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

FIX path

d6447b6dc19d9ee153f0bbf476e661cfb517cd0b authored over 3 years ago by oliveralka <[email protected]>

Add third-party binaries to PATh

4520b108dbe1eba14b470780df1698326b97956f authored over 3 years ago by oliveralka <[email protected]>

remove OMSSA

52409a331a70dfe3c44e62eaeb062d322215717e authored over 3 years ago by Timo Sachsenberg <[email protected]>

add cd to source dir

f8f179592d2d88ce16818dab8e2a7b1bcb08359c authored over 3 years ago by oliveralka <[email protected]>

upstream branch

9a54c6fabf0166d8f9e632ee84773f28b78d2dfa authored over 3 years ago by oliveralka <[email protected]>

test branch

8a0b1b987550e9d5e0efb7a1ac9b5718c4910f96 authored over 3 years ago by oliveralka <[email protected]>

[FIX] style

dde97c16b640a4fbfff3bdebeb57b5e9eb94125c authored over 3 years ago by oliveralka <[email protected]>

add THIRDPARTY; add search_engine_search_dir

93662787f2f1f780a57ab29cbccb73ba48bae9f5 authored over 3 years ago by oliveralka <[email protected]>

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

e7b25610a27e01f13acf8d243e50f63a0c5eb9f4 authored over 3 years ago by oliveralka <[email protected]>

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

88cf01f95c171b67327d4a3fa3be595eef771b91 authored over 3 years ago by oliveralka <[email protected]>

Update src/openms/include/OpenMS/ANALYSIS/OPENSWATH/TargetedSpectraExtractor.h

Co-authored-by: Oliver Alka <[email protected]>

d8afb55dbb1cf5268f35ce1c01a216ba5546f6e0 authored over 3 years ago by bertrandboudaud <[email protected]>

[REFACTOR] Modify check in addModificationsSequences_ refactor and add a specific test based on PR feedback

915790c0bbb7be81d4bc17174305c92c0fe3fc91 authored over 3 years ago by singjc <[email protected]>

[REFACTOR] Modify check in addModificationsSequences_ refactor and add a specific test based on PR feedback

b4944f054b82dee84312fa80231ee76676a263e8 authored over 3 years ago by singjc <[email protected]>

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

6be63dbbba42293fd66b877546a0d460d5f7d307 authored over 3 years ago by oliveralka <[email protected]>

fix build (#5358)

Co-authored-by: timosachsenberg <[email protected]>

83a4849740629a46df0620df93e79e9ded4db863 authored over 3 years ago by Timo Sachsenberg <[email protected]>

Update IDFilter.pxd (#5356)

* Update IDFilter.pxd

1dd705e44b6f5a1ba2d016f76bfc52a0ea8ff032 authored over 3 years ago by Timo Sachsenberg <[email protected]>

Warn if only one file provided as input to MapAlingerPoseClustering (#5355)

* Warn if only one file provided as input to MapAlingerPoseClustering & MapAlignerIdentification

1324ba9ecf8c23e9bf1f0ec8b9ee8292753e60a5 authored over 3 years ago by Timo Sachsenberg <[email protected]>

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

9d577b52373c082293cf9c2154da29cbab27ec2c authored over 3 years ago by oliveralka <[email protected]>

Merge branch 'develop' into feature/FLASHDeconv

00999bf7cdacb56078730856549416cc1b01270d authored over 3 years ago by JihyungKim <[email protected]>

Merge branch 'feature/TargetedSpectraExtractor_storeSpectra_for_pr' of https://github.com/bertrandboudaud/OpenMS into feature/TargetedSpectraExtractor_storeSpectra_for_pr

d6d6556c67d56ecdc098e4acddc129475ecdb198 authored over 3 years ago by Bertrand Boudaud <[email protected]>

fixed insertion operator for unit test

f3574e3b423051f35d98ddd4e8b7bd9f1ede45d5 authored over 3 years ago by Bertrand Boudaud <[email protected]>

Update src/openms/include/OpenMS/ANALYSIS/OPENSWATH/TargetedSpectraExtractor.h

Co-authored-by: Oliver Alka <[email protected]>

f512ccf6247731d7d12b0c78c73b00c8ae948580 authored over 3 years ago by bertrandboudaud <[email protected]>

Update src/pyOpenMS/pxds/TargetedSpectraExtractor.pxd

Co-authored-by: Oliver Alka <[email protected]>

a5a194e29833c80c77d96bed298c6fc821fbc9eb authored over 3 years ago by bertrandboudaud <[email protected]>

Update src/openms/include/OpenMS/ANALYSIS/OPENSWATH/TargetedSpectraExtractor.h

Co-authored-by: Oliver Alka <[email protected]>

ec752a85c37103d5c06b66757dcef0585aefd76b authored over 3 years ago by bertrandboudaud <[email protected]>

Update src/openms/include/OpenMS/ANALYSIS/OPENSWATH/TargetedSpectraExtractor.h

Co-authored-by: Oliver Alka <[email protected]>

e9bcc7607c85a7b90e1020e188f405c17dcdf82a authored over 3 years ago by bertrandboudaud <[email protected]>

Update src/openms/include/OpenMS/ANALYSIS/OPENSWATH/TargetedSpectraExtractor.h

Co-authored-by: Oliver Alka <[email protected]>

85e7c35c8d3c5bf1b920770a4a2b1bc7ebb5aa18 authored over 3 years ago by bertrandboudaud <[email protected]>

set value to double (trigger ci)

29459b30dccdd6b906b4c993ab19f3f7d1bea4dd authored over 3 years ago by Bertrand Boudaud <[email protected]>

FLASHDeconv beta+

1b4deed181c95df4e527d30613488dcd46e91771 authored over 3 years ago by kyowonjeong <[email protected]>

FLASHDeconv beta+

87ed0f6e48a80180f716bc0b995cc6b3fe767cc1 authored over 3 years ago by kyowonjeong <[email protected]>

fix wrong gitignore; add missing sources.cmake (#5353)

* fix wrong gitignore; add missing sources.cmake

* fix duplicate

* fix linter errors

29187a6b2d0c614437dc7099f5089e9620fa226d authored over 3 years ago by Chris Bielow <[email protected]>

Merge pull request #16 from OpenMS/fix/hendrik_idfile_integration

[FIX] handle multiple file origins in ProtID Runs, transfer IDs with CFeat.Obs.

6e39e1d5eb5d4f2a6e33ecb4cd7e5b22cf414005 authored over 3 years ago by hendrikweisser <[email protected]>

[FIX] Modify check in addModificationsSequences_ fix typo in debug log message

aa08ed92cde35bf0eae62efbe8ae19748222aa3a authored over 3 years ago by Justin Sing <[email protected]>

put back the tests

07c8f9a64f6249ca96282f87b76d01b0700e31fd authored over 3 years ago by Bertrand Boudaud <[email protected]>

commented mergeFeatures, annotateSpectra and storeSpectraTraML tests

5fea7dfffe1df21ae80d77d7b273fc909eeddefe authored over 3 years ago by Bertrand Boudaud <[email protected]>

Merge pull request #5342 from noraw61/seq-align

Replace SeqAn alignment with Needleman Wunsch

da39ff4bafb1b5d84cc8433452416e43a1a4a321 authored over 3 years ago by Chris Bielow <[email protected]>

test reducing template recursion level (#5347)

* test reducing template recursion level

* Also reduce max Tensordimension

a3afd27050a90312571078c8383e52e2a9619b84 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Fixed linux compilation

4a635452de4c982f198ea957fcc9d7678931413f authored over 3 years ago by Bertrand Boudaud <[email protected]>

[FIX] Modify check in addModificationsSequences_ add debug log message

bd1e98cc8fb18fba0e62f0e696aed9f8d95876bc authored over 3 years ago by Justin Sing <[email protected]>

[UPDATE] Update AUTHORS and CHANGELOG files

0aee42d16c4119b8315893232934c9744225c0a3 authored over 3 years ago by Justin Sing <[email protected]>

[FIX] Modify check in addModificationsSequences_ to allow cases of no restriction of specificty (i.e. X) or for specificity of current assessed residue

5090ab126549dbcfb2600139f284c7f2440b2fa2 authored over 3 years ago by Justin Sing <[email protected]>

[FIX] Modify check in addModificationsSequences_ to allow cases of no restriction of specificty (i.e. X) or for specificity of current assessed residue

3e6e9e0b3b29c4460136c73d064b8fa9612dcb0a authored over 3 years ago by Justin Sing <[email protected]>

[FIX] Modify check in addModificationsSequences_ to allow cases of no restriction of specificty (i.e. X) or for specificity of current assessed residue

f5fd24bebed203ec3320cdebbc73f705c00bb0c6 authored over 3 years ago by Justin Sing <[email protected]>

[FIX] Modify check in addModificationsSequences_ to allow cases of no restriction of specificty (i.e. X) or for specificity of current assessed residue

2856fe62157a89e23d33778fddef9b5527652995 authored over 3 years ago by Justin Sing <[email protected]>

Merge branch 'develop' into feature/TargetedSpectraExtractor_storeSpectra_for_pr

d2e7d834f95d7ba7763f519d41695059b807a418 authored over 3 years ago by Bertrand Boudaud <[email protected]>

removed empty line

4067b4d955019b0693c78184ad06fb7c68105c61 authored over 3 years ago by Bertrand Boudaud <[email protected]>

simplifies mergeFeatures

ab7e38eb8db161bca5a6c04caf44a712d7e6b470 authored over 3 years ago by Bertrand Boudaud <[email protected]>

simplified storeSpectraMSP

971906bdac5e2e673ae1d85aa01e8193bbc15e87 authored over 3 years ago by Bertrand Boudaud <[email protected]>

simplified storeSpectraMSP

356f73ce346908f1c68646e7f4b09dd08c38c60d authored over 3 years ago by Bertrand Boudaud <[email protected]>

Fixed codefactor-io reported issues

7a6583747520b420dec0c1822d019fcefb2553f2 authored over 3 years ago by Bertrand Boudaud <[email protected]>

[FIX] Modify check in addModificationsSequences_ to allow cases of no restriction of specificty (i.e. X)

da4e0077d66d7c97a015eb2ab5f7c9000ae4ea71 authored over 3 years ago by Justin Sing <[email protected]>

[FIX] Modify check in addModificationsSequences_ to allow cases of no restriction of specificty (i.e. X)

dba538842108c8fdfcf489492086b2e896272a1f authored over 3 years ago by Justin Sing <[email protected]>

[FIX] Modify check in addModificationsSequences_ to allow cases of no restriction of specificty (i.e. X)

46a3a9a5ecb5ae7929dff091fe9682bc4d57c123 authored over 3 years ago by Justin Sing <[email protected]>

[FIX] Add a check in addModificationsSequences_ to ensure C/N Terminal modification can only be added to correct residue based on modification database

996802609dc502e6deb24e59985d1bf7a394b53b authored over 3 years ago by Justin Sing <[email protected]>

Merge pull request #5326 from vmusch/maxQuant

export MaxQuant Evidence File

dd7a23fee72808a585a964e966d1f50aa7cebe31 authored over 3 years ago by Chris Bielow <[email protected]>

[FEATURE ]Additional features in SimpleSearchEngine (#5325)

* Additional features in SimpleSearchEngine

* add missing constants

* update test file

...

3e70dd0b4bac7982df96d4e8d80477d8e19d8f69 authored over 3 years ago by Timo Sachsenberg <[email protected]>

refactor comment

2d542fc811867668958995612a921464550d8e3a authored over 3 years ago by Vincent Musch <[email protected]>

delete some whitespaces

9da2ca67162c51065898e087819bd9e8e3d38a08 authored over 3 years ago by Vincent Musch <[email protected]>

Merge pull request #5324 from OpenMS/feature/move_mpg

[REFACTOR] moved modified peptide generator to chemistry folder

4142f13999923b5770b06941029890094da0e761 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Merge branch 'develop' into seq-align

507f5f3fc98be4d19fae25fc382daf834a396323 authored over 3 years ago by Timo Sachsenberg <[email protected]>

[UPDATE] to SIRIUS 4.8.2 (#5338)

* [ADD] THIRDPARTY master (SIRIUS 4.8.2); [UPDATE] Version and Tests

d601404fe917d1b2db74c8e1a9a3aab2d20baed7 authored over 3 years ago by Oliver Alka <[email protected]>

Bugfix MSFragger engine (#5344)

* Bugfix MSFragger engine

* Update PosteriorErrorProbabilityModel.cpp

Co-authored-by: Timo...

27a7599acd5d3f90e3c84ce5bc66c348b2d31345 authored over 3 years ago by tillenglert <[email protected]>

default constructor etc

8067f51c5c7df6a8aae0cae6bffe46b133fbc49c authored over 3 years ago by Nora Wild <[email protected]>

Merge pull request #5343 from tillenglert/feature/MSFragger

Include MSFragger engine in the PEPModel

9d6604119ff8f8379e584ba47b02c43b8f23a50e authored over 3 years ago by Julianus Pfeuffer <[email protected]>

PEPModel include MSFragger engine

095a3537d6704b01973693f73a1004cf39807911 authored over 3 years ago by tillenglert <[email protected]>

docu

28bb4570bcd0d4912a7f73fbd422f583e70961f9 authored over 3 years ago by Nora Wild <[email protected]>

Merge branch 'fix/hendrik_idfile_integration' of https://github.com/OpenMS/OpenMS into fix/hendrik_idfile_integration

ab3acd615b733851e44f5faa8fdd69a869ff1680 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Danke für das nette Praktikum

1d1c9f152ce096593bdddfba17869b9d1dfc5059 authored over 3 years ago by Vincent Musch <[email protected]>

Added CHANGELOG entry

a0fff4465f9d0d13235239b78cee55754648f069 authored over 3 years ago by Bertrand Boudaud <[email protected]>

TargetedSpectraExtractor: cleaning

12a8abc022b626077f3c2cb032a502bd38a84835 authored over 3 years ago by Bertrand Boudaud <[email protected]>

updated pxd

902601b4bcec7863c9f4ee0225908afadd12f441 authored over 3 years ago by Bertrand Boudaud <[email protected]>

unit test for searchSpectrum

3b3ccad7140744bfc72c85e72842576c24c238db authored over 3 years ago by Bertrand Boudaud <[email protected]>

unit test for storeSpectraMSP

150c35813556407de0c65d3f139c1974a2d347a8 authored over 3 years ago by Bertrand Boudaud <[email protected]>

more review comments

b8a44e8d471f7d96d732579128975dd2243db125 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Apply suggestions from code review

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

12edbbc767a0ed07f3864837748b64f12efc27fd authored over 3 years ago by Julianus Pfeuffer <[email protected]>

unit test for storeSpectraTraML

a85082b55da198f930d57491babe24f2baa2c16f authored over 3 years ago by Bertrand Boudaud <[email protected]>

unit test for annotateSpectra

55209ba7b7def57b2cae036726b9728714ba5033 authored over 3 years ago by Bertrand Boudaud <[email protected]>

unit test for mergeFeatures

f90881852964c66aaa4491d50a99896eb5cbc19e authored over 3 years ago by Bertrand Boudaud <[email protected]>

changed Test_file_equal to similar

44cad96f21c2725c908fd9fbe84b9119f8a27a31 authored over 3 years ago by Vincent Musch <[email protected]>

Forgot to register ObsMatches. Adapted tests.

54d3da67852c0f573981e1390432a47d3a856cf4 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

MQEvidence_test gefixed vo.2

dff4eb533193da597cdd08aa7f539a65e7fc7d68 authored over 3 years ago by Vincent Musch <[email protected]>

MQEvidence_test gefixed

5e9508dffd72f9ae2dbf90dc2d242bfb7961ca0a authored over 3 years ago by Vincent Musch <[email protected]>

getMatrix()

da20bc32446a895da938321edad3511e7c808c4f authored over 3 years ago by Nora Wild <[email protected]>

Einrückung und Doku folgt noch

e96b2c78bdfac19062e9ac1c889d931885e43fd3 authored over 3 years ago by Nora Wild <[email protected]>

removed useless parameters

c4f6575286c5ac730439dbe13a531d24465bd044 authored over 3 years ago by Bertrand Boudaud <[email protected]>

Implementation of annotateSpectra, searchSpectrum, mergeFeatures, storeSpectraTraML and storeSpectraMSP

271c66a9696e428a544e9217be2d3620dd83bf42 authored over 3 years ago by Bertrand Boudaud <[email protected]>

Merge pull request #5321 from OpenMS/py_nightly_test

[test] pyopenms nightly actions

d175779572395bb7860dfb48ba3aececcbf6eedb authored over 3 years ago by Julianus Pfeuffer <[email protected]>

[Fix] Prevent crash when TOPP tool/util executable cannot be found (#5335)

* [fix] Stop TVToolDiscovery from crashing when a tool/util executable cannot be found

* Upda...

a811da6dacd0a55c5324a0d5bcda4efd1b085a70 authored over 3 years ago by David Voigt <[email protected]>

remove cp code

d5e69a83316fe58e62b82877fac7c630ad53b8d8 authored over 3 years ago by oliveralka <[email protected]>

committing before changing branches

c8e6d5fe548f716dc1b5ae01dd7ee657b7be0309 authored over 3 years ago by Nora Wild <[email protected]>

set matrix

5f55b0b63ce67d31a5a254d89876060daf51a36a authored over 3 years ago by Nora Wild <[email protected]>

QC test fix

70962dde734a76bd001fcb55a065512b0ed85efd authored over 3 years ago by Vincent Musch <[email protected]>

testdateien

a9b0e4baeb03e34e6c0c0f8a78c394ac4fa90314 authored over 3 years ago by Vincent Musch <[email protected]>

clean up, set cmake win,mac,lnx

66167b65ba353e378c59d098fe2dd85fc5034b30 authored over 3 years ago by oliveralka <[email protected]>

leer taste hinzugefügt

c61b95ffd68e84ecf7a820c7b5b439bcdbb1a874 authored over 3 years ago by Vincent Musch <[email protected]>

reset path each iteration

4cc263277052a29ef10f0f7151d4686cbdf34db0 authored over 3 years ago by oliveralka <[email protected]>

check paths

3b1e642150ca1bda70e4250c4c85df2e36cb8269 authored over 3 years ago by oliveralka <[email protected]>

coding style

c47934b17442a7882330a2ecd3287e416ebb2b96 authored over 3 years ago by Vincent Musch <[email protected]>

Overlap removing bug fixed (last mass ignored before) + topFD output per charge in peakgroup

5f92159bb4a7407debbe9c243bd6a77f48a9cc55 authored over 3 years ago by kyowonjeong <[email protected]>

Merge

0e44f3e410c4107a62cbc21f8a9b3d7a8ed4b673 authored over 3 years ago by valentin-noske <[email protected]>

Changed UInt64 to Size

5012981415b6b80eac8f121ca318a66b55d30f4e authored over 3 years ago by valentin-noske <[email protected]>