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

[API] various changes to IsotopeLabelingMDVs

3de54836bcb1a06c01a32ad02a617e79ec465a5d authored almost 4 years ago by Ahmed Khalil <[email protected]>

enable double/single clicking of rows in DIA view;

show the transitions with bands marking the feature-groups

1c0fbe301550e2672710e73b724108f93680fb44 authored almost 4 years ago by bielow <[email protected]>

show the correct menu entries when chromatogram data is present

1cb9cff9453b91112f02d465e20bd40aeb2a68b9 authored almost 4 years ago by bielow <[email protected]>

move data conversion for chomatogram to spectrum for 1D widget to a better place.

Reduce redundant code.
(this is still not ideal)

66477a0631a95ac0945affe387b8bfa546eee3e6 authored almost 4 years ago by bielow <[email protected]>

extend VerticalLineItem for 1D plot to show a band and actually use the color (if given) and a transparency

59a1b0d9ddc2dc49de1e75e4ce7711ced3f71792 authored almost 4 years ago by bielow <[email protected]>

Added comment to FLASHDeconvAlgorithm.h

f54a3b5f506dcf3e7ae88c09e7e466ae708ba3d1 authored almost 4 years ago by kyowonjeong <[email protected]>

Scoring stabilized again and again. ..

57afa2db9dc3c37655367f80171374792f6a6152 authored almost 4 years ago by kyowonjeong <[email protected]>

Add quantify decoys option to FFid (#5065)

* add option to quantify decoys

* quantif decoys if report decoys option is choosen

* quan...

66cdb1fb595590041a767800af26083f7a9128b4 authored almost 4 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #5063 from OpenMS/feature/plfq_decoys

keep decoys

f6dc6716d2fbd14dd699217974534b1264b43475 authored almost 4 years ago by Timo Sachsenberg <[email protected]>

Update FeatureFinderIdentificationAlgorithm.cpp

bb701b5e07aeae5a286431fcaa7e6be99c622381 authored almost 4 years ago by Timo Sachsenberg <[email protected]>

Scoring stabilized..

2f680e12aee1f1f9fa10e5328183489d549e5d1f authored almost 4 years ago by kyowonjeong <[email protected]>

CI warning

de607b49f1ac9bad5200f853bdfea5bdd66fb6a3 authored almost 4 years ago by Timo Sachsenberg <[email protected]>

Update FeatureFinderIdentificationAlgorithm.cpp

4f4f7b542ee2e92a3ac8f5c85e8b061cdb21d515 authored almost 4 years ago by Timo Sachsenberg <[email protected]>

update tests after fix

99b58c20db8d275d9cdac7b6fb265d3080b14356 authored almost 4 years ago by Timo Sachsenberg <[email protected]>

readd decoys

b73f70d7dbbf3daff3919745502af25ed6d4d4da authored almost 4 years ago by Timo Sachsenberg <[email protected]>

replaced int* with vector<int> etc.

f5a3fe1559808574ee260451f2720150c108cb43 authored almost 4 years ago by kyowonjeong <[email protected]>

Harmonic error removed. More optimization on scoring done.

72b4a1ce7bfc03506e64cf23392cc403c475a13b authored almost 4 years ago by kyowonjeong <[email protected]>

Charge cosine removed. Instead, a peak is assigned to a single PeakGroup

d1ed397fde5378f6abdea9ea1ac3ed908a24c2f0 authored almost 4 years ago by kyowonjeong <[email protected]>

reduce to one version -debug

138872ef05108375227e7172151bdd164050b38a authored almost 4 years ago by oliveralka <[email protected]>

TODO: copy decoys back into consensusmap

ec838444d72952ff987bfe6412e31ee8c5d06b79 authored almost 4 years ago by Timo Sachsenberg <[email protected]>

[FIX] test

5081b1e727d18de2273db61696fe59f8d680b5c0 authored almost 4 years ago by oliveralka <[email protected]>

Update MascotGenericFile.cpp

71462e8dbe7aae77f7d3c718710831e4eb9328b0 authored almost 4 years ago by Timo Sachsenberg <[email protected]>

Removed PeakGroupScoring.cpp. Also changed scoring part..

aeb55c402cd49462e132283a307c75eb61c72a6b authored almost 4 years ago by kyowonjeong <[email protected]>

keep decoys

3ba2356d005de4c5b78dc3a60d40e447d7bb0cd3 authored almost 4 years ago by Timo Sachsenberg <[email protected]>

[API] various changes to IsotopeLabelingMDVs - using OpenMS::Math::MeanAD() in calculateMDVAccuracy()

9e57662f392f78999dc23d052d3410c9a4be33d3 authored almost 4 years ago by Ahmed Khalil <[email protected]>

debug only latest version; fix paths auditwheel

abbdb22da5f1e628bf16d018c26d4e7806f09fd2 authored almost 4 years ago by oliveralka <[email protected]>

Removed PeakGroupScoring.cpp. Also changed scoring part..

753f51eac262278f935874f46b51c0a984944fd3 authored almost 4 years ago by kyowonjeong <[email protected]>

bash array syntax

17fa424439c3d3e1e8f618bd2d9bebc4518a9e00 authored almost 4 years ago by oliveralka <[email protected]>

use bash via shell command; rm eval; fixed loop

ec6877b2c9439b18315be5ec53d04b5db9fceeed authored almost 4 years ago by oliveralka <[email protected]>

try bash

cafeba2829ab484a64b36968f9c7a3505e8cdc4a authored almost 4 years ago by oliveralka <[email protected]>

test - debug

211662d86c3632fc13f75f75deb954af3db06f74 authored almost 4 years ago by oliveralka <[email protected]>

Removed PeakGroupScoring.cpp. Also changed scoring part..

57aa884fb2d071fdd0429627df2e2d4c2f3c7935 authored almost 4 years ago by kyowonjeong <[email protected]>

fix loops

a5539d4242509a25f6a120271984cc54aaeb74ef authored almost 4 years ago by oliveralka <[email protected]>

3 py versions linux; suppress warnings

58a7a2594d05758cd318558bce9086310a0c4433 authored almost 4 years ago by oliveralka <[email protected]>

try fix THIRDPARTY

307eb4cc2a636eba4c28bd7626189f589c4ac770 authored almost 4 years ago by oliveralka <[email protected]>

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

bc39d90ad13b45fd39c27907e2a38b117f172c09 authored almost 4 years ago by oliveralka <[email protected]>

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]>