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

add tests for the new param.

93816efdf31dd2a9f4d4f455695d19e7872c407b authored over 4 years ago by Julianus Pfeuffer <[email protected]>

typo

d74139a1d427e7fb33566016560382904f05465d authored over 4 years ago by jpfeuffer <[email protected]>

updated test files of comet

c986f4cfe178b601d819f4ca40516f8565a8b2ef authored over 4 years ago by Timo Sachsenberg <[email protected]>

removed tmp output

f465fe65ee4162541aaa29c38b15e997c5f49aae authored over 4 years ago by Timo Sachsenberg <[email protected]>

update MSGF+ test file

c5c5bae869e357c9936f7229aee1a9e3f8d590f8 authored over 4 years ago by Timo Sachsenberg <[email protected]>

added binary groups

fcb1903b83a3fb1dadb76f0784cf3ef791691451 authored over 4 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #4612 from OpenMS/feature/removeEmptyCFsIsobaric

[FEATURE] Remove unquant. ConsFeats w/o ID after IsobaricAnalyzer

8ff9a1d4741dd6868ebd7cfb598d8f12c6c5f598 authored over 4 years ago by jpfeuffer <[email protected]>

Merge pull request #4611 from OpenMS/fix/winExternalCode

[FIX] make external CMakeLists win compatible

0e93a62767cb62bb981bc1f9b65d08436e03e837 authored over 4 years ago by jpfeuffer <[email protected]>

Update CometAdapter.cpp

7ecfdd152a73441369445113aae5b5cc4c04ea82 authored over 4 years ago by Timo Sachsenberg <[email protected]>

Merge remote-tracking branch 'origin/develop' into feature/update3rdparty

f5ce570797dcd9caebdc0005d5c41d725d57e72e authored over 4 years ago by Timo Sachsenberg <[email protected]>

Update .gitmodules

b6b16e981493de5a9524e73496df541eef636296 authored over 4 years ago by Timo Sachsenberg <[email protected]>

[FEATURE] Remove unquant. ConsFeats w/o ID after IsobaricAnalyzer

4257a6e0b6ee995c89a2211cbcbf11fbb3667d42 authored over 4 years ago by jpfeuffer <[email protected]>

added basic test

01b5c5f2f107b16a361f0216d6d61f252bf98b9c authored over 4 years ago by Timo Sachsenberg <[email protected]>

make external CMakeLists win compatible

da7b7a46336ffa230dda30e3135972c9c4c4a7f3 authored over 4 years ago by jpfeuffer <[email protected]>

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

749ca3b9b1764b603d2aaa453cc2187b3eeabb68 authored over 4 years ago by Timo Sachsenberg <[email protected]>

update parameters to comet 2019.01 rev 4

3acba1732d6001e45d397bc70f78f32d4dc0b518 authored over 4 years ago by Timo Sachsenberg <[email protected]>

update docs

2ec2c16e7f938fdbabcb156a66e54007fd759d5e authored over 4 years ago by Chris Bielow <[email protected]>

finalize split of ConsensusMap; support for TMT/iTRAQ in QC

3344631d7b27d48e25aeaf09947f40ece94fb1fd authored over 4 years ago by Chris Bielow <[email protected]>

Merge branch 'develop' into feature/update3rdparty

34d7fefa99bef01a628bf2fcd7a4567479aaffbc authored over 4 years ago by Timo Sachsenberg <[email protected]>

more fixes and options

f1b28b44a645c323af07a524482e245b8f7db4ad authored over 4 years ago by Julianus Pfeuffer <[email protected]>

add test stub for DecoyGenerator

f3cfdc62863b277eadab8b32c43281345b9e8e71 authored over 4 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #4602 from jpfeuffer/fix/installIncludes

[FIX] Adds missing includes to be exported

90e3ce53386100764d5151d34ec8557b35ef91a3 authored over 4 years ago by jpfeuffer <[email protected]>

Merge remote-tracking branch 'origin/develop' into feature/update3rdparty

8cac0ab114d05e25856a88cc84d59d6b314a09c7 authored over 4 years ago by Timo Sachsenberg <[email protected]>

fix bad submodule commit

96e429af2776f0fe47cfac6ef7947cfd65bc6537 authored over 4 years ago by Timo Sachsenberg <[email protected]>

update THIRDPARTY

6b52932699c569730491cc41e38ea5ca6438ff2d authored over 4 years ago by Timo Sachsenberg <[email protected]>

[TEST] updated .oms input files for MapAlignerIdentification test

c8e105d086cb16ee63454bbce91f3d7e0f1b8ba8 authored over 4 years ago by Hendrik Weisser <[email protected]>

make add_decoys an advanced option in MSGF+ adapter (#4605)

* make add_decoys an advanced option in MSGF+ adapter

rarely used as we need to index we a t/...

b8fcdc8828d502b0ec0b362616a7148b1f01984f authored over 4 years ago by Timo Sachsenberg <[email protected]>

Added findHighestInWindow in MSSpectrum. Changed PrecursorCorrection … (#4606)

* Added findHighestInWindow in MSSpectrum. Changed PrecursorCorrection accordingly.
A piece of ...

ffda609d41621aa87cc773b610876b45474471bb authored over 4 years ago by JihyungKim <[email protected]>

[TEST] updated order of results in IDFileConverter test file

e045f030435bbdf01ff2be540b68b9ff1a494e56 authored over 4 years ago by Hendrik Weisser <[email protected]>

remove todo

1badfaa9488aa76f8c119639cd54a45b5e8bae68 authored over 4 years ago by Julianus Pfeuffer <[email protected]>

add openmp

46c0f45668a0f6d9dbc1865b499cea1a2c228625 authored over 4 years ago by jpfeuffer <[email protected]>

remove todo

ffbeb6feb0e79f7ce425d291e08141ab970fc419 authored over 4 years ago by Julianus Pfeuffer <[email protected]>

Fix compile and test.

82320d30e0276aeda4a7f696060eb290dd89b9fe authored over 4 years ago by Julianus Pfeuffer <[email protected]>

Use a merge index metavalue to keep track of the primaryMSRun path of

IDs during merging.

09164724b3c9978d399bedbf19ac864fbf1e7ae0 authored over 4 years ago by Julianus Pfeuffer <[email protected]>

Update .gitpod.Dockerfile

99d56e323d86e9a3bc69f2d4172832d57b3ddd05 authored over 4 years ago by Timo Sachsenberg <[email protected]>

Update DecoyGenerator.pxd

1af330dd3580dfae418cbc934d435dce5296efb0 authored over 4 years ago by Timo Sachsenberg <[email protected]>

added icon

28686474ddde84ae85c0e8c930520b150c177fc0 authored over 4 years ago by Chris Bielow <[email protected]>

Merge branch 'develop' into feature/FLASHDeconv

c88399d7aea250b0f63291ee7079aed6506d13f5 authored over 4 years ago by JeeK <[email protected]>

Merge branch 'feature/FLASHDeconv' of https://github.com/JeeH-K/OpenMS into feature/FLASHDeconv

cf6c415f92f3c77db977cff5e9d766d910425b3b authored over 4 years ago by JeeK <[email protected]>

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

9478c734a4f4fbb4c077b53bfb9c4f920c1775d5 authored over 4 years ago by JeeK <[email protected]>

Added a test and pyOpenMS binding for MSSpectrum, and fixed bugs for PrecursorCorrection

cf45588b1791c55d3e22a8cb72a59d1d1b61d2f8 authored over 4 years ago by JeeK <[email protected]>

Added findHighestInWindow in MSSpectrum. Changed PrecursorCorrection accordingly.

A piece of PrecursorCorrection code is extracted to findHighestInWindow for further use.

4634689f336d245943c8e5b670c9b3186ca415fb authored over 4 years ago by JeeK <[email protected]>

[NOP] retrigger

730199f00fe9ff6063302e8f7a0984d573b2afae authored over 4 years ago by jpfeuffer <[email protected]>

Avoid interaction in gitpod dockerfile

1f65231784a32027e3c02c210a68113a0aa11579 authored over 4 years ago by jpfeuffer <[email protected]>

Added a test and pyOpenMS binding for MSSpectrum, and fixed bugs for PrecursorCorrection

410993ea7abae9907f43f3dff78f8b8aea3f8bf0 authored over 4 years ago by JeeK <[email protected]>

Add Qt requirement to external CMakeLists

b64961fec331e0c97bd0527ffdcd1bc4dc745c3e authored over 4 years ago by jpfeuffer <[email protected]>

Deleted unused file

a583463aa1bc8c41e5d3931b5422c76950df42e2 authored over 4 years ago by JeeK <[email protected]>

Added findHighestInWindow in MSSpectrum. Changed PrecursorCorrection accordingly.

A piece of PrecursorCorrection code is extracted to findHighestInWindow for further use.

898dfd608f953152bda6bb38d888f78677e04df4 authored over 4 years ago by JeeK <[email protected]>

Merge pull request #4540 from bernt-matthias/topic/fido-test-6

use separate testfile for FidoAdapter tests

9d2282c40359c6cbd8e13e8bd220c8737b4e377a authored over 4 years ago by jpfeuffer <[email protected]>

Merge pull request #4553 from bernt-matthias/topic/Mascot-out-formats

MascotAdapter: specify allowed output formats

96e4a993e614b5f89ac61ab7f08e745cb22ca910 authored over 4 years ago by jpfeuffer <[email protected]>

use separate testfile for FidoAdapter tests

Before test1 and test6 used the same file for the comparison
which is fine if compared with Fuzz...

62c7eeae406a430cd634606680f67babd97d3d34 authored over 4 years ago by M Bernt <[email protected]>

add out_type parameter for TOPPAS and tests

6b4a2cabc81ece726cea5f50112f3a9396ef7a32 authored over 4 years ago by jpfeuffer <[email protected]>

Add php and clangd to gitpod Dockerfile for Intellisense

b705b33848ac875c99d53783510bc72c69b01db8 authored over 4 years ago by jpfeuffer <[email protected]>

Adds missing includes to be exported

f84a595ba84b7337dc3db124aee32a75737e6149 authored over 4 years ago by jpfeuffer <[email protected]>

adapt tests

ed89e3dbd81b7df73170a5ca18bf347e02a91b7c authored over 4 years ago by jpfeuffer <[email protected]>

first merge

5c5845666b60b52e39a91edff65e8e64c67f6fe0 authored over 4 years ago by Chris Bielow <[email protected]>

adding input files

c86e551df80aae7da49c78f6e6c25d3e3b297734 authored over 4 years ago by Chris Bielow <[email protected]>

Merge pull request #4594 from jpfeuffer/feature/inferenceCXML

[Feature] Allow inference on consensusXML

e7bfe5d9aa3794b8bde77cca7ee1cbd66e4a4ca0 authored over 4 years ago by jpfeuffer <[email protected]>

add ostream to cpp

d22ddebf47dbc61d81d27169228ad2be8d4d475b authored over 4 years ago by Julianus Pfeuffer <[email protected]>

Remove ostream includes in headers 2

7ce62b1ec7aa6a98668a361fd39ce8155ed94989 authored over 4 years ago by Julianus Pfeuffer <[email protected]>

Remove ostream includes in headers

67aaab0cb11de6965d5c67c060c99679ee82c586 authored over 4 years ago by Julianus Pfeuffer <[email protected]>

Toolbar items for SwathWizard

ffb8df3bbe36b88eebb69584166ce9b9f5336880 authored over 4 years ago by Chris Bielow <[email protected]>

preparatory changes to InputFileList

37ccc7f689cf74e0ff1a8773d8725639dcbba4b2 authored over 4 years ago by Chris Bielow <[email protected]>

add additional debug options and prelimary support for percolator 3.0… (#4591)

* add additional debug options and prelimary support for percolator 3.04 features

* unify use...

e9cc7a64cfc41579b00095ec09cbe90a2d290f32 authored over 4 years ago by Timo Sachsenberg <[email protected]>

Merge branch 'develop' into feature/inferenceCXML

3f3d6b6ed3c899ba223a3070a52a865a0364149f authored over 4 years ago by jpfeuffer <[email protected]>

Merge pull request #4593 from jpfeuffer/feature/epifanyGroupFDR

[FEATURE] Allow calculation of FDR from protein group scores.

3ab2d35572700a998041ba6d8da47e77e558f743 authored over 4 years ago by jpfeuffer <[email protected]>

codacy

8f61e3ca3c02cee5df8d35d2a9329625aa1a1f55 authored over 4 years ago by Julianus Pfeuffer <[email protected]>

includes for newer clangs

8932f30091dc8fb3a7818be6276a6d275272f260 authored over 4 years ago by Julianus Pfeuffer <[email protected]>

address comments by cbielow. Cleanups, especially for openmp.

3a8328452f33589e67cd0f5c2e5ff98bb86ad759 authored over 4 years ago by Julianus Pfeuffer <[email protected]>

address comments by cbielow. Cleanups, especially for openmp.

f375caa8f25bc776a5614d8db46414edd67a443a authored over 4 years ago by Julianus Pfeuffer <[email protected]>

update .gitpod.yml

9b3741c8ff69350de7002c35d7b22b2a918ba002 authored over 4 years ago by Timo Sachsenberg <[email protected]>

change title

9e209b6ba96bae77124afe54e6457a83f2237553 authored over 4 years ago by Chris Bielow <[email protected]>

update .gitpod.yml

b9bf7df839eaf1c37d09b7bc0b08910d851052c6 authored over 4 years ago by Timo Sachsenberg <[email protected]>

Update .gitpod.yml

9309706cdbf8be22dc12befc2284a1d9e9a45f81 authored over 4 years ago by Timo Sachsenberg <[email protected]>

Update .gitpod.yml

6ac1c5c22a687192b26359ee7371a782068612c0 authored over 4 years ago by Timo Sachsenberg <[email protected]>

update gitpod

11607c686652be4b458ef802ce3d212eb7b62e9f authored over 4 years ago by Timo Sachsenberg <[email protected]>

update

d22a4d12b39d1c75f89da492d6fa9152d1fcd710 authored over 4 years ago by Timo Sachsenberg <[email protected]>

add path

4f90a49898408ae17306a65039bf37c854705c5f authored over 4 years ago by Timo Sachsenberg <[email protected]>

Update .gitpod.yml

e217dc05f894302fbb73d6e58a938db5ebe89008 authored over 4 years ago by Timo Sachsenberg <[email protected]>

Update .gitpod.Dockerfile

c660a1fac31b8dfd093873ea6cf88cd8df96543e authored over 4 years ago by Timo Sachsenberg <[email protected]>

Svg fix (#4596)

* [fix] fixed detection in Spectrum1DWidget of SVG

* [nop] removed obsolete FIXME

7d7d0159e551766f66366f85cd6c2c1ca165b190 authored over 4 years ago by Samuel Wein <[email protected]>

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

7c67c6899e5a347ff6133bdd69dfc4c8f8782275 authored over 4 years ago by Timo Sachsenberg <[email protected]>

address most of the comments.

0038becfe7188f2a7b3df50109d74ceba56d92a6 authored over 4 years ago by Julianus Pfeuffer <[email protected]>

[nop] removed obsolete FIXME

4622026c2b1a6a2c3782dc83c905538889b9d502 authored over 4 years ago by Samuel Wein <[email protected]>

merge develop

f97e3bae288dc7b33ceb4a25c1669450b1c4bea1 authored over 4 years ago by Julianus Pfeuffer <[email protected]>

old boost/gcc does not have hash for tuple. switch to a struct

Signed-off-by: Julianus Pfeuffer <[email protected]>

270570bd6765b266c8f33e717c6b4a6dbf39537a authored over 4 years ago by Julianus Pfeuffer <[email protected]>

Update .gitpod.yml (#4595)

* Update .gitpod.yml

* Update .gitpod.Dockerfile

0162ffd5fb648a5704a6f01870d7d443852df27a authored over 4 years ago by Timo Sachsenberg <[email protected]>

[fix] fixed detection in Spectrum1DWidget of SVG

0cef76ef60ef186721b5c73e747fa040cdd92524 authored over 4 years ago by Samuel Wein <[email protected]>

remove for loop copies. fix boost optional for older boosts

24a5b91413c81766174e70c97ceefecd734605cc authored over 4 years ago by Julianus Pfeuffer <[email protected]>

fix unused var and accidental const change.

98bcacf7026648868c4b75fa2315237d70c19d03 authored over 4 years ago by Julianus Pfeuffer <[email protected]>

codefactor issues

Signed-off-by: Julianus Pfeuffer <[email protected]>

8de224407c2a879cd239c4ca1eae872106756c44 authored over 4 years ago by Julianus Pfeuffer <[email protected]>

add compile flag for older boosts

Signed-off-by: Julianus Pfeuffer <[email protected]>

ca55bd587ed4340b63a3179756f70928cc622bec authored over 4 years ago by Julianus Pfeuffer <[email protected]>

more documentation

7a9e2da01d604f692978746b4a465379fe04c297 authored over 4 years ago by Julianus Pfeuffer <[email protected]>

oops

de8b61faef73e564a20523d9c6459ea903515f0b authored over 4 years ago by Julianus Pfeuffer <[email protected]>

fix other test with new groups

Signed-off-by: Julianus Pfeuffer <[email protected]>

2142064aa7b2009232cf13a4c2f1510ee6f9a8b5 authored over 4 years ago by Julianus Pfeuffer <[email protected]>

fix bayesian test where i was experimenting

Signed-off-by: Julianus Pfeuffer <[email protected]>

101db5529559802be4a364c46506eafcae599d45 authored over 4 years ago by Julianus Pfeuffer <[email protected]>

Finished test for the new graph based resolution.

b53e805cdb90fb27ddcc92d0bd8a7febd3ef6a75 authored over 4 years ago by Julianus Pfeuffer <[email protected]>

Mini tests seem to pass now but needs to be thoroughly tested.

5f35eaeb773c563169796f3ed45fa8cdacd605ea authored over 4 years ago by Julianus Pfeuffer <[email protected]>

Allow calculation of FDR from protein group scores.

Signed-off-by: Julianus Pfeuffer <[email protected]>

8af61302e7738ad44cd7adbf27e1cef0fdb6c384 authored over 4 years ago by Julianus Pfeuffer <[email protected]>

Smaller fixes.

1649fedcb2f9c69cf746c14dd4c07000500eb2f8 authored over 4 years ago by Julianus Pfeuffer <[email protected]>