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

[FIX] IdentificationData: add adducts to move c'tor and 'swap'

6d4d1dca85eff87fd5bffa64d4e90ec3fc737007 authored over 3 years ago by Hendrik Weisser <[email protected]>

minor

ae0166a47c93e5a340a40454375127669092bbe3 authored over 3 years ago by bielow <[email protected]>

fix compile error

ec3363283ebea96bdf454bd18ab818a031702b67 authored over 3 years ago by bielow <[email protected]>

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

7ca9af8083c8a662334b5d14177bd6aae451badd authored over 3 years ago by bielow <[email protected]>

switch to last 3 python versions

e36563be22c79903678d3f5a078f75c9f5d151b0 authored over 3 years ago by oliveralka <[email protected]>

fix TOPPAS crash when double clicking disconnected output node

3c37e01428f6c3eb6d9505fd214214849fada294 authored over 3 years ago by bielow <[email protected]>

fix seed for internalcalibration tests

239760c590fded89afc3571f956f735f8956a9f1 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

use only 3.9 to see if it is a specific issue; print path windows

578b3495b2d78ec91aadb5f03d5bb72cad011242 authored over 3 years ago by oliveralka <[email protected]>

TextExporter output filetype(s) (#5121)

* add out_type option to TextExporter with tsv, csv support

* adjusted .ini files

* remove...

7b267436d473a1ba35c2955d6e20fa7265d2fd63 authored over 3 years ago by RobertDeibel <[email protected]>

update travis script (#5171)

b3915b88214f9abeb20fe994b3c937537e423b9e authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Extends precondition check bounds to equality (#5170)

85924bf475c4e4cd2ea585d21b91371918357fc3 authored over 3 years ago by bertrandboudaud <[email protected]>

mascot batch processing (#5162)

* batch processing

* fix

* online edits ftw

* fix

* fix
...

fe8f3082d434ef04fd3a475eba32a4b9ed81b1c0 authored over 3 years ago by Timo Sachsenberg <[email protected]>

[API,TEST] IdentificationData: added convenience function 'getMatchesForObservation'

c19b489180052465cad8fc9c92cf5ce142916a2d authored over 3 years ago by Hendrik Weisser <[email protected]>

[FEATURE] IdentificationData: remove unused adducts in 'cleanup' function

126fff960bc0c8b90b05255e1c18d7b32571e0e2 authored over 3 years ago by Hendrik Weisser <[email protected]>

[TEST] test loading of IDs on feature maps from SQLite file

4d2e7712f5f7d619427e155f6bbc0e4059781f98 authored over 3 years ago by Hendrik Weisser <[email protected]>

[FEATURE] SQLite file format for feature maps: support meta infos on 'DataProcessing' items

cac3e3d50cbdbf43656f8272a3c64c1580288b98 authored over 3 years ago by Hendrik Weisser <[email protected]>

[INTERNAL] IdentificationData: renamed 'InputItem' -> 'Observation', 'InputMatch' -> 'ObservationMatch'

08cbe98371e4233086252e76a2e00a38b0aedd7b authored over 3 years ago by Hendrik Weisser <[email protected]>

[TEST] test for reading/writing of feature maps from/to SQLite

15939f8822bd5ec258f224abaa72f46b45ed9c6a authored over 3 years ago by Hendrik Weisser <[email protected]>

[TEST] test for conversion of ID data in feature maps

ceb6366dd657d4de3a6a6ff2f3e1d453faec27d2 authored over 3 years ago by Hendrik Weisser <[email protected]>

[API] added conversion functions for ID results stored in feature maps ('Peptide-'/'ProteinIdentification' <-> 'IdentificationData')

335873539a57caee117c773b8f4be0c0ec60da56 authored over 3 years ago by Hendrik Weisser <[email protected]>

[FIX] fixes for reading/writing of feature maps to/from SQLite

5de205b5875e9e545fd8bfc0c0be34ed827bcee5 authored over 3 years ago by Hendrik Weisser <[email protected]>

[NOP] slight formatting change

0b089ed0f21bfbe0201f4c99117c23c3f4c8940f authored over 3 years ago by Hendrik Weisser <[email protected]>

[API] IdentificationData: added 'setMetaValue' overloads

c23979ab5965f0952175d16eea9479021d3b3368 authored over 3 years ago by Hendrik Weisser <[email protected]>

testing second compute function

32c85f38bf19c8b556122169cec7e78555e32a3e authored over 3 years ago by Tom Waschischeck <[email protected]>

catching ppms = 0

6147ab64cfff41ca10a59f0d33c1341385df3fed authored over 3 years ago by Tom Waschischeck <[email protected]>

docu

fef2056391d67eba626cad87acc292e202608f57 authored over 3 years ago by Tom Waschischeck <[email protected]>

Merge pull request #5167 from Waschi97/feature/SpecRefInNovorAdapter

Writting Spectrum Reference in NovorAdapter

a7e8b05472fd7f0407ca1bf881bd00bd3564d412 authored over 3 years ago by Chris Bielow <[email protected]>

avoid copy

fb2ba71b2eefa2ec659b10a71f01d6af3aae02ce authored over 3 years ago by Chris Bielow <[email protected]>

MetadataOnly and MSLevel 2 while loading MzML

72391d48297c02fff2bb8f566a6099a23b1f86d1 authored over 3 years ago by TomW <[email protected]>

FLASH Ida log file is now read by FLASHDeconv!!

5aa41c2bdf8dd566942305e3db770dc29dcf4453 authored over 3 years ago by kyowonjeong <[email protected]>

SpectrumLookup used for SpecRef, test file changed accordingly

b5cac288cc6c9ac2e01d1519e0949304adead530 authored over 3 years ago by Tom Waschischeck <[email protected]>

forward declaring

511addbafb271c57b70923cd998bb5210382fe88 authored over 3 years ago by Tom Waschischeck <[email protected]>

second compute for vector<PepID> input

457067a0cc8e632d98579ea181b050803791fad8 authored over 3 years ago by Tom Waschischeck <[email protected]>

Merge pull request #5166 from OpenMS/doc/FFMID

[DOC] FFMetaboIdent supports raw&centroided

b68a89c2e352df6568b9cb2bf0b300bbc84ea392 authored over 3 years ago by Chris Bielow <[email protected]>

[DOC] FFMetaboIdent

1b16076793d730d1a8d869d5968fce9b6d9385c6 authored over 3 years ago by Timo Sachsenberg <[email protected]>

FLASH Ida log file is now read by FLASHDeconv!!

02a9a83b46b1c2a407e08c489409b7453513a4fe authored over 3 years ago by kyowonjeong <[email protected]>

QScore bug (feature vector has only 0 elements) fixed!!

d2734fd439fe65aa02f342a50725ae111455aec0 authored over 3 years ago by kyowonjeong <[email protected]>

A searchengine base (#5157)

* a first go at a searchengine base

* fix codefactor

* add tests

* lb

* change to si...

3aa2f4f2ac2f98c9aa5f279bec10ed05067ab106 authored over 3 years ago by Chris Bielow <[email protected]>

IDMapper map ids by native_id (#5120)

* IDMapper map ids by native_id

* Apply suggestions from code review

Co-authored-by: Julia...

3a2f985d966b962b99fdc39d61ffe625972fa2b6 authored over 3 years ago by RobertDeibel <[email protected]>

[FEATURE] Allow skipping MS2 isotope scores in SWATH and disable it in FFID. (#5161)

* [FEATURE] Allow skipping MS2 isotope scores in SWATH And disable it in FFID.

* reverted ord...

f30d5cd28a6ffab278137a7422dca4cd4a7f8ccd authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Negative mode charge resolved. Still need test functions...

1b8b82d9460bbde94a75737bac29097f44e5f35d authored over 3 years ago by kyowonjeong <[email protected]>

Merge pull request #5150 from jpfeuffer/feature/ExposeFFMSettingsPLFQ

[FEATURE] Expose a few FFM settings in PLFQ for finetuning.

dd584853c8e9ac1236c7f77948745e149814bf78 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Negative mode charge resolved. Still need test functions...

d3dc37ce299361e1845b366034c9fd63602d2cc3 authored over 3 years ago by kyowonjeong <[email protected]>

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

# Conflicts:
# src/openms/source/DATASTRUCTURES/QTCluster.cpp

722fe3a5bea6d8774fc175a4d9a1f09216dfd823 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

cleanup and style

09e53ee990882a5128e82dc65aa5686005c07f33 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

New Qscore weights..

ef23ad9551fe540718f8f3c832f53c87faeaa76a authored over 3 years ago by kyowonjeong <[email protected]>

Update QTCluster.cpp

589c843f209a5afacd2b912e1c80ea8b1d1a35d3 authored over 3 years ago by Timo Sachsenberg <[email protected]>

tests

e8c742011e405d5239c958b5ea1ae189be0e510c authored over 3 years ago by Julianus Pfeuffer <[email protected]>

More comments and try to pop at beginning since it is safer

be7566bc637b658fc2e3b0d0ff660c54050bd5e4 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

fixes to QtClusterFinder

c20e9fad52b2e8dd0323f1d6f9c89b03be542c3e authored over 3 years ago by Julianus Pfeuffer <[email protected]>

fix percolator URL (#5159)

ba426a2c8395536937ad00b24f72c8bcb2353b02 authored over 3 years ago by M Bernt <[email protected]>

Low mass coverage succeeded!! only need to remove min_charge_ for MSn

3aaa7908bb824b52a2e81dbc4a608076c8af3c8f authored over 3 years ago by kyowonjeong <[email protected]>

Low mass coverage succeeded!! only need to remove min_charge_ for MSn

2510f67cb38bfd0aa4fde791a3ff91a94db84750 authored over 3 years ago by kyowonjeong <[email protected]>

trigerred peaks are now included for deconvolution ...

702da254f91ec206842ca7da0af8fd7ee7f56f25 authored over 3 years ago by kyowonjeong <[email protected]>

trigerred peaks are now included for deconvolution ...

beacb07d2743b997a41dc39e9b1bc02878cd4afe authored over 3 years ago by kyowonjeong <[email protected]>

Fatal bug in MS2 deconvolution fixed

87526cd4f6240845b11a713122124c50120ad19a authored over 3 years ago by kyowonjeong <[email protected]>

avoid errors through register keyword in seqan

2188f933e7ed44a724bd0cf99f5491877e78400f authored over 3 years ago by Julianus Pfeuffer <[email protected]>

revert

86d2d05c1cea1a225dbf330ffc155a812bc02b24 authored over 3 years ago by Timo Sachsenberg <[email protected]>

Update .travis.yml

2971924319e241849e1357d0fab5959518b72f5f authored over 3 years ago by Timo Sachsenberg <[email protected]>

Expose a few FFM settings in PLFQ for finetuning

9e60a4664468068f58a3ce20a6181c71dbe6e966 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

allow reading in a mod as protein-nterm in mzIdentML (#5143)

* allow reading in a mod as protein-nterm in mzIdentML

* adding a test ...

* check all mod...

91bead89d1810f9c1511234060008dee73c32cda authored over 3 years ago by Chris Bielow <[email protected]>

FLASHIda part updated new color 'g' introduced

0cbe15ddc07c10adcb338c12726fa47b23c15a85 authored over 3 years ago by kyowonjeong <[email protected]>

Update python, cython and autowrap on travis

812919e8df851b4ce1ed5041dca7721721ff8e11 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

FLASHIda update

ede5688afe462919f0dfafb25e3279001ebac65f authored over 3 years ago by KyowonJeong <[email protected]>

cleanup using statements in TOPPAS.cpp

592fc59bbfcfa4508b6e4b498d349e098a7999e0 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Change TextExporter Output to Display Accession Details (#5137)

* [FEATURE,TEST] Change TextExporter output to display accession details

[FEATURE,TEST] Chang...

053ad836ce97c128983c5974a698ca9ce2b7959e authored over 3 years ago by emilpaulitz <[email protected]>

rearrange swathwizard using decls

a60120d1f4b17ac10d3a1f7366af86c177d083b6 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Merge pull request #5147 from jpfeuffer/feat/IDlinking

Make quantile function safer

61a7abe6851fc33edb2b33e50779661af51ddfd7 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Fixed Nightly Build Error (#5148)

* functionality in IDConverter

* ms lvl and precursor info written in TSG::getSpectrum

* r...

03867c61b834f73329b9e6e4b6241f1fae03361a authored over 3 years ago by TomW <[email protected]>

include

050fc017a6a3a59cc9780d744abb643a4299fbb6 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Merge remote-tracking branch 'origin/feat/IDlinking' into feat/IDlinking

996d42d1a70f05241f08e40f413a263e795e6f14 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

quantile even safer

cb4cca841f894cb27f0551e9f97be269fbaea0f0 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Mass bin level harmonic and charge off by one elimination : huge improvement in sensitivity and specificity

efbf5299da3549819884e3d17edd68cbd8157842 authored over 3 years ago by kyowonjeong <[email protected]>

Mass bin level harmonic and charge off by one elimination : huge improvement in sensitivity and specificity

f9becc409ee59f1acf54661704f1c6eef229b4af authored over 3 years ago by kyowonjeong <[email protected]>

Merge pull request #5145 from jpfeuffer/feat/IDlinking

[FIX] some smaller fixes for the ID-based filtering during linking

b67fbeaeb8c3e3c3759ca80285e6264c1f7e54ac authored over 3 years ago by Julianus Pfeuffer <[email protected]>

.

ce2c304080c331aabf43768467692a742079eb6d authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Double

2f50717331a4b0b6bb6c0564e8a5f9a1adee85e0 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Oops

962e2b840337e8a258d5cb037925a6f45c96e5b2 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

debug code

68ff36d9475b62f9ae118a5e7c87f17ec2f2d282 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

[FIX] some smaller fixes for the ID-based filtering during linking

23f25e7bde21d2d1264595b4b5527732a60d3225 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Mass bin harmonic removal activated.

18ef3331bc0874d2fb7cf794009a6efd019a6c47 authored over 3 years ago by kyowonjeong <[email protected]>

desperate

421fc5a76dc44e555981ce0b4655a3937a913363 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Option to Convert a Fasta to a mzML File in IDFileConverter using TSG (#5136)

* functionality in IDConverter

* ms lvl and precursor info written in TSG::getSpectrum

* r...

30f79a16b0d9b5017917e43ed8fe4f9ec4f46722 authored over 3 years ago by TomW <[email protected]>

[HOTFIX] QTClusterFinder

eea9e58d88f2c63c072b520a027aa7d4fd0cc0bb authored over 3 years ago by Julianus Pfeuffer <[email protected]>

[FIX] more RANSAC pyopenms

346792e45356051333899dab86dba71f051260aa authored over 3 years ago by Julianus Pfeuffer <[email protected]>

[HOTFIX?] buffer overflow QTClusterFinder

62b4a7fe079b1e19ef7f07a33c4c107d09157bd9 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

update cpplint

743e24c8c4533f6ee23dc33df1bd7d84694bced6 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

ransac pyopenms fixes

851567b4ac50fedc7e77b6c9a47147ec16f9f4c3 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Merge pull request #5144 from OpenMS/gitpod-add-clang-tidy

add clang-tidy

7be93bad9b61214f5bbc71bec03e90a54b9eb916 authored over 3 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #5138 from jpfeuffer/update/cmakeMinVersion

Silence CMake warnings about deprecated version

79acb60c1d228bccf45b9aa37e4fcb642162bb0b authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Merge pull request #5142 from cbielow/feat_recentfilesmenu_for_TOPPAS

[FEATURE] add a `recentFiles` menu to TOPPAS

f4ae0e72f2d9651b9dcabc4e772f013b8f62464b authored over 3 years ago by Chris Bielow <[email protected]>

add java 11 and plugin

9f78442e86e30183e5f4a64e48986e6d8daa0e9f authored over 3 years ago by Timo Sachsenberg <[email protected]>

add clang-tidy

4e0afd7558c68e34b2fbddeda43c46b2f05852c1 authored over 3 years ago by Timo Sachsenberg <[email protected]>

Parameter names ending with _ fixed + multiple spectra examined for precursor search for real time deconv added

6d284aa05ddb182f59e6cc98cf8136a7172a30f4 authored over 3 years ago by kyowonjeong <[email protected]>

update flags for pyopenms

de29584294794ac6905fd8c13a0f91eee0cad318 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

ransac random error?

bf988f4a9034752e7cc5cc7d8bdef7245fb463f5 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

remove *nary_function

854cde1fa858220de62aae93a19ab83bfffce90a authored over 3 years ago by Julianus Pfeuffer <[email protected]>

add a `recentFiles` menu to TOPPAS

9deee390fae5edfb6141e990d038e2cb80ade599 authored over 3 years ago by bielow <[email protected]>

Merge pull request #5141 from cbielow/fix_pngprofile

fix png color profile warning

931262b1d4e6b2984a1675927bc2db5a9771caab authored over 3 years ago by Chris Bielow <[email protected]>

fix warning 'warning: iCCP: known incorrect sRGB profile' when opening TOPPView, TOPPAS because some PNGs use a shady embedded PNG color profile

a35603540842edc5dffdb91a42ee525b97dc3179 authored over 3 years ago by bielow <[email protected]>