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

Merge pull request #3872 from lars20070/feature/SplineSpectrumExtension

SplineSpectrum API extended for chromatograms

6326b34f81a7261cbdff792d4af37f1216039621 authored almost 6 years ago by Timo Sachsenberg <[email protected]>

Merge remote-tracking branch 'origin/feature/SiriusAdapter_output' into refactor/AssayGeneratorMetabo

f4695e68881033bb455b4c1fd732cb2fa9bb5a59 authored almost 6 years ago by oliveralka <[email protected]>

Merge remote-tracking branch 'origin/develop' into refactor/AssayGeneratorMetabo

a63a1f4c9e44c463de374e938e70a66ed4578292 authored almost 6 years ago by oliveralka <[email protected]>

[ADD] Deisotper param, strucutre for SIRIUS

8e686404c4440acb723740034fc01a38919b7290 authored almost 6 years ago by oliveralka <[email protected]>

[FIX] Rename FragmentAnnotation to SiriusFragmentaAnntotation, fix

pyopenms

11a3a3ba81f582de73061f98c56c1c4126a3318d authored almost 6 years ago by oliveralka <[email protected]>

Update SplineInterpolatedPeaks.pxd

a712982714469423b626eec8fb66f6155f0f4c89 authored almost 6 years ago by Hannes Roest <[email protected]>

Merge branch 'fix/xfdr_labeled' of https://github.com/enetz/OpenMS into feature/OPXL_speedup_by_simplification

e3a1f2e1382bc11cfac9be97c024068661688dac authored almost 6 years ago by enetz <[email protected]>

Merge branch 'fix/xfdr_labeled' of https://github.com/enetz/OpenMS into fix/xfdr_labeled

771b19809e683b21aa1ba963d1c44f63a4458cce authored almost 6 years ago by enetz <[email protected]>

[TEST] adapted tests to fixed alignment

378a82dafc703be2b5577d6c637353c20900c79d authored almost 6 years ago by enetz <[email protected]>

attempt to fix Navigator Cython error

a8650aa3ee055be53be87b050809c5bc9ef0b6c9 authored almost 6 years ago by lars20070 <[email protected]>

[FIX] OpenPepXL: fixed a major error in spectrum alignment algorithm

this error caused a few wrong MS2 peak matches way outside the tolerance window

95b1daa92d3906fc7b7ac3487c1effa914d20873 authored almost 6 years ago by enetz <[email protected]>

[FIX] OpenPepXL: fixed a major error in spectrum alignment algorithm

this error caused a few wrong MS2 peak matches way outside the tolerance window

de2a567dd78a9f6f45b1aa9046d2e8fb0aa008f9 authored almost 6 years ago by enetz <[email protected]>

[FEATURE] OpenPepXL: better filtering of spectra in preprocessing

5bc13c69897b4b51596d759d74660e13a268bb54 authored almost 6 years ago by enetz <[email protected]>

fix typo

e12b24ee95572001981d55abb341efa06212454c authored almost 6 years ago by lars20070 <[email protected]>

Merge pull request #3876 from oliveralka/script/whl_python_pyopenms

[FIX][ADD] pyOpenMS whl mac

4902e996a3c64fe8d0beb8f49eaa54408da925c0 authored almost 6 years ago by Timo Sachsenberg <[email protected]>

[FIX] fixed an ambiguous case where the first residue can have a terminal or a side chain cross-link

ca13018dfa46834e5bf64e6bcdf00adc7590abb2 authored almost 6 years ago by Eugen Netz <enetz@>

Remove (currently unused) ignore_adduct parameter from FLKD

Found out that FLKD currently doesn't use adduct information (doesn't use FeatureDistance ), so ...

6d9e688d9d8b76182e02db270c4d1119e4024cee authored almost 6 years ago by FabianAicheler <[email protected]>

fix python wrapper

efcc5c270b750c468baef63bed6e4b3a474af5f1 authored almost 6 years ago by lars20070 <[email protected]>

[FIX] style

6d7f8e51423b069a0fa0b342a9bf39cae783e53b authored almost 6 years ago by oliveralka <[email protected]>

[FIX] FeatureMapping

6bcfa2594ad669565cb8ddf09371be11a20160ae authored almost 6 years ago by oliveralka <[email protected]>

[FIX] newline

6c094bdee1e661d277cad0ead487dc9c8dd6ea1a authored almost 6 years ago by oliveralka <[email protected]>

[ADD] script build whl

c8af66fb674cbb6b236e8cfa91089d09d43fbb95 authored almost 6 years ago by oliveralka <[email protected]>

Merge remote-tracking branch 'origin/develop' into feature/SiriusAdapter_output

5f3d270f6e4d1e3a670ad82a1eaf6441e4811652 authored almost 6 years ago by oliveralka <[email protected]>

[ADD] SiriusAdapterAlgorithm, pxds, fix test

f1b12484d7bd1ae33cd01e39eaffda4317f11012 authored almost 6 years ago by oliveralka <[email protected]>

Merge pull request #45 from hendrikweisser/rna-lfq

[FIX] TOPPView: fixed display of 'a-B' ions in sequence diagrams for RNA

69ae785799d881ac1613e32ffdcc60c0e1620660 authored almost 6 years ago by Samuel W <[email protected]>

[TEST, FIX] fixed incorrect test dependency

4d330a189e347d2578ef6ccaaeb119c514b87668 authored almost 6 years ago by enetz <[email protected]>

[FIX] TOPPView: fixed display of 'a-B' ions in sequence diagrams for RNA; made a debug output conditional

000128d004e652bc5462acdb68430ee169b68096 authored almost 6 years ago by Hendrik Weisser <[email protected]>

[PARAM] OPXLLF: changed parameter name of cross-linker mass

the previous parameter name (cross_linker:mass_light) does not make sense for label-free cross-l...

3389b8e343195f9e9e847018153c474f5dc4352f authored almost 6 years ago by enetz <[email protected]>

[LOG] fixed spelling error in debug output

0918e2fa341d555783d96db86f2ab122258b7b7d authored almost 6 years ago by enetz <[email protected]>

[TEST] added OpenPepXL test with a zero-length cross-linker

Zero-length cross-linkers can have a negative total delta mass,
which caused some problems in th...

27f65ef5bb041292f1c196486fa77b4994a55f55 authored almost 6 years ago by enetz <[email protected]>

[API] fix python bindings

8205273fbeefdc58ca92ca0c707cf283e225299c authored almost 6 years ago by lars20070 <[email protected]>

[API] move step width scaling from constructor to navigator

436632b4ce70852d5bddececaf8ec255b68a75a5 authored almost 6 years ago by lars20070 <[email protected]>

docs: improve warning in computeScore_() (newline)

96d23195b3f0ff3939e5f99e46d58af3bb2ea9db authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

fix: avoid division by 0 when input is empty

aaf53e9c29bf7c321dbf83696dcc089c81725e16 authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

chore: remove old .pxd file

b19424e668be711ef2f2c0a1f4c4c1ed8faf5025 authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

[DOCU] fix docu

fad2723e6ba3a6cc60c9f588331e6918babcde60 authored almost 6 years ago by lars20070 <[email protected]>

Merge pull request #3865 from Leon-Bichmann/fix/IDFileConverter

IDFileConverter - NativeID prior to RT lookup

f80dc42551140d48c955121dd6aec6b50d11b060 authored almost 6 years ago by Timo Sachsenberg <[email protected]>

[FIX] TSGXLMS: check for negative theoretical peak masses where they actually happen

afc3817807eb354b28d3ff3f34065cbc5955af37 authored almost 6 years ago by enetz <[email protected]>

[IO] OPXLHelper: turned off LOG_DEBUG output

d9a713a67f4b4fbe7acfa7f0eb46482ef42e8d52 authored almost 6 years ago by enetz <[email protected]>

[FIX, IO] OpenPepXLLF: moved LOG_DEBUG access into critical sections

and turned it off by default

374bd598b091bbc8f3a71d12d75d3afcb87648e2 authored almost 6 years ago by enetz <[email protected]>

[FIX, IO] OpenPepXL: moved LOG_DEBUG access into critical sections

and turned them off by default

36c60dbb2bc1069e30de00c2647a87cee6c9c5bd authored almost 6 years ago by enetz <[email protected]>

[DOC] add mitivation to docu

98332002c90c66329e8c502ef1eb6941f997c370 authored almost 6 years ago by lars20070 <[email protected]>

[DOC] extended docu

8c88b15be7edf5887c119b600c4546c9d752ef16 authored almost 6 years ago by lars20070 <[email protected]>

[DOC] docu for scaling factor

7cd037133e303427326d4390e1fc79e20d6d0a80 authored almost 6 years ago by lars20070 <[email protected]>

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

35c2c7d058fe22f69bfa6c64e3d333613e9a12f7 authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

refactor: make methods static in MRMBatchFeatureSelector

1fe3ac65e1bc8846b4ad0a3e609457e8cef04190 authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

remove lookup empty

ff4a395339a3e0ecc955804c58ff6c27e76c9da5 authored almost 6 years ago by Leon Bichmann <[email protected]>

Merge pull request #3847 from lars20070/fix/PeakIntegratorTest

problematic example for Simpson rule added to PeakIntegrator class test

a8012316ae75451b803f2e0c183ef4c922c0ea06 authored almost 6 years ago by Timo Sachsenberg <[email protected]>

[FIX] TSGXLMS: check for negative theoretical peak masses

this is a quick fix until I can figure out, how and why negative masses are calculated, but it s...

5f79fc610799233972029ad480d0ccbfb1b64cc1 authored almost 6 years ago by enetz <[email protected]>

[FIX] OPXLHelper: made debug output OpenMP safe

in this state, debug output is activated

9d1438e001debddfd1942f66cb6faa3e8269c221 authored almost 6 years ago by enetz <[email protected]>

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

ca46398ce26cb9a9ecb1bd03270fb0e4777004be authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

style: rename MRMFeatureScheduler to MRMBatchFeatureSelector

e2c3533a213863ab9461c1c95878ddb34c55eadc authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

[API] replace any mz by pos (i.e. mz or rt)

ab2e2728eb3eda4d7455f4542b62f68932f9e6c3 authored almost 6 years ago by lars20070 <[email protected]>

refactor: remove class parameters, pass parameters through arguments

cb7123e1bb8061f0009e5636eeeca83e19fd125e authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

[API] rename SplineSpectrum --> SplineInterpolatedPeaks

10273bbd0e38d21708598253d2d774bbeef4966d authored almost 6 years ago by lars20070 <[email protected]>

extend class test for chromatograms

576de092b8487e83a045920fe3262c95b89e83d0 authored almost 6 years ago by lars20070 <[email protected]>

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

53db2d4c9d86449e66fe566b1a75e7ec305131c9 authored almost 6 years ago by lars20070 <[email protected]>

update docu

ecabed8f2993296451605d1d9cb6cfa9ad9ef221 authored almost 6 years ago by lars20070 <[email protected]>

use auto loops, pass as const

c8730e09112149ec388fb8d3a48adefe48a512ad authored almost 6 years ago by lars20070 <[email protected]>

use optional params in API

e69f98c32af0f7154f266706c0a819ea9eea51b9 authored almost 6 years ago by lars20070 <[email protected]>

Update FineIsotopePatternGenerator.cpp

072491adcd635cf9015eeebde81877217a3e1dbf authored almost 6 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #3867 from oliveralka/fix/pyopenms_mac_240

[FIX] compile issue on MacOS

9421dd1734f0dae2f37e1e65752097eaad600bd6 authored almost 6 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #3780 from michalsta/develop

Improvements for IsoSpec integration

d272a98ee456a5e3a5a0115d11b986cabb570232 authored almost 6 years ago by Timo Sachsenberg <[email protected]>

[FIX] fix compile issue on MacOS

1ecd64fa08f305c6fdd72e8641dc2e51e9a33a03 authored almost 6 years ago by oliveralka <[email protected]>

trying to set spectrum reference NativeIDlookup prior to RTlookup

f174f785db8b88089aaaafe082cadf64b851ae2c authored almost 6 years ago by Leon Bichmann <[email protected]>

Add the possibility to use total_probability in FinePatternGenerator

9d7ab2313cc3cd43af52cf7abefef9d99c82660e authored almost 6 years ago by michalsta <[email protected]>

Merge pull request #3862 from OpenMS/fix/3424

fix #3424 in TOPPViewBase.cpp

686cd97152ee6dac982424ca3cee368c6e50da63 authored almost 6 years ago by Timo Sachsenberg <[email protected]>

[TEST] added new XFDR test with labeled linkers

eaae1b9935b08e13485a52868146d545a80f6aef authored almost 6 years ago by enetz <[email protected]>

[TEST] updated XFDR test files

4fed9cf6bad10eec923d9ae26bbb8a9d00791cc5 authored almost 6 years ago by enetz <[email protected]>

[TEST] updated OpenPepXL test files

8b967da20a1c8fd59bd7a2493ac58fca998720f4 authored almost 6 years ago by enetz <[email protected]>

[FIX] added a missing parameter to XLMS mzid parsing

c8e5dc34216fed1e9ebe3dfe8553161fa83a82b1 authored almost 6 years ago by enetz <[email protected]>

[TEST] updated OpenPepXLAlgorithm test, now fewer reported hits

f31d02c4fb5efa8464f08bd15e047393fd0c9f50 authored almost 6 years ago by enetz <[email protected]>

[FIX] OpenPepXL and XFDR: grouping of top ranked hits by light spectrum

for labeled linkers the top x hits for each spectrum pair were treated separately,
which resulte...

d026d01561e2fcb2e06ec032a29ead6ac1a2e4f3 authored almost 6 years ago by enetz <[email protected]>

[TEST] added new test for XFDR

test for robustness in case of some missing values in an input xquest.xml

cafa87ec1cef11a2a52ab89d93e8b77ec21d17f9 authored almost 6 years ago by enetz <[email protected]>

[TEST] updated new XFDR test files

754d607bac2f13d3bdd4f59b079c86fb61711c09 authored almost 6 years ago by enetz <[email protected]>

Update TOPPViewBase.cpp

b65984b26e38093a03f262e87b52d70058bea304 authored almost 6 years ago by Timo Sachsenberg <[email protected]>

[FEATURE] added novel scoring with other ion types

775b0dfb67285c062cc8a2a2156f4317d4673489 authored almost 6 years ago by Timo Sachsenberg <[email protected]>

[REFACTOR] moved combined scoring to static method

6ee28052d0267a9a2d8a90a8bb9c330bef405a48 authored almost 6 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #3859 from oliveralka/fix/pqp_MIMEType

[ADD] pqp to KNIME MimeType

c1988426f8085b7a6bbfd692af5c2af80ae8b0aa authored almost 6 years ago by jpfeuffer <[email protected]>

add pqp

7dc36328bdeca7a2ba3cad35c143d2e788d658f4 authored almost 6 years ago by Oliver Alka <[email protected]>

[TEST] added additional test files for OpenPepXL

a8804056fff4426cc106e738d86c7fb8b13cfa89 authored almost 6 years ago by enetz <[email protected]>

Merge pull request #3850 from OpenMS/doc/pc_info

added missing newline. add more information why correction failed

1ee4446e13d287b715254875c9d8e7b27dfe9875 authored almost 6 years ago by Hannes Roest <[email protected]>

docs: scheduler improvements

5ef8b4e631179ed4b375b63f40346ae4216985a3 authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

[FIX] fixed parsing decoy database path from xQuestXML format

37762e059dbbc2ff5e81c7930228725cfa89c80e authored almost 6 years ago by enetz <[email protected]>

[ADD] LOG SiriusAdapter; Class Test FragmentationAnnotation

2f93043a37702d3710232f5f0fa3873d454436da authored almost 6 years ago by oliveralka <[email protected]>

pqp MIMETYPE

bded4a317de34d33b1e024e2c65d827cbdb73980 authored almost 6 years ago by Oliver Alka <[email protected]>

Merge pull request #44 from hendrikweisser/rna-lfq

Tidying up loose ends, addressing reviewer comments

69bd1f504abbf8b85eae22a3189b12387d04c5c2 authored almost 6 years ago by Samuel W <[email protected]>

[FIX] fixed ambiguous cross-linker names in parsing XQuest xml files

20dc9fc60782801aa825376a01b0440cc6c28cdd authored almost 6 years ago by enetz <[email protected]>

[REFACTOR] FragmentationAnnotation class to functions only

5a0229cc55c2f34b7b019a4fb72a2b15840d9b09 authored almost 6 years ago by oliveralka <[email protected]>

[COMMENT] updated year in copyright notice

8412f205d66daf1abe17f7099096279f3e539145 authored almost 6 years ago by Hendrik Weisser <[email protected]>

[INTERNAL] changed implementation of 'IdentificationData' move c'tor to use 'std::move' instead of 'swap'

5a01ce4bdcc4f192448f0320c3a35fdc6fcff528 authored almost 6 years ago by Hendrik Weisser <[email protected]>

[DOC] small documentation updates

59d9edc753b226b6c40298f73b7b2b46b5527448 authored almost 6 years ago by Hendrik Weisser <[email protected]>

[INTERNAL] replaced include guards with '#pragma once'; updated some author/maintainer entries

e76eca1b97a8e2b05972a2754c04277bfba56b1e authored almost 6 years ago by Hendrik Weisser <[email protected]>

Merge branch 'poshul/hendrikweisser-rna-ms2-id' of https://github.com/poshul/OpenMS into rna-lfq

a2f00df80de906411e5c0cd3f67cc774699c0b93 authored almost 6 years ago by Hendrik Weisser <[email protected]>

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

cdd64dcc4c2ec53f57d86d4bc9c2e27a64aef740 authored almost 6 years ago by timosachsenberg <[email protected]>

Merge remote-tracking branch 'origin/develop' into feature/SiriusAdapter_output

7c5f36b8450ea105687aaab5745075cf1fd47b17 authored almost 6 years ago by oliveralka <[email protected]>

[TEST] fix ms test; add draft class_test

eea2e694197a5ced4865adfedec8eb8dcf493682 authored almost 6 years ago by oliveralka <[email protected]>

[ADD] class FragmentAnnotation; Minor fixes; remove comments

deef69eaea2b1d75654547a10ec033247fff2b48 authored almost 6 years ago by oliveralka <[email protected]>

[fix] fixed pyopenms bindings

2ecffdf7552de50ac3935dbb04abc9bb793ae3f1 authored almost 6 years ago by poshul <[email protected]>

[fix] fixed NASE progress bar

b4acc4a09289f2145c14066c30ab37d2c8457bbe authored almost 6 years ago by poshul <[email protected]>