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

Merge pull request #4857 from cbielow/pepind_auto

PeptideIndexer explicit 'auto' mode for enzyme

6fb63c9d8913efba7f81425d5a18f18641023f56 authored about 4 years ago by Chris Bielow <[email protected]>

Merge pull request #4855 from enetz/fix/projection_val_names

[FIX, GUI] fixes OpenMS#4828, wrong labels in the projections

e6c58439c5f10d2f96b4486c663fd29f9b60dd6c authored about 4 years ago by Timo Sachsenberg <[email protected]>

* use 'auto' as default for enzyme and specificity

25c0b7f7dd59e9fd5c3d9a678d96141f2ff84f55 authored about 4 years ago by Chris Bielow <[email protected]>

[FIX, GUI] fixes OpenMS#4828, wrong labels in the projections

6bbc7c59076ecc833a7259650a45d06e401cd366 authored about 4 years ago by Eugen Netz <[email protected]>

add warning to PSMFeatureExtractor

257d0751f810db600801673e0662d24ad63839a2 authored about 4 years ago by Leon-Bichmann <[email protected]>

Create PULL_REQUEST_TEMPLATE.md

c9133a753ed43263757c4b851f5a192403cdd470 authored about 4 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #4849 from Leon-Bichmann/fix/scan_regex

Adapt Regex when parsing XTandem Percolator output files

cbd54972bf43a7138ea73c2c6586971432df105c authored about 4 years ago by Timo Sachsenberg <[email protected]>

Try "txt" as intermediate format for InspectAdapter

50ccda38b114b87d011459301ed73badf7f6de29 authored about 4 years ago by jpfeuffer <[email protected]>

add dollar to regex

58d13a9842eb2b2ccfd16bfcbe188d367d777fc8 authored about 4 years ago by Leon-Bichmann <[email protected]>

write out native ids and spectrum references

094dd728710b40b7a69819a2cdb299032e97780f authored about 4 years ago by timosachsenberg <[email protected]>

Merge pull request #4840 from Waschi97/develop

Fixed Bug in MzTabFile which yielded a Compiler Error

7dc73bf9e3cb526c116c50d4e04e316559d529fd authored about 4 years ago by jpfeuffer <[email protected]>

Merge branch 'develop' into feature/exportDBSuitToLibrary

merging bug fix

73649efddf6bff1127d0f2275f791ceb0eca9c6a authored about 4 years ago by Tom Waschischeck <[email protected]>

bug fix in MzTabFile

f039796df8f4de27eb5fe51b2d03342f2d8b5257 authored about 4 years ago by Tom Waschischeck <[email protected]>

Update mimetypes.xml

b9f7c9d956e05e9cfa388ae32f36df2e08fea0db authored about 4 years ago by jpfeuffer <[email protected]>

moved all functions to Suitability class - not compiling atm

6f5f89441a5c134e7bad575d08fa3a0a38db51d3 authored about 4 years ago by Tom Waschischeck <[email protected]>

Add more to mime.types

c8e54da30f41ceb2b23b389761f482a57020e38d authored about 4 years ago by jpfeuffer <[email protected]>

Add splib to mimetypes

f089ad3d7bc3be98d2054b3d4d0bf8770978bba4 authored about 4 years ago by jpfeuffer <[email protected]>

Merge pull request #4838 from cbielow/FileInfo_ext

Fixes

922a11192bf5960c749437e6cff19aa7269c3634 authored about 4 years ago by Chris Bielow <[email protected]>

fix tests which are writing to source tree

d546aaffd5508ac6293042202803f60f4ff265f6 authored about 4 years ago by Chris Bielow <[email protected]>

make -out optional

628fbef31c6a9dbd5795bf62454621f04a0c9520 authored about 4 years ago by Chris Bielow <[email protected]>

Merge pull request #4837 from cbielow/FileInfo_ext

[DOC ] add SwathWizard documenation

02ec4d48fbd3ab6a3056ab4ce58a74d96b72b153 authored about 4 years ago by Chris Bielow <[email protected]>

add SwathWizard documenation

fa00cc753f583f088a02b1d0a192c92394803f17 authored about 4 years ago by Chris Bielow <[email protected]>

Merge pull request #4836 from cbielow/FileInfo_ext

[FEATURE] FileInfo: more information for Raw files

ba5decd97cb156cd21fbf64e59ae175ea7c51048 authored about 4 years ago by Chris Bielow <[email protected]>

remove empty line for CI

d268ef7969120bf9ed194a0d82828eb08a760aaa authored about 4 years ago by Chris Bielow <[email protected]>

add distribution information for charge and activation-method of MS2 data in raw(mzML etc) files

dc93495e93ba3918279f8acb91b4b61f448ad138 authored about 4 years ago by Chris Bielow <[email protected]>

std::min to std::min<unsigned long> in line 3187

5c361f5671f6c8548b52838434acae2e33214d20 authored about 4 years ago by KyowonJeong <[email protected]>

Merge branch 'feature/FLASHDeconv' of https://github.com/JeeH-K/OpenMS into feature/FLASHDeconv

5a364142023c5371397d0839242ec2d8ca54d821 authored about 4 years ago by KyowonJeong <[email protected]>

.

c3530fd3ad965570f3c61a9f08db0ad8e2f8b6bf authored about 4 years ago by KyowonJeong <[email protected]>

Merge pull request #4829 from OpenMS/fix/consIDSPLocation

[FIX] ConsenusID reading from wrong meta data

902f74bdbb674137bc37595eaaf546389ed04a5d authored about 4 years ago by jpfeuffer <[email protected]>

Fix splitting of modifications for ConsensusID after Percolator.

50216c2b0f89d6bc1e5fcad89ef6fe2545111434 authored about 4 years ago by Julianus Pfeuffer <[email protected]>

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

fabdfa250cd376f839b35ecfcfe861c90df9f281 authored about 4 years ago by kyowonjeong <[email protected]>

Negative mode implemnted

9609b1407b66a471183186fcdd7b35d5b90cfeda authored about 4 years ago by kyowonjeong <[email protected]>

Merge pull request #1 from poshul/feature/FLASHDeconv

Feature/flash deconv

c361bda3424eff73831825b95a1a0baed8e19b56 authored about 4 years ago by JihyungKim <[email protected]>

[fix] fixed inconsistent capitalization

c1ac269005afdd305b319cc24271b5f6be001fe9 authored about 4 years ago by Samuel Wein <[email protected]>

[fix] Corrected capitalization error to match other FLASHIda* file. Pruned old MassTraceDetection files

Reverted some comments in MSSpectrum.cpp

2d3d701312709491354b2dd4ee31515a9a4268bb authored about 4 years ago by Samuel Wein <[email protected]>

Merge pull request #4831 from cbielow/toppview_chrom

Minor INI/TOPPAS improvements

c1cf9bb1e7b1279e61f952faeb914887c2ec4e75 authored about 4 years ago by Chris Bielow <[email protected]>

[fix] fixed capitalization issue in sources.cmake file

f02f0a3ec6bfb4f981be9d077be610abc77e6cdd authored about 4 years ago by Samuel Wein <[email protected]>

Merge remote-tracking branch 'JeeH/feature/FLASHDeconv' into HEAD

027f48ea1389b6c9e86133634531ef71aa138d74 authored about 4 years ago by Samuel Wein <[email protected]>

Make the initial Parameter editor big enough && label store and load buttons more precisely

41f77f9f45c499a0d703005bde4fea0775453214 authored about 4 years ago by Chris Bielow <[email protected]>

[FIX] ConsenusID reading from wrong meta data

5da3b4783bdf06b27aafcbcf1988ec235b257323 authored about 4 years ago by jpfeuffer <[email protected]>

output polising for new release..

52c68569cdb67b23bb3a806b06a37eb1220ea7fb authored about 4 years ago by kyowonjeong <[email protected]>

Merge branch 'develop' of https://github.com/OpenMS/OpenMS into update/unimod_2020

75719107295cf653f708f3a0a2606d934dd3c69e authored about 4 years ago by Eugen Netz <[email protected]>

[COMMENT] fixed a comment

9f8182d640655cab632a4e8ce10b9aa3e3ea4a71 authored over 4 years ago by Eugen Netz <[email protected]>

[TEST] updated test files

a02cf725cc6ee6a2818697c9654714bfebdd5222 authored over 4 years ago by Eugen Netz <[email protected]>

[FIX,TEST] updated class tests for multiple neutral losses for mod residues

d949e86344f4de74750b7086db00578b2a872a27 authored over 4 years ago by Eugen Netz <[email protected]>

[FIX] updated OMSSAAdapter for multiple neutral losses for modified residues

As the OMSSAAdapter expects only one loss, the first in the vector is used.

8d7233dd5dad8054eb42f7d5fd13ca1cf15cdbfb authored over 4 years ago by Eugen Netz <[email protected]>

[FIX] Support for multiple neutral losses for modified residues

d2cfc140d2da22ff8de601b809a928137ad1105a authored over 4 years ago by Eugen Netz <[email protected]>

Parameter description polished.

523ab284b3a98e958bf9600d94b0aa2376ef0dec authored over 4 years ago by kyowonjeong <[email protected]>

FLASHDeconvAlgorithm.cpp rewritten + bug fixed

0f69aefd8cab927c6e47557765c0fade475868fe authored over 4 years ago by kyowonjeong <[email protected]>

FLASHDeconvAlgorithm.cpp rewritten + bug fixed

e8476635bbd733948fddcb3cf69cc72fac90b959 authored over 4 years ago by kyowonjeong <[email protected]>

FLASHDeconvAlgorithm.cpp rewritten

4529df7ce7ca0697da664f5f41f31e29ffd9bb7a authored over 4 years ago by kyowonjeong <[email protected]>

FLASHIda.cpp memory menaged..

f593e85df93bb2b4b55406e73860ca614a96d80e authored over 4 years ago by kyowonjeong <[email protected]>

Merge pull request #4823 from cbielow/doc_extra

Doc extra

e6774d1d7800a47e453f0b1be1944d1948961c73 authored over 4 years ago by Chris Bielow <[email protected]>

.

04e74a7c72b255542fc9f9d34c2b34c3b822e7a2 authored over 4 years ago by KyowonJeong <[email protected]>

Memory leak 100% resolved for FLASHIda

e4db574b50cab5994103f5019f45914c142c656d authored over 4 years ago by KyowonJeong <[email protected]>

Merge pull request #4820 from jpfeuffer/fix/mzTabColRestriction

[FIX] PR enforcing equal column sizes showed bug probably introduced …

b81909b51b9762c8c856a4ef0171a368597bc093 authored over 4 years ago by Timo Sachsenberg <[email protected]>

* add documentation how 'conf' file behaves

* print stderr on error without requiring debug flag

26a3c854b0495229899412e737e7e1a700c62362 authored over 4 years ago by Chris Bielow <[email protected]>

allow returning of stderr/out from external process

7691280690bcb4e99c15853c19b04cd17462a374 authored over 4 years ago by Chris Bielow <[email protected]>

.

6760e136bd8c1c576483f929e86bcf3c39690df1 authored over 4 years ago by KyowonJeong <[email protected]>

FLASHIda.cpp memory menaged..

20ee9265070ef6ae608d6afc21cf3b248541c531 authored over 4 years ago by kyowonjeong <[email protected]>

Merge pull request #4822 from cbielow/doc_extra

Doc extra

d7fed205a776a3b950cd1036e8a89859f420a12b authored over 4 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #4815 from OpenMS/timosachsenberg-patch-2

[FIX] change spectrum index to integer type in novoradapter

d46119e5b2dfb615ad3a26c91c7a66161a1417ae authored over 4 years ago by Chris Bielow <[email protected]>

fix ci

6e5fdc53a48186cb557fc245c912f03393094934 authored over 4 years ago by Chris Bielow <[email protected]>

FLASHIda.cpp memory menaged..

b1585046331f177833fb889629fd183b47ae92d9 authored over 4 years ago by kyowonjeong <[email protected]>

fix file-not-open warning and compile errors

7651c051ce54eb15f38d3135f4796c902fa79a56 authored over 4 years ago by Chris Bielow <[email protected]>

fix test

362c9d12b64d9ce283b0ad1c43a74657884883a7 authored over 4 years ago by Chris Bielow <[email protected]>

fix Ci error

9c5912d55d78c5a0384393b26ea5bd0cdad5ad23 authored over 4 years ago by Chris Bielow <[email protected]>

add docu that only plain mzML is supported by X!Tandem

8b023c47f8ba9fd3daae031cb5af692e00c40f52 authored over 4 years ago by Chris Bielow <[email protected]>

add configuration file option to MSGF+

44de91ac0e1423a01e9ce29d394169806b7aa067 authored over 4 years ago by Chris Bielow <[email protected]>

FLASHIda.cpp memory menaged..

a77b097b0495f0e92f75bc57f873f759b231631a authored over 4 years ago by kyowonjeong <[email protected]>

added some statistics for excluded calibration points

26045ead537cf6ad50893a11d614855b0e0d4ee7 authored over 4 years ago by Chris Bielow <[email protected]>

FLASHIda.cpp memory menaged..

0f221d9d2a6388d92daa215ddede82d3d8438d8d authored over 4 years ago by kyowonjeong <[email protected]>

Memory leak resolved..

707ea4b6d12f5dccde31f64bdb72a545b441ca34 authored over 4 years ago by kyowonjeong <[email protected]>

Add Search Engine information for idXMLs

df46c92d03687e6571aaa9d9f504e1681f79d95a authored over 4 years ago by Chris Bielow <[email protected]>

[FIX] PR enforcing equal column sizes showed bug probably introduced in stream export.

ada210436dcc7c3de2f2b98f39473644d9a91189 authored over 4 years ago by Julianus Pfeuffer <[email protected]>

output rearranged.

7c82690c6b8f85da5117c07a38b7cd19339bea5f authored over 4 years ago by kyowonjeong <[email protected]>

QScore.cpp added

333fef78b69ac53000ab9e43d2423df85c4be0f0 authored over 4 years ago by kyowonjeong <[email protected]>

Merge pull request #4818 from OpenMS/fix/consensusID_SP

[FIX] Add rest of search params during ConsensusID

789651072233f537f003cca4df97530566f9871d authored over 4 years ago by jpfeuffer <[email protected]>

[FIX] Add rest of search params during ConsensusID

58ab9790e5071021994c36e26e35bb5c04845e48 authored over 4 years ago by jpfeuffer <[email protected]>

FLASHDeconv parameter renamed + mzml out implemented

8b943fb9a6430504073cce24b1a6ef5036425d66 authored over 4 years ago by kyowonjeong <[email protected]>

Merge pull request #4814 from Waschi97/feature/DBSuitabilityTool

FDR filtering in DBSuitability Tool

f8ee6bb2d0bb0022c483ac02fac7c8db43bd28b6 authored over 4 years ago by jpfeuffer <[email protected]>

change spectrum index to integer type in novoradapter

9fdc45478031d0807f8b9ab6f8580436f50301b6 authored over 4 years ago by Timo Sachsenberg <[email protected]>

FLASHIda interface polishing.. 4

5f50824688909e6c374576f1e2137ee8b21a67ed authored over 4 years ago by kyowonjeong <[email protected]>

readability changes

9ee2837e248937c3dd1d9ea4667db6a999158f2f authored over 4 years ago by Tom Waschischeck <[email protected]>

sorting hits, tests changed, minor other changes

67fe1d0f19290e215f64d372b347a85e6625c6a0 authored over 4 years ago by Tom Waschischeck <[email protected]>

[FIX] FeatureFinderIdentification: fixed handling of custom peptide modifications defined only by mass shift

7ee4a97184c2c8522b5420dba8cb7c7da1dce950 authored over 4 years ago by Hendrik Weisser <[email protected]>

FDR filtering in DBSuit

5a26db72aa841ba6b84bd06e115b314a2e70c34d authored over 4 years ago by Tom Waschischeck <[email protected]>

[FIX] FeatureFinderIdentification: fixed oversights from adapting algorithm to new ID data structures

1b5ebffde942637dfe110ecde5ecb95b835521b9 authored over 4 years ago by Hendrik Weisser <[email protected]>

[DOC] IdentificationDataConverter (export to legacy structures): clarified that output is appended without clearing

72bbfb21e3bb6ba24fd6c2ec9985b4499b02064f authored over 4 years ago by Hendrik Weisser <[email protected]>

[INTERNAL] IdentificationDataConverter (export to legacy structures): append output without clearing; better handling of charge parameter information

272e26bc3653a22dae3a3819ca0d80da62f4538a authored over 4 years ago by Hendrik Weisser <[email protected]>

.

c310ddba559df0cac04352fc374120aa7c571e3a authored over 4 years ago by KyowonJeong <[email protected]>

[FIX,TEST] fixed IDMerger (.oms input) test - missing var. mods

4dbed1da78a8dd06fb90066b6af2e41c16776c81 authored over 4 years ago by Hendrik Weisser <[email protected]>

[FIX,TEST] small update to NucleicAcidSearchEngine test

14eee773b86ce3cd5a7e71f1dcc6ce83b589426e authored over 4 years ago by Hendrik Weisser <[email protected]>

[FIX] redo change lost in previous merge

2939896f6fd954fed8ca010e16f25747fc1c16ef authored over 4 years ago by Hendrik Weisser <[email protected]>

Merge branch 'id-file-format' into idfile-integration

064fc31d4c4622fc82caf373f66292f539994f92 authored over 4 years ago by Hendrik Weisser <[email protected]>

[FEATURE] IdentificationDataConverter (export): sort peptide IDs by RT for increased reproducibility

8bba7db1d0724f9f9212aaa493c05ff822b2c70e authored over 4 years ago by Hendrik Weisser <[email protected]>

Merge branch 'develop' of https://github.com/OpenMS/OpenMS into id-file-format

b2e3f9f0e40c64d028ebdf320d816802ab483567 authored over 4 years ago by Hendrik Weisser <[email protected]>

beta version

829204ae0cd5e848eeaa75218ef5978e53c0f204 authored over 4 years ago by KyowonJeong <[email protected]>

Merge pull request #4791 from Waschi97/feature/DBSuitabilityTool

Database Suitability TOPP Tool

c1e6b66ffa2c41cae58580c35e918e55eaf86750 authored over 4 years ago by jpfeuffer <[email protected]>

charges and avg mass output from getIsolationWindoes

edbc85758760c99e479b6966980d781f304655e1 authored over 4 years ago by KyowonJeong <[email protected]>