Ecosyste.ms: OpenCollective

An open API service for software projects hosted on Open Collective.

github.com/OpenMS/OpenMS

The codebase of the OpenMS project
https://github.com/OpenMS/OpenMS

changes regarding to merge conflict

bd5bdba75e9a6242ab479a07b8e82b2a5953a444 authored over 5 years ago by swew98 <[email protected]>
MZCalculation version1b

547feb1bddaea9deb01378119b303aa67688c81b authored over 5 years ago by jschmacht <[email protected]>
MZCalculation version1a

b3c10550c6b56a3e2fc0d13575e05be41ef7916b authored over 5 years ago by jschmacht <[email protected]>
MZCalculation version1

09ad75def301bbef1a13ef343fafb0020e5064db authored over 5 years ago by jschmacht <[email protected]>
changes regarding do pullrequest

38111239db01cadf9ba20fecc8cbdebf97c565fe authored over 5 years ago by swew98 <[email protected]>
Merge branch 'develop' into Contaminants

8065f2d1d859b32e0e922b35020adbbdd9befec4 authored over 5 years ago by Dominik Sebastian Schmitz <[email protected]>
solved merge conflict

cc093627004ea2863d0db1d8f55b3800a485bee7 authored over 5 years ago by Dominik Sebastian Schmitz <[email protected]>
removed the loops and added ifs instead

d7dfd58fdbe2819954e33a6d66e172758b287f0b authored over 5 years ago by Dominik Sebastian Schmitz <[email protected]>
Update src/openms/include/OpenMS/CHEMISTRY/ModificationsDB.h

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

813189965c821f1723802b55363a42fdfd933a57 authored over 5 years ago by Hannes Roest <[email protected]>
Update src/openms/include/OpenMS/CHEMISTRY/ModificationsDB.h

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

a6ee135c262b2a2bb1b0fda766fa662601058593 authored over 5 years ago by Hannes Roest <[email protected]>
Update src/openms/source/FORMAT/HANDLERS/MzIdentMLHandler.cpp

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

184d3138248a66c62530edf8da363902b349a8b6 authored over 5 years ago by Hannes Roest <[email protected]>
Update src/openms/include/OpenMS/APPLICATIONS/OpenSwathBase.h

7b1e23a0d9a345b5ff48a5e6d3c8bef9e8995208 authored over 5 years ago by Hannes Roest <[email protected]>
Update src/openms/include/OpenMS/APPLICATIONS/OpenSwathBase.h

00a5dd32146de1f550b684b58b3be7ae14bff79c authored over 5 years ago by Hannes Roest <[email protected]>
[DOC] improved documentation for NucleicAcidSearchEngine (and RNA mods. resource file)

fbc8103ca1e68696ce8ea64394359d097e3bb9a2 authored over 5 years ago by Hendrik Weisser <[email protected]>
[INTERNAL] theoretical spectrum generation for nucleotide sequences: calculate using masses, not chemical formulas, to save time

9f5310e00ac421314042d662147b1974cb9308d8 authored over 5 years ago by Hendrik Weisser <[email protected]>
[TEST] small simplification in test for class 'TheoreticalSpetrumGenerator'

2a51a2ebc347364d93682503857f3547f79b2af4 authored over 5 years ago by Hendrik Weisser <[email protected]>
Merge branch 'develop' of https://github.com/cbielow/OpenMS into develop

2ff9f9e297739c36bfc4a15cdd45b8959b375db3 authored over 5 years ago by TomW <[email protected]>
Merge pull request #39 from Waschi97/FEATURE_QC_TIC

[FEATURE] QC TIC metric

f3c0afc317fdb068c911b6a13d160aec3b1aa40c authored over 5 years ago by Chris Bielow <[email protected]>
minor docu changes

91594cb0e62bc7812c4358fd48224c13bed2c807 authored over 5 years ago by TomW <[email protected]>
TOPPTool adjusted to metric, renamed forceflag in metric

93c1df898490ec82a7e516d052d1cf078429eb64 authored over 5 years ago by swew98 <[email protected]>
changed getTIC(), now with optional binning and corresponding section in MSExperiment_test

dbb51a3c20d24042c03bbfbaa4e1e6b367993299 authored over 5 years ago by TomW <[email protected]>
Update AASequence_test.cpp

f4516b05bf18c7acb203fee9d2785de52e2ae0b2 authored over 5 years ago by Hannes Roest <[email protected]>
[FIX] make it work for lowercase sqmass files

7d9c295069192dd8a38cbf527445100345c499aa authored over 5 years ago by Hannes Roest <[email protected]>
works

6c049ffde13868945c504cbff112a895592a927e authored over 5 years ago by Hannes Roest <[email protected]>
works

49361a57423a287fb0b4add67df759e79669adce authored over 5 years ago by Hannes Roest <[email protected]>
[DOC] add docu

7fe7a9a7db2ae7172367b8780c1ddde8ca6303ec authored over 5 years ago by Hannes Roest <[email protected]>
fix

55d6dfd5566dd5f1ed73179e4f7a2413490c339d authored over 5 years ago by Hannes Roest <[email protected]>
fix ?

15b39d89b1d82a4fc131c8ddeab55505591eb66b authored over 5 years ago by Hannes Roest <[email protected]>
works?

ca4331206a426f2aa16a09e77cfbe3f82a15cb8e authored over 5 years ago by Hannes Roest <[email protected]>
applied changes, MSExperiment::getTIC() not changed

b960de20a91772994d5e77a5a755f45f89cecc00 authored over 5 years ago by TomW <[email protected]>
[INTERNAL] removed obsolete functions for theoretical spectrum generation of nucleotide sequences

e5863ac909285d56053880c97e4fba1a3ef19907 authored over 5 years ago by Hendrik Weisser <[email protected]>
[DOC] improved parameter documention in class 'TheoreticalSpectrumGenerator' (differences between amino acid and nucleotide sequences)

0fe5f23951e2da2c32975898e16f983dcb4dae11 authored over 5 years ago by Hendrik Weisser <[email protected]>
[FIX] fixed generation of theoretical spectrum peaks for 'a1-B' ions of nucleotide sequences

9382e484d07f9400447b580c676854f644c329f6 authored over 5 years ago by Hendrik Weisser <[email protected]>
Test with empty MSExperiment added

a1fc7acaef43dd6a4ea245898a75d6974e2c61ba authored over 5 years ago by TomW <[email protected]>
finished Test class, implemented ==operator in BaseClass

25f9ee4b58292fa6f50b3fc29e49dfcd5029ac57 authored over 5 years ago by swew98 <[email protected]>
working Test for TIC

3d2216c7abf4d6952f316c61485a760fee438a7f authored over 5 years ago by TomW <[email protected]>
[TEST] updated test for class 'TheoreticalSpectrumGenerator' to recent changes

a6f11300c2b52dd2ec5f0c4cb7c9471ed93b6fcc authored over 5 years ago by Hendrik Weisser <[email protected]>
[FEATURE] much faster theoretical spectrum generation for nucleotide sequences

01c7269114124f384c534b30cf1ef65343238e34 authored over 5 years ago by Hendrik Weisser <[email protected]>
[LOG] better error logging when reading RNA modification data from file

55166579198ae9fe292dbb896974b07372f5823a authored over 5 years ago by Hendrik Weisser <[email protected]>
[INTERNAL] NucleicAcidSearchEngine: explicitly don't include precursor peaks in theoretical spectra

318f412a686599b3af4d2637bc16bc0623db2d88 authored over 5 years ago by Hendrik Weisser <[email protected]>
Merge pull request #4008 from oliveralka/add/adducts_compound_osw

[Add] Adducts and Annotations for compounds (tsv, traml, pqp)

857e6b97c6015af66587fa73d3afdf9f2849928a authored over 5 years ago by Timo Sachsenberg <[email protected]>
Update src/openms/source/FORMAT/HANDLERS/MzIdentMLHandler.cpp

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

f72fe6736ce43cad3fd5c9b7eda41e286447192a authored over 5 years ago by Hannes Roest <[email protected]>
Update src/openms/source/FORMAT/HANDLERS/MzIdentMLHandler.cpp

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

110e2c67a71b0db7bcf98cdac45f6889ad1c0adf authored over 5 years ago by Hannes Roest <[email protected]>
Merge pull request #4012 from OpenMS/hroest-patch-4

[FIX] fix mzML index overflow on Windows

ac51714c14797db3b348282d785585716772b3ac authored over 5 years ago by Chris Bielow <[email protected]>
Merge remote-tracking branch 'upstream/develop' into add/adducts_compound_osw

e9d965dd4548c9a6ee9ab80ae33b4d24be8bedc4 authored over 5 years ago by oliveralka <[email protected]>
[ADD] python bindings, fix test (adducts), fix comments

72aec71a8c66bd5665d216f666400d25490bfc54 authored over 5 years ago by oliveralka <[email protected]>
Merge pull request #4003 from oliveralka/update/SiriusAdapterOutput_rt_mz

[ADD] mz, rt and nativeID to SiriusAdapter mzTab output

0575fc04dfc53ca0dcbecdcfcd07a9a3f16b8b36 authored over 5 years ago by Lukas Zimmermann <[email protected]>
[PYOPENMS] fix inheritance for MetaInfoInterface

[TEST] fix test

0e7db73ab57c3d2ab3cc02f706c3cf4d165ef016 authored over 5 years ago by Hannes Roest <[email protected]>
[TEST] test fix

07f59b60b0414d193add3bfbb140fded27987807 authored over 5 years ago by Hannes Roest <[email protected]>
[FIX] also fix mzIdentML

a5a2fb28f2b6da9917d1ed74a1ba089ffd7cf250 authored over 5 years ago by Hannes Roest <[email protected]>
[FIX] ammend fix

95040016b00236df8059190694a1789b159f3d02 authored over 5 years ago by Hannes Roest <[email protected]>
[FIX] fix overflow on Windows

Ensure that we actually use 64 bit integers to store spectra / chromatogram offsets on all platf...

d58fcd690d7682d3d0d08bdc3d0bbe52b39e2e19 authored over 5 years ago by Hannes Roest <[email protected]>
exceptions in cpp, added Testcases but implementation still incomplete

c43be7094ce10c4661c9a9f8c01e3b8d284d330d authored over 5 years ago by swew98 <[email protected]>
TIC commented, preemptively add TIC to TOPPQC

4276acbb312feda0986e063d0576c876c8bbabf7 authored over 5 years ago by TomW <[email protected]>
added test file

695d274cc7ebbb25a57dbcba87667c386df6ef66 authored over 5 years ago by Dominik Sebastian Schmitz <[email protected]>
merged from develop

bb50de8dc5d509656350ed8ff53bf530cfb8fc63 authored over 5 years ago by Dominik Sebastian Schmitz <[email protected]>
Merge branch 'develop' of https://github.com/cbielow/OpenMS into develop

0fad60d5f967653f399e3be59db0821f67a4468c authored over 5 years ago by Dominik Sebastian Schmitz <[email protected]>
replaced construct with hashset

8e6131d4050a5d300bd3b0adaf7644a02fdf514d authored over 5 years ago by Dominik Sebastian Schmitz <[email protected]>
TIC done, TODO: Docu

219b26c1fe8dbe888368e5fd5d120d9a1582c07f authored over 5 years ago by TomW <[email protected]>
tried to save TIC, and failed

808ded0c3a49237ab950c3a4fb7678341fe0cbfe authored over 5 years ago by TomW <[email protected]>
TIC in .gitignore

b062fda25afd3f1c13c418e9d0e858acab6b7d84 authored over 5 years ago by TomW <[email protected]>
testclass update

b73dcdec991d1a491987116fe7190189d9a16673 authored over 5 years ago by swew98 <[email protected]>
Merge branch 'develop' of https://github.com/OpenMS/OpenMS into rna-lfq-ambivar

64d2946bdead1fdb2077f84e557696e2e9b52a08 authored over 5 years ago by Hendrik Weisser <[email protected]>
wrote test class

2aa516f2d33260793351c78d0cf2b5ebb5912525 authored over 5 years ago by swew98 <[email protected]>
[FEATURE,PARAM] NucleicAcidSearchEngine: improved support for 'ambiguous' modifications, including two search modes (parameter 'modifications:resolve_ambiguities')

cda9d47f2820ebd7e8efb8a760714df6c02e6190 authored over 5 years ago by Hendrik Weisser <[email protected]>
start of TIC QC

7ca1e4c07034d38af3e971e5ab95a778d911ac6b authored over 5 years ago by TomW <[email protected]>
added digested_db_

587834b9ee26ce03308688bf4dca24eb0ab6b972 authored over 5 years ago by Dominik Sebastian Schmitz <[email protected]>
memory leak solved

8a007c57f55c3bfe61950a4b592bebd7d4205076 authored over 5 years ago by kyowonjeong <[email protected]>
memory leak solved

5ef7ee3eba6534d3855d7532b174087c125e2c9a authored over 5 years ago by kyowonjeong <[email protected]>
[PARAM,TEST] NucleicAcidSearchEngine: removed option for fixed modifications (not useful for RNA)

7d7d29c81d712b1a1d4edcad43490168acdd79e4 authored over 5 years ago by Hendrik Weisser <[email protected]>
[RESOURCE] extended list of OpenMS-specific RNA modification codes

a91a9347da55a7aa167bbf0b59989d7e7edea636 authored over 5 years ago by Hendrik Weisser <[email protected]>
Merge branch 'develop' of https://github.com/cbielow/OpenMS into identificationRate

297dda84dad28f5b6e6ad5fe4db7288d79398f97 authored over 5 years ago by swew98 <[email protected]>
changes for base class, create test class

6f15174c4ee188ab209c8313780bf77950e284c8 authored over 5 years ago by swew98 <[email protected]>
Update PepXMLFile.cpp

b1e1df69a1e09e7d11938e857c2545ed149f545d authored over 5 years ago by Timo Sachsenberg <[email protected]>
Merge pull request #38 from Waschi97/TOPPQualityControl

Topp quality control

fa093cfa774ac8a22533f6af79c08acd46c36376 authored over 5 years ago by Chris Bielow <[email protected]>
forgot one last change

1c8dbbf4f551e718cc8010ceb256efd6d987cb9e authored over 5 years ago by TomW <[email protected]>
status should now actually work, changed & to |

f510acf51816a06e3f9b8190962e599882249eee authored over 5 years ago by TomW <[email protected]>
applied changes

ca5f8b099e454ea1ed9775cf389bfd282f91b8e1 authored over 5 years ago by TomW <[email protected]>
new base class, Tool is already using it

466112073e3ad61754729cc463ffc45126850184 authored over 5 years ago by TomW <[email protected]>
moved Tool from utils to topp

aae7b1f162c096fede643730f67b122e01f73e30 authored over 5 years ago by TomW <[email protected]>
reworked Tool for QCBase

24b074d559433df97c568a229680458464e0734d authored over 5 years ago by TomW <[email protected]>
max charge reduced

ff385950850f221ce7afd86ef933974eee5598e2 authored over 5 years ago by kyowonjeong <[email protected]>
max charge reduced

f1113a5ea752725b92637414ba85c7db64332bac authored over 5 years ago by kyowonjeong <[email protected]>
merge conflict in sources.make

99eb9f2121391951274b4fa6d91a068702dd29ef authored over 5 years ago by swew98 <[email protected]>
Ms2IdentificationRate, added exceptions, adjust input, added clear function

2b4154fd12684dc7d74d539ce85f2f2dd87124b0 authored over 5 years ago by swew98 <[email protected]>
ChargeDistribution1

9a57afad189af61dba753d49486c976a4271d567 authored over 5 years ago by jschmacht <[email protected]>
cleared merge conflict

88cb14ac7f07ebaa38d70a37f93ff7f221cf45da authored over 5 years ago by Dominik Sebastian Schmitz <[email protected]>
added Contaminants.cpp and .h

976bf201bc353e6a2619ebc8656c2fdca22df129 authored over 5 years ago by Dominik Sebastian Schmitz <[email protected]>
Merge branch 'develop' into TOPPQualityControl

f84ccc6ea0b9f49c6b8b23638b2613b6f39b314e authored over 5 years ago by TomW <[email protected]>
Merge pull request #35 from Waschi97/QCBaseClass

[FEAT] QC base class

e201326c665be26b1818dfcd2b9cbc74972bbe5c authored over 5 years ago by Chris Bielow <[email protected]>
max charge reduced

4d0309d2bc452bba139a9345ebf08eef5dd345e8 authored over 5 years ago by kyowonjeong <[email protected]>
changes applied

6c9e46034e0932979409b8b9f83ef3455554eeb9 authored over 5 years ago by TomW <[email protected]>
Base class working

078f194e9ace933edddfc6386afc2989d4547c84 authored over 5 years ago by TomW <[email protected]>
enum exist, class doesn't work right now

033f3854b1dd01ea327a70a4e8f00edd9e4f35fa authored over 5 years ago by TomW <[email protected]>
[INTERNAL] removed unused code in TheoreticalSpectrumGenerator (for nucleic acids)

c3ed4555522302908ad94b21dd22a2a48f209715 authored over 5 years ago by Hendrik Weisser <[email protected]>
[FIX] NucleicAcidSearchEngine: fixed handling of queuosine mod. (replaces 'G')

da22b3c232ca3bea0cc91b6f52c598e1a5fb614e authored over 5 years ago by Hendrik Weisser <[email protected]>
[QC] reading works

084a4105fff298b0285564b208085709e6a1daeb authored over 5 years ago by TomW <[email protected]>
[RESOURCE] extended list of OpenMS-specific RNA modifications

60edc7bd193025ea697118cdfe633572411b8622 authored over 5 years ago by Hendrik Weisser <[email protected]>
incomplete Identification addition

de8513a6e2dfe4e67cfce688172879019b4988bf authored over 5 years ago by swew98 <[email protected]>
incomplete identificationRate

2e91325d780721bb13ff709f18eb89934357515a authored over 5 years ago by swew98 <[email protected]>