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

Fixed rest of the tests again.

Signed-off-by: Julianus Pfeuffer <[email protected]>

e1252fe3a6e464f71b52d9c022b1687356e5df1d authored about 5 years ago by Julianus Pfeuffer <[email protected]>

Added TOPP test for handling interleaved MS3 levels

on the example of IsobaricAnalyzer.

Signed-off-by: Julianus Pfeuffer <[email protected]>

2859356fee118c9c4fe513d7ef3f0f0dc1459f7e authored about 5 years ago by Julianus Pfeuffer <[email protected]>

Fixed mzML test after changing the mzML Handler

Signed-off-by: Julianus Pfeuffer <[email protected]>

725977ec6c85f6dad22d89f131612561515f7f62 authored about 5 years ago by Julianus Pfeuffer <[email protected]>

Write optional attributes in precursor section of mzML.

Signed-off-by: Julianus Pfeuffer <[email protected]>

91559578a013179736ec2b72c73a55218901a025 authored about 5 years ago by Julianus Pfeuffer <[email protected]>

[Fix] Precursor lookup and cxml default labelled experimental design (#4217)

* Fixes bugs encountered in a full TMT pipeline:
- When consensusXML is merged rowwise instead ...

f7905ceea3c0af9898101954fe2b36c6dfb7dd83 authored about 5 years ago by jpfeuffer <[email protected]>

Fixes bugs encountered in a full TMT pipeline: (#4213)

- When consensusXML is merged rowwise instead of colwise, files in the
ID structures might not ...

8bb81964e0482a26c83c6c2d4a3b3f86089347b4 authored about 5 years ago by jpfeuffer <[email protected]>

[INTERNAL] use new option for default value when querying meta values

01434ff324d2a224067190c18e2e14c5c9d446cb authored about 5 years ago by Hendrik Weisser <[email protected]>

[TEST] updated MetaInfo(Interface) tests to changes in 'get(Meta)Value'

8aac57a41b4413ae08b0d373adfd2eae2dd6ac78 authored about 5 years ago by Hendrik Weisser <[email protected]>

[API] added optional default value to 'MetaInfo::getValue' and 'MetaInfoInterface::getMetaValue'

44621cf52aee89fe3e0e6d68b220eba2bb7987dd authored about 5 years ago by Hendrik Weisser <[email protected]>

[NOP] coding style/whitespace adjustments

06ff56ecdb9572ec67ff3ed992a18a135e22bc23 authored about 5 years ago by Hendrik Weisser <[email protected]>

Merge pull request #4210 from timosachsenberg/fix/primary_ms

[FIX] set primary MS run support in more tools

085cb957e5aae1548ec85884fb5da218ca0080c3 authored about 5 years ago by jpfeuffer <[email protected]>

Merge pull request #4199 from hendrikweisser/fix-precursor-mz

Improve handling of precursor m/z when reading/writing mzML

163c13c86c4ce3b6ebb22f126d4667615da7e834 authored about 5 years ago by hendrikweisser <[email protected]>

[FIX-#4168] use 'isolation window target m/z' information if available to show precursor isolation window in TOPPView (fixes #4168)

0f5e45f0a0fc20138063bf36929dd5a66ded79c9 authored about 5 years ago by Hendrik Weisser <[email protected]>

missing tests

c47103b5328522e67dffe5d05c6013a9f4ee5294 authored about 5 years ago by Timo Sachsenberg <[email protected]>

add more warnings

6f8b6bc5b773dbeb3112ba2a59816f786e4278ca authored about 5 years ago by Timo Sachsenberg <[email protected]>

[FIX] replaced auto with proper type (error on GCC9.1) (#4211)

2571cf318df17ed00224eca977b3e71ce8ceba24 authored about 5 years ago by Timo Sachsenberg <[email protected]>

pyOpenMS bindings

aeff5642ce073ec6c2e98ba64515cddf0a26006a authored about 5 years ago by Timo Sachsenberg <[email protected]>

[FIX] set primary MS run support in more tools

80dd9f235b8546dc4251eb4611428d893130791a authored about 5 years ago by Timo Sachsenberg <[email protected]>

[FIX] Opt-out dark mode MacOS (#4209)

e7037f0a5fb8a3f606f5eb8165c454c5c5d56910 authored about 5 years ago by Oliver Alka <[email protected]>

Merge pull request #4207 from jpfeuffer/feature/msstatsrefcol

[FEATURE] Added Reference column to MSstats output

3804820fc0f503839eac1e1397c5cd637ad10646 authored about 5 years ago by jpfeuffer <[email protected]>

fix random segfaults if identified spectra were browsed (#4208)

* fix random segfaults if identified spectra were browsed

* Update LayerData.cpp

79943d4015ad47ea72c189d90fc450456ac49f80 authored about 5 years ago by Timo Sachsenberg <[email protected]>

Refactored csv style parameters. Uses quotes to escape Ref column now.

Signed-off-by: Julianus Pfeuffer <[email protected]>

4253dfa058ef1e1989ce60d8d71d7bf640902f11 authored about 5 years ago by Julianus Pfeuffer <[email protected]>

Added Reference column to MSstats output

Signed-off-by: Julianus Pfeuffer <[email protected]>

4da4ec4f09d59cc10786858dd42d3d515833dae0 authored about 5 years ago by Julianus Pfeuffer <[email protected]>

Merge pull request #4204 from timosachsenberg/fix/mix_hash

[FIX] avoid mixing hashes

3d3bb80985a44a864c51a07c1778754dad90b8d5 authored about 5 years ago by jpfeuffer <[email protected]>

Update String.cpp

0f8f805eb61604930368c95f4f53e790ef21a3cc authored about 5 years ago by jpfeuffer <[email protected]>

Update String.cpp

8e23a6a467aefc84ae30b17ce4db268810cd3a80 authored about 5 years ago by jpfeuffer <[email protected]>

Update String.cpp

d68f14dd85dc28f0900f653edd2977d9595bcd7b authored about 5 years ago by jpfeuffer <[email protected]>

Update String.cpp

c11734284a5563573e1aacfc0bd8aaecc6032424 authored about 5 years ago by jpfeuffer <[email protected]>

Update String.h

42d9256cc4d1cec442d4686e84fd22c6507dab88 authored about 5 years ago by jpfeuffer <[email protected]>

Update String.h

4bbbe8fd4fecf433fdeafc5febe0bd8f5b69c176 authored about 5 years ago by jpfeuffer <[email protected]>

Update String.cpp

52f3eed77bd850f79b3a8e779213c01a9260725b authored about 5 years ago by jpfeuffer <[email protected]>

[FIX] OPXLHelper::computeDeltaScores, added checks for the number of PeptideHits (#4206)

* [FIX] simplified OPXLHelper::computeDeltaScores

* [FIX] computeDeltaScores sorts PeptideHit...

c310a36ed65a4e7f9af1b868e3a3078de1c332c4 authored about 5 years ago by Eugen Netz <[email protected]>

Merge remote-tracking branch 'origin/fix/mix_hash' into fix/mix_hash

84e05c5972b6a1fbd4efadafffb01069a3396df5 authored about 5 years ago by Timo Sachsenberg <[email protected]>

Merge remote-tracking branch 'upstream/develop' into fix/mix_hash

22e87fb58e1f616938fcd6aca9df948dffa23fe0 authored about 5 years ago by Timo Sachsenberg <[email protected]>

[FIX] simplified OPXLHelper::computeDeltaScores (#4205)

* [FIX] simplified OPXLHelper::computeDeltaScores

* [FIX] computeDeltaScores sorts PeptideHit...

6f0e6049982218668917b58e0699d05d89e12022 authored about 5 years ago by Eugen Netz <[email protected]>

[FIX] avoid mixing hashes

4be9a2da7b13e867001e2a7252b0995ff7f1dccb authored about 5 years ago by Timo Sachsenberg <[email protected]>

Update MRMIonSeries.cpp

c8301b2debd8e599a6eb685997dfada1be99f2c9 authored about 5 years ago by Timo Sachsenberg <[email protected]>

NucleicAcidSearchEngine improvements (#4187)

* [FEATURE] NucleicAcidSearchEngine: use precursor intensity to find RT pos. for label-free quan...

8f6886302b55bd1881a45c62cc77b7fb7ba7e9d6 authored about 5 years ago by hendrikweisser <[email protected]>

[NOP] tabs to spaces

5cf3c492256a12ca1cce791855101f3f52f2be14 authored about 5 years ago by jpfeuffer <[email protected]>

Simplification of the XL-MS PeptideIdentification / PeptideHit ID structures (#4201)

* [TEST] updated XLMS mzid output files

* [RESOURCE] updated psi-ms.obo CV file

* [TEST] u...

2b09dd10fd3608f37503e26b02b248897e390ca1 authored about 5 years ago by Eugen Netz <[email protected]>

Fixed wrong erase idiom in MzTab.

31422197bc1745e2222443e56f4fc9149b8c4772 authored about 5 years ago by jpfeuffer <[email protected]>

Update lnx-cibuild.sh

c16026ddfb5af954e7708d4dbe6cf28d282b6107 authored about 5 years ago by jpfeuffer <[email protected]>

Update install-linux.doxygen

0565e3816c08efdc8dcbc3aabeced7fe11758df4 authored about 5 years ago by jpfeuffer <[email protected]>

Mini fix for assertions in debug mode.

09d0dfb30e59fa4080e808e6d5c231b59f12f2a1 authored about 5 years ago by jpfeuffer <[email protected]>

Merge pull request #4182 from jpfeuffer/feature/proteomicLFQandInference

[FEATURE] ProteomicsLFQ workflow tool and additional inference tools

a86f58cd7f26a0284ca690703c513e29e55c19fa authored about 5 years ago by Timo Sachsenberg <[email protected]>

IDPEP python fix.

Signed-off-by: Julianus Pfeuffer <[email protected]>

6f4bac126911bd4367b58e85caaaf632912a6217 authored about 5 years ago by Julianus Pfeuffer <[email protected]>

[COMMENT] added explanatory comment (writing precursor meta data to mzML)

fdd2d3274096f7d607e9f9f2c39bbfe2c713e90f authored about 5 years ago by Hendrik Weisser <[email protected]>

Building docu and IDPEP python fix.

Signed-off-by: Julianus Pfeuffer <[email protected]>

209896098f884077388992aa9c71ea8580b50c79 authored about 5 years ago by Julianus Pfeuffer <[email protected]>

IDPEP python tests

Signed-off-by: Julianus Pfeuffer <[email protected]>

02d19e939e9c558d84d8e15752eccbc1247bc027 authored about 5 years ago by Julianus Pfeuffer <[email protected]>

Codacy shell style fixes

Signed-off-by: Julianus Pfeuffer <[email protected]>

e547083b7ae03b137175862d9c7da9d3314ceaa6 authored about 5 years ago by Julianus Pfeuffer <[email protected]>

Codacy shell style fixes

Signed-off-by: Julianus Pfeuffer <[email protected]>

726edd107d5d44169e679df275010f9d905ccbb4 authored about 5 years ago by Julianus Pfeuffer <[email protected]>

Last style error.

Signed-off-by: Julianus Pfeuffer <[email protected]>

65a3c1da1ee7e635a620e0f85e43158e1a0e177d authored about 5 years ago by Julianus Pfeuffer <[email protected]>

Style errors. Compatibility with old boost. MSstats switch

to mod sequence and remove unnecessary stuff.

Signed-off-by: Julianus Pfeuffer <jpfeuffer@fu-ber...

598f9f65cb777987a4e5bf751b93ebbb18d9045b authored about 5 years ago by Julianus Pfeuffer <[email protected]>

Merge remote-tracking branch 'origin/feature/proteomicLFQandInference' into feature/proteomicLFQandInference

54d94692851cf7d4aed16473356a93858befbb30 authored about 5 years ago by Julianus Pfeuffer <[email protected]>

Fixed old py bindings.

Signed-off-by: Julianus Pfeuffer <[email protected]>

00832a6082d5ccc261ef024361b97aefe213cbe9 authored about 5 years ago by Julianus Pfeuffer <[email protected]>

attempt to fix failing MapAlignerID test

02dd143bd799b6b9dca9de57a78ea52972e9edde authored about 5 years ago by Timo Sachsenberg <[email protected]>

Addressed some remaining comments. Mostly introducing typedefs.

Add whitelist to ProteomicsLFQ test

Signed-off-by: Julianus Pfeuffer <[email protected]>

42635b8de2a089ff5b8c7e47099d0f0b968fed4d authored about 5 years ago by Julianus Pfeuffer <[email protected]>

[TEST] updated tests to recent changes

d25a3412f3236156dba32bdf7937989153544c48 authored about 5 years ago by Hendrik Weisser <[email protected]>

[FIX] fixed handling of precursor m/z when 'isolationWindow' is missing from mzML

d00dc5a8ac4398061ac1b797ef8843914045fb26 authored about 5 years ago by Hendrik Weisser <[email protected]>

Merge pull request #4198 from grosenberger/fix/sangle_nan

[FIX] OpenSWATH: Patch to prevent NaN from spectral angle score

bc2b18cb610eed8eee8d3dc44ad48176a83fdad6 authored about 5 years ago by Timo Sachsenberg <[email protected]>

[FEATURE] improved support for handling of two sources for precursor m/z values in mzML files (see #4168)

cb71e836d7b932a501b2b4c58b0b8c34980ca2c7 authored about 5 years ago by Hendrik Weisser <[email protected]>

[FEATURE] added peak file option to select source for precursor m/z values in mzML files (see #4168)

1c4f73e72aa4f4febb0d4f147329781d3fca92d5 authored about 5 years ago by Hendrik Weisser <[email protected]>

Use fixed online XSL for consensusXML. Fix tests.

Signed-off-by: Julianus Pfeuffer <[email protected]>

6ff40f370f388171722b372e390d19e8121654b8 authored about 5 years ago by Julianus Pfeuffer <[email protected]>

Tried to circumvent compiler bug but failed -> raise min version to 4.9

Signed-off-by: Julianus Pfeuffer <[email protected]>

b1f670c6edc68b5f9f59993519d5814e25a894c1 authored about 5 years ago by Julianus Pfeuffer <[email protected]>

Refactored getting and setting of IDScores in FDR.

Signed-off-by: Julianus Pfeuffer <[email protected]>

4f67f34ca76805be4454125f096eca5f92f65e58 authored about 5 years ago by Julianus Pfeuffer <[email protected]>

Put more stuff to Debug output.

Add test for ProteomicsLFQ (faking PEPs in the example files).

Signed-off-by: Julianus Pfeuffer ...

0f9c58d765de868f82e92e60525cb8759c9c9957 authored about 5 years ago by Julianus Pfeuffer <[email protected]>

Merge remote-tracking branch 'origin/feature/proteomicLFQandInference' into feature/proteomicLFQandInference

907e8ccca3405dcc71c2a0f9c9f412b2724a00ce authored about 5 years ago by Julianus Pfeuffer <[email protected]>

minor changes

Signed-off-by: Julianus Pfeuffer <[email protected]>

cfb46d2320f6a61284b875d443ab87895ce82866 authored about 5 years ago by Julianus Pfeuffer <[email protected]>

Major refactor of MSstatsFile.

Signed-off-by: Julianus Pfeuffer <[email protected]>

e8a438986285f6a65c065f3339138b2e1f2336c0 authored about 5 years ago by Julianus Pfeuffer <[email protected]>

[NOP] use auto-for loop

0b8a2365abeeb8b8c345f82c25f66f1366fd39f8 authored over 5 years ago by Hannes Roest <[email protected]>

[FIX] bugfix: use lower_bound like other impl

350ffa46b382c9cbcab75caf2b5df21149591746 authored over 5 years ago by Hannes Roest <[email protected]>

[FIX] bugfix: ensure that ion mobility is always present

e4627e2a1d67aaa0b7804beef139dc1548484cd5 authored over 5 years ago by Hannes Roest <[email protected]>

[FIX] bugfix (older libraries)

8b1ea85c26a60f939a139ce1e2f142e084a36cdf authored over 5 years ago by Hannes Roest <[email protected]>

[NOP] removed extra spaces (indentation)

a2bcff1e01da7e00ea7c7c7e61a2957aff670e8b authored over 5 years ago by Hendrik Weisser <[email protected]>

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

5841068a2e9353492b58da9c16b6bec6151588ed authored over 5 years ago by timosachsenberg <[email protected]>

minor fixes

486f4368f0d20d7e599ea358e723169a3d6de33b authored over 5 years ago by timosachsenberg <[email protected]>

Merge pull request #4190 from hendrikweisser/fix-toppview-annotations

Disable automated m/z annotations in TOPPView by default

081c4600de18c39656a3cb0a2902a97ebf89f622 authored over 5 years ago by Timo Sachsenberg <[email protected]>

Forgot reverting test stuff for win.2

Signed-off-by: Julianus Pfeuffer <[email protected]>

6a3eb801ffa57b00dde98b12cdfd694d32f8f1d4 authored over 5 years ago by Julianus Pfeuffer <[email protected]>

Forgot reverting test stuff for win.

Signed-off-by: Julianus Pfeuffer <[email protected]>

04dd4674d68a083698712bfd4638e2757225a4f9 authored over 5 years ago by Julianus Pfeuffer <[email protected]>

cosmetics

Signed-off-by: Julianus Pfeuffer <[email protected]>

d1c4f551ca9513602a194bd7188889a4ba7e95cd authored over 5 years ago by Julianus Pfeuffer <[email protected]>

Tried to fix horrible merge conflict. Of course tests fail..

Nested namespace fix.

Signed-off-by: Julianus Pfeuffer <[email protected]>

d335015a6a3f9725e4096b31ef642acd3fe3d0b3 authored over 5 years ago by Julianus Pfeuffer <[email protected]>

Merge remote-tracking branch 'remotes/upstream/develop' into feature/proteomicLFQandInference

# Conflicts:
# src/openms/source/FORMAT/MSstatsFile.cpp

fcf42fd4dbe4332cf71a281f5110b40cb70b4b80 authored over 5 years ago by Julianus Pfeuffer <[email protected]>

fix catch by ref warning.

Signed-off-by: Julianus Pfeuffer <[email protected]>

b1c7bcaa8c8b245631da894145c58480d087a323 authored over 5 years ago by Julianus Pfeuffer <[email protected]>

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

e6a4220f12d3cb054f5c61a8f95d040c0120ad05 authored over 5 years ago by Julianus Pfeuffer <[email protected]>

More comments addressed. Especially namespace stuff.

Use 0/1 for Metavalue bool.
GridSearch test.
Allow skipping unassigned peptides in ConsensusMap a...

3d6cada5e227c4ab2de89213756e92151f0fca44 authored over 5 years ago by Julianus Pfeuffer <[email protected]>

Windows fixes.

62957188258d9120e2db0c3a10f60b9a0356c444 authored over 5 years ago by jpfeuffer <[email protected]>

Merge pull request #4188 from hendrikweisser/imagecreator-data-range

ImageCreator improvements

6b6c92ac38eb0d40e2012dac415345cafa1a11eb authored over 5 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #4185 from bernt-matthias/topic/either-or

minor wording fixes

664a616f7be94302285e251e19f6c6a4c52cfaa7 authored over 5 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #4181 from oliveralka/update/MSstatsTMT

[Update] MSstatsConverter (TMT)

332fb388f72929915a87bf00992427b2415cf7ba authored over 5 years ago by Timo Sachsenberg <[email protected]>

[FIX] comments

5a162febf7220465ccabe787833b236548984994 authored over 5 years ago by oliveralka <[email protected]>

Fixed Fido tests with new inference annotation.

Completely reverted String, trying to fix Windows hash bug.
Fix filtering in BasicProtInference.
...

acfe43b7e89f5d4198b021f5147acec39a82277c authored over 5 years ago by Julianus Pfeuffer <[email protected]>

[TEST] updated ImageCreator tool tests after recent changes

6ca5b7d83dec2bbdff55b4605dbbc27b2e64cdea authored over 5 years ago by Hendrik Weisser <[email protected]>

[FIX] typo

e125f6f9dd660332515daf4612b713ce5db7b308 authored over 5 years ago by oliveralka <[email protected]>

[COMMENT] fix comment (spectrum -> chromatogram)

Co-Authored-By: Hannes Roest <[email protected]>

7a7a887cdcdcdf3992747040ff0afee937dee72b authored over 5 years ago by hendrikweisser <[email protected]>

[ADD] constructFile function with tempalte argument, general clean-up

ebfdf93c023f4c333ceb61f04158d5736b63e482 authored over 5 years ago by oliveralka <[email protected]>

Merge pull request #4192 from biosustain/chromeleon_new_raw_data_header

[FEATURE/FIX] ChromeleonFile handles raw data header

1f1dd633e583a28c35ef7a93c1ec71aeab2c4be2 authored over 5 years ago by Hannes Roest <[email protected]>

no using directives. try fix weird String hash bug on windows by completely going back to "develop"

Signed-off-by: Julianus Pfeuffer <[email protected]>

b9daf20da23519971f469743708714b5a8121ca9 authored over 5 years ago by Julianus Pfeuffer <[email protected]>

More namespace fixes. Plus some Adapter test fixes.

Signed-off-by: Julianus Pfeuffer <[email protected]>

76a259eebf079235e3af5121747b19b444a54c44 authored over 5 years ago by Julianus Pfeuffer <[email protected]>

feat: Replace std::getline() with TextFile::getLine()

ea8ec4cf44db29bec1b9f2c3b622fc8ecece043e authored over 5 years ago by Pasquale Domenico Colaianni <[email protected]>

feat: Update regex to handle empty values for metadata

feat: Handle possible '\r' in lines (discard it right away)

feat: Replace regex_search with reg...

0b5bbea4d1056fb928301eef1bf15dfd4651ee80 authored over 5 years ago by Pasquale Domenico Colaianni <[email protected]>