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

[FIX] NucleicAcidSearchEngine: fixed problem with multithreaded progress logging (due to dynamic scheduling)

c2997d463263d36c4e46c4a3856ed2f02aa1fc3b authored almost 6 years ago by Hendrik Weisser <[email protected]>

Merge pull request #43 from hendrikweisser/rna-lfq

[FIX] NucleicAcidSearchEngine: fixed multithreading (OpenMP)

77f2e92defa7555225cf91d9a10dbb5d8cf81f36 authored almost 6 years ago by Samuel W <[email protected]>

Merge branch 'rna-lfq' of https://github.com/hendrikweisser/OpenMS into rna-lfq

813469bf92efb6ba18270524a7bc0a4e67ecc03f authored almost 6 years ago by Hendrik Weisser <[email protected]>

[FIX] NucleicAcidSearchEngine: fixed multithreading (OpenMP)

c79530e3e5f278c671518b4ed914e863466a2549 authored almost 6 years ago by Hendrik Weisser <[email protected]>

[FIX] NucleicAcidSearchEngine: fixed multithreading (OpenMP)

d3d36a21a46648307aed553b1f89a10e8237bd8b authored almost 6 years ago by Hendrik Weisser <[email protected]>

[DOCU] update docu

0c69f8b4bc029ce0db99fb321afee052a4febd12 authored almost 6 years ago by lars20070 <[email protected]>

[DOCU] negative areas documented

10b89b57f76c7bab10fee031825532f9acf04c9c authored almost 6 years ago by lars20070 <[email protected]>

Revert "[BUILD] travis cache restart"

This reverts commit 89c5cd7f2d9d343b3d63fc6bab18e08dcd969c05.

949028ea15f02fb80248861f42f0582729ba74e4 authored almost 6 years ago by Hannes Roest <[email protected]>

[BUILD] travis cache restart

- only build TOPP tools in order to reset the ccache and allow travis to
complete an OpenMS bu...

4949f78c725a45e5e83ac16d7267f481a72e45c2 authored almost 6 years ago by Hannes Roest <[email protected]>

Remove obsolete remark from docs

c4cbdb3b0d73a848039ab05ad243972235c29439 authored almost 6 years ago by Michał Startek <[email protected]>

Rewrok API: split wrappers into generator and non-generator versions

87f96792dd7580c7ee60403f466edc5cafc6791f authored almost 6 years ago by Michał Startek <[email protected]>

Merge pull request #42 from hendrikweisser/rna-lfq

Label-free quantification of RNA

680a744c03ee83ca4ca4f494c0e82c938188eeae authored almost 6 years ago by Samuel W <[email protected]>

Docs clarification

14578e79bb52ea71ff6210c7c33378c581ed9f37 authored almost 6 years ago by Michał Startek <[email protected]>

Typo fix

9c5c1a9cf342a3b82ac100e18541e9a2ea4b3b79 authored almost 6 years ago by Michał Startek <[email protected]>

Merge branch 'rna-ms2-id' into rna-lfq

492874d9053d0b414f9940625d4abb3e08db7b8d authored almost 6 years ago by Hendrik Weisser <[email protected]>

[FIX] fixed unspecific digestion of RNAs (now ignores missed cleavages), simplified code

c791f655b0b4ddf4550516b46f5ed5499580e8e0 authored almost 6 years ago by Hendrik Weisser <[email protected]>

[fix] fixed IdentificationData constructor.

1f5159af7288071c1db451f1c5466572733b1417 authored almost 6 years ago by poshul <[email protected]>

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

347722843d2bede417fe150abf29c64f3c3f9e59 authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

Merge pull request #41 from hendrikweisser/rna-ms2-id

Improved tests for class "IdentificationDataConverter", and related fixes (EDIT: and "Identifica...

0db0468530baa2966635de98317f70cff4871de3 authored almost 6 years ago by Samuel W <[email protected]>

Merge branch 'rna-ms2-id' into rna-lfq

241d825a539be2250c9f1d86530be020a32a035e authored almost 6 years ago by Hendrik Weisser <[email protected]>

Merge branch 'rna-ms2-id' of https://github.com/hendrikweisser/OpenMS into rna-ms2-id

179977376d7e5ff249489c43045e92686342fb1e authored almost 6 years ago by Hendrik Weisser <[email protected]>

Merge branch 'develop' of https://github.com/OpenMS/OpenMS into rna-ms2-id

0549ecef83787bc1908cc458c1976c0c4fb8784b authored almost 6 years ago by Hendrik Weisser <[email protected]>

[FIX,TEST] updated numbering of PSMs in mzTab exported via 'IdentificationDataConverter', updated test file

b05584f4626d3f98ab45b1e13ccbbfc782814309 authored almost 6 years ago by Hendrik Weisser <[email protected]>

[FIX] replace hostname in mascot query

Was replacing all occurrences of the hostname. Wrong in case of equal servername.
This is on to...

e9721b71859e50acf31037079beaeaab6b521671 authored almost 6 years ago by jpfeuffer <[email protected]>

added missing newline. add more information why correction failed

76f38df98a4a8ab4c9301f6a62462b1072a11a29 authored almost 6 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #3846 from Leon-Bichmann/fix/CometAdapter

delete valid strings for comet version

09ebd2eaecd3bf1a702e633e4a3545bf10e99fc0 authored almost 6 years ago by Timo Sachsenberg <[email protected]>

Update IsoSpec sources to 1.9.1

432113ba334f9fdbcc96e294c35f33a068228234 authored almost 6 years ago by michalsta <[email protected]>

Merge branch 'poshul/hendrikweisser-rna-ms2-id' into rna-ms2-id

a671a1f8b99505b6add77c09062e40be82106e10 authored almost 6 years ago by hendrikweisser <[email protected]>

Merge pull request #2874 from hendrikweisser/FFMetId

New tool: FeatureFinderMetaboIdent

1bfc5587a541bfe466dc2b4e3aa2945de67be3c7 authored almost 6 years ago by Timo Sachsenberg <[email protected]>

[FEATURE] improved export of scores in 'IdentificationDataConverter::exportIDs'

ca059e3dea20e67555ab384b5e1e71c7c720bee3 authored almost 6 years ago by Hendrik Weisser <[email protected]>

[FIX,TEST] small fix in 'IdentificationDataConverter::exportIDs'

590f69ffbe3a3376bc5744aff08569d34186f319 authored almost 6 years ago by Hendrik Weisser <[email protected]>

[TEST] updated test file for mzTab output from 'IdentificationDataConverter'

d4e477fd961f91350b739ccd72f5868882c92ea1 authored almost 6 years ago by Hendrik Weisser <[email protected]>

[FEATURE] improved export to mzTab in 'IdentificationDataConverter', incl. sorting of rows

ddb36f4c3ca5dce783ba20523f40d7e20d743c6d authored almost 6 years ago by Hendrik Weisser <[email protected]>

[API] reference score types in software tools (to allow prioritization), not the other way around, in 'IdentificationData' and related classes

fb259092d97720251dda50a46bc345761a7d91f9 authored almost 6 years ago by Hendrik Weisser <[email protected]>

[API] refactored handling of scores and processing steps in 'IdentificationData' and related classes

a1e92573490689b3131a24a3917825f01c920eb8 authored almost 6 years ago by Hendrik Weisser <[email protected]>

[INTERNAL] replaced include guards with '#pragma once' in 'IdentificationData' header files

05c7b1b3e3ca4adf617421a099f060b133afcb90 authored almost 6 years ago by Hendrik Weisser <[email protected]>

[INTERNAL] moved new class 'AppliedProcessingStep' to its own file, registered new header files

a1d0855019341bccab2887080817de0a5f24d863 authored almost 6 years ago by Hendrik Weisser <[email protected]>

[COMMENT] NucleicAcidSearchEngine: removed outdated comment

3f39a79db994a8cceba5d39078a33ddca9aee44e authored almost 6 years ago by Hendrik Weisser <[email protected]>

[FIX] NucleicAcidSearchEngine: reverted faulty renaming of parameter 'decharge_ms2', made that parameter advanced

b81766f1398abcce8cb3fb0609548b1783184139 authored almost 6 years ago by Hendrik Weisser <[email protected]>

[PARAM] NucleicAcidSearchEngine: updated defaults of some 'precursor' parameters ('isotopes': 0-4, 'max_charge': -20, 'potential_adducts': Na+)

3ffd646be84cac187a58caa45c5b01a29146395a authored almost 6 years ago by Hendrik Weisser <[email protected]>

[FEATURE] include adduct information in mzTab output generated by 'IdentificationDataConverter'

5ce14096201918ad5cdb6c79fd4b756753c1db97 authored almost 6 years ago by Hendrik Weisser <[email protected]>

[INTERNAL] revert renaming of c'tor arguments in class 'MoleculeQueryMatch'

7f0cda4f1ba83d698c1b909e1fa4af09b6bf6750 authored almost 6 years ago by Hendrik Weisser <[email protected]>

update description

92939e511a281d0132f95ecb1ff5be945baae815 authored almost 6 years ago by Leon Bichmann <[email protected]>

[TEST] problematic example for Simpson rule added

aceeb4f68ef6eec807fd97ffef6b808e00adb6a3 authored almost 6 years ago by lars20070 <[email protected]>

delete valid strings for comet version

70a3da12c6f98f2f3340025c9d47d45938a7ae9f authored almost 6 years ago by Leon Bichmann <[email protected]>

Merge pull request #3840 from lars20070/fix/IDMapper

change default params in IDMapper

bac0c7dc52e5f4658b81c7d8a0422fd63f0422ce authored almost 6 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #3836 from lars20070/feature/SpectrumHelper

new makePeakPositionUnique() method for SpectrumHelper

8408374f07904ae674fcc6daea1f428c33c4544d authored almost 6 years ago by Timo Sachsenberg <[email protected]>

Merge branch 'develop' into feature/MRMFeatureSelector

61f19714c18b8f75055d0e1008db46edbeb3d460 authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

refactor: Move SelectorParameters to MRMFeatureSelector. Pack parameters into a single object.

ca01c9b68f0c9345673949069566153b0ba7b3a6 authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

docs: optimize in derived classes

e549ccdc73659e3e082a89865a6543f59707f02c authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

[ADD] CompoundInfo struct; all struct to header; reset des, sumformula

to unkown; beginning to add extracComment function

da476848affbde9a54a4b65a76ce0d84078fd3cb authored almost 6 years ago by oliveralka <[email protected]>

Merge pull request #3843 from OpenMS/pix_cython025

pin cython version to 0.25

30967de1619590710dab6393a7ac3f03e02722ec authored almost 6 years ago by Timo Sachsenberg <[email protected]>

pin cython verison to 0.25

a79ec33907bf88e1e7fd0df187864160e1501ea5 authored almost 6 years ago by Timo Sachsenberg <[email protected]>

docs: Document class parameters

6029f85886039723502cddac45a266b05b3ba2e9 authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

refactor: replace strings with enum class

e705740fb30286cad1ce5aa395e7806c3b40cfb2 authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

contrib fix?

7accbf2f5d259f98705541d49d7471843728946b authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

Update ModificationDefinitionsSet.pxd

de650e2a47c606da37c971ed10ff4a491716e904 authored almost 6 years ago by Timo Sachsenberg <[email protected]>

Update ModificationDefinitionsSet.pxd

7e9218faec43097f1eb7fb99becf84fe672d6c9b authored almost 6 years ago by Timo Sachsenberg <[email protected]>

Merge branch 'develop' into feature/MRMFeatureSelector

519783c8855ef77f3cf3917b6de6718149bc9c91 authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

Merge pull request #3841 from OpenMS/timosachsenberg-patch-3

[NOP] small warning fix

0327194808b7e78649a58d56a1a0192ea8d8c5ae authored almost 6 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #3816 from FabianAicheler/fix/FixNegativeModeGrouping

fixed negative mode decharging for charge!=0 features from FF

3c8f9ce402a99a4367f6bbd367ba04615c374496 authored almost 6 years ago by Timo Sachsenberg <[email protected]>

chore: remove wonderful whitespace

4361ea3a57a850d1444cf251ea62b06adfec770e authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

docs: MRMFeatureSelector

47d40cd3d4a6c88fb2e5a6fba1e9cbb095243658 authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

style: avoid underscore in method names

5a95db7347445db4138774ca788b05bffb217f3b authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

docs: MRMFeatureFilter::getDefaultParameters()

6c5c737093265a036711ebd236049936192f421b authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

[FIX] rm cout

aa876729389916fc80b3fb38376f3e02539420a1 authored almost 6 years ago by oliveralka <[email protected]>

remove legacy code

5e14a288e48f2df7adc0e1f0cd0ae02236c7d22d authored almost 6 years ago by lars20070 <[email protected]>

[ADD] adducts AMS, add sourcefile info, add accessioninfo

3f90a9ffe73c3fea17df0118f50e702110b9b63a authored almost 6 years ago by oliveralka <[email protected]>

updated testfiles to new output

f3c8a4f3c81ae9efc98dc13be45eb59749d05f30 authored almost 6 years ago by FabianAicheler <[email protected]>

style: newline on output of AbsoluteQuantitation

83cc3fea6146321e23f6881251bf2124ffeb489d authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

group annotation to all featureXML output features

453c92d8ce6e92925d3b9016934a2d9640dd57ef authored almost 6 years ago by FabianAicheler <[email protected]>

chore: codacy code quality guidelines

7e7b8e4f829c8a3a31c042d98b0c422799b427f2 authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

[ADD] add deisotoping

29aea540aa7acaa369739e471f6144831f2a4a76 authored almost 6 years ago by oliveralka <[email protected]>

Make the IsoSpec_test produce a lot less unnecessary messages

eb7c73341937687ec89875314d26c24624fed5f5 authored almost 6 years ago by Michał Startek <[email protected]>

Make IsoSpecWrapper throw OMS Exception, not std::logic_error

bd247215a98aafb81c2e11d3b6545f5b4bab08f0 authored almost 6 years ago by Michał Startek <[email protected]>

Full tests for entire IsoSpec*Wrapper APIs

0ac5303e83da104f47e31b39dbdd40248b2e2b2e authored almost 6 years ago by Michał Startek <[email protected]>

Some more cleanups in IsoSpec tests

1968c7dadbce29f55c570e935bff71270de22a5d authored almost 6 years ago by Michał Startek <[email protected]>

[COMMENT] NucleicAcidSearchEngine: removed outdated comment

f99eed2c10d406e7b34f104a2bc5cbd1e2e2a635 authored almost 6 years ago by Hendrik Weisser <[email protected]>

[FIX] NucleicAcidSearchEngine: reverted faulty renaming of parameter 'decharge_ms2', made that parameter advanced

569ef949c801863a12c23cff85c1c89da51520f9 authored almost 6 years ago by Hendrik Weisser <[email protected]>

use string instead of flag for use_centroid_rt param

efea71faac14afe9ef74ddda7276d0784ecc6295 authored almost 6 years ago by lars20070 <[email protected]>

Clean up test code a little bit, upgrade for IsoSpecTotalProbWrapper

2b37ddb24ba60fc00047b0a80fa3a213168f5cde authored almost 6 years ago by Michał Startek <[email protected]>

[PARAM] NucleicAcidSearchEngine: updated defaults of some 'precursor' parameters ('isotopes': 0-4, 'max_charge': -20, 'potential_adducts': Na+)

ece81a70d8ee60e7973d4b461a067d51109f3f1c authored almost 6 years ago by Hendrik Weisser <[email protected]>

[REFACTOR] CleanUp FeatureMapping

dd7efc23777a6ef7b699990bb3472d85fce0ddb1 authored almost 6 years ago by oliveralka <[email protected]>

style: Size and String

0d13f728878f3761d027bb841c0961a54834971b authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

style: braces on same column

b78945b84da0f4fd1f71e14aeadb6b40ea81ae36 authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

Merge branch 'develop' into feature/MRMFeatureSelector

95d4b309ccbb87478a67e05cedfd40e258f06ac4 authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

feat: MRMFeatureScheduler.pxd pyopenms wrapper

5ebcc17b9c6252462aa84cc7fe12e19de8194f75 authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

chore: remove unnecessary #includes

0d295e4c92e18000be0524fafc8a2f7ed4a7fc05 authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

docs: complete documentation

style: rename methods to reflect openms style guidelines

6df57405df3646f0e8c917c141da0134d70cf2a4 authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

[NOP] small warning fix

8c987e955928b8975783bbdaa3f18a6716192967 authored almost 6 years ago by Timo Sachsenberg <[email protected]>

[FIX] rename functions

48ef2bd51d765ff34da5b25a0b4dde9488d5a019 authored almost 6 years ago by oliveralka <[email protected]>

Pull in IsoSpec-1.9.0 (stable)

0a44e0e23a77707e5cf9e85e742ff2d770621359 authored almost 6 years ago by michalsta <[email protected]>

Merge pull request #3839 from OpenMS/fix/warning

[NOP] remove compile warning (expression always true)

d80f3960369d32162e3025a2cf0a7cce3bde87a5 authored almost 6 years ago by Hannes Roest <[email protected]>

Expose trim in API in anticipation of 2.0 changes; improve & clarify the docstrings a bit

5b115d52145acf95c4443c7f234d41e401dde1e7 authored almost 6 years ago by Michał Startek <[email protected]>

Merge pull request #3830 from mwalzer/pthread-cmake-find

added pthread find to cmake

824a6b7f7bc5bb71a0f974f9b7b42b029a9292e5 authored almost 6 years ago by Timo Sachsenberg <[email protected]>

docs: MRMFeatureSelector wip

88ba4ed2abc2ca29700bc5a69d55ffff09b16074 authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

[ADD] Remove duplicate entries (sort, unique)

0fd2bc92e530fd487d3c2648d159a9eb82a9efb4 authored almost 6 years ago by oliveralka <[email protected]>

fix tests

6c8bdd8b7ffcb28b96a2866f37a01b2ec8f9f416 authored almost 6 years ago by lars20070 <[email protected]>

docs: MRMFeatureScheduler

19918328a2deb9863e2de8c6beef48b478dfe1f8 authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

set use_centrois_mz = true

49a9a8f1a7cb4071f97e32eb7321a1015b238d9d authored almost 6 years ago by lars20070 <[email protected]>