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

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 Adduct::toAdductString for ion formatting

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

update FeatureLinkerUnlabeledKD tests

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

add TextExporter IIMN test

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

use Adduct::toAdductString in MetaboliteFeatureDeconvolution

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

add explanation for graph

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

use Adduct::toAdductString in FeatureGrouping

95aa955b43ec860aed33dfcbd9c9b1a7ab4fa6f9 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]>

hash partners mv

7ae057419516d99071a7e13c0fa2c5cdd0f89363 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]>

update TextExporter

4ea6ac4367b665c4c7f95d3e2c6f63b8237dde2c 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 partners mv from all features Group mv

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

annotate IIMN only when necessary

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

use boost graph library

40eb259ca27598bd183f0bdd04ce07e9ba490e02 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]>

update Constants

988133441d18d718c3cd11bae3c4e69c940e5fe6 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]>

add best_ion and partners MVs for FeatureLinkerUnlabeledQT

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

fix TextExporter ConsensusMap header

4b2a56ae739a61b3bc9aa260182515a54283722c 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]>

add linkAdductPartners for FeatureLinkerUnlabeledQT

0b4e5c9c223d774edc06ad4e44f252d5fd399e28 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 Group mv to Constants

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

add annotation network number

5e7924feb26fe2c02f449706b6b9fc0abeb76749 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]>

correct partners and row ID for KD

b6bd87464646e8000327c61048dd08430ad9c869 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]>

remove log

3c742936af5610bce983ff1cb8d8e92c6735a22a 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]>

Replace OpenMS::Map with std::map

52f999cb12512ebe2316f3b93275b03608e2f11b authored over 2 years ago by matteopilz <[email protected]>

new isotope interface working

a4c17c59796c7d06f3657cb20f1a36feca01fe34 authored over 2 years ago by Tom Waschischeck <[email protected]>

fix tests by adding new parameter

d5af4a0a43ea46314d104fc7f0c4139f36230672 authored over 2 years ago by bielow <[email protected]>

new interface for isotopes, only gui

4e8c9025c597c6c96fb38c02d372c526b9473488 authored over 2 years ago by Tom Waschischeck <[email protected]>

Merge pull request #5860 from cbielow/fix_fileTypeSelection

GUI: improvements, mostly better File-save dialogs

621e338ed00cb96723d8a211bef5ec0004bc06fe authored over 2 years ago by Timo Sachsenberg <[email protected]>

copy paste error

6f40c82c24b781f201537b3e355b29ada6475bf9 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

[FIX] add tests and allow Asp/Pro cleavage even for 'no cleavage'

eb69f4aefa3d26cb67ac413131a97b3c4e0b4358 authored over 2 years ago by bielow <[email protected]>

Merge branch 'feature/FLASHDeconv' into feature/FLASHDeconvOnly

c1ba00f8f4477f8afc7561ff39b37e768471f04f authored over 2 years ago by JeeH-K <[email protected]>

fix missing checkboxes, new datastructures for checkbox backend

c02ca516445da2f1189dbc5b6bcf8530478e33a5 authored over 2 years ago by Tom Waschischeck <[email protected]>

fix test

1f8eac74c6122ff0c738bae9241efb8e8beecb59 authored over 2 years ago by bielow <[email protected]>

Update GNPSExport.cpp

Corrections on bold text, code text and ref of MetaboAdductDecharger

3aca99366e0cdc58162722a4e39f1d5769714834 authored over 2 years ago by Efi Kontou <[email protected]>

Docu/iso (#5858)

* [DOC] fix documentation for isotopes

* [DOC] documentation expansion for isotopic patterns

ec3250d20e318cd569356ffee5fd976433b19aa2 authored over 2 years ago by Hannes Roest <[email protected]>

[FEATURE] add `getSaveFilename` function with predefined OpenMS data types for less boilerplate

38e8dad6a6e419b4ac86a666790f3453c6b2a500 authored over 2 years ago by bielow <[email protected]>

move FileTypes out for shorter names

6586e0bec26eee3b4c9dcf6806e2e72690dca1d1 authored over 2 years ago by bielow <[email protected]>

[TEST,FIX] add test and fix a bug in OverlapDetector

42ef18f38b4b0063d2e1c779844fa07d1c5af66f authored over 2 years ago by bielow <[email protected]>

[NOOP] move code

f80350984c731eaf3ba9b70c655ef9701e652b03 authored over 2 years ago by bielow <[email protected]>

[FEATURE] add convenience function to create a Qt file filter from OpenMS filetypes; and read back what type was selected

5c2110c2000f3394f768ec69b622e458c511304e authored over 2 years ago by bielow <[email protected]>

Feature/im pyopenms (#5827)

* add IM Types

* [PYOPENMS] drift time functions

* [PYOPENMS] add tests and function

- ...

dad3146c260d889ebf416b91ac9825b2be97c82f authored over 2 years ago by Hannes Roest <[email protected]>

more detailed error message (#5856)

c26d432c31e94edd74bc67e8dabdbf8fbd92eaff authored over 2 years ago by Timo Sachsenberg <[email protected]>

[DOC] fix documentation for isotopes (#5852)

d5f7935dcb387ead9fd119f7b535c76eb721da5c authored over 2 years ago by Hannes Roest <[email protected]>

fix compile warning

ee54aa77907abc713cafa01bdbe31d7a2850f221 authored over 2 years ago by Timo Sachsenberg <[email protected]>

[release-prep] new version iteration

3ce4524f6279f01eb7dd6520b844a91d9c693546 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

new changelog iteration

f1356f937f048743a20c214b5b7b11610f133964 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Merge pull request #5855 from jpfeuffer/develop

Merge back release into develop

3ea6fc1792bc64fce25e0f511897391ad8e16aad authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Merge branch 'release/2.8.0' into develop

f73a969004847f37f15500893a2d57253b338135 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Merge pull request #5846 from OpenMS/feature/nosharePYOMS

[FEATURE] No share option for pyopenms

4cd74a93ed5626ecc51ead0b90d48358e70997ac authored over 2 years ago by Julianus Pfeuffer <[email protected]>

fix warning

9fce010a3afd2f3d4cf9ab221e145998b85dfa45 authored over 2 years ago by Timo Sachsenberg <[email protected]>

Update DataValue.h (#5850)

fix copy-paste error in documentation

2e223ba7eea73e0d36fa2777e1753215c124162a authored over 2 years ago by Hannes Roest <[email protected]>

updated authors and changelog

d1b7809494e82712ed0b32493f2625106a09c47b authored over 2 years ago by zhuchcn <[email protected]>

fix (PeptideIndexing): variable name was spelled wrong

fc3c0a9fb0a22283483c2b0ee93334433665af1e authored over 2 years ago by zhuchcn <[email protected]>

fix (PeptideIndexing): updated in upstream, so changes were not added to the correct place of `allow_nterm_protein_cleavage`

575643e729948dd21bc378b6c512c3d58303d677 authored over 2 years ago by zhuchcn <[email protected]>

Merge pull request #5795 from khuenm/mutualInfoSparse

[PERFORMANCE] Rewrite mutual information calculation and remove MIToolbox

10bd462b115f2297cb62f0fe883e3fd2ed63459e authored over 2 years ago by Chris Bielow <[email protected]>

Merge pull request #5848 from OpenMS/jpfeuffer-patch-7

[FEATURE] strip files in installers with cpack

47fc5dd262f070362f4e7f4157b98b52efd990ea authored over 2 years ago by Chris Bielow <[email protected]>

[FEATURE] strip files in installers with cpack

9a206e69fcb9c55239c5ef432ab5688e2724b1c3 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

[FEATURE] No share option for pyopenms

943a66f9fb9d9cb7502cc246dba7086ded8b5224 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

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

957b8a43f4b6ad401e9a8a511d9966aa99e46e96 authored over 2 years ago by Timo Sachsenberg <[email protected]>