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

Finished work on most SEs

47b3555acffd010e4ed70e3a85078101e8e30c32 authored over 4 years ago by jpfeuffer <[email protected]>

more refactoring

7da0f0c0665deb9b028578200a8e4ca7401c3fcf authored over 4 years ago by timosachsenberg <[email protected]>

First try on memory efficient streaming/checking for mzmls in SE adapter

c01201e81fcbccceca7601c9c88e22734c583392 authored over 4 years ago by jpfeuffer <[email protected]>

Total signal within isotope window is used for PeakGroup.h selection in precursor

72e51ceaae9ae0002f2d206856d07667f0c3625b authored over 4 years ago by kyowonjeong <[email protected]>

more streaming

6d650d49447709c69819165664c9f743aec09478 authored over 4 years ago by timosachsenberg <[email protected]>

MapAlignerTreeGuided: new option

the user has the choice to copy or reload the input data for the
alignment (decision between lon...

6ae50c83138321100f69b914267f1862219b7f8c authored over 4 years ago by JuliaThüringer <[email protected]>

initial refactoring for streaming

dc00edb4eeb8c6634227fba98e99177e1c1f77db authored over 4 years ago by timosachsenberg <[email protected]>

[DOC] updated RNAMassCalculator documentation

eb76448107a8941323763ef85ca85fe195dfff97 authored over 4 years ago by Hendrik Weisser <[email protected]>

[TEST] updatd RNAMassCalculator test

d460df026a4337186c227eabd1d9de1d481be247 authored over 4 years ago by Hendrik Weisser <[email protected]>

MapAlignmentAlgorithmTreeGuided: save memory

* vector of input maps is given as reference instead of a copy
* FeatureMaps that are no longer ...

95badfb4ba3b8cdf734a24fbf12b3e572a0bce2e authored over 4 years ago by JuliaThüringer <[email protected]>

Merge pull request #4673 from OpenMS/fix/pyomsnightly

pyopenms-nightly - change date format

07894e975c6fea790f7584543166c05d8baa9563 authored over 4 years ago by jpfeuffer <[email protected]>

Forgot one return

2c29d4b1cfd48b1ff2c20655e6b364b4a10e1d66 authored over 4 years ago by IceFreez3r <[email protected]>

replace more calls to getAllChildTerms

db00e1dbc28b20452d30a67ed6741ea331de72ad authored over 4 years ago by Anton Levin Kriese <[email protected]>

less branches in checkFreatureQuality_

Instead of changing feature_ok to false and returning it at the end, just instant return false. ...

47c96f11ce30890dcaa4ffc32df2f97567112b43 authored over 4 years ago by IceFreez3r <[email protected]>

FIX to correct inital format

68ebc4a4eafdeb39502ae9b581fcf7b2d9c7bbb2 authored over 4 years ago by oliveralka <[email protected]>

Merge pull request #4669 from OpenMS/feature/scoreFinding

Allow auto finding of scores in PLFQ and IDPEP

274167660e06cbe14ffef59661921e000d6e115f authored over 4 years ago by jpfeuffer <[email protected]>

Merge pull request #4672 from OpenMS/fix/protQntMzTabCXMLInfrc

[FIX] Correctly use inference run for mztab export in proteinquantifier

cf718d10d2ac5abc5a5399fed89b439db3a3aabe authored over 4 years ago by jpfeuffer <[email protected]>

fix: added fwrd decl

fbd36d655b20c784a98e4ffc34162d9950dcf981 authored over 4 years ago by Douglas McCloskey <[email protected]>

change date format

83505d181c770a6bb1ecb2d863e35ca80cb085ac authored over 4 years ago by oliveralka <[email protected]>

Correctly use inference run for mztab export in proteinquantifier

853356b275ec3dc798709bc201db6b2f83de2df6 authored over 4 years ago by jpfeuffer <[email protected]>

more fixes and test update

b1df55a8b2d0c2d3c3e500e9d5c37a2dd31061a4 authored over 4 years ago by jpfeuffer <[email protected]>

fixes and docu

c1fad3aed31042d96b5c46031ca196339aadc2ac authored over 4 years ago by jpfeuffer <[email protected]>

Harmonic mass deletion via massSNR added

2bc02c86e5eb69ac1f3a506b57bbf3cc71d3f71e authored over 4 years ago by kyowonjeong <[email protected]>

remove some calls to getAllChildTerms

0ff39372e72894b857b2117bd2cb4783c3e807d7 authored over 4 years ago by Anton Levin Kriese <[email protected]>

make checkAndGetTermByName() return CVTerm*

25570d522712f6dfe2905cfc427ecdde4d2f72c4 authored over 4 years ago by Anton Levin Kriese <[email protected]>

more fixes

8157a555520b5edd7c8b321f30e864fd88b50483 authored over 4 years ago by jpfeuffer <[email protected]>

fix function decl

7695b96fe4d82cfa2221753ecfa69230d1eb2bc0 authored over 4 years ago by jpfeuffer <[email protected]>

Allow auto finding of scores in PLFQ and IDPEP

b835b938aa4edca7a1b69b2512864e51dee80f64 authored over 4 years ago by jpfeuffer <[email protected]>

static variables in FLASHDeconvAlgorithm.cpp::deconv

bae325653346a613f249c70de4d8fc4840bbe3aa authored over 4 years ago by kyowonjeong <[email protected]>

static variables in FLASHDeconvAlgorithm.cpp::deconv

72f17c95e398414e8e36c04f3c887f3cf477349d authored over 4 years ago by kyowonjeong <[email protected]>

Merge pull request #4666 from OpenMS/fix/pyomsnightly

[FIX] pyopenms-nightly - variable for push

eeca6bf2c147c65350e0a82d3ef7566ed17996c2 authored over 4 years ago by jpfeuffer <[email protected]>

cachedTerms

959f051069866a86799445b43e06831e412c4591 authored over 4 years ago by Anton Levin Kriese <[email protected]>

FIX Variable for push

b5c2a45483bc2eeb9f43553f66dcc657bc23a5ea authored over 4 years ago by oliveralka <[email protected]>

Update CMakeLists.txt

1de8bd9abbc786e2f569103a1a4c0839c696d851 authored over 4 years ago by jpfeuffer <[email protected]>

Merge pull request #4665 from cbielow/fix_MATreeGuided

MapAlignerTreeGuided: fix segfault when featureXML contains no IDs

619fe5270266a0345056371e6e38abe10139cc0f authored over 4 years ago by jpfeuffer <[email protected]>

[FEATURE] added output of sum formulas to RNAMassCalculator

5daf7dbc249e9b0b4540c2bff58ab3d3a8ae19a9 authored over 4 years ago by Hendrik Weisser <[email protected]>

[FEATURE,IO] support for RNA and compound IDs in FeatureFinderIdentification via IdentificationData/.oms file input (not yet tested)

9f7e4df18d55aa2b08002d416e0525c31e0dab69 authored over 4 years ago by Hendrik Weisser <[email protected]>

Precursor selection and train dataset output done...

a46a48411ab2d81ce812d9d98f0ebebc060a7784 authored over 4 years ago by kyowonjeong <[email protected]>

Replace containsChildTerm() with iterateAllChildren()

20d8431fdc9be40ea171b2160d5647b710f52737 authored over 4 years ago by Anton Levin Kriese <[email protected]>

Precursor selection and train dataset output done...

ed0af1e81a894eb64923348bac6a593cf76194f1 authored over 4 years ago by kyowonjeong <[email protected]>

Update pyopenms-wheels.yml

b573e7e3981eca7c979c5b0db1787dab44786784 authored over 4 years ago by jpfeuffer <[email protected]>

Merge pull request #4651 from OpenMS/fix/pyomsnightly

[FIX] pyopenms-nightly

1e1ea78c6cef8936408c9cd3960243a88848195d authored over 4 years ago by jpfeuffer <[email protected]>

Precursor selection and train dataset output done...

a36e33373a20cfb9f0ad9b9c7c668b3cbd9c857d authored over 4 years ago by kyowonjeong <[email protected]>

[FIX] fixed public/protected declarations in CoarseIsotopePatternGenerator

9e179917d8c5a81c1a23da65925435ce4564977a authored over 4 years ago by Hendrik Weisser <[email protected]>

[FIX] updated IDFileConverter and NucleicAcidSearchEngine to recent change in IdentificationDataConverter

454e5565321acb0a94b7699637750bbe3730103f authored over 4 years ago by Hendrik Weisser <[email protected]>

fix compile error

a1f4c9efa181f1fdbf0dc28f9509f846ba5cac8f authored over 4 years ago by Chris Bielow <[email protected]>

fix segfault when featureXML contains no IDs

44136c377730a1865941bc79674ecd7a6adb0d67 authored over 4 years ago by Chris Bielow <[email protected]>

Small change

Small changes similar to the commits before

e5210037bc815ae639ee605417678706a47f1776 authored over 4 years ago by IceFreez3r <[email protected]>

[API] IdentificationData: added function to set meta values on stored molecule-query matches

22b6b8bbc7e83cd619e7a28b68c816b78e9fb019 authored over 4 years ago by Hendrik Weisser <[email protected]>

[API] IdentificationDataConverter: export data of any type (protein/RNA/compound), incl. mixed; added public method for exporting parent molecule (e.g. protein) matches

5593ab02e92826d15dd3b312073d0073da7cac7b authored over 4 years ago by Hendrik Weisser <[email protected]>

Again GitHub Actions

2a3301fae46371fc2a04f45b0a78d03555bbb09f authored over 4 years ago by oliveralka <[email protected]>

Swtich to OpenMS_GIT_LC_DATE

8819b45c576667bdea4acf2f40415864da653b7c authored over 4 years ago by oliveralka <[email protected]>

source code big clean : PeakGroup.cpp DeconvolutedSpectrum.cpp added.. Still needs quite a lot of work..

0186a8c40793c876e1a6767369a55f13f1a42ee8 authored over 4 years ago by kyowonjeong <[email protected]>

test cmake timezone

11447540b5cb804723547189f7d94a09edf7cd8b authored over 4 years ago by oliveralka <[email protected]>

TEST cmake date

e9683ba8f355d5a9d6a32260b2ea7abbc2d0bb68 authored over 4 years ago by oliveralka <[email protected]>

Merge pull request #4661 from jpfeuffer/updatecontrib

Update contrib

79fbc97c22a3dd39b480d556b326e3cb2bb80fa4 authored over 4 years ago by jpfeuffer <[email protected]>

Add Function Description, beautify code

88be285ff098d3b5fc510eeb047505b6cf9bebc6 authored over 4 years ago by Anton Levin Kriese <[email protected]>

Optimize locateTerm

261c71fee496ae3fb696e5bf20d930098495d431 authored over 4 years ago by Anton Levin Kriese <[email protected]>

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

ac291109fe9b7746b14fb8ba6e4a93ec939d21ea authored over 4 years ago by Builder <[email protected]>

update contrib

78dd09311f19b9f8345a6fb4c7757a9ec10da743 authored over 4 years ago by Builder <[email protected]>

Ranged based for-Loops, OMP-Checks removed

Changed all for-Loops to ranged based for-Loops where CLion recommended it
Removed checks for OM...

9345dcb283e475a6ca68fca6fdf6644e71454b1b authored over 4 years ago by IceFreez3r <[email protected]>

Merge pull request #4660 from cbielow/develop

some minor warning fixes

0daed1e884bc29b82b1999e92a6f4443d42586e0 authored over 4 years ago by Chris Bielow <[email protected]>

[HOTFIX] ASAN new/delete char[] mismatch

3c57e6cf6fe369957429078bfd822f5225fd481b authored over 4 years ago by jpfeuffer <[email protected]>

const readded

fb5e03254fbfcc0c0fa71fa558627da007d9849d authored over 4 years ago by IceFreez3r <[email protected]>

Merge pull request #4659 from cbielow/fix_mssim_types

added citation for FFCentroided

6a6d8dfc0053343c2b313813631c086fe9a14e68 authored over 4 years ago by Timo Sachsenberg <[email protected]>

Introduce ControlledVocabulary::containsTermRecursively

6db3fe59705d08eac16345bff5117945184acdbf authored over 4 years ago by Anton Levin Kriese <[email protected]>

added citation for FFCentroided

719f2c76e4f45c6c16e1d2f88b0fa0f3d7408fcf authored over 4 years ago by Chris Bielow <[email protected]>

Step 2 Performance 1/2

Removed scores-vector. Working on the trace_score (double) should be sufficient here.
Stored map...

7b701bc10a85297a6e94f15a2f7302b119d25355 authored over 4 years ago by IceFreez3r <[email protected]>

Merge pull request #4647 from cbielow/swath_wizard

Swath wizard

3e7e3f38e0c7650552ae1cbe53ca42a4f959fa5d authored over 4 years ago by Timo Sachsenberg <[email protected]>

more fixes

496d5b4567591aa2782024b0eaed69047bdef5b9 authored over 4 years ago by Chris Bielow <[email protected]>

fix compile errors

420e5304dcc68f20f233dc7b22e49a837c4372d3 authored over 4 years ago by Chris Bielow <[email protected]>

Add shell;run

63f24135b41ccfbb886a21f5bb03f17ca4553c69 authored over 4 years ago by oliveralka <[email protected]>

fix contrib install names

6f5fa857272023988c31446e80cdd051cca7a182 authored over 4 years ago by oliveralka <[email protected]>

MetaboliteAdductDecharger: don't write to opt out if absent (#4552)

* MetaboliteAdductDecharger: don't write to opt out if absent

* add tests

* Adapted tests;...

bdb3cc3bb271014a5e949737df810e480cb7bd3f authored over 4 years ago by M Bernt <[email protected]>

Merge pull request #4630 from jpfeuffer/feature/cXMLProtGroups

[Feature][Fix] consensusXML and mzTab protein group support

8c7375eac70b1ec3db8abc5ff92717645d033d24 authored over 4 years ago by jpfeuffer <[email protected]>

Merge branch 'develop' into feature/cXMLProtGroups

dde10123fd9d3db4f891293d8bbabe8fb8e4e9f0 authored over 4 years ago by jpfeuffer <[email protected]>

add some constness

bf2f4d097c558c63569f7415b0253c68af07c3b5 authored over 4 years ago by Julianus Pfeuffer <[email protected]>

Merge pull request #4657 from OpenMS/feature/check_missing_id_plfq

check for missing identifications

aeaa56a06360f147fa464f52585d0e0f1e6216b8 authored over 4 years ago by jpfeuffer <[email protected]>

Update FeatureFinderCentroided.cpp

46aca501060eabc9802d8e788e8d8f8e97d2af98 authored over 4 years ago by Timo Sachsenberg <[email protected]>

check for missing identifications

and fail with error message

aa5ded033cbcc94528e7c2c5fff71b775cbbf449 authored over 4 years ago by Timo Sachsenberg <[email protected]>

fixed missing docs

78ef15f7b25465d6b6a1ca22d6f6284c5ccca10b authored over 4 years ago by Chris Bielow <[email protected]>

[FEATURE] FeatureFinderCentroided Performance (#4652)

* Filter spectra in FeatureFinderCentroided

Filter out spectra in FeatureFinderCentroided wit...

1bd22ced82588a784882a8b8f97094c751d98f33 authored over 4 years ago by IceFreez3r <[email protected]>

ADD pytz

e30fb630cfbb3d8c562eac99faccd23e794aef56 authored over 4 years ago by oliveralka <[email protected]>

Merge pull request #4653 from cbielow/fix_cometmzML

[FIX] CometAdapter always writes indexed mzML
[FEATURE] comet version is determined automatically

c3352dedafbb8ab512b4552e480b907d84363cc4 authored over 4 years ago by Chris Bielow <[email protected]>

check MS3 as well

277dbfa20ff3cd7d3604b0b8b7a001c15a177e22 authored over 4 years ago by Chris Bielow <[email protected]>

rewrite for MS3 as well

672b808c30c34268f4c7bf715e7b1896e6dd209b authored over 4 years ago by Chris Bielow <[email protected]>

update INI files (remove comet_version parameter)

995155a04356fd7658896700844fa1e9546b5f09 authored over 4 years ago by Chris Bielow <[email protected]>

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

# Conflicts:
# src/topp/CometAdapter.cpp

3f683f3d743ccf3c4792f4c6b184183f75a22d6d authored over 4 years ago by Chris Bielow <[email protected]>

add warning. fix compile error on gcc/clang

2bcefe52bac94f4116c4db503a9572beb9c0997e authored over 4 years ago by Chris Bielow <[email protected]>

[FIX] fixes indexedMZML problem (#4348, always write an Index)

[FEATURE] CometAdapter does now read the comet version. No need for the user to specifiy it via c...

72b6658d4333882b8f96efccd07fc21bb1415db9 authored over 4 years ago by Chris Bielow <[email protected]>

comment out unused meta param in other overloads

c698fac251cadd50b26329f678c42615c99e21bb authored over 4 years ago by Julianus Pfeuffer <[email protected]>

adapt last tests.

610fdd55127a73be989a3f9ce7b5da93a25da372 authored over 4 years ago by Julianus Pfeuffer <[email protected]>

repository changed miniconda

27c3e87e4222c35f849a86cc708d78fdd8032a55 authored over 4 years ago by oliveralka <[email protected]>

test, set timezone in python

5db0e60961ddc69258bd42910a1dbe2b0d49acae authored over 4 years ago by oliveralka <[email protected]>

[ADD] action on push for debugging

f30c8afd4936614e518ed52456508a0e2a1768e7 authored over 4 years ago by oliveralka <[email protected]>

FIX timezone, download contrib

a8857be9fa19f7b97a5341284ab908fb98162a5c authored over 4 years ago by oliveralka <[email protected]>

[FIX] updated call after API change

fccc99f2199c2371a1e3939bf687da7500bd4c98 authored over 4 years ago by Hendrik Weisser <[email protected]>

[API] IdentificationData: created separate class for identified molecules (variant), moved corresp. functions from MoleculeQueryMatch

b1bd122315b3d37a70b8062e754693e34bd12661 authored over 4 years ago by Hendrik Weisser <[email protected]>

[FIX] disable frequent warning message in SN estimator (as done in OpenSWATHWorkflow by default). (#4649)

c34ac70932f876928066fca33e43962b8b3304bd authored over 4 years ago by Timo Sachsenberg <[email protected]>

reset THIRDPARTY module

b2350c5619543c6c987b5a543bac28827bcf9a40 authored over 4 years ago by Julianus Pfeuffer <[email protected]>