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

minor PR changes & CONCAT_PEPTIDE constant

8503e3d392a8dd9fcc9a8506f7185193a64341e3 authored over 4 years ago by Tom Waschischeck <[email protected]>

basic tool structure

f81b52eca9d004700edb843933c5ae53c9cc4f79 authored over 4 years ago by Tom Waschischeck <[email protected]>

test for idXML to fasta

a2bee04f3635a75205742b3d36886fcc2fbfa43a authored over 4 years ago by Tom Waschischeck <[email protected]>

negativ #hits results in export of all hits

50f6a03c7ad68d4f5fd14493446841c6583eb440 authored over 4 years ago by Tom Waschischeck <[email protected]>

Merge pull request #4784 from OpenMS/timosachsenberg-patch-1

add 'algorithm' include for gcc10

274b63075a7e3f511c0ec1b5f324d1be45575527 authored over 4 years ago by Chris Bielow <[email protected]>

fix Issue 4765

https://github.com/OpenMS/OpenMS/issues/4765

65db9502d24e046ca0c894d5e2c379ad9432714a authored over 4 years ago by Timo Sachsenberg <[email protected]>

PR changes & 'number of hits' option

065868df33e12b995690cbd04cddb457cda14d70 authored over 4 years ago by Tom Waschischeck <[email protected]>

fixed typo

1c1f284b4d67bddc17e710293c59f745d3dd5c24 authored over 4 years ago by Tom Waschischeck <[email protected]>

comments

ec355c2fe3bd46f14f5a42d2ac6ea6c71519a2c6 authored over 4 years ago by Tom Waschischeck <[email protected]>

writing fasta with FASTAFile methodes

5d09ab133d24130fb7ad544c1d0464034f3cd90e authored over 4 years ago by Tom Waschischeck <[email protected]>

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

TOPPAS error fixed

84b5124a2724c9b9f280471a1f8d07b1b964dcba authored over 4 years ago by Tom Waschischeck <[email protected]>

concatenate option set with flag

09ea557297a717138991bedeecaf05b702b3cfe5 authored over 4 years ago by Tom Waschischeck <[email protected]>

Good Fix for FeatureLinkerUnlabeledQT Segfault Issue (#4778)

* hotfix precondition

* coding style fix

* Quick fix for segfault

* Removed temporary f...

e46d7728567adfddc81b1f051ad11d1cf3065463 authored over 4 years ago by Felix-Droop <[email protected]>

Merge pull request #4780 from cbielow/TOPPAS_filerenamefix

TOPPAS fixes

eb60687284d21177ea1551527292bc55baa3adef authored over 4 years ago by Chris Bielow <[email protected]>

Merge pull request #4755 from jpfeuffer/fix/pepXMLModParsing

[FIX] Comet pepXML modification parsing

9fee773cabb2f17d9aea2d9556cf2efee7d30504 authored over 4 years ago by jpfeuffer <[email protected]>

clang-tidy apply initializers for bools and other members

bd2fb661b025f7704209776460f18b7d87b91436 authored over 4 years ago by Julianus Pfeuffer <[email protected]>

fix compile error

52835dd0335060d761185934e095e7bab2fb8e36 authored over 4 years ago by Chris Bielow <[email protected]>

add endline

45a3df2ee9312173f933ab8f35c21357a1dff12c authored over 4 years ago by Chris Bielow <[email protected]>

[FIX] prevent Exception from skipping over important cleanup code (might lead to inoperable pipelines which cannot be executed anymore)

57581e2a3edd925dedfffb86ed3064bbb715a6a6 authored over 4 years ago by Chris Bielow <[email protected]>

new default

796af27991b4ddcfaf21e112340be36cfeda583f authored over 4 years ago by Chris Bielow <[email protected]>

[FEATURE] new RAII cleanup class which allows executing arbitrary code at the end of a scope (no matter if exceptions occurred)

2643b62c9ad8c1c104fa4228bd0ce5c87872186f authored over 4 years ago by Chris Bielow <[email protected]>

fix 'FileNotWritable' exception in TOPPAS when temporary filenames only differ in case (upper vs lower) and thus renaming deletes the source

18e8d07857d1efa00c714e843e26d41eca26c671 authored over 4 years ago by Chris Bielow <[email protected]>

fix typo

ccf707cb4a810fd8fe98695d6ef268e88649291d authored over 4 years ago by Chris Bielow <[email protected]>

adapt tests

9c5d7e985d410527f77ac7ffbef37a84cf918a12 authored over 4 years ago by Julianus Pfeuffer <[email protected]>

adapt tests

0945f63e7adff9f07ccdf4d14a39a434a21fd4d5 authored over 4 years ago by Julianus Pfeuffer <[email protected]>

Optimization in TheoreticalSpectrumGenerator and MSSpectrum + Fixing multithreaded SimpleSearchEngine (#4709)

* Alternative sortByPosition() and added String generation optimization

* further work on spe...

71a9ddb7b5131a5684da937ef8574fc1f8b0535b authored over 4 years ago by akriese <[email protected]>

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

70ab78b4ab4d75c3b4d9981d1534b70e0b908c06 authored over 4 years ago by Timo Sachsenberg <[email protected]>

another warning

1010a749f12105f1f0e6394cdff3dd4a21e24847 authored over 4 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #4777 from timosachsenberg/fix/mscrhom

potential fix for MSChromatogram merge

faeda8ce9ce8c266672efb10134651f52756a220 authored over 4 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #4772 from timosachsenberg/feature/loc

[FEATURE] export localization scores in mzTab

25e94d98a88d663ed0af10c55676e3be0e6ef9b1 authored over 4 years ago by Timo Sachsenberg <[email protected]>

fix warning

1d06a90c6efc81a51a34d4644cd9464f557a8af5 authored over 4 years ago by Timo Sachsenberg <[email protected]>

quick fix

f7f031d1714e06176043b59e1b17a87b181a2aa3 authored over 4 years ago by Timo Sachsenberg <[email protected]>

forgot one file

a39656efb70b2121631ea6aaa01b069de307a22a authored over 4 years ago by timosachsenberg <[email protected]>

Update MSChromatogram.cpp

aea9beefa43b5026ebfbb693e4592cfd00b0f688 authored over 4 years ago by Timo Sachsenberg <[email protected]>

potential fix for MSChromatogram merge

326940e3ab791952cdedd8817374814fc08dc2c2 authored over 4 years ago by timosachsenberg <[email protected]>

update test file

fed8edc6a97f276bb0351ab33e8e6cce0b20baf8 authored over 4 years ago by timosachsenberg <[email protected]>

move localization meta data to search parameters

8d1718610e66cb76d79e02a43e2e8015f9c515ca authored over 4 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #4773 from cbielow/swath_wizard

Swath wizard

3e314f50cd3cb1c9f3081db0500b436f8daca751 authored over 4 years ago by Timo Sachsenberg <[email protected]>

Omit conda deactivate to have correct env for setuptools?

9da987635d25bebf000e2b1661ff6da8006bcc4b authored over 4 years ago by jpfeuffer <[email protected]>

refactor loop calls

17ed06c79c7cf73cb4e686fbcc65621c79c6ebc7 authored over 4 years ago by Chris Bielow <[email protected]>

export localization scores in mzTab

5637bf1ca4fad433c346f54a8e2c58e323f72fa6 authored over 4 years ago by timosachsenberg <[email protected]>

allow reading of decoy information from (Comet's) pepXML

1ac934fb8f2387052b005cd6acea37a7d207424d authored over 4 years ago by Julianus Pfeuffer <[email protected]>

Merge pull request #4771 from timosachsenberg/feature/luci

[FEATURE] store which modifications were used for localization

b1730645fec216bd5fb543ad214d1379faef4a85 authored over 4 years ago by Timo Sachsenberg <[email protected]>

make interface slimmer

ca3cfd62b1a9d1f918964dc2c00c8cad94133ee1 authored over 4 years ago by Chris Bielow <[email protected]>

Merge pull request #4767 from OpenMS/feature/mztab_main

[Feature/Fix] only export main score, derive nativeID from data

c5fd6e5dda945ee10f9778e2e81eb9bcc2fcb528 authored over 4 years ago by Timo Sachsenberg <[email protected]>

Update LuciphorAdapter.cpp

725deba3a26edf7961dce6e75842065330957568 authored over 4 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #4769 from cbielow/swath_wizard

Swath wizard

ab3ff6ef9b4b1007b12f1f0a0c26ecd2d92148a1 authored over 4 years ago by Timo Sachsenberg <[email protected]>

Merge branch 'develop' into feature/luci

df2bbae2f3a59fa74a33f35ca6197d4fd11105cd authored over 4 years ago by Timo Sachsenberg <[email protected]>

[FEATURE] store which modifications were used for localization

a569d3fa311a6f3f48afe4ba434ff78ea5831e03 authored over 4 years ago by timosachsenberg <[email protected]>

compiler fixes

089786329b45fcb3a09d7017cccb716262571a75 authored over 4 years ago by Chris Bielow <[email protected]>

some preparation for localization

d3db1ee67fd682543f304e031011c37349a2d3e0 authored over 4 years ago by Timo Sachsenberg <[email protected]>

fixes

3747056648b9ed76448f68d80fcfb381ae15484f authored over 4 years ago by Chris Bielow <[email protected]>

Merge pull request #4768 from OpenMS/jpfeuffer-patch-3

[FIX] Update novor tests to precision changes

a97bb507695eb94a79dac3b7ee1b1912ef4fe7f1 authored over 4 years ago by jpfeuffer <[email protected]>

fix linter errors

832e67aa0105adf745208237f13dc5033679e335 authored over 4 years ago by Chris Bielow <[email protected]>

more detailed error message

6495f6bba9d6f904e7e01545d1dd09fc706acc27 authored over 4 years ago by Chris Bielow <[email protected]>

cleanup

49f6876111f8717c18d3466af78675533804654c authored over 4 years ago by Chris Bielow <[email protected]>

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

# Conflicts:
# src/topp/CometAdapter.cpp

885fffaafeb6ffa8879da06305486818f76e9c43 authored over 4 years ago by Chris Bielow <[email protected]>

run PyProphet and TRIC;

open result folder;
keep output directory in sync

3647f08fe5853730d2779f95c2304f46c288d761 authored over 4 years ago by Chris Bielow <[email protected]>

add ExternalProcess class to run external processes conveniently

7e9981b8e41e97498fe91a128f5ee132113c81be authored over 4 years ago by Chris Bielow <[email protected]>

some minor fixes for search adapters

61250da910147e5c47c02c867a15ea65f59d0926 authored over 4 years ago by Chris Bielow <[email protected]>

fix MSGF+ docs and error message

b80e308c884ca83d679e81e34d9651b39dd90cdc authored over 4 years ago by Chris Bielow <[email protected]>

fix mem leaks

4c82de8a51b0b8cf39f9e3c059c76ebbcebf73ec authored over 4 years ago by Chris Bielow <[email protected]>

change to new Qt signal/slot style

3589060e78a05df82516d4d6b164aafea90f0f66 authored over 4 years ago by Chris Bielow <[email protected]>

Merge remote-tracking branch 'origin/feature/mztab_main' into feature/mztab_main

afe1a37cfe500da9721ef29055a9f2b894f7ab75 authored over 4 years ago by Timo Sachsenberg <[email protected]>

fixed test files

5ffc9cc9d3ac6f5f28b42908cf3cb11295580a5b authored over 4 years ago by Timo Sachsenberg <[email protected]>

Cherry-picked commits for feature (#4754)

* Cherry-picked commits for feature

* [feature] implements performance improvements.

* [no...

02d1c60ac95063ef0c48b183cb2e7cfbb498662d authored over 4 years ago by Samuel Wein <[email protected]>

Update novor tests to precision changes

d15ec6d6ed2e9dec4a85e6ff064291f339ecbb94 authored over 4 years ago by jpfeuffer <[email protected]>

Update MzTab.cpp

f66392436452fe77145a74d1b8584c778b2184f5 authored over 4 years ago by Timo Sachsenberg <[email protected]>

added missing CV term

539af0094caa6beaef99be9567a4f8e6b08755f6 authored over 4 years ago by Timo Sachsenberg <[email protected]>

determine native id from data

a1e0aa52b5f89dac065ea7f66e8a454f1163aa03 authored over 4 years ago by Timo Sachsenberg <[email protected]>

only export main search engine score

8466eea14feb03fa1f49935041a066805755eff4 authored over 4 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #4750 from akriese/getchildterms

[FEATURE/PERFORMANCE] Caching of validated CV terms in MzMLHandler + Alternative to getAllChildT...

4125788da613519618247e598a6bf1a0c39b2120 authored over 4 years ago by Chris Bielow <[email protected]>

Comments for cached_terms_

23b9ea0d2b7bffc02ceb17f22f08749a32f00def authored over 4 years ago by Anton Kriese <[email protected]>

refactoring, increase readability

62a9eefa1e621646d635e3f6c722337339722b46 authored over 4 years ago by Anton Kriese <[email protected]>

Merge pull request #4758 from cbielow/swath_wizard

Swath wizard

d05d38c10fc4f0a7accaec4d3a36e5ae00246c50 authored over 4 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #4726 from timosachsenberg/feature/plfq_spec_count

Feature/plfq spec count

eb418007d98dd2a86abc226025239f3a218c21a8 authored over 4 years ago by Timo Sachsenberg <[email protected]>

Merge branch 'id-file-format' of https://github.com/hendrikweisser/OpenMS into id-file-format

5aa03c3129ca598965b428bdab0b8ca68ce82856 authored over 4 years ago by Hendrik Weisser <[email protected]>

[TEST] updated IDFileConverter test (SQLite file format)

029ee6ed010ac9db9bcc899c728d512bc82824a9 authored over 4 years ago by Hendrik Weisser <[email protected]>

Merge branch 'develop' of https://github.com/OpenMS/OpenMS into id-file-format

1084b71447328240e7878396a5baa27abf14a930 authored over 4 years ago by Hendrik Weisser <[email protected]>

add OPENMS_GIT_LC_DATE defaults (#4759)

* Default for OPENMS_GIT_LC_DATE

* Update CMakeLists.txt

Co-authored-by: IceFreez3r <39794...

5c80aa78faf16a5c3be8ab22b6565e60d2d3755e authored over 4 years ago by Chris Bielow <[email protected]>

Quick/Ugly/Temporary Fix for fibonacci heap optimization segfault issue (#4760)

* hotfix precondition

* coding style fix

* Quick fix for segfault

ffd7bf6416dc739132beaee63a518984961400f2 authored over 4 years ago by Felix-Droop <[email protected]>

fix CI

65ebc790ae2377a2ab0ad8cce7244da172710e8d authored over 4 years ago by Chris Bielow <[email protected]>

added pyprophet and TRIC computation

a8e5a32d00f6e72638520c73e6399477b11c8aae authored over 4 years ago by Chris Bielow <[email protected]>

correctly set the module status

7ccd14f694513ff4cf2d102e9de6e1c29ee3fc85 authored over 4 years ago by Chris Bielow <[email protected]>

update CWD more consistently (when using add/remove buttons)

33c5a433477bb2fcd5b0bb8e55ff994bc9abe207 authored over 4 years ago by Chris Bielow <[email protected]>

react to changes in TextEdit field with a 'directoryChanged' signal

45a03784f4e95feae50492df0989c61a1745d092 authored over 4 years ago by Chris Bielow <[email protected]>

code cleanup

27a7f61b6ac0346f80fa9bc2fff27c3d066bd031 authored over 4 years ago by Chris Bielow <[email protected]>

Merge pull request #4733 from michalsta/develop

Update IsoSpec sources to v 2.1.0

628e6b0d0f4ba975f444e6bde4fa6d25ae83b6f5 authored over 4 years ago by Timo Sachsenberg <[email protected]>

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

42f4c2c4eb9f6672019bbc60bd73cd502f7c85fb authored over 4 years ago by timosachsenberg <[email protected]>

Hotfix PRECONDITION after optimization for QTCluster (#4756)

* hotfix precondition

* coding style fix

a538f8d57a91bef20d6fc32fda3fa70f1d4a6e1a authored over 4 years ago by Felix-Droop <[email protected]>

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

2fe39290260623e69ec658ec87c8edc066b7a6d4 authored over 4 years ago by Michał Startek <[email protected]>

Sync to IsoSpec at v2.1.0 final release

680add0a6af95381ae0cbd05c9c54a58ed4e85b0 authored over 4 years ago by Michał Startek <[email protected]>

Bit of defensive coding: define some consts for IsoSpec before the includes, be immune to some platform.h mishaps

3c60b62b200d47307585db106a5aeb94ef4ab58a authored over 4 years ago by Michał Startek <[email protected]>

Rename vscode folder and init during gitpod startup (#4757)

562d402ac1b89e0c1b99d28dc837f04094a0fc41 authored over 4 years ago by jpfeuffer <[email protected]>

Try removing explicit arguments from swap to use ADL

397a48de6a6512fa88c587beaa7b39f2ad797f70 authored over 4 years ago by jpfeuffer <[email protected]>

fix masses. little refactor

f3c1b48b7aae18d5af25e0d989fe7b6157ad69d8 authored over 4 years ago by Julianus Pfeuffer <[email protected]>

small error during refactor

3e0633ed466c1c97219d2fdef80d3952491c112f authored over 4 years ago by Julianus Pfeuffer <[email protected]>

simplified MSstats code a bit

7179a8f26c6a320baa4a462598600e909e702f5f authored over 4 years ago by timosachsenberg <[email protected]>

Add missing header

a9382762d7011aa73d5a75d60bc779418f8861a8 authored over 4 years ago by Michał Startek <[email protected]>

[FIX] Avoid putting terminal modifications to internal AAs when reading pepXML. Instead put them as unknown delta_mass.

3ded22630d26b1303dfead7a9f205b40693f8db2 authored over 4 years ago by Julianus Pfeuffer <[email protected]>