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

hopefully fixed https://github.com/OpenMS/OpenMS/issues/5714

871a48ee30cc3bed7756de1a42db40e909360985 authored almost 3 years ago by bielow <[email protected]>

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

# Conflicts:
# src/openms_gui/include/OpenMS/VISUAL/LayerDataBase.h
# src/openms_gui/include/Ope...

ca16a545d45e5882b8936012b01d963990e77fe8 authored almost 3 years ago by bielow <[email protected]>

- replace manual switching of layer type with Visitor pattern

- cleanup of LayerStatistics (separate model from view)
- visualization improvements (show ints a...

f2268cd4e426e6d64b832efd58a3d0d03dc512b6 authored almost 3 years ago by bielow <[email protected]>

[REFACTOR] New RangeManager (#5703)

* refactor RangeManager

* add Ranges to all Layer types

* Fix bug: set only m/z visible ar...

acaba98aae3c363364f38d0a3dd44e17d714a2b7 authored almost 3 years ago by Chris Bielow <[email protected]>

MapAlignerPoseClustering: print error message and fall back to identity if no data provided (#5711)

* print error message and fall back to identity if no data provided

* Update MapAlignerPoseCl...

5ebaf1dd7f2d3456f6a51687e815e1f783011df1 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

fix (#5712)

574e5c45d04427b3f9a7d2f6ee760ac0ba2f94ba authored almost 3 years ago by Oliver Alka <[email protected]>

use on disc experiment (#5709)

* use on disc experiment

* Update GNPSExport.cpp

6a7a38b0e908e85c9ce54d9d206c020495c910d2 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

Update .clang-format

b49dcf184ff5e8b5572256f882f2a3294e08b855 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

Bug fixed in precursor registration

+ isolation windows crawling implemented in FLASHIda

8836d5ac6a355fcfbf6908f389e85f352e941db6 authored almost 3 years ago by KyowonJeong <[email protected]>

fix chromatogram range

221a8d1aef077a3680f4290f17ab1b3f31112e6f authored almost 3 years ago by bielow <[email protected]>

remove some remnants

c8f346d9705d21cdc1d36aaf9b92622a248cbfc4 authored almost 3 years ago by bielow <[email protected]>

fix python bindings (wrap doc RANT!!)

currently our pyopenms build will include any CPP it finds, even its it not in the build system.....

3dffb3613fd807cf5397dbd479ddcf36e0bc2760 authored almost 3 years ago by bielow <[email protected]>

fix python bindings

90e680301ce859b4172c927db9ed5b8d801e8f69 authored almost 3 years ago by bielow <[email protected]>

fix pyOpenMS build on Windows with multiple threads by adding `if __name__ == '__main__':`. Avoids infinite recursion for spawning new processes

c773dc0951f86e4850bfa5480de3f9ddb77ff065 authored almost 3 years ago by bielow <[email protected]>

Update PULL_REQUEST_TEMPLATE.md

d124416d7654e68762cefb8103dfa3d8ba3ceec8 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

fix range for cf

5ceea76f6ef4dfe6a9e20413d80f8b7e6076e9ba authored almost 3 years ago by bielow <[email protected]>

fix pyopenms script for Windows

dd6e95e96e36d50848ad95b9b2f90231b3b114a5 authored almost 3 years ago by bielow <[email protected]>

adapt clang format (#5706)

19321c9005290c684aa7da2a686965dc3f94bf8e authored almost 3 years ago by Timo Sachsenberg <[email protected]>

fixes, more docs from review

2e9f22df672a3d8e205680f7c7fb8f0817ee1969 authored almost 3 years ago by bielow <[email protected]>

[FEATURE] add python compatible get precursor spectrum (#5704)

* [FEATURE] add python compatible get precursor spectrum

* Update MSExperiment.pxd

6005e498335b6ce95ac51ce3590bdc14ea5fd23b authored almost 3 years ago by Timo Sachsenberg <[email protected]>

[ADD] GitHub Action Clang Format (#5577)

* test_clang_format

* Add path to actions_checkout

* [FIX] style

* Ren...

6612e16d9fd8f38af415a88cb28135beb8a7d50a authored almost 3 years ago by Oliver Alka <[email protected]>

extend test; fix last remnants

ca25bacdb28db9b65871051232fedc71231495c2 authored almost 3 years ago by bielow <[email protected]>

Fix bug: set only m/z visible area, not mz+intensity

f1aff7e94b9c504c7697ca8a8a985830b5bad3a3 authored almost 3 years ago by bielow <[email protected]>

add Ranges to all Layer types

3d0b984a3bb762bcf1129bd2dd0b84d31e00ac8e authored almost 3 years ago by bielow <[email protected]>

fix imputation bug on single peak mass traces (#5702)

72ff959c8050b23a607d96f0bb043677621956ac authored almost 3 years ago by Timo Sachsenberg <[email protected]>

Correct a-B fragment masses for DNA (#5587)

* [fix] correct a-B ion masses for deoxy ribo nucleotides

* [fix] fix bone-headed syntax erro...

0810ebf7269532e6bbef7acc0114d89cd3ac0c44 authored almost 3 years ago by Samuel Wein <[email protected]>

refactor RangeManager

66d5fe3ddc58703811769fad8279b7222097120e authored almost 3 years ago by bielow <[email protected]>

[INTERNAL] OMSFileStore: wrap SQLite interaction in transactions to improve runtime

a8150b3ef0af9e2b99d9a7e803c821b469d8a2db authored almost 3 years ago by Hendrik Weisser <[email protected]>

[FIX] fixed merge error in (Metabolite)FeatureDeconvolution

1536f259b0e8b61b19a9a2f8ea8f6180dad977a8 authored almost 3 years ago by Hendrik Weisser <[email protected]>

Merge branch 'idfile-integration' of https://github.com/hendrikweisser/OpenMS into idfile-integration

8f93f1f52de7716a803cc9214a6fb0d364fe7d75 authored almost 3 years ago by Hendrik Weisser <[email protected]>

[INTERNAL] store prepared SQL queries in 'OMSFileStore' to avoid recreating them, improve runtime

a9a6f1440b87921a9edaa7af00237f7282ae4fa3 authored almost 3 years ago by Hendrik Weisser <[email protected]>

[FEATURE] increased fault tolerance in 'IdentificationDataConverter::importIDs' to allow converting problematic idXML

fd184779e5970aba01d1ebb91634d2608d720c15 authored almost 3 years ago by Hendrik Weisser <[email protected]>

Merge branch 'develop' into idfile-integration

c75d04657b279b499ce0f96bb9edf8784353e387 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

Bug in mass determination... fixed and being tested

9cd4ff2dd1f1cb5d70db6e38e89a90c0d2385daf authored almost 3 years ago by KyowonJeong <[email protected]>

New harmonic removal added (after deconvolution, in monoisotopic mass level) in FLASHDeconvAlgorithm.cpp removeHarmonics function

ba3c536e3475badc4d782c2cf376b300e496a0f6 authored almost 3 years ago by KyowonJeong <[email protected]>

New harmonic removal added (after deconvolution, in monoisotopic mass level) in FLASHDeconvAlgorithm.cpp removeHarmonics function

0b55bd659f1cb87de0529daba05026eaa1f915ea authored almost 3 years ago by KyowonJeong <[email protected]>

[INTERNAL] use function 'addMetaValues' where appropriate

a836527e6b65fde46e686ed24a7e85dec0d4eee0 authored almost 3 years ago by Hendrik Weisser <[email protected]>

[COMMENT] removed unhelpful comment

a270793a7b2ee4f7ae8a66cf6336a1f1c21b90e7 authored almost 3 years ago by Hendrik Weisser <[email protected]>

Merge pull request #5696 from cbielow/layer_refactor

Layer refactor #2

ce6a7b71486121ab9b902e0e65e8ce4f6be21126 authored almost 3 years ago by Chris Bielow <[email protected]>

fix include

e1653b1ca792d12964e67fc5f62d9ee5d307b60d authored almost 3 years ago by bielow <[email protected]>

add missing header for gcc/clang

4de63c8be5f2d6fe2b05a19e015ff0ac732fae5f authored almost 3 years ago by bielow <[email protected]>

Revert "simplification"

This reverts commit c1bf0a2fb2b26f6772efbbc7c9a26234ec98b931.

e94c30151730f84304375083ead4fd39ab145742 authored almost 3 years ago by bielow <[email protected]>

simplification

c1bf0a2fb2b26f6772efbbc7c9a26234ec98b931 authored almost 3 years ago by bielow <[email protected]>

avoid superfluous virtual keyword

e0cdd47afcb5b5e9192ea68cf10049d73bd44719 authored almost 3 years ago by bielow <[email protected]>

precompute end. much faster

6d5382e1225f7479443e9eed090d55f68f783c22 authored almost 3 years ago by bielow <[email protected]>

remove needless extension of range (recalculate_ranges_ already extends by 4%)

f84866042066791f5441439a614f9e02ecbf24cb authored almost 3 years ago by bielow <[email protected]>

noop

83909060f5626c33863cd4bc4bf7aa8ab3424f6d authored almost 3 years ago by bielow <[email protected]>

cleanup ctor

ee7486f22937b8bfe6241744fd0fb9f791d0fd4b authored almost 3 years ago by bielow <[email protected]>

[fix] added 3' phosphate gain for unspecific cleavage of nucleotides.… (#5694)

* [fix] added 3' phosphate gain for unspecific cleavage of nucleotides. This is consistant with ...

e03d5848572027d312fda7cca5540fcfb3062127 authored almost 3 years ago by Samuel Wein <[email protected]>

Hide IsoSpec using pimpl and add some clang-tidy performance fixes on top (#5681)

* cppcoreguidelines-virtual-class-destructor,misc-redundant-expression,performance-trivially-des...

48f80b3cda933c4dc5f2d20444d1cabd58f64d34 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

add convenience function

efad1292147aae1e03c3d71d1e7048f6e87d799a authored almost 3 years ago by bielow <[email protected]>

cleanup unused includes

92fae7ac5c68e19532e555c4a21482a476ea52eb authored almost 3 years ago by bielow <[email protected]>

min/maxIntensity moved into function

5f69702381b1e5b26cf3ecb723c94b9d9e54d1d2 authored almost 3 years ago by bielow <[email protected]>

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

cd9cd790e3d52b4bf063f4f74a0ca2b6fd535365 authored almost 3 years ago by bielow <[email protected]>

shorten code

3c981aea6d27ccc267b28338e67e281af9bfddc9 authored almost 3 years ago by bielow <[email protected]>

Merge pull request #5682 from cbielow/layer_refactor

GUI Layer refactoring -- preparations

42d6def5e466714cb0b9a31b9b1b446d92524bbd authored almost 3 years ago by Chris Bielow <[email protected]>

removing non-FLASHDeconv dependant files

ee800acd8041d110bda1b62233b5091723f8a278 authored almost 3 years ago by JeeH-K <[email protected]>

removing non-FLASHDeconv dependant files

66293bde9c2fdaf96720f4a6c0f9f8f294ebe09b authored almost 3 years ago by JeeH-K <[email protected]>

[DOC] improved doc. on merging in IdentificationData

43d709155681de3e7ddbfa4995e029d70d4e84e9 authored almost 3 years ago by Hendrik Weisser <[email protected]>

[DOC] improved doc. related to IdentificationData in BaseFeature and FeatureMap (incl. grouping of functions)

b29508f5169adb1c7eadd6f826d006223ecaa9d7 authored almost 3 years ago by Hendrik Weisser <[email protected]>

[INTERNAL] replaced boost::optional with std::optional in BaseFeature

9b6a68a9439b82626e3207cc3b37ae92c39d3d10 authored almost 3 years ago by Hendrik Weisser <[email protected]>

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

ed4311a2a3d7c04e53649410315b9c1eb8908e80 authored almost 3 years ago by bielow <[email protected]>

remove wrong noexcepts

ab64cf7f28fd2b3363932b38d36203ce54fae576 authored almost 3 years ago by bielow <[email protected]>

[COMMENT] removed outdated comment

e14a39dda07c8455c7b2794c18628b2af323d150 authored almost 3 years ago by Hendrik Weisser <[email protected]>

[DOC] documented public interface of OMSFileLoad and OMSFileStore

2c10e8adee3aac3e6f09b0173c803b1783b231cc authored almost 3 years ago by Hendrik Weisser <[email protected]>

Merge branch 'develop' into layer_refactor

5c76cdee77bbd9e82a9c0775277fe2fd018d2e21 authored almost 3 years ago by Chris Bielow <[email protected]>

clang-tidy add const to methods and replace size() == 0 with empty (#5673)

* add const to methods and replace size() == 0 with empty

* fixed small issues introduced by ...

a1055245fc89f4e9f0b97fa06e58323bad30e2ed authored almost 3 years ago by Timo Sachsenberg <[email protected]>

[FIX] deal with missing filename when converting seeds to IdentificationData for ProteomicsLFQ (fixes failing ProteomicsLFQ_3 test)

1dff915f4738703ed3e56605dad5f8de104b4e39 authored almost 3 years ago by Hendrik Weisser <[email protected]>

[INTERNAL] guard against empty spectrum file names when converting ProteinIdentification to IdentificationData

ca2d93e8caee80613030016242c7092f442d534f authored almost 3 years ago by Hendrik Weisser <[email protected]>

[NOP] indentation fix

1af307e12932ee73948844c3af97fb5d463b5aa4 authored almost 3 years ago by Hendrik Weisser <[email protected]>

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

5da9ba49018497c4987131f4f07fd2afc6a24b06 authored almost 3 years ago by bielow <[email protected]>

add suggestions from review

f5d1cb1eb26db14bddb1c9b78c95b0325b798a83 authored almost 3 years ago by bielow <[email protected]>

[COMMENT] added explanatory comments in IdentificationData and ObservationMatch

c09cf7995ccfb636dec4f9082913eed4b4016044 authored almost 3 years ago by Hendrik Weisser <[email protected]>

[DOC] improved doc. for IdentificationData::mergeScoredProcessingResults_

f4d3a90f75657366f4b515c551318fb1eccf4705 authored almost 3 years ago by Hendrik Weisser <[email protected]>

[DOC] add thread-safety warning for IdentificationData

a86da88af0d2d3b3f33f35720bcdac3bdce01ced authored almost 3 years ago by Hendrik Weisser <[email protected]>

[COMMENT] added explanatory comments for IdentificationData references in features; style improvements

d4b224cf38897b8c51541ef8343c70feeba58d14 authored almost 3 years ago by Hendrik Weisser <[email protected]>

[DOC] improved doc. of BaseFeature::updateIDReferences and Feature::updateAllIDReferences

420d41f4076e2fe804dd46f64cff0b9f64afe522 authored almost 3 years ago by Hendrik Weisser <[email protected]>

[DOC] improved doc. of IdentificationData-related functions in IDFilter and MapAlignmentAlgorithmIdentification

57c185a2d91085d6797028e279a8e630355ac54e authored almost 3 years ago by Hendrik Weisser <[email protected]>

Decumentation in average function in SpectraMerger.h added.

5941be2b82ea4396ba4f6b98e494245fc652b404 authored almost 3 years ago by KyowonJeong <[email protected]>

Bug in average funtion in SpectraMerger.h fixed.

5bf926ee7ebe6c1f01e5ae256a3c094469cf4935 authored almost 3 years ago by KyowonJeong <[email protected]>

1. FLASHDeconv documentation added.

2. SpectraMerger run for all ms levels (for gaussian and tophat) if ms_level is set to be 0.

6530d5bfe5f2d456f1620558914b7aa862360d3d authored almost 3 years ago by KyowonJeong <[email protected]>

bug fixing according to the codefactor comments

d52b3ce3d2b6e40c709d056c9ec0378fbdb0d236 authored almost 3 years ago by JeeH-K <[email protected]>

[INTERNAL] moved OMSFile helper classes (OMSFileStore, OMSFileLoad) to separate .cpp/.h files

98656f05c5be92a6be822e65f6c6f450f37e4a83 authored almost 3 years ago by Hendrik Weisser <[email protected]>

[INTERNAL] use 'FeatureFinderIdentificationAlgorithm::run' overload for legacy ID formats where appropriate

ed4a34d0b6fd2437753d9454b0fb51a741d8f499 authored almost 3 years ago by Hendrik Weisser <[email protected]>

[API] added 'FeatureFinderIdentificationAlgorithm::run' overload for legacy ID formats (for ProteomicsLFQ and pyOpenMS)

104fa9e6d7279ada428808275f4d980760f8a6a1 authored almost 3 years ago by Hendrik Weisser <[email protected]>

[FIX] add move constructor and assignment operator (#5686)

3c4a078ad4687677393c138d4acb91bb444a7c7b authored almost 3 years ago by Hannes Roest <[email protected]>

add FileFilter option to overwrite precursor charge (#5684)

* add FileFilter option to overwrite precursor charge

* fix some typos

* nop

6987211e42360201b2a094bc98b9405c6fe387d4 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

Remove max_peak and max_peak_sec matrix from XCorr

3522c6a9355c8ea90b2c8846248ad0234ff418c8 authored almost 3 years ago by khue.nm <[email protected]>

move templates to cpp file to reduce Seqan exposure (#5516)

* move templates to cpp file to reduce Seqan exposure

* add dll export

3b6c0eedfd33dee76d9e9f8819700ce28312fc3c authored almost 3 years ago by Timo Sachsenberg <[email protected]>

Update src/openms_gui/source/VISUAL/APPLICATIONS/TOPPViewBase.cpp

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

96acbf1c0f1cf26f62dd06cbf37e90743316c466 authored almost 3 years ago by Chris Bielow <[email protected]>

[SUBMODULE] add pyopenms-extra as submodule (#5665)

fb12c851f0703a9db540c99741fdf1a49baeb3b9 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

add noexcept to move and move assignment ctors

03951abd4fc6f7c00268312fb735c9f3cd060545 authored almost 3 years ago by bielow <[email protected]>

workaround for rare segfault in elution peak detection (#5677)

b8d69c74622167d1b4799ebcbe55188b5a4e4b07 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

clang-tidy performance-inefficient-vector/string-operation (#5676)

* performance-inefficient-vector-operation

* Apply suggestions from code review

Co-authore...

b391237bb8e4f5a3dc79ab0cdd663bbfa663c47b authored almost 3 years ago by Timo Sachsenberg <[email protected]>

fix return to reference (#5679)

8594c2ad50b1e3d3263235ea592ed02049dbcb11 authored almost 3 years ago by Timo Sachsenberg <[email protected]>

[FEATURE] peptide export from feature map for pyOpenMS (#5672)

* Add assigned peptide export from FeatureMap

- collect PeptideHits from each feature
- add ...

66b3e7d422d4154758c797cf8b6cd8cf35190390 authored almost 3 years ago by axelwalter <[email protected]>

fix bug introduced earlier

245a4693be7d9e7260000bf76ccb39f4897406bb authored almost 3 years ago by bielow <[email protected]>

move peptide member of IdentLayer to derived class

705eaf21d7c46a4aa5eabe0855d20efceafd1f97 authored almost 3 years ago by bielow <[email protected]>

fixes a race condition when multiple threads call newFile() and the reference gets invalidated (happened in TOPPView, when requesting a temporary file for INI's) (#5674)

12ec65593063bebd148d07f34545cb6a1e9be8ef authored almost 3 years ago by Chris Bielow <[email protected]>

Fix seg fault

a74bb0d40d9628880c91ec59514521a523b960a1 authored almost 3 years ago by khue.nm <[email protected]>