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

[FIX] fix shadow warnings

0fdb4aa32fac56f5ad8805c773ce5df5b4c9d815 authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] add virtual destructor

b2713b16b99c0fe4bf1bcc00e7540f6e6cbe692a authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] fix unused parameter warning

42327c181b9343cf486d2ccd6fd6ec90c7bb97d7 authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] fix unreachable code

a43f7e7e6b1281f0a88852fb3b440b6cc4b71693 authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] add prototype

90e5bf69ec910ecd8ba8ebc9e5bfec1fbae8134a authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] warning eof

4476ea0e85bbd3910c204cee866c4c2278692c8a authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] fix unused member warning

bb1ab2ffe123357bfccd81ee332eefe9f9415ff5 authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] fix unreachable code

4fe1963b2182f2f35797289fd8084a390bdb8a0f authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] fix shadow warnings, cleanup

9ce97e1ffbb6ef307489b03a99d89f177d7cdd7a authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] fix shadow warnings

3a61df3afacdcab851d8f6072cd6bbe1ba2ff5cc authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] fix Wreorder warning

5e6739630cbbd237249bc17d85fd4f9da8b03f86 authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] fix integer constant warning

8ac87727444e4904b9a7cba4fbed20a1b3a58f25 authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] fix extra semicolon

466a17579bf9f634e1223ffb90b3dbe6bcd3b628 authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] fix unused parameter

a1c81b1aee6ecc54ad3ef8fda6b3b1d9f2fb7434 authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] fix unused variable

412bf7b9c2f206a9d37e4078248ab90969230e78 authored over 10 years ago by Hannes Roest <[email protected]>

[TEST] adopt tests to class interface

912274e79be5ab8e8d59c14e3f1eef22315a531c authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] adopt to new class interface

b04d220f207ffe74b2e3c5490987fd2fddd99a8e authored over 10 years ago by Hannes Roest <[email protected]>

Merge pull request #730 from hroest/feature/PeakPickerSNPerformance

Feature/peak picker sn performance

13c40ec1515f5c055d4d7a38aa81f921cf31156b authored over 10 years ago by Hannes Roest <[email protected]>

Implemented further feedback

98a6730a230e924a210ba0d491038b9e4b37b8d8 authored over 10 years ago by George Rosenberger <[email protected]>

Merge branch 'develop' into feature/PeakPickerSNPerformance_github

d7781487092909a9c3afe12a6338092f70b6c789 authored over 10 years ago by Hannes Roest <[email protected]>

Revert "[TEST] Speedtest"

This reverts commit ab3f43c75fa5f2893ffb8c92ef9d1104ef194835.

de46d2a7e53ad6480621153cb5b9d9cdd5ed887e authored over 10 years ago by Hannes Roest <[email protected]>

Merge pull request #1 from hroest/fix/small_fix

[FIX] fix error from 5b5bb90673145db3dd21927c591f2b925ca55a6a

5752df7413ad73d9feb94ba9fc5d911a784c0ae1 authored over 10 years ago by grosenberger <[email protected]>

Merge pull request #817 from hroest/fix/spline_derivative

[FIX] fix spline derivative for cubic spline

fa9b7e5b38c5bf304ed7ceb96e3101ae74c9a440 authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] remove extra bracket

- some compilers (gcc > 4.6) try to honor the extra bracket and compute
x*x explicitly, leadin...

08091c8d501cbf39d9330329454717a86301fbf9 authored over 10 years ago by Hannes Roest <[email protected]>

Implemented feedback from hroest

78a674d8a4e2f419e8673a46021dd05a7798dabf authored over 10 years ago by George Rosenberger <[email protected]>

[TEST] adapt and fix tests

25b6a2e1c87b1c8466f2df1d98310b14bfc79cbd authored over 10 years ago by Hannes Roest <[email protected]>

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

bde5c162845bac1431edf47262a82ec506f8ce7c authored over 10 years ago by lars20070 <[email protected]>

[TEST] adopt tests to cubic spline interpolation

26d29d7ec25d17da78fc7b8318f32af3c45a9a70 authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] fix spline derivative for cubic spline

fixed spline derivative for cubic spline

90e0805f63374379340ae889609f9e14a3bde656 authored over 10 years ago by Hannes Roest <[email protected]>

[FEATURE] switch to CubicSpline2d

167dabdb046759a32a6f1130a637105ee4cf71ef authored over 10 years ago by Hannes Roest <[email protected]>

Merge branch 'develop' into feature/PeakPickerSNPerformance_cr

2536391545ea7723ec27a748a61f1b734395a4dd authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] fix error from 5b5bb90673145db3dd21927c591f2b925ca55a6a

690005dd1d758d65105350e04ff70bd55b1dd06b authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] cleanup, add documentation

5e5c0c4df00ac337b2445b0953edd58d64664e32 authored over 10 years ago by Hannes Roest <[email protected]>

[INTERNAL] less copying

7ae967d532d1182de49947af6fd8116c9ddd2613 authored over 10 years ago by lars20070 <[email protected]>

[INTERNAL] less copying

fdec552a5386d2b98880b1570d4d31cfaafa0fb6 authored over 10 years ago by lars20070 <[email protected]>

[INTERNAL] const methods added

94a7a6cdd5d7b45464092001b2bc25d6b683a319 authored over 10 years ago by lars20070 <[email protected]>

[NOP] public/private interchanged

270f2dbbb1f0dea042b3ef9ade5e2cffab10bb21 authored over 10 years ago by lars20070 <[email protected]>

[FIX] adapted to change in AASequence class

e4220897b1a51d124dcc7145faa8105eccb954c9 authored over 10 years ago by Hendrik Weisser <[email protected]>

[API,TEST] getSpline removed

89eba0ea7af2414ff80dd5f1afa09ca8bd2fdb7d authored over 10 years ago by lars20070 <[email protected]>

[FEATURE] ConvertTSVToTraML: Support for SpectraST MRM Transition Lists

5b5bb90673145db3dd21927c591f2b925ca55a6a authored over 10 years ago by George Rosenberger <[email protected]>

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

520e55c905506e52b6f544cb5da106f86cc90ea3 authored over 10 years ago by Hendrik Weisser <[email protected]>

Merge pull request #812 from hroest/fix/cppcheck

[FIX] per cppcheck

54a10fe876e368c48df0ddcfa6e765e28114fe8d authored over 10 years ago by timosachsenberg <[email protected]>

Merge pull request #813 from hroest/fix/openswath

Fix/openswath

d55e89ace92528314b0a4ea1aaee61535c219175 authored over 10 years ago by Hannes Roest <[email protected]>

[DOC] correct documentation

- csv is not a valid input format here

47474725886eb0dbae4cc4385950e5097f370f0c authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] bugfix for TSV reader

- ProteinName is now a required field

490311052a7de97d5f98aea4d0dca308c8b9099f authored over 10 years ago by Hannes Roest <[email protected]>

Merge pull request #811 from hroest/fix/SwathDebug

[NOP] add better debug information and error handling

2d4b646c04b77670ac0c842d12cf36cd884cd99d authored over 10 years ago by Hannes Roest <[email protected]>

[API,TEST] evalNonNegative removed

82a6a402aa58a20f58f190918317e6e81f148739 authored over 10 years ago by lars20070 <[email protected]>

[FIX] per cppcheck

15b86df34f666ad512ae11cb49b6274c9284a229 authored over 10 years ago by Hannes Roest <[email protected]>

[TEST] SplinePackage test corrected

cef5b5e65f86a7e774410d17129662de785debe4 authored over 10 years ago by lars20070 <[email protected]>

[FIX] per cppcheck

65e77c7fc0d0971cb463d674dce6b8637003fb59 authored over 10 years ago by Hannes Roest <[email protected]>

[NOP] add better debug information and error handling

- better debug information and error handling for swath windows file
- add debug information abo...

a91e4d6fecaab0011a9c4570dbf9b89b4288aeed authored over 10 years ago by Hannes Roest <[email protected]>

[INTERNAL] Eigen splines replaced by CubicSpline2d

c8900e9040521348af73c17c052ec000a26aa275 authored over 10 years ago by lars20070 <[email protected]>

[API,TEST] non-negative eval for cubic spline added

a9675993832ab90a802e07fc6b82e2d3ea622c4b authored over 10 years ago by lars20070 <[email protected]>

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

db13b74f9ddc62aa9b8b815a9b6c8066955e2d26 authored over 10 years ago by lars20070 <[email protected]>

Merge pull request #810 from lars20070/feature/CubicSpline2d

[FIX] improvements/code fixes of cubic spline interpolation

21ef0e60bef91c0f505e89fef4b8e736b6923477 authored over 10 years ago by Stephan Aiche <[email protected]>

[INTERNAL] template remnants removed

8567354d96c31d31e49d21780a3569ed9c4fe730 authored over 10 years ago by lars20070 <[email protected]>

[TEST] sections in tests corrected

0edd6f13b98f41832cff2688443c300f9f41e69d authored over 10 years ago by lars20070 <[email protected]>

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

3ca37cf2c391a3ba9908373b0ec6e20962252cc5 authored over 10 years ago by lars20070 <[email protected]>

[NOP] indention changed

47c3791aa60bb7581b971ec81a8f267e3ab17b07 authored over 10 years ago by lars20070 <[email protected]>

[FIX] addendum to 5f818b0bbb8aabb35bb3502287ed2e06d8371b72; fixed now invalid call to AASequence(char *) by repaling it with AASequence::fromString()

2332f8c29aec267dcbfcfb5e0cfdbe980364d83c authored over 10 years ago by Stephan Aiche <[email protected]>

[NOP] uncrustified

09a9a592c48d0f787201243b1e8e7bb85762b660 authored over 10 years ago by lars20070 <[email protected]>

Merge branch 'develop' into fix-msgfplusadapter

fabcc6e72b4813eec42b3d16874b96e2afdc1672 authored over 10 years ago by Petra Gutenbrunner <[email protected]>

[NOP] uncrustified

28cbf88c559feca409095dab20c3db4ab05444d8 authored over 10 years ago by lars20070 <[email protected]>

[TEST] CubicSpline2d test split in several sections

9e9a786e08505cb3f4f680a96087bced033c34ed authored over 10 years ago by lars20070 <[email protected]>

[API] DLL macro added

2624900ce870632ea7553fc4d04aa26db9d75f6a authored over 10 years ago by lars20070 <[email protected]>

[API] add cpp for CubicSpline2d

418fb0b8c96b68025dcfd8bb9470582661828e7e authored over 10 years ago by lars20070 <[email protected]>

Merge pull request #792 from timosachsenberg/feature/AASequence_refactoring

[FEATURE] AASequence refactoring

5f818b0bbb8aabb35bb3502287ed2e06d8371b72 authored over 10 years ago by Stephan Aiche <[email protected]>

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

15322f9093d603cc1733710cbb3f5b6d4f4636d9 authored over 10 years ago by lars20070 <[email protected]>

[FIX] fixes for RTNormalizer

- as discussed in https://github.com/hroest/OpenMS/pull/4
- use a percentage cutoff in the RT gr...

8e84c52b86694d8b678a0356f626d782b4da920f authored over 10 years ago by Hannes Roest <[email protected]>

Merge pull request #4 from grosenberger/feature/custom_iRT

[FEATURE,FIX]: Small changes for RTNormalizer

f0d21ab70a005c4530158d64aa1737a9afddcf49 authored over 10 years ago by Hannes Roest <[email protected]>

Merge pull request #804 from grosenberger/fix/mrmdecoy

[FIX] MRMDecoy: Fix neutral losses for higher charge states

3add7a7deedc45bc95523795e10364252ea0137c authored over 10 years ago by Hannes Roest <[email protected]>

Merge pull request #807 from lars20070/feature/CubicSpline2d

cubic spline implementation

bfbd8ea62541947815972a65f2e768899adf15f9 authored over 10 years ago by Hannes Roest <[email protected]>

[API, TEST] templates removed from interface, class tests added

108279825f25bc0fefe6c3c177386710ff576c4b authored over 10 years ago by lars20070 <[email protected]>

[FIX #803] Add decoy hits to output

Set show_decoy = 1 to keep the decoy hits

modified: ../src/topp/MSGFPlusAdapter.cpp

285dc5817e39a8788ca010ed6fc47d2f0bf7a6de authored over 10 years ago by Petra Gutenbrunner <[email protected]>

[API, INTERNAL] cubic spline interpolation added

11fc2c1d61a196e461be9c0feaeaae1db6c707f2 authored over 10 years ago by lars20070 <[email protected]>

[FIX #806] ConsensusID

TOPP ConsensusID FileType idXML:
- after reading a peptide identification, sort their peptide hi...

dbf928d18e8dbb11818765657b177e1308c908f4 authored over 10 years ago by Petra Gutenbrunner <[email protected]>

Merge pull request #805 from uweschmitt/pyopenms_adapted_pxd_declarations

[PYOPENMS] added getters/setters for MZ and RT in PeptideIdentification....

238817ed43430e973b87fc2211dd53b69d579a9c authored over 10 years ago by Hannes Roest <[email protected]>

[PYOPENMS] added getters/setters for MZ and RT in PeptideIdentification.pxd

d87794dd9383b27af015e825606fc5f18d908b6e authored over 10 years ago by Uwe Schmitt <[email protected]>

[TEST] OpenSwathDecoyGenerator: Fix of second test

e7424bc4aa00625d7a0c4476e12880de810daa44 authored over 10 years ago by George Rosenberger <[email protected]>

[FIX] Get m/z from input file, because after converting to tsv the value is rounded.

The searchengine throws an error if you create an outputnode for the .mzid file, because the file...

5de86fc31bafc9448fc82737d1ab83945d853f70 authored over 10 years ago by Petra Gutenbrunner <[email protected]>

[FIX] write original intensities instead of scaled ones

630bad908f0cb619749d7e155aa96f487045904e authored over 10 years ago by Hendrik Weisser <[email protected]>

[FIX] MRMDecoy: Implementation of feedback

9272f84b3ef0ab2dfe175155e1c8e36b951efcfd authored over 10 years ago by George Rosenberger <[email protected]>

[TEST] OpenSwathDecoyGenerator: Fixed TOPP tests

d6c1caf2bc7f83f42b1a2e522e4a7958a365d05e authored over 10 years ago by George Rosenberger <[email protected]>

[FIX] MRMDecoy: Hack to enable specific losses with shuffling

ebafdfa2ffe28e7177261a51f6755bbcaa4abbd2 authored over 10 years ago by George Rosenberger <[email protected]>

[FIX] various fixes to get feature (elution peak) detection working

a7822c6fa82ac89700f589be3979664726b4f54b authored over 10 years ago by Hendrik Weisser <[email protected]>

[FIX] MRMDecoy: Fix losses for higher charge states

7cbb6c13cd5526cdb0faab605b2c1aa4f8e4fe58 authored over 10 years ago by George Rosenberger <[email protected]>

[FIX] MRMDecoy: Fix losses for higher charge states

b3b2d490654c4d2752e911d2ccbf9b2387a131e6 authored over 10 years ago by George Rosenberger <[email protected]>

Merge branch 'develop' into feature/AASequence_refactoring

0dc616dce7ea8dafff79d67d3afd9b6f56b34ba3 authored over 10 years ago by Timo Sachsenberg <[email protected]>

[DOC,STYLE] documented exception, improved formating

367772c388ec268eefb8d533a0f50cee38e27428 authored over 10 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #802 from hendrikweisser/fix-toppbase-message

[FIX] fixed copy-paste mistake in TOPPBase error message

9501b517f4958d78ab52c9b0ba7b9c267bbb7138 authored over 10 years ago by Stephan Aiche <[email protected]>

[MSGFPlus Adapter Coding Conventions]

2 spaces instead of tab

modified: ../src/openms/source/APPLICATIONS/ToolHandler.cpp

180dea1413509af85ad7c8d5f3005dbe1a5f37d8 authored over 10 years ago by Petra Gutenbrunner <[email protected]>

[FIX] fixed copy-paste mistake in error message

(However, the error message itself also seems dubious to me: Couldn't "NaN" be used to represent...

e202b480d838028e1b4e8a2610c3c4b6104d73be authored over 10 years ago by Hendrik Weisser <[email protected]>

[FEATURE] more work on feature detection (adding meta data to features: m/z, charge, peptide IDs)

bb05752dc4e32ddfb5e7be54ce1766bb634a57f8 authored over 10 years ago by Hendrik Weisser <[email protected]>

Merge branch 'develop' into fix-msgfplusadapter

7078e96eb1f06af1c817d49f0bb7ae5e8fda72af authored over 10 years ago by Petra Gutenbrunner <[email protected]>

[STYLE] fixed some style issues in AASequence.cpp

7ffb7c3d944bdfcc8e7a3a2c6ed3d3db5b0ec939 authored over 10 years ago by Timo Sachsenberg <[email protected]>

[API] removed classes irrelevant for pull request #800

2d32d15d47ac396e21f5461760fc751e2dc0aa7d authored over 10 years ago by lars20070 <[email protected]>

[API] removed classes irrelevant for pull request #800

15dde460a2e245c379fb2bb68fa793c1b3fbe4af authored over 10 years ago by lars20070 <[email protected]>

[FEATURE, TEST] removed FeatureSetFinder tool and its tests

41d2b58c415918a0d705b97c0ac8939b59ca06b4 authored over 10 years ago by lars20070 <[email protected]>

[NOP] uncrustify on SplinePackage and SplineSpectrum

05b225de3fd3d300f65d60ec19e2a065c9b55cec authored over 10 years ago by lars20070 <[email protected]>

[TEST] class tests for SplinePackage and SplineSpectrum completed

07e8ee8094f21bf2709de823f6a898b764810740 authored over 10 years ago by lars20070 <[email protected]>