Ecosyste.ms: OpenCollective

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

github.com/OpenMS/OpenMS-1

The codebase of the OpenMS project
https://github.com/OpenMS/OpenMS-1

refactor LayerView into own class

097654eacd94bf5390fed7cb4d35b241e9a0a7ca authored about 4 years ago by Chris Bielow <[email protected]>
? forgot to commit output?

510bdd21f2c11de457275cd4e71760f87b158a48 authored about 4 years ago by Julianus Pfeuffer <[email protected]>
merging origin changes

95abfb9db585819b2f195f3a610660be340e261d authored about 4 years ago by Tom Waschischeck <[email protected]>
more class docu, instances novo_fract in docu replaced with new name

5b8cfb98a572e25342ac4dc87e784869946b6528 authored about 4 years ago by Tom Waschischeck <[email protected]>
Fixed some TODOs, a small copypaste error. Added more tolerant lookups which added another Modification that was found.

4ffcdf9012e09ad36d2bfcb41875957748585c27 authored about 4 years ago by Julianus Pfeuffer <[email protected]>
remove unused method

f622512ca55f47bfb97a262efdccfee037c92e3a authored about 4 years ago by Chris Bielow <[email protected]>
fix CI

1e588d802b2c31267414059113bd61ebeec0e71b authored about 4 years ago by Chris Bielow <[email protected]>
use set for specs

06ae91d2001d7e66542528e7a79bb411153f8d0f authored about 4 years ago by jpfeuffer <[email protected]>
another small fix

0d33e5898ccab1ff0f68452c41ba08b5302d1300 authored about 4 years ago by Julianus Pfeuffer <[email protected]>
Do not use direct initialization

b2b81046dabca612a2c9e4f90e89225b7cb00d67 authored about 4 years ago by Julianus Pfeuffer <[email protected]>
small error

4c9c1e0550df2c0af67a25f90a940786368c5aca authored about 4 years ago by Julianus Pfeuffer <[email protected]>
Feature/pyopenms acquisitioninfo access (#4329)

* [FIX][pyOpenMS] Enable access to AcquisitionInfo items, ..

.. enable access to metainfointe...

548abfaa87a7ef345fcd051e10ee93e240bc3ff8 authored about 4 years ago by Mathias Walzer <[email protected]>
[FEATURE] combine SE settings during ConsensusID (instead of taking 1st)

2e11d9365a7ef6e3f46f142129072f8ab4d9f54b authored about 4 years ago by jpfeuffer <[email protected]>
Raised tolerance

3685c8aef089945a8139e8c590cead5e322f810d authored about 4 years ago by Julianus Pfeuffer <[email protected]>
Remove unused variable.

91ba516ab5916b96755c8364896f3047adb7f1c4 authored about 4 years ago by Julianus Pfeuffer <[email protected]>
Improved tolerance to match pepXML precision.

Cleanup.

7a103123784ece3b9f6d4c43d317cb6a0cfbc3a6 authored about 4 years ago by Julianus Pfeuffer <[email protected]>
Complete rewrite of mod-parsing in pepXML. Fixes huge bugs:

- fixed modifications were not considered if not explicitly annotated at the sequence (Mascot)
- ...

c17c3a21f738aefbc7451eb41aee967714480000 authored about 4 years ago by Julianus Pfeuffer <[email protected]>
[FEATURE] correct return value for operator[] (#4536)

* [FEATURE] correct return value for operator[]

* Update AcquisitionInfo.pxd

Co-authored-b...

0af37e2de11d6589d0b5735e03f001eb2e9920fa authored about 4 years ago by Hannes Roest <[email protected]>
bump autowrap in travis CI (#4888)

71c0d01f4d7da9939ccd66cc9cfbc31b7d165570 authored about 4 years ago by Timo Sachsenberg <[email protected]>
PercolatorAdapter and CruxAdapter: use underscore in arguments (#4529)

* PercolatorAdapter: use underscore in arguments

instead of dashes. makes it consistent and a...

97fbc6bbed05c9abf44801d9ab67fc5699265226 authored about 4 years ago by M Bernt <[email protected]>
subsitute vector<double> for map<PeakType, double> in SignalToNoiseEstimator (#4884)

* subsitute vector<double> for map<PeakType, double> in SignalToNoiseEstimator

* new version
...

e75a3616ba4ef48040909f180a7c15a6c7e0d317 authored about 4 years ago by Chris Bielow <[email protected]>
Merge branch 'develop' of https://github.com/OpenMS/OpenMS into toppview_refactor

# Conflicts:
# src/openms_gui/source/VISUAL/APPLICATIONS/TOPPViewBase.cpp

3fa90133092d4b9d08c56bdd7a27ce29ff2da468 authored about 4 years ago by Chris Bielow <[email protected]>
Merge pull request #4443 from bernt-matthias/topic/OpenSwathDIAPreScoring-out-fix

OpenSwathDIAPreScoring: fix outputs

5b1fda0e85418655e4d6c439261c23b144ea48d7 authored about 4 years ago by Hannes Roest <[email protected]>
[FEATURE] support adducts in FeatureFinderIdentification (work in progress)

52b639b6008b2576e0d7839b004aeb27be419d79 authored about 4 years ago by Hendrik Weisser <[email protected]>
DBSuitability.cpp change

b8bab8dc5560e110da2716f44f7f1c413fa4b03b authored about 4 years ago by TomW <[email protected]>
DBSuitability.h change

c2f967f9607a2831825eb6d492e2d25e1c6edbb9 authored about 4 years ago by TomW <[email protected]>
[FIX] IdentificationDataConverter: re-enabled output of adducts in mzTab

b2885fc413a09c4f0805bad0fbffa596ee5359bb authored about 4 years ago by Hendrik Weisser <[email protected]>
review

3ef2a9991888dd82dacb88fe59417f571cdeb072 authored about 4 years ago by Julianus Pfeuffer <[email protected]>
clean up TabBar handling

a292fe5dc3ddf5026929b8c3c1f17689032c5119 authored about 4 years ago by Chris Bielow <[email protected]>
more docu and Suitability to DBSuitability

94937efc46924797d684509b1329cbccbb75a07d authored about 4 years ago by Tom Waschischeck <[email protected]>
Labeling support (#4832)

* remove redundant code

* make interface safer (avoid memory leaks and dangling pointers)

...

4514827e20e18246cefa02e84fb0023110a246f0 authored about 4 years ago by Chris Bielow <[email protected]>
Add comments and bogus tests

3237d261e72ff5f50ddb5be8aa500742eaadcc16 authored about 4 years ago by Julianus Pfeuffer <[email protected]>
some invariants for DataFilters

31d3cb31a75efe86aebcb3421b98fde593af12de authored about 4 years ago by Chris Bielow <[email protected]>
Better pepXML support with still a lot of TODOs

f3fb2334890a96132e53a38741756c7691c0e0f1 authored about 4 years ago by Julianus Pfeuffer <[email protected]>
Merge branch 'develop' into feature/FLASHDeconv

7b3c87e28bdcf9c0d49721ad20014dd4129cb17a authored about 4 years ago by JeeK <[email protected]>
fixing error: FLASHDeconv test

e37dc923c26cd1a3dfbb7871db1b6930d521d79f authored about 4 years ago by JeeK <[email protected]>
[FIX] docu for tools (#4883)

* [FIX] docu for tools

* Update MetaboliteAdductDecharger.cpp

1bdb8937ce82140eda2fd0606a191c31b92bb9f1 authored about 4 years ago by jpfeuffer <[email protected]>
[FORMAT,TEST] added support for adducts in SQLite file format for IDs (.oms); added corresp. tests

06fc05936f9728707b2973e2aa75710ed2e9b367 authored about 4 years ago by Hendrik Weisser <[email protected]>
[TEST] added tests for handling adducts in 'IdentificationData'

d782646852be5f80f3ebf5ac04347436d65bf183 authored about 4 years ago by Hendrik Weisser <[email protected]>
Toppview refactor (#4880)

* switching to Qt's compile-time connect()

* fix #4812

* avoid linker for missing MOCs err...

46f3c9039511a45d9f4cd4cfa93bd351460ba617 authored about 4 years ago by Chris Bielow <[email protected]>
[API] added functions ('getMolMultiplier', 'operator==') to class 'AdductInfo'

16f8aab4a556e21f86d624868098ccd61c23a7a2 authored about 4 years ago by Hendrik Weisser <[email protected]>
wrong ratio

a1cbd38b08b5cdb8da3549db754c5c85743a2cf9 authored about 4 years ago by Julianus Pfeuffer <[email protected]>
Added review comments. Extend allowed test ratio for numbers.

c9c836e126f732ce2adffab3463f4c68cdc13a2f authored about 4 years ago by Julianus Pfeuffer <[email protected]>
fix TOPPView test (order of destruction)

4e17630ff49cde1bc5ff51023ef88a5a61fdc1ef authored about 4 years ago by Chris Bielow <[email protected]>
Merge pull request #4881 from OpenMS/fix/msgfEnzymeOut

[FIX] Let MSGFAdapter overwrite the enzyme from mzid w/ our nomenclature

17af278b314fb37b98559067a0dbd3082892961f authored about 4 years ago by jpfeuffer <[email protected]>
Merge branch 'develop' into topic/OpenSwathDIAPreScoring-out-fix

69fb8b3f2c7be615720e84480f0637d89fb46df4 authored about 4 years ago by Hannes Roest <[email protected]>
[FIX] Let MSGFAdapter overwrite the enzyme from mzid w/ our nomenclature

409eeaedc3c4feef73cbdc6402aaf46cf463e2c8 authored about 4 years ago by jpfeuffer <[email protected]>
error while registering input options, Re-check writability of output file

b9da89f7f30b5e800a4e096df1dd7ed5227db06c authored about 4 years ago by Tom Waschischeck <[email protected]>
deleted whiteline

7dba99bf89d7533b29efea3710bee98d963ba7ac authored about 4 years ago by Tom Waschischeck <[email protected]>
final PR changes

01dbfab24baf5906fc4c8a1ad095b80e8a38bd69 authored about 4 years ago by Tom Waschischeck <[email protected]>
Added a gitattributes file to prevent git from changing line endings when checking out on windows.

608d2a3c7ad7bc371428159c888a40d296b26d46 authored about 4 years ago by Julianus Pfeuffer <[email protected]>
fix wrong signal/slot

dce6b1f071bb6fb9b99a59dc2c9ebafe273c4d78 authored about 4 years ago by Chris Bielow <[email protected]>
[INTERNAL] IdentificationData: added typedef 'AdductOpt' for optional adduct; include adduct in key for molecule-query match

84986d8e68615eb27985b144a43dbd1791c85262 authored about 4 years ago by Hendrik Weisser <[email protected]>
convert connect() to new Qt5 method

6eb7ac93c143f248cc3d600f2ecee8380f24d705 authored about 4 years ago by Chris Bielow <[email protected]>
avoid linker for missing MOCs error when switching to Qt5 connect with FileWatcher

cb7182451bc6e2e8f1e0dcbc02d4ccee63c176d1 authored about 4 years ago by Chris Bielow <[email protected]>
Add precursor mz to selected ion m/z (mzML) (#4861)

* add precursor mz to selected ion m/z

* tests

* FIX: missing test

Co-authored-by: Timo...

e7fa45f84e377e6d21fa297d0a3698f08f336207 authored about 4 years ago by Oliver Alka <[email protected]>
Merge pull request #4879 from OpenMS/fix/hugeDocs

Exclude some files for dot creation from doc install

feeeafe075ca7fb7eb0b718cd84ffad888456adb authored about 4 years ago by jpfeuffer <[email protected]>
fix #4812

cd13b63ba133cae501d52bb469fb62f4bcb95556 authored about 4 years ago by Chris Bielow <[email protected]>
switching to Qt's compile-time connect()

43bd39ef43f77c9c3497858f3cdb7f7f9cca032d authored about 4 years ago by Chris Bielow <[email protected]>
fix output/input files to PTModel and PTPredict (#4856)

* adapt PTModel and PTPredict

* small fix

* small changes

* change back

* remove emp...

5fe10ecf976e72a88225322331293bda3b4c4388 authored about 4 years ago by Leon-Bichmann <[email protected]>
Switch to (interactive) svg format and limit depth

347e734db30ed4af46f22e35db77d29e62b32bbf authored about 4 years ago by jpfeuffer <[email protected]>
Exclude some files for dot creation from doc install

41c79a92a2f8ebb87f4159fe9a965ff09a62bb05 authored about 4 years ago by jpfeuffer <[email protected]>
[INTERNAL] avoid using 'EmpiricalFormula(String)' c'tor where possible

c56ed55024febd48345b3e097c5271b763634492 authored about 4 years ago by Hendrik Weisser <[email protected]>
[API,TEST] added static functions to efficiently generate often-used empirical formulas (hydrogen, water)

56037135b7eb930dc4272ceee4f52c84acb8fb10 authored about 4 years ago by Hendrik Weisser <[email protected]>
[NOP] fixed whitespace in pointer/reference declarations

9e7d5d54143936815006f2fce6d5cf5b6ce8b2da authored about 4 years ago by Hendrik Weisser <[email protected]>
Merge branch 'develop' of https://github.com/OpenMS/OpenMS into idfile-integration

67959df679796769b767d3a15715d7ada10932cd authored about 4 years ago by Hendrik Weisser <[email protected]>
forgot test file

e95d3d4720407ae36d0655afa0e43efdcc504cfe authored about 4 years ago by Tom Waschischeck <[email protected]>
some more PR changes

fdc15eb4762a980a6f9fec548575707950daae24 authored about 4 years ago by Tom Waschischeck <[email protected]>
fixed error message and some docu

e3f307cba4effd55c8e1a198f21a9607b1726b1e authored about 4 years ago by Tom Waschischeck <[email protected]>
add unknown modifications as chemmod (#4841)

* add unknown modifications as chemmod

* added test file

* ammend

* moved code to stati...

c4d9a9b843c961e27a3a0e98fefa889dbaee9430 authored about 4 years ago by Timo Sachsenberg <[email protected]>
Forgot test file result

b82e1ac2d0772aabaa322e20402859073df038c3 authored about 4 years ago by Julianus Pfeuffer <[email protected]>
Merge pull request #4876 from cbielow/fileinfo_extra

[FEATURE] Fileinfo: more info

016175943b42e88e9bf7c7a69c5b6600ade9cd56 authored about 4 years ago by Timo Sachsenberg <[email protected]>
some more PR changes, DBSuit test input to be without FDR, TOPPTool docu changed

4eac72c806bc8ef3d18cc80b27e1b361d2040605 authored about 4 years ago by Tom Waschischeck <[email protected]>
* extend mslevel + fragmentation method information

3b8271a18666a17b21e37cfbf4dc0f5db0431a8e authored about 4 years ago by Chris Bielow <[email protected]>
fix test

0ed914c7fb62e3cd22855c4e5ae6a54af2a9d060 authored about 4 years ago by Chris Bielow <[email protected]>
Merge pull request #4871 from OpenMS/PeptideIndexer_rework

[FEATURE] PeptideIndexer more user friendly using 'auto' mode

f53519586b29109b8a428fe303476ff09b037507 authored about 4 years ago by Chris Bielow <[email protected]>
[FIX] Protein terminal mods in AASequence

cd1a3fa006abca35ab23b8d754c5cca44ed40e76 authored about 4 years ago by Julianus Pfeuffer <[email protected]>
PR changes & target/decoy lookup bug fix

d248329666a167b6d156d61e45ff856fade22163 authored about 4 years ago by Tom Waschischeck <[email protected]>
Fix ProteinIdentification::SearchParameters::getChargeRange (solves #4872) (#4873)

* [FIX] fixed parsing of charge states from comma-separated list in 'ProteinIdentification::Sear...

307a248f7ac95b1cd82e4557bf68d77ad4163b4b authored about 4 years ago by hendrikweisser <[email protected]>
class test for Suitability

6844ab0eb4767d017bc2ede98b90c1722a46025f authored about 4 years ago by Tom Waschischeck <[email protected]>
computeSuitability to compute

3c5d4bf4afa470ccec50656fd4142ea1a56d1068 authored about 4 years ago by Tom Waschischeck <[email protected]>
minor fix

bae116a60d917af8b9b1ebf2b80769c155ad71ce authored about 4 years ago by Chris Bielow <[email protected]>
Merge branch 'develop' of https://github.com/OpenMS/OpenMS into PeptideIndexer_rework

44df9b7784899e16a5c7b5ddc09148e7f08c9b21 authored about 4 years ago by Chris Bielow <[email protected]>
Merge pull request #4803 from enetz/update/unimod_2020

[UPDATE] Unimod xml and obo files

3794925b9684b83a2954079f1ffe6dc4ab4eb96d authored about 4 years ago by jpfeuffer <[email protected]>
[TEST] small improvements to IdentificationDataConverter_test

600b87eceb7910633b838ea0d81e3cd9a043d00b authored about 4 years ago by Hendrik Weisser <[email protected]>
[FIX] fixed parsing of charge states from comma-separated list in 'ProteinIdentification::SearchParameters::getChargeRange'

7bb0bc2a44bb1ec667995b5e78c5e3bf55d3565c authored about 4 years ago by Hendrik Weisser <[email protected]>
Update CHANGELOG for 2.6 Release

a258a5eeea99529eb94cf26134594edea4fd2b8d authored about 4 years ago by FabianAicheler <[email protected]>
Merge branch 'develop' of https://github.com/OpenMS/OpenMS into PeptideIndexer_rework

# Conflicts:
# src/topp/PeptideIndexer.cpp

7ba5e7ef433a9495dfec2ac4cd000159075d36f9 authored about 4 years ago by Chris Bielow <[email protected]>
* auto mode for settings in PeptideIndexer

* allow removing weird peptides produced by XTandems's special cleavage rules ('X' is a stop cod...

4d5da564f7ffb6f08fc127d020052ecd1701efa8 authored about 4 years ago by Chris Bielow <[email protected]>
Merge pull request #4868 from cbielow/toppview_layers

minor GUI improvements

710106f20633346b0d81b60703c73cc225b7d4a1 authored about 4 years ago by Chris Bielow <[email protected]>
[TEST] updated boost version < 1.56 MRMAssay test files

edeb946e068825866a3190eea7d67509cfdd5985 authored about 4 years ago by Eugen Netz <[email protected]>
Update IDMassAccuracy.cpp

6009845de5b2ee1c76dcfaea96fe474622d145c2 authored about 4 years ago by Timo Sachsenberg <[email protected]>
[FIX] suppress misleading warning messages about unknown parameters (#4864)

a55cb658f9c2e7dfb408377013f3e07caca764f7 authored about 4 years ago by Eugen Netz <[email protected]>
clicking 'edit' when no item is selected, uses the first item

f62f2100e33a618988196338e85dcc5f4196c5f5 authored about 4 years ago by Chris Bielow <[email protected]>
Merge branch 'develop' of https://github.com/OpenMS/OpenMS into toppview_layers

ceea347974d40d4b11896ed5e00afcc143214ea0 authored about 4 years ago by Chris Bielow <[email protected]>
[TEST] updated test files

470bbe25147819e948d9654a39bc9356d4c3a6e7 authored about 4 years ago by Eugen Netz <[email protected]>
[TEST] updated class tests

75e9b80323e3594944d8b8ed178d900d526125d3 authored about 4 years ago by Eugen Netz <[email protected]>
[FIX] only parse neutral losses with an existing formula from unimod

afeaddc74c9bce43ece9c027258f48276e27038d authored about 4 years ago by Eugen Netz <[email protected]>