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

cleanup using statements in TOPPAS.cpp

592fc59bbfcfa4508b6e4b498d349e098a7999e0 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Change TextExporter Output to Display Accession Details (#5137)

* [FEATURE,TEST] Change TextExporter output to display accession details

[FEATURE,TEST] Chang...

053ad836ce97c128983c5974a698ca9ce2b7959e authored over 3 years ago by emilpaulitz <[email protected]>

rearrange swathwizard using decls

a60120d1f4b17ac10d3a1f7366af86c177d083b6 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Merge pull request #5147 from jpfeuffer/feat/IDlinking

Make quantile function safer

61a7abe6851fc33edb2b33e50779661af51ddfd7 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Fixed Nightly Build Error (#5148)

* functionality in IDConverter

* ms lvl and precursor info written in TSG::getSpectrum

* r...

03867c61b834f73329b9e6e4b6241f1fae03361a authored over 3 years ago by TomW <[email protected]>

include

050fc017a6a3a59cc9780d744abb643a4299fbb6 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Merge remote-tracking branch 'origin/feat/IDlinking' into feat/IDlinking

996d42d1a70f05241f08e40f413a263e795e6f14 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

quantile even safer

cb4cca841f894cb27f0551e9f97be269fbaea0f0 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Mass bin level harmonic and charge off by one elimination : huge improvement in sensitivity and specificity

efbf5299da3549819884e3d17edd68cbd8157842 authored over 3 years ago by kyowonjeong <[email protected]>

Mass bin level harmonic and charge off by one elimination : huge improvement in sensitivity and specificity

f9becc409ee59f1acf54661704f1c6eef229b4af authored over 3 years ago by kyowonjeong <[email protected]>

Merge pull request #5145 from jpfeuffer/feat/IDlinking

[FIX] some smaller fixes for the ID-based filtering during linking

b67fbeaeb8c3e3c3759ca80285e6264c1f7e54ac authored over 3 years ago by Julianus Pfeuffer <[email protected]>

.

ce2c304080c331aabf43768467692a742079eb6d authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Double

2f50717331a4b0b6bb6c0564e8a5f9a1adee85e0 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Oops

962e2b840337e8a258d5cb037925a6f45c96e5b2 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

debug code

68ff36d9475b62f9ae118a5e7c87f17ec2f2d282 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

[FIX] some smaller fixes for the ID-based filtering during linking

23f25e7bde21d2d1264595b4b5527732a60d3225 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Mass bin harmonic removal activated.

18ef3331bc0874d2fb7cf794009a6efd019a6c47 authored over 3 years ago by kyowonjeong <[email protected]>

desperate

421fc5a76dc44e555981ce0b4655a3937a913363 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Option to Convert a Fasta to a mzML File in IDFileConverter using TSG (#5136)

* functionality in IDConverter

* ms lvl and precursor info written in TSG::getSpectrum

* r...

30f79a16b0d9b5017917e43ed8fe4f9ec4f46722 authored over 3 years ago by TomW <[email protected]>

[HOTFIX] QTClusterFinder

eea9e58d88f2c63c072b520a027aa7d4fd0cc0bb authored over 3 years ago by Julianus Pfeuffer <[email protected]>

[FIX] more RANSAC pyopenms

346792e45356051333899dab86dba71f051260aa authored over 3 years ago by Julianus Pfeuffer <[email protected]>

[HOTFIX?] buffer overflow QTClusterFinder

62b4a7fe079b1e19ef7f07a33c4c107d09157bd9 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

update cpplint

743e24c8c4533f6ee23dc33df1bd7d84694bced6 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

ransac pyopenms fixes

851567b4ac50fedc7e77b6c9a47147ec16f9f4c3 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Merge pull request #5144 from OpenMS/gitpod-add-clang-tidy

add clang-tidy

7be93bad9b61214f5bbc71bec03e90a54b9eb916 authored over 3 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #5138 from jpfeuffer/update/cmakeMinVersion

Silence CMake warnings about deprecated version

79acb60c1d228bccf45b9aa37e4fcb642162bb0b authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Merge pull request #5142 from cbielow/feat_recentfilesmenu_for_TOPPAS

[FEATURE] add a `recentFiles` menu to TOPPAS

f4ae0e72f2d9651b9dcabc4e772f013b8f62464b authored over 3 years ago by Chris Bielow <[email protected]>

add java 11 and plugin

9f78442e86e30183e5f4a64e48986e6d8daa0e9f authored over 3 years ago by Timo Sachsenberg <[email protected]>

add clang-tidy

4e0afd7558c68e34b2fbddeda43c46b2f05852c1 authored over 3 years ago by Timo Sachsenberg <[email protected]>

Parameter names ending with _ fixed + multiple spectra examined for precursor search for real time deconv added

6d284aa05ddb182f59e6cc98cf8136a7172a30f4 authored over 3 years ago by kyowonjeong <[email protected]>

update flags for pyopenms

de29584294794ac6905fd8c13a0f91eee0cad318 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

ransac random error?

bf988f4a9034752e7cc5cc7d8bdef7245fb463f5 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

remove *nary_function

854cde1fa858220de62aae93a19ab83bfffce90a authored over 3 years ago by Julianus Pfeuffer <[email protected]>

add a `recentFiles` menu to TOPPAS

9deee390fae5edfb6141e990d038e2cb80ade599 authored over 3 years ago by bielow <[email protected]>

Merge pull request #5141 from cbielow/fix_pngprofile

fix png color profile warning

931262b1d4e6b2984a1675927bc2db5a9771caab authored over 3 years ago by Chris Bielow <[email protected]>

fix warning 'warning: iCCP: known incorrect sRGB profile' when opening TOPPView, TOPPAS because some PNGs use a shady embedded PNG color profile

a35603540842edc5dffdb91a42ee525b97dc3179 authored over 3 years ago by bielow <[email protected]>

Merge pull request #5135 from cbielow/feat_ParamEditorStringListEdit

ParamEditor with more convenient StringList editing

2676ed66531a5042a657841e1cfab3ac3fce405a authored over 3 years ago by Chris Bielow <[email protected]>

What?

7d4c18ccbdbb19ff62172a4de09b66801fd1bf8b authored over 3 years ago by Julianus Pfeuffer <[email protected]>

augment CHANGELOG

e8d66423759404ebd11b8954cc83d28efd42c6bb authored over 3 years ago by bielow <[email protected]>

remove *nary_function and add note about stupid cmake

7af6475743072984638a04ee2104193d26ccf9db authored over 3 years ago by Julianus Pfeuffer <[email protected]>

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

4fdd0e6c4f6ac44e06c33fdf60c88bd081314e62 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

no aggregate-init for c17 due to bug in boost <1.70

8d93c7a09f1571cb308db6854f83ea90e40f51ab authored over 3 years ago by Julianus Pfeuffer <[email protected]>

enable gcc7

c2c4a37a422b8d120aa74369bbae6aef5d1a58ef authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Merge remote-tracking branch 'origin/fix/clangwarnings' into fix/clangwarnings

3a9f8197ee109446efa38955fb6e46780a23e68d authored over 3 years ago by Julianus Pfeuffer <[email protected]>

wildcard filter with escape func and tooltip

d0ad90e0dcb28389d4cc1545b7d494a1f4068172 authored over 3 years ago by bielow <[email protected]>

fix rest of executables

bd36635428e53d0a43c34e2e637010ee1de53bbe authored over 3 years ago by Julianus Pfeuffer <[email protected]>

fix non-committing of QLineEdit values

51e71746cb388b8d9a75999472aee8c2ca1d0733 authored over 3 years ago by bielow <[email protected]>

use the new class in origin decoygenerator

7bdabc9391a976347240745f286bb32c688eb604 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

introduce portable_random_shuffle

2a1b77ee0b02b3ecaa7853396a2d9bbdbb6a810a authored over 3 years ago by Julianus Pfeuffer <[email protected]>

mistake

82147b686c31ff2b0838a52d38d93ab3d8a21966 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

[FEATURE] c17

52e04b7131d62196faadf67cee21352b1fb37ba3 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Parameter names ending with _ fixed + multiple spectra examined for precursor search for real time deconv added

febe365b1f55398c24c26bbdd5c50143aa68b802 authored over 3 years ago by kyowonjeong <[email protected]>

regex mistake

14490ae55f236d2d7dcde45963b9b9939b2c302a authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Silence CMake warnings

2f46db13a13192ecfecbc374a6717900aad6a9a3 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Merge pull request #5124 from jpfeuffer/feat/IDlinking

[FEATURE] Infer linking tolerance from RT distances of IDs in RT bins

2951410a094038a59d1bbd3ed6d300f275e84dfc authored over 3 years ago by Timo Sachsenberg <[email protected]>

pyopenms + codestyle

e237725e640bd0b4145baffd9ab8b69df2befc0e authored over 3 years ago by Julianus Pfeuffer <[email protected]>

[TESTS] double overwrites??

e40fc9efc5d142e804e3fddd67c6b01cde7ac8a3 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

[TESTS] double overwrites??

2e2652cf1d22ff4b559234604d13e78e8bf5d28c authored over 3 years ago by Julianus Pfeuffer <[email protected]>

[TESTS] double overwrites??

0281ac1253a6e652d7bb932524afddf5e3f1208f authored over 3 years ago by Julianus Pfeuffer <[email protected]>

[TESTS] fix hopefully most tests

f310772ee12f6ddf5dd523370481e0fd1c1f6335 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Merge branch 'develop' into feat/IDlinking

fc2777791ea8841825fe5be90a68d85165642bea authored over 3 years ago by Julianus Pfeuffer <[email protected]>

[TESTS] fix hopefully most tests

a359294a54025c039e7f4e5aea62dfecdef3f518 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

MS-Level and Precursor Information Written in TheoreticalSpectrumGenerator (#5126)

* ms lvl and precursor info written in TSG::getSpectrum

* removed writting ms lvl and precurs...

8fc23fe5c7eca9157c95fe9e7832f5087426ccbd authored over 3 years ago by TomW <[email protected]>

rename

d7f47647c298c5f1ee74371298550827f1ffe624 authored over 3 years ago by bielow <[email protected]>

[API] IdentificationData: simplified 'MoleculeType' and 'MassType' enums

a36f9bacf6b5e66ac222928fcb95f123c82ccdc9 authored over 3 years ago by Hendrik Weisser <[email protected]>

[API] store matching IDs in features by referencing 'input items' (e.g. MS2 spectra), rather than 'input matches' (e.g. PSMs)

43a9fff89fa3de16f9741ffde3ee39851ff0cce4 authored over 3 years ago by Hendrik Weisser <[email protected]>

Merge pull request #5122 from ahmedskhalil/feat/aut509

[Feat/aut509] - Refactoring Support for Isotopic Labelling Experiments (MDV) IsotopeLabelingMDVs

9d2951760e313ad1a5d20ad21e9fe679c18738d5 authored over 3 years ago by Timo Sachsenberg <[email protected]>

[FIX] more charge errors. adapt tests

738d247544cb39d2505b9f36e674092971e67c63 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

more rename

b9097335c99fc537be404ac51c098de661e8368d authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Use int for charge everywhere in DIA and use abs for safety. Try to reproduce old code.

e5368c18ffef06ea28f334387a7ca00986213dbe authored over 3 years ago by Julianus Pfeuffer <[email protected]>

fix CI

e9eba566ba35405649bb0122348a9012927258c6 authored over 3 years ago by bielow <[email protected]>

fix bug when data is comitted even though the user cancelled the Editor dialog

b97ae2c661298e0c7b31e3d8a2f063724a40caa2 authored over 3 years ago by bielow <[email protected]>

added tootips

48a8068fae76d690e35094ad2d4595aa8bbd816f authored over 3 years ago by bielow <[email protected]>

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

53506ca013a2727a44c57f71b2c48b40dbc146b7 authored over 3 years ago by bielow <[email protected]>

ParamEditor with more convenient StringList editing when restrictions apply (mostly for fixed/variable modifications)

011f587ec1223976cae5d4aed64343518842b977 authored over 3 years ago by bielow <[email protected]>

Update PULL_REQUEST_TEMPLATE.md (#5132)

2a858ba1251177d1110dd11a3772e9400147285c authored over 3 years ago by Timo Sachsenberg <[email protected]>

First PR stage seems to be done.. All sytle problem is addressed. Pointers in class removed. Comments updated.

694a624ed710a0d1b7ddc660f4b8cb0131ff783c authored almost 4 years ago by kyowonjeong <[email protected]>

First PR stage seems to be done.. All sytle problem is addressed. Pointers in class removed. Comments updated.

46b9af2ef4137181151e6cedbca4ac38a98ecece authored almost 4 years ago by kyowonjeong <[email protected]>

[REVIEW] coding style

a53cb8612ac7834232fc7cf6cd680e64242ef527 authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

[FIX] Fixed bug in QTCluster that assumed consecutive map_indices, which not even the test adhered to.

904be7e2189e7db42307a76aef16985979a10ada authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

Merge remote-tracking branch 'upstream/develop' into feat/aut509

c79a91c3aa69275dd10df4a7b86b094a8dd459a6 authored almost 4 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #5127 from cbielow/fix_glpk5

Support glpk5

567cd605ce926821354c2775349f081b670f741c authored almost 4 years ago by Chris Bielow <[email protected]>

FLASHDeconvAlgorithm.cpp local and private ones style fixed..

06b5d630aea93c5c8c57a3d466f92da6396cf926 authored almost 4 years ago by kyowonjeong <[email protected]>

[TEST] add test for negative charge and fixed dotprod

105dc582e7cbdc9336357b9d5bc557011569aa0c authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

[REVIEW] most review comments

[FIX] DIAScoring MS1 Negative charges would be casted to unsigned with nonsense values
[FIX] Smal...

a7a410f6fbff1405b9c177d32522c23760886937 authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

changed names of local variable based on OpenMS conventions

3c74b0598874b288e3ca4cbc19b8dcfedc1bbb15 authored almost 4 years ago by JeeK <[email protected]>

except for local variables, variable sytle done. Comments should be changed. Feature finder bug fixed.

0efbaca3ced645ac4a9f48facfd28b3c10a6cbe4 authored almost 4 years ago by kyowonjeong <[email protected]>

except for local variables, variable sytle done. Comments should be changed. Feature finder bug fixed.

109553b00c5c5a1600dc7b045109509460ba391f authored almost 4 years ago by kyowonjeong <[email protected]>

Parameters sorted.

b936384029eda62a532e654c78960fce4773a922 authored almost 4 years ago by kyowonjeong <[email protected]>

[SCRIPT] Add script to automatically overwrite TOPP test outputs.

82e382340e34ceaa56167d939b7fa3e697611ec8 authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

[FIX] Spelling (#5111)

* [FIX] spelling

* [FIX] INIUpdater_test

3f9aae0bc1dc5e551937d95b98b9c5c5e4c001d0 authored almost 4 years ago by Oliver Alka <[email protected]>

forgot

4c99428b219c1045eb20e6042fdda771bc7022fc authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

Small changes

04b85f94953f80f5ab7ba1eb89832b2cb1d399c4 authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

[FIX] Remove sqrt since we actually can get negative values now.

9bdf17629debd9935018605a5897bb2006f8ac3d authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

[FIX] Unused param2

429984c174745166a835af6de92615de9efff340 authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

[FIX] Unused param

6af76b6036fed71d06123ca75c1fa422b88cd4d9 authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

[FIX] Unused var. Cleanups.

6118a16f9b03e3607983cef28a3c5c47c074b1c0 authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

[API] - debugging pyOMS : excluding calculateIsotopicPurities(..., libcpp_vector[DoubleList]) - retriggering CI

bc89512eb4c1784e61f786348963166ccc0147f3 authored almost 4 years ago by Ahmed Khalil <[email protected]>

[FIX] Fixes some isotope related scoring functions in OpenSwath. Changes usage of scores in FFID. Some cleanups.

77de0102f5a350d77f7f257c19da2bf1a5f3301a authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

[FIX] preserve native id format in FileHandler (#5130)

* take first native id format as represenative

* Apply suggestions from code review

Co-aut...

9446dc620ea734179ba4b9e338bf0ae2cd07a84c authored almost 4 years ago by Timo Sachsenberg <[email protected]>