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

SiriusAdapter: do not change in the executable dir

hopefully fixes https://github.com/OpenMS/OpenMS/issues/6068

386870dbed0ff1030fa62dc4bf18133aa1d7d843 authored over 2 years ago by Matthias Bernt <[email protected]>

Merge branch 'develop' into idfile-json-export

f1bfa32eeeecd37210ee725dd3963396f232bbeb authored over 2 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #6119 from OpenMS/fix/mzML_dpForDAs

[FIX] mzml: Dont write empty DataProcessing for DataArrays

14f7c887a79730c12ad46a26b12b516d5aa6204d authored over 2 years ago by Julianus Pfeuffer <[email protected]>

[FIX] class test

eb429fa6d1a5141939097dd3211b3557f7673fa6 authored over 2 years ago by jpfeuffer <[email protected]>

[FIX] tool tests

b1722f1f87cbbdfbecbb8aaeb17f3d97c9f46763 authored over 2 years ago by jpfeuffer <[email protected]>

[FEATURE, TEST] added test mode flag to xQuest spec.xml output format (#6117)

* [TEST] commented out OpenPepXLS's spec.xml tests

These tests are unstable due to difference...

a039f216a0ab8ea8592bcad155284e0af1a41bbb authored over 2 years ago by Eugen Netz <[email protected]>

progress..

16e91178f9c42029e0f5eee04dddad386e6b01b4 authored over 2 years ago by bielow <[email protected]>

[FIX] mzml: Dont write empty DataProcessing for DataArrays

cca2f1dd4ca2c008a1fc6e68cd56ae3f0c5f7bb5 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

revert last commit. should be on branch

5859883114b6f13160331341d7a52dfbb0b3bed7 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

[FIX] Do not write empty DataProcessing for DataArrays

7aaab598d031d9991fdc8c37139c8caf214b669a authored over 2 years ago by Julianus Pfeuffer <[email protected]>

use OpenMS string split method to handle synonyms in MSPGenericFile::store

f200aad7460b72f6964a78efbdd637f4bc5d9634 authored over 2 years ago by bertrandboudaud <[email protected]>

Factorized code in organizeMapWithSameIdentifier using a lambda

1820cd8ef7596db3bd04417c697daf94d3df5568 authored over 2 years ago by bertrandboudaud <[email protected]>

Factorized code for annotateSpectra using lambda

54c733e5e9636fed71ff213c4bf54b5a0323002e authored over 2 years ago by bertrandboudaud <[email protected]>

Started to prepare MQMsmsExporter a little for the addition of MQExportHelper. But not complete yet!

6a3a6c80ecdc5f1476ca87390980e99367604a40 authored over 2 years ago by Virginia Rossow <[email protected]>

[TEST] commented out OpenPepXLS's spec.xml tests (#6116)

These tests are unstable due to differences in number to string conversions between versions of ...

921d3dae57d9bf52c5777c4fad0869cfcabfe32e authored over 2 years ago by Eugen Netz <[email protected]>

update -- trying to abstract away MSSpectrum from Canvas1D

162ae186793b3983c946abec5b18928376acd17b authored over 2 years ago by bielow <[email protected]>

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

274f65e0ccbc9551590171d3eb7af3bab8bc6ae1 authored over 2 years ago by beschorneh32 <[email protected]>

const verload for findHit, get gene name from description

b82126204d23ec14b480e8800b111b22d4d1e4d7 authored over 2 years ago by beschorneh32 <[email protected]>

annotated preoteindescription to featuremap instead of consensus....

4959f597aea8c6b19b8ae1a1c3d5c3442079ab16 authored over 2 years ago by lennykovac <[email protected]>

Removing commented lines from RT Transition list construction

26cec5a9b0bf937925428c20828d9cde2efa9ea8 authored over 2 years ago by bertrandboudaud <[email protected]>

fix: missing RT in transition list

1addd55730f7cde5747eb7ca9b347a9b1134201e authored over 2 years ago by dmccloskey <[email protected]>

MQEvidenceexporter now fixed -> working quality control, mapping from feature to protein name / gene name

589efd278ecee5bf1abe9559a58b3ce9c24d20ba authored over 2 years ago by beschorneh32 <[email protected]>

Using OpenMS::String's prefix method

ad0987c9ccfe8330a6caf6a261d7815182c9bda6 authored over 2 years ago by bertrandboudaud <[email protected]>

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

073eec2ab6034c77affecdf0c9b5321ee2c3fff6 authored over 2 years ago by Hendrik Weisser <[email protected]>

[TEST] added tool tests for JSONExporter (incl. test files)

cb3f70480891269a78d321bff361c6ba42c9d3aa authored over 2 years ago by Hendrik Weisser <[email protected]>

Added comment on how we extract adduct

1cf9c432ee8aa2d23302ac5ebaafd4cbdd93e934 authored over 2 years ago by bertrandboudaud <[email protected]>

fix: missing RT in transition list

f4078fd68b085935563496780f1e41886c8ed036 authored over 2 years ago by dmccloskey <[email protected]>

Changed API of extractSpectra, removed the compute_features flag

8b3ff0c7717f4a63693c10cdfc4ac569433c659a authored over 2 years ago by bertrandboudaud <[email protected]>

Update stale.yml

b7f296d361c43c1e922fe4fc83ce4308b3206c61 authored over 2 years ago by Timo Sachsenberg <[email protected]>

cleaned up a bit, not final ...

ac73f4ed407ad50b9e6d08439df6ce02a013b7af authored over 2 years ago by lennykovac <[email protected]>

[FEATURE] JSON export of OMS (SQLite) files: peak annotations, meta info, applied processing steps

587f128933540f671fdb777befbf8784b5933d21 authored over 2 years ago by Hendrik Weisser <[email protected]>

[FORMAT] OMS (SQLite) file format: added unique constraint for labels of parent group sets

4b6551a5f5edfed9b2aa33cebb7bdeb452a5d808 authored over 2 years ago by Hendrik Weisser <[email protected]>

[FIX] removed unneeded variable

75d520f7f57f51ce910834bf3cc8727159fe78a9 authored over 2 years ago by Hendrik Weisser <[email protected]>

Fasta Indexing done, functionality seems correct. QualityControl still crashing.

06866f333b69f17c423d0b4b8555bf492cccb47b authored over 2 years ago by lennykovac <[email protected]>

add_unknown_features renamed add_unidentified_features

d2207bf2979bc871794b1a5f03ea056b21f629d8 authored over 2 years ago by berbou <[email protected]>

Removed constexpr for std::array that is init with std::string (non literal)

780b843c1f2469b778a29e3455f281bc0c20e06c authored over 2 years ago by berbou <[email protected]>

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]>

Removed debug traces

2191f9e399ac7b8d3a49fa8e71d34db37cad64b1 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]>

Store retention time in msp files

8188cc4c499fcd2d9d915ce6860bf01c2b0a0de2 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]>

fix: added check for unannotated spectra in

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

Fixed doc

9405c89d8bf2d1ae197123536cdc2023410cc3dc 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]>

Fixed OpenMS unit test after changes related with PeptideRef

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

Added extractSpectra to pxd

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

Added extractSpectra unit test

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

Removed unused variable

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

Added extractSpectra's documentation

b47ae4d7d98eadeca144963101afc639f1f585c4 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]>

Store MSP: do not store spectrum with no peaks.

90a8e9892de59a4b913b3bbea3a858a3ebb794b0 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]>

Added one option to return unknown feature in searchSpectrum

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

Removed debug traces

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

storeSpectraTraML renamed constructTransitionsList

06e476a5780914d1a87c6ca514dc7fa7bab923c2 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]>