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

Merge pull request #5135 from cbielow/feat_ParamEditorStringListEdit

ParamEditor with more convenient StringList editing

2676ed66531a5042a657841e1cfab3ac3fce405a authored over 3 years ago by Chris Bielow <[email protected]>

What?

7d4c18ccbdbb19ff62172a4de09b66801fd1bf8b authored over 3 years ago by Julianus Pfeuffer <[email protected]>

augment CHANGELOG

e8d66423759404ebd11b8954cc83d28efd42c6bb authored over 3 years ago by bielow <[email protected]>

remove *nary_function and add note about stupid cmake

7af6475743072984638a04ee2104193d26ccf9db authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Merge branch 'fix/clangwarnings' of https://github.com/jpfeuffer/OpenMS into fix/clangwarnings

4fdd0e6c4f6ac44e06c33fdf60c88bd081314e62 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

no aggregate-init for c17 due to bug in boost <1.70

8d93c7a09f1571cb308db6854f83ea90e40f51ab authored over 3 years ago by Julianus Pfeuffer <[email protected]>

enable gcc7

c2c4a37a422b8d120aa74369bbae6aef5d1a58ef authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Merge remote-tracking branch 'origin/fix/clangwarnings' into fix/clangwarnings

3a9f8197ee109446efa38955fb6e46780a23e68d authored over 3 years ago by Julianus Pfeuffer <[email protected]>

wildcard filter with escape func and tooltip

d0ad90e0dcb28389d4cc1545b7d494a1f4068172 authored over 3 years ago by bielow <[email protected]>

fix rest of executables

bd36635428e53d0a43c34e2e637010ee1de53bbe authored over 3 years ago by Julianus Pfeuffer <[email protected]>

fix non-committing of QLineEdit values

51e71746cb388b8d9a75999472aee8c2ca1d0733 authored over 3 years ago by bielow <[email protected]>

use the new class in origin decoygenerator

7bdabc9391a976347240745f286bb32c688eb604 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

introduce portable_random_shuffle

2a1b77ee0b02b3ecaa7853396a2d9bbdbb6a810a authored over 3 years ago by Julianus Pfeuffer <[email protected]>

mistake

82147b686c31ff2b0838a52d38d93ab3d8a21966 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

[FEATURE] c17

52e04b7131d62196faadf67cee21352b1fb37ba3 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Parameter names ending with _ fixed + multiple spectra examined for precursor search for real time deconv added

febe365b1f55398c24c26bbdd5c50143aa68b802 authored over 3 years ago by kyowonjeong <[email protected]>

regex mistake

14490ae55f236d2d7dcde45963b9b9939b2c302a authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Silence CMake warnings

2f46db13a13192ecfecbc374a6717900aad6a9a3 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Merge pull request #5124 from jpfeuffer/feat/IDlinking

[FEATURE] Infer linking tolerance from RT distances of IDs in RT bins

2951410a094038a59d1bbd3ed6d300f275e84dfc authored over 3 years ago by Timo Sachsenberg <[email protected]>

pyopenms + codestyle

e237725e640bd0b4145baffd9ab8b69df2befc0e authored over 3 years ago by Julianus Pfeuffer <[email protected]>

[TESTS] double overwrites??

e40fc9efc5d142e804e3fddd67c6b01cde7ac8a3 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

[TESTS] double overwrites??

2e2652cf1d22ff4b559234604d13e78e8bf5d28c authored over 3 years ago by Julianus Pfeuffer <[email protected]>

[TESTS] double overwrites??

0281ac1253a6e652d7bb932524afddf5e3f1208f authored over 3 years ago by Julianus Pfeuffer <[email protected]>

[TESTS] fix hopefully most tests

f310772ee12f6ddf5dd523370481e0fd1c1f6335 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Merge branch 'develop' into feat/IDlinking

fc2777791ea8841825fe5be90a68d85165642bea authored over 3 years ago by Julianus Pfeuffer <[email protected]>

[TESTS] fix hopefully most tests

a359294a54025c039e7f4e5aea62dfecdef3f518 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

MS-Level and Precursor Information Written in TheoreticalSpectrumGenerator (#5126)

* ms lvl and precursor info written in TSG::getSpectrum

* removed writting ms lvl and precurs...

8fc23fe5c7eca9157c95fe9e7832f5087426ccbd authored almost 4 years ago by TomW <[email protected]>

rename

d7f47647c298c5f1ee74371298550827f1ffe624 authored almost 4 years ago by bielow <[email protected]>

[API] IdentificationData: simplified 'MoleculeType' and 'MassType' enums

a36f9bacf6b5e66ac222928fcb95f123c82ccdc9 authored almost 4 years ago by Hendrik Weisser <[email protected]>

[API] store matching IDs in features by referencing 'input items' (e.g. MS2 spectra), rather than 'input matches' (e.g. PSMs)

43a9fff89fa3de16f9741ffde3ee39851ff0cce4 authored almost 4 years ago by Hendrik Weisser <[email protected]>

Merge pull request #5122 from ahmedskhalil/feat/aut509

[Feat/aut509] - Refactoring Support for Isotopic Labelling Experiments (MDV) IsotopeLabelingMDVs

9d2951760e313ad1a5d20ad21e9fe679c18738d5 authored almost 4 years ago by Timo Sachsenberg <[email protected]>

[FIX] more charge errors. adapt tests

738d247544cb39d2505b9f36e674092971e67c63 authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

more rename

b9097335c99fc537be404ac51c098de661e8368d authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

Use int for charge everywhere in DIA and use abs for safety. Try to reproduce old code.

e5368c18ffef06ea28f334387a7ca00986213dbe authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

fix CI

e9eba566ba35405649bb0122348a9012927258c6 authored almost 4 years ago by bielow <[email protected]>

fix bug when data is comitted even though the user cancelled the Editor dialog

b97ae2c661298e0c7b31e3d8a2f063724a40caa2 authored almost 4 years ago by bielow <[email protected]>

added tootips

48a8068fae76d690e35094ad2d4595aa8bbd816f authored almost 4 years ago by bielow <[email protected]>

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

53506ca013a2727a44c57f71b2c48b40dbc146b7 authored almost 4 years ago by bielow <[email protected]>

ParamEditor with more convenient StringList editing when restrictions apply (mostly for fixed/variable modifications)

011f587ec1223976cae5d4aed64343518842b977 authored almost 4 years ago by bielow <[email protected]>

Update PULL_REQUEST_TEMPLATE.md (#5132)

2a858ba1251177d1110dd11a3772e9400147285c authored almost 4 years ago by Timo Sachsenberg <[email protected]>

First PR stage seems to be done.. All sytle problem is addressed. Pointers in class removed. Comments updated.

694a624ed710a0d1b7ddc660f4b8cb0131ff783c authored almost 4 years ago by kyowonjeong <[email protected]>

First PR stage seems to be done.. All sytle problem is addressed. Pointers in class removed. Comments updated.

46b9af2ef4137181151e6cedbca4ac38a98ecece authored almost 4 years ago by kyowonjeong <[email protected]>

[REVIEW] coding style

a53cb8612ac7834232fc7cf6cd680e64242ef527 authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

[FIX] Fixed bug in QTCluster that assumed consecutive map_indices, which not even the test adhered to.

904be7e2189e7db42307a76aef16985979a10ada authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

Merge remote-tracking branch 'upstream/develop' into feat/aut509

c79a91c3aa69275dd10df4a7b86b094a8dd459a6 authored almost 4 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #5127 from cbielow/fix_glpk5

Support glpk5

567cd605ce926821354c2775349f081b670f741c authored almost 4 years ago by Chris Bielow <[email protected]>

FLASHDeconvAlgorithm.cpp local and private ones style fixed..

06b5d630aea93c5c8c57a3d466f92da6396cf926 authored almost 4 years ago by kyowonjeong <[email protected]>

[TEST] add test for negative charge and fixed dotprod

105dc582e7cbdc9336357b9d5bc557011569aa0c authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

[REVIEW] most review comments

[FIX] DIAScoring MS1 Negative charges would be casted to unsigned with nonsense values
[FIX] Smal...

a7a410f6fbff1405b9c177d32522c23760886937 authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

changed names of local variable based on OpenMS conventions

3c74b0598874b288e3ca4cbc19b8dcfedc1bbb15 authored almost 4 years ago by JeeK <[email protected]>

except for local variables, variable sytle done. Comments should be changed. Feature finder bug fixed.

0efbaca3ced645ac4a9f48facfd28b3c10a6cbe4 authored almost 4 years ago by kyowonjeong <[email protected]>

except for local variables, variable sytle done. Comments should be changed. Feature finder bug fixed.

109553b00c5c5a1600dc7b045109509460ba391f authored almost 4 years ago by kyowonjeong <[email protected]>

Parameters sorted.

b936384029eda62a532e654c78960fce4773a922 authored almost 4 years ago by kyowonjeong <[email protected]>

[SCRIPT] Add script to automatically overwrite TOPP test outputs.

82e382340e34ceaa56167d939b7fa3e697611ec8 authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

[FIX] Spelling (#5111)

* [FIX] spelling

* [FIX] INIUpdater_test

3f9aae0bc1dc5e551937d95b98b9c5c5e4c001d0 authored almost 4 years ago by Oliver Alka <[email protected]>

forgot

4c99428b219c1045eb20e6042fdda771bc7022fc authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

Small changes

04b85f94953f80f5ab7ba1eb89832b2cb1d399c4 authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

[FIX] Remove sqrt since we actually can get negative values now.

9bdf17629debd9935018605a5897bb2006f8ac3d authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

[FIX] Unused param2

429984c174745166a835af6de92615de9efff340 authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

[FIX] Unused param

6af76b6036fed71d06123ca75c1fa422b88cd4d9 authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

[FIX] Unused var. Cleanups.

6118a16f9b03e3607983cef28a3c5c47c074b1c0 authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

[API] - debugging pyOMS : excluding calculateIsotopicPurities(..., libcpp_vector[DoubleList]) - retriggering CI

bc89512eb4c1784e61f786348963166ccc0147f3 authored almost 4 years ago by Ahmed Khalil <[email protected]>

[FIX] Fixes some isotope related scoring functions in OpenSwath. Changes usage of scores in FFID. Some cleanups.

77de0102f5a350d77f7f257c19da2bf1a5f3301a authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

[FIX] preserve native id format in FileHandler (#5130)

* take first native id format as represenative

* Apply suggestions from code review

Co-aut...

9446dc620ea734179ba4b9e338bf0ae2cd07a84c authored almost 4 years ago by Timo Sachsenberg <[email protected]>

[API] support for loading feature maps from SQLite (class OMSFile)

957ae22784ce650a201f97d73c554a06167ae535 authored almost 4 years ago by Hendrik Weisser <[email protected]>

[API] OMSFile: store feature map meta data using SQLite; begin work on loading feature maps

d6669f3a83e0caf81d09ba109894695adadf3a72 authored almost 4 years ago by Hendrik Weisser <[email protected]>

add to CHANGELOG

662c1e219c7248058e1d454f69ddbb3a6169e8da authored almost 4 years ago by bielow <[email protected]>

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

# Conflicts:
# src/openms/source/DATASTRUCTURES/LPWrapper.cpp

ac2814b9c59a22f7f8999de3309703e9c4c9ce3c authored almost 4 years ago by bielow <[email protected]>

avoid includes and remove some warnings

eed4eaf98dcc29ebb3d039cceb277d2ba531881c authored almost 4 years ago by bielow <[email protected]>

fixes as suggested in #5123

fcde6151cd8de3902988b07b136b410e6856cefe authored almost 4 years ago by bielow <[email protected]>

[FIX] min RT fixes

614d4826ab8bf8a57da82917ef00de21d44873a5 authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

[NOP] removed extra whitespace

e8cb525859b04929b86ff35188c83430a754a443 authored almost 4 years ago by Hendrik Weisser <[email protected]>

[FEATURE]

- Parameterize new tolerance estimation.
- Allow noID penalty.
- Do not use MS2 SWATH scores i...

1078cf8515f5232008a911ba270047f05d76e2a9 authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

[API] - debugging pyOMS : excluding calculateIsotopicPurities(..., libcpp_vector[DoubleList])

78b8251e2848c58117486734e4b3e446375e9da6 authored almost 4 years ago by Ahmed Khalil <[email protected]>

Parameters sorted.

7ccb483aaabd202c906a209f688618a4a5553d09 authored almost 4 years ago by kyowonjeong <[email protected]>

[FEATURE] store input matches on features using SQLite (class OMSFile)

649967d20ec434e2be7e1f75e01a372fe30461e6 authored almost 4 years ago by Hendrik Weisser <[email protected]>

[FEATURE] support for storing feature maps using SQLite (class OMSFile) - work in progress

2f0da7c3c0fba730550095bee11ac0dac2eecadc authored almost 4 years ago by Hendrik Weisser <[email protected]>

[API] added accessors for ID data in FeatureMap

5513072794aa09dff42c7c908fdfef302c728c03 authored almost 4 years ago by Hendrik Weisser <[email protected]>

[API] - debugging pyOMS

971485216f62d8c2cb7d577062ad561055d37ad7 authored almost 4 years ago by Ahmed Khalil <[email protected]>

[API] - debugging pyOMS

54d8663683f891b86901c3d026cc13ef9d643e60 authored almost 4 years ago by Ahmed Khalil <[email protected]>

[API] - debugging pyOMS

aa9a24f3caddc2f1e4503854eac27845b71d4d98 authored almost 4 years ago by Ahmed Khalil <[email protected]>

[API] - debugging pyOMS

d0a5a0187f35783e9359534bbee1087975dd7d4a authored almost 4 years ago by Ahmed Khalil <[email protected]>

[FEATURE] Infer linking tolerance from RT distances of IDs in RT bins

e9fd34dce3d3a038e26e9b5775a01698d1f9f9f9 authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

[REFACTORING] ResidueDB (#5096)

* remove XML file and store data locally in ResidueDB

* fix indentation of certain lines

*...

4f1dee95fd4a86ab80abd59bd4ddf7a5bde1fc22 authored almost 4 years ago by Timo Sachsenberg <[email protected]>

Automatically detected all avialable tools in ToolsDialog (#5117)

* Automatically determine all available tools based on the layer type.

* Refactoring

* Fix...

0a6f9ba37f399e1425f5460446094c2c2bf878dd authored almost 4 years ago by David Voigt <[email protected]>

[API] - debugging pyOMS

246293c76d73c82241955721ce9d638cffaa2c1b authored almost 4 years ago by Ahmed Khalil <[email protected]>

[API] add 'swap' and 'clear' functions to IdentificationData (for use in FeatureMap)

71c4dcc652283c6a90d8e2e54a5449c6d292a2a1 authored almost 4 years ago by Hendrik Weisser <[email protected]>

[API] start integrating new ID data structure into Feature[Map]

40b6b1fcd650c0cebd293158cad2a0f36ebeded2 authored almost 4 years ago by Hendrik Weisser <[email protected]>

[API] - debugging pyOMS

06c58be197ebfb912ba6842e35ecfe02abfe93a7 authored almost 4 years ago by Ahmed Khalil <[email protected]>

query decoy result (#5113)

* query decoy result

* export decoys after target export has been downloaded

* Update Masc...

eb342e0cf8806872bb589424cf5bc66c987144ec authored almost 4 years ago by Timo Sachsenberg <[email protected]>

[API] - debugging pyOMS - libcpp_map

b828fda504920cb4a69bf2ffd1b0eb137975ecbd authored almost 4 years ago by Ahmed Khalil <[email protected]>

[API] - debugging pyOMS

f5def7def6b2d57cbbf3456c8693d916d5cc3fd6 authored almost 4 years ago by Ahmed Khalil <[email protected]>

[API] - debugging pyOMS

3fea59459716f9866b755c56df841e7d0ab9ea91 authored almost 4 years ago by Ahmed Khalil <[email protected]>

[API] - minor change

82cb7e1d07776da31ef366380a921537bf087488 authored almost 4 years ago by Ahmed Khalil <[email protected]>

[API] - minor correction

07ff61b8cfdeb8b0f4f6451c882455bccd138134 authored almost 4 years ago by Ahmed Khalil <[email protected]>

[API,TEST,DOC] - refactoring IsotopeLabelingMDVs()

da1c93fbf9c5de4001bd1e8bd8f8289caba3ee9c authored almost 4 years ago by Ahmed Khalil <[email protected]>

Merge remote-tracking branch 'openms_upstream/develop' into feat/aut509

40fc099432e1431ac703bb297131bb378163b896 authored almost 4 years ago by Ahmed Khalil <[email protected]>

[API,TEST] updating calculateMDVAccuracies and related tests

a6808eb9adf3c5b61b3056cb06dfbf346956dee8 authored almost 4 years ago by Ahmed Khalil <[email protected]>

[API] Adding logic handle feature_name in IsotopeLabelingMDVs::calculateMDVAccuracy

7a69da8bdb50797e60f96fa15dd0d95765150999 authored almost 4 years ago by Ahmed Khalil <[email protected]>

[API] Discarding FeatureName in IsotopeLabelingMDVs and other minor changes

3478fe756bf67699632da79045a6a97b4f48130f authored almost 4 years ago by Ahmed Khalil <[email protected]>