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

[FEATURE] major speed improvement for FuzzDiff

4cc856eddd61d87e23be2431e56db8184732660b authored almost 6 years ago by Chris Bielow <[email protected]>

Merge pull request #3910 from cbielow/sim_fix

[FIX] MSSimulator thread-safe now

d303e9c061c5239e7cc65b80bc494343245ab7fd authored almost 6 years ago by Timo Sachsenberg <[email protected]>

[TEST] test new feature

0b6ccb72baea3253b2b5c3009741f055d84f2299 authored almost 6 years ago by Hannes Roest <[email protected]>

[FEATURE] UTF8 conversion for String return values

attempts to convert all String return values to UTF8 unicode strings if
possible (instead of byt...

50469f29ce9f172801b890bb0675f0a707eba4c3 authored almost 6 years ago by Hannes Roest <[email protected]>

[FIX] conversion fix for zero-bytes

691bf6fff7e28fe23bf2c242c1c2140e12bee0a0 authored almost 6 years ago by Hannes Roest <[email protected]>

runExternalProcess function adapted

4dbf0d1fb36994a59918433a7b6a8c09242a46b9 authored almost 6 years ago by Leon Bichmann <[email protected]>

changed runExternalProcess to qProcess

6f49bc48caab685909f01503afc8460d07fa65c1 authored almost 6 years ago by Leon Bichmann <[email protected]>

add empty check back again

3ac9749aa0d3d1464fd50a83926f847ef8fa71cc authored almost 6 years ago by Leon Bichmann <[email protected]>

test abundance exception

ba27b24fb723a3a77928f6d5ce6b904d4079d40e authored almost 6 years ago by Chris Bielow <[email protected]>

remove unneeded ifdef (unsupproted pragmas are ignored anyways)

596716dc6277c3705dd89a04ab84252c9b28c761 authored almost 6 years ago by Chris Bielow <[email protected]>

MaRaClusterAdapter exectuable check moved to qprocess exit code

90e0279fdace9567013de07a7bc38c9018e69a9e authored almost 6 years ago by Leon Bichmann <[email protected]>

[FIX] catch bad_alloc when protein intensity is too high (float -> int overflow conversion)

5521d815c0d2a551730c8b3bcddaf9f76dfa8e20 authored almost 6 years ago by Chris Bielow <[email protected]>

[FIX] avoid crash when using multiple threads during simulation (Boost RNG is not threadsafe)

5c47eb3655a265871ed519bce23f83b6b5c125dc authored almost 6 years ago by Chris Bielow <[email protected]>

[FIX] make compatible with Python 3

743d5f2804c599a1442c0e0be9bb9ec5c40e1041 authored almost 6 years ago by Chris Bielow <[email protected]>

Merge pull request #3826 from oliveralka/fix/SpectrumLookup_wiff

[FIX] SpectrumLookup::extractScanNumber wiff regex

3bf4fc9b390c6bcabb1f81fb31fef568ed883ca1 authored almost 6 years ago by Hannes Roest <[email protected]>

Merge remote-tracking branch 'upstream/develop' into feature/MRMFeatureSelector

259ace14a809acac03a232a0488a2d126c01624e authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

[FIX] comments, insert (instead of push_back)

d2647e5392e0f15a6038f700bdc50aaeaa642c6c authored almost 6 years ago by oliveralka <[email protected]>

[FIX] add error

25493fd492dcffb0bdf37b96c699d4f5a5f01bbe authored almost 6 years ago by oliveralka <[email protected]>

Merge pull request #3908 from hendrikweisser/fix-ffmetid-overlaps

Fixed infinite loop during overlap resolution in FeatureFinderMetaboIdent

af5be1693385c4aa11f0bada0bf8d9aa901dfe7f authored almost 6 years ago by Timo Sachsenberg <[email protected]>

Merge branch 'fix-ffmetid-overlaps' into rna-lfq

c43684304eeb2353a4b599845f3190d3947f0098 authored almost 6 years ago by Hendrik Weisser <[email protected]>

[FIX] fixed infinite loop during overlap resolution in FeatureFinderMetaboIdent

cb686c8866ddb086d51014622c536e3c9f8fa48f authored almost 6 years ago by Hendrik Weisser <[email protected]>

[RESOURCE] added RNase H to the list of RNA digestion enzymes (currently requires increasing the number of missed cleavages to work)

1dc68d6d2000b20b4306ddbc717a4dac53ea3399 authored almost 6 years ago by Hendrik Weisser <[email protected]>

Merge pull request #3906 from cbielow/develop

Fix ElementDB and Elements.xml

d0c889231c38e5a19fd65c8fb5c52b7377d05268 authored almost 6 years ago by Chris Bielow <[email protected]>

Update src/openms/source/CHEMISTRY/ElementDB.cpp

Co-Authored-By: cbielow <[email protected]>

46d3b493922b924c8ad6f198036e9a00767354e4 authored almost 6 years ago by Hannes Roest <[email protected]>

Update src/openms/source/CHEMISTRY/ElementDB.cpp

Co-Authored-By: cbielow <[email protected]>

cf37b9dfd09b49ccbb5c4cac1dcec755bf8a235f authored almost 6 years ago by Hannes Roest <[email protected]>

Update src/openms/source/CHEMISTRY/ElementDB.cpp

Co-Authored-By: cbielow <[email protected]>

5849c7baca99b9e307f756eae873df9fd0e6e8d3 authored almost 6 years ago by Hannes Roest <[email protected]>

[FIX] Elements.xml -- disable heavy isotopes of Hydrogen since they trigger a Warning now when parsed (due to identical atomic numbers, which would lead to mem-leak in ElementsDB)

10361b11e7625e3aae991cd40d3c934ae57af84e authored almost 6 years ago by Chris Bielow <[email protected]>

Merge pull request #3905 from FabianAicheler/feature/MetaboDechargerPPM

Feature/metabo decharger ppm

e109918ac92e7f5828ff835ad033903cedb41bc2 authored almost 6 years ago by Timo Sachsenberg <[email protected]>

[FIX] Elements.xml : fix mass of Pb208

614b3537214e3b676e7f7d2ebaefc7a4b686ec1a authored almost 6 years ago by Chris Bielow <[email protected]>

[FIX] ElementDB: memory leak (lost pointer) and double free (duplicate pointer to same Element)

[FIX] ElementDB: fix properties of last element 'Samarium' in File (not constructed correctly)
[F...

a5b79038a2b3b997558c94a835cd6415825a0647 authored almost 6 years ago by Chris Bielow <[email protected]>

[FIX] make construction of ElementDB thread-safe

08b9f1439ed690c6e383f573b008f31f01edaf8a authored almost 6 years ago by Chris Bielow <[email protected]>

[OPT] minor optimization

149e3fdbc6b4e0fa8fd694b1e29f76f2ebe54e6b authored almost 6 years ago by Chris Bielow <[email protected]>

undo unordered_map

7340bc991d1aa0c2d6e1c5ac18883c518ddaa6eb authored almost 6 years ago by timosachsenberg <[email protected]>

replaced ppm test featureXML with consensusXML

8625154418184a2db1b944c5aaccd0648ff7c670 authored almost 6 years ago by FabianAicheler <[email protected]>

added exception for invalid unit parameter

75f1aa8c780a1933c37c962e241dc1195310eb29 authored almost 6 years ago by FabianAicheler <[email protected]>

Merge remote-tracking branch 'upstream/develop' into feature/MRMFeatureSelector

5dd5841247a717e73238cdd0d2d64df49b552bee authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

Merge remote-tracking branch 'origin/develop' into fix/SpectrumLookup_wiff

2a4edfa8883924222b49a7e0d2e11c05d0f93e93 authored almost 6 years ago by oliveralka <[email protected]>

[FIX] SpectrumLookup for wiff

d3c909b995b1c598b0e9cfaf3176152339e412fc authored almost 6 years ago by oliveralka <[email protected]>

No sorting 5000 intensity filtering, even faster - yeast per spec 1.5msec, less stringent parameters...

805b09982bd6fbde34da2cbf6ad6f17722047295 authored almost 6 years ago by kyowonjeong <[email protected]>

fixed merge conflict

a58e808b33a1852181736888ec119f5027d95ef1 authored almost 6 years ago by FabianAicheler <[email protected]>

adapted test to new DC output format

21d18b6c328af99ff393ba0ef4404e076a36b0da authored almost 6 years ago by FabianAicheler <[email protected]>

No sorting 5000 intensity filtering, even faster - yeast per spec 1.5msec

d87e583759844291c0e57eb8ce4548294dd90932 authored almost 6 years ago by kyowonjeong <[email protected]>

Merge pull request #3852 from FabianAicheler/feature/reworkDechargerOutput

Feature/rework decharger output

1c0d43492bc0e4a6c0382c80330cdf354e0eec73 authored almost 6 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #3883 from oliveralka/fix/SiriusAdapter_20181204

[FIX] SiriusAdapter: negative mode feature_only

1b9a70e7b0ae181baa53ac7735a71bc492f20ca4 authored almost 6 years ago by Timo Sachsenberg <[email protected]>

No sorting 5000 intensity filtering, very fast - yeast per spec 2msec

5ceb6b12c774f2be83d3ccd104f8fba11ed8fdf3 authored almost 6 years ago by kyowonjeong <[email protected]>

Merge pull request #3904 from biosustain/ChromeleonFile_acq_method_name

[FEATURE] add "acq_method_name" metavalue to ChromeleonFile parser

897e87e70019a82ad706a551443a5ceae4713ae3 authored almost 6 years ago by Timo Sachsenberg <[email protected]>

test: smaller experiment file, both integer and continuous cases

9db13c3c4a07330d84abfe5be4e911976fe1e5f9 authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

Merge branch 'develop' into feature/MRMFeatureSelector

63c5d8de84313919caba990cdf745526a83d1fc8 authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

feat: add acq_method_name metavalue to ChromeleonFile parser

c16ffd2fa5a94518249492a11fef7c1ebb01f06d authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

[FIX]update test files

71dc0df9137ecffff9323ee01dc7b886d6d40eab authored almost 6 years ago by timosachsenberg <[email protected]>

Merge pull request #3893 from hroest/feature/drift_time

Drift time unit

e33c9a64bf19e9fe4f9bb74d17a86b48321e07f2 authored almost 6 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #3900 from lars20070/fix/RegressionTest

[TEST] regression test checking that modified mass shift has effect

80d04f81f0196b9bcb053ccb6f43d6f55a0bac47 authored almost 6 years ago by Timo Sachsenberg <[email protected]>

add ppm mode

e0bd89ecdc6fde2f4f3502aead16d13adca5240d authored almost 6 years ago by FabianAicheler <[email protected]>

added test

4ce3c62f5f1088e260cd575d28630b696158a0ee authored almost 6 years ago by FabianAicheler <[email protected]>

added test

749b7c856aaacee6162e506de21fc47e2712eefc authored almost 6 years ago by FabianAicheler <[email protected]>

[FIX] error due to past-the-end iterator

30966a9ed632d76627295ef4254cab5f3024b7c3 authored almost 6 years ago by oliveralka <[email protected]>

[ADD] writeDebug (SiriusAdapterAlgorithm param)

7a5485cda369b98b6a111be52dfb26587d918651 authored almost 6 years ago by oliveralka <[email protected]>

add ppm mode

f156db9211b2e4f1a54f0ae50a7d316a05c2e70d authored almost 6 years ago by FabianAicheler <[email protected]>

Merge remote-tracking branch 'upstream/develop' into feature/MRMFeatureSelector

8a3a629c7bee277837470786066d493e994a6491 authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

test: produce output debugging info

5f5b49b26afb927389b7bbd7bba0f0f0e6e3577e authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

test: add one test

6c24d7ba3b07c5baf0f36fd2adc5bfa7dc44e4d8 authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

Merge branch 'develop' into poshul/hendrikweisser-rna-ms2-id

e48994943140fa80a70e7f67de54fd4c16ca4c4c authored almost 6 years ago by Samuel W <[email protected]>

Merge branch 'develop' into fix/RegressionTest

e9d8ca994ab81b68b9ad0aaf2fad0ecfd6bb0eee authored almost 6 years ago by Hannes Roest <[email protected]>

Merge pull request #3886 from enetz/feature/OPXL_speedup_by_simplification

[Feature] OpenPepXL speedup by simplification

476cf2abbc1d97c79a192247ed10a1c4718be3d0 authored almost 6 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #3896 from lars20070/fix/AveragineSimilarityScaling

re-scaling of averagine similarity in FeatureFinderMultiplex

3dbec63bb3077235ab0fd42b09ad0b27231181b6 authored almost 6 years ago by Timo Sachsenberg <[email protected]>

[TEST] regression test checking that modified mass shift has effect

1201c1d21458a394f5fcf1139a7bc8277a1f3635 authored almost 6 years ago by lars20070 <[email protected]>

filterSpectrum implemented but takes too long (>3msec per spec)

e499a5ab7c3addf9c8dbb944ba938b1b90260754 authored almost 6 years ago by kyowonjeong <[email protected]>

Novel scoring

Merge remote-tracking branch 'remotes/origin/feature/RNPxl_logReg' into feature/RNPxl_logReg

Con...

d7b6ff729d0c94fe7dde80aa620d73f46a61d15d authored almost 6 years ago by timosachsenberg <[email protected]>

[FIX] speed up partial loss generation

8ade43b87b37545d04050b8c44c051a9e924ec9e authored almost 6 years ago by timosachsenberg <[email protected]>

In the middle of filterSpectrum implementation...

195b7cab605649ad96b2b260957f3b79853efa29 authored almost 6 years ago by kyowonjeong <[email protected]>

simple log likelihood ratio scoring function implemented.

Tested with CytoC, Myo and works well.

77f05203ca2d7131b44ba618583ffd3d5adccbf6 authored almost 6 years ago by kyowonjeong <[email protected]>

[TEST] parenthesis, std

6631819aad330776c575abdcf59dc026e95caba8 authored almost 6 years ago by oliveralka <[email protected]>

[TEST]

6e7fb4917efc4fbf9cd2f732ba8874f36aca2e31 authored almost 6 years ago by oliveralka <[email protected]>

[INTERNAL] correct scaling factor for singlet searches

faac223124adfc1a0754e80e99985fc14c67f051 authored almost 6 years ago by lars20070 <[email protected]>

[INTERNAL] igonore averagine_similarity_scaling for singlet-only searches

fc589bf1c76a204109b6be23a4daf354be1676d8 authored almost 6 years ago by lars20070 <[email protected]>

[FIX] style

0b7a91940283ff5dde916c4787bc133b74974d05 authored almost 6 years ago by oliveralka <[email protected]>

[TESTS] add dependencies, switch

fef2187561c8906916c6b167e0a3fb277bfe6db2 authored almost 6 years ago by oliveralka <[email protected]>

[INTERNAL] remove legacy code

49158261b356f0d88b148f31c5f48743049f3e05 authored almost 6 years ago by lars20070 <[email protected]>

Merge remote-tracking branch 'upstream/develop' into feature/MRMFeatureSelector

54d7a06684145089195c6eebf4580d291173bd10 authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

simple log likelihood ratio scoring function implemented.

Tested with CytoC, Myo and works well.

165f790ebaa5348b41f3af6fd4e2425b964faee0 authored almost 6 years ago by kyowonjeong <[email protected]>

[TEST] no re-scaling required for pure (!) singlet searches, only for knockouts

04250147fc7080b613cdce3bbf32a0ae5086ffd5 authored almost 6 years ago by lars20070 <[email protected]>

[TEST] add TOPP test (averagine_similarity_scaling = 1.0 => no singlets)

d8ee5ec960b5b77171db43b79e49b7e5e8b8b196 authored almost 6 years ago by lars20070 <[email protected]>

[INTERNAL] re-scaling averagine similarity for singlet detection (profile mode)

14123f3fa75f2d69b8f7ee0cdf978cbe89b04692 authored almost 6 years ago by lars20070 <[email protected]>

[FEATURE] IDFilter... remove hit by meta value

07dffe1c9c2168dd13d52b02a5c4d42a8138dae5 authored almost 6 years ago by timosachsenberg <[email protected]>

[INTERNAL] re-scaling averagine similarity for singlet detection

ba3d301de2ba668133e0989535d2cb15127690c8 authored almost 6 years ago by lars20070 <[email protected]>

Merge pull request #3889 from biosustain/lpwrapper_const_args_no_pointers

[STYLE] LPWrapper: avoid pointers, use const, use STL containers

802d4a0de14d2a52a3401cf468861636031f93ed authored almost 6 years ago by Timo Sachsenberg <[email protected]>

Update LPWrapper.cpp

58f0afb0c74c986c3069617968c0ad90e68ae436 authored almost 6 years ago by Hannes Roest <[email protected]>

[FIX] fix indent and test

7836617eb0c359573ca6d9dc8e373a853506c1cb authored almost 6 years ago by Hannes Roest <[email protected]>

[FIX] warning fix for obo

38a4811d68b10a000a007193bdc746499a1d93c3 authored almost 6 years ago by Hannes Roest <[email protected]>

[NOP] removed unused member

baa28b6973aaafadda5c5004ba021ac19fba6b8c authored almost 6 years ago by timosachsenberg <[email protected]>

simple log likelihood ratio scoring function implemented.

Tested with CytoC, Myo and works well.

f3b0f7ca914fe3184819e83517904a4e7218abd4 authored almost 6 years ago by kyowonjeong <[email protected]>

Add LogMzPeak struct

7561298f13db81b85a30458975f1a27911860c3b authored almost 6 years ago by JeeK <[email protected]>

yeast dataset per spec 1.88msec

1e67460e1dea2ce031f3364f51c130cf437f4201 authored almost 6 years ago by kyowonjeong <[email protected]>

a little bit change

ab8e6247fcef5f18d3c4f91446b91b96059660b6 authored almost 6 years ago by kyowonjeong <[email protected]>

[DOC] improved descriptions of the three TSG classes

47de5a9063f0d63d032534974170b0d9ba8ab469 authored almost 6 years ago by enetz <[email protected]>

[FIX] fix FileConverter

4e2b6780d40cabc5a004e27dd96f41fddad9a88b authored almost 6 years ago by Hannes Roest <[email protected]>

[FIX] forgotten

4bf407d3a454248441281e5157694b96c9ff89e5 authored almost 6 years ago by Hannes Roest <[email protected]>

[TEST] add tests

a5af41137f628ca75f1a157b6238d0a6c31d0197 authored almost 6 years ago by Hannes Roest <[email protected]>

[FIX] also write out when unit is not set

b8c129ce5038cc8418b81b4879969b82c6c673c8 authored almost 6 years ago by Hannes Roest <[email protected]>

[FIX] misc

b31bfe6931d4bda07131538f10986e9532bc78e8 authored almost 6 years ago by Hannes Roest <[email protected]>