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

Fix clang warnings

a6b6debec8d5db06b6ed596ea14c117c2de832b7 authored about 6 years ago by michalsta <[email protected]>

generate elution peak clusters - in progress

- collect close apexes : done
- clustering : in progress

3f91f60ca6c7824b643ad4452848403c3434ac54 authored about 6 years ago by JeeK <[email protected]>

Merge pull request #3821 from enetz/fix/TV_IDView

[FIX] TOPPView IDs with theoretical spectra

736d2568a1bfd1a5af423fa4d493120e7cea7ba4 authored about 6 years ago by Timo Sachsenberg <[email protected]>

Fix some cpplint complaints

543028a037e52954447e33dfdf32b1a27c496796 authored about 6 years ago by michalsta <[email protected]>

Replace bzero with the more-widely available memset

e585f1159bc003c6983895a2d7b6c9a84411bc7f authored about 6 years ago by michalsta <[email protected]>

Reserve the vector size before extracting configurations into it

95146416d862af60a6353d124c8a6acfa1362e4a authored about 6 years ago by michalsta <[email protected]>

Fix mman.h detection in IsoSpec

20f294ae4fe81cfdf8726fcc0597939a95a890b8 authored about 6 years ago by michalsta <[email protected]>

Rework the wrapper's interface a bit in preparation to expose the Layered algo

5879ea3202732b1ecd5b34d07d1f6d70be70cfd7 authored about 6 years ago by michalsta <[email protected]>

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

1207b9d489ae04be0e4745c27a6ec7c183e62fa9 authored about 6 years ago by michalsta <[email protected]>

Update IsoSpec to 1.9.0beta1

221d74244c3aa0832a5ceed717584f853a4f0f17 authored about 6 years ago by michalsta <[email protected]>

Pull in IsoSpec v1.9.0alpha3

5275c281004a3d9e928884dfd94fedf75edab11b authored about 6 years ago by michalsta <[email protected]>

Fix wrong macro names

9266b1d691c641cf02ebf60f2f5e5a4da8595d85 authored about 6 years ago by michalsta <[email protected]>

FIX

ff745a9795c7b51b2c0dacb8e66c926c7429d303 authored about 6 years ago by Hannes Roest <[email protected]>

Delete mman.h

9dd9b6af7582440ad74da8eb2f151ca9d820eb50 authored about 6 years ago by Hannes Roest <[email protected]>

Delete mman.c

5d285f6e69ad30a604b356d93201f3cd96fb994e authored about 6 years ago by Hannes Roest <[email protected]>

Bring IsoSpec implementation up to d41e5f89924d12518e0c96904baa88edac37c667

361c146c88d299a802b9bc9c7325f3c8b3729b7b authored about 6 years ago by michalsta <[email protected]>

Update isoMath.cpp

b2187dc586d7f7bd8bc9c180f83f0ee7719bfe17 authored about 6 years ago by Hannes Roest <[email protected]>

[FIX] Fix issue mentioned in comment https://github.com/OpenMS/OpenMS/pull/3780#discussion_r223198483

a9e9496620dfebca2f603600d09bd9f746c58ad2 authored about 6 years ago by michalsta <[email protected]>

Comment out Ordered and Layered for now; remove tabulators

2deed1f3090e3ba0b519ace30015aa95d413e9bf authored about 6 years ago by michalsta <[email protected]>

Delete mman.c

95e97ca2af14eddbca4e7e056513754a8e8f11d0 authored about 6 years ago by Hannes Roest <[email protected]>

FIX

22cf000950653dda3cb275b6b4d5aa9f4e60b99f authored about 6 years ago by Hannes Roest <[email protected]>

Update IsoSpecWrapper.cpp

fe6919edfcb101707c3d8de53dc1b16d1cfaea40 authored about 6 years ago by Hannes Roest <[email protected]>

Update isoMath.cpp

a438c0efc89beb9f471dd093d2e1c55791173ad8 authored about 6 years ago by Hannes Roest <[email protected]>

Rename IsoSpec class to IsoSpecWrapper to avoid name clashes with IsoSpec namespace

8ebe32b79d6ab6a0c1b4a04835816dbe5fb0aeb6 authored about 6 years ago by michalsta <[email protected]>

Rename the IsoSpec.cpp/.h files to IsoSpecWrapper.cpp/.h to match the name of classes inside

b1510bc8c925d12dfbadea5b191e4f8dcebc5212 authored about 6 years ago by michalsta <[email protected]>

Bring IsoSpec implementation up to d41e5f89924d12518e0c96904baa88edac37c667

5f33da5208a0033f0be81b15cc7bab47e178cbd8 authored about 6 years ago by michalsta <[email protected]>

Delete mman.h

2a3c68be7d0c3963a6f03a049a831ee4e03745c4 authored about 6 years ago by Hannes Roest <[email protected]>

Pull a bugfix from main IsoSpec repo

29b46307e7ea3fd6dee8872388e4ea6b53ad22e2 authored about 6 years ago by michalsta <[email protected]>

Avoid some memory copies by having IsoSpec generate right into a vector<Peak1D>

4f9a354d3b23d2dc1195adb0f375158f80d863f0 authored about 6 years ago by michalsta <[email protected]>

[FIX] fix memleak

c1781bd072a17a209b34e9e1b09ee68fd33c0eba authored about 6 years ago by Hannes Roest <[email protected]>

[TEST] fix test

bb38ca8aee20947cefebda2565c9ad46d1333b14 authored about 6 years ago by Hannes Roest <[email protected]>

[FIX] SiriusAdapter_5_output.ms (converter_mode)

ce542cb7e29aad8bb953173ce3a924cddddd3895 authored about 6 years ago by oliveralka <[email protected]>

[FIX] extractScanNumber, test (SpectrumLookup, SiriusAdapter)

a110b673ee79a7845a4744a00d65c3334bff12fa authored about 6 years ago by oliveralka <[email protected]>

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

f1f9410d9c2e6683e27ae7116738b0f7c288d8f8 authored about 6 years ago by oliveralka <[email protected]>

[ADD] Comments to .ms files

b95430715d0664a7e08bfeb2a961a57ab46a1730 authored about 6 years ago by oliveralka <[email protected]>

[FEATURE] add advanced option to skip non-cross-linked files

a65449a0ad4cb02ff81c355811c14c652f05a433 authored about 6 years ago by timosachsenberg <[email protected]>

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

63712b10d7b6d13b25a39951628dbe2b134193f1 authored about 6 years ago by timosachsenberg <[email protected]>

Merge pull request #40 from hendrikweisser/rna-ms2-id

Fix for Windows compile error

cbdbc341200bf15e1a8e71ab8aae55735bc6e538 authored about 6 years ago by Samuel W <[email protected]>

Merge pull request #3824 from OpenMS/fix/openmpcmake

[FIX] Made new OpenMP CMake code backwards compatible

8345b7be5f8875c2346dbcd4bc3345f77695988f authored about 6 years ago by Hannes Roest <[email protected]>

Merge pull request #3823 from FabianAicheler/feature/improveMetaboDechargerDoc

Feature/improve metabo decharger doc

75012e0278436e9d5bfcb7143deadc30fdcf4c93 authored about 6 years ago by Hannes Roest <[email protected]>

Merge pull request #3815 from jpfeuffer/fix/pepidx_xtandem

[FIX] PepIdxer correctly parsing Xtandem results

02faa40ef8eb34bb2f540649067e7356cbb51bd7 authored about 6 years ago by Hannes Roest <[email protected]>

[FIX] Made new OpenMP CMake code backwards compatible

OpenMP_CXX_FOUND only exists in newer CMakes

07aa625b5af15a2c2de28b223033a9aa50859fdc authored about 6 years ago by jpfeuffer <[email protected]>

extended potential_adducts parameter format and rules explanation.

5f511d470c4564e78ff6bad00d322145c41f31e2 authored about 6 years ago by FabianAicheler <[email protected]>

feat: manage score weights through setter (no default handler support for this one)

8dd949025ab3ea1ad290f9fcdedc4031d0159976 authored about 6 years ago by Pasquale Domenico Colaianni <[email protected]>

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

32b638d055c55ffaf5b3b814c7ad7d8040684830 authored about 6 years ago by Hendrik Weisser <[email protected]>

[FIX] fixed Windows compile error (no hash for 'String')

6f460dc52c7e561c2f1e321665858444c5b5a03b authored about 6 years ago by Hendrik Weisser <[email protected]>

chore: add const to scheduler methods

2865bf3334e8ae237de807f28234c7d29157a5af authored about 6 years ago by Pasquale Domenico Colaianni <[email protected]>

fix: parameters types for scheduler and selector (Int instead of double)

da42974b0c8ef05499e0783339ce05b06001f521 authored about 6 years ago by Pasquale Domenico Colaianni <[email protected]>

extended Util doxy for output mass behavior.

f54ff1b0aa24d26ed7ec82b9d13e80d42cf3d8ba authored about 6 years ago by FabianAicheler <[email protected]>

style: MRMFeatureScheduler remove custom constructor / destructor

style: replace [i] with bound-check .at(i)

chore: do not inherit from DefaultParamHandler

c7e1e92301bf4f84ed8386e64717a53d5785f8d3 authored about 6 years ago by Pasquale Domenico Colaianni <[email protected]>

style: replace cast (String)value with constructor call String(value)

d136a205f82e4670c012edd05b8da073c2bbf53c authored about 6 years ago by Pasquale Domenico Colaianni <[email protected]>

style: replace iterators with range-for loops, use count(), add const, to select_MRMFeatures()

c43bf7e6a7f68485f74e8c980545b4f18b4924ac authored about 6 years ago by Pasquale Domenico Colaianni <[email protected]>

style: replace iterators with range-for in select_MRMFeature() #1

2f35994ce08d41e855769f52864a24d0402c9df8 authored about 6 years ago by Pasquale Domenico Colaianni <[email protected]>

style: use const and reorder variables in qmip::optimize()

36ebae7ddc9321c30acc03fd30152572c6a61272 authored about 6 years ago by Pasquale Domenico Colaianni <[email protected]>

style: use range-for in score::optimize()

dd58b335e0f19b377432f1452dd8923641eaf0c6 authored about 6 years ago by Pasquale Domenico Colaianni <[email protected]>

[nop] Undid variable name changes in MolecularQueryMatch

463c55e569bfe045009160333eec45d691d04240 authored about 6 years ago by poshul <[email protected]>

Update NASequence.pxd

bb8ef092914837ac54847695829f47a043b95730 authored about 6 years ago by Hannes Roest <[email protected]>

generate interval - in progress

- detect apexes : done
- sortng with RT : in progress

2af7d9ba673cca8dd81b8f8238a078b5bb36063c authored about 6 years ago by JeeK <[email protected]>

test: add check for output_selected size

5d350196a0f2d7567b0160065cd3a8c6d9cb31bb authored about 6 years ago by Pasquale Domenico Colaianni <[email protected]>

[FIX] added check for nullptr

0877f77bc578b42b31dfea87bba48998450e5d9a authored about 6 years ago by enetz <[email protected]>

Merge pull request #3819 from oliveralka/feature/add_param_processor_SiriusAdapter

[ADD] Param: processors (SiriusAdapter)

81cdd8486c91adca0be89ef124224b2a0d708c56 authored about 6 years ago by Timo Sachsenberg <[email protected]>

Update IsoSpec to 1.9.0beta1

ffb3fe49bce0e910bce15c9c92ae820ebd965263 authored about 6 years ago by michalsta <[email protected]>

[feature] Added pyopenms support for IdentificationDataConverter, and basic support for IdentificationData

578bad4b34d48d044ec37553eb97dd5f97b673d9 authored about 6 years ago by Samuel Wein <[email protected]>

[fix] commented out [] operator of NASequence allowing pyopenms to compile

23e30e502de7d7d509efca3c2ddbb0c6c4ab0f86 authored about 6 years ago by Samuel Wein <[email protected]>

[FIX] remove OpenMP, give threads directly

6bc90b0cd9951ec0961a309b0c438a08c949a039 authored about 6 years ago by oliveralka <[email protected]>

[DOC] improve parameter documentation of OpenSwathWorkflow

1dcdd8bb6b21eed1ed72842ce68e4cf5bb4ecf2d authored about 6 years ago by Chris Bielow <[email protected]>

[FIX] reverted unintentional change

5e6b59fc7aa67c029d25549174fb131f53a9747f authored about 6 years ago by enetz <[email protected]>

[FIX] TOPPView IDs from theo spectra

Because of synchronization between peak labels and PeptideHits,
PeakAnnotations were generated a...

4cb114c0167023646b8699d56297ed3e3d70dc1d authored about 6 years ago by enetz <[email protected]>

[FIX] solution with OpenMP

66d2ea9865cd1b5c052df4c1cddf1d32a4126df0 authored about 6 years ago by oliveralka <[email protected]>

feat: MRMFeatureFilter::getDefaultParameters()

4cb6bdb3bef5f8406e649d27396375faa2d86555 authored about 6 years ago by Pasquale Domenico Colaianni <[email protected]>

[ADD] param processors

cc36b7cc4031bdee464311f141a385eadecfb562 authored about 6 years ago by oliveralka <[email protected]>

Merge branch 'feature/TDdeconv' of https://github.com/JeeH-K/OpenMS into feature/TDdeconv

7eb13fe3b01058e5c8dd875af9597202ac538af4 authored about 6 years ago by JeeK <[email protected]>

generate interval - in progress

3af74892751e2b95afac2b6dafcbc79413e19415 authored about 6 years ago by JeeK <[email protected]>

Merge pull request #3818 from lars20070/fix/FFM

simplify blacklist initialisation in FeatureFinderMultiplex

62cf75fd10e453cc0909f138f3159f18f9222af6 authored about 6 years ago by Timo Sachsenberg <[email protected]>

[INTERNAL] simplify blacklist initialisation

60bb91b7a160a9c46dd4cea9b6821798f1d83c76 authored about 6 years ago by lars20070 <[email protected]>

fixed negative mode decharging for charge!=0 features from FF

76b305e20f20f22c889f5d97b0da886e5d900302 authored about 6 years ago by FabianAicheler <[email protected]>

[FIX] PepIdxer correctly parsing Xtandem results

5087eadd2d7938cdf6050d1e8a411ec6896e8847 authored about 6 years ago by Julianus Pfeuffer <[email protected]>

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

48fa43fe33c4e722ef3359b541a9d8bead7b7b29 authored about 6 years ago by oliveralka <[email protected]>

Merge pull request #3806 from OpenMS/fix/warning

change warning to info as in precursor correction

c71c0d52b5858dc61a0375e25166aa12999d4e4e authored about 6 years ago by oliveralka <[email protected]>

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

26eefdd1bad129f3098e448e1f1de1158edb50b9 authored about 6 years ago by enetz <[email protected]>

[feature] started pyopenms bindings for NASequence Ribonucleotide and RibonucleotideDB

bc3e761b58d5cc2806a6f263e65a73d50a1dc34a authored about 6 years ago by poshul <[email protected]>

Merge pull request #3787 from oliveralka/fix/SiriusAdapterWorkspaceOutput

[FIX] QT copy directory recursively (sirius_workspace)

d92e7adc2e6aa09fe2e12d379f8bcdeeb002f501 authored about 6 years ago by Chris Bielow <[email protected]>

Merge pull request #3809 from hroest/feature/py

Feature/py

e542edbb8d70fc9d5f0b2bff7b13cacd052b476a authored about 6 years ago by Hannes Roest <[email protected]>

[FIX] default ctor fix

a59849a7bc398afb67046b58349272ac0ba1a0c7 authored about 6 years ago by Hannes Roest <[email protected]>

[FIX] improve code gen for static methods

b6e78503bcc08e44a4c4bca2743df1929289050f authored about 6 years ago by Hannes Roest <[email protected]>

[FIX] improve code gen for const

ecf4b5f71565f7bc6019475d5a9e5807fd4117c9 authored about 6 years ago by Hannes Roest <[email protected]>

Update src/openms/source/FILTERING/CALIBRATION/PrecursorCorrection.cpp

3b5188512c68d539798a257aaa7a737116cd840c authored about 6 years ago by Hannes Roest <[email protected]>

[FIX] Error in OpenSwathWorkflow_21 in debug mode

Fixes #3764 . Prevents successful nightlies. This should be the easy way. Not sure if it makes s...

af7e1fb769b163e4c86cf1fe8caa2dd5041b15df authored about 6 years ago by jpfeuffer <[email protected]>

Merge pull request #3807 from jpfeuffer/fix/knime/percolatorTabMimeType

[FIX] Added percolator Tab file as possible mime type in KNIME

0df0b7737cf5946d1f5664c3ec535d23ad15170d authored about 6 years ago by Timo Sachsenberg <[email protected]>

[FIX] Added percolator Tab file as possible mime type in KNIME

031e6ff807786abece7bc031a40788e89999081e authored about 6 years ago by Julianus Pfeuffer <[email protected]>

Update PrecursorCorrection.cpp

change warning to info as in precursor correction

471c73d11d0876fd34b2107ab2581ac4feb2cb0c authored about 6 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #3799 from jpfeuffer/feature/omp_macos

[FEATURE] Updated OpenMP inclusion to modern target based CMake to si…

3a5595621e730e2aaee9356564c99768ffaede20 authored about 6 years ago by jpfeuffer <[email protected]>

[NOP] indenting

b74cac1bdfdecc74e61d6f8bee5b59862851b965 authored about 6 years ago by Julianus Pfeuffer <[email protected]>

[FIX] Restructure sumformula

e613f7a31664711a98dc9e87b11bdeadb327229b authored about 6 years ago by oliveralka <[email protected]>

[FEATURE] add -out_qc flag to OpenSwathWorkflow and OpenSwathFileSplitter

65cd0cf8da53a310ec7e60a2d027c274dca4bb41 authored about 6 years ago by Chris Bielow <[email protected]>

[FEATURE] add SwathQC file (Charge Distribution support for now)

5212eb923d1967caca33c87b3198d90a11436b1d authored about 6 years ago by Chris Bielow <[email protected]>

[FEATURE] add JSON to known filetypes

0cab9657e145e020c4cafc89407cdd5dc46bf53c authored about 6 years ago by Chris Bielow <[email protected]>

[FIX] test_win

42f7945898412d8b091b2456d361daad75bdaf69 authored about 6 years ago by oliveralka <[email protected]>

style: move constants from OpenMS namespace to class

test: update tests values with same ones returned in python version

599eb91e066b11eb973795ed0a79fa5f7a95ec51 authored about 6 years ago by Pasquale Domenico Colaianni <[email protected]>

[FIX] change switch,case; update_tests

97fb57168ad21d827dbf60a2703bb98960224a9f authored about 6 years ago by oliveralka <[email protected]>