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

Merge pull request #5887 from bernt-matthias/update-unimod

Update unimod

2765546ccc1a656bcee9002a85f2a30d6d4cb6a8 authored over 2 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #5883 from Waschi97/fix/TheoSpecDialog

Fix TheoreticalSpectrumGenerationDialog - closes #5787

82c847f41a83d72d34b7951d0f82b72ddd0bb276 authored over 2 years ago by TomW <[email protected]>

Major change in MS2 deconvolution

- added isotope pattern based harmonic detection : both in mass bin and peak levels
- changed the...

c934181a7d42ef0de7c667beccc78810047a5455 authored over 2 years ago by kyowonjeong <[email protected]>

added changes to CHANGELOG

17449fd7e606df2578f89d7c5eadf52701c5d929 authored over 2 years ago by Tom Waschischeck <[email protected]>

Major change in MS2 deconvolution

- added isotope pattern based harmonic detection : both in mass bin and peak levels
- changed the...

4fb05bc59ca01637e3523cac60bf2769fa4e3b32 authored over 2 years ago by kyowonjeong <[email protected]>

add more modifications

xref https://github.com/OpenMS/OpenMS/pull/5887#issuecomment-1059098323

5bebe8b9a526ae7cf69142430267f3882dc6a650 authored over 2 years ago by Matthias Bernt <[email protected]>

Update src/openms/source/ANALYSIS/DECHARGING/ILPDCWrapper.cpp

Co-authored-by: Hannes Roest <[email protected]>

4dfa5e10896270a255a459baf800444bed1a6a4e authored over 2 years ago by Matteo Pilz <[email protected]>

Update src/openms/source/ANALYSIS/DECHARGING/ILPDCWrapper.cpp

Co-authored-by: Hannes Roest <[email protected]>

23772d2f708362dac6eab9e19b91d6046275a4fa authored over 2 years ago by Matteo Pilz <[email protected]>

removed recently added elements with unknown / zero abundance

50155fd768c3f8b07560a3beb01b0bfb6a771d93 authored over 2 years ago by Timo Sachsenberg <[email protected]>

[FIX] bugfixes / compile fixes

ab60e312f9b84d701e9407ecc69cca74607fcd71 authored over 2 years ago by Hannes Roest <[email protected]>

update VS version in pyoms GH actions

b2a35be4c747edb19473bc0dc964b2f69d2e0ae0 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

fix debug statement in gh actions

a1a504c565b7772082e5effc72e2662920d958ea authored over 2 years ago by Julianus Pfeuffer <[email protected]>

[FIX] bugfix (new behavior)

6aeecd7096d5d8e14b9b05d27681ae6993d39416 authored over 2 years ago by Hannes Roest <[email protected]>

[FIX] compile fixes

52717546115744515c4ee319ffa784470029d628 authored over 2 years ago by Hannes Roest <[email protected]>

na seq only info from parameter desc to comment

f3fb8e2306d4830235a54b588c535c05ba0599b3 authored over 2 years ago by Tom Waschischeck <[email protected]>

[FIX] compile fixes for DigestionEnzymeDB

b19fa09aa01cb4c0b2f2e7db1df688e7dd8b9f4b authored over 2 years ago by Hannes Roest <[email protected]>

parameter description for nucleic acid only ions updated

d28f662cbb83a6a24a5350cff5810927e1390665 authored over 2 years ago by Tom Waschischeck <[email protected]>

[FIX] conversion providers for CVTerm-maps

126f3f9fe4e81ea0853fab6e318ffbb1bc5de995 authored over 2 years ago by Hannes Roest <[email protected]>

[FIX] compile fixes, remove leftover Map

2e818759e1b51c75f5d8e704886d9fa76c94080b authored over 2 years ago by Hannes Roest <[email protected]>

[FIX] compile fixes

8401b5580844261bb9902af2557dad72101e3d0d authored over 2 years ago by Hannes Roest <[email protected]>

[FIX] compile fixes

e00bf84ff8cc55daa0fed476950e17852960c350 authored over 2 years ago by Hannes Roest <[email protected]>

add cusom modifications

f62172e727dc7825787a307399b212c5407c7be1 authored over 2 years ago by Matthias Bernt <[email protected]>

update unimod.xml

fixes https://github.com/OpenMS/OpenMS/issues/5874

caa230bd1a2834f3abc4f15bbe8d844270957db8 authored over 2 years ago by Matthias Bernt <[email protected]>

check if vertex in graph with map

0df8bc211bea4260cbbd01925162de1a92011515 authored over 2 years ago by axelwalter <[email protected]>

Replace OpenMS::Map with std::map

45bcc8a90deeada033f8201d351f79b5005abdb2 authored over 2 years ago by matteopilz <[email protected]>

parameter description for peptide only ions updated

f5c1f5be5c713932122869315a47f8e37bd33409 authored over 2 years ago by Tom Waschischeck <[email protected]>

hiding instead of disabling, automatic resizing, added myself to authors

028e83c2f4d7a7926b17721b9fbc1cbaf01677ce authored over 2 years ago by Tom Waschischeck <[email protected]>

simplify comparison

93edddbbb0fe1a44886c7b7608bea872257dffca authored over 2 years ago by axelwalter <[email protected]>

use unordered_map for partners

ae8ba1680c30c92ca0c59827c8afe5dbf5726bb1 authored over 2 years ago by axelwalter <[email protected]>

more efficient partner annotation

7f6b23e3ffce6d830c9b761896ac765b39f63e06 authored over 2 years ago by axelwalter <[email protected]>

improve documentation

85ad1cad13da65b66d2352312496b6e10ee88635 authored over 2 years ago by axelwalter <[email protected]>

Merge pull request #5886 from OpenMS/feature/remove_empty_string_restrictions

[FIX, BREAKING] replace empty strings in restrictions with meaningful value

58ac2727f251f14febb1e2ddc063472f4113ee43 authored over 2 years ago by Timo Sachsenberg <[email protected]>

new signal slot syntax

2d6345e44c82cb7cfa00ddf2d6bdb5aa04fd6324 authored over 2 years ago by Tom Waschischeck <[email protected]>

RNA spectrum generation interface with working backend, checkbox datastructures to cpp, return const ref

3495160f80dc6a1b8a5741b774c727d25acb336f authored over 2 years ago by Tom Waschischeck <[email protected]>

Major change in MS2 deconvolution

- added isotope pattern based harmonic detection : both in mass bin and peak levels
- changed the...

62e1340cebc76f1680c5444d34fe4278dbfca99f authored over 2 years ago by kyowonjeong <[email protected]>

Merge remote-tracking branch 'upstream/remove_Map' into remove_Map

b5167e701ccded99b7ed583ce92a407edadcf524 authored over 2 years ago by matteopilz <[email protected]>

Replace OpenMS Map with libcpp.map

b3dc3ffe55bc09280e6e7be8d5eb41b96c607d03 authored over 2 years ago by matteopilz <[email protected]>

Merge pull request #5863 from eeko-kon/patch-2

Update GNPSExport.cpp

f7828b04a3ebe5b2d6d2fefb815aaa7c05090569 authored over 2 years ago by Timo Sachsenberg <[email protected]>

remove Map_test

5a101a878b08dbaef862b3604319936e8c7957ec authored over 2 years ago by Timo Sachsenberg <[email protected]>

Merge remote-tracking branch 'origin/develop' into remove_Map

bed2a43b92c55536581e508225848eaa60fe9330 authored over 2 years ago by Timo Sachsenberg <[email protected]>

Update TransformationModelLinear.cpp

b2cfc1eb966cfc6ab49fe70253678e72732f4951 authored over 2 years ago by Timo Sachsenberg <[email protected]>

Merge remote-tracking branch 'upstream/remove_Map' into remove_Map

7f09d4de25e995e7e55a449650a7a0d4a2b7f5a2 authored over 2 years ago by matteopilz <[email protected]>

Replace OpenMS Map with libcpp.map

1b48749cdc1f08c93c3547e6689596c099fbcd05 authored over 2 years ago by matteopilz <[email protected]>

forgot some tests

0a022ee5fae09de0096c764b7430f9d1d2312431 authored over 2 years ago by Timo Sachsenberg <[email protected]>

update test files

504f6573b43829461203b212cb069d5a3b333364 authored over 2 years ago by Timo Sachsenberg <[email protected]>

use x and y for identity to be consistent

333ebe745bd4b211f0f6ec851bc560db34a2d70d authored over 2 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #5873 from bernt-matthias/idripper-use-prefix

use prefix parameter for out

51e5ef6cd07f1c320486235f2d4dba4fefc23578 authored over 2 years ago by Timo Sachsenberg <[email protected]>

more replacements

ede172ce33db356bb4800035a109a2b34c424e54 authored over 2 years ago by Timo Sachsenberg <[email protected]>

replace empty weight

1536c026417c3ffeaca1a17342b1b4eba38a2d21 authored over 2 years ago by Timo Sachsenberg <[email protected]>

Update src/openms/source/ANALYSIS/MAPMATCHING/FeatureGroupingAlgorithmKD.cpp

Co-authored-by: Timo Sachsenberg <[email protected]>

5f6fb632c4ebc70788cb06f30666c83a709941cb authored over 2 years ago by axelwalter <[email protected]>

add explanation for graph

90fc28300520f9f062779d6fee87fd117f3983db authored over 2 years ago by axelwalter <[email protected]>

add Adduct::toAdductString for ion formatting

44c87c73cf9c59813e70ef241bf4214e163974a9 authored over 2 years ago by axelwalter <[email protected]>

use Adduct::toAdductString in FeatureGrouping

95aa955b43ec860aed33dfcbd9c9b1a7ab4fa6f9 authored over 2 years ago by axelwalter <[email protected]>

add TextExporter IIMN test

60f0b36565a34465d9480017983571b61e4919cf authored over 2 years ago by axelwalter <[email protected]>

rename Constant BEST_ION to IIMN_BEST_ION

76076cbf2cb38fc0659d010d372106c2b85bcfad authored over 2 years ago by axelwalter <[email protected]>

update FeatureLinkerUnlabeledKD tests

ff072159673c53e1979d9abdde55736a5a78ff84 authored over 2 years ago by axelwalter <[email protected]>

use Adduct::toAdductString in MetaboliteFeatureDeconvolution

1b6c64182e7d90e1f1aaedadedc490182cd79b5f authored over 2 years ago by axelwalter <[email protected]>

TextExporter export best_ion and partners mv from ConsensusMap

0a01bae978e5e46ca891318961230c589e095202 authored over 2 years ago by axelwalter <[email protected]>

use boost graph library

40eb259ca27598bd183f0bdd04ce07e9ba490e02 authored over 2 years ago by axelwalter <[email protected]>

add linkAdductPartners for FeatureLinkerUnlabeledQT

0b4e5c9c223d774edc06ad4e44f252d5fd399e28 authored over 2 years ago by axelwalter <[email protected]>

best ion as meta value for FeatureGroupingAlgorithmKD

68b6390f4abaefdcc286f2ae76e1cf586e05fa46 authored over 2 years ago by axelwalter <[email protected]>

add partners mv from all features Group mv

dfc2fea4e1e9ac9cca6248df1e2240c3336e150c authored over 2 years ago by axelwalter <[email protected]>

update TextExporter

4ea6ac4367b665c4c7f95d3e2c6f63b8237dde2c authored over 2 years ago by axelwalter <[email protected]>

annotate IIMN only when necessary

5fb3e15d30e43c85de4d945dc63add26fb8a4e26 authored over 2 years ago by axelwalter <[email protected]>

add dc_charge_adducts mv to Constants

2838a12ff3c4c80b204949586d5e4d8b0a2c0717 authored over 2 years ago by axelwalter <[email protected]>

update Constants

988133441d18d718c3cd11bae3c4e69c940e5fe6 authored over 2 years ago by axelwalter <[email protected]>

add annotation network number

5e7924feb26fe2c02f449706b6b9fc0abeb76749 authored over 2 years ago by axelwalter <[email protected]>

correct partners and row ID for KD

b6bd87464646e8000327c61048dd08430ad9c869 authored over 2 years ago by axelwalter <[email protected]>

hash partners mv

7ae057419516d99071a7e13c0fa2c5cdd0f89363 authored over 2 years ago by axelwalter <[email protected]>

add Group mv to Constants

bfa47d65c6d5213524125368730fed41e6b5b879 authored over 2 years ago by axelwalter <[email protected]>

fix TextExporter ConsensusMap header

4b2a56ae739a61b3bc9aa260182515a54283722c authored over 2 years ago by axelwalter <[email protected]>

remove groups mv after processing

9a8e08dba41f33c35be41a5c793399a3801b0f80 authored over 2 years ago by axelwalter <[email protected]>

add FeatureGroupingAlgorithm::linkAdductPartners and implement in FeatureLinkerUnlabeledKD

60f797150cc0225e9695097f937550b4abb28189 authored over 2 years ago by axelwalter <[email protected]>

store Group mvs as vector in partners mv

081bb3aa41dfd862fdc91bc05546466ecebe545d authored over 2 years ago by axelwalter <[email protected]>

add best_ion and partners MVs for FeatureLinkerUnlabeledQT

0ce00acb8a5d421b949cc76df5cbd93055842019 authored over 2 years ago by axelwalter <[email protected]>

remove log

3c742936af5610bce983ff1cb8d8e92c6735a22a authored over 2 years ago by axelwalter <[email protected]>

use own connected components approach

3764ab3d07b1770b462e8956159467159c52711c authored over 2 years ago by axelwalter <[email protected]>

add best ion formatting for pos ions

49b704c42cf2d9484589882b9b6b474479e1092d authored over 2 years ago by axelwalter <[email protected]>

Merge pull request #5872 from bernt-matthias/test/fix-msfragger

fix msfragger test

75c3c795861255e94314a6966c95e3e8585d714a authored over 2 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #5881 from cbielow/fix_logscale

TOPPView: fix log scale display (caused by negative intensity in visible area)

5796cba21b227952c79d8d8e5572fca0d13f3eb0 authored over 2 years ago by Timo Sachsenberg <[email protected]>

const ref loops and some design

3ed87f9370fb5228721ea08729822b77f8198c3a authored over 2 years ago by Tom Waschischeck <[email protected]>

design

34770980a0d72f276e87d590b7bdba49158e78c2 authored over 2 years ago by Tom Waschischeck <[email protected]>

fix log scale display (caused by negative intensity in visible area)

ef34f8b222ed440898494126d5919f73430e1fce authored over 2 years ago by bielow <[email protected]>

TheoSpecDialog as member of TOPPViewBase

578dd031401d84c9a06407e3d0074a8512e41c22 authored over 2 years ago by Tom Waschischeck <[email protected]>

catching corner case to avoid seq fault in MSSpectrum

bbeb60c91bd3c10c31d2e748ac5d606c51275ca5 authored over 2 years ago by Tom Waschischeck <[email protected]>

Merge branch 'develop' into fix/TheoSpecDialog

b0aead61a8dab6032e6ec6b918a4cfee58cf5d22 authored over 2 years ago by Tom Waschischeck <[email protected]>

commenting

a38fc6223e4bfbf4f649e86d387823c198cb2c19 authored over 2 years ago by Tom Waschischeck <[email protected]>

Merge pull request #5878 from hroest/fix/bugfix_py

[FIX] do not clear data arrays when setting peaks

11148e0248a5a9370707e7b88ee639596accc734 authored over 2 years ago by Timo Sachsenberg <[email protected]>

Update src/tests/class_tests/openms/source/HiddenMarkovModel_test.cpp

Co-authored-by: Hannes Roest <[email protected]>

8d440a9c12c528e727c67c343a662c91adbfca9e authored over 2 years ago by Timo Sachsenberg <[email protected]>

Update src/tests/class_tests/openms/source/SeedListGenerator_test.cpp

Co-authored-by: Hannes Roest <[email protected]>

33004be0e45a4e24e94884a2566cd1572b4c1c20 authored over 2 years ago by Matteo Pilz <[email protected]>

[FIX] do not clear data arrays when setting peaks

- fixes bug #5876
- set_peaks() no longer clears data arrays, only clears the peak data

7215fc74afb34a7ddb8b06f91b19ad20264d0ab8 authored over 2 years ago by Hannes Roest <[email protected]>

Merge pull request #5853 from zhuchcn/fix/peptide_indexer_no_cleavage

[FIX] PeptideIndexer support 'no cleavage' with full specificity

df159dbe45b4143500715974bc60aa4ab1fd1226 authored over 2 years ago by Chris Bielow <[email protected]>

update doc

eb88e083673b4f130138511b10a5a62747ce3f58 authored over 2 years ago by Matthias Bernt <[email protected]>

spectrum generation and corresponding errors within dialog

893e5f4b2fd5420f7ebcde903fbf7356cbe4fa6a authored over 2 years ago by Tom Waschischeck <[email protected]>

use prefix parameter for out

d371c85f755fe54f939f33fc037fa0cf5576134e authored over 2 years ago by Matthias Bernt <[email protected]>

reformatting

646e8317174110e0af031643c52914743d9f5731 authored over 2 years ago by Matthias Bernt <[email protected]>

Replace OpenMS::Map with std::map

644398d26414be8a0b1212070625a8a7a5f311f6 authored over 2 years ago by matteopilz <[email protected]>

Replace OpenMS::Map with std::map

9e9e753fe3892765fc5c4040d4b6ce19aacd8c26 authored over 2 years ago by matteopilz <[email protected]>

Replace OpenMS::Map with std::map

7fa17753405e870e351a225b4f7e633b6f507c24 authored over 2 years ago by matteopilz <[email protected]>

fix msfragger test

add missing parameter `-license yes`

ed6b75a0d013ab66f993b8b543d5040ec9ff93ab authored over 2 years ago by Matthias Bernt <[email protected]>