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

[FEATURE] include version information in .oms export to JSON

0b0995d4b6faf6ea47da38b4fafa00285e0d6a76 authored over 2 years ago by Hendrik Weisser <[email protected]>

Merge branch 'develop' of https://github.com/OpenMS/OpenMS into idfile-json-export

51fb503836dd6060927e86d0dca3fa96fa8dc603 authored over 2 years ago by Hendrik Weisser <[email protected]>

[COMMENT] add to-do comment (JSON export of protein groups)

9b45bbe586c7e781dabb02879c2a02bc29c90d61 authored over 2 years ago by Hendrik Weisser <[email protected]>

Fixed the Test, changed the filename of the additional_info_file and made some minor fixes in QualityControl

d4b169155facbb0e39416c16076a75ee045f82f5 authored over 2 years ago by lennykovac <[email protected]>

Big performance boost by introducing recurteAllPeaksInSepctrum in PeakGroup.cpp. Changing PeakGroup so scoring is included inside as private functions. 70% done.

730151e86d9a6451e7b43ffa03610b9e282ae7f3 authored over 2 years ago by kyowonjeong <[email protected]>

minimal support for IM Frame data in 2D

bf132c6d28eafb2826d1fff5a07d41020ad211d0 authored over 2 years ago by bielow <[email protected]>

Merge pull request #6196 from OpenMS/Delete-uncrustify-config-and-uncrustify_branch.sh-file

Delete uncrustify config and uncrustify_branch.sh file

23e67e187650b0b656d6343cf7c977da738d1b40 authored over 2 years ago by Samuel Wein <[email protected]>

Big performance boost by introducing recurteAllPeaksInSepctrum ins PeakGroup.cpp. Changing PeakGroup so scoring is included inside as private functions. 50% done.

ff855adcf17af05aa45e10e2df80e128616b80fd authored over 2 years ago by kyowonjeong <[email protected]>

Add CMake test explorer to gitpod

4643431f4026f02622b35d1154cd5c6e6ad617eb authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Big performance boost by introducing recurteAllPeaksInSepctrum ins PeakGroup.cpp. Changing PeakGroup so scoring is included inside as private functions.

35c188033b1dfabe175c086c785c08710d4469b4 authored over 2 years ago by kyowonjeong <[email protected]>

fix, wip: debugging spectral library matching

13a201d4407a07a7c1698b7c9cd1d0da27908160 authored over 2 years ago by dmccloskey <[email protected]>

Big performance boost by introducing recurteAllPeaksInSepctrum ins PeakGroup.cpp. This function collects all peaks from each mass before scoring. Fine tuning will follow.

da5512d3bac82582953fcbb956e4d879019b22bd authored over 2 years ago by kyowonjeong <[email protected]>

Big performance boost by introducing recurteAllPeaksInSepctrum ins PeakGroup.cpp. This function collects all peaks from each mass before scoring. Fine tuning will follow.

d2224d1a5ff6cc2810f35f4b6462e40c1e184560 authored over 2 years ago by kyowonjeong <[email protected]>

fix, wip: refining matchSpectra and library generation routines

d12d83330c3f4f7677fddfc93bb9bc92aa6858dd authored over 2 years ago by dmccloskey <[email protected]>

fix: cleaned up AnnotateSpectra to reduce reudandant code

f9733c175d99937a393fd99bfb8dda4fdae956d5 authored over 2 years ago by dmccloskey <[email protected]>

+ allow showing a single spectrum in 2D view (fix RT margins)

+ update axis when switching intensity mode

8a15772cfc9329b57705d66e0b65ceaceb20cae5 authored over 2 years ago by bielow <[email protected]>

support Chroms in 1D natively

lots of fixes and simplifications

d2621c3392e848d2331a206428778a62407c355e authored over 2 years ago by bielow <[email protected]>

fix: updated ConstructTransitionList transition creation logic to account for duplicate names and RTs

18e4ab03d2c757debdeccb9131131a06089b06e5 authored over 2 years ago by dmccloskey <[email protected]>

Merge pull request #6173 from OpenMS/fix/psmpepfdr_plfq

[Fix] PSM and Pep FDR in PLFQ

394b1492e732625f44b4036f8a873a22258d15cc authored over 2 years ago by Julianus Pfeuffer <[email protected]>

removed uncrustify_branch.sh

3ea5b86134d102bf2475f084476ebd286ef6d079 authored over 2 years ago by matteopilz <[email protected]>

Delete uncrustify.cfg

d9b392e1efd91de8fcfd879b398a15358fe9af1a authored over 2 years ago by Matteo Pilz <[email protected]>

Bug fixes in negative MS mode

844920b868457c285c3399b7e771c19129d06fbf authored over 2 years ago by kyowonjeong <[email protected]>

fix: bugs from merge

d1b04f5cf1f9fb4e2386d0a62d3bd1491c38c2a6 authored over 2 years ago by dmccloskey <[email protected]>

Merge pull request #6167 from tapaswenipathak/delete-dups

Delete: duplicate pages in openms rtd and doxgen

9905029a1d9b5e8e65c1387f322abd0f835e76c6 authored over 2 years ago by Samuel Wein <[email protected]>

Merge branch 'delete-dups' of github.com:tapaswenipathak/OpenMS into delete-dups

75e150f6dc6ad532b214357be068dd0d0abf0f55 authored over 2 years ago by Tapasweni Pathak <[email protected]>

Add OpenMS tut pages on RTD

7a704cc3b25282ab3b2acc101b86d028a2f05d25 authored over 2 years ago by Tapasweni Pathak <[email protected]>

Add TOPPAS Tutorial RTD link

602a9f50f56c551b09ac3d6a3a01a28ca5d5d9d0 authored over 2 years ago by Tapasweni Pathak <[email protected]>

merge develop

efb805ca3e7b5bc567558c3cbe179ff25c6b63f9 authored over 2 years ago by dmccloskey <[email protected]>

Merge branch 'develop' into delete-dups

588f514dc34f16189b3a662fda32ca02132393fc authored over 2 years ago by Tapasweni Pathak <[email protected]>

Merge branch 'develop' into fix/psmpepfdr_plfq

0add0f4b09a1220d6abc56e88bba135db8092a93 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Merge pull request #6193 from bertrandboudaud/fix/pyOpenMS_storeSpectraTraML_not_found

Fixed pyOpenMS build: storeSpectraTraML has been renamed constructTra…

7fcfaf66fee9678713faf759b8b2dbda39610585 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Fixed pxd for extractSpectra

8d132e137c4a8814f6340b21295ccb042fa6dab8 authored over 2 years ago by bertrandboudaud <[email protected]>

Fixed pyOpenMS build: storeSpectraTraML has been renamed constructTransitionsList

fd4c8bef86cfc4e21f3622e23a6bba6d03a9e617 authored over 2 years ago by bertrandboudaud <[email protected]>

Merge branch 'develop' into fix/psmpepfdr_plfq

659e9c93f1a919b538e05fd701094a151db38b14 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

[FIX] some style and pyopenms

7295a715ec305f754e3c3c3edc2c62a79ef600a9 authored over 2 years ago by jpfeuffer <[email protected]>

[FIX] Last fixes for pepFDR in plfq

6aaaebff8030edf436741a93c8e446149b95a741 authored over 2 years ago by jpfeuffer <[email protected]>

Merge remote-tracking branch 'upstream/develop' into feature/FLASHDeconv

f8eab28b3ada5d570d4cebfafdf646be2711d2e9 authored over 2 years ago by JeeH-K <[email protected]>

Merge pull request #6182 from OpenMS/new_doc_categories_for_tools

Update TOPP.doxygen

851f10050549407512a42c1b87f90d9d8c49f83e authored over 2 years ago by Timo Sachsenberg <[email protected]>

Merge branch 'develop' into delete-dups

ce984968136806f59ae86f35426923a66e82d561 authored over 2 years ago by Tapasweni Pathak <[email protected]>

fix a grammatical error

Co-authored-by: Julianus Pfeuffer <[email protected]>

f14a897e31e76008c86e55384f4b72efd491e62c authored over 2 years ago by Tapasweni Pathak <[email protected]>

Merge pull request #6186 from greengypsy/fix_indentation_developer_faq

fixed indentation in developer-faq.doxygen by adding closing ul tag

7a84a045758b2704b60122a08614c7b4a2d40bdc authored over 2 years ago by greengypsy <[email protected]>

fixed indentation in developer-faq.doxygen by adding closing ul tag

4b71662e88ee048adbd6912e6ca664e02346604f authored over 2 years ago by greengypsy <[email protected]>

Apply suggestions from code review

Co-authored-by: Julianus Pfeuffer <[email protected]>

8adb0d587092f8c2aba89c854b15c60a6fb09ad9 authored over 2 years ago by Timo Sachsenberg <[email protected]>

fixing typo

9d13c7cd1e50fd7ccb943470f816ff6038f2ae54 authored over 2 years ago by JeeH-K <[email protected]>

Update TOPP.doxygen

738509fb1243d9f4907efa8fae19f9e3b02b6877 authored over 2 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #6180 from bertrandboudaud/fix/unknown_feature_counter

fixed compilation error unknown_feature_counter unused variable

381879df9c4d94865746a0655fe8a11072897b01 authored over 2 years ago by Timo Sachsenberg <[email protected]>

fixed compilation error unknown_feature_counter unused variable

0fbf19089bf92fb03967cd848f02fcb9f9010188 authored over 2 years ago by bertrandboudaud <[email protected]>

fixing typo

730c626bb25c5df4919f5d86e08185f20e60f42c authored over 2 years ago by JeeH-K <[email protected]>

Merge branch 'feature/FLASHDeconv' into feature/FLASHDeconvOnly

d02f74aed47ae2510cb52aab8a82963b490aa148 authored over 2 years ago by JeeH-K <[email protected]>

Merge remote-tracking branch 'upstream/develop' into feature/FLASHDeconvOnly

a24a02457c8da8614477ccaf74775cd895c5393d authored over 2 years ago by JeeH-K <[email protected]>

polishing codes to remove warnings

be4647695b6b21c9f146748d33991ccfe31d1eb4 authored over 2 years ago by JeeH-K <[email protected]>

Merge branch 'develop' into fix/psmpepfdr_plfq

68bf5b52c0b934cbeb8d4fdf0b40b5a18deb318f authored over 2 years ago by jpfeuffer <[email protected]>

[FIX] Some docu changes. Always keep all PSMs also with Bayes.

35f4a7b709d8042e9801975f2198f495992ab2ca authored over 2 years ago by jpfeuffer <[email protected]>

Merge pull request #6174 from OpenMS/fix/better_error_message

Update XMLHandler.cpp

97d7742022572cd9f1eeae92e9b440ae7dc9e843 authored over 2 years ago by Timo Sachsenberg <[email protected]>

Merge branch 'develop' into feature/FLASHDeconv

d0b3123cb8666a8f56a6b83391f0694bf07ad29b authored over 2 years ago by JeeH-K <[email protected]>

fixing bugs for ctests

ff484ed189480c27a2047e9b5676502b5b65b1cf authored over 2 years ago by JeeH-K <[email protected]>

Merge pull request #6106 from bertrandboudaud/feature/searchSpectrum_extended

Feature/search spectrum extended

1d4f5c9f50346e5bffa344977acf2e28e6c0d797 authored over 2 years ago by Timo Sachsenberg <[email protected]>

Update XMLHandler.cpp

better error message if run identifiers are not unique

e5d7f19e6ac2d3e21e6bf11300f540095fca1f90 authored over 2 years ago by Timo Sachsenberg <[email protected]>

Cleaned up some comments

ea3a6f945c59625224e142124bb4ac90aaccb669 authored over 2 years ago by Virginia Rossow <[email protected]>

fixes

d237a406430c5633de3efd36929a028f99c44aec authored over 2 years ago by jpfeuffer <[email protected]>

Merge pull request #6145 from greengypsy/convert_to_doxygen

Add OpenMS wiki pages to OpenMS API reference Doxygen documentation

831ee90f501f53c9d5496a100b3b869b1d2acf15 authored over 2 years ago by greengypsy <[email protected]>

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

3b27b3db423d5110c71fff5522b11e9ea0d16a19 authored over 2 years ago by jpfeuffer <[email protected]>

[FIX] FDR applyBasic. Add pepFDR to PLFQ.

0072ee36622dcb3befcca2c956f04c8b32a443b6 authored over 2 years ago by jpfeuffer <[email protected]>

[FIX] FDR applyBasic. Add pepFDR to PLFQ.

56345ff458983139d29a8cf4985233239a5746cb authored over 2 years ago by jpfeuffer <[email protected]>

[FEATURE] Add iBAQ to ProteinQuantifier (#6107)

* update

* added iBAQ to ProteinQuantifier

* removed outdated iBAQQuantitation.cpp

* re...

ab260e1aad2b23c81ea50a62f3ebf69b6b7a6a13 authored over 2 years ago by Matteo Pilz <[email protected]>

infra-fix: don't lint deleted files (#6172)

3af93c27d4b96291498e41cb24aaf3b9b81cbe0b authored over 2 years ago by Simon Gene Gottlieb <[email protected]>

Merge pull request #6171 from SGSSGene/fix/github-workflow

Fix/GitHub workflow

9cea4b51096f54e6823545d185a047676f89eb51 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

update: github workflow uses tj-actions and DoozyX

005a0fbb958dc7926f96f53561d28245bb4b4dda authored over 2 years ago by Simon Gene Gottlieb <[email protected]>

infra-fix: don't lint deleted files

ea6a0f18f06b851c5b85a85782ac4425abba57ee authored over 2 years ago by Simon Gene Gottlieb <[email protected]>

fixed indentation and replaced {cpp} and {sh} with {.cpp} and {.sh} as discussed

4c030a2659c9ac2176c93e38d91bc903b892ea6c authored over 2 years ago by greengypsy <[email protected]>

add peptide level fdr/q-values (#6132)

* add peptide level fdr/q-values

* use emplace

* add option to enable/disable FDR calcuati...

5f93c53c7201a8a84d5475354a8b27a50a006655 authored over 2 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #6169 from axelwalter/fix/GNPS-meta-values-from-consensusmap

[Fix] GNPSMetaValueFile get mzML file names from ConsensusMap

8e4aae3815c7a0dcd8ba6a03143af5b07f56cbe0 authored over 2 years ago by axelwalter <[email protected]>

Merge branch 'develop' into feature/searchSpectrum_extended

25837556a8b3ef717a93d88a81eb198a5b2c18f2 authored over 2 years ago by Timo Sachsenberg <[email protected]>

alternative method to get mzML file paths

1181dd2e6c422fb34033d7441d1c9133f013d796 authored over 2 years ago by axelwalter <[email protected]>

update tests

1154c77a2ef8d1e332bfd1897116fb4d576fd0ed authored over 2 years ago by axelwalter <[email protected]>

use ConsensusMap as input for GNPSMetaValueFile

654dee6b85e9b8664112c5bcfecd412afafb1e5b authored over 2 years ago by axelwalter <[email protected]>

Merge remote-tracking branch 'upstream/nightly' into feature/FLASHDeconv

38c66f5403e103663469d17ccfcf92e89d3cbd6e authored over 2 years ago by JeeH-K <[email protected]>

Merge remote-tracking branch 'upstream/develop' into delete-dups

03fb606803db8a29ef0aa9fa32535dbc263b583f authored over 2 years ago by Tapasweni Pathak <[email protected]>

update changelog

fb509babb544916254ba534329286c1d430dceaf authored over 2 years ago by Tapasweni Pathak <[email protected]>

Delete: duplicate pages in openms rtd and doxgen

Ref: https://github.com/OpenMS/OpenMS-docs/issues/4#issuecomment-1125150286.

22141b3490deb89eb85948a960c527b8d93d1ccc authored over 2 years ago by Tapasweni Pathak <[email protected]>

made changed to documentation according to feedback

a36baf23b48e8bb81e06f9d7e90f6b6a92c299b6 authored over 2 years ago by greengypsy <[email protected]>

Merged develop and added metavalue num_of_datapoints.

f9f4581bd9c9e64fcd2842288a6354a313996041 authored over 2 years ago by Virginia Rossow <[email protected]>

Merge branch 'develop' into maxquant-output

72209fc950fef1c32a22502d03193d69ab5d5292 authored over 2 years ago by Virginia Rossow <[email protected]>

Added the compatible version of MSFragger into the MSFraggerAdapter documentation. (#6154)

a686a995efc5d2f38519666039d856566a571654 authored over 2 years ago by tillenglert <[email protected]>

Feature/GNPSexport_split_files (#6152)

* Separate class for GNPSQuantificationFile and adding GNPSMetaValueFile

* add new files

*...

1acb92a7d2ded2f5fc706045be36b6bf87ca1f5b authored over 2 years ago by Timo Sachsenberg <[email protected]>

fixed signed and unsigned int comparison (#6150)

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

988bfef13dd389a6b973bc70e0b4c35b70d6c320 authored over 2 years ago by KyowonJeong <[email protected]>

[PARAM, FEATURE] FileConverter, disable zlib compression flag (#6151)

db0229516839ba59004032f0b9e04ab553bb81a6 authored over 2 years ago by Eugen Netz <[email protected]>

fix unneded pragma warning in cpp (#6148)

ac113412ef7524d51f648e696f81fecceab3de98 authored over 2 years ago by Timo Sachsenberg <[email protected]>

added pull request checklist link

de5d92d770adcd488b2ccb8392d09bc1f61cf064 authored over 2 years ago by greengypsy <[email protected]>

modified developer-faq to include questions not included in contributor-faq.md

40c0a14276cf1b574960dae58c60f37701fbe76a authored over 2 years ago by greengypsy <[email protected]>

Merge pull request #6136 from zhuchcn/uclacds-develop

Add support of "no cleavage" for XTandemAdapter & CometAdapter

1f903c020948ae0ddfea70b21440047b6e328c23 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

fixes

8952f5f98e7f710aa19a008d79495a9e2766dce4 authored over 2 years ago by bielow <[email protected]>

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

# Conflicts:
# src/openms/source/CONCEPT/CommonEnums.cpp
# src/openms_gui/source/VISUAL/ANNOTATI...

0f637941b4db69b8f22e4c0dbf9d107c63c8f538 authored over 2 years ago by bielow <[email protected]>

progress...

66c4132380f901ad57954d8932770939ee426f5e authored over 2 years ago by bielow <[email protected]>

added discussed doxygen files

572a9a2a218b67a407e401707474562947cb6e56 authored over 2 years ago by greengypsy <[email protected]>

Msms works + test added

abdc0a9d2658a5d4eac7d3393397b3d3737aceb3 authored over 2 years ago by Virginia Rossow <[email protected]>

Merge branch 'OpenMS:develop' into develop

969cf912d2adb7a8c0bc3430ddc85a85a0cb0a35 authored over 2 years ago by greengypsy <[email protected]>

Merge pull request #6141 from cbielow/api_extensions

some preps for upcoming GUI PR

e0e8d0ebdd89b5f43cda84b5a6548d5af6772a9e authored over 2 years ago by Chris Bielow <[email protected]>

MQEvidence Test now working with fasta

9c865feb468d5ed941f854a971fca676421ea2ee authored over 2 years ago by lennykovac <[email protected]>

add tests

6e9dda69331a78b2555281bb2774899c4dad02d9 authored over 2 years ago by bielow <[email protected]>