github.com/OpenMS/OpenMS-1 commits | Ecosyste.ms: OpenCollective

[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]>

Various enhancements to IsotopeLabelingMDVs

cf24043b89e33fd580d3dbd02871782ed7e38227 authored almost 4 years ago by Ahmed Khalil <[email protected]>

Updating IsotopeLabelingMDVs to handle multiple entries

d75a26458eff91f373b0d7dd85421b36cdfba18f authored almost 4 years ago by Ahmed Khalil <[email protected]>

Use pointer (#5116)

bbde6e5271ae549012dbc936f8ac9032c73f184c authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

[FEATURE] Prefer adapter modification when loading pepXML (#5114)

* Start on allowing preferred mods eg from adapter when parsing PepXML

* [FEATURE] Prefer ada...

4706e6ed8aa45a7f794423e9e2e940bb026c1c79 authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

Merge pull request #4935 from ahmedskhalil/feat/aut509

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

72e8515369d74f5b4dd144a23e9c3f34d0308e2e authored almost 4 years ago by Timo Sachsenberg <[email protected]>

remove unneeded code

ebebf99701651a1f4d3d7aa2a91219b3e9514ad4 authored almost 4 years ago by Chris Bielow <[email protected]>

Update StatisticFunctions_test.cpp

ea533815d882e1935bae7b6c5545c7e25dbf745b authored almost 4 years ago by Chris Bielow <[email protected]>

[FEATURE] RT tolerance specific to seeds (#5112)

* lower rt window for seeds

* update test files

e96731ed0ca7077d5a7b48afd3715f21e873248e authored almost 4 years ago by Timo Sachsenberg <[email protected]>

FLASHDeconv.cpp input output polished !! And segment fault bug fixed..

78f93724de8593d2b67fd52c7f406c6d04df962a authored almost 4 years ago by kyowonjeong <[email protected]>

FLASHDeconv.cpp input output polished !!

d97d39f275aac84c12f2d00d28cdb2e0713176bb authored almost 4 years ago by kyowonjeong <[email protected]>

[TEST,API] minor changes

dd7f2329c4dfca528029013cb00b702bdc07321b authored almost 4 years ago by Ahmed Khalil <[email protected]>

MS2 small mass bug fixed

c53d8ed9141b8cca79021f2cbd620b7b3ae4415d authored almost 4 years ago by kyowonjeong <[email protected]>

[TEST] minor changes

fae8ee034ebdacce9c927ce7763929c95de5e970 authored almost 4 years ago by Ahmed Khalil <[email protected]>

[API] minor changes

b17134e7cf01cf1daea1143ba141a8022aeb1dbb authored almost 4 years ago by Ahmed Khalil <[email protected]>

MS2 small mass bug fixed

e32bfd6d97ad2a41d8262e2a105894f73a2222e5 authored almost 4 years ago by kyowonjeong <[email protected]>

[API] minor changes

eb1d9287a95ca5880e5d516c0e4b42f6c4041da6 authored almost 4 years ago by Ahmed Khalil <[email protected]>

[FIX] More plfq fixes. Triqler PP export. TraML debug file problem. (#5108)

* [FIX] More plfq fixes. Triqler PP export. TraML debug file problem.

* Update FeatureFinderI...

e419ca310a084ca033d6ce78f259eec3d17dfd7a authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

Allow SSEngine in IDPEP (#5107)

* Allow SSEngine in IDPEP

* opening brackets

* minor fix

Co-authored-by: Timo Sachsenbe...

b8a95c81a783c94313ce518a13de9863f509b044 authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

[API] minor changes

5921887cba994d280bf006674bb49239d94a4aaa authored almost 4 years ago by Ahmed Khalil <[email protected]>

[FIX] Sort results from getModFromDiffMass (#5103)

* [FIX] Sort results from getModFromDiffMass

* Only use the closest mass mod for non-integer ...

ab9774ad704f01137549a19338fc000fa67ddb22 authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

Merge pull request #5104 from cbielow/TV-DIA-table

SwathWizard: support opening results in TOPPView

63c8b74d8cc33e25a1e1e948ee9a103853c63146 authored almost 4 years ago by Chris Bielow <[email protected]>

ci fixes

e28d45f11a402c9c7eb9c747fa0d2a6451981f2a authored almost 4 years ago by bielow <[email protected]>

[API] minor changes

6bcbe335204500a61e8b39dddfbfbad00b949b55 authored almost 4 years ago by Ahmed Khalil <[email protected]>

[API] minor changes

97cfae938868ff81f3db7d0dff2decd6584a7e87 authored almost 4 years ago by Ahmed Khalil <[email protected]>

[API] minor changes

9b169afa18f0bbdae92adf74777c8ce1c5d8e608 authored almost 4 years ago by Ahmed Khalil <[email protected]>

ci fixes

88ec44ac4133ef577d25628869e0da8232697fab authored almost 4 years ago by bielow <[email protected]>

[API] minor changes

f1f158886eb9eefac05081eeea589458ce148e44 authored almost 4 years ago by Ahmed Khalil <[email protected]>

[API] switching to std::map for correction_matrices_

2b08a83f7e1bd7131f0f9c0566abff955c30eb1d authored almost 4 years ago by Ahmed Khalil <[email protected]>

ci fixes

591263ef019182b964bec37f09fa122c5bf1b8b4 authored almost 4 years ago by bielow <[email protected]>

[API] moving correction_matrices_ to IsotopeLabelingMDVs::isotopicCorrection

1542683ecfae1348f3e37dc0739e0170bed27f1c authored almost 4 years ago by Ahmed Khalil <[email protected]>

[API] renaming IsotopeLabelingMDVs_DerivatizationAgent

b01bd1bc72f953ed460f8b452dfe5aaeadae9cf4 authored almost 4 years ago by Ahmed Khalil <[email protected]>

[API] updating correction_matrices_ mapping

87e03485ef9a4703228e3af3e747b658a9df9f43 authored almost 4 years ago by Ahmed Khalil <[email protected]>

[API] implementing OpenMS::IsotopeLabelingMDVs::DerivatizationAgent, OpenMS::IsotopeLabelingMDVs::FeatureName and OpenMS::IsotopeLabelingMDVs::MassIntensityType enum classes in pyOpenMS

547c294374b13ece50b8a8d6e4d5d643a22ff11d authored almost 4 years ago by Ahmed Khalil <[email protected]>

Update PULL_REQUEST_TEMPLATE.md

cc603d84e4f51dce0e697804899387e81968e399 authored almost 4 years ago by Timo Sachsenberg <[email protected]>

Update PULL_REQUEST_TEMPLATE.md

3a7f50ea771bb605c2f7a4eb19d388968dae0618 authored almost 4 years ago by Timo Sachsenberg <[email protected]>

Still QScore adjusting...

a7471c3fbdd1eda94e871e54c7868edd8eedd6d8 authored almost 4 years ago by kyowonjeong <[email protected]>

charge score added!

d4a4bba4a17550ca4021eef2a4e9648b8c95eb07 authored almost 4 years ago by kyowonjeong <[email protected]>

charge score added!

d995239c3fc7c74843432857fed16a2a54027fd7 authored almost 4 years ago by kyowonjeong <[email protected]>

Merge branch 'develop' of https://github.com/OpenMS/OpenMS into feat/aut509

34ab5783036e8150a2a9562d1625c47bef55850c authored almost 4 years ago by Ahmed Khalil <[email protected]>

[API,CI] updating TransitionTSVFile::createPeptide_(..) to handle SumFormula MetaValue, merging travis ci build scripts

f3c41925725b3657c7cae01ba130cadffd57c55b authored almost 4 years ago by Ahmed Khalil <[email protected]>

QScore relative intensity used

79b2cb872ab128c6966825f7364563731332977a authored almost 4 years ago by kyowonjeong <[email protected]>

[REFACTOR] remove some unneeded methods, use std::array instead of c … (#5102)

* [REFACTOR] remove some unneeded methods, use std::array instead of c array

* trying to remo...

ee70bd4e3a0ae2dcea202f7130cb24f558e55ce5 authored almost 4 years ago by Timo Sachsenberg <[email protected]>

qscore final version + 0.0 parameter bug fixed

5ea31b8cb09ef0a27f056b01261ab01fe83f2f21 authored almost 4 years ago by KyowonJeong <[email protected]>

QScore relative intensity used

6c6dcdb24810fa7f581ad680acebed35eb4bd607 authored almost 4 years ago by kyowonjeong <[email protected]>

Merge branch 'develop' of https://github.com/OpenMS/OpenMS into TV-DIA-table

# Conflicts:
# src/openms_gui/include/OpenMS/VISUAL/TableView.h
# src/openms_gui/source/VISUAL/S...

39e6c533b5ec38112306736f83c48335cd7c3249 authored almost 4 years ago by bielow <[email protected]>

[FEATURE] support opening Wizard results in TOPPView

b29a9e3216230a175d84baff83ddca2fb8657d3a authored almost 4 years ago by bielow <[email protected]>

QScore relative intensity used

70c5d66aa76c2a5733886f814ad28e349c91c395 authored almost 4 years ago by kyowonjeong <[email protected]>

QScore relative intensity used

9b7889f1cde7551cb0566fca1faf085df6f592ca authored almost 4 years ago by kyowonjeong <[email protected]>

[Feature] Add info output to MzMLHandler store (#5101)

* [FEATURE] Add info output to MzMLHandler store

MzMLHandler now prints out how many spectra ...

4201cb84c9e25eae134219b07da1431007de7228 authored almost 4 years ago by Ruben Grünberg <[email protected]>

TopPic output bug fixed..

513b286dc5fdcd1bddc11eedd7ded7557bd8927c authored almost 4 years ago by kyowonjeong <[email protected]>

Merge pull request #5097 from OpenMS/feature/expSubsetPLFQ

[FEATURE] allow subset of exp design to be given to PLFQ

2e5e643aaa6b592820b5bae1a34e77cb8b1f9141 authored almost 4 years ago by Julianus Pfeuffer <[email protected]>

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

9835d1d92c283f213f7ee7973a2e2ccbb109c762 authored almost 4 years ago by jpfeuffer <[email protected]>

[NOP] style

9ae69b06c8ac46a4b62f4921b15446a9cb3c128d authored almost 4 years ago by jpfeuffer <[email protected]>

FLASHIda coloring algorithm implemented.

9fbd7d29b0c458267f2de6358aac08b4ec735947 authored almost 4 years ago by kyowonjeong <[email protected]>

added underlying motivation

427d5c1333f10e2432512f39cc4374baf2141eb6 authored almost 4 years ago by Chris Bielow <[email protected]>

Code review and more logging improvements

46abc09cb909bf755f68d7d9d904b3729dfaebf1 authored almost 4 years ago by jpfeuffer <[email protected]>

TOPPView SpectraID view fixes (#5100)

* fixes empty cells in IDView table for common metavalues

* fixes #5098

18dfc487d31ebcbec083bc657b794fab021015f6 authored almost 4 years ago by Chris Bielow <[email protected]>

FLASHIda.cpp and .h take max Q value for each mass and mz

mass and mz are used to find consecutive masses..

edfbd5eb1ed49fada08c31fad970144f66b6ab61 authored almost 4 years ago by kyowonjeong <[email protected]>

Merge branch 'develop' of https://github.com/OpenMS/OpenMS into TV-DIA-table

388009c94e5cbff45da453e50f02cdf8e17b459b authored almost 4 years ago by bielow <[email protected]>

FLASHIda.cpp oiptimized

23b5c202cf3995cc2f81370aad8487406af99acb authored almost 4 years ago by kyowonjeong <[email protected]>

fixes #5098

985ea7e48d72512b1c2563634b299f1b47c3961d authored almost 4 years ago by bielow <[email protected]>

fixes empty cells in IDView table for common metavalues

5399c69f19dca4dfd7d7c0a63c97505ed353b6b3 authored almost 4 years ago by bielow <[email protected]>

codefactor

74ebc7195bdb89e8dcb8f9977b64e228f8f60d93 authored almost 4 years ago by jpfeuffer <[email protected]>

[FIX] use config.h instead of compiler definition

f2c44abe5514efa3d831146cbe6074ce6800395f authored almost 4 years ago by jpfeuffer <[email protected]>