Ecosyste.ms: OpenCollective

An open API service for software projects hosted on Open Collective.

github.com/OpenMS/OpenMS

The codebase of the OpenMS project
https://github.com/OpenMS/OpenMS

[INTERN] lower bound index fixed

e3422ca10f9252ea18275fdbc2b6a0ffb8404611 authored about 10 years ago by lars20070 <[email protected]>
Merge pull request #911 from aiche/fix/ff-centroided-exception-miuse

[FIX] FFCentroided replace exception handling with proper check

bd45e8b4b432f1d0c85cdce13c75ee7423d0a716 authored about 10 years ago by Hannes Roest <[email protected]>
[FIX] addendum to 8fef18dda7b904850981f303ec5964eb5826a5b2 (findNearest - try/catch - fix)

68e26379265dfb1e5b3acbec63890e8c01fe093c authored about 10 years ago by Stephan Aiche <[email protected]>
[FIX] fixed try/catch misuse for findNearest also in MassTraceDetection

8fef18dda7b904850981f303ec5964eb5826a5b2 authored about 10 years ago by Stephan Aiche <[email protected]>
[TEST] CubicSpline2d eval() at input nodes tested

6939b4a0275dd4d6c5d32d4e712fb12e96ed877b authored about 10 years ago by lars20070 <[email protected]>
[FIX] replace exception handling with proper check

in ff centroided the precondition of findNearest was handled by adding
a try/catch around it ins...

4dff13aa364b0c9c43b0d7dd3f4b7651efe9f0c5 authored about 10 years ago by Stephan Aiche <[email protected]>
Merge pull request #821 from hroest/fix/suppress-warnings

[FIX,BUILD] suppress clang warnings

2a0c9edcc1b2ca6816c18e0f516020335c10d00d authored about 10 years ago by Stephan Aiche <[email protected]>
[BUILD] ignore additional warnings for clang

5d78d1e6092b878f95b6115acf198b0cf991c1e2 authored about 10 years ago by Hannes Roest <[email protected]>
[FIX] added pragmas

- suppress warnings in certain positions where we either believe that
the code is correct (or ...

6dfbd77935ba4b2019196ba7f7460bffdc7c1f66 authored about 10 years ago by Hannes Roest <[email protected]>
[BUILD] suppress certain warnings

- suppress undef macros because of platform-specific macros
- add Wno-unknown-pragmas for gcc on...

11e391a918ecffee4026570aa507e22f5f6fbbbd authored about 10 years ago by Hannes Roest <[email protected]>
Merge pull request #910 from aiche/fix/unity-build

[FIX] fixed unity build error introduced in #845

1d75c75694047887e14df22dc17c5c2f3aaa3463 authored over 10 years ago by Hannes Roest <[email protected]>
[CI] added unity to ci build name

cb9f22fdbe8d41beef25b893a8977630f38d87c5 authored over 10 years ago by Stephan Aiche <[email protected]>
[CI] added unity build test to travis

11bd2308552ee6fa086ee8c9c72fd8047f68284a authored over 10 years ago by Stephan Aiche <[email protected]>
[FIX] fixed unity build error by renaming internal namespace in IndexedMzMLDecoder

9a2170f3101e03494d25d1eddb0adeadaeec58c5 authored over 10 years ago by Stephan Aiche <[email protected]>
Merge pull request #903 from hroest/fix/mzXML_fix

[FIX] mzXML fix (filterLine, basePeakMz)

8d77eb89856c8ece1cf4755a8b1abe619e5dc8e8 authored over 10 years ago by Stephan Aiche <[email protected]>
[INTERNAL] ratios corrected

031ce6e09c9a0234a1d9006b56deb80858a06165 authored over 10 years ago by lars20070 <[email protected]>
[INTERNAL] ratios calculated from profile intensities

6a26ad7fc585b81cbd632d0eed2d61403e03b038 authored over 10 years ago by lars20070 <[email protected]>
[INTERNAL] complete consensus positions written

3a7d8b8dd1f7eff2f6c28ca25596d8e2522758b5 authored over 10 years ago by lars20070 <[email protected]>
[INTERNAL] incomplete consensus map generated and written

2d754e650fe551c50d52c4ad196c1961ad35f6c6 authored over 10 years ago by lars20070 <[email protected]>
[INTERNAL] incomplete consensus map generated and written

f117395029976732a9ca0ef9d650db8ad80d348d authored over 10 years ago by lars20070 <[email protected]>
Merge branch 'feature/MZID' of https://github.com/mwalzer/OpenMS into feature/MZID

c7e6778dbffd5bc9419deb344ebab4bb1f60d1c2 authored over 10 years ago by mwalzer <[email protected]>
[FIX] fixed proteinhit reading

8e263c39d5369d22e88108c7e64121b7e748991b authored over 10 years ago by mwalzer <[email protected]>
[INTERNAL] full iteration

752b0677e8bfe1c11973bbb1655ef94592d3d904 authored over 10 years ago by lars20070 <[email protected]>
[INTERNAL] consensus map generated

361250f8d3cbf9f2524dfb3234516de8fb50a9a6 authored over 10 years ago by lars20070 <[email protected]>
[INTERNAL] iterating through filter and cluster results

4d75c0f9cee36b69335bb7d8bba709bbd7dba1fa authored over 10 years ago by lars20070 <[email protected]>
[API] writing to debug output directory

4d2dd3dadcc9db3d95013fac1ae9174508286be0 authored over 10 years ago by lars20070 <[email protected]>
Merge pull request #898 from hendrikweisser/mgf-compact

More compact format for MGF files (fixes #890)

0bc45d8a1e1f63cf3396a29bd54fb87fffa12e6a authored over 10 years ago by Hannes Roest <[email protected]>
Merge pull request #894 from aiche/feature/better-lib-finding

[FEATURE] improved 3rd party lib finding

f9e3e9d0c5c8a502775c6b0743ca0e3b7253524f authored over 10 years ago by Hannes Roest <[email protected]>
[API] writing final output started

373e0b636a66dc2fb9272566059a5a4d618d0e47 authored over 10 years ago by lars20070 <[email protected]>
Merge pull request #845 from hroest/feature/StringUtils

[FEATURE] replace String classes with StringUtils

ce574da812e42941b686b4a905ebd1cd4ac9e813 authored over 10 years ago by Hannes Roest <[email protected]>
[INTERNAL] main() restructured

70c8394555655f3e96a9bbfbe9dfe350459754a7 authored over 10 years ago by lars20070 <[email protected]>
[INTERNAL] peak pattern generated

19e231212a50942f2dcd000e28672181a2c7a4eb authored over 10 years ago by lars20070 <[email protected]>
[INTERNAL] knock-out mass shifts generated

edf37704f7e9737e0c147125ccd08993b1d7dc55 authored over 10 years ago by lars20070 <[email protected]>
[FIX] small edit of last commit.

ec7e0dbcdde3f14d7080a109c5afe9ac9a4eaf7d authored over 10 years ago by liangoaix <[email protected]>
[FEATURE] add conversion of tandem.xml output into idXML.

add test files for tandem.xml conversion.

97b324b8141e67fa3b5164e04df2a55cbcb65128 authored over 10 years ago by liangoaix <[email protected]>
[INTERNAL] knock-out parameter added

c6b17e0e248d96e006815a45ad27f7ed5daac385 authored over 10 years ago by lars20070 <[email protected]>
[INTERNAL] mass patterns for SILAC, Dimethyl and ICPL

b23825a280bd46ee17d6f0a941ad0e3268a9d667 authored over 10 years ago by lars20070 <[email protected]>
Merge branch 'develop' into pepXMl

ef27e27a52b4e0d965e8529026804c9b066f1b29 authored over 10 years ago by liangoaix <[email protected]>
[INTERNAL] generate mass patterns

2f5eeee1ba03863730fa6afe524883a8cd952085 authored over 10 years ago by lars20070 <[email protected]>
[FIX] added scannumber to metainfo of PeptideIdentification

f04e0444a87779bc1fd3afaebc44c6ab0be9f9fa authored over 10 years ago by mwalzer <[email protected]>
[INTERNAL] labels string split

5e970fad35dba8e06dbc310543c56c8a0bfc1dd4 authored over 10 years ago by lars20070 <[email protected]>
[INTERNAL] labelling detected

af4a33535f66d1d659d3f74adf862fe32df882ab authored over 10 years ago by lars20070 <[email protected]>
[INTERNAL] user parameters updated

ff2e570afc914ebf016c9b22f8f603c76cfe0dfc authored over 10 years ago by lars20070 <[email protected]>
[INTERNAL] user parameters updated

21af2e131a1a9acac9e91a16a67e3fc8efc4d203 authored over 10 years ago by lars20070 <[email protected]>
[INTERNAL] user parameters updated

afc915ed44348dde8fc17bac9f45b8a82e7355c0 authored over 10 years ago by lars20070 <[email protected]>
[INTERNAL] user parameters updated

7a143c25f51caffcc0f62db07d40b3c51d90a03a authored over 10 years ago by lars20070 <[email protected]>
[INTERNAL] user parameters updated

c0bfcf186c7cb3851a281f5aa3cdeb1df7a20178 authored over 10 years ago by lars20070 <[email protected]>
[INTERNAL] reset decimal precision of stream after storing MGF file

65d5838a9f59c82e120e56c6eaabbea72d194b26 authored over 10 years ago by Hendrik Weisser <[email protected]>
[INTERNAL] user parameters updated

31fd5302b1e03b16043d134baab7c02f198a8b35 authored over 10 years ago by lars20070 <[email protected]>
[TEST] added test for storing MGF in compact format

691c8e54607e4cff5a75c69b9a56e3ff8e0e18ec authored over 10 years ago by Hendrik Weisser <[email protected]>
[INTERNAL] use preprocessor constants for decimal precision values

6c6366857fcfcd75ebb42ae5ce924ccb9e1743f4 authored over 10 years ago by Hendrik Weisser <[email protected]>
[INTERNAL] user parameters updated

6cdd3c1d71bb99a9ab9576ea6af19b69bc15987b authored over 10 years ago by lars20070 <[email protected]>
[INTERNAL] user parameters updated

bbd4a7635f5a36f040b064dbd24d7769395d2d20 authored over 10 years ago by lars20070 <[email protected]>
[INTERNAL] labels updated

295b8cd49ee60862b402a13d5443670f4a60a9a8 authored over 10 years ago by lars20070 <[email protected]>
[INTERNAL] user parameters modified

42439ec4834476f7b7f3d679073343071c5ac7b2 authored over 10 years ago by lars20070 <[email protected]>
[FIX] add new mzXML attribute: basePeakMz

- [TEST] new test file (where attribute is non-zero as well)

e8a964c3dbf191d9cbbb80b3d456127bc9b3a41d authored over 10 years ago by Hannes Roest <[email protected]>
[TEST] fix tests

316ca7b7a96d661232808c882566ae78093200fb authored over 10 years ago by Hannes Roest <[email protected]>
[FIX] read and write the filterLine attribute

- fix MzXML file handling, no longer ignore filterLine attribute

ff3c99cb84fb2c7425c75dd0dc6dc36b88b59505 authored over 10 years ago by Hannes Roest <[email protected]>
[INTERNAL] move xml escape function

- move xml escape function from XMLFile to XMLHandler
- Handler usually has the task to properly...

dbe57b6bf01dc60398fab4bae8fccfa198116db3 authored over 10 years ago by Hannes Roest <[email protected]>
[BUILD] new tool fully registered

e9d12628d396f9a7ee995bfd9b3138e44af32735 authored over 10 years ago by lars20070 <[email protected]>
[API] FeatureFinderMultiplex tool added

e8f8e45d69d1c4f154d1d96c64259dfd56224adf authored over 10 years ago by lars20070 <[email protected]>
Merge remote-tracking branch 'upstream/develop' into feature/MultiplexClustering2

664650c781ab99fbe8dc7de02b80ee9b96c23fb0 authored over 10 years ago by lars20070 <[email protected]>
Merge branch 'develop' into feature/better-lib-finding

f2f33899f681c0d4915ced7be1db8f06ee50ffa3 authored over 10 years ago by Stephan Aiche <[email protected]>
[BUILD,PYOPENMS] temporary workaround for pyOpenMS

* see #900

53e87963f3c11551da50755a857e25e4ee34a79a authored over 10 years ago by Stephan Aiche <[email protected]>
Merge pull request #902 from hroest/fix/pyOpenMS_fix

[FIX,PYOPENMS] fix pyOpenMS after #875, #896

5ed44c310325cdce803bd233ce1f45e4b54c5fbf authored over 10 years ago by Stephan Aiche <[email protected]>
[FIX] fix pyOpenMS files

46193ca0e2072c2235d9893a95f96a053e90e355 authored over 10 years ago by Hannes Roest <[email protected]>
Merge pull request #904 from hroest/feature/fixPeakBoundaries

Feature/fix peak boundaries

303d16ae980ea3a83976e29af8f6365b5dfa5eb1 authored over 10 years ago by Hannes Roest <[email protected]>
[FIX] pepXML: replace spaces by tabs; adapt the raw_data type; edit documentation.

48e09d171ea0f3dc49d96807c3eff702eb9b7de9 authored over 10 years ago by liangoaix <[email protected]>
[FIX] add test data for PepXMLFile and XTandemAdapter.

[FIX] Fix the spectrum_query in test data for PepXMLFile().store.

6cdd88796a0c95d5ee55ba3ccfc38744cca38dbe authored over 10 years ago by liangoaix <[email protected]>
[FIX] pepXML writing format.

c770dbc9e2e67c9886934c767f40229bf5dcb158 authored over 10 years ago by liangoaix <[email protected]>
[FIX] Distinguish PeptideProphet_pepXMl and raw_pepXMl.

[FIX] RT_index information from XTandem is added to spectrum id and scan_id in stored pepXML fil...

8ea5cfbb7c2fdcf243ae3d8528069aca42eb5cf9 authored over 10 years ago by liangoaix <[email protected]>
[TEST] MultiplexClustering test extended

2ad75cdd826e4b8e4e011b42a8ac65d7f84bae01 authored over 10 years ago by lars20070 <[email protected]>
[TEST] MultiplexFiltering and MultiplexClustering tests fixed

970a438e4c30ccd783fd69d5e4504f6cbb1ccefe authored over 10 years ago by lars20070 <[email protected]>
[TEST] MultiplecClustering test

0f9f8e638171350afd9934ff6f6681ff16b6a23a authored over 10 years ago by lars20070 <[email protected]>
[TEST] test added

1d5c430d87f168274242113a69edb22d2d88889a authored over 10 years ago by lars20070 <[email protected]>
[INTERNAL] exception more detailed

61ab9e4714f4067804d7ed192ffad336413de755 authored over 10 years ago by lars20070 <[email protected]>
[TEST] MultiplexClustering test fixed

3217c9f38949ac68d8016db2335cf3828a90903b authored over 10 years ago by lars20070 <[email protected]>
[FIX] fix peak boundary extension

- no extension of peak boundaries if zero value is encountered
- analogous to #880

6959a92bd2b3ebbb199400033cf59d1a788c3e07 authored over 10 years ago by Hannes Roest <[email protected]>
[TEST] add test for zero cutoff

ed710b49614d1ecc991d11c3086894a5a2e03600 authored over 10 years ago by Hannes Roest <[email protected]>
[INTERNAL] exception more detailed

c1d7127dfa03d9b8947a070a67137a6bb899fb79 authored over 10 years ago by lars20070 <[email protected]>
Merge remote-tracking branch 'upstream/develop' into feature/MultiplexClustering2

bf997045f6967c275233137dd3b67b58bce7918e authored over 10 years ago by lars20070 <[email protected]>
[API] HashGrid2 renamed

14ad63683561a561fe4a783eae39b7125083b4c5 authored over 10 years ago by lars20070 <[email protected]>
Merge pull request #901 from OpenMS/feature/fix893

[FIX] fix MS level for DTA file reader

e582cbc11b620c4886b155d70b95cb99cc9faefa authored over 10 years ago by Hannes Roest <[email protected]>
[NOP] uncrustified

cbafa458141dbcf556d65f7a06417e50fd399f36 authored over 10 years ago by lars20070 <[email protected]>
[MOVE] move pyOpenMS files to src

311c73734d856f7af428d4882f7f717c25a7177e authored over 10 years ago by Hannes Roest <[email protected]>
[FIX] fix test

157bc97c6dc5c4b776fe62e9f75a18aa61a23441 authored over 10 years ago by Hannes Roest <[email protected]>
[FIX] last fix

012df2d172aab8840077fad41ca75ac786f9f28b authored over 10 years ago by Hannes Roest <[email protected]>
[FIX,PYOPENMS] fix pyOpenMS after #875

- fromUnmodifiedString function was removed

08b309ad1b65687765bde762cf801d6fbe60ae1f authored over 10 years ago by Hannes Roest <[email protected]>
[FIX] fix MS level for DTA file reader

fixes #893

482b0d51c6ec5c4a6ede691c4c56691bada577bf authored over 10 years ago by Hannes Roest <[email protected]>
Merge pull request #899 from timosachsenberg/fix/ModificationsDB_doc

[DOC] some minor documentation addition

7eaa06854f0d556c2eec305a888aff1fd99fb395 authored over 10 years ago by Hannes Roest <[email protected]>
[BUILD] removed last traces of old contrib finding code

e5cc09ed069245fe69fa08bd7d7db1bdd8ce1874 authored over 10 years ago by Stephan Aiche <[email protected]>
Merge pull request #897 from cbielow/develop

(feature for Windows developers) added a small Windows .reg file

3ff63c18a3a1257b59e7d72cc2206e5a8810cd9f authored over 10 years ago by cbielow <[email protected]>
[DOC] some minor documentation addition

cd344096658c3bebf208230ae6d58f658dcdb225 authored over 10 years ago by Timo Sachsenberg <[email protected]>
[FORMAT] removed unnecessary newlines in MGF output

b4c9f9a8c30a7f551309a51192a6d88a0c8ccf86 authored over 10 years ago by Hendrik Weisser <[email protected]>
(feature for Windows developers) added a small Windows .reg file, which allows to change file extensions on Windows to another OpenMS instance

949a1dcfb355db5fd160a8af216e2dfbcab9541d authored over 10 years ago by Chris Bielow <[email protected]>
[PARAM,DOC] added option to write compact MGF; small doc improvements

bd05b05a8921fb40010e48ddb52c1070ca032ef8 authored over 10 years ago by Hendrik Weisser <[email protected]>
[FORMAT] adjusted decimal precision for writing compact MGF

776e66a5c09ffc0dc252802c6a198dc305c4b06b authored over 10 years ago by Hendrik Weisser <[email protected]>
Merge pull request #896 from cbielow/lipids

[FEATURE] added scan-polarity filter to FileFilter

b469379641b93899639dc20802767e410200f131 authored over 10 years ago by Stephan Aiche <[email protected]>
added scan-polarity filter to FileFilter; RangeUtils speed improvement by 24% via XOR; minor fixes

5b6e330dffccfe73cbc82cec4a4ef6ecaff4d342 authored over 10 years ago by Chris Bielow <[email protected]>
[TEST,PARAM] updated test with new signatures of 'store' methods

318d59284d0163988c7282cf73d658719284b7fd authored over 10 years ago by Hendrik Weisser <[email protected]>