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

Additional fix macOS script

a57fd9efb5eda5bfa5a73dac9c9099c87967763f authored over 3 years ago by oliveralka <[email protected]>

Update PSI-MS ontology (#5211)

* Add files via upload

* Update psi-ms.obo

* fixed some mzML tests

* fixed some mzML te...

3b29bfcefdbf51047776ade4a6cadfcaea1be893 authored over 3 years ago by Timo Sachsenberg <[email protected]>

add THIRDPARTY branch with fixed start scripts

3a2ad7edec0d64370553a87833a113a1e04b955f authored over 3 years ago by oliveralka <[email protected]>

remove unnecessary files

3ac40ffc1af454f31fb538e357e77419f4d72eee authored over 3 years ago by JeeK <[email protected]>

Merge branch 'develop' into feature/FLASHDeconv

f1e5468bb5903b8e67a0892260a19274c8588560 authored over 3 years ago by JeeK <[email protected]>

FLASHDeconv 2.0 beta release version. Parameter problem fixed

0783a186461c5c575e98ccdb29f7d3ddcfd8b2e8 authored over 3 years ago by kyowonjeong <[email protected]>

revert sirius_binray; use THIRDPARTY fix sirius moved from bin dir

e544af336209fc72b45fb16a3bbdf48b3fd89b05 authored over 3 years ago by oliveralka <[email protected]>

split SIRIUS FINDBINARY statements

a0e9be559ef6a1f89bd11f9281ba42ab15473b0b authored over 3 years ago by oliveralka <[email protected]>

[nop] fixed whitespace

453f9db4ca6e3a4782a831f7bb999aa27cbc1e30 authored over 3 years ago by Samuel Wein <[email protected]>

[feature] enable multi nucleotide specificity in RNases. Multiple successive nucleotides must be separated by , in the CutsAfter and CutsBefore regexes (see mazF as an example)

a1476751a38abf6d1c344cb36a04f665f486bbbe authored over 3 years ago by Samuel Wein <[email protected]>

test jenkins

c0b398da34ec8704f2f20201d19286c2b8b71daa authored over 3 years ago by oliveralka <[email protected]>

QC test files updated

5a36631534d7206bd895c2b0e6272de842cc793a authored over 3 years ago by Tom Waschischeck <[email protected]>

metavalue name for PSMExplainedIonCurrent in Constants::UserParam

e3193cf5a2a22ba8e508ff6882d1bfe222732532 authored over 3 years ago by Tom Waschischeck <[email protected]>

moved getTheoSpectrum to TSG::generateSpectrum

1e96bc1b08d58df904d1d2e528b109553a381db2 authored over 3 years ago by Tom Waschischeck <[email protected]>

fix bug in BPIA and add tie resolution (#5204)

* fix bug in BPIA and add tie resolution

* proper tie resolution for all hits

* add conven...

5cacd520a6e6eb3cf510c63adc53a8b63230473e authored over 3 years ago by Timo Sachsenberg <[email protected]>

Refactoring and Integration of SIRIUS 4.6.0 (#4725)

* [REFACTOR] SiriusAdapter: First adaption to new SIRIUS version

* [ADD] Additional parameter...

664f8361a70948b67caa646d09420bb0c6e58fd9 authored over 3 years ago by Oliver Alka <[email protected]>

no variance for vectors of size < 2

5bf89eafe49b7ec9f193c18a5115b9df84338051 authored over 3 years ago by Tom Waschischeck <[email protected]>

Ci/GitHub actions for OpenMS builds without python and pyopenms (#5174)

* initialize openms yml

* delete pyopenms and python parts from ci yml

* underscore

* r...

0113f970a975c66b2c109021fd40c07e0c06bed6 authored over 3 years ago by Leon-Bichmann <[email protected]>

catching error for peptide hit variance & update QC test files

299e6283ede737b67d6e5f371198dcb536f348a6 authored over 3 years ago by Tom Waschischeck <[email protected]>

DBSuit topp to original state

93e2e72a0f30b65d713a1caf7f2dab1a7e3c1c81 authored over 3 years ago by Tom Waschischeck <[email protected]>

rename PSMCorrectness -> PSMExplainedIonCurrent

a25d79010618a981d0c1e35bc20e26d2ead7cec0 authored over 3 years ago by Tom Waschischeck <[email protected]>

FLASHDeconv 2.0 beta release version. Parameter problem fixed

cc63a8144385d66d5c0f17fffe48c47dec7dd44b authored over 3 years ago by kyowonjeong <[email protected]>

whoops, undoing change from a wrong branch

42a37f2ea6b22e5bf3fcc78aa59d01238a922e17 authored over 3 years ago by Tom Waschischeck <[email protected]>

variance for each peptide hit as meta value

463ee24e69e4e6fa64d06eacd165eab0cbf67498 authored over 3 years ago by Tom Waschischeck <[email protected]>

docu

121db7b9fc55ff996a5202aad0f3de0debcc6593 authored over 3 years ago by Tom Waschischeck <[email protected]>

FLASHDeconv 2.0 beta release version. Parameter problem fixed

847bb13e6d9a2369e75862bb76e9634766933d6d authored over 3 years ago by kyowonjeong <[email protected]>

PSMCorrectness in DBSuit

7052b803d8617cd2c456a518483ae399bb17fce4 authored over 3 years ago by Tom Waschischeck <[email protected]>

fixed variance calculation

8d70988828aa6ef1c763bb75f62579b280739501 authored over 3 years ago by Tom Waschischeck <[email protected]>

Merge branch 'feature/FMEInterface' of https://github.com/Waschi97/OpenMS into feature/FMEInterface

fa5f0e4eb0e4d6dd5398336ba2b54b83d65600b8 authored over 3 years ago by Tom Waschischeck <[email protected]>

updated contrib, merged develop

23e518379b576b1779b0aee8cca404635049f8cc authored over 3 years ago by Tom Waschischeck <[email protected]>

move avg calc, metavalue name in Constants, FMEStatistics renamed

ea7671c27921cbea93658425e337a56803794372 authored over 3 years ago by Tom Waschischeck <[email protected]>

catching ppms = 0

ee4dde358e876e0d1cdb03af2e884faef3bddd94 authored over 3 years ago by Tom Waschischeck <[email protected]>

testing second compute function

2da83b19bca90f4420891a36a75ec622d4962c54 authored over 3 years ago by Tom Waschischeck <[email protected]>

forward declaring

4376a2ae6d8ff3a88160071afae2aaa77ec6779a authored over 3 years ago by Tom Waschischeck <[email protected]>

docu & FME test

b762240a9cc64395c7151cad7fda2705c579a64e authored over 3 years ago by Tom Waschischeck <[email protected]>

docu

5e4b4e429acd50698d0f6d1af587eeffdcc663f2 authored over 3 years ago by Tom Waschischeck <[email protected]>

second compute for vector<PepID> input

96b3c353a055db377620b9c29d91d9d91c673f4b authored over 3 years ago by Tom Waschischeck <[email protected]>

Merge branch 'develop' into feature/FMEInterface

9ac4f7f3275e8383945e37d3716255734b55f40d authored over 3 years ago by Tom Waschischeck <[email protected]>

new lines at end of file

20008cc545f33df45ecc3be619daf962f736466c authored over 3 years ago by Tom Waschischeck <[email protected]>

remove seqan from contrib and place into main tree (#5214)

* remove seqan from contrib and place into main tree

* forgot one file

* remove hidden mac...

8be26bac2ffcbf0454cfe9c875e9b8feb6226a2e authored over 3 years ago by Timo Sachsenberg <[email protected]>

FLASHDeconv 2.0 beta release version. Parameter problem fixed

dcf86a47c182e4944b6bf912564d99e9e54bced7 authored over 3 years ago by kyowonjeong <[email protected]>

FLASHDeconv 2.0 beta release version. Parameter problem fixed

fc675f1d5b0ac1afc406575bf37b399cc6a0acac authored over 3 years ago by kyowonjeong <[email protected]>

update description of colicin_E5

301fa5a1d9171d9696e2bc3142b0b843bfc7f9cf authored over 3 years ago by Samuel Wein <[email protected]>

Merge branch 'RNA_enzymes' of ssh://github.com/poshul/OpenMS into RNA_enzymes

475989d3afa8d844d81881c46ce230a792df278c authored over 3 years ago by Samuel Wein <[email protected]>

[fix] fixed Colicin E5 specificity to match https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1635277/

d0836b433ea26d447e6030eb1db7d748d4448f3f authored over 3 years ago by Samuel Wein <[email protected]>

fixed QC test files

0f70d7c45c6e66b9e31a08cefe08864b12de8f61 authored over 3 years ago by Tom Waschischeck <[email protected]>

Merge pull request #5212 from oliveralka/fix/scan_number_handling

ADD: SpectrumLookup - MS_Agilent_MassHunter_nativeID_format

1e1ada2950496570f1491b2dde78f09d173f4615 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Merge pull request #5210 from OpenMS/doc/install_win

Update install-win.doxygen

1cec5cac2aaf35ff43240fd7f95b5bf3c617eeb2 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

PSMCorrectness docu

fb18872f4fcc07bc6dfe75059c20ae4506154b66 authored over 3 years ago by Tom Waschischeck <[email protected]>

FLASHDeconv 2.0 beta release version

d58cdf5088ff9e30ca693a0742ab1682bd16c138 authored over 3 years ago by kyowonjeong <[email protected]>

FLASHDeconv 2.0 beta release version

c43c06fd39f66a55a53bc685fe956fde8d4fafb8 authored over 3 years ago by kyowonjeong <[email protected]>

docu in FME test

b5bf423974bd4143bd7985056017329862ee0f4a authored over 3 years ago by Tom Waschischeck <[email protected]>

test for PSMCorrectness and additional catches

488469ca2a7309c66d94820e07b1bbf740aa2113 authored over 3 years ago by Tom Waschischeck <[email protected]>

Update install-win.doxygen

13de1fe8affec6741dfcb716487c21134b7556f8 authored over 3 years ago by Timo Sachsenberg <[email protected]>

ADD: MS_Agilent_MassHunter_nativeID_format

d748f79aa633439e120aa7fc03585f9b79d72a30 authored over 3 years ago by oliveralka <[email protected]>

Update install-win.doxygen

10be6244c245a55f35a635287f556dca8c75b172 authored over 3 years ago by Timo Sachsenberg <[email protected]>

use default move; try fix string operations

187671864a87284d3a3bd3847f968f1e940f4df5 authored over 3 years ago by oliveralka <[email protected]>

Update install-win.doxygen

36aec54ca71fea3b295cae31c86d81c607365782 authored over 3 years ago by Timo Sachsenberg <[email protected]>

Update install-win.doxygen

ab32f49f729ef0c267d1580b147a6e606e302bac authored over 3 years ago by Timo Sachsenberg <[email protected]>

add move constructor; fix cleanup FeatureMap; fix charge parsing PeptideRef inFFMID

9bbb414b0d5055a563bd76ad09e18e293b03e44e authored over 3 years ago by oliveralka <[email protected]>

FIX: MapAlignerIdentification

6c839ea6af0127c0927b63e03b610e676894687c authored over 3 years ago by oliveralka <[email protected]>

FIX: FeatureFinderIdentification

f4b306d4c91f93025e10b150963a27ab5445154d authored over 3 years ago by oliveralka <[email protected]>

Implementation of MSPGenericFile::store (#5206)

* Implementation of MSPGenericFile::store

* Added Python bindings

* fixed Redundant blank ...

f113da71517230f5a751c32bac6acb58b4187992 authored over 3 years ago by bertrandboudaud <[email protected]>

QScore has mass error feature..

15761dd785edf2f3bd0c32a162078c3ce2049ea9 authored over 3 years ago by kyowonjeong <[email protected]>

QScore has mass error feature..

7960d6913b841167b98e92ef705967311fd789b2 authored over 3 years ago by kyowonjeong <[email protected]>

FIX: IDMerger; IDFileConverter

942fe96d4509eee2dba8b3f7bd38f6c1855ca8fb authored over 3 years ago by oliveralka <[email protected]>

[feature] added more RNA digestion enzymes

dca042eb2fd6c9457c4ed838ccc0287b428787fd authored over 3 years ago by Samuel Wein <[email protected]>

QScore has mass error feature..

5ca54f199339e6787491b2819ecc3f1474494148 authored over 3 years ago by kyowonjeong <[email protected]>

[FIX] fix compile errors and warnings

d4c98736a9d75a77e7a9f88bfccb3132558963bf authored over 3 years ago by Hendrik Weisser <[email protected]>

[DOC] DefaultParamHandler: mention that 'defaultsToParam_()' calls 'updateMembers_()'

252d194e8bc1e18948da94a65be5d6c3ca3cfe6f authored over 3 years ago by Hendrik Weisser <[email protected]>

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

de477d9b46ee2270f252341d179670214efcc57c authored over 3 years ago by Hendrik Weisser <[email protected]>

Merge pull request #5199 from oliveralka/fix/AMS_mass_error

FIX: mass error calculation multiplier AMS

64c260cb84228ad14dfd30a842cd09854d7d6ef2 authored over 3 years ago by FabianAicheler <[email protected]>

Merge pull request #5203 from OpenMS/oliveralka-patch-1

pyopenms_dev_to_latest

67909b5efa4875efa86f99bba429538a2191bbc2 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

pyopenms_dev_to_latest

34feac65dab4f0ea9062ef84bf8633e9cc94268d authored over 3 years ago by Oliver Alka <[email protected]>

[feature] added more RNA digestion enzymes

20ee767bccc8ce74087a795e5f9b5dc5dc92a393 authored over 3 years ago by Samuel Wein <[email protected]>

change type to UInt

48ca2d3be77ed733a7466eea629f514bc01928e2 authored over 3 years ago by oliveralka <[email protected]>

FIX: Check mol_multiplier zero

fe675b32c9e3bb46fa0226f4070ec9d3b7608500 authored over 3 years ago by oliveralka <[email protected]>

FIX: mass error calcualtion multiplier AMS

e10e86f6bccb089bbe422885891d64b179ab1283 authored over 3 years ago by oliveralka <[email protected]>

fix minor warning

38285354b7ad9e08747ca6c9f92ef660c59245dd authored over 3 years ago by Timo Sachsenberg <[email protected]>

fix default operators (#5197)

d46c1a24fa9a86fd6f9505fba9049047bd290dbb authored over 3 years ago by Timo Sachsenberg <[email protected]>

fix

3a7f680bce4aa22fe27f976d26463041f894a8cb authored over 3 years ago by Timo Sachsenberg <[email protected]>

QScore has mass error feature..

cef0822f6c8cd2e3b7875be28ef3e98594b0a9ad authored over 3 years ago by kyowonjeong <[email protected]>

QScore has mass error feature..

bf1dfd60b6e081e22d190df3defd593c543acb01 authored over 3 years ago by kyowonjeong <[email protected]>

QScore has mass error feature..

b41bec806e727e5dae3f3e9047a840c443aa92af authored over 3 years ago by kyowonjeong <[email protected]>

more gcc 9 fixes (#5196)

c792811b710747a76ee3678d7a1e23fc85e8a313 authored over 3 years ago by Timo Sachsenberg <[email protected]>

FLASHDeconv ver 2.0 beta before test...

924262ea62e9ea6784ed00cfb0f9deb9ba9df4e3 authored over 3 years ago by kyowonjeong <[email protected]>

QC topp test outputs adapted

93836f33eb5e7008898ed248d8150c9be2656f9a authored over 3 years ago by Tom Waschischeck <[email protected]>

ToleranceUnit moved to QCBase, added PSMCorr to QC topp

caec5d33338b0d45137efabc9359c2d77822ed76 authored over 3 years ago by Tom Waschischeck <[email protected]>

new metric PSMCorrectness

fa34ecff80573d2f390e25e33403bfde44625730 authored over 3 years ago by Tom Waschischeck <[email protected]>

made getTheoSpec static member function of FME

db74f0aa18e6be8c38e943484406d78a97f147c4 authored over 3 years ago by Tom Waschischeck <[email protected]>

Merge pull request #5193 from OpenMS/oliveralka-patch-1

Revert changes due to cython 0.29.2

3eee4b79bf42aa618574aaa1caf19ec5c2a5a5df authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Revert changes due to cython 0.29.2

Autowrap fix See uweschmitt/autowrap#99
Should work with python 3.6, cython 0.29.22 and autowra...

e26093fa6272044d4ae569100b76f0de1cc5760a authored over 3 years ago by Oliver Alka <[email protected]>

Compile error fixes OpenMS/OpenMS#5186 (#5187)

* Fixes OpenMS/OpenMS#5186

* some more fixes

* fix

* Fix Cython to last version before ...

c481073b25351a9c524ea7c605b136942e4b46d9 authored over 3 years ago by Timo Sachsenberg <[email protected]>

FLASHDeconv ver 2.0 beta before test...

82ea5acb62e5fdb74356bb70b5e0feb50d14ea2c authored over 3 years ago by kyowonjeong <[email protected]>

FLASHDeconv ver 2.0 beta before test...

c435f8fbd3257c1e0c549d464cc78718978d8b69 authored over 3 years ago by kyowonjeong <[email protected]>

Merge pull request #5190 from cbielow/mgf_spec_annotation

more robust SearchEngineBase

988b883dff70c58a3301ea7d31b2c5c4eae78af8 authored over 3 years ago by Chris Bielow <[email protected]>

CI fixes

cefab27fc867733a8f439deb2c302136c79552b3 authored over 3 years ago by bielow <[email protected]>

amend

c8eb488ca2bc989e1ed6f3422a184d072db36ff1 authored over 3 years ago by bielow <[email protected]>

make SearchEngineBase robust against empty MS2 spectra

5614a8854186522197fc501fe6e281e845193a53 authored over 3 years ago by bielow <[email protected]>

Merge branch 'develop' into feature/FMEInterface

26da52e07e2608de4c4957d75c8071069df2c54b authored over 3 years ago by Tom Waschischeck <[email protected]>