Ecosyste.ms: OpenCollective

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

github.com/OpenMS/OpenMS

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

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]>
[FEATURE] cut filepath from DEBUG logs. Add debug info to PLFQ. Add filtering warning.

49c76132c37d5968972edd110dcf20d8af8afca1 authored almost 4 years ago by jpfeuffer <[email protected]>
[FEATURE] allow subset of exp design to be given to PLFQ

c86b3019f4e950617856dbe701c98a462b974c63 authored almost 4 years ago by jpfeuffer <[email protected]>
FLASHIda.cpp oiptimized

564b6e436976a4d7e992a4fa8e1cbee65233a8e8 authored almost 4 years ago by kyowonjeong <[email protected]>
remove XML file and store data locally in ResidueDB (#5092)

* remove XML file and store data locally in ResidueDB

* fix indentation of certain lines

*...

49383fcf6e7e1d2f9a5574bee5d86e03c6f17542 authored almost 4 years ago by Timo Sachsenberg <[email protected]>
Fix: Bug in MRMFeatureQCFile (#5094)

* fix, tests: bug in MRMFeatureQCFile where an out of range error for an empty vector would be t...

3422ac3bf2effd8e3c2d44f385a8bf5b58d3ed52 authored almost 4 years ago by Douglas McCloskey <[email protected]>
FLASHIda.cpp oiptimizing

0a4b35851b40b2fe04c24cd9140cd54a304a5768 authored almost 4 years ago by kyowonjeong <[email protected]>
FLASHIda.cpp oiptimizing

c40432135215170c970fdd41fbf0593461e970f4 authored almost 4 years ago by kyowonjeong <[email protected]>
FLASHIda.cpp oiptimizing

2e34d6a2633006ce994bffff1ade602059bf36b4 authored almost 4 years ago by kyowonjeong <[email protected]>
QScore.cpp train att write added ..

af15ea42a4429d51df03bd645102b23ef3552e69 authored almost 4 years ago by kyowonjeong <[email protected]>
fix: bug in AbsoluteQuantitation (#5093)

* fix: changed the term to apply the dilution factor to

* tests: added tests for dilution fac...

0ba6a15f285fae7ac2d1229cab36f529d072f016 authored almost 4 years ago by Douglas McCloskey <[email protected]>
SQL: common ID for sqMass and OSW (#5089)

* create common UID for sqMass and OSW file when generated by OpenSwathWorkflow

* [FIX] preve...

41c2c94ac2041b3043ddcfb7f78a7f255b07d7c3 authored almost 4 years ago by Chris Bielow <[email protected]>
[REFACTOR] turn inheritance from QDataTime into private composition (#5082)

turn inheritance from QDataTime into private composition

9b2d373e6d308a1ed101a0419c0e064247af59f8 authored almost 4 years ago by Timo Sachsenberg <[email protected]>
fix py

0f79f4ac707444c10e7ba12942476c5353e44d0a authored almost 4 years ago by bielow <[email protected]>
fix compile error

d58b33aac1c452637ec9f49746e52a1a7fce27cb authored almost 4 years ago by bielow <[email protected]>
fix compile error

25b7dfe7b17d76f71ab449f718f59c9d4c0d13fd authored almost 4 years ago by bielow <[email protected]>
revive good error message by making it dependent on the template type -- otherwise the static_assert will trigger even without instanciation!

3672a940b1900e08ca97ea1115fa95c54fcddd89 authored almost 4 years ago by bielow <[email protected]>
fix pyOpenMS bindings

28421fc4723cea4197cb4741b6f2e8d2439adbe1 authored almost 4 years ago by bielow <[email protected]>
Merge pull request #5084 from jpfeuffer/feature/betterDebugPLFQ

[FEATURE] Better debug messages and values.

44ed5efe027bfce51c816dd203805afbaff0f909 authored almost 4 years ago by Julianus Pfeuffer <[email protected]>
attempt to fix weird compile error

1b1e11741568e8a678e9846d982f7d451f0b3fdd authored almost 4 years ago by bielow <[email protected]>
QScore.cpp train att write added ..

b59020229744c8aba7e0b893b26ad3b1ca127178 authored almost 4 years ago by kyowonjeong <[email protected]>
QScore.cpp train att write added ..

7802bf854fab45b96dfd5090424ab52780f09684 authored almost 4 years ago by kyowonjeong <[email protected]>
refactor sign-bit removal for save storing to sqlite integer type (if using stringified insert statements...)

b12dcf622ef8664ce5cb17a7ea330325a5bca325 authored almost 4 years ago by bielow <[email protected]>
QScore.cpp train att write added ..

5305a64c97d9714c491e1470eaa07a85e2e512e3 authored almost 4 years ago by kyowonjeong <[email protected]>
remove unneeded meta value

f5c248c7d7846f7124740d9584f00cdc93a17a6d authored almost 4 years ago by Timo Sachsenberg <[email protected]>
[FEATURE] add common unique identifier to sqMass and OSW files

[TEST] fix some testing bugs (exp == exp, instead of exp==exp2) and make tests faster by removing...

b89a4f25c50817118be54eb91b9e87bd4d06e331 authored almost 4 years ago by bielow <[email protected]>
Added min_mass_count parameters in FLASHIda.cpp FLASHDeconvAlgorithm.cpp

705a00cfa3cba6a6ea4206835d09352e26def100 authored almost 4 years ago by kyowonjeong <[email protected]>
[FIX] prevent SqlConnector from silently creating an sqlite file if the file does not exist and not reporting an error, when all we wanted was to read from the file

522732d8be7d85ede245870bdd3291aad1bd1e74 authored almost 4 years ago by bielow <[email protected]>
Comment added to all .h (Except for QScore.h - what should I do with this will be determined soon...)

5a196e730f7f911e9b2523007bf908a2d6587f23 authored almost 4 years ago by kyowonjeong <[email protected]>
create common UID for sqMass and OSW file when generated by OpenSwathWorkflow

52a3e7c2ad4afff5c79b1378c39151cdce7208db authored almost 4 years ago by bielow <[email protected]>
Merge pull request #5085 from cbielow/TV-DIA-table

TOPPView convenience (commandline, locking) and DIA plotting

551bdcd8541e32e4d55fd7ed710482773716fee4 authored almost 4 years ago by Timo Sachsenberg <[email protected]>
fix conversion warning

4fe5ffe3e6b58b23901b50e110bffcfa5c58ec1b authored almost 4 years ago by bielow <[email protected]>
fix bugs

e03e566a316d505a801f84dde6027cfe25283a8b authored almost 4 years ago by bielow <[email protected]>
fix conversion error

095141c0234ea8c6844f98382958612170cd248f authored almost 4 years ago by bielow <[email protected]>
fix aggregate init for std::array -- C++ defects for the win... :(

e94c4581fa993cd412ff71598a57d1ff157c02a3 authored almost 4 years ago by bielow <[email protected]>
fix codefactor

6ac8c70e935e2d288e66e01f915ad3bf3b7ebaa1 authored almost 4 years ago by bielow <[email protected]>
automatic tab selection and enable/disable

e5070a15591623c9cf97f19f4e9b75d5e7d05fd0 authored almost 4 years ago by bielow <[email protected]>