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

re-implement StopWatch to allow for 'resume()' and querying time while still running...

a7cf8f38b9b8d062bab8994752b7ae42d956c9ec authored about 4 years ago by Chris Bielow <[email protected]>

minor rename

86ce04968081d965a21b9619f67012dbac4056d1 authored about 4 years ago by Chris Bielow <[email protected]>

add FLASHProFilterAlgorithm

67b3db45036ccf43b7933227e23ec300acb869b1 authored about 4 years ago by kyowonjeong <[email protected]>

RNA avg model applied with

input arg "use_RNA_averagine 1"

85d266e7d68faa5acec531c90093e8fb2b7dd6af authored about 4 years ago by kyowonjeong <[email protected]>

Merge pull request #4893 from dmccloskey/fix/OptionalStrict

made strict_ param in MRMFeatureFinderScoring an optional parameter

2a6f1cb1fe74c2ff5013d63b678b8448ff7dd532 authored about 4 years ago by Hannes Roest <[email protected]>

[API, TEST] implemention and testing for IsotopeLabelingMDVs::calculateIsotopicPurity(...)

a106c4e6a8843bee36e8f78479ef307bd539ed32 authored about 4 years ago by Ahmed Khalil <[email protected]>

minor rename

ba015d878755e744a1c1b2a74dd748f2cc0a5732 authored about 4 years ago by Chris Bielow <[email protected]>

fix: GLPK thread safety (#4902)

* fix: removed unneccessary calls to deallocate GLPK memory when using COINOR and added some str...

cabf408f039c08a4dcf2008da6a3581527c0c5a2 authored about 4 years ago by Douglas McCloskey <[email protected]>

Merge pull request #4903 from jpfeuffer/fix/keepSamePeps

[FIX] mzTab opt columns bug, now also for PEP section

6f843005b52fb69f3a3823e09a626d3f78845c4f authored about 4 years ago by jpfeuffer <[email protected]>

Added consensusID to software CV terms

437331fa4a1564304839d30cb9b89cba52a5836f authored about 4 years ago by Julianus Pfeuffer <[email protected]>

Adapted tests

1ae7e434dcae644db508b356ea49a79b283574fc authored about 4 years ago by Julianus Pfeuffer <[email protected]>

fixes mzTab opt columns bug, now for PEP section

53e09e6a72cee069a2e51a34d6850f59afce4e4e authored about 4 years ago by Julianus Pfeuffer <[email protected]>

[API, TEST] implementing and testing IsotopeLabelingMDVs::isotopicCorrection(...)

6fa36d16ecaffaefd65608c043e731d8658989d9 authored about 4 years ago by Ahmed Khalil <[email protected]>

Merge pull request #4898 from jpfeuffer/fix/keepSamePeps

[FEATURE] Improve PSI MS ontology support in mzTab

bc70c82ab7139ce0553e925166755a1938ff6b40 authored about 4 years ago by jpfeuffer <[email protected]>

gcc tries

10a54bf6a2f35dfb8f079a0ee7a34b48c6f081f6 authored about 4 years ago by Julianus Pfeuffer <[email protected]>

old gccs..

7ec04791cdf05171c32e5fe187e2b386dd61b8f0 authored about 4 years ago by Julianus Pfeuffer <[email protected]>

Adapt tests to bugfix

310ca1ff33c597fc6dce8f20d7d70145a70312aa authored about 4 years ago by Julianus Pfeuffer <[email protected]>

how did it not fail on my computer???

bcd964772109d3ae3fe4aa082bf03292352311d5 authored about 4 years ago by Julianus Pfeuffer <[email protected]>

Fixes bug with metavalues and whitespaces. Fixes other tests.

8484b3cdaa8a9eb7af80d0b1acb18e561248aa82 authored about 4 years ago by Julianus Pfeuffer <[email protected]>

Added more CV terms. Small restructuring.

9a2e949494b882b28d71648ebfb192dfb2552712 authored about 4 years ago by Julianus Pfeuffer <[email protected]>

Carry over Percolator infos in ConsensusID. Adapt some CVs.

e26d9c06e4f5e50587d59ef35a3202090f714cce authored about 4 years ago by Julianus Pfeuffer <[email protected]>

Apply GHactions pyoms path fix from #4779

571d820633365b43aec243bb9829df8a61358fce authored about 4 years ago by jpfeuffer <[email protected]>

MzMLToMatlab.cpp added in utils

b8860e640d6881cf8bf95bb6613bf610999b8c5b authored about 4 years ago by kyowonjeong <[email protected]>

Improve PSIMS ontology support in mzTab

6c43645203ff96f36297b72df8cbb7ba55b83681 authored about 4 years ago by Julianus Pfeuffer <[email protected]>

[COMMENT] IdentificationData: added to-do comment (adduct names)

301ea003ff57f8b0f37419edc2cb4133c6df2900 authored about 4 years ago by Hendrik Weisser <[email protected]>

[LOG] FeatureFinderIdentification: added explanatory message for negative 'targets without features' number

e5c5cee7aef4a0ff15a98ebd173c85880a840055 authored about 4 years ago by Hendrik Weisser <[email protected]>

Merge pull request #4896 from cbielow/doc_mte

[DOC] add missing INI documentation for TOPP tools

bed0ff7eb2d5bbd555789a1b3243ab633f3c65bc authored about 4 years ago by Chris Bielow <[email protected]>

add missing INI documentation for TOPP tools

a7f8b3de135c477f6f483497c3ab5d8d467731c6 authored about 4 years ago by Chris Bielow <[email protected]>

update percolator parameters (#4895)

* [PARAM] set post-processing-tdc = true by default

* [TEST] fix Percolator TOPP test

* [T...

7c10a168507f9183da9fb15376e4bfc2225804fb authored about 4 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #4866 from Waschi97/feature/exportDBSuitToLibrary

DatabaseSuitability functions exported into the library

8ea152127ec9ebdca4d15b92c93c72468d4c977a authored about 4 years ago by jpfeuffer <[email protected]>

fixed tests, sort increasing

9e720c5415fdc5156d5776d81a0ec7945cbd5e64 authored about 4 years ago by Tom Waschischeck <[email protected]>

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

merging to fix dbsuit test error

8777715ded59163f0b51e67770d0c75408f2824c authored about 4 years ago by Tom Waschischeck <[email protected]>

[FEATURE] FeatureFinderIdentification: add label with ID to features (for TOPPView)

a2f58c649c25ca90cef65242f16f4cda0fc43605 authored about 4 years ago by Hendrik Weisser <[email protected]>

[FIX,INTERNAL] FeatureFinderIdentification: fixed handling of external IDs; some refactoring

ae3eeb3e49d0e17ea734c8f26f61e41f64b24906 authored about 4 years ago by Hendrik Weisser <[email protected]>

always use traML for valid formats (#4863)

1f4bc12263daa1f0c4aaea11c208f27947e2d257 authored about 4 years ago by M Bernt <[email protected]>

PR changes, min to max change

56fb8a44a0db67ef883310cc453d4be2fca032bf authored about 4 years ago by Tom Waschischeck <[email protected]>

remove duplicated code

d20daba6adb5fef9aad76d796ca60c3ed22a002d authored about 4 years ago by Chris Bielow <[email protected]>

remove unused parameters; make parsing more efficient

c8ab4aee2b1718e758e33b692c0dc248e36d9972 authored about 4 years ago by Chris Bielow <[email protected]>

signal rename

56cf588f749409c0accbe82f8ff53ea96330fbe5 authored about 4 years ago by Chris Bielow <[email protected]>

better docs

a4f62bcd2208867ccc855bb066f3b37acbf84598 authored about 4 years ago by Chris Bielow <[email protected]>

[API, TEST] calculateMDV(..) : changing calculation routines and adding test cases

5a95c69704ddffd36c9162c183a1bd8533708464 authored about 4 years ago by Ahmed Khalil <[email protected]>

update THIRDPARTY

5dfa4e9d80e602c86ebef419c9aa938750d1ca82 authored about 4 years ago by Timo Sachsenberg <[email protected]>

Update rebase.yml

d6c8f3a74cf5e7cdc433a94adc843e011801dcdb authored about 4 years ago by Timo Sachsenberg <[email protected]>

Update rebase.yml

9f9c04b2d72ee45ebe5657775d2aaee4f3afd42b authored about 4 years ago by Timo Sachsenberg <[email protected]>

fix: made strict_ param in MRMFeatureFinderScoring an optional parameter

92c6566974d5211c3183895486c4f3fdfb8575cb authored about 4 years ago by Douglas McCloskey <[email protected]>

Merge pull request #4894 from jpfeuffer/fix/MzTabSearchEngines

Only export main SE to mzTab. Correct scoretype. Keep scores and localization as Metavals in PLFQ.

d0dbeb6f7d141094e2c1d3c99de8b0a662e01568 authored about 4 years ago by jpfeuffer <[email protected]>

Update src/openms/source/FORMAT/MzTab.cpp

86a8ba6820ca3eb6c501ed1c033eb0328666de5d authored about 4 years ago by jpfeuffer <[email protected]>

Fix tests

3f1cb873337d36995f335d9e50d7f864cf43143f authored about 4 years ago by Julianus Pfeuffer <[email protected]>

[LOG] improved log output of FeatureFinderIdentification

c913cbd3f8057486c0b4a421b546778b9262f7d0 authored about 4 years ago by Hendrik Weisser <[email protected]>

Only export main SE to mzTab. Correct scoretype. Keep scores and localilzation as Metavals in PLFQ.

d5695fa53f9b049f394d3756d64e4a56cad0de7b authored about 4 years ago by Julianus Pfeuffer <[email protected]>

refactor menu and Recent files submenu into separate classes

4aa59508bee0375a6d4bc5440dc92ccc9eb7027c authored about 4 years ago by Chris Bielow <[email protected]>

no warning if rerank_percentile to high, (1-rerank_percentile) to just rerank_percentile

2a3d46ab0173e34f0eff39ce13c8aec2be20cf8a authored about 4 years ago by Tom Waschischeck <[email protected]>

Merge branch 'develop' of https://github.com/OpenMS/OpenMS into idfile-integration

74fd88e440ea54587a4270542ae883457fe6297a authored about 4 years ago by Hendrik Weisser <[email protected]>

switching QCBase to FlagSet

de1837f04406ba53f4e50fac27d2658edeb42189 authored about 4 years ago by Chris Bielow <[email protected]>

[FIX] FeatureFinderIdentification: fix m/z values of mass traces for adducted molecules

01ecf822a0bde7c8391776e85d958f540250fa05 authored about 4 years ago by Hendrik Weisser <[email protected]>

[FIX] take electrons into account when calculating mass shifts caused by adducts

cf06fa782852e1a5d9835fe7e2809bdd72b529ee authored about 4 years ago by Hendrik Weisser <[email protected]>

[FEATURE,PARAM] support for adducts in MapAlignerIdentification; new parameter 'algorithm:use_adducts'

8a583377a0d6982667d80de8875a9dc9f16a1e3c authored about 4 years ago by Hendrik Weisser <[email protected]>

add FlagSet class to model combinations of enum values

a6e1245ad3c18101712910699a17ba6aa77afcb1 authored about 4 years ago by Chris Bielow <[email protected]>

[FEATURE,PARAM] support for adducts in FeatureFinderIdentification; new parameter 'extract:max_isotopes'

526c0982d02f554f01595ccb7e484c68ee341a0e authored about 4 years ago by Hendrik Weisser <[email protected]>

[INTERNAL] simplified implementation of 'CoarseIsotopePatternGenerator' c'tors using default values

802d16b06c5603fa9affb5558733619dcc5c8e5b authored about 4 years ago by Hendrik Weisser <[email protected]>

Merge pull request #4874 from jpfeuffer/fix/AASeqProteinNTerm

[FIX] Protein terminal mods in AASequence

8062249e8558a9f355a178e1b91fde06265eb930 authored about 4 years ago by jpfeuffer <[email protected]>

Last cleanup.

150295f98e8deb694eedbc230f40ca53992f0d15 authored about 4 years ago by Julianus Pfeuffer <[email protected]>

...

e10646357c648de030f1da1fc2ea996c6b5b71d1 authored about 4 years ago by Julianus Pfeuffer <[email protected]>

forgot whitelist in test

9b873b7057cd3ca0e03520a5219b30082c52e321 authored about 4 years ago by Julianus Pfeuffer <[email protected]>

small percentile now tested in class test, also some phrasing

b78b81f3a440009bc45b3abdea38e21b602e6aa5 authored about 4 years ago by Tom Waschischeck <[email protected]>

returning smallest diff instead of throwing error when index out of bounce

aa38301ab6b06d50795e2715ca4367e3c553b3d6 authored about 4 years ago by Tom Waschischeck <[email protected]>

Improve enzyme handling in pepXML

4bc93c05e7f63a3d1424c473abf535eaf5fb4546 authored about 4 years ago by Julianus Pfeuffer <[email protected]>

Revert "Update function names in addons/ConvexHull2D.pyx"

This reverts commit 633b977f33ff5699e087adae6089cf3c8c4ea0b7.

d533744dfa31834411ac14b94ccfd784f149f2a5 authored about 4 years ago by Shekhar Shukla <[email protected]>

Revert "Updated name of align in addons/MapAlignmentAlgorithmIdentification.pyx"

This reverts commit b2f2937c178eb989055855ba267b40a9c32110b7.

db6a11e051966919edff9ae77e84df91ff241f46 authored about 4 years ago by Shekhar Shukla <[email protected]>

changed rerank_cutoff_percentile default to 0.99

9085b38d74cd4bfabcebca1eb105269fbd69587a authored about 4 years ago by Tom Waschischeck <[email protected]>

Updated name of align in addons/MapAlignmentAlgorithmIdentification.pyx

b2f2937c178eb989055855ba267b40a9c32110b7 authored about 4 years ago by Shekhar Shukla <[email protected]>

Update function names in addons/ConvexHull2D.pyx

633b977f33ff5699e087adae6089cf3c8c4ea0b7 authored about 4 years ago by Shekhar Shukla <[email protected]>

[API] calculateMDV(..) : removing unnecessary assignments

ff3dbc95d6fa8c6675b59b164d5336ac5262606f authored about 4 years ago by Ahmed Khalil <[email protected]>

[API] Moving calculateMDV(..) to IsotopeLabelingMDVs class

cd9888e800d5172acdedb20df0af5c6970ac0f17 authored about 4 years ago by Ahmed Khalil <[email protected]>

Merge branch 'develop' into fix/AASeqProteinNTerm

ed74f83e87bb0a9632819b37b99d5f2d1ee9b445 authored about 4 years ago by jpfeuffer <[email protected]>

revert debug mode of test

cd24de61927ee4a7e858a0143a524225500b6a01 authored about 4 years ago by Julianus Pfeuffer <[email protected]>

Enabled MSFraggerAdapter and adapt tests. At the same time upgraded our "private" Thirdparties for testing to MSFragger 3.0.

311083646c4fab15654b3fc1655a4accfd434a39 authored about 4 years ago by Julianus Pfeuffer <[email protected]>

Merge pull request #2 from jpfeuffer/patch-1

[FIX] Add new DBsearchDeconvMass util to list of executables to be built (and documented)

cbe6794e25f08d2bfc376500741eb75a944bce2c authored about 4 years ago by JihyungKim <[email protected]>

[FIX] Add new DBsearchDeconvMass util to list of executables to be built (and documented)

7a473ca6788f21536ada202693d7bebfd702685e authored about 4 years ago by jpfeuffer <[email protected]>

Adapter Parameters Written as MetaValues to SearchParameters (#4887)

* function in DefaultParamHandler

* meta values written in comet- & msgf+ adapter, test missi...

62899d6211aedc666ba8d4f31c65dbc958afdc24 authored about 4 years ago by TomW <[email protected]>

section for algorithm parameters in TOPP tool, some renaming

c2557323c6c9b26c533718055f6047aa86984276 authored about 4 years ago by Tom Waschischeck <[email protected]>

Always remove zips for notarization. Otherwise they stay in the dmg when it fails.

7c93e22e9cc8430614a5989531471c36111ef528 authored about 4 years ago by jpfeuffer <[email protected]>

remove version from autowrap to always have the latest

52ab750b1e6d6ec3609e22b87dfc05ff5a0c0a68 authored about 4 years ago by jpfeuffer <[email protected]>

LogWindow cleanup

60d8db26acadd828ddeb999a6ea042d4e4670295 authored about 4 years ago by Chris Bielow <[email protected]>

use signal/slot instead of pointer (unsafe due to order of destruction)

5978d02f396d9d73ea7fe8687a6b16a5a1c46112 authored about 4 years ago by Chris Bielow <[email protected]>

Merge pull request #4889 from OpenMS/feature/combineSEsettingsConsID

[FEATURE] combine SE settings during ConsensusID (instead of taking 1st)

309c0a856306ae149421c719499171c70d1ffb78 authored about 4 years ago by jpfeuffer <[email protected]>

Last style fixes.

f4feec6c4dbf9c449083c2bb3513ee1339d813e2 authored about 4 years ago by Julianus Pfeuffer <[email protected]>

exclude loop

2896bc8c21ac554740c34ba989f26f3a9498948d authored about 4 years ago by jpfeuffer <[email protected]>

[CI] rebase using /rebase (#4890)

* [CI] rebase using /rebase

writing /rebase in a comment will automatically attempt to rebase...

018d479e8fb8aa09a7168a2094031e04659f4413 authored about 4 years ago by Timo Sachsenberg <[email protected]>

Added check for db basename and consider unknown_enzyme. Add a force flag to IDMerger to be safe.

101bf0121460010b929c47a370ec841c9707d2c8 authored about 4 years ago by jpfeuffer <[email protected]>

Consider units and disagreeing enzymes.

0515131768a03dd9093c749accdd55c5383ccae0 authored about 4 years ago by jpfeuffer <[email protected]>

[API] Adding calculateMDV to AbsoluteQuantitation class

84c084a995788b6169dd81751d69d7cdd4838395 authored about 4 years ago by Ahmed Khalil <[email protected]>

phrasing changes

2b7cc223373c35d8b8142e0818e1d70eedc155d7 authored about 4 years ago by Tom Waschischeck <[email protected]>

refactor log to separate class

8b5064cd07755898f3d0005e877163f5d58b8ca0 authored about 4 years ago by Chris Bielow <[email protected]>

add doc

22949783291e8ea15d9061fa7da94361679a1dd8 authored about 4 years ago by Chris Bielow <[email protected]>

add free function

dbc5c151f83312b7083baad49dfea8976631d290 authored about 4 years ago by Chris Bielow <[email protected]>

add member function hasPeptideIds

fd84b105aebfde9892c5b0c5b1f67b10b0514b9a authored about 4 years ago by Chris Bielow <[email protected]>

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

cf1184a46f1d70bee12fbf23007d01e2ea5e54af authored about 4 years ago by Chris Bielow <[email protected]>

Some refactoring and errors/warnings/todos

48dd1f4c4f379ed21474a81e754163ab154d5d7b authored about 4 years ago by Julianus Pfeuffer <[email protected]>

fix compile error

fea07fae7b695b30f4a07312c524a90747574a5c authored about 4 years ago by Chris Bielow <[email protected]>