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

fixes after merge

a4599665631771f5b4ad15531cf0303e4a5a877c authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

merge dev

9c5cc2f852d1ce01868feeddd303d42b56e6ec19 authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

Fix plfq tests

b5eab24c1918e12820cbf633e863be1db7f633af authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

Fix tests and UID MV as String

1d294ff518221c42e5d899f33e4c1a1f459c5ca7 authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

[FEATURE] Better debug messages and values.

4accf70c22b160823259ba6600f9376312046b36 authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

TOPPView: support annotion of layers from commandline

6bbbf253fc33c923e89fdf7293885312cbc11f2d authored almost 4 years ago by bielow <[email protected]>

highlight all OSW features; plot them only once;

3ca3dda1a5c48cff8988bad3a1127a47caa38904 authored almost 4 years ago by bielow <[email protected]>

allow conversion of distances in widget(plot) coordinates to MS-data coordinates and vice versa

f0efda7b1d40ab11a928cd7299e6a7febc8f4daf authored almost 4 years ago by bielow <[email protected]>

a 14 color palette of distinct colors

8f1c4aa959fd75421a8d9ca8cc08a5d5ffda83cf authored almost 4 years ago by bielow <[email protected]>

Comment added to all .h (Except for QScore.h - what should I do with this will be determined soon...)

ebe2e6a52f7dba359eb5ff8e447d4080611c0eb9 authored almost 4 years ago by kyowonjeong <[email protected]>

Comment added to all .h (Except for QScore.h - what should I do with this will be determined soon...)

8d3220e2f0532e043d4fe6a05b1463a82b91d45d authored almost 4 years ago by kyowonjeong <[email protected]>

[FIX] Correctly sync greedy resolution in PLFQ with quant data (#5081)

* [FIX] Correctly sync greedy resolution in PLFQ with quant data

* [FIX] refactor and fix ID/...

735f9bdc894e3298a505373ab11eba6a509c1893 authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

use numpy 1.19.3 for win

e58a792c5dd63610c3bbd1011186327e5d203f71 authored almost 4 years ago by oliveralka <[email protected]>

FLASHIda peakgroup ordering by QScore added

5f7528e17b6b00581fa6c2285714f6575ce709e0 authored almost 4 years ago by kyowonjeong <[email protected]>

max_mass bug fixed

816e16355f3903deec8177f3ea96894925383619 authored almost 4 years ago by kyowonjeong <[email protected]>

flashida masscount fixed

c82288a4c1030f44cbe485b860c7d46a73d592dc authored almost 4 years ago by KyowonJeong <[email protected]>

flashida parameter bug fixed

ec117f5b13ba14f3a8fe3785cd30c216ba940e54 authored almost 4 years ago by KyowonJeong <[email protected]>

plot DIA features' text non-overlapping, and avoid duplicate transitions

6173e89bc966701a36b5b2c5f42893f1d2ae4d89 authored almost 4 years ago by bielow <[email protected]>

allow dashed lines

fb043f278d88f7c2081aae8fbbc087d3a9ab2e8a authored almost 4 years ago by bielow <[email protected]>

[API] adding SIZE_OF_DERIVATIZATIONAGENT to enum class DerivatizationAgent

88d7740805c2aaefb5417fd6693a37d03a8385b6 authored almost 4 years ago by Ahmed Khalil <[email protected]>

[FIX] Correctly sync greedy resolution in PLFQ with quant data (#5079)

* [FIX] Correctly sync greedy resolution in PLFQ with quant data

* removed unused variable

...

5efe148b482b4af205d4e1323168785527381d75 authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

min_mass bug fixed

99bec5520d23f5722ed19a59ef3012ba759f2b02 authored almost 4 years ago by kyowonjeong <[email protected]>

converted PeakGroup.cpp into a class.

So many getter and setter.. probably should be changed somehow...

3a042f53a7e253cb83823a3d9a8f62291cddbde9 authored almost 4 years ago by kyowonjeong <[email protected]>

query text dimension of annotation item

a107fc32f91c09061e72598a85e86dc9cd6ca1bb authored almost 4 years ago by bielow <[email protected]>

new function to estimate text dimension when plotting

7b07be88a310c3defa3ff972af737793aaa3a63b authored almost 4 years ago by bielow <[email protected]>

[FEATURE] lock GUI when annotating IDs in TOPPView

e995f6ebf97ff48cb73c45aae6645f7ad0ecdd9d authored almost 4 years ago by bielow <[email protected]>

allow nullptr for locking (does nothing)

9d6bb59635d1179cbd6067b20cd9b09ecc4757bc authored almost 4 years ago by bielow <[email protected]>

fix bug in GUILock: undo wait cursor after finished locking

8e755a9455aab458c1268e70026d769e88da87c2 authored almost 4 years ago by bielow <[email protected]>

MS2 deconvolution problem addressed!

66b1bc3a8d1904a170fc54ee83528ecf0ea5846a authored almost 4 years ago by kyowonjeong <[email protected]>

[FEATURE, PARAM] updated default parameters of OpenPepXLLF (#5043)

* [FEATURE, PARAM] updated default parameters of OpenPepXLLF

OpenPepXLLF default parameters s...

4d404aa51b6370b57e8bb2ad2b8fc235d78a933b authored almost 4 years ago by Eugen Netz <[email protected]>

Merge pull request #5076 from OpenMS/feature/fix_sc

regression test for decoys in spectral counting

4d2a65ab3c867f5e16383f7a93e3be9b37dde76a authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

Merge pull request #5075 from cbielow/TV-DIA-table

TOPPView DIA data browsing

9e3ee16b1b07a12a3218b6df17fe2de8f9971e53 authored almost 4 years ago by Chris Bielow <[email protected]>

properly disable GUI when loading a file ....

7eddd6109be08964d2b96ebeb74712c417fd4153 authored almost 4 years ago by bielow <[email protected]>

fix linter warnings

9ab0b1f38b27b4a6b2c463c8307c89b3a178a1fc authored almost 4 years ago by bielow <[email protected]>

add regression test

10efb99aad4969ffe5cad2b8bea23d21f8486417 authored almost 4 years ago by timosachsenberg <[email protected]>

Use 4 latest python versions

87d7b211f237d47add086bb288d3005b778be729 authored almost 4 years ago by oliveralka <[email protected]>

regression test for decoys in spectral counting

0ceb9a99c244d53d0793f056c928d1503cacb04a authored almost 4 years ago by Timo Sachsenberg <[email protected]>

fix: map native IDs to chrom indices

3037591c55dfdbfb2c1813b0552f4f9f4dd70a21 authored almost 4 years ago by bielow <[email protected]>

fix bug (peptides get repeatedly added when browing data)

723602aff0b669c6dd13e6c72054685193c65401 authored almost 4 years ago by bielow <[email protected]>

- allow Annotation1DVerticalItem to be a band (and actually use its color member)

- annotate OSW features using a band

686224cf2831954376ddfbd53713651798238f4c authored almost 4 years ago by bielow <[email protected]>

rm vsenv.bat; try action

9246dd782fdfb6b185062cc40cfcbd81e236808f authored almost 4 years ago by oliveralka <[email protected]>

faster sqMass reading (7%)

41a802653b04154ca11f1f57b90f08892a00ba39 authored almost 4 years ago by bielow <[email protected]>

test set utf8 chcp

b0ef72f8a36d070961810b430a9e12d0c62dda58 authored almost 4 years ago by oliveralka <[email protected]>

debug1

0bcc6f34b7322885efa1b3a20d4bb712ed59baf6 authored almost 4 years ago by oliveralka <[email protected]>

debug

825b9addc083f211324afced70868ca4439cee33 authored almost 4 years ago by oliveralka <[email protected]>

[FEATURE, PARAM] updated default parameters of OpenPepXL (#5042)

* [FEATURE, PARAM] updated default parameters of OpenPepXL

OpenPepXL default parameters set t...

ef3f57d99cabaa83a6790e9093317ef3a868c942 authored almost 4 years ago by Eugen Netz <[email protected]>

test_contrib

dd8c8133f01fef0394cb5c06e34f063bc8e387c2 authored almost 4 years ago by oliveralka <[email protected]>

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

1c271a1e2cc14969fb0d01afe71fe1fbd7511d94 authored almost 4 years ago by oliveralka <[email protected]>

[FIX] rare underflow error in OpenPepXLAlgorithm (#5041)

* [FIX] rare underflow error in OpenPepXLAlgorithm

Fixed an underflow error in calculating th...

6542533ab40bfcbd9957992f4f0c7fc3a6248555 authored almost 4 years ago by Eugen Netz <[email protected]>

[FIX] rare underflow error in OpenPepXLLF (#5040)

* [FIX] rare underflow error in OpenPepXL

* [FIX] second charge underflow error in OpenPepXLL...

b2ab86fe42e062bc5c87e48d95051f3bf2f62b04 authored almost 4 years ago by Eugen Netz <[email protected]>

Update vsenv.bat

8c7c1a662e4efcd49390a7332e259a0f67f3123b authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

Try to link to XercesC again

4295d652b172a5277abc4a7cbc692ce426f9f8f9 authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

Update pyopenms-wheels.yml

e70fb53bd41c5e001cd200e36243e1fe4a086b44 authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

Merge pull request #5073 from OpenMS/feature/importTgtXerces

Add imported target for Xerces

8b9da31b18737bfb58adf439f2d5c64fccf41daa authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

[FIX] PATH

ac4b5e0da257b63fb74449efe663445df49c9f0f authored almost 4 years ago by oliveralka <[email protected]>

Add imported target for Xerces

be5d0a46f0f3d524a805173ef7db1eaf178a83fc authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

auditwheel verbose

7b4b55f493b3dcf5486b6aa0e9e56073c2d04b41 authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

initial Triqler export (#5066)

* Triqler support

adapt pLFQ tool

fix

add tool to tool handler

added Triqler tests
...

64323d4c815b2f116b5f1149c5d87df52384b45d authored almost 4 years ago by Timo Sachsenberg <[email protected]>

fixed test (#5070)

140a60a0dd1a547ab9b84a68f87f55f48aaba91e authored almost 4 years ago by Oliver Alka <[email protected]>

add regression test (#5069)

99d45296df399de5910217bbc936f489a3beb4bf authored almost 4 years ago by Timo Sachsenberg <[email protected]>

FLASHIda.cpp reimplemented based on new structure of FLASHDeconvAlgorithm.cpp

7900242549d766895e6f2b83c70830483c18e0c1 authored almost 4 years ago by kyowonjeong <[email protected]>

Added comment to FLASHDeconvAlgorithm.h

68f569e103e7e4ae6e58763fe3e4f1439933a2b4 authored almost 4 years ago by kyowonjeong <[email protected]>

Added comment to FLASHDeconvAlgorithm.h

db8f3f24ca55d4d6cdc50f5f1e5b65e8ed364b01 authored almost 4 years ago by kyowonjeong <[email protected]>

fix for removed decoys in pLFQ (#5068)

de830c3ebc45c3e7a530a55f222480e26817705c authored almost 4 years ago by Timo Sachsenberg <[email protected]>

[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]>