github.com/OpenMS/OpenMS-1 commits | Ecosyste.ms: OpenCollective

[FIX] fix binned spectrum interface

9a688c1989f77b7ec652412e365989ef820df15c authored almost 3 years ago by Hannes Roest <[email protected]>

[DOC] improved IM set/get documentation (#5614)

* extended docs

* augment

e75e5e43ef903f10a263501769fe072f184b89cb authored almost 3 years ago by Chris Bielow <[email protected]>

doppelungen in initialize entfernt

a13267384c4b785b803f73be1dc3982fb52e80c0 authored almost 3 years ago by Vincent Musch <[email protected]>

augment

c620b7b3d21377f923eb3d5dac51fdaabee03d72 authored almost 3 years ago by bielow <[email protected]>

extended docs

69bbfbc6243bec07afeb9acd5b03a4133fb65bf7 authored almost 3 years ago by bielow <[email protected]>

fix xcorr_precursor_combined & contrast

73e9cceec5c186d2f88fa0d1a9889f2a44487f1e authored almost 3 years ago by Vincent Musch <[email protected]>

[REVERT] revert changes in MRMAssay

- switching from boost::unordered_map to std::unordered_map breaks the
regression tests due di...

c9bb40cc85c0529eae606961758fa80340d1ed53 authored almost 3 years ago by Hannes Roest <[email protected]>

Merge branch 'develop' into feature/header_cleanup

5fdc6a314babad8842dd00e2aeebb572b7676570 authored almost 3 years ago by Hannes Roest <[email protected]>

const und ref

9f9c7719dda5a92c48af39efd5b92feb02f34073 authored almost 3 years ago by Vincent Musch <[email protected]>

Merge pull request #118 from OpenMS/develop

update to latest

3dfce80cc1143ad362b40fbbc8254f47cdf98bde authored almost 3 years ago by Chris Bielow <[email protected]>

[FEATURE] speed improvement in OpenSwathAssayGenerator

5c990cab6f170c9c8ec1ac0989cc73f5b0985a2e authored almost 3 years ago by Hannes Roest <[email protected]>

[FIX] remove intermediate storage of transitions in large vector

- lower memory footprint of PQP storage

52d204008174111ef362ff7f900c0b2df9e3932f authored almost 3 years ago by Hannes Roest <[email protected]>

[FEATURE] lower memory footprint

- lower memory footprint of PQP file writing by storing transitions
repeatedly while iterating...

ad698b0b3ebcaa1c9c503ae493032baef321c5ea authored almost 3 years ago by Hannes Roest <[email protected]>

[FIX] use set instead of map

bcb62b9aac2a985609b72e2dee3a0f5cc9c81c0a authored almost 3 years ago by Hannes Roest <[email protected]>

remove problematic progress loggers

4f1d94ca2ab4cb4edb687a5225921a3071d2ea5f authored almost 3 years ago by Hannes Roest <[email protected]>

[FEATURE] add rvalue functions for TargetedExperiment

947d22545b5b7f84b68b3f75b1ccd7277c6d7748 authored almost 3 years ago by Hannes Roest <[email protected]>

[FEATURE] use rvalue addition

b79b56033cd42fe47db193ae96dc9d896c39153a authored almost 3 years ago by Hannes Roest <[email protected]>

[FEATURE] DecoyGenerator speedup

c67054e30e98503941a3ceffba8d3aaed775aaab authored almost 3 years ago by Hannes Roest <[email protected]>

[FEATURE] filter in-place

627cb3726211b2b04a40f0da5391b94d8d450980 authored almost 3 years ago by Hannes Roest <[email protected]>

neue Matrixstruktur in MRM Scoring

96c4f65c555af8e4c6a66298ba8c947ea5251c08 authored almost 3 years ago by Vincent Musch <[email protected]>

prep for quick MS1 peak accession for pyOpenMS / numpy (#5606)

* prep for quick MS1 peak accession for pyOpenMS / numpy

* Update MSExperiment.h

* Update ...

62dfd22e9dd91be62422b1752a345ec3e5b9e188 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

Merge branch 'develop' into feature/header_cleanup

a2a61378a369d79561589afe2475e986ee2303a3 authored almost 3 years ago by Hannes Roest <[email protected]>

Merge pull request #5610 from hroest/feature/header_cleanup_inc

Feature/header cleanup inc

c0466511c156b8faf0f8196a85d69df9906732d2 authored almost 3 years ago by Chris Bielow <[email protected]>

[FIX] Windows fix

28f94dbc1b83e8d4b61e48a05837ad2f2e6d1d63 authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] windows fix?

9d01d505b41ef24af21f25e468074e81863b7b21 authored about 3 years ago by Hannes Roest <[email protected]>

fixes

e9c306ba5d4b3ba26d9ff64b9758eb2174351aed authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] move back to boost (Clang)

db87c9df531375fd3c91b1c34d5676eb3ab8cba7 authored about 3 years ago by Hannes Roest <[email protected]>

Merge branch 'develop' into feature/header_cleanup_inc

51a9b9a9575108a2363e6742d65e87a1baec433b authored about 3 years ago by Hannes Roest <[email protected]>

Update Deisotoper.pxd

a761c325a5bcd4b80300ca4dcff1a425c24f6f83 authored about 3 years ago by Timo Sachsenberg <[email protected]>

[FIX] move MaxLikeliFitter1D to cpp

9b89cde2a6ab8adb00df26882573b32d4d7b87a2 authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] move XMLHandler to cpp

- remove STL dependencies

2a2596dbec764e253d6d15bbf7e361a874c19584 authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] move FastLowessSmoothing function to cpp

- remove STL dependencies

f0be6f23023c259a7bc337e2f04764626e965336 authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] move GaussFilter to cpp (I/O)

- remove LogStream dependencies

eeb120d5f21f6890db7eb319e0088f1e020c3547 authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] move TargetedSpectraExtractor to cpp (I/O)

57f594047f21fb0d21dda2c29da700f2a7b6d531 authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] move ConsensusMap to cpp (I/O)

115b197d0acfc4faa642f2a0a64ade2cc8b095c4 authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] move LevMarqFitter1D to cpp

- remove Eigen dependency from header file

7bf70ed22b5a80b9019c4cf80730922fd9977143 authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] move GumbelMaxLikelihoodFitter function to cpp

- remove Eigen dependency from header file

f9dba4f099933140f994c4f26836c22c37b16894 authored about 3 years ago by Hannes Roest <[email protected]>

Merge branch 'develop' into feature/header_cleanup

b102743bf6a3421233f7714d46d899b3a44136b0 authored about 3 years ago by Hannes Roest <[email protected]>

Merge pull request #5609 from cbielow/fix_doxy

Fix doxygen warnings

f99a891af86c7ee254d9cc719059bf921e6429e5 authored about 3 years ago by Chris Bielow <[email protected]>

Merge branch 'develop' into fix_doxy

d4a494adc4d8c3325dd4c0fcc7c2363fe6bbc834 authored about 3 years ago by Chris Bielow <[email protected]>

[pyopenms] use np.empty instead of np.zeros (#5607)

* [pyopenms] use np.empty instead of np.zeros

for a little bit of speed. We know we will init...

6052e35a363f70577ffcdd966615be447680306b authored about 3 years ago by Julianus Pfeuffer <[email protected]>

Feature/header cleanup inc (#5608)

* [FIX] move Qt headers

* [MOVE] split String Utils

- split into StringConversions (uses b...

92be666110942d43987e12f5639fef084229f73f authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] Windows fix

c92087a38192f6c707e93d1e28ef667380103ff7 authored about 3 years ago by Hannes Roest <[email protected]>

Merge branch 'develop' into feature/header_cleanup

b4d5ddb66e71c4643c775d14dda65bb63f8e3713 authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] missing Windows include

977a63c7fa177f19869b60013f280ddfab1559db authored about 3 years ago by Hannes Roest <[email protected]>

fix forgotten include

a51d68068c28cfc449253ddc8af669dbfcdfdb14 authored about 3 years ago by Hannes Roest <[email protected]>

fix

f0c57e93cca5c0b57919ab82ea52a9c9bb8dfb18 authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] check for self-assignemnt

cb1983a726bd1821bc1c7649d91d6ffb348809ac authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] go back to boost because of clang

7b63a863d6e350dfbc452d50653ed6d58f417469 authored about 3 years ago by Hannes Roest <[email protected]>

[PYOPNEMS] remove fxn

96c12bd8981cb886b66fc5d9d22e4fde1ef55d81 authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] Windows fix

cb2c2925847dff020c10909bc354ab59e41e9f02 authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] Windows fix

8eda721c28e8da136c9e9b92adb4162c9883f8e9 authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] compile fix

f0d95c2cbebc8966c18753e30ce35bf6bc15f23e authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] add LogStream where required

82cfede9610925bbe5b23ec3730f50f3656bf53a authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] test fix

1f7fb53a334bcf6cd3a2f40dc87d74b27bb60ed5 authored about 3 years ago by Hannes Roest <[email protected]>

fix doxygen warnings

8cb90e31e7069a5be0e5c8437c706b048dbc1df0 authored about 3 years ago by bielow <[email protected]>

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

fb364fa8c3ddf409f26c7c91b98915dc090ae30a authored about 3 years ago by bielow <[email protected]>

[pyopenms] fix wrapping of idXML store (#5605)

0596a671b0f41dc33fb4ede9ded9f92c58e8c248 authored about 3 years ago by Timo Sachsenberg <[email protected]>

[pyopenms] deisotoper add other (common) wrapping of optional parameters

515640d614a85015cbc3b158964c39d4008b846e authored about 3 years ago by Timo Sachsenberg <[email protected]>

Fix/comparator utils (#5601)

* add missing elements

* replace comparator with lambda expression

* refactor mapalignerba...

32942281e0c707ddbbd7ecd3f9ae5cb187dec9ed authored about 3 years ago by JangJang3 <[email protected]>

[FIX] move MaxLikeliFitter1D to cpp

b933787a7b8c49c050d672c6e685cc991758b631 authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] several boost header fixes

3e96a2eacd0f7568c0e85ea4e9c7a157a18cbb48 authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] fix LogStream headers

11544ae89756e211d6bc95c9763c51516e69a088 authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] fix STL headers

- remove STL dependencies
- remove <algorithm> headers where appropriate

052cbd455bb8b7d78cd8f8e76faf624e839163ce authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] move GaussFilter to cpp (I/O)

- remove LogStream dependencies

48cd6c49357adf44bf2aa88861da0238f55041a0 authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] move TargetedSpectraExtractor to cpp (I/O)

d986426db6bb6a5eb84401d03f8f86d79268cad2 authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] fix iostream headers

- remove STL dependencies

fa5214a5bf033b0f214e1f4c1a963dc4978f1081 authored about 3 years ago by Hannes Roest <[email protected]>

[MOVE] extract StringView

- remove STL dependencies
- extract StringView.h into its own header file
- otherwise String.h p...

e333f629867be464bc2ef31ccc4eb67bfa0a9f05 authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] move FastLowessSmoothing function to cpp

- remove STL dependencies

de8039ec5b22fffa9b4af4d88c79ecc0bcd121f8 authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] move XMLHandler to cpp

- remove STL dependencies

f862ba9eb8336dba910f33ceefc70c9c16323ccb authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] remove boost::lexical_cast where possible

- remove boost dependencies

e153e912730a821ad2e88100b75f2167fd3dfe80 authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] move ConsensusMap to cpp (I/O)

26468d04f01d0d81c2004b62573a54cdb125b5bc authored about 3 years ago by Hannes Roest <[email protected]>

[MOVE] move BinnedSpectrum

b05a16e9b42a589ddafc7cbaf04a734e772c010e authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] replace boost::unordered

- remove boost dependencies

2fb468d3efa6def32495c259034623bc950cae72 authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] move TwoDOptimization to cpp

- remove Eigen dependency from header file

410f8f6a008a16a5736c00f51ec4aed30203b9a5 authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] move LevMarqFitter1D to cpp

- remove Eigen dependency from header file

afc5d31609ecb215ee349c9fed289ee2b25a2294 authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] move GumbelMaxLikelihoodFitter function to cpp

- remove Eigen dependency from header file

8015c70d99156642b97f065ac3baf088265feaed authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] move Eigen dependencies to cpp

a206bf1be8c1d0facae5e10ec97b8ffa02de76b1 authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] move Eigen to cpp

d1bbbdfb58d1ed3691a9f710f19c9d11f36e8064 authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] move ConfidenceScoring to cpp (boost)

144a5367b30163629508a9ebdbcb6c92bfa4f4f6 authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] move boost includes

- replaced boost::math::cyl_bessel_i with std::cyl_bessel_i function

36a0ef96105feff092552e1861134256f9d788e2 authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] move boost includes

1f8c860fd4058c1d0c3bfe8748ace6d787c4fff5 authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] remove unused fxn

940f24ccc25add550e1734340c50660d6ba65b29 authored about 3 years ago by Hannes Roest <[email protected]>

[MOVE] split String Utils

- split into StringConversions (uses boost::spirit)
- split into StringUtilsSimple (no Qt, no bo...

2c930cb8613f2a53f945fe458ab9ad7d790f7e14 authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] move Qt headers

a2614a87dee88f8bf32e07cb86cdfc9ccde48af4 authored about 3 years ago by Hannes Roest <[email protected]>

FLASHDeconv peak count limit = 20k per spectrum.

848f08d779160f444675f6b831fe25582e122198 authored about 3 years ago by kyowonjeong <[email protected]>

Spectra are not stored if only meta data is read. (#5600)

5cb7abbf28a04ce698eb10953e0a511f691e3add authored about 3 years ago by Timo Sachsenberg <[email protected]>

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

dc07a82bc50cac2cdeac2600f5138bcb71cb73d1 authored about 3 years ago by Hendrik Weisser <[email protected]>

[FIX] FeatureFinderIdentificationAlgorithm: small fixes after last merge

5a681d21b787f4e04798dd7f94100f63db429646 authored about 3 years ago by Hendrik Weisser <[email protected]>

[FIX] IDFilter: small fix after variable rename; removed unused variables

1609eb6a7a6a24f04edb726469bde17665fdf676 authored about 3 years ago by Hendrik Weisser <[email protected]>

[TEST] added missing include in OMSFile test

93a6ce81b7844e1fae86dbdc1f89e78d359aa97e authored about 3 years ago by Hendrik Weisser <[email protected]>

[PARAM] IDMerger: ignore 'annotate_file_origin' (now on by default) for .oms inputs

d94980afd5920a6a1f3a441b01a3f03786804d27 authored about 3 years ago by Hendrik Weisser <[email protected]>

Feature/im calibration bugfix (#5595)

* [FIX] bugfix (actually use MS1 map)

* [FIX] use ms1 and ms2 for variable names

* [DOC] p...

e66b2c45ae29fab5fb97e4c4d0e69e75e1849b91 authored about 3 years ago by Hannes Roest <[email protected]>

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

5cd2dfde99375df740c7575a4d633ff6b30c177a authored about 3 years ago by Hendrik Weisser <[email protected]>

fixed unused variable warnings (#5597)

* fixed unused variable warnings

* Update IDFilter.cpp

Co-authored-by: timosachsenberg <sa...

0531793f20f0f3b1537955a08479fe76a0e3f1a0 authored about 3 years ago by Timo Sachsenberg <[email protected]>

[TEST] extended test of IdentificationData copy c'tor

83f48d5caea8c500d390ff9961cd91813ac271fd authored about 3 years ago by Hendrik Weisser <[email protected]>

[FEATURE,IO] FileConverter: convert between .featureXML and .oms (SQLite format) - thanks to Oliver Alka

1f7d3956896cf1f50e94cb27343b6d22f0c555ae authored about 3 years ago by Hendrik Weisser <[email protected]>

ParseMsAlign bug in windows fixed

ea822271206bc6334d0c3b8cb67f7ecdd9e59878 authored about 3 years ago by KyowonJeong <[email protected]>

SpectraMerger modified so precursor mass filter can be used.

d80455f61e91cbe4f5770ea9c050c10864b47ec7 authored about 3 years ago by kyowonjeong <[email protected]>

SpectraMerger modified so precursor mass filter can be used.

a251584ad0fc050551b9595d581f976c9afff2a3 authored about 3 years ago by kyowonjeong <[email protected]>