github.com/OpenMS/OpenMS-1 commits | Ecosyste.ms: OpenCollective

[DOC] documented public interface of OMSFileLoad and OMSFileStore

2c10e8adee3aac3e6f09b0173c803b1783b231cc authored almost 3 years ago by Hendrik Weisser <[email protected]>

Merge branch 'develop' into layer_refactor

5c76cdee77bbd9e82a9c0775277fe2fd018d2e21 authored almost 3 years ago by Chris Bielow <[email protected]>

clang-tidy add const to methods and replace size() == 0 with empty (#5673)

* add const to methods and replace size() == 0 with empty

* fixed small issues introduced by ...

a1055245fc89f4e9f0b97fa06e58323bad30e2ed authored almost 3 years ago by Timo Sachsenberg <[email protected]>

[FIX] deal with missing filename when converting seeds to IdentificationData for ProteomicsLFQ (fixes failing ProteomicsLFQ_3 test)

1dff915f4738703ed3e56605dad5f8de104b4e39 authored almost 3 years ago by Hendrik Weisser <[email protected]>

[INTERNAL] guard against empty spectrum file names when converting ProteinIdentification to IdentificationData

ca2d93e8caee80613030016242c7092f442d534f authored almost 3 years ago by Hendrik Weisser <[email protected]>

[NOP] indentation fix

1af307e12932ee73948844c3af97fb5d463b5aa4 authored almost 3 years ago by Hendrik Weisser <[email protected]>

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

5da9ba49018497c4987131f4f07fd2afc6a24b06 authored almost 3 years ago by bielow <[email protected]>

add suggestions from review

f5d1cb1eb26db14bddb1c9b78c95b0325b798a83 authored almost 3 years ago by bielow <[email protected]>

[COMMENT] added explanatory comments in IdentificationData and ObservationMatch

c09cf7995ccfb636dec4f9082913eed4b4016044 authored almost 3 years ago by Hendrik Weisser <[email protected]>

[DOC] improved doc. for IdentificationData::mergeScoredProcessingResults_

f4d3a90f75657366f4b515c551318fb1eccf4705 authored almost 3 years ago by Hendrik Weisser <[email protected]>

[DOC] add thread-safety warning for IdentificationData

a86da88af0d2d3b3f33f35720bcdac3bdce01ced authored almost 3 years ago by Hendrik Weisser <[email protected]>

[COMMENT] added explanatory comments for IdentificationData references in features; style improvements

d4b224cf38897b8c51541ef8343c70feeba58d14 authored almost 3 years ago by Hendrik Weisser <[email protected]>

[DOC] improved doc. of BaseFeature::updateIDReferences and Feature::updateAllIDReferences

420d41f4076e2fe804dd46f64cff0b9f64afe522 authored almost 3 years ago by Hendrik Weisser <[email protected]>

[DOC] improved doc. of IdentificationData-related functions in IDFilter and MapAlignmentAlgorithmIdentification

57c185a2d91085d6797028e279a8e630355ac54e authored almost 3 years ago by Hendrik Weisser <[email protected]>

Decumentation in average function in SpectraMerger.h added.

5941be2b82ea4396ba4f6b98e494245fc652b404 authored almost 3 years ago by KyowonJeong <[email protected]>

Bug in average funtion in SpectraMerger.h fixed.

5bf926ee7ebe6c1f01e5ae256a3c094469cf4935 authored almost 3 years ago by KyowonJeong <[email protected]>

1. FLASHDeconv documentation added.

2. SpectraMerger run for all ms levels (for gaussian and tophat) if ms_level is set to be 0.

6530d5bfe5f2d456f1620558914b7aa862360d3d authored almost 3 years ago by KyowonJeong <[email protected]>

bug fixing according to the codefactor comments

d52b3ce3d2b6e40c709d056c9ec0378fbdb0d236 authored almost 3 years ago by JeeH-K <[email protected]>

[INTERNAL] moved OMSFile helper classes (OMSFileStore, OMSFileLoad) to separate .cpp/.h files

98656f05c5be92a6be822e65f6c6f450f37e4a83 authored almost 3 years ago by Hendrik Weisser <[email protected]>

[INTERNAL] use 'FeatureFinderIdentificationAlgorithm::run' overload for legacy ID formats where appropriate

ed4a34d0b6fd2437753d9454b0fb51a741d8f499 authored almost 3 years ago by Hendrik Weisser <[email protected]>

[API] added 'FeatureFinderIdentificationAlgorithm::run' overload for legacy ID formats (for ProteomicsLFQ and pyOpenMS)

104fa9e6d7279ada428808275f4d980760f8a6a1 authored almost 3 years ago by Hendrik Weisser <[email protected]>

[FIX] add move constructor and assignment operator (#5686)

3c4a078ad4687677393c138d4acb91bb444a7c7b authored almost 3 years ago by Hannes Roest <[email protected]>

add FileFilter option to overwrite precursor charge (#5684)

* add FileFilter option to overwrite precursor charge

* fix some typos

* nop

6987211e42360201b2a094bc98b9405c6fe387d4 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

Remove max_peak and max_peak_sec matrix from XCorr

3522c6a9355c8ea90b2c8846248ad0234ff418c8 authored almost 3 years ago by khue.nm <[email protected]>

move templates to cpp file to reduce Seqan exposure (#5516)

* move templates to cpp file to reduce Seqan exposure

* add dll export

3b6c0eedfd33dee76d9e9f8819700ce28312fc3c authored almost 3 years ago by Timo Sachsenberg <[email protected]>

Update src/openms_gui/source/VISUAL/APPLICATIONS/TOPPViewBase.cpp

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

96acbf1c0f1cf26f62dd06cbf37e90743316c466 authored almost 3 years ago by Chris Bielow <[email protected]>

[SUBMODULE] add pyopenms-extra as submodule (#5665)

fb12c851f0703a9db540c99741fdf1a49baeb3b9 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

add noexcept to move and move assignment ctors

03951abd4fc6f7c00268312fb735c9f3cd060545 authored almost 3 years ago by bielow <[email protected]>

workaround for rare segfault in elution peak detection (#5677)

b8d69c74622167d1b4799ebcbe55188b5a4e4b07 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

clang-tidy performance-inefficient-vector/string-operation (#5676)

* performance-inefficient-vector-operation

* Apply suggestions from code review

Co-authore...

b391237bb8e4f5a3dc79ab0cdd663bbfa663c47b authored almost 3 years ago by Timo Sachsenberg <[email protected]>

fix return to reference (#5679)

8594c2ad50b1e3d3263235ea592ed02049dbcb11 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

[FEATURE] peptide export from feature map for pyOpenMS (#5672)

* Add assigned peptide export from FeatureMap

- collect PeptideHits from each feature
- add ...

66b3e7d422d4154758c797cf8b6cd8cf35190390 authored almost 3 years ago by axelwalter <[email protected]>

fix bug introduced earlier

245a4693be7d9e7260000bf76ccb39f4897406bb authored almost 3 years ago by bielow <[email protected]>

move peptide member of IdentLayer to derived class

705eaf21d7c46a4aa5eabe0855d20efceafd1f97 authored almost 3 years ago by bielow <[email protected]>

fixes a race condition when multiple threads call newFile() and the reference gets invalidated (happened in TOPPView, when requesting a temporary file for INI's) (#5674)

12ec65593063bebd148d07f34545cb6a1e9be8ef authored almost 3 years ago by Chris Bielow <[email protected]>

Fix seg fault

a74bb0d40d9628880c91ec59514521a523b960a1 authored almost 3 years ago by khue.nm <[email protected]>

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]>