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

rm THIRDPARTY; comment

b59ef77d22a619c00eaf0d1de72de789fc3e622a authored almost 4 years ago by oliveralka <[email protected]>

revert

d3e8ac83e116cf6789884133405edab746d5100f authored almost 4 years ago by oliveralka <[email protected]>

rm restrict python

3df83eed3ede0b01785d106db74ad11e3967fada authored almost 4 years ago by oliveralka <[email protected]>

test

e7c100f56b2570033696443164c5d8facd9aa3c0 authored almost 4 years ago by oliveralka <[email protected]>

comment fix; add use last three python versions - via array

1b60d70ab31ca31a8f5b25e8cf4210c4fafc6811 authored almost 4 years ago by oliveralka <[email protected]>

Merge pull request #5058 from cbielow/TV-DIA-table

TOPPView: new data tab for DIA/OSW data

c3f7e41944a35a120d4841e5e858689eb588164a authored almost 4 years ago by Chris Bielow <[email protected]>

fix CI

f92bbbe346ec81787e6b4c004bd47d6d6240e4ed authored almost 4 years ago by bielow <[email protected]>

Removed SpectrumDeconvolution class. Merged into FLASHDeconvAlgorithm.cpp so functions do not take many parameters.

0a3eee0a109400f64e530d7226ae39d1f994c653 authored almost 4 years ago by kyowonjeong <[email protected]>

initial version of controller

755e1b852b1dfc77821af0c76b19df52dd5b6213 authored almost 4 years ago by bielow <[email protected]>

Added comment by half

0e4785253d85e06ed75192141810fd30832bc9d1 authored almost 4 years ago by kyowonjeong <[email protected]>

starting to hate CI ...

788a9e6a28631a5ea4850719e792f078afa0b356 authored almost 4 years ago by bielow <[email protected]>

add new container for manylinux

a720f56bfc2c0db16b2b0a9c1989a10e1c0f15d1 authored almost 4 years ago by oliveralka <[email protected]>

ci fix

7a40245f6a33a0650bfeefe55e40ac14061351f9 authored almost 4 years ago by bielow <[email protected]>

fix CI

a2f1c245556735dda79503eacbe8bfd6d2caacd4 authored almost 4 years ago by bielow <[email protected]>

fix CI

6f7791a934893e2b4c88638d7e37a12853b316f0 authored almost 4 years ago by bielow <[email protected]>

addressed PR comments

b73f53fd8d9491aaf2c100c96c158548ca0c6416 authored almost 4 years ago by bielow <[email protected]>

[API] various changes to IsotopeLabelingMDVs - deducing calculateMDVAccuracy()

b3e3ef761cb3538ef6fc6ddbd12065e4ea95ffbf authored almost 4 years ago by Ahmed Khalil <[email protected]>

make CodeFactor happy

08797d9ddf9ffc88a3ef98b31c44684517efb088 authored almost 4 years ago by bielow <[email protected]>

more renaming

0c7c517485284831d09bac41728a40c201f3ae2c authored almost 4 years ago by bielow <[email protected]>

rename signal/slots to more meaningful descriptors

b6278039b942756a806ca870b9bbcdaa3a43f3b4 authored almost 4 years ago by bielow <[email protected]>

fix segfault when DIA tab is active, but no data is available

00d056459ba46ba5ccdf751956cd7b61cf5634fb authored almost 4 years ago by bielow <[email protected]>

Speed boosted.. Need to put comments

d478c3e50191b9e1a04948bc187120bca6d9b7ea authored almost 4 years ago by kyowonjeong <[email protected]>

const accessor added (for const LayerData)

832d73de268d4ac4e0f8f51ad7dfbcca127d2bec authored almost 4 years ago by bielow <[email protected]>

avoid useless indirections

472ac0f12bc74bafc941932d5c1ea33fcc12e912 authored almost 4 years ago by bielow <[email protected]>

use sharedPtr to point to OSWData, to avoid copy between layers (2DView and 1DView)

7002d4609286097cc01df1fcbd82693c8ae1f20b authored almost 4 years ago by bielow <[email protected]>

initial DIA-OSW tab (shows table data, but cannot show chromatogram data yet)

e41c5866634a62846133f48ade30a6a6d67af70a authored almost 4 years ago by bielow <[email protected]>

fix compile error

a041d126d6ff5762da35d6d8d9b8410423a99061 authored almost 4 years ago by bielow <[email protected]>

allow OSWData to load more data from source file

2c1d31527cefa76aecc7f078e9361ec7cf9b9384 authored almost 4 years ago by bielow <[email protected]>

make interface cleaner

336d3fd590659cc20c8a7a4b9df0a074e8e87d86 authored almost 4 years ago by bielow <[email protected]>

Speed boosted.. Need to put comments

b849c0515fc9fd7de5c81db008fd79dac81f4d35 authored almost 4 years ago by kyowonjeong <[email protected]>

Speed boosted.. Need to put comments

c1c03c9dcecb0bf6d5fbe345d96f01b66da541ad authored almost 4 years ago by kyowonjeong <[email protected]>

Merge pull request #5057 from OpenMS/fix/mascot_decoys

added decoy parameter to mascot search

03fda657546db090a1dca5812609261dd49e988f authored almost 4 years ago by Timo Sachsenberg <[email protected]>

DefaultParameterHandler inherit done. Super slow as it is. Need to find bottlenecks..

7cf4dde7aff16a33b23800854c7a3350cf33dbfa authored almost 4 years ago by kyowonjeong <[email protected]>

Merge pull request #5036 from jpfeuffer/feature/PLFQProfiling

[Feature][Performance] ProteomicsLFQ performance + addition of MapAlignerTreeGuided

c344e41fb3448e0ee97f02e0ff69721b92a9f776 authored almost 4 years ago by Timo Sachsenberg <[email protected]>

added decoy parameter to mascot search

065ccdb27f67438c9543a4253873757c9714eefc authored almost 4 years ago by Timo Sachsenberg <[email protected]>

[API] various changes to IsotopeLabelingMDVs - adding MassIntensityType and FeatureName enum classes

c1199bcb1e28df343d92a3ee8e6525a7dd466245 authored almost 4 years ago by Ahmed Khalil <[email protected]>

[API] various changes to IsotopeLabelingMDVs

c3f4dc77896494c8e93531c3046df6d4c27de012 authored almost 4 years ago by Ahmed Khalil <[email protected]>

refactor some code into a new TreeView (extends QTreeWidget)

302920f9962d8b5d3a2dc3c54e01e2176ce2af3f authored almost 4 years ago by Chris Bielow <[email protected]>

fix style

a12e3d5dfca30ffe6d05acb7fd79e74d3e31fcca authored almost 4 years ago by oliveralka <[email protected]>

add test

84f69249128bad81196d69146edd89cf569e218f authored almost 4 years ago by oliveralka <[email protected]>

[ADD] python 3.9 to CMakeLists

7d3a6630a5944bf10e6ac07c19a0ed534aa7cd7d authored almost 4 years ago by oliveralka <[email protected]>

Merge pull request #5054 from cbielow/TV-DIA-table

Rename Table/Tree widgets

5748862c413cdc68eff9e4c239b059007b839c61 authored almost 4 years ago by Chris Bielow <[email protected]>

set UTF-8 encoding

401dee078d5732decf7d35fa742b41ca7fc6fa52 authored almost 4 years ago by oliveralka <[email protected]>

more renaming

442096ff47ddae2554589cd7e9db891b3151f187 authored almost 4 years ago by Chris Bielow <[email protected]>

rename filename occurrences

c980128f1e3f5ce55bcd556b5070b7cabb77fe83 authored almost 4 years ago by Chris Bielow <[email protected]>

rename SpectraTreeTab

1bb513bdf523624386e3ba4487f6d1bd1efec03d authored almost 4 years ago by Chris Bielow <[email protected]>

rename to SpectraIDViewTab

620c491bd0bcc61f6b48e012e7cc0b70a9fca927 authored almost 4 years ago by Chris Bielow <[email protected]>

Merge branch 'develop' of https://github.com/OpenMS/OpenMS into TV-DIA-table

ce18e0c13c8ca774da920cd300683c3f025230a9 authored almost 4 years ago by Chris Bielow <[email protected]>

[TEST] PATH

1409fb9795998c7efa765c2d80f0e0d0ed05ef5f authored almost 4 years ago by oliveralka <[email protected]>

Tv dia table (#5051)

* minor cleanup

* avoid useless conversion of numbers to qstring. Name roles properly.

* p...

f015737332d9c64286ca2eaf8e4fe93ba6c8a0f4 authored almost 4 years ago by Chris Bielow <[email protected]>

include optimization

8f2fd21a295c1cd93be2ab631ee3a6cbb1f1ff3e authored almost 4 years ago by Chris Bielow <[email protected]>

fix linter

803d7ba2612194338066c8458e25a00cb3613870 authored almost 4 years ago by Chris Bielow <[email protected]>

Merge branch 'develop' into feature/FLASHDeconv

1632ac1d85be52bd86b6e8be37520dd5bb5a453d authored almost 4 years ago by Timo Sachsenberg <[email protected]>

const iterators

489cbf5f0381ba14382099bb474266f39e1fe1a6 authored almost 4 years ago by Chris Bielow <[email protected]>

DefaultParameterHandler inherit merging.. Not tested yet.

b88dc5c661bdf217a19a35a771b5a6d686e908f9 authored almost 4 years ago by kyowonjeong <[email protected]>

further changes

7ac5bc65d018cee95867b74f5fec0ddd0d8d637e authored almost 4 years ago by oliveralka <[email protected]>

rm remote branch

3f95616c123694bc5911aaf73f93dd24540d470a authored almost 4 years ago by oliveralka <[email protected]>

[FIX] branch

19320f33c99bcd522eb136e7834f1cc0a2d155fa authored almost 4 years ago by oliveralka <[email protected]>

[TEST] new env_variables

bc2e4aca17dd15630104d8fcf403cf0801d43af7 authored almost 4 years ago by oliveralka <[email protected]>

fix ref error

29642a7508c74b05702490e66790438ab6b0c311 authored almost 4 years ago by Chris Bielow <[email protected]>

get rid of unneeded and dangerous exposure to internal data;

allow drag'n'drop of single chromatogram data from SpecView table to new Window

37f28608991b4ea0b034c17c619a6dfa0ed561ac authored almost 4 years ago by Chris Bielow <[email protected]>

fix bug, which caused the LayerMenu not to refresh when clicking a single chrom transition in SpectraView

3288acc040395fd1c89ddfa76e6da55ab30b7a48 authored almost 4 years ago by Chris Bielow <[email protected]>

properly pupulate columns via enum indices (fixes wrong layout)

e1c0412ab51ebbd13789be5f18903c50a0e06e15 authored almost 4 years ago by Chris Bielow <[email protected]>

avoid useless conversion of numbers to qstring. Name roles properly.

325c981f4b3a6f8c3119b1149143486effe1c7bb authored almost 4 years ago by Chris Bielow <[email protected]>

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]>