511d3f2bf010bf85b295f authored almost 3 years ago by Vincent Musch <[email protected]>

FLASHIda default parameters updated

f9de15225b086a3eaf46daae9e6c7378fe7bbe76 authored almost 3 years ago by kyowonjeong <[email protected]>

Noise peak in isotope envelope = max peak intensity between signal isotopes

077c473dd732b47ec60bad7151c08abdefd01810 authored almost 3 years ago by kyowonjeong <[email protected]>

Update Scoring.cpp

4e0e64c9b072862ca18bff7613fdb960a6a8ec11 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #5624 from OpenMS/feature/percolator_warn_missing_features_in_psm

Update PercolatorInfile.cpp

3a598d6e9cd176f705cc355c78b518adf7ab5bb6 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

reduce output to summary of warnings

8475ccb23b89e70ebf5557fb47a4cfd816beeebc authored almost 3 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #5654 from OpenMS/emf_test_and_ffmid_move

Emf test and ffmid move

16826c0c5e24832bf671f716ddf13ba87633a789 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

Update src/openms/include/OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinderIdentificationAlgorithm.h

5306c675c382d8d5f0667f5190bb539c8ddf5f73 authored almost 3 years ago by Hannes Roest <[email protected]>

delete old function

3e5924721c6a697a84251b6501c133598034f3dc authored almost 3 years ago by Vincent Musch <[email protected]>

new computeRank

2aa9ff749bf8a28d6b973053f3c53cb1df146947 authored almost 3 years ago by Vincent Musch <[email protected]>

ammend

6a5df993ead0715775b80e26693757baf8c0acff authored almost 3 years ago by Timo Sachsenberg <[email protected]>

add test and move assignment to FFAID

42a4fb1dc89856dc2898dae8fe2e15357a12458c authored almost 3 years ago by Timo Sachsenberg <[email protected]>

Merge branch 'develop' of https://github.com/OpenMS/OpenMS into swath4

88fb258f9d33880056e755b9a5466e99aa4b529c authored almost 3 years ago by Vincent Musch <[email protected]>

aktualisiern

dc65a58b28e923950f880097890bd6eec298aa28 authored almost 3 years ago by Vincent Musch <[email protected]>

fix check for same feature set

891cc65b81772997db0af2abaa4727dccc42aa8d authored almost 3 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #5652 from OpenMS/feature/fix_ffmid

[fix] Elution peak detection: rare segfault if no features were detected (e.g., in blanks)

646d49398c518e4517e412d2c08ea44fd947bc64 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

fix rare exception if no features were detected (e.g., in blanks)

bc265d49eb19909bd644d27af6c96fbdda48c8f2 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #5651 from OpenMS/feature/ffmid_MS1_only

only detect features on MS1 (don't mix levels)

7933346ab452c06c427ce81df39cfd218de4423a authored almost 3 years ago by Timo Sachsenberg <[email protected]>

only detect features on MS1 (don't mix levels)

7f2003bf06d0a63226c2a0774075a59855d3a093 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

code simplification

1d52bacb7fa6690d08a35d6e360c27e309d2a840 authored almost 3 years ago by bielow <[email protected]>

Merge pull request #5648 from OpenMS/fix/disable_SN_warning

the amount of SN warnings in FFMid are just too much for jupyter note…

7d3fd3afb2af5105875ffb5c687ff834f08dc39e authored almost 3 years ago by Timo Sachsenberg <[email protected]>

the amount of SN warnings in FFMid are just too much for jupyter notebooks

eb486abd0594d67b46408ff6b72209d8c4959ca8 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #5635 from vmusch/swath

move MRMScoring to OpenMS lib

8fb42eca245b70bc79818a4f37e6243f67225c1a authored almost 3 years ago by Chris Bielow <[email protected]>

Apply suggestions from code review

Co-authored-by: Timo Sachsenberg <[email protected]>

a6a18fff0683ef119650610cfa98345d01cda3d6 authored almost 3 years ago by Chris Bielow <[email protected]>

Update src/openswathalgo/source/OPENSWATHALGO/ALGO/Scoring.cpp

Co-authored-by: Timo Sachsenberg <[email protected]>

7871176a111a3db0a9992b4b2b49f38eeee66a94 authored almost 3 years ago by Chris Bielow <[email protected]>

Noise peak in isotope envelope = max peak intensity between signal isotopes

cdf0767f4f19ef54b104ab1774b8afffb91a0f9c authored almost 3 years ago by kyowonjeong <[email protected]>

Merge pull request #5647 from hroest/feature/pphires_wrap

[PYOPENMS] wrap check_spectrum_type parameter for pphires

7dc444e43a81508e19b5c4c8d9eb726aec1f9ae5 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

Added getMostAbundantDelta in FLASHDeconvHelperStructs.cpp

1feabac4e42c91fbc3a683230d6216d71ad65c71 authored almost 3 years ago by kyowonjeong <[email protected]>

Merge pull request #5626 from hroest/feature/separate_interfaces

Feature/separate interfaces

186893847d17382e0463f0ba355022031c7b4d5b authored almost 3 years ago by Timo Sachsenberg <[email protected]>

[PYOPENMS] wrap check_spectrum_type parameter for pphires

dfe3e123645f733492e8d5922451dec16e6ee428 authored almost 3 years ago by Hannes Roest <[email protected]>

Merge pull request #5644 from cbielow/perf_mini

Perf mini

c7ae2a94fbc7fc94156ef11ae45ecbda9802c77e authored almost 3 years ago by Timo Sachsenberg <[email protected]>

Merge branch 'develop' of https://github.com/OpenMS/OpenMS into perf_mini

53b2d9a1d4aa957c5d82f9fba8662bde3e285e15 authored almost 3 years ago by bielow <[email protected]>

mini example for performance opt. This yields 2x speed...

0229023e12db3b4f4ab90992dda51737e9d9a7a3 authored almost 3 years ago by bielow <[email protected]>

mrmscoring.pxd

7f082257dc35b33efff96dff58ba2937c31f0011 authored almost 3 years ago by Vincent Musch <[email protected]>

matrix

6d061979eeb05392bffc0102cabc84947bc263b9 authored almost 3 years ago by Vincent Musch <[email protected]>

[FIX] Some CodeFactor issues

7f3bb03fac54d2b36460be11ab80a2bb64ee8d5b authored almost 3 years ago by oliveralka <[email protected]>

Merge remote-tracking branch 'upstream/develop' into idfile-integration

f0ddbbefe7ad70ed5c00721e91826a18bbcd5baf authored almost 3 years ago by oliveralka <[email protected]>

[FIX] PLFQ tests

b33e6e4e5231df9f70202b2f035224ed66067c3c authored almost 3 years ago by oliveralka <[email protected]>

Update CHANGELOG

b9744c6b2cae4517fc7c547fc198f75272f140ab authored almost 3 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #5633 from emilpaulitz/IsoDistrApprox

Isotopic distribution approximation

cceb3d3f27a8603dab7c73609f72905f944027b9 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

change include in pyOpenMS

b225dc3952112ed8376710fa5d251ebb40b8ffd9 authored almost 3 years ago by Vincent Musch <[email protected]>

[FIX] merge issue FeatureMap

1ee4138397609e3ac78bd500112039d0c5be3884 authored almost 3 years ago by oliveralka <[email protected]>

removed uint8_t to fix python binding problem

4477673dd95e8f699ea02aead1ee1631d7f29163 authored almost 3 years ago by emilpaulitz <[email protected]>

Merge branch 'IsoDistrApprox' of https://github.com/emilpaulitz/OpenMS into IsoDistrApprox

a564aff6cab537784c1b07eaf45f20a3146a1160 authored almost 3 years ago by emilpaulitz <[email protected]>

Update python bindings

be7cd82920c55910f04cca034b9ae2bed59c65ca authored almost 3 years ago by emilpaulitz <[email protected]>

fix double_t

f5c6e24240beb1b3aeb33b1b0a2dd00399be20cc authored almost 3 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #5622 from axelwalter/feature/pandas-dataframes

add pandas df conversion

84d15f108c0c15d7f192b11169c9205b9de4129e authored almost 3 years ago by Julianus Pfeuffer <[email protected]>

bug fix for windows

c855df9a829c6d5954c648b56ed384a7fdb0a223 authored almost 3 years ago by Vincent Musch <[email protected]>

skip unidentified in main iteration

8ecb4aaa84670aa805d2635eaf0e7bbd4433c2f1 authored almost 3 years ago by Julianus Pfeuffer <[email protected]>

Merge branch 'develop' into idfile-integration

96308276c15b8d4475ae1f326f0e82413dac07bc authored almost 3 years ago by Oliver Alka <[email protected]>

add TODO for filtering PeptideHits in main iteration

8377fc73edca549ff24e76cacb742da0cb0d189f authored almost 3 years ago by axelwalter <[email protected]>

fix missing values for peptide identification meta values

c5e7cfba64fdcf9a14a317de3d1c5df75f0dd980 authored almost 3 years ago by axelwalter <[email protected]>

delete old mrmscoring from the cmake file

3786b0d6ce9619bd007458cb2a0169d5bec4d081 authored almost 3 years ago by Vincent Musch <[email protected]>

Update CoarseIsotopePatternGenerator.cpp

6f50d8e59ebe60541f029ebe8c5b47dadb96896c authored almost 3 years ago by Timo Sachsenberg <[email protected]>

Update CoarseIsotopePatternGenerator.h

e0ff15e371bd945b8f2b0d82098300f8e11672ca authored almost 3 years ago by Timo Sachsenberg <[email protected]>

Per charge SNR use per charge cosine

2b6e1447a52f053987bafe0a960a2e0a1e4fe948 authored almost 3 years ago by kyowonjeong <[email protected]>

Updated description

a73d9a9332e88866d84037533dca1d2995338c63 authored almost 3 years ago by emilpaulitz <[email protected]>

Fixed faculty overflow issue

By including the running faculty into the double of result, early overflow is not a problem anym...

2c17611d0ec228e685ec2166ef2d069e5b14424d authored almost 3 years ago by emilpaulitz <[email protected]>

Updated types and description

made num_peaks unsigned, approximateIntensities now returns vector<double>, used the OpenMS type...

eab432b84d21df2b9d2e3984b1bcdb63021a1c42 authored almost 3 years ago by emilpaulitz <[email protected]>

Update to m/z calculation

Detailed description and added charge parameter

47182e417847683092ded1b07d03c7112290ff0d authored almost 3 years ago by emilpaulitz <[email protected]>

Fix tool scan on strong machines (#5640)

Should also go into 2.7.1

9a4225030e6a25631d42c83989ed14199773e732 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

MRMScoring nach OpenMS

2f17e30db1079c10ce4d4b5c01ed9997a23b3aa6 authored almost 3 years ago by Vincent Musch <[email protected]>

add test for PeptideIdentifications to df

72eb3f739e06676637d9982e83c833534ff50773 authored almost 3 years ago by axelwalter <[email protected]>

missing charge values to pandas.NA

6bab1a6eaa70c4c643f4eff767f66aea79414644 authored almost 3 years ago by axelwalter <[email protected]>

little fix

d3ee09708dc7e190c24e85672f53879d4511a772 authored almost 3 years ago by Vincent Musch <[email protected]>

delete whitespaces

8ec36273d089516af89c877e358addcb1684c001 authored almost 3 years ago by Vincent Musch <[email protected]>

Skip non existent wheels

55329c87dff14893ec0d278cdf7a2899ddbea9ff authored almost 3 years ago by Julianus Pfeuffer <[email protected]>

new computeRanks, only in MIcombinedMatrix

d25139f690f214900fbf0dbc580ba19607c5bdb4 authored almost 3 years ago by Vincent Musch <[email protected]>

Merge branch 'feature/pandas-dataframes' of https://github.com/axelwalter/OpenMS into feature/pandas-dataframes

21a6c04f5b04607b3c77bd7c3d7db34ad3fc32d1 authored almost 3 years ago by axelwalter <[email protected]>

Merge remote-tracking branch 'origin' into feature/pandas-dataframes

050ecb9792be013d563642f1c3bcaf4d3e6135be authored almost 3 years ago by axelwalter <[email protected]>

add MSExperiment().get_df() test

e5001e0ee1c961276975b7883aee90baee4e173b authored almost 3 years ago by axelwalter <[email protected]>

[DOC] update documentation

ec458fbc965e944e316860ee8083373f509e7771 authored almost 3 years ago by Julianus Pfeuffer <[email protected]>

fix python msvc requirements

d35e49f6da53d0a84fca4faa90b9bcd531987387 authored almost 3 years ago by Julianus Pfeuffer <[email protected]>

Merge branch 'feature/pandas-dataframes' of https://github.com/axelwalter/OpenMS into feature/pandas-dataframes

631d179dcc2a8c159c266ab18af61d1bc89533ff authored almost 3 years ago by axelwalter <[email protected]>