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

remove large test case

97b93b7c415a14d06e7694a7e9eff6639d649637 authored over 3 years ago by Abi Sarvepalli <[email protected]>

refactor write to file as method

bea1e5d463949e27ae8f0394110bdde6aabb5b1d authored over 3 years ago by Abi Sarvepalli <[email protected]>

use emplace_back to prevent creating duplicate structs

23ed6cb53e1179aa66dc304e21a6e991afebf456 authored over 3 years ago by Abi Sarvepalli <[email protected]>

fixed output errors:

- prefix "e_" when specifying consensusElement feature id
- change feature_charge to int
- clamp ...

edf8a05c2123d134e8064513e7612b6e8dac0030 authored over 3 years ago by Abi Sarvepalli <[email protected]>

[fix] pass ms2_block to write method by reference rather than value

bd46c1ed479ba6f8da087354702d45701898cd95 authored over 3 years ago by Abi Sarvepalli <[email protected]>

fix documentation; updated generateMSMSSpectrumBins_ with overloaded method accepting MSSpectrum

Signed-off-by: Abinesh Sarvepalli <[email protected]>

dd8eda367678dc67c40044cde85245a290407af4 authored over 3 years ago by Abinesh Sarvepalli <[email protected]>

fix: trailing whitespaces and extra blank lines

12aee8d4ab777e2f17595e944e8a2559e4cf7c7d authored over 3 years ago by Abinesh Sarvepalli <[email protected]>

Addressed PR 4761 to OpenMS/openms

https://github.com/openms/openms/pull/4761

Added...
- Technical documentation to method headers
...

59c43b3dd1cc73678a54de61d8bc9bf569c94aa6 authored over 3 years ago by Abinesh Sarvepalli <[email protected]>

upd test suite

3d146a0101296d29ef1eb737f319e4a639d4616f authored over 3 years ago by Abi Sarvepalli <[email protected]>

pass args by value into sort helper funcs

eb75504fd98773303e7c3a902cbe62fd6107fd6a authored over 3 years ago by Abi Sarvepalli <[email protected]>

updated GNPSExport module

2129705a4e8eaf9ef8dbd9e63f9f0aa340a44c8a authored over 3 years ago by Abi Sarvepalli <[email protected]>

add small result struct to DetectedCompounds

75b13cf25a537381af4df42e53e7bf3d3434b881 authored over 3 years ago by axelwalter <[email protected]>

adding missed file

6e7ba5757bb2c3ce1f3152b63255a48880c202e1 authored over 3 years ago by JeeH-K <[email protected]>

added output format checkboxes and changed wizard name

8a53f6303b9ea5df6bf7681b667a809081a47500 authored over 3 years ago by JeeH-K <[email protected]>

fix TIC relative intensity calculation

d4fe4e6c31acc328c329f2332d18671da40fbb0f authored over 3 years ago by axelwalter <[email protected]>

add detected compound QC metric

bd196a923ee2e4e01cab4bb2fc30dcf1706ecd40 authored over 3 years ago by axelwalter <[email protected]>

Update CHANGELOG

ad30d3e0d6a62990b9b18c285e2faabafe43d6d7 authored over 3 years ago by Samuel Wein <[email protected]>

[fix] updated the config storage path for linux

21f6614d2fff43428da1698d8c2f078797a44c52 authored over 3 years ago by Samuel Wein <[email protected]>

noop

4c638b548103b89bf875352dd0f2fb9c10ee0282 authored over 3 years ago by bielow <[email protected]>

fix test condition

9ad04f96d2daed0d5615dae6f892ecc38ec51571 authored over 3 years ago by bielow <[email protected]>

remove test -- its unclear why it should fire

df9fed30bd8195fed68506a51935ee0833ba413a authored over 3 years ago by bielow <[email protected]>

fixed parameter handling

e86109d47925c87094fe17a1bab7651219384289 authored over 3 years ago by JeeH-K <[email protected]>

Merge pull request #5384 from OpenMS/jpfeuffer-patch-1

[FIX] segfault in NeedlemanWunsch

64802a57fd97acf6b784cc9abc0803b7e002b31b authored over 3 years ago by Julianus Pfeuffer <[email protected]>

[FIX] segfault in NeedlemanWunsch

breaks nightlies

2d62314275156894874aa299e00b7295427fd205 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

setting FLASHDeconvWizard (parameter part not done)

4b287605606e58caf8c9e5f615c3f2cec272d8df authored over 3 years ago by JeeH-K <[email protected]>

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

1ed19762c8f67571f928774192bfbc4854c3239e authored over 3 years ago by bielow <[email protected]>

fix ABORT_IF's unexpected behaviour

ec11b43cf6ab1e1fbaebead6ff7a4308a266b648 authored over 3 years ago by bielow <[email protected]>

Merge pull request #5381 from cbielow/fix_static_initsegfault

fix segfault when starting any executable

60ebf3d7f27ee475fc93a861b19f8bdd69aee3b1 authored over 3 years ago by Chris Bielow <[email protected]>

* removed unused mz_right_lim and mz_left_lim

* using Logging mechanisms instead of std::cout
* use if (! x.empty()) instead of if (x.size())

e3877cf1d2bb4178d9631b957b8713cd17f58f84 authored over 3 years ago by Bertrand Boudaud <[email protected]>

fix segfault when starting any executable which was linked with

which results in
Program received signal SIGSEGV, Segmentation fault.
0x00007ffff7893f00 in xerce...

f29631567ac45adf083162faa3e2709451449714 authored over 3 years ago by bielow <[email protected]>

massively reduce build time (#5377)

* massively reduce build time by removing includes from ClassTest.h

* fix linux compile error...

f0f3b9411164256e8a9a266faaea757d547cdfe0 authored over 3 years ago by Chris Bielow <[email protected]>

support for IM data conversion (#5375)

* support for IM data conversion

* fixed tests

* fix

* extend test

* fix fallthrough...

9810f53ea6715d9d4b957cb4bdbd8cc57ae6fe86 authored over 3 years ago by Chris Bielow <[email protected]>

add complete TIC and MS2 TIC for mzqc

d90aad291b9d5e7df88b97be8662dbd9b11357f5 authored over 3 years ago by axelwalter <[email protected]>

review comments

02b63b76d2bdb7152c9d45eaf89cf084ca05f099 authored over 3 years ago by bielow <[email protected]>

fix linter errors

55257ea188541e4f05a3cb0dba45475015a6f7e1 authored over 3 years ago by bielow <[email protected]>

fix linux compile error

68b2f43c1fd548da170fbc4a866c883b58d959ff authored over 3 years ago by bielow <[email protected]>

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

89e74fe9fa1e4453a1e82a283be4359b290e6cef authored over 3 years ago by bielow <[email protected]>

massively reduce build time by removing includes from ClassTest.h

bbe0beded94bae282d88ff59b42afe4c99b511c4 authored over 3 years ago by bielow <[email protected]>

add ms_level parameter to MSExperiment::getTIC()

45a392709653428fbc329784672d62784c032bb9 authored over 3 years ago by axelwalter <[email protected]>

Fixed mergeFeatures unit test

2e8c746169f0f09eee2b39bd5df33c2c83dbd5ad authored over 3 years ago by Bertrand Boudaud <[email protected]>

Merge pull request #5351 from singjc/fix/ipf_peptidoform_gen

Fix/ipf peptidoform gen

ad726f579de423c20852c871ae572df933f06a55 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

[FIX] Adjust braces on multiline if-else statements to match consistent code style

e9d599894eb394994e0a334b03e3fc826c7fb28a authored over 3 years ago by Justin Sing <[email protected]>

Merge pull request #5374 from OpenMS/py_nightly_test

[TEST] PyOpenMS Nightly Linux failing

4389ed7dec33354c15852c62dcab52e74d8f830e authored over 3 years ago by Julianus Pfeuffer <[email protected]>

reformat patch

908bc0c756fb6cc8c95da1b534a98a8d89481e04 authored over 3 years ago by oliveralka <[email protected]>

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

a42d77e5b62166ba6ed4ec6acfeba071695f0c7a authored over 3 years ago by oliveralka <[email protected]>

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

b54873efd15dc1dfeb93997ad128b83ec270440d authored over 3 years ago by oliveralka <[email protected]>

format

c68a8790584df28f857399219539a6c0b864af46 authored over 3 years ago by oliveralka <[email protected]>

test1

d86531571420d6b4e510b324b4af89301e9eb519 authored over 3 years ago by oliveralka <[email protected]>

test

3e9071285202f478f9e457358343acf53dd76353 authored over 3 years ago by oliveralka <[email protected]>

Disallow IL_equiv with enzymes that potentially distinguish them. (#5368)

25e5034768f8fa897edc695fd03cfc5903dc2594 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

make getOpenMSDataPath thread-safe (#5372)

* make getOpenMSDataPath thread-safe

* Update File.cpp

6365587b5ee42d1dea730c9619df679c16a199c5 authored over 3 years ago by Timo Sachsenberg <[email protected]>

Update src/openms/include/OpenMS/ANALYSIS/OPENSWATH/TargetedSpectraExtractor.h

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

6a00f8ec1145f2ed226db556c0b6e8b40780da06 authored over 3 years ago by bertrandboudaud <[email protected]>

add missing meta data to FFMultiplex output (#5371)

* add missing meta data to FFMultiplex output

* Apply suggestions from code review

* set c...

1645a2233380df34d69fe7388c3c6b935adbfeca authored over 3 years ago by Lars Nilse <[email protected]>

Add option for compile time tracing (#5364)

383408f0555372116a72385d962632688af8e6a5 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

remove superhirn (#5369)

* remove superhirn

* remove also algo

68cc62d87b8716bb051909f26082291ab182a591 authored over 3 years ago by Timo Sachsenberg <[email protected]>

insert Element.xml info into ElementDB file (#5279)

* insert Element.xml info into ElementDB file

* changed String, Map to std::string, std::map;...

c096c1185f8c9fb21b3c1695bfd445760913f682 authored over 3 years ago by JangJang3 <[email protected]>

only considering the 1st identifier in organizeMapWithSameIdentifier

f7d28e0495f2a3af7d1c487b86c2275f117472ff authored over 3 years ago by Bertrand Boudaud <[email protected]>

moved include

8700e2397b05886ccd7a3242235ea36b779176c6 authored over 3 years ago by Timo Sachsenberg <[email protected]>

update toppas workflow in share

26acfb33e41d5b1e170e036b24d27a3f433f58b1 authored over 3 years ago by timosachsenberg <[email protected]>

Merge pull request #5363 from OpenMS/add/openms_ci_thirdparty_tests

[TEST] openms-ci THIRDPARTY tests

5934031ea4e8f3dc8d5d5c27a538c38a3cd8c417 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Merge branch 'feature/TargetedSpectraExtractor_storeSpectra_for_pr' of https://github.com/bertrandboudaud/OpenMS into feature/TargetedSpectraExtractor_storeSpectra_for_pr

da8e0abfd6a05585bc200100a9396e8e32cbde5c authored over 3 years ago by Bertrand Boudaud <[email protected]>

added max_precursor_mass_threashold_ parameter

1a835957af4570aa94a608fddbcd81f8b0e6c628 authored over 3 years ago by Bertrand Boudaud <[email protected]>

added and apply AMSE parameters

cf4faa84a0992b7c3d3e25a94f1254ea8d45159b authored over 3 years ago by Bertrand Boudaud <[email protected]>

switch to loop

ca19c1c514282a17042699a2eedb1bfadbcdb552 authored over 3 years ago by oliveralka <[email protected]>

FIX path

d6447b6dc19d9ee153f0bbf476e661cfb517cd0b authored over 3 years ago by oliveralka <[email protected]>

Add third-party binaries to PATh

4520b108dbe1eba14b470780df1698326b97956f authored over 3 years ago by oliveralka <[email protected]>

remove OMSSA

52409a331a70dfe3c44e62eaeb062d322215717e authored over 3 years ago by Timo Sachsenberg <[email protected]>

add cd to source dir

f8f179592d2d88ce16818dab8e2a7b1bcb08359c authored over 3 years ago by oliveralka <[email protected]>

upstream branch

9a54c6fabf0166d8f9e632ee84773f28b78d2dfa authored over 3 years ago by oliveralka <[email protected]>

test branch

8a0b1b987550e9d5e0efb7a1ac9b5718c4910f96 authored over 3 years ago by oliveralka <[email protected]>

[FIX] style

dde97c16b640a4fbfff3bdebeb57b5e9eb94125c authored over 3 years ago by oliveralka <[email protected]>

add THIRDPARTY; add search_engine_search_dir

93662787f2f1f780a57ab29cbccb73ba48bae9f5 authored over 3 years ago by oliveralka <[email protected]>

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

e7b25610a27e01f13acf8d243e50f63a0c5eb9f4 authored over 3 years ago by oliveralka <[email protected]>

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

88cf01f95c171b67327d4a3fa3be595eef771b91 authored over 3 years ago by oliveralka <[email protected]>

Update src/openms/include/OpenMS/ANALYSIS/OPENSWATH/TargetedSpectraExtractor.h

Co-authored-by: Oliver Alka <[email protected]>

d8afb55dbb1cf5268f35ce1c01a216ba5546f6e0 authored over 3 years ago by bertrandboudaud <[email protected]>

[REFACTOR] Modify check in addModificationsSequences_ refactor and add a specific test based on PR feedback

915790c0bbb7be81d4bc17174305c92c0fe3fc91 authored over 3 years ago by singjc <[email protected]>

[REFACTOR] Modify check in addModificationsSequences_ refactor and add a specific test based on PR feedback

b4944f054b82dee84312fa80231ee76676a263e8 authored over 3 years ago by singjc <[email protected]>

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

6be63dbbba42293fd66b877546a0d460d5f7d307 authored over 3 years ago by oliveralka <[email protected]>

fix build (#5358)

Co-authored-by: timosachsenberg <[email protected]>

83a4849740629a46df0620df93e79e9ded4db863 authored over 3 years ago by Timo Sachsenberg <[email protected]>

Update IDFilter.pxd (#5356)

* Update IDFilter.pxd

1dd705e44b6f5a1ba2d016f76bfc52a0ea8ff032 authored over 3 years ago by Timo Sachsenberg <[email protected]>

Warn if only one file provided as input to MapAlingerPoseClustering (#5355)

* Warn if only one file provided as input to MapAlingerPoseClustering & MapAlignerIdentification

1324ba9ecf8c23e9bf1f0ec8b9ee8292753e60a5 authored over 3 years ago by Timo Sachsenberg <[email protected]>

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

9d577b52373c082293cf9c2154da29cbab27ec2c authored over 3 years ago by oliveralka <[email protected]>

Merge branch 'develop' into feature/FLASHDeconv

00999bf7cdacb56078730856549416cc1b01270d authored over 3 years ago by JihyungKim <[email protected]>

Merge branch 'feature/TargetedSpectraExtractor_storeSpectra_for_pr' of https://github.com/bertrandboudaud/OpenMS into feature/TargetedSpectraExtractor_storeSpectra_for_pr

d6d6556c67d56ecdc098e4acddc129475ecdb198 authored over 3 years ago by Bertrand Boudaud <[email protected]>

fixed insertion operator for unit test

f3574e3b423051f35d98ddd4e8b7bd9f1ede45d5 authored over 3 years ago by Bertrand Boudaud <[email protected]>

Update src/openms/include/OpenMS/ANALYSIS/OPENSWATH/TargetedSpectraExtractor.h

Co-authored-by: Oliver Alka <[email protected]>

f512ccf6247731d7d12b0c78c73b00c8ae948580 authored over 3 years ago by bertrandboudaud <[email protected]>

Update src/pyOpenMS/pxds/TargetedSpectraExtractor.pxd

Co-authored-by: Oliver Alka <[email protected]>

a5a194e29833c80c77d96bed298c6fc821fbc9eb authored over 3 years ago by bertrandboudaud <[email protected]>

Update src/openms/include/OpenMS/ANALYSIS/OPENSWATH/TargetedSpectraExtractor.h

Co-authored-by: Oliver Alka <[email protected]>

ec752a85c37103d5c06b66757dcef0585aefd76b authored over 3 years ago by bertrandboudaud <[email protected]>

Update src/openms/include/OpenMS/ANALYSIS/OPENSWATH/TargetedSpectraExtractor.h

Co-authored-by: Oliver Alka <[email protected]>

e9bcc7607c85a7b90e1020e188f405c17dcdf82a authored over 3 years ago by bertrandboudaud <[email protected]>

Update src/openms/include/OpenMS/ANALYSIS/OPENSWATH/TargetedSpectraExtractor.h

Co-authored-by: Oliver Alka <[email protected]>

85e7c35c8d3c5bf1b920770a4a2b1bc7ebb5aa18 authored over 3 years ago by bertrandboudaud <[email protected]>

set value to double (trigger ci)

29459b30dccdd6b906b4c993ab19f3f7d1bea4dd authored over 3 years ago by Bertrand Boudaud <[email protected]>

FLASHDeconv beta+

1b4deed181c95df4e527d30613488dcd46e91771 authored over 3 years ago by kyowonjeong <[email protected]>

FLASHDeconv beta+

87ed0f6e48a80180f716bc0b995cc6b3fe767cc1 authored over 3 years ago by kyowonjeong <[email protected]>

fix wrong gitignore; add missing sources.cmake (#5353)

* fix wrong gitignore; add missing sources.cmake

* fix duplicate

* fix linter errors

29187a6b2d0c614437dc7099f5089e9620fa226d authored over 3 years ago by Chris Bielow <[email protected]>

Merge pull request #16 from OpenMS/fix/hendrik_idfile_integration

[FIX] handle multiple file origins in ProtID Runs, transfer IDs with CFeat.Obs.

6e39e1d5eb5d4f2a6e33ecb4cd7e5b22cf414005 authored over 3 years ago by hendrikweisser <[email protected]>

[FIX] Modify check in addModificationsSequences_ fix typo in debug log message

aa08ed92cde35bf0eae62efbe8ae19748222aa3a authored over 3 years ago by Justin Sing <[email protected]>

put back the tests

07c8f9a64f6249ca96282f87b76d01b0700e31fd authored over 3 years ago by Bertrand Boudaud <[email protected]>

commented mergeFeatures, annotateSpectra and storeSpectraTraML tests

5fea7dfffe1df21ae80d77d7b273fc909eeddefe authored over 3 years ago by Bertrand Boudaud <[email protected]>

Merge pull request #5342 from noraw61/seq-align

Replace SeqAn alignment with Needleman Wunsch

da39ff4bafb1b5d84cc8433452416e43a1a4a321 authored over 3 years ago by Chris Bielow <[email protected]>

test reducing template recursion level (#5347)

* test reducing template recursion level

* Also reduce max Tensordimension

a3afd27050a90312571078c8383e52e2a9619b84 authored over 3 years ago by Julianus Pfeuffer <[email protected]>