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

Merge branch 'develop' into fix/clang-tidy-fixes

165c9151cc868393b2602fe0a25a28ff6b57dd97 authored over 5 years ago by jpfeuffer <[email protected]>

update contrib

0dfbfad29eb594086a5154df91be5f27c1953977 authored over 5 years ago by Timo Sachsenberg <[email protected]>

from LOG_INFO to OPENMS_LOG_INFO

dda67fcd25acef9d8646edf62fff6a1a981d3312 authored over 5 years ago by JeeK <[email protected]>

minor fixes

595a7780bb0eb63d8ec6ec227b54f1cce134ed04 authored over 5 years ago by Chris Bielow <[email protected]>

Fix protein identifiers associated to PepIDs (#4111)

* [FIX] segfault in RiboNucleotideDB if string is empty, i.e. back() is forbidden

* [FIX] use...

b9f6fb3a6ff2480f0c8a5f9f968f517eb050f9f9 authored over 5 years ago by Chris Bielow <[email protected]>

Fix 32bit to 64bit

1UL is legitimately only 32bits (on VS at least). This should be 1ULL <<63 to ensure the shift i...

004358380b6fbc6d5dd6cd26a88d7f611cd0e4eb authored over 5 years ago by Hannes Roest <[email protected]>

Merge pull request #4114 from hroest/feature/doc

[DOC] topp/utils docu

0cf87cf0d172f867d28abbef202f5194f1c722ab authored over 5 years ago by Hannes Roest <[email protected]>

Merge branch 'develop' into feature/TDdeconv

ee03247b9681ca978b71e86f6be6db54cb57d384 authored over 5 years ago by JeeK <[email protected]>

Modification file needed for DBsearchDeconvMass

179699ee099f03d40e98bc152192fb9588084bf2 authored over 5 years ago by JeeK <[email protected]>

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

8bb513892e9159c6f53bdcdc8375616f6b8afbed authored over 5 years ago by JeeK <[email protected]>

Change structure to multimap and give tolerance as ppm. Mono mass and Average mass are both available.

1c63055626c4e07f948a8e0f006c3fbf505fc5e3 authored over 5 years ago by JeeK <[email protected]>

[ADD] Output SIRIUS workspace

bb23c27951848a03acf5f08ed17dba6150a8fc0e authored over 5 years ago by oliveralka <[email protected]>

add test for non-unique protIDs

f4d369515546a074f5a963956c9ed9ab64bbed76 authored over 5 years ago by Chris Bielow <[email protected]>

check protIDs when writing XML files

05c94be7be2a1a1a0257c144b29797701094a51a authored over 5 years ago by Chris Bielow <[email protected]>

[DOC] topp/utils docu

3e35eeb3bfb28238bc22da0da225d01399529d44 authored over 5 years ago by Hannes Roest <[email protected]>

[FIX] move output to end of TSV file

f32c134e6e10960e70cc09c60e2001a29539b791 authored over 5 years ago by Hannes Roest <[email protected]>

[DOC] add documentation for output format

f14a9bde7efdaffc3b2e2006ac38b97ddd25edd9 authored over 5 years ago by Hannes Roest <[email protected]>

[FIX] bugfix

10eadfd5219201e9b7f3f83336fd811fe36f940b authored over 5 years ago by Hannes Roest <[email protected]>

[FIX] skip fasta header files, test with PEFF

0b3e832a93f799409eb4a82e3564bef78bed6251 authored over 5 years ago by Hannes Roest <[email protected]>

[DOC] add documentation for output format

9c26843316c7663bf0a570678c61079de014a5d4 authored over 5 years ago by Hannes Roest <[email protected]>

Merge pull request #4106 from hroest/feature/prm

Feature/prm

e87e6d8c478d4be631c5911edbef70adce05db06 authored over 5 years ago by Hannes Roest <[email protected]>

Suggestions from code review

- [NOP] easier to read
- [FIX] more efficient computation for nominal_mass

e6a9944e252f66164aac078b03da5271a3b6671e authored over 5 years ago by Hannes Roest <[email protected]>

fix CI warnings

7c94497a0b758e228fdb08a16e7fc91b59fc60c4 authored over 5 years ago by Chris Bielow <[email protected]>

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

# Conflicts:
# src/openms/source/QC/TopNoverRT.cpp

0b68acbe0eb75b8a587a02554e5bda405c2dc42e authored over 5 years ago by Chris Bielow <[email protected]>

minor

83d0070e25a15031c55a8b1a5542fefd7bb8cb78 authored over 5 years ago by Chris Bielow <[email protected]>

Merge pull request #68 from Waschi97/feature/QC/SpectraRefForEmptyPepIDs

spectra ref for empty pep i ds

3e46de2ce1cb13467552d228205bdb1b9b670cda authored over 5 years ago by Chris Bielow <[email protected]>

Update QualityControl.cpp

e6c4449bea996ab69d21f1afac3e54c7f113b48c authored over 5 years ago by Chris Bielow <[email protected]>

Update QualityControl.cpp

0e41aba188bc3d68e09213cc0ead82dc3d50edff authored over 5 years ago by Chris Bielow <[email protected]>

Update TopNoverRT.cpp

99451a31a132e3d0b83df2c6a040f9b8322acf17 authored over 5 years ago by Chris Bielow <[email protected]>

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

8109b8010571bb5ecb347c78b208f3a506b4eeec authored over 5 years ago by Chris Bielow <[email protected]>

[FIX] use unique ID when parsing ProteinIdentifications so allow merging of them without worrying about creating amgiguities for PepIDs associated via .setIdentifier(). fixes #70

056cdf3c69683e97da8bd2c794dc951126427317 authored over 5 years ago by Chris Bielow <[email protected]>

[FIX] segfault in RiboNucleotideDB if string is empty, i.e. back() is forbidden

2bcb5b3d645e601f0a8273ac7d98853f3d7c85cd authored over 5 years ago by Chris Bielow <[email protected]>

Update test000.py

cb9259555122247c9beeb5c8010f274ab2cace94 authored over 5 years ago by Hannes Roest <[email protected]>

Header - fixed to MonoisotopicMass

Nominal mass removed

27bb150676a9ee4c46962d6f63cca7df90e1362d authored over 5 years ago by kyowonjeong <[email protected]>

Add HDF5 license

7c8acd985de57edf700849d84d6f38965a34f42e authored over 5 years ago by jpfeuffer <[email protected]>

Merge branch 'develop' into feature/QC/SpectraRefForEmptyPepIDs

c167c00fe42f1dfede21fdc684c7e46a4b950cfa authored over 5 years ago by TomW <[email protected]>

added a mapping to find the identifier

11120a39bd28b63c449c2e608e60b9990cf93ea1 authored over 5 years ago by TomW <[email protected]>

Merge pull request #67 from Waschi97/feature/QC/SpectraMapping

Feature/qc/SpectraMapping

74df57de49081c30d279e1e86c4bdf582d87a40a authored over 5 years ago by Chris Bielow <[email protected]>

Update QCBase.cpp

a4861ce1c193c39138b6e2fc864add3e9ecc47c7 authored over 5 years ago by Chris Bielow <[email protected]>

Merge pull request #63 from dominikschm/tutorial

QC Tutorial

ab53e2a816d18db22946e718f5028af89e741413 authored over 5 years ago by Chris Bielow <[email protected]>

Update TOPP_scripting.doxygen

8436ae703bce241f3a092eec05e966ef08b02bad authored over 5 years ago by Chris Bielow <[email protected]>

identifier and spectrum_reference now at TopNoverRT's new PepIDs

9a9fc096f96b30bf0e3bda48628e571409d66efb authored over 5 years ago by TomW <[email protected]>

finished wordings and added another metric

1110fc37349fc066fd0063092f9cce5ce37a4192 authored over 5 years ago by Dominik Sebastian Schmitz <[email protected]>

Merge pull request #4104 from bblum9/develop

Add missing elements for HMDB 4

d4b667c8e2eb926d3dc49ddee210dfa3aa3f1860 authored over 5 years ago by jpfeuffer <[email protected]>

added missing include

79bcdf3f0a02cd37b676a8a755dc469f46100535 authored over 5 years ago by TomW <[email protected]>

PR changes

aca03fae2fc8dad2fee870fcb69a4fa9822bd060 authored over 5 years ago by TomW <[email protected]>

[FIX] do not use underscore replacement for mzTab cells (#4103)

* [FIX] do not use underscore replacement for mzTab cells

* fix test files

18c715cc808c9df41e2c6a7df6b4f46505efff29 authored over 5 years ago by Chris Bielow <[email protected]>

prepared for merge

1240d868df7968fd6d43376a172a3bf8c6f173b6 authored over 5 years ago by TomW <[email protected]>

started to fix wordings

54755e1221de2afc9d3f9e97d92087639d6361c6 authored over 5 years ago by Dominik Sebastian Schmitz <[email protected]>

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

b77c4f0890691a6593c0c0d9b73eae4337a19886 authored over 5 years ago by Dominik Sebastian Schmitz <[email protected]>

Update src/openms/source/ANALYSIS/OPENSWATH/OpenSwathWorkflow.cpp

c0a195e0b40da095ec40a065e3244ff16589a1ce authored over 5 years ago by Hannes Roest <[email protected]>

[FIX] segfault

211beb10aedd29aab8ac4e3ee8afb0da4db0119b authored over 5 years ago by Hannes Roest <[email protected]>

[FIX] fix pre-scoring for empty chromatograms

c6aa0ee7adc2d97a3ee51c72a540ccea216fe01c authored over 5 years ago by Hannes Roest <[email protected]>

[FIX] fix filtering

6841139b4459f1df57deb36fff93c7ccabaead5b authored over 5 years ago by Hannes Roest <[email protected]>

Merge branch 'develop' into feature/QC/SpectraMapping

3a1db5b6b004b79fbb5d3319f7ff84a1f29b3175 authored over 5 years ago by TomW <[email protected]>

[TEST] add test

b1d10e92f4d0197cd4594eb47d116b79057e8484 authored over 5 years ago by Hannes Roest <[email protected]>

[FEATURE] add prm option for OpenSwath

bb026b461ad92a373b7af86121b4171d6b0599aa authored over 5 years ago by Hannes Roest <[email protected]>

[FIX] also provide center of SWATH window

e7db847c0e045160a419b7cd7eb6f39c0138db64 authored over 5 years ago by Hannes Roest <[email protected]>

Merge pull request #4080 from hroest/feature/pyopenms2

Feature/pyopenms2

2a0932d85e221eafa89346aa25013d9226b5bd70 authored over 5 years ago by Hannes Roest <[email protected]>

finished the changes

88e1021f689b2e20dfd3332b6928a70f103a5b85 authored over 5 years ago by Dominik Sebastian Schmitz <[email protected]>

Spectrum corresponding to PepID now via mapping and not RT

a13d759285c2201029ae4ecabdd6ffb0027d0e4b authored over 5 years ago by TomW <[email protected]>

Merge pull request #66 from swewagner/matchedIterator

FragmentMassError with MatchedIterator

fb6d870eb5c0a492acffc5e2c13da5298ab993cf authored over 5 years ago by Chris Bielow <[email protected]>

lowcase in names_of_toleranceUnit, ref, delete cout

4bf42e1078dff2ae4dbdb9c68b1edf8378213135 authored over 5 years ago by swew98 <[email protected]>

fix test files

50b43eb67d981503f3f12afcfe12cad249d0d874 authored over 5 years ago by Chris Bielow <[email protected]>

Merge pull request #4097 from grosenberger/fix/sqlite2

[FIX] OpenSWATHOSWWriter: Separate score fix

f11db200c9d1c23c257f8712ee0c00dcab03ad41 authored over 5 years ago by Hannes Roest <[email protected]>

Merge pull request #1 from bblum9/bblum9-patch-1

Add missing elements

101498a3afed044a349b33fccb633523e301bc53 authored over 5 years ago by bblum9 <[email protected]>

fix includes and docs and metavalue names

14c0f59e103319ec95478b5e49e5bd134ffb7c85 authored over 5 years ago by Chris Bielow <[email protected]>

started to remove the brief and shorten the output col

866d6be4d0f386befc67fddfc95bb67bdf4583a8 authored over 5 years ago by Dominik Sebastian Schmitz <[email protected]>

[FIX] prevent TOPPAS crash on Windows when copying output files (if allowed output type of upstream node is only a single type which at the same time has lower/uppercase differences to the default, e.g. ConsesusXML vs consensusXML) (#4100)

41106e1da525b38d46312480b11fb589dccf21d7 authored over 5 years ago by Chris Bielow <[email protected]>

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

8507e53ecbae7083e56ff37df546139155c323fe authored over 5 years ago by Chris Bielow <[email protected]>

[FIX] do not use underscore replacement for mzTab cells

098da026dceb26232bcdc78f5b770b70c4a973c4 authored over 5 years ago by Chris Bielow <[email protected]>

Merge pull request #65 from Waschi97/feature/QC/TopNoverRT/CIC_and_BPI

Feature/qc/top nover rt/cic and bpi

51824a6c4560acd220abc785be55308ab5ef6143 authored over 5 years ago by Chris Bielow <[email protected]>

bpi and tic are calculated in one function

45e31032366d854d2305f287c51b64c7b3d4ac5d authored over 5 years ago by TomW <[email protected]>

framework for spectra mapping

fdf76c2fcf4e1ad6cb9b504b56684a201e98cc5d authored over 5 years ago by TomW <[email protected]>

changed some wordings

34d88757a391cf00d5b0ca9fdb864544507bf9f2 authored over 5 years ago by Dominik Sebastian Schmitz <[email protected]>

comment

6d61c6b7e0dc9902cf5b6e2e7508e5aceb82dd11 authored over 5 years ago by swew98 <[email protected]>

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

9296a7296acf23275618d7f143913d3d87d0ab4b authored over 5 years ago by swew98 <[email protected]>

changed test regarding to auto

79ee92f5fddbf08b5ed53671f9c387784d2a75d4 authored over 5 years ago by swew98 <[email protected]>

added test for CIC & BPI meta values

24aa05b5e61c8e70ae43195d459c9c7a612e32c4 authored over 5 years ago by TomW <[email protected]>

merged from develop

59d91cedff40a1857b9bb8c0ddb2a373e533077e authored over 5 years ago by TomW <[email protected]>

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

a88db9705eb5b571703d0ccba51a783df044c8fe authored over 5 years ago by Chris Bielow <[email protected]>

fix output type names

59f3ecef80cdf7f53aefa4682e649aa5de7fa983 authored over 5 years ago by Chris Bielow <[email protected]>

[FIX] prevent TOPPAS crash on Windows when copying output files (if allowed output type of upstream node is only a single type which at the same time has lower/uppercase differences to the default, e.g. ConsesusXML vs consensusXML)

64ca3ca5d58c3dc95e2f5e86d58c64bdbab2b022 authored over 5 years ago by Chris Bielow <[email protected]>

Small improvement

eb60e611e35b7b041b3062b28d5db8d682455dad authored over 5 years ago by kyowonjeong <[email protected]>

PERFECT.

Even tic

need to speed up

2fed87cc577a243c14d5cc1317f6ba47d4d2ad82 authored over 5 years ago by kyowonjeong <[email protected]>

PERFECT.

Even tic

need to speed up

6f6b4a7697c54c57e7889423a036a02dab89b58d authored over 5 years ago by kyowonjeong <[email protected]>

mass bin out of range in getpeaksfrommassbin bug fixed

d71dd7613fb19d5c5378a4a8c5289c930a2842ab authored over 5 years ago by kyowonjeong <[email protected]>

mass bin out of range in getpeaksfrommassbin bug fixed

c2c832acce57cc9c1ae038ecf3f0991683cc45eb authored over 5 years ago by kyowonjeong <[email protected]>

thermo std perfect

d350701e1a157c0f1e761c2f4713ab4c39ba39cb authored over 5 years ago by kyowonjeong <[email protected]>

thermo std perfect

b6377d80c9556e3265db0f51d87ac7425c3d5255 authored over 5 years ago by kyowonjeong <[email protected]>

thermo std perfect

fb157c112b8dc1d4f0bfee94c7cd5967fd18f671 authored over 5 years ago by kyowonjeong <[email protected]>

Merge pull request #64 from Waschi97/feature/QC/exportEmptyPepIDs

Empty PepIDs now appear in MzTab

289f4b95df0b8359d8be4ead1a5b2dad9ce11f51 authored over 5 years ago by Chris Bielow <[email protected]>

Merge branch 'develop' into feature/QC/exportEmptyPepIDs

4e584c2c6e60a540f5aa6073957373e88821476a authored over 5 years ago by Chris Bielow <[email protected]>

[FIX] some compile warnings on GCC 81 about catching exceptions by value (#4098)

95b83646e8e17e04836cb131c81dc4ab5c1d5ca9 authored over 5 years ago by Timo Sachsenberg <[email protected]>

MzTab can export empty PepIDs, TopNoverRT returns new PepIDs and doesnt append FeatureMap

b35c7a14fe8e70feb3b45fc23d430dfd886a9366 authored over 5 years ago by TomW <[email protected]>

enum instead of bool, for tolerance unit

8335d6e815500af1112563fcfb7c7a8612b358d8 authored over 5 years ago by swew98 <[email protected]>

forgot semicolon

5b14c1724645df6d2816d1c334c7b72535ed8d47 authored over 5 years ago by jpfeuffer <[email protected]>

[FIX] Lifetime of temporary lambda function object not extended when captured as reference.

4c9f9dd47da75740318a3b23e398327b6738def3 authored over 5 years ago by jpfeuffer <[email protected]>

doc

293562a92007e8c34f7a57391eccc433de870e09 authored over 5 years ago by TomW <[email protected]>

[FIX] SQLite fix

aba6d46002b4d3626094ba8a7bb58e8bd1605fa1 authored over 5 years ago by George Rosenberger <[email protected]>