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

[FIX] docu for tools (#4883)

* [FIX] docu for tools

* Update MetaboliteAdductDecharger.cpp

1bdb8937ce82140eda2fd0606a191c31b92bb9f1 authored about 4 years ago by jpfeuffer <[email protected]>

[FORMAT,TEST] added support for adducts in SQLite file format for IDs (.oms); added corresp. tests

06fc05936f9728707b2973e2aa75710ed2e9b367 authored about 4 years ago by Hendrik Weisser <[email protected]>

[TEST] added tests for handling adducts in 'IdentificationData'

d782646852be5f80f3ebf5ac04347436d65bf183 authored about 4 years ago by Hendrik Weisser <[email protected]>

Toppview refactor (#4880)

* switching to Qt's compile-time connect()

* fix #4812

* avoid linker for missing MOCs err...

46f3c9039511a45d9f4cd4cfa93bd351460ba617 authored about 4 years ago by Chris Bielow <[email protected]>

[API] added functions ('getMolMultiplier', 'operator==') to class 'AdductInfo'

16f8aab4a556e21f86d624868098ccd61c23a7a2 authored about 4 years ago by Hendrik Weisser <[email protected]>

wrong ratio

a1cbd38b08b5cdb8da3549db754c5c85743a2cf9 authored about 4 years ago by Julianus Pfeuffer <[email protected]>

Added review comments. Extend allowed test ratio for numbers.

c9c836e126f732ce2adffab3463f4c68cdc13a2f authored about 4 years ago by Julianus Pfeuffer <[email protected]>

fix TOPPView test (order of destruction)

4e17630ff49cde1bc5ff51023ef88a5a61fdc1ef authored about 4 years ago by Chris Bielow <[email protected]>

Merge pull request #4881 from OpenMS/fix/msgfEnzymeOut

[FIX] Let MSGFAdapter overwrite the enzyme from mzid w/ our nomenclature

17af278b314fb37b98559067a0dbd3082892961f authored about 4 years ago by jpfeuffer <[email protected]>

Merge branch 'develop' into topic/OpenSwathDIAPreScoring-out-fix

69fb8b3f2c7be615720e84480f0637d89fb46df4 authored about 4 years ago by Hannes Roest <[email protected]>

[FIX] Let MSGFAdapter overwrite the enzyme from mzid w/ our nomenclature

409eeaedc3c4feef73cbdc6402aaf46cf463e2c8 authored about 4 years ago by jpfeuffer <[email protected]>

error while registering input options, Re-check writability of output file

b9da89f7f30b5e800a4e096df1dd7ed5227db06c authored about 4 years ago by Tom Waschischeck <[email protected]>

deleted whiteline

7dba99bf89d7533b29efea3710bee98d963ba7ac authored about 4 years ago by Tom Waschischeck <[email protected]>

final PR changes

01dbfab24baf5906fc4c8a1ad095b80e8a38bd69 authored about 4 years ago by Tom Waschischeck <[email protected]>

Added a gitattributes file to prevent git from changing line endings when checking out on windows.

608d2a3c7ad7bc371428159c888a40d296b26d46 authored about 4 years ago by Julianus Pfeuffer <[email protected]>

fix wrong signal/slot

dce6b1f071bb6fb9b99a59dc2c9ebafe273c4d78 authored about 4 years ago by Chris Bielow <[email protected]>

[INTERNAL] IdentificationData: added typedef 'AdductOpt' for optional adduct; include adduct in key for molecule-query match

84986d8e68615eb27985b144a43dbd1791c85262 authored about 4 years ago by Hendrik Weisser <[email protected]>

convert connect() to new Qt5 method

6eb7ac93c143f248cc3d600f2ecee8380f24d705 authored about 4 years ago by Chris Bielow <[email protected]>

avoid linker for missing MOCs error when switching to Qt5 connect with FileWatcher

cb7182451bc6e2e8f1e0dcbc02d4ccee63c176d1 authored about 4 years ago by Chris Bielow <[email protected]>

Add precursor mz to selected ion m/z (mzML) (#4861)

* add precursor mz to selected ion m/z

* tests

* FIX: missing test

Co-authored-by: Timo...

e7fa45f84e377e6d21fa297d0a3698f08f336207 authored about 4 years ago by Oliver Alka <[email protected]>

Merge pull request #4879 from OpenMS/fix/hugeDocs

Exclude some files for dot creation from doc install

feeeafe075ca7fb7eb0b718cd84ffad888456adb authored about 4 years ago by jpfeuffer <[email protected]>

fix #4812

cd13b63ba133cae501d52bb469fb62f4bcb95556 authored about 4 years ago by Chris Bielow <[email protected]>

switching to Qt's compile-time connect()

43bd39ef43f77c9c3497858f3cdb7f7f9cca032d authored about 4 years ago by Chris Bielow <[email protected]>

fix output/input files to PTModel and PTPredict (#4856)

* adapt PTModel and PTPredict

* small fix

* small changes

* change back

* remove emp...

5fe10ecf976e72a88225322331293bda3b4c4388 authored about 4 years ago by Leon-Bichmann <[email protected]>

Switch to (interactive) svg format and limit depth

347e734db30ed4af46f22e35db77d29e62b32bbf authored about 4 years ago by jpfeuffer <[email protected]>

Exclude some files for dot creation from doc install

41c79a92a2f8ebb87f4159fe9a965ff09a62bb05 authored about 4 years ago by jpfeuffer <[email protected]>

[INTERNAL] avoid using 'EmpiricalFormula(String)' c'tor where possible

c56ed55024febd48345b3e097c5271b763634492 authored about 4 years ago by Hendrik Weisser <[email protected]>

[API,TEST] added static functions to efficiently generate often-used empirical formulas (hydrogen, water)

56037135b7eb930dc4272ceee4f52c84acb8fb10 authored about 4 years ago by Hendrik Weisser <[email protected]>

[NOP] fixed whitespace in pointer/reference declarations

9e7d5d54143936815006f2fce6d5cf5b6ce8b2da authored about 4 years ago by Hendrik Weisser <[email protected]>

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

67959df679796769b767d3a15715d7ada10932cd authored about 4 years ago by Hendrik Weisser <[email protected]>

forgot test file

e95d3d4720407ae36d0655afa0e43efdcc504cfe authored about 4 years ago by Tom Waschischeck <[email protected]>

some more PR changes

fdc15eb4762a980a6f9fec548575707950daae24 authored about 4 years ago by Tom Waschischeck <[email protected]>

fixed error message and some docu

e3f307cba4effd55c8e1a198f21a9607b1726b1e authored about 4 years ago by Tom Waschischeck <[email protected]>

add unknown modifications as chemmod (#4841)

* add unknown modifications as chemmod

* added test file

* ammend

* moved code to stati...

c4d9a9b843c961e27a3a0e98fefa889dbaee9430 authored about 4 years ago by Timo Sachsenberg <[email protected]>

Forgot test file result

b82e1ac2d0772aabaa322e20402859073df038c3 authored about 4 years ago by Julianus Pfeuffer <[email protected]>

Merge pull request #4876 from cbielow/fileinfo_extra

[FEATURE] Fileinfo: more info

016175943b42e88e9bf7c7a69c5b6600ade9cd56 authored about 4 years ago by Timo Sachsenberg <[email protected]>

some more PR changes, DBSuit test input to be without FDR, TOPPTool docu changed

4eac72c806bc8ef3d18cc80b27e1b361d2040605 authored about 4 years ago by Tom Waschischeck <[email protected]>

* extend mslevel + fragmentation method information

3b8271a18666a17b21e37cfbf4dc0f5db0431a8e authored about 4 years ago by Chris Bielow <[email protected]>

fix test

0ed914c7fb62e3cd22855c4e5ae6a54af2a9d060 authored about 4 years ago by Chris Bielow <[email protected]>

Merge pull request #4871 from OpenMS/PeptideIndexer_rework

[FEATURE] PeptideIndexer more user friendly using 'auto' mode

f53519586b29109b8a428fe303476ff09b037507 authored about 4 years ago by Chris Bielow <[email protected]>

[FIX] Protein terminal mods in AASequence

cd1a3fa006abca35ab23b8d754c5cca44ed40e76 authored about 4 years ago by Julianus Pfeuffer <[email protected]>

PR changes & target/decoy lookup bug fix

d248329666a167b6d156d61e45ff856fade22163 authored about 4 years ago by Tom Waschischeck <[email protected]>

Fix ProteinIdentification::SearchParameters::getChargeRange (solves #4872) (#4873)

* [FIX] fixed parsing of charge states from comma-separated list in 'ProteinIdentification::Sear...

307a248f7ac95b1cd82e4557bf68d77ad4163b4b authored about 4 years ago by hendrikweisser <[email protected]>

class test for Suitability

6844ab0eb4767d017bc2ede98b90c1722a46025f authored about 4 years ago by Tom Waschischeck <[email protected]>

computeSuitability to compute

3c5d4bf4afa470ccec50656fd4142ea1a56d1068 authored about 4 years ago by Tom Waschischeck <[email protected]>

minor fix

bae116a60d917af8b9b1ebf2b80769c155ad71ce authored about 4 years ago by Chris Bielow <[email protected]>

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

44df9b7784899e16a5c7b5ddc09148e7f08c9b21 authored about 4 years ago by Chris Bielow <[email protected]>

Merge pull request #4803 from enetz/update/unimod_2020

[UPDATE] Unimod xml and obo files

3794925b9684b83a2954079f1ffe6dc4ab4eb96d authored about 4 years ago by jpfeuffer <[email protected]>

[TEST] small improvements to IdentificationDataConverter_test

600b87eceb7910633b838ea0d81e3cd9a043d00b authored about 4 years ago by Hendrik Weisser <[email protected]>

[FIX] fixed parsing of charge states from comma-separated list in 'ProteinIdentification::SearchParameters::getChargeRange'

7bb0bc2a44bb1ec667995b5e78c5e3bf55d3565c authored about 4 years ago by Hendrik Weisser <[email protected]>

Update CHANGELOG for 2.6 Release

a258a5eeea99529eb94cf26134594edea4fd2b8d authored about 4 years ago by FabianAicheler <[email protected]>

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

# Conflicts:
# src/topp/PeptideIndexer.cpp

7ba5e7ef433a9495dfec2ac4cd000159075d36f9 authored about 4 years ago by Chris Bielow <[email protected]>

* auto mode for settings in PeptideIndexer

* allow removing weird peptides produced by XTandems's special cleavage rules ('X' is a stop cod...

4d5da564f7ffb6f08fc127d020052ecd1701efa8 authored about 4 years ago by Chris Bielow <[email protected]>

Merge pull request #4868 from cbielow/toppview_layers

minor GUI improvements

710106f20633346b0d81b60703c73cc225b7d4a1 authored about 4 years ago by Chris Bielow <[email protected]>

[TEST] updated boost version < 1.56 MRMAssay test files

edeb946e068825866a3190eea7d67509cfdd5985 authored about 4 years ago by Eugen Netz <[email protected]>

Update IDMassAccuracy.cpp

6009845de5b2ee1c76dcfaea96fe474622d145c2 authored about 4 years ago by Timo Sachsenberg <[email protected]>

[FIX] suppress misleading warning messages about unknown parameters (#4864)

a55cb658f9c2e7dfb408377013f3e07caca764f7 authored about 4 years ago by Eugen Netz <[email protected]>

clicking 'edit' when no item is selected, uses the first item

f62f2100e33a618988196338e85dcc5f4196c5f5 authored about 4 years ago by Chris Bielow <[email protected]>

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

ceea347974d40d4b11896ed5e00afcc143214ea0 authored about 4 years ago by Chris Bielow <[email protected]>

[TEST] updated test files

470bbe25147819e948d9654a39bc9356d4c3a6e7 authored about 4 years ago by Eugen Netz <[email protected]>

[TEST] updated class tests

75e9b80323e3594944d8b8ed178d900d526125d3 authored about 4 years ago by Eugen Netz <[email protected]>

[FIX] only parse neutral losses with an existing formula from unimod

afeaddc74c9bce43ece9c027258f48276e27038d authored about 4 years ago by Eugen Netz <[email protected]>

Revert "[TEST] updated MRMAssay class test files for boost < 1.56"

This reverts commit c246eb12fd201e5b5a9db942dc90f1f2e03b54d7.

9814643208c5b276cf6b5d2466cbe164f9211ded authored about 4 years ago by Eugen Netz <[email protected]>

Ms2IDRate tests

fcf424db94bb02150dfc5cb7ce049eeeb46c4be8 authored about 4 years ago by Tom Waschischeck <[email protected]>

changed error message

2cc23e78e43cc3f0641c888df9760285e6331ac7 authored about 4 years ago by Tom Waschischeck <[email protected]>

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

aebdd57737e40bf11e24286e6c03d35ca5833ff3 authored about 4 years ago by Eugen Netz <[email protected]>

Merge pull request #4852 from timosachsenberg/fix/omssa

write out native ids and spectrum references

be297b8d5e17a5f00143d36b67047e5466ae10ce authored about 4 years ago by Timo Sachsenberg <[email protected]>

[INTERNAL] use class 'AdductInfo' for adducts in NucleicAcidSearchEngine

2d7c6d357692a5d12584f9ebb2f1eb53896e0270 authored about 4 years ago by Hendrik Weisser <[email protected]>

[API,FEATURE] added support for adducts to class 'IdentificationData' (based on class 'AdductInfo')

f69d5b641a729d40ceadaaade9e107b0c828d3f3 authored about 4 years ago by Hendrik Weisser <[email protected]>

[API] moved class AdductInfo out of AccurateMassSearchEngine; added function to calculate mass shift caused by an adduct

7421bdde127c067b41bf59abbb346a8a124b3033 authored about 4 years ago by Hendrik Weisser <[email protected]>

[TEST] added proteomics example to IdentificationData test (courtesy of Timo)

6208b1dd0b499edd5c6a0024fdaa938314ca307c authored about 4 years ago by Hendrik Weisser <[email protected]>

SpectralQuality removed from source.cmake files, number unique novo seqs re-added to DBSuit TOPP

d27ef1767f17466d856df6ec954e294dc390b56f authored about 4 years ago by Tom Waschischeck <[email protected]>

fixed param error in Suitability Constructor, deleted SpectralQuality since functionality in Ms2IDRate

e6840c6e7c041a33c81959547ba5cdbf851c8b47 authored about 4 years ago by Tom Waschischeck <[email protected]>

documentation changes, renamed no_fdr to no_pep_index, spectral quality calculated with MS2IDRate, DbSuit test changed accordingly

065201d5e1792d5b6cf089cde4db19af08f97548 authored about 4 years ago by Tom Waschischeck <[email protected]>

second compute in Ms2IDRate for vec<PepID> input

0cb8945f7be895eeee1e4414fa61f4250cfc1d7a authored about 4 years ago by Tom Waschischeck <[email protected]>

Merge pull request #4859 from enetz/fix/mzid_nonstandard_scores

[FIX] parsing mzid with nonstandard, non-CV-term scores, fixes #4607

ffac143a57ed143b38f2229c0e8fe77d0af9f33f authored about 4 years ago by jpfeuffer <[email protected]>

[PYOPENMS] updated ResidueModification python bindings

a22c50e069e539ad151d29e6a112ca53cf231d05 authored about 4 years ago by Eugen Netz <[email protected]>

Params of Suitability with DefaultParamHandler

300e4dc1235e4aef52acb0a9b76f0280d1f19bca authored about 4 years ago by Tom Waschischeck <[email protected]>

Update PULL_REQUEST_TEMPLATE.md

b0653a20ea693be273c05592b2ce82140a9b9c2c authored about 4 years ago by Eugen Netz <[email protected]>

open folder by double clicking

416b0c9ba34d0c63da9fbfeb53b723e9f897a0ee authored about 4 years ago by Chris Bielow <[email protected]>

[INTERNAL] changed a variable name to fit its content better

ca9aa39f9c2a467c2096f27c48e26883dbf53859 authored about 4 years ago by Eugen Netz <[email protected]>

Update PULL_REQUEST_TEMPLATE.md

Added Python bindings to checklist

9da758862128da77870129e979f2506e75e3ffd8 authored about 4 years ago by Eugen Netz <[email protected]>

use build in method

88b140f5fd45c23d5897d412076a5676990c14f6 authored about 4 years ago by timosachsenberg <[email protected]>

* remove redundant code

f2e558bd44196d9f0fdf268714b4b78a60d18ac3 authored about 4 years ago by Chris Bielow <[email protected]>

update test

a86db9828e091342dae500556c0a73b69b19aa6a authored about 4 years ago by timosachsenberg <[email protected]>

Merge pull request #4853 from Leon-Bichmann/warn/PSMFeatureExtractor

Warn about multiple runs when using PSMFeatureExtractor

6d397f1a3a689c74211759444bd20c213094dd9e authored about 4 years ago by Leon-Bichmann <[email protected]>

[FIX] added check for empty vector in OMSSAAdapter

c0b75e9be11d856b739e97101597f0276d59055e authored about 4 years ago by Eugen Netz <[email protected]>

Merge pull request #4860 from timosachsenberg/develop

update THIRDPARTY

4ebd22b9d503e32042d46d0249b122025c3c5efc authored about 4 years ago by Timo Sachsenberg <[email protected]>

[TEST] updated MRMAssay class test files for boost < 1.56

c246eb12fd201e5b5a9db942dc90f1f2e03b54d7 authored about 4 years ago by Eugen Netz <[email protected]>

Merge pull request #4850 from OpenMS/fix/inspectFormats

Try "txt" as intermediate format for InspectAdapter

4188b2f6e6eae100bd0242efec21f6d73b915c35 authored about 4 years ago by jpfeuffer <[email protected]>

Merge pull request #4839 from OpenMS/fix/syncMIMEandFileTypes

Sync mimetypes and filetypes

0ab4d83c73d52ad433e26d13e0975c20938bd695 authored about 4 years ago by jpfeuffer <[email protected]>

update THIRDPARTY

06835fc33962e9dd770b6b839b54d6786e4de1be authored about 4 years ago by timosachsenberg <[email protected]>

Update ConsensusXML_1_7.xsd

500593e74d355fb40168bfe775d9715b9db0cf9e authored about 4 years ago by Timo Sachsenberg <[email protected]>

[COMMENT] updated authorship of MzIdentMLDOMHandler

5ecd47c2e72599f088a52569d1dc6679cd39f734 authored about 4 years ago by Eugen Netz <[email protected]>

[TEST] added missing test files

6f2cf2cc40818ea5bf4403eff2116357e77fdc06 authored about 4 years ago by Eugen Netz <[email protected]>

[TEST] added test for mzid files without recognized score

45d72a31ee219476c42868a7b2f8fc68cab59f05 authored about 4 years ago by Eugen Netz <[email protected]>

[FIX, IO] fixed reading mzid files without a recognized score

64b4cb0d15227ab5cde86de01de2ec678ac02280 authored about 4 years ago by Eugen Netz <[email protected]>

fix

487218625bbd243e1ba37e3da7133975e9bd0852 authored about 4 years ago by Timo Sachsenberg <[email protected]>

FDR calculated in Suitability, flag in TOPPTool to disable this, docu and errors in SpectralQuality

e9b7b64cea856a074c27cf6c3e5cdb873b4f13d5 authored about 4 years ago by Tom Waschischeck <[email protected]>

SpectralQuality and DBSuitability moved from TOPPTool to own classes

78b840ff672eba2c550202ce63211f9e862f51ed authored about 4 years ago by Tom Waschischeck <[email protected]>