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

minor cleanup

6ba65375fad6b64f597372e65b6a141209d68ab3 authored almost 4 years ago by Chris Bielow <[email protected]>

[refactor] rename spectr* components to plot* to reflect that they a… (#5046)

* rename spectra components to plotwidget/canvas to reflect that they are not restricted to spec...

973674372b1e97e542acdb6d59295f492b3c051c authored almost 4 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #5049 from cbielow/OSW_datamodel

Refactor TableViews in TOPPView

cc1c7025ffceabff34ff17172637fa3c5752b45f authored almost 4 years ago by Chris Bielow <[email protected]>

address comments and compiler warnings

85f8ac9cfb8416c0c7e4958493f0e03024acd83b authored almost 4 years ago by Chris Bielow <[email protected]>

fix typo

8a8e23b325cca263972b474bbea7c1fe17cbf995 authored almost 4 years ago by Chris Bielow <[email protected]>

codefactor fixes

308af2320a3726a3542cd1950150aa829de7447f authored almost 4 years ago by Chris Bielow <[email protected]>

fixes

31fa681f223755c678efde42758073d844c6fd8c authored almost 4 years ago by Chris Bielow <[email protected]>

better docs

71b059b8615a39be59660034d5362fcad1c15f4e authored almost 4 years ago by Chris Bielow <[email protected]>

remove unused signals; unifiy existing ones

6abcbf99312dacf04f6e3d0284d6ae0f03b4f69e authored almost 4 years ago by Chris Bielow <[email protected]>

major rework of SpecIDWidget

4244dce943524f2ba8e2d897440b66963278305c authored almost 4 years ago by Chris Bielow <[email protected]>

[DOC] adding a comment for an else case

f137c798702fb8a44ab8d897ecca462c5328b7aa authored almost 4 years ago by Ahmed Khalil <[email protected]>

[API] Python bindings and vairous updates to coding conventions for Isotopic Labelling Experiments

6f7c8c6458005d3e1325816774a5eb443fbeb0d9 authored almost 4 years ago by Ahmed Khalil <[email protected]>

Update FeatureFinderIdentificationAlgorithm.cpp

881f869e6c178688f99fbe2ffa894121171849d7 authored almost 4 years ago by Timo Sachsenberg <[email protected]>

Travis errors

d3661bdadd296f5e83280c00262e8817609f940f authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

last changes

f72055574181ad1642b60667ea9e083fc9df1bd0 authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

Parametrize new fitter options. Fix parameter passing bug. Adapt tests.

81cd8f67f0a3690874f6e60fe2141bf0a01fdf71 authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

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

# Conflicts:
# src/openms_gui/include/OpenMS/VISUAL/LayerData.h

97cbd4a3b36ffdc67ea07bc7c798794fca71e4b8 authored almost 4 years ago by Chris Bielow <[email protected]>

start OSW view

7f4636298f4b706ce712b19a402d6ffebbcd7796 authored almost 4 years ago by Chris Bielow <[email protected]>

Merge pull request #5037 from OpenMS/refactor/TVController

[REFACTOR] some small name changes

0b29c657aa56bd698d91010f50b1f963d19c48a3 authored almost 4 years ago by Chris Bielow <[email protected]>

more fixes

4f8c7292abbc65bf13985e2af5d403d3d745e5e5 authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

change variable names

496027da029f25e56e383941744c036d53c50dea authored almost 4 years ago by Timo Sachsenberg <[email protected]>

more fixes

0c5eef5966bd2155244525a43acf0cb72466a753 authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

[REFACTOR] some lass name changes

dc1f861ce306eb34c876ea835c05e01ffbd586a8 authored almost 4 years ago by Timo Sachsenberg <[email protected]>

Fix masstracedetection test by correct sorting. Fix warnings and style.

1a9fdc12fc0539326ab7157bde233111f11bc9b5 authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

review comments

e0f34bb802f588a88238c2d50a2a6a2d90d1a91a authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

[REFACTOR] rename SpectraSelectionTab to express that it can be used … (#5035)

* [REFACTOR] rename SpectraSelectionTab to express that it can be used for other data as well

...

be5f5cadd3d29f6842de483de9120f7578ad04f7 authored almost 4 years ago by Timo Sachsenberg <[email protected]>

[Performance] Convolution fillgaps, multithread MRMFeatureScoring, quit UpdateCheck process

[Feature] MapAlignerTreeGuided for ProteomicsLFQ

11b20fd1a269422be6ce29b49f7ce8f0f99dd27f authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

fix ToppView crash and Preferences menu status (#5034)

* [DOC] fix doxygen warnings

* more DOC fixes

* add 15N config file for X!Tandem-Adapter t...

66afb97c8c6cf412be83bf5890e50f391f083258 authored almost 4 years ago by Chris Bielow <[email protected]>

[FIX] tool categories & additional checks. (#5032)

* [FIX] tool category; [ADD] check duplication, UTILS

* use exceptions instead of a warning
...

daa7d0483d877de19719ebd771a9f427abf1e6fd authored almost 4 years ago by Oliver Alka <[email protected]>

Merge pull request #5033 from OpenMS/feature/aas_add_mz

[FEATURE] added getMZ as convinience method to AASequence

43fbffeaa92ef41c62cdb96933af802c3fc49065 authored almost 4 years ago by Chris Bielow <[email protected]>

Update AASequence_test.cpp

4f549d2c07996ab3c319aef07165179b96c510db authored almost 4 years ago by Timo Sachsenberg <[email protected]>

Update AASequence.h

b75d51470a05c7195206f1f122397fe28748b006 authored almost 4 years ago by Timo Sachsenberg <[email protected]>

Adding comments ...

c973036b3e5fad0b8837d946ed2903183961bb29 authored almost 4 years ago by kyowonjeong <[email protected]>

fix test

73e16c35b185b2a260ebf8821704018bf80b074b authored almost 4 years ago by Timo Sachsenberg <[email protected]>

Update AASequence_test.cpp

54d3cc50761391cd8838cbe78ec513e5307b19ae authored almost 4 years ago by Timo Sachsenberg <[email protected]>

[Multithreading] Partially convolution, fully FFMultiplex filtering. TODO benchmark convolution since the work in the loop is quite small

5bd0ba714d0e8575894ec05295e985116ffba5d4 authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

Update MzIdentMLHandler.cpp

b284fec1c7c8f04c5f084a69c5ece2c1929bab4b authored almost 4 years ago by Timo Sachsenberg <[email protected]>

Update Tutorial_AASequence.cpp

3cceab17ddcb514eb1afed04017228e576463571 authored almost 4 years ago by Timo Sachsenberg <[email protected]>

[FEATURE] added getMZ as convinience method to AASequence

9ae9d5fbe9f87d732cd20233f85fe637c8d7d9af authored almost 4 years ago by Timo Sachsenberg <[email protected]>

[Performance] Some improvements based on profiling ProteomicsLFQ

6d4daabe1015ed5e0019a9a6352c797ff46e0c14 authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

removing redundant blank spaces

205a54573cd7d281b464e4a20391587ff7a8dbc5 authored almost 4 years ago by JeeK <[email protected]>

Polishing and adding comments

3057edf9acdc5146d80877a175d94a8e62e9d3ad authored almost 4 years ago by kyowonjeong <[email protected]>

[REFACTOR] introduce behavior base class (#5027)

* [REFACTOR] introduce behavior base class

* address reviewer comments

591cc3f1f130374b5aca12f38cd4c7b1fbf65508 authored almost 4 years ago by Timo Sachsenberg <[email protected]>

Topp view fix pref (#5031)

fix Preferences Dialog not instantiable

18d4410d5bcd338751ccc4f039a872535ea58c27 authored almost 4 years ago by Chris Bielow <[email protected]>

Merge pull request #5030 from OpenMS/mergemaster

Merge remote-tracking branch 'origin/master' into mergemaster

961ea416b53e65c31655412b459e38974300e01b authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

Merge pull request #5024 from OpenMS/fix/consID_oldMode_proteins

[FIX] ConsID not taking over proteins in "linking" mode

2cbd5691c8a428e24b2d738b90cbecc11763e12c authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

fixing Jenkins builder error

8a1f7cfc6615c7a78131d44abaabc398ad137270 authored almost 4 years ago by JeeK <[email protected]>

Merge remote-tracking branch 'origin/master' into mergemaster

efe3a78502007e5bac0836b27cbaa911dd532cb9 authored almost 4 years ago by jpfeuffer <[email protected]>

15N mod file for XTandemAdapter (#5026)

* [DOC] fix doxygen warnings

* more DOC fixes

* add 15N config file for X!Tandem-Adapter t...

6e8378b60580115ec23b5f2de4c5f32d19f8de69 authored almost 4 years ago by Chris Bielow <[email protected]>

adding header file for setprecision

e2a044655fae29306fc730ff3a5709c769b28d59 authored almost 4 years ago by JeeK <[email protected]>

Merge branch 'develop' into feature/FLASHDeconv

191caf097c748415b42cfcf8830ff36351b1dae6 authored almost 4 years ago by JeeK <[email protected]>

change the location of first OPENMS_LOG_INFO

05d737d2815b415e4a64da005c81e3a5b9abf5df authored almost 4 years ago by JeeK <[email protected]>

Polishing #include in .h files...

41f9820cc80f8a5d78b5e0bdd50232d1ea483286 authored almost 4 years ago by kyowonjeong <[email protected]>

Replaced pointers with vectors and vector<vector<>> with Matrix

fca7963e642e3bd4ec4f1346d6521a211dbdb8cc authored almost 4 years ago by kyowonjeong <[email protected]>

Review comments

739c3beb8ac64d878175e1d73611270be123703e authored almost 4 years ago by jpfeuffer <[email protected]>

Addressed most comments by Timo. Major modification is still necessary.

caf8b806b711743a87890382874fcb9473dd66c7 authored almost 4 years ago by kyowonjeong <[email protected]>

remove files not needed

24e6f4a4fb25ae7494ab68bd401618cbc255f966 authored about 4 years ago by JeeK <[email protected]>

[FIX] ConsID not taking over proteins in "linking" mode

0b9d9a82a0464def594346ec8d74139a8becd759 authored about 4 years ago by jpfeuffer <[email protected]>

[DOC] fix doxygen warnings (#5021)

* [DOC] fix doxygen warnings

* more DOC fixes

7b706518faf289213158507a5be9d0ce30c440f1 authored about 4 years ago by Chris Bielow <[email protected]>

Merge pull request #5022 from ahmedskhalil/fix/5020

[FIX] Failed to compile with VS2019 MSVC 14.2

2c50ccdbaac0a32df4a35250867768d0807a9b7f authored about 4 years ago by Chris Bielow <[email protected]>

[DOC] Updated Authors list

ad0306c217cad0dbe0bed5990bbf7ee9433b4e85 authored about 4 years ago by Ahmed Khalil <[email protected]>

[FIX] Reinstating a missing include which std::sort depends on - MSVC Error C2039

9f0c40c3f9ae4023ae5a9fdac39b23d1ba740c83 authored about 4 years ago by Ahmed Khalil <[email protected]>

Merge pull request #5018 from OpenMS/feature/gitpodExtensions

[GITPOD] Better integration of CMake plugin with debugger + update of extensions

84da68a91f805310193d589915205b3af76ac25b authored about 4 years ago by jpfeuffer <[email protected]>

Update .gitpod.yml

c59be09c1ffa3927f5a2142aee6eb5919c961f96 authored about 4 years ago by jpfeuffer <[email protected]>

[GITPOD] Better integration of CMake plugin with debugger + update of extensions

117953850b73848c1663fa4a4a3c4f372acfe062 authored about 4 years ago by jpfeuffer <[email protected]>

resolving some comments on minor issues

c235cbff98c743d127b83784ecdfe3dcd5ac3398 authored about 4 years ago by JeeK <[email protected]>

remove not needed file

afa501c9a75e0c545715f2553e8dffa4556026ee authored about 4 years ago by JeeK <[email protected]>

adding comment

71abf06386e70f64c4d4ebf79c67c9bd83ea510f authored about 4 years ago by kyowonjeong <[email protected]>

adding comment

78ce362ed8fefce349f802ca38402381761f431f authored about 4 years ago by kyowonjeong <[email protected]>

Update MapAlignerTreeGuided.cpp (#5013)

0e538d9141eaabad8f99fc6309b8c091f6340527 authored about 4 years ago by Timo Sachsenberg <[email protected]>

mzTab move static to member (#5012)

* move from static to member

* disabled FFId test 4

Co-authored-by: timosachsenberg <sachs...

886cdb2cee1b91db3c5284e6268420df8293a17a authored about 4 years ago by Timo Sachsenberg <[email protected]>

adding comment

66a32482c531d13f808f912cd3d8206490ac2cd7 authored about 4 years ago by kyowonjeong <[email protected]>

adding comment

00b6acc2e6e71f3608bdaa90cd990b8623e33fc2 authored about 4 years ago by kyowonjeong <[email protected]>

ToppView: Show selected layer in Apply TOPP tool dialog (#558) (#5007)

8db2e8f49d66716e81a7da673f527ba05ba36e02 authored about 4 years ago by Lukas Zimmermann <[email protected]>

[FEATURE] first prototype of Annotation1DVerticalLineItem (#5005)

* Adding Annotation1DVerticalLineItem based on Annotation1DDistanceItem

* Vertical line drawi...

ee16987dc6606d7135e575cf8d64a0214243425a authored about 4 years ago by JihyungKim <[email protected]>

fix variable names, rename enum due to macro clash, some refactoring (#5004)

efde088ad3489a840d370fec57a92f8857558cc7 authored about 4 years ago by Chris Bielow <[email protected]>

fix variable names, rename enum due to macro clash, some refactoring

efe0fce75beb1eaa040ab40c49aa737bcdae0ae7 authored about 4 years ago by Chris Bielow <[email protected]>

fix name clash of FeatureFinderIdentification test (#5003)

* fix name clash of FeatureFinderIdentification test

in particular the clash of the output na...

860dfe76b6b88d3b0b40a5530a09425d3412f607 authored about 4 years ago by Timo Sachsenberg <[email protected]>

Update OpenMS_Tutorial.doxygen (#5000)

* Update OpenMS_Tutorial.doxygen

415864ce7073905eab788b76ac1a7a56cfe135d1 authored about 4 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #4981 from cbielow/OSW_datamodel

an OSW datamodel

6c0ddc0cad2275bf3ad70b7c397981d30956e5bb authored about 4 years ago by Chris Bielow <[email protected]>

FIX: CSI:FingerID parsing (#4976)

* FIX test CSI:FingerID

* REFACTOR path parsing

* [FIX] style, duplicated comparison funct...

708e48ceef2f26a416eb6ef0bd26e26e2de4385a authored about 4 years ago by Oliver Alka <[email protected]>

fix pyBindings

9523d91aa8ba74f54a68f5372c919eb88aafe360 authored about 4 years ago by Chris Bielow <[email protected]>

[DOC] improvements

51414bdab91746bf004fd7279c0ae7ea2ef4eb53 authored about 4 years ago by Chris Bielow <[email protected]>

some refactoring

4c286425a0698341ec059e75eb28f6ebb493ea8c authored about 4 years ago by Chris Bielow <[email protected]>

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

a2f292e4ce472e77dbcdc8a05c90b6e8a3d936b4 authored about 4 years ago by Chris Bielow <[email protected]>

fix CI

cf4ff08734312fd22d37992807514d73951a57cd authored about 4 years ago by Chris Bielow <[email protected]>

make OpenSwathDIAPreScoring outputs mandatory (#4999)

I think I forgot this in https://github.com/OpenMS/OpenMS/pull/4443

If not given causes a seg...

3052bef486bd8c74e7f1c6465d2557051e1c4e30 authored about 4 years ago by M Bernt <[email protected]>

better data model with stepwise loading

0303e9237ca1e0410f1888ab00950c75d19eaa01 authored about 4 years ago by Chris Bielow <[email protected]>

[CI] Add --output-on-failure to travis ctest invocations (#4983)

adda0846e59f6630ce45140a94bfbf4ddb38a6d7 authored about 4 years ago by Leon Kuchenbecker <[email protected]>

fix more warnings

73d1d04e37af188ca7873570c7c7ef1d148c8bf2 authored about 4 years ago by Chris Bielow <[email protected]>

fix warnings

2bb0b4bc8297451e001353730c90f9cc33ee1694 authored about 4 years ago by Chris Bielow <[email protected]>

more fixes

8813055d51d8858454875c2b1530e2821817a609 authored about 4 years ago by Chris Bielow <[email protected]>

Scan number as in spectrum + toppic output for MS1

4f7bfa5d0a16706fa95da0fd7fc084e69a75d5c3 authored about 4 years ago by kyowonjeong <[email protected]>

revert

102bddfd911d0610d97d6e95449037eb80712323 authored about 4 years ago by Chris Bielow <[email protected]>

[API,TEST] Adding an option to the isotopicCorrection functions to be able to use the internally stored derivatization agent correction matrices, added TBDMS correction matrix.

773dbdb397bfc1d0e6fc834496b1eedce8176cec authored about 4 years ago by Ahmed Khalil <[email protected]>

[FEATURE] retain top n spectra (better spectrum = better PSM) (#4994)

* [FEATURE] retain top n spectra (better spectrum = better PSM)

* moved exception code out of...

d17026048a70f95973867bf618b46eb0c222e4d4 authored about 4 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #4985 from OpenMS/doc/htmlHeaderWarning

[DOC] Add opt-in include to display a warning and link to latest docu

55598cf39c73a2092365fbdb51e63defa9b29c6f authored about 4 years ago by jpfeuffer <[email protected]>

Merge pull request #4984 from OpenMS/doc/toollinks

Make documentation links point to the exact version of the tool

22ef09f924dcfb8538eb0943bf5571ca2af3b4e5 authored about 4 years ago by jpfeuffer <[email protected]>

[fix] projection button (#4987)

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

531eebddd090ab70f34e663f5108a594b6cdd14c authored about 4 years ago by Timo Sachsenberg <[email protected]>

properly load OSW data in batch

13b7d986da1476f2d358ea39ac2de8330db4049e authored about 4 years ago by Chris Bielow <[email protected]>