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

Update src/openms/source/ANALYSIS/OPENSWATH/TargetedSpectraExtractor.cpp

Co-authored-by: Chris Bielow <[email protected]>

f6ba8fe920ce91ed4fe960c27bde0d324dfa889a authored over 2 years ago by Bertrand Boudaud <[email protected]>

Update src/openms/source/FORMAT/MSPGenericFile.cpp

Co-authored-by: Chris Bielow <[email protected]>

41dc7c6f8c52ec04091d70372f9341c324d9d4a7 authored over 2 years ago by Bertrand Boudaud <[email protected]>

Update src/openms/source/ANALYSIS/OPENSWATH/TargetedSpectraExtractor.cpp

Co-authored-by: Chris Bielow <[email protected]>

0ce748375e1fd50a5588c37a05e0867989a355b6 authored over 2 years ago by Bertrand Boudaud <[email protected]>

Update src/openms/source/ANALYSIS/OPENSWATH/TargetedSpectraExtractor.cpp

Co-authored-by: Chris Bielow <[email protected]>

95e323d0cf75d530b2a9e33633a0fc2430121827 authored over 2 years ago by Bertrand Boudaud <[email protected]>

Update src/openms/source/ANALYSIS/OPENSWATH/TargetedSpectraExtractor.cpp

Co-authored-by: Chris Bielow <[email protected]>

02f5d081c68ca6c17ebba09d1299cf3ce6ed970f authored over 2 years ago by Bertrand Boudaud <[email protected]>

repaired MQevidencexport.h, someone messed up the function arguments. Fasta handeling done, indexing will be finished tomorrow

07f74e39d1d5c830ecc64e9fd4120a2e0e97a996 authored over 2 years ago by lennykovac <[email protected]>

Merge branch 'maxquant-output' of https://github.com/vrossow/OpenMS into maxquant-output

944048c218027a71e0a9091f8d45c3e510454b68 authored over 2 years ago by lennykovac <[email protected]>

added fasta to qualitycontroll, and made the MQEvidenceTest compile (rather cheap for now)

1f5208445fc6ff6cbe2a1cee9065c638b7a4eb10 authored over 2 years ago by lennykovac <[email protected]>

[FEATURE] JSON export of OMS (SQLite) files: identified molecules, adducts, observation matches

e4494fed7808e18634b5254e66b4098b4d6ca03c authored over 2 years ago by Hendrik Weisser <[email protected]>

[API] add helper function to create database views in class 'OMSFileLoad'

e15fc2382996a2c5616485b622871602053ef35a authored over 2 years ago by Hendrik Weisser <[email protected]>

Update openms_clang_format_add_and_commit.yml

f08c25b0011a7384c7fc8278aeb9b64fac812098 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

[FEATURE] JSON export of OMS (SQLite) files: observations, parent sequences, parent groups

777bbffef875a9023556d743db5cd5caf44661d9 authored over 2 years ago by Hendrik Weisser <[email protected]>

added MSExperiment and some fixes

b7312c97167eb19a42fc263c2a9aaf2f10efe338 authored over 2 years ago by beschorneh32 <[email protected]>

[FEATURE] JSON export of OMS (SQLite) files: improved handling of processing steps

4a9a31d7bddc1ad871363226715114981a9ba69f authored over 2 years ago by Hendrik Weisser <[email protected]>

fixes for MouseCursor position reporting (correct units now).

Using new QT signal/slot in more places

450732674ff3462d122bf055e613fc8adc873b32 authored over 2 years ago by bielow <[email protected]>

WIP, TODO list made, and no fasta requiered for now

943b5ab3e5fb772b085e4f9debb9436987572221 authored over 2 years ago by lennykovac <[email protected]>

[FEATURE] JSON export of OMS (SQLite) files: improvements for assigned scores, processing steps

5fb2b5b31fc5fb8d9b7e2510ddc1321ec08940eb authored over 2 years ago by Hendrik Weisser <[email protected]>

[FEATURE] JSON export of OMS (SQLite) files: processing software, assigned scores, processing steps

60a128a93364366a9a7c2eee40491e8a3e30b8fc authored over 2 years ago by Hendrik Weisser <[email protected]>

it compiles!

d94655f87f0e5f758f3f29817282648faca1fe48 authored over 2 years ago by bielow <[email protected]>

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

bc42d5094169cf632f9cb3ffcaf18047e7774dac authored over 2 years ago by Hendrik Weisser <[email protected]>

Support for enzyme term specificity (DB search params.) in OMS (SQLite) files (#6105)

* [NOP] removed extra whitespace

* [FIX] added enzyme term specificity to comparison operator...

2372bdf011eee8fea2e8113b753318ec25ba9cf5 authored over 2 years ago by hendrikweisser <[email protected]>

fixing compile errors; simplify interfaces

66bab7fc903c5ebcdf6be9f3528cd4ffdda97b06 authored over 2 years ago by bielow <[email protected]>

Merge branch 'maxquant-output' of vrossow/OpenMS into lennykovac/maxquant-output

792e0728c3c0b31a03bb6e4ca38f641104d50c13 authored over 2 years ago by lennykovac <[email protected]>

functionality implemented, extract genenames&protnames in the evidenceExporter

1fb240bd43476d8f2296e45a06c34da57f0a426f authored over 2 years ago by lennykovac <[email protected]>

[FEATURE] added JSONExporter util to export OMS (SQLite) files to JSON

2c29b8b4bafd6006cbbc54bb52c53f263ce91a9c authored over 2 years ago by Hendrik Weisser <[email protected]>

[API,FEATURE] added functions for exporting OMS (SQLite) files to JSON - work in progress

fd726234d3d7adf06b1c5658145a1b1500406b53 authored over 2 years ago by Hendrik Weisser <[email protected]>

[FIX] small fix (Qt SQL query)

cfaef0205a7b8bca1655e0c54a23d9df90d68e25 authored over 2 years ago by Hendrik Weisser <[email protected]>

[FIX] small fix (string literal with comment)

b0787d987a0470b36ee69430312ec58513777cbf authored over 2 years ago by Hendrik Weisser <[email protected]>

[FIX] OMS (SQLite) files: load enzyme term specificity as part of DB search params. (depending on version, for backwards compatibility)

f5ebfae6e87cad4fd3041ee4cb00cc6575adef5a authored over 2 years ago by Hendrik Weisser <[email protected]>

[FIX] OMS (SQLite) files: store enzyme term specificity as part of DB search params., increase version number

94b1c51ca4379ad374b8fe377d3910e6dbd4e94c authored over 2 years ago by Hendrik Weisser <[email protected]>

[FIX] added enzyme term specificity to comparison operator in 'DBSearchParam'

060a9dc66aaea0254ea5f24aae9ca0c34a0050a9 authored over 2 years ago by Hendrik Weisser <[email protected]>

start of MQMsmsExporter

cfb919a0a6a509f4fb0b79c8a2fef48c5cf2f31d authored over 2 years ago by beschorneh32 <[email protected]>

[NOP] removed extra whitespace

9896325fd12c3710193808b7ab62a8bd667ac9f2 authored over 2 years ago by Hendrik Weisser <[email protected]>

some progress

00fc3f289835e6ed037efc936527b3e3806d304e authored over 2 years ago by vrossow <[email protected]>

Updated CHANGELOG

d801817aaf72670ececadf63cb0e6328446f1ed3 authored over 2 years ago by bertrandboudaud <[email protected]>

fix: small updated to library intensity in construct transition list

73325b73ef45437d1ded650c5c71bb8949ed895f authored over 2 years ago by dmccloskey <[email protected]>

Fixed doc

9405c89d8bf2d1ae197123536cdc2023410cc3dc authored over 2 years ago by bertrandboudaud <[email protected]>

Fixed OpenMS unit test after changes related with PeptideRef

6b6460f723b811cbc5d145d510ab40f8c62a1412 authored over 2 years ago by bertrandboudaud <[email protected]>

fix: major modifications to DDA related code to allow for transition list construction and spectral export

9958ffe7d4201ffdb3a0232fe3d6e1f31211a05e authored over 2 years ago by dmccloskey <[email protected]>

Added extractSpectra unit test

0f25bb3cce87d0b8c00e845b1af6c681a377ef6d authored over 2 years ago by bertrandboudaud <[email protected]>

Added extractSpectra to pxd

3dbc756d6fbe5eec6320eeff8d6055742601b3e0 authored over 2 years ago by bertrandboudaud <[email protected]>

Store MSP: do not store spectrum with no peaks.

90a8e9892de59a4b913b3bbea3a858a3ebb794b0 authored over 2 years ago by bertrandboudaud <[email protected]>

Store retention time in msp files

8188cc4c499fcd2d9d915ce6860bf01c2b0a0de2 authored over 2 years ago by bertrandboudaud <[email protected]>

Added one option to return unknown feature in searchSpectrum

70c03fb90af8d7256d01a04bbd29ea45f64c307a authored over 2 years ago by bertrandboudaud <[email protected]>

Store retention time in msp files

3c77b58368a17d211549532353809c53873a0297 authored over 2 years ago by bertrandboudaud <[email protected]>

Added extractSpectra's documentation

b47ae4d7d98eadeca144963101afc639f1f585c4 authored over 2 years ago by bertrandboudaud <[email protected]>

Store MSP: do not store spectrum with no peaks.

338ab6104d19c1a4b3563420a1d3e810c275f9f6 authored over 2 years ago by bertrandboudaud <[email protected]>

Cleaning

70ef13cf81cc204d29681ff3ed29026e3220b1a2 authored over 2 years ago by bertrandboudaud <[email protected]>

fix: added check for unannotated spectra in

21f23ba6b39947acc40ecd8dd5f85af2fe470e5a authored over 2 years ago by dmccloskey <[email protected]>

Removed unused variable

2b72be2684f8e7ee9e7094444bfa25ad8ec483aa authored over 2 years ago by bertrandboudaud <[email protected]>

Removed debug traces

2191f9e399ac7b8d3a49fa8e71d34db37cad64b1 authored over 2 years ago by bertrandboudaud <[email protected]>

storeSpectraTraML renamed constructTransitionsList

06e476a5780914d1a87c6ca514dc7fa7bab923c2 authored over 2 years ago by bertrandboudaud <[email protected]>

Added one option to return unknown feature in searchSpectrum

0ab07ea9327124b423d582cd0f678ed32a94b7f7 authored over 2 years ago by bertrandboudaud <[email protected]>

Added new extractSpectra method for DDA

3baa7ccbd9720d7938b5ea95369951d8a2c340ed authored over 2 years ago by bertrandboudaud <[email protected]>

Removed debug traces

697be1968b4f69b5baf47fa6144b51a32dbfd29c authored over 2 years ago by bertrandboudaud <[email protected]>

[FEATURE] Some refining ... added auto and changed var names. (#6104)

* Naming vars is art. Changed some names to represent their functionality and added some auto's ...

ba8469382f479ccbb22ebf2e5c6b7b15f1c06d2b authored over 2 years ago by Lenny Kovac <[email protected]>

OpenSwathDecoyGenerator remove duplicates (#6054)

* change switchKR behaviour with nontryptic peptide

Previously if peptide did not end in K or...

0fa86cb123470928a273f22fffe4e88a9274c0b5 authored over 2 years ago by Joshua Charkow <[email protected]>

AnnotationItems1D done

2d6f8daa41448d10c766c904c25a2df3b68ff153 authored over 2 years ago by bielow <[email protected]>

compile warning fix

6e68fec42260933f4e3fb99ba762c2f8abd723fa authored over 2 years ago by Timo Sachsenberg <[email protected]>

Cleanup

5f35554242dab269a291bdfdfa564657093fe822 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Fix AGM tests

689f2354d91f4a8411f3960b627320f121711f74 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Export all candidate annotations, not just the best.

b1b5414bf663609fa5c3257e4d99e452a88dc12c authored over 2 years ago by Julianus Pfeuffer <[email protected]>

[FIX]: wrange-loop-contruct (#6098)

14cbb01541cf6241923abb4aae99ac479f6b5a9d authored over 2 years ago by AMIT KUMAR MISHRA <[email protected]>

read swath window file with no header try #2 (#6077)

* read swath window file with no header

In response to https://github.com/OpenMS/OpenMS/issue...

71a1a27c31bc30d2de5bdefd1366519c0dcc3817 authored over 2 years ago by Joshua Charkow <[email protected]>

Allow missing score types in IDDData conversion (#6097)

* warning

* conversion works

* Apply suggestions from code review

Co-authored-by: Chris...

f3f35c9c9e7face3c5194b453ed2b1d9a48e8360 authored over 2 years ago by Timo Sachsenberg <[email protected]>

more columns filled and some removed again

ddda072e51d03ac713a7057d3bda45a930a8f1d7 authored over 2 years ago by vrossow <[email protected]>

working on AnnotationItems

729a9f6e62c0d9c45b6cecaa8b7448f098b37efb authored over 2 years ago by bielow <[email protected]>

[FIX] Suppress -Wunused-private-field warnings (#6046)

* Suppress unused sonar_ in osw writer

* (fix) remove unused private field

Remove pos_min_...

c289655514e3a4d46cb2984a53d37eb924008c31 authored over 2 years ago by Matchy <[email protected]>

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

600c7047bb9dc060a5bec452b8ace151c0c95279 authored over 2 years ago by vrossow <[email protected]>

Merge pull request #6095 from OpenMS/timosachsenberg-patch-1

Update stale.yml

360dd58a3d47062400de79a245870c5f64ab5d77 authored over 2 years ago by Samuel Wein <[email protected]>

Update stale.yml

let's reduce times gradually

aaa74797186d46bee146bdf73cf775fe2f2e6d58 authored over 2 years ago by Timo Sachsenberg <[email protected]>

Update stale.yml

e1d64bde6dd9362cc574167858641871a9780ede authored over 2 years ago by Timo Sachsenberg <[email protected]>

All missing column names added and started filling them with the correct info. And test file changed.

50258b67d01351ddb1398263d8dfe9adbd6c0732 authored over 2 years ago by vrossow <[email protected]>

[FEATURE] std::move to spectra merger (#6063)

* [FEATURE] MicroOptimazations: auto in some for-loops, got rid of unnecessary allocations & if ...

f58bfb93d6ebefcaef66ca707b37039bb6213b80 authored over 2 years ago by Lenny Kovac <[email protected]>

Add the native_id identifier to the list of spectrum references (#6078)

Co-authored-by: Timo Sachsenberg <[email protected]>

c59e7fab3d33ce23c45c4672871d03672ecc2e67 authored over 2 years ago by tillenglert <[email protected]>

Season of Docs application - My edits (#6064)

* test edit of QuickStart.doxygen

* minor edits to QuickStart.doxygen file

* added a short...

cbf1a2921ed66a14edf2c1bddcabfc6596ba085e authored over 2 years ago by greengypsy <[email protected]>

[FIX]: deprecated Qprocess::execute(const Qstring& command) (#6086)

* [FIX]: deprecated Qprocess::execute(const Qstring& command)

* [FIX]: deprecated Qprocess::e...

15ffe52a06365756ccc8d702f978774cc256996a authored over 2 years ago by AMIT KUMAR MISHRA <[email protected]>

[FIX]: suppressed deprecated QRegion::rects() (#6089)

6a9a000d6fcc5c9f192f5d44de5abab0753212f3 authored over 2 years ago by AMIT KUMAR MISHRA <[email protected]>

[FIX]: suppressed deprecated QWheelEvent::x() const (#6088)

* [FIX]: suppressed deprecated QWheelEvent::x() const

* update contrib

Co-authored-by: Tap...

5c93b16bcca2bc9dd7ab755d84783e66ad6d6df3 authored over 2 years ago by AMIT KUMAR MISHRA <[email protected]>

[FIX]: deprecated addRoundRect (#6085)

* [FIX]: deprecated addRoundRect

* update contrib

4306b58b27ffe3ffe606e2de9aad9d77598bd01f authored over 2 years ago by AMIT KUMAR MISHRA <[email protected]>

[FIX]: deprecated setBackgroundColor (#6084)

* [FIX]: deprecated setBackgroundColor

* update contrib

Co-authored-by: Timo Sachsenberg <...

4b5401991b46ce4aa132111318e8ffe724e7b320 authored over 2 years ago by AMIT KUMAR MISHRA <[email protected]>

Merge remote-tracking branch 'origin/feature/FLASHDeconv' into feature/FLASHDeconvOnly

3537731d3958df1b5dcb6f0ae0251372de74c989 authored over 2 years ago by JeeH-K <[email protected]>

Change printProgress to OpenMS ProgressLogger

283a579c9e50e9542bbaaf383a1db56f029fb33e authored over 2 years ago by JeeH-K <[email protected]>

revert to "mass_error_da_" version to avoid test errors from other tools

cd78291fbe3ec4b460ad6d9c881a6c6e53f264bf authored over 2 years ago by JeeH-K <[email protected]>

debug error while merging

683c4d02ed7ad7170bee7be32b4ffa205b3a5407 authored over 2 years ago by JeeH-K <[email protected]>

Merge remote-tracking branch 'origin/feature/FLASHDeconv' into feature/FLASHDeconvOnly

bf374bffa4a136c2557342dda31b2789a7bb44c8 authored over 2 years ago by JeeH-K <[email protected]>

Addressing Chris' comments - FLASHIda sort bug fixed3

63b6fd6c3aab023c7159f9f5cd0af584749e73e7 authored over 2 years ago by kyowonjeong <[email protected]>

Merge branch 'develop' into feat/specAnnotationSirius

12c207110a16aced1968aa9e39d62becf0943b8e authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Merge pull request #6090 from poshul/add_sponsor

added funding.yml

19013e5841c7fe2f32e12cfd688b0dc0e05cb8a3 authored over 2 years ago by Samuel Wein <[email protected]>

smaller headers in PR template

c0917f20d957127f49d09ed451aa09eef1056a45 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

added funding.yml

4bbf66be85ec05602887fe95287b692f645dfefc authored over 2 years ago by Samuel Wein <[email protected]>

Merge branch 'develop' into develop

65cef8bfc1137f21d69975944b550dbf6f088b9c authored over 2 years ago by greengypsy <[email protected]>

Ordered the header of evidence.txt and started to add missing column names/data

da7970abd9612e60b3caf4147dc02a59fb20eb42 authored over 2 years ago by vrossow <[email protected]>

remove indent from QuickStart.doxygen and add approved text from pull request

ff34b143fb84a1d2ece9434c255031fb9e19181e authored over 2 years ago by greengypsy <[email protected]>

Rename pyopenms-extra to pyopenms-docs (#6087)

* Update CHANGELOG

* Add Tapasweni Pathak in AUTHORS

* Rename submodule pyopenms-extra to ...

5fc379a455dac3d66b7ee58c935706bad422fbd9 authored over 2 years ago by Tapasweni Pathak <[email protected]>

Merge pull request #5915 from OpenMS/jpfeuffer-patch-7

Uncomment wrapping of other operators in Empirical Formula

09c7143ba919840569d7b54ab76e0b495475339c authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Comment mul since autowrap requires same type

21031fb9ff546f696a3aa4a4b1b562c76ecfa8e7 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Update PULL_REQUEST_TEMPLATE.md with information on reformat (#6076)

* Update PULL_REQUEST_TEMPLATE.md

Co-authored-by: Julian...

fdb295b65a5dc695a0f20ef321a7477655864e74 authored over 2 years ago by Timo Sachsenberg <[email protected]>

Merge branch 'develop' into develop

77c8207e33ec5f32783488b8d9d500bc6c30baeb authored over 2 years ago by Timo Sachsenberg <[email protected]>

[CI] Rename tools/travis to tools/ci (#6075)

* Rename travis folder

* Fix GHA yml config

c046c222850041069f55fe9f3423f61bfdbfac86 authored over 2 years ago by Matchy <[email protected]>