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

[FEATURE] cut filepath from DEBUG logs. Add debug info to PLFQ. Add filtering warning.

49c76132c37d5968972edd110dcf20d8af8afca1 authored almost 4 years ago by jpfeuffer <[email protected]>

[FEATURE] allow subset of exp design to be given to PLFQ

c86b3019f4e950617856dbe701c98a462b974c63 authored almost 4 years ago by jpfeuffer <[email protected]>

FLASHIda.cpp oiptimized

564b6e436976a4d7e992a4fa8e1cbee65233a8e8 authored almost 4 years ago by kyowonjeong <[email protected]>

remove XML file and store data locally in ResidueDB (#5092)

* remove XML file and store data locally in ResidueDB

* fix indentation of certain lines

*...

49383fcf6e7e1d2f9a5574bee5d86e03c6f17542 authored almost 4 years ago by Timo Sachsenberg <[email protected]>

Fix: Bug in MRMFeatureQCFile (#5094)

* fix, tests: bug in MRMFeatureQCFile where an out of range error for an empty vector would be t...

3422ac3bf2effd8e3c2d44f385a8bf5b58d3ed52 authored almost 4 years ago by Douglas McCloskey <[email protected]>

FLASHIda.cpp oiptimizing

0a4b35851b40b2fe04c24cd9140cd54a304a5768 authored almost 4 years ago by kyowonjeong <[email protected]>

FLASHIda.cpp oiptimizing

c40432135215170c970fdd41fbf0593461e970f4 authored almost 4 years ago by kyowonjeong <[email protected]>

FLASHIda.cpp oiptimizing

2e34d6a2633006ce994bffff1ade602059bf36b4 authored almost 4 years ago by kyowonjeong <[email protected]>

QScore.cpp train att write added ..

af15ea42a4429d51df03bd645102b23ef3552e69 authored almost 4 years ago by kyowonjeong <[email protected]>

fix: bug in AbsoluteQuantitation (#5093)

* fix: changed the term to apply the dilution factor to

* tests: added tests for dilution fac...

0ba6a15f285fae7ac2d1229cab36f529d072f016 authored almost 4 years ago by Douglas McCloskey <[email protected]>

SQL: common ID for sqMass and OSW (#5089)

* create common UID for sqMass and OSW file when generated by OpenSwathWorkflow

* [FIX] preve...

41c2c94ac2041b3043ddcfb7f78a7f255b07d7c3 authored almost 4 years ago by Chris Bielow <[email protected]>

[REFACTOR] turn inheritance from QDataTime into private composition (#5082)

turn inheritance from QDataTime into private composition

9b2d373e6d308a1ed101a0419c0e064247af59f8 authored almost 4 years ago by Timo Sachsenberg <[email protected]>

fix py

0f79f4ac707444c10e7ba12942476c5353e44d0a authored almost 4 years ago by bielow <[email protected]>

fix compile error

d58b33aac1c452637ec9f49746e52a1a7fce27cb authored almost 4 years ago by bielow <[email protected]>

fix compile error

25b7dfe7b17d76f71ab449f718f59c9d4c0d13fd authored almost 4 years ago by bielow <[email protected]>

revive good error message by making it dependent on the template type -- otherwise the static_assert will trigger even without instanciation!

3672a940b1900e08ca97ea1115fa95c54fcddd89 authored almost 4 years ago by bielow <[email protected]>

fix pyOpenMS bindings

28421fc4723cea4197cb4741b6f2e8d2439adbe1 authored almost 4 years ago by bielow <[email protected]>

Merge pull request #5084 from jpfeuffer/feature/betterDebugPLFQ

[FEATURE] Better debug messages and values.

44ed5efe027bfce51c816dd203805afbaff0f909 authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

attempt to fix weird compile error

1b1e11741568e8a678e9846d982f7d451f0b3fdd authored almost 4 years ago by bielow <[email protected]>

QScore.cpp train att write added ..

b59020229744c8aba7e0b893b26ad3b1ca127178 authored almost 4 years ago by kyowonjeong <[email protected]>

QScore.cpp train att write added ..

7802bf854fab45b96dfd5090424ab52780f09684 authored almost 4 years ago by kyowonjeong <[email protected]>

refactor sign-bit removal for save storing to sqlite integer type (if using stringified insert statements...)

b12dcf622ef8664ce5cb17a7ea330325a5bca325 authored almost 4 years ago by bielow <[email protected]>

QScore.cpp train att write added ..

5305a64c97d9714c491e1470eaa07a85e2e512e3 authored almost 4 years ago by kyowonjeong <[email protected]>

remove unneeded meta value

f5c248c7d7846f7124740d9584f00cdc93a17a6d authored almost 4 years ago by Timo Sachsenberg <[email protected]>

[FEATURE] add common unique identifier to sqMass and OSW files

[TEST] fix some testing bugs (exp == exp, instead of exp==exp2) and make tests faster by removing...

b89a4f25c50817118be54eb91b9e87bd4d06e331 authored almost 4 years ago by bielow <[email protected]>

Added min_mass_count parameters in FLASHIda.cpp FLASHDeconvAlgorithm.cpp

705a00cfa3cba6a6ea4206835d09352e26def100 authored almost 4 years ago by kyowonjeong <[email protected]>

[FIX] prevent SqlConnector from silently creating an sqlite file if the file does not exist and not reporting an error, when all we wanted was to read from the file

522732d8be7d85ede245870bdd3291aad1bd1e74 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...)

5a196e730f7f911e9b2523007bf908a2d6587f23 authored almost 4 years ago by kyowonjeong <[email protected]>

create common UID for sqMass and OSW file when generated by OpenSwathWorkflow

52a3e7c2ad4afff5c79b1378c39151cdce7208db authored almost 4 years ago by bielow <[email protected]>

Merge pull request #5085 from cbielow/TV-DIA-table

TOPPView convenience (commandline, locking) and DIA plotting

551bdcd8541e32e4d55fd7ed710482773716fee4 authored almost 4 years ago by Timo Sachsenberg <[email protected]>

fix conversion warning

4fe5ffe3e6b58b23901b50e110bffcfa5c58ec1b authored almost 4 years ago by bielow <[email protected]>

fix bugs

e03e566a316d505a801f84dde6027cfe25283a8b authored almost 4 years ago by bielow <[email protected]>

fix conversion error

095141c0234ea8c6844f98382958612170cd248f authored almost 4 years ago by bielow <[email protected]>

fix aggregate init for std::array -- C++ defects for the win... :(

e94c4581fa993cd412ff71598a57d1ff157c02a3 authored almost 4 years ago by bielow <[email protected]>

fix codefactor

6ac8c70e935e2d288e66e01f915ad3bf3b7ebaa1 authored almost 4 years ago by bielow <[email protected]>

automatic tab selection and enable/disable

e5070a15591623c9cf97f19f4e9b75d5e7d05fd0 authored almost 4 years ago by bielow <[email protected]>

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]>