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

fix tests

9ba7fcd1f7b6b920538330f80b06ce7857ff5862 authored almost 6 years ago by lars20070 <[email protected]>

[NOP] remove compile warning (expression always true)

2770ef930ec51dc668a8194400f9adaf7a191537 authored almost 6 years ago by Timo Sachsenberg <[email protected]>

style: remove strings constants (not used often)

d5b885a080464212dfc727dc34d7d4f3981aa7a3 authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

style: rename setParameters to setSchedulerParameters (same for getter)

4e0cd36e6b53190d58539d7e542dc5198b1c87b1 authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

refactor: replace String with bool where possible (parameters)

26dc6d52321599614b3d8155fd1aa90163233d94 authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

test: make methods private and test them

674a3ebe3550f916643adaa58e72ca5a9b118a80 authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

set mz_reference = peptide

132ed19aa2dcd74a5b05e3d5369375282136c8aa authored almost 6 years ago by lars20070 <[email protected]>

fix tests

3f473c871ac9fa3dad4fe499652277dd3ff136a6 authored almost 6 years ago by lars20070 <[email protected]>

make ignore_charge advanced

7d42740b9c4a67b4eee331a02042807c883c7ea3 authored almost 6 years ago by lars20070 <[email protected]>

[FIX] FeatureFinderMetaboIdent: fixed segfault caused by misconfiguration when 'model:type' was 'none'

d3ee8aed0840bd64f026b1055d13bf823dbe262f authored almost 6 years ago by Hendrik Weisser <[email protected]>

[FIX] FeatureFinderMetaboIdent: fixed segfault caused by misconfiguration when 'model:type' was 'none'

f7ff651c9b4307a45d303748f7f70b5f7d72fcae authored almost 6 years ago by Hendrik Weisser <[email protected]>

chore: rename functions

01aaeff8f0028954f8fbe9e2ec6ee2d95f45ba8b authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

Merge branch 'FFMetId' into rna-lfq

2b7e55bbec2bc7c917dc9d902bab4061fc4b9a96 authored almost 6 years ago by Hendrik Weisser <[email protected]>

chore: remove debug couts

f2d12ff87979395eed5120e031a9812b4df074dc authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

Merge branch 'develop' into feature/MRMFeatureSelector

08f707bdb8a89d444b046be6f63e754dba852984 authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

refactor: remove DefaultParamHandler, implement SelectorParameters struct

cf835854e8e145c7f8449cb9def660b768d14379 authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

[FEATURE] NucleicAcidSearchEngine: support for adducts in output for label-free quantification

9f575696b792d3e420f5fe860c98d85d230da57c authored almost 6 years ago by Hendrik Weisser <[email protected]>

fix: threshold

test: integer and continuous cases

7e69bfe62f492dc84ff9457d7b8470829ef5d566 authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

add id of group to ion feature

3435668f5cf6b1c8b6a3889b9b74cee71c0769b9 authored almost 6 years ago by FabianAicheler <[email protected]>

small restructure and cleanup

afd92e5777e0d0ff799bf36137b756504d672625 authored almost 6 years ago by FabianAicheler <[email protected]>

Added adducts userParams to consensus; changed monosisotopic decharged mz to feature mz

0b285595b41983254ba630bb9314624550ab39c1 authored almost 6 years ago by FabianAicheler <[email protected]>

Removed charge userParam

465091cc8bcd3f4d2ad9832b4500eb23c5907461 authored almost 6 years ago by FabianAicheler <[email protected]>

Cleaned up output userParams

ed76d81f46e285254939eebb40b522842492fc89 authored almost 6 years ago by FabianAicheler <[email protected]>

[FEATURE] include adduct information in mzTab output generated by 'IdentificationDataConverter'

42e83fd29b6d1970465815080966af628bde1d60 authored almost 6 years ago by Hendrik Weisser <[email protected]>

[DOCU] typo

5131bb489b2b11a49fff10a17a0c93fcfc9ce5dc authored almost 6 years ago by lars20070 <[email protected]>

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

a8885f295819a08a80400ea984fea41a1be5fa05 authored almost 6 years ago by oliveralka <[email protected]>

[ADD] further TODO

bc7f6da9c3a409412bd9cc32b4e08ed951e24464 authored almost 6 years ago by oliveralka <[email protected]>

Merge pull request #3805 from cbielow/SWATH_CD

SwathQC output

caf885743805ff09a03c068bd0c578b6576e2ee4 authored almost 6 years ago by Timo Sachsenberg <[email protected]>

[FIX] fixed TOPPView segfault (display of FeatureFinderMetaboIdent results)

e4df547d5d43d63e3e4b9ad379917fcb2582c2f2 authored almost 6 years ago by Hendrik Weisser <[email protected]>

Update ConstRefVector.h (#3832)

* Update ConstRefVector.h

second one

* Update ConstRefVector.h

5afe7058870592182328dd6239f9bb505b97af98 authored almost 6 years ago by Timo Sachsenberg <[email protected]>

[COMMENT] FeatureFinderMetaboIdent: added doc comments to functions

f744012b7e6a94eeaeae0839090414c2edf9e9c9 authored almost 6 years ago by Hendrik Weisser <[email protected]>

[FIX] FeatureFinderMetaboIdent: fixed m/z calculation for negative charges

772c1735d8d3df1f72fe61ab0cf7216cb6506c1b authored almost 6 years ago by Hendrik Weisser <[email protected]>

change enum values to all caps

36d917470877a6a54b402fd768f83a61231cc813 authored almost 6 years ago by lars20070 <[email protected]>

[FIX] FeatureFinderMetaboIdent: fixed m/z calculation for negative charges

18ac963bc768795678983dbff6f203bed90f9629 authored almost 6 years ago by Hendrik Weisser <[email protected]>

[PARAM] NucleicAcidSearchEngine: added option to write out coordinates for label-free quantification via FeatureFinderMetaboIdent

a07fd1d6cdfb5afaeb877ee1babeeb3ec0e03991 authored almost 6 years ago by Hendrik Weisser <[email protected]>

[INTERNAL] revert renaming of c'tor arguments in class 'MoleculeQueryMatch'

173a36b9643eb8c8612a5d5e92d901e39c7ce7b7 authored almost 6 years ago by Hendrik Weisser <[email protected]>

Merge branch 'FFMetId' into rna-lfq

0c6787e1a7b7801706ef324c894180853b66963a authored almost 6 years ago by Hendrik Weisser <[email protected]>

check for float, integer and string data arrays

d4952f7742e19e9d011ac6066a816a3d437af95d authored almost 6 years ago by lars20070 <[email protected]>

use enums, add sum as method, add warning, fix tests

7ffe7959e75b04c61ad5f22b84d33168dbc4e1ca authored almost 6 years ago by lars20070 <[email protected]>

Update FineIsotopeDistribution_test.cpp (#3837)

b38d5b1b5de4ceb3e52084f0bc49343cdfe919a9 authored almost 6 years ago by Timo Sachsenberg <[email protected]>

fix test

0cb77c6e5525b6461dbcbc8a6c71f85016bb75ba authored almost 6 years ago by Chris Bielow <[email protected]>

[TEST] add class test

b3820f75e836ab9baf9d1f6c2266fb8a27f0b9c0 authored almost 6 years ago by lars20070 <[email protected]>

[API] new makePeakPositionUnique() method

895092480164f51f8f197f715da53fc145ed5b8e authored almost 6 years ago by lars20070 <[email protected]>

[NOP] release cleanup (#3831)

* [NOP] removed execute rights from source files.

* [NOP] Added copyright header to cmake fil...

1d9c0ace4baca940ca9252c645441592611d6cec authored almost 6 years ago by jpfeuffer <[email protected]>

Merge pull request #3835 from heckendorfc/sa-qprocfail

Postpone QProcess.close() until after error handling

8efd41bb259379ed608b711eaad96c22d16789a0 authored almost 6 years ago by Timo Sachsenberg <[email protected]>

Minor improvements to documentation

5a2242dc2d1c10362db25688462e524a43b22e77 authored almost 6 years ago by Michał Startek <[email protected]>

Add tests for IsoSpecOrderedWrapper

ca48e08de463e4e5ddc373f7222de2ee0ce0399e authored almost 6 years ago by Michał Startek <[email protected]>

Fix GCC8 warnings

9a69f8e315878b1e0ee8bbff4980df3b5270ebff authored almost 6 years ago by Michał Startek <[email protected]>

Add unit tests for IsoSpecTotalProbWrapper

ded243273b261173ef489c86f8c652296dfe96ee authored almost 6 years ago by Michał Startek <[email protected]>

Postpone QProcess.close() until after error handling

c4ff7b6c19acb344b22fbda03f37211f98135084 authored almost 6 years ago by Christian Heckendorf <[email protected]>

[TEST] updated FeatureFinderMetaboIdent test file after changes in OpenSWATH

1f68d5724a2bc7132466b1ccd036e0d10987299f authored almost 6 years ago by Hendrik Weisser <[email protected]>

[FIX] updated FeatureFinderMetaboIdent to changes in isotope pattern generation

b5e3c944971166d0c0f7e15c5f5766d907235501 authored almost 6 years ago by Hendrik Weisser <[email protected]>

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

a16bb6c6cd1f2c9f16745e1b533fd31b9a0aecc7 authored almost 6 years ago by Hendrik Weisser <[email protected]>

revert travis hack

b86b75f335049679bab7b510ecaec7c94f9dcb00 authored almost 6 years ago by Chris Bielow <[email protected]>

fix gcc

c5c1bfe568fc823027e119a95dcafeb51ecd9fc3 authored almost 6 years ago by Chris Bielow <[email protected]>

[BUILD] travis cache restart

- only build TOPP tools in order to reset the ccache and allow travis to
complete an OpenMS bu...

37d1fd1f45e25c995c14ae5c6ef905bb7250c976 authored almost 6 years ago by Hannes Roest <[email protected]>

fix: condition to insert selected results

69a0b3efc6c77142972cb212d488ca295e64dbf5 authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

fix: set continuous variable type when necessary in optimize()

bda7212bafb57c65786c190c0490cf29d8ebd5fd authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

feat: reduce cast calls

36e541720771895b51085aa72c12ed2e50a015bb authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

feat: use remove_spaces()

5b67a9c59f9fec5e59a74a1a88871199335e9126 authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

style: indent

0cff15c178cbfb9968cc1041df0eacd85e09b5cb authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

feat: move more computation into parent loop

46ae3c0d19655bd1de3a82ff18031a0ae0ee9e07 authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

fix: reduce computation (moving it to parent loop)

376e7428c660871f6955576f8c0bfda9c6fe29e6 authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

Add documentation for IsoSpecWrapper

31039a882dced95b98ffaec3f192e9f4a3253cc3 authored almost 6 years ago by Michał Startek <[email protected]>

fix: optimize (qmip), start_iter integer underflow

eb9c6aac7f5709b205258370fdbe3f37614efe5a authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

feat: avoid unnecessary scores update when exponent is 1 (i.e. score_weights_.size() == 1)

226dcaaed2660c87a01f8b6098362d43f528681c authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

test: make_score()

4b6514eccc16bace2f0c0276f59d09e48af63ad6 authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

fix codacy

428d4d02bce52801dcdabee45b7e76855f99831c authored almost 6 years ago by Chris Bielow <[email protected]>

fix - revert change

539ab0e7b8204723766f49f850e8c7f1e902e652 authored almost 6 years ago by Chris Bielow <[email protected]>

[TEST] added test for mzTab export and expanded other tests for 'IdentificationDataConverter'

6c72ef0413423edab57d516e7bc546ab94be5487 authored almost 6 years ago by Hendrik Weisser <[email protected]>

[FIX] fixed export of peptides to mzTab in 'IdentificationDataConverter'

38889223c5e7a885dc8cfa13dc17ea6f185f37af authored almost 6 years ago by Hendrik Weisser <[email protected]>

[FIX] when exporting from 'IdentificationData' to 'Peptide-'/'ProteinIdentification', handle X! Tandem charge notation and sort certain data

30068d6b40c39437ab31c100d76b03e3de1eb0f4 authored almost 6 years ago by Hendrik Weisser <[email protected]>

[NOP] removed execute bits from txt and cmake files

cc8b58d36abda166b17c3500ebf08e8bd7b5603e authored almost 6 years ago by Julianus Pfeuffer <[email protected]>

[NOP] Added copyright header to cmake files.

8e71fe840d445cf7ea3a181c9920fb02c5005f11 authored almost 6 years ago by Julianus Pfeuffer <[email protected]>

[FIX] Set finding pthreads up as early as possible in cmake process

needed by prior 12ac3fe

790f53c00bbec08dc6bcd4b9afecd88c1117477d authored almost 6 years ago by walzer <[email protected]>

[NOP] removed execute rights from source files.

1f2948d1f593d2c1509fac508949abebea1bb641 authored almost 6 years ago by Julianus Pfeuffer <[email protected]>

[FIX] added pthread to the linked cmake libs for FeatureFinderSuperHirn

0dad15bc7a572f66c8e9215f2108eeec8ceae655 authored almost 6 years ago by mwalzer <[email protected]>

style: avoid cast to double in optimize()

b302b7a31b9c0d18682de08c378e49dbfccc8fdb authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

fix tests

99d4959e466f2394f80c52d68d98592c21cedc86 authored almost 6 years ago by Chris Bielow <[email protected]>

chore: remove cast

e81c0d31544552e263f11efb979985a67d97a6f7 authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

test: weight_func()

89e724c2f1af53d5b4988b710a1d334b0515d9d4 authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

fix: integer division

7b3e56497286e96a38499167d89d0fe3b7063a6a authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

refactor: separate To_list() (in python) construction

test: constructToList()

26980d9788a43b8169312e8efcec735996ea5090 authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

[FEATURE] enable collection of SwathQC data when mzML data is loaded

bd53b755e761ed17729b48109aaec907b54641a9 authored almost 6 years ago by Chris Bielow <[email protected]>

[FIX] Deistoper class now correctly deals with DataArrays which are already attached to the spectrum

7ef81fe61e0c639ce5515843612dd7c419c39928 authored almost 6 years ago by Chris Bielow <[email protected]>

[TEST] more thorough import/export comparison in class test for 'IdentificationDataConverter'

91cf6309b444ac2add10d80d9da7db279927968b authored almost 6 years ago by Hendrik Weisser <[email protected]>

Remove the remaining visibility workarounds (not needed anymore)

b6f4e7d646971cf3ec955eed3c96b613d45d5c35 authored almost 6 years ago by michalsta <[email protected]>

Fix visibility problems with IsoSpec

d70e9c326aac648caf1dc8e9f64bb2ffada397be authored almost 6 years ago by michalsta <[email protected]>

Return IsotopeDistribution from Iso*Wrapper run() method

664346946166950f24c557e8686ab898f8760022 authored almost 6 years ago by michalsta <[email protected]>

Now that we're using OMS isotope frequencies, correct test results are slightly different

892159a3a0691bdcd78f40307dd46295ffa3bed1 authored almost 6 years ago by michalsta <[email protected]>

Use OMS empirical formula parser and isotope frequencies instead of IsoSpec's

cfda47dd2048250cf85f7d1b4f496fc57ccf4ccf authored almost 6 years ago by michalsta <[email protected]>

Update $Authors

916c93bef2bb7481f4d8943edf1a128e9a194758 authored almost 6 years ago by michalsta <[email protected]>

Merge pull request #3829 from jpfeuffer/fix/ompMacLogStream

[FIX] Fixes concurrency issues for LogStream on Mac and avoids access…

89125c95dcd29879fda2a784835e6a16b725241c authored almost 6 years ago by Timo Sachsenberg <[email protected]>

Removed legacy blocking parentheses

ea79e750e950b2dd1168fb47b68dcdca947d2ebc authored almost 6 years ago by jpfeuffer <[email protected]>

[DOC] Describe omp log stream issue on mac better

Co-Authored-By: jpfeuffer <[email protected]>

dac958315745aeba32ebf3740b66be9a44a27855 authored almost 6 years ago by Hannes Roest <[email protected]>

Expose the Ordered generator

093fab7252d909b6a9b574eb2b909b64db0cd9da authored almost 6 years ago by michalsta <[email protected]>

Expose the Layered algorithm

a8b26e87556af21a2db7b0f55ec42b22ee80ee63 authored almost 6 years ago by michalsta <[email protected]>

Rework the IsoSpecWrappers to be more elegant, expose generator functionality

339f0a1e7004c15232d4ce615941ff407a697ac3 authored almost 6 years ago by michalsta <[email protected]>

Pull in IsoSpec v1.9.0beta2

e95f68da3b43a536452a207ef398d0ba657e2a6b authored about 6 years ago by michalsta <[email protected]>

[FIX] Fixes concurrency issues for LogStream on Mac and avoids accessing omp symbols in dtor in case of premature closing.

0d882fef4b59a515ba0bb5c7a82781580d28e0eb authored about 6 years ago by Julianus Pfeuffer <[email protected]>