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

[Feature] added MetaInfo objects to the userparams and the other way

around for mzid write/read

e63c90bc1b758a5d500e38e06f16946cc7cf2d45 authored about 10 years ago by mwalzer <[email protected]>

[FIX] switched to mzid stream writing, first attempt to handle a huge

family of errors with cv/user params in very custom mzid files

992019381127474a4e657d93f05aa58d402ab67c authored about 10 years ago by mwalzer <[email protected]>

[FIX] mzid writing (both stream and dom) fixed technically - not

semantically

fdf2211f78563d944ea6a3fb72e5e63c13e41522 authored about 10 years ago by mwalzer <[email protected]>

[FIX] fixed correct number of proteinhits

75a677b426e78fa471ae90bb0038012c0b6d399a authored about 10 years ago by mwalzer <[email protected]>

[FIX] Fixed SpectrumIdentificationList_Ref hickup

51f0808249a7ea2293a17ef693cb57acfd6cbfec authored about 10 years ago by mwalzer <[email protected]>

[FIX] try to fix rebase conflict

9a5bce4cbf0706e8aeddb514e4708d25eb44898b authored about 10 years ago by mwalzer <[email protected]>

[FIX] fixed proteinhit reading

c219b64e2109580485db5a89ef2ed4322e133315 authored about 10 years ago by mwalzer <[email protected]>

[FIX] added scannumber to metainfo of PeptideIdentification

a3ea1b1711a8dd5571d8acb99e96b560fa570131 authored about 10 years ago by mwalzer <[email protected]>

[FEATURE] added mzid support via DOM parsing

- starting with read functionality on handler level
- new branch(!), after merge/rebase nightmare...

45920dbebb0fe9bf6884a26e38fd3ba6ecd03845 authored about 10 years ago by mwalzer <[email protected]>

[FIX] fixed SpectraData write for mzid with MetaValue spectra_data -

this will be empty if read from idxml (not captured there at all, yuk!)
then set to UNKNOWN in mzid

516f70d11b3d7691140c4a5c52c6404124398d97 authored about 10 years ago by mwalzer <[email protected]>

[FIX] fixed SpectrumID write for mzid with MetaValue spectrum_reference

-
this will be empty if read from idxml (not captured there at all, yuk!)
then set to MZ:...@RT:....

d1a3e2278171e47a56e169b9bebacddadfa37452 authored about 10 years ago by mwalzer <[email protected]>

[Featrue] added DOMHandler to the FileHandler, showcased with FileInfo

0b63caad84b31e9373980f7f913033b7ccd1591f authored about 10 years ago by mwalzer <[email protected]>

[FIX] added generic fragmentation table entry in mzid

33230f57b4956ab5c531c8dd1751d472c459d2a7 authored about 10 years ago by mwalzer <[email protected]>

[FIX] mzid writing (both stream and dom) fixed technically - not

semantically

224adf9c05d31f4cc3a37a0b6d7c202285d23438 authored about 10 years ago by mwalzer <[email protected]>

[FIX] Fixed SpectrumIdentificationList_Ref hickup

adef15c7ebc43f9d399ba8f0901daed78405d212 authored about 10 years ago by mwalzer <[email protected]>

[Feature] added MetaInfo objects to the userparams and the other way

around for mzid write/read

606cf5010b4fa77aa44e95933a5fb0c7f1b8864a authored about 10 years ago by mwalzer <[email protected]>

[UNKNOWN] just added debug hack in FileInfo (toberemoved! afterwards)

and some TODO comments - due to urgent workplace shift

25f77b06945791b36504b1c7faa7fe2f5823e75c authored about 10 years ago by mwalzer <[email protected]>

[FIX] corrected mzid header write (id & date)

b84d1ba0d308a0e1aaea00e96eba5714b7fcbe3e authored about 10 years ago by mwalzer <[email protected]>

[FIX] fixed mzid searchdatabase read/write

c7ed9aabc62da062fdcf1278dedf673873f5241e authored about 10 years ago by mwalzer <[email protected]>

[FIX] fixed correct number of peptideevidences

f5478aad8118c3a6eb01781f9049df26b8dce8eb authored about 10 years ago by mwalzer <[email protected]>

[FIX] mzid AdditionalSearchParams are written, redundant pepevidence

fixed, broke spectrumidentificationresult - see FIXMEs

67f77ea5bff129b75bf7d092686ad3d77e2e7acb authored about 10 years ago by mwalzer <[email protected]>

[FIX] switched to mzid stream writing, first attempt to handle a huge

family of errors with cv/user params in very custom mzid files

24f6449c4324206e805b05ca5cb51403298e756d authored about 10 years ago by mwalzer <[email protected]>

[FIX] fixed correct number of proteinhits

389fd39f5a035b9b1af264e72311688c6c5a4d8f authored about 10 years ago by mwalzer <[email protected]>

[FEATURE] added mzid support via DOM parsing

- starting with read functionality on handler level
- new branch(!), after merge/rebase nightmare...

a25148b2057ff6dd7c6bc6876586707fa83c0e84 authored about 10 years ago by mwalzer <[email protected]>

[FIX] added scannumber to metainfo of PeptideIdentification

afb468ce1ee17129ab08532957997773fd37bdcc authored about 10 years ago by mwalzer <[email protected]>

[FIX] fixed proteinhit reading

24eb4f6b2e00ef41127dcb346619120440bafd75 authored about 10 years ago by mwalzer <[email protected]>

[FIX] check for presence of target and decoy proteins (Fido requires both)

0da5a30e0bf922bb8d9cd5ff3f2fb0b539b74451 authored about 10 years ago by Hendrik Weisser <[email protected]>

Added TopPerc to TOPPAS

9e3d3faa3aa28d6dac84220a01460a598afc747c authored about 10 years ago by Andreas Simon <[email protected]>

Set output from idXML to mzid

2c3cd5dc37238391ecaf5c9adaf0330b5cf44643 authored about 10 years ago by Andreas Simon <[email protected]>

now everything up

6ef3734bc02309f453085aa2a19d90c3a3f548ee authored about 10 years ago by Andreas Simon <[email protected]>

after some trouble, i hope TopPerc is with mathias newest dom reader online

1e042a8b39eeeb27f44be962ef744af843be60dc authored about 10 years ago by Andreas Simon <[email protected]>

asd

5735590a55290e4cc31d41b20e2a8a1f5e319c13 authored about 10 years ago by Andreas Simon <[email protected]>

Merge pull request #936 from mwalzer/feature/QCML

[FIX] fixed the 'variable' consumption of xslt files for a QcML file.

cccbc5d872320f197091596db275f35b4d0458cd authored about 10 years ago by Hannes Roest <[email protected]>

[NOP] uncrustified

07e4bde8a93bfa9428a561c72f6117b5291f3ba8 authored about 10 years ago by lars20070 <[email protected]>

[DOC] FeatureFinderMultiplex docu updated

ca613e7d604279b8419b7d53e1bdebc50b54ba63 authored about 10 years ago by lars20070 <[email protected]>

[TEST] FeatureFinderMultiplex TOPP test added

29600d429ff87f80cd0022b3f00cef97b5b23cce authored about 10 years ago by lars20070 <[email protected]>

[API] progress logger added to MultiplexClustering

00065f5b1b8ed2c62f2dba8e24c00c7ec96ed98d authored about 10 years ago by lars20070 <[email protected]>

[API] progress logger added to MultiplexClustering

a17a3bee2e92ff8e60e88949572c56de8f196623 authored about 10 years ago by lars20070 <[email protected]>

[API] progress logger added to MultiplexFiltering

b005e4814ff4b13a62e2f8d58c3f84ef11876f8d authored about 10 years ago by lars20070 <[email protected]>

[TEST] MultiplexClustering class test fixed

0e848c00d4b7176132523a79a375e632221ed0d5 authored about 10 years ago by lars20070 <[email protected]>

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

ac7cd8ed7761558d57d84a0a3a024cb552ee952e authored about 10 years ago by lars20070 <[email protected]>

Merge pull request #946 from lars20070/fix/GridBasedClustering

OPENMS_DLLAPI removed from GridBasedClustering

88324a36ae9e452fae6761a67afb6802a12b7a6a authored about 10 years ago by Hannes Roest <[email protected]>

[NOP] cleanup

98db770226d253c7f2e77d866fac0f5530825177 authored about 10 years ago by Hannes Roest <[email protected]>

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

64bdfed6bd02e5ee30a965305aa9456d7372ec17 authored about 10 years ago by lars20070 <[email protected]>

[API] OPENMS_DLLAPI removed from GridBasedClustering

134a78d112fa26bdaf1efb90dbcbe00d2ccca81e authored about 10 years ago by lars20070 <[email protected]>

[FIX] fix for case where meta-value does not exist

fb538706a6de1c84902a491dc6af73a44eec5ca7 authored about 10 years ago by Hannes Roest <[email protected]>

[INTERNAL] msq file written

0c806b2f35b88b9a48799b618b55c995891e0a27 authored about 10 years ago by lars20070 <[email protected]>

[INTERNAL] msq file written

e896dec157b405850dcf9d269fb1bc79318947da authored about 10 years ago by lars20070 <[email protected]>

[INTERNAL] results added to msq

7fa4ec1fe5e37db850ac6cb05219f67a5281303b authored about 10 years ago by lars20070 <[email protected]>

[INTERNAL] labels ordered

a677000b64cf07b0857f3ca3949b8680b94cde5e authored about 10 years ago by lars20070 <[email protected]>

[FIX] explicit constructor

d0f3596541615713b4a7a404963b00da7177524f authored about 10 years ago by Hannes Roest <[email protected]>

[FEATURE] also output precursor intensity in tsv

59324f6e46ae2d6ce4b10278c88fe3a4c5235327 authored about 10 years ago by Hannes Roest <[email protected]>

[TEST] fix tests

a7f0070f849ab80da204bc7ed37aa635f7a91b72 authored about 10 years ago by Hannes Roest <[email protected]>

[DOC] add documentation about deprecated methods

597e69b526410b29ffaef8e337525c91aa257c2a authored about 10 years ago by Hannes Roest <[email protected]>

[FIX] also output MS1 features

b64e5888ce79b05dd26beafa1230aca45133d599 authored about 10 years ago by Hannes Roest <[email protected]>

[FIX] remove non-working tests again

9ffe9a64e48e8be282f6ba16b45f53aa4a510fdf authored about 10 years ago by Hannes Roest <[email protected]>

[FEATURE] also write out chromatograms to mzML

e15f793cdef56cd2413bd64d884a58da3e35c5ad authored about 10 years ago by Hannes Roest <[email protected]>

[FIX] fix deleted test from ef9e6684be4959f909d7b364fd521ce395e3976a

4c47762cf4f8761b7aef8692836c9fe46238ebcc authored about 10 years ago by Hannes Roest <[email protected]>

[FEATURE] new CLI flag for using MS1 traces

370ff4ab930e5703165ee72a978ad731cdd6ad9d authored about 10 years ago by Hannes Roest <[email protected]>

[TEST] test with and without MS1 precursor trace

e74e298b17c45aba43cdc49d0c26e8eee77fb973 authored about 10 years ago by Hannes Roest <[email protected]>

[TEST] additional tests for MS1 based scores

- also test isotope overlap score on MS1 level

48a47cc4f1c02fda0eab0fa92d419f41e5cfbeda authored about 10 years ago by Hannes Roest <[email protected]>

[BUILD,INTERNAL] add macro for OpenSwath assertions

1cda407c3eee449c99ffe3e5c8e8ca5da01a6512 authored about 10 years ago by Hannes Roest <[email protected]>

[FIX] do not add xic of the precursor chromaotogram to total

9583030bf972050e17ce8959487f1c22d30457f3 authored about 10 years ago by Hannes Roest <[email protected]>

[FEATURE] compute second score for isotope overlap

- also compute maximal ratio score
- use the maximal ratio for precursor based scoring

bf48f2c638eb9dd8d8b1ec65fa17b6f1e250eae3 authored about 10 years ago by Hannes Roest <[email protected]>

[TEST,FIX] fix DIAScoring test

7d2ee708d3da130b6794f6b430014def193f85a1 authored about 10 years ago by Hannes Roest <[email protected]>

[FIX] add ms1 scores to tsv output

d7b1f01275015021417fd36da45f782d87adbe31 authored about 10 years ago by Hannes Roest <[email protected]>

[TEST] extend test

cf19a95ed6b43937d8c7747ef77e12c424d593a2 authored about 10 years ago by Hannes Roest <[email protected]>

[INTERNAL] labels added to MSQuantification

9df8ab2a0f483c3d7456ed53573fee13522eff7a authored about 10 years ago by lars20070 <[email protected]>

[API] refactored

bca91e632407a7b805d4ab2dc18a3b070ccac9c8 authored about 10 years ago by lars20070 <[email protected]>

[FIX]final after rebase fix

789700ca3d0ed02ed7dccac8327f6580328e533e authored about 10 years ago by mwalzer <[email protected]>

[INTERNAL] bounding boxes for features added

3a0015acc63187d0dfb4591bd2572ddd623226d6 authored about 10 years ago by lars20070 <[email protected]>

Merge branch 'feature/MZID' of https://github.com/mwalzer/OpenMS into feature/MZID

Conflicts:
src/openms/source/FORMAT/HANDLERS/MzIdentMLHandler.cpp

502dbdbe00c8c367153ffea1f1ee263bc7bc8f1f authored about 10 years ago by mwalzer <[email protected]>

[FIX] fixed SpectraData write for mzid with MetaValue spectra_data -

this will be empty if read from idxml (not captured there at all, yuk!)
then set to UNKNOWN in mzid

47234f001b33fc64d5fcf20640c2cb8f49657782 authored about 10 years ago by mwalzer <[email protected]>

[FIX] fixed SpectrumID write for mzid with MetaValue spectrum_reference

-
this will be empty if read from idxml (not captured there at all, yuk!)
then set to MZ:...@RT:....

ef605cb544235d882513cc56324a14621d417dcd authored about 10 years ago by mwalzer <[email protected]>

[FIX] try to fix rebase conflict

a087d2e9a9850a8e010e108cb5599e41184154d5 authored about 10 years ago by mwalzer <[email protected]>

[Feature] added MetaInfo objects to the userparams and the other way

around for mzid write/read

14277a3914176a0785ef9071bd572731cc00a03a authored about 10 years ago by mwalzer <[email protected]>

[UNKNOWN] just added debug hack in FileInfo (toberemoved! afterwards)

and some TODO comments - due to urgent workplace shift

bbd1fecea552b3a0e4293767874f337fa528b351 authored about 10 years ago by mwalzer <[email protected]>

[FIX] corrected mzid header write (id & date)

e134ecb0ca8737f8b0d168e3e291ac8c0a1c65dc authored about 10 years ago by mwalzer <[email protected]>

[FIX] fixed mzid searchdatabase read/write

e77bc240dc733494a85283784942e2b4567f112e authored about 10 years ago by mwalzer <[email protected]>

[FIX] fixed correct number of peptideevidences

8f403d831356fea05ce21102bf9bd5e6284c78eb authored about 10 years ago by mwalzer <[email protected]>

[FIX] mzid AdditionalSearchParams are written, redundant pepevidence

fixed, broke spectrumidentificationresult - see FIXMEs

c72ad62c1ca58417cc92b659bac6869ca850004b authored about 10 years ago by mwalzer <[email protected]>

[FIX] switched to mzid stream writing, first attempt to handle a huge

family of errors with cv/user params in very custom mzid files

b0943d33b82febea89d49383a0d7abf6ca13af4b authored about 10 years ago by mwalzer <[email protected]>

[FIX] fixed correct number of proteinhits

362453fcb0b0943897699ffeb1cc671e9d3942ae authored about 10 years ago by mwalzer <[email protected]>

[Featrue] added DOMHandler to the FileHandler, showcased with FileInfo

c3695811d4d2c8e05399f6852423cc1fead51335 authored about 10 years ago by mwalzer <[email protected]>

[FIX] added generic fragmentation table entry in mzid

fb5e3c728bc38f4bdf7fe53e88560921a5b5b096 authored about 10 years ago by mwalzer <[email protected]>

[FIX] Fixed SpectrumIdentificationList_Ref hickup

d3d29263f5adae6f0b4422eaace433453da697c5 authored about 10 years ago by mwalzer <[email protected]>

[FIX] mzid writing (both stream and dom) fixed technically - not

semantically

d68a190f8fa180ab7dc0557d3cb785cf4a7b70f8 authored about 10 years ago by mwalzer <[email protected]>

[FIX] try to fix rebase conflict

c891f3b00c6ca221139a65f83c36331413a5bbb8 authored about 10 years ago by mwalzer <[email protected]>

[FIX] try to fix rebase conflict

31a10c1a31dcfae432e7fa2ff8a9f5fb633fe857 authored about 10 years ago by mwalzer <[email protected]>

[FIX] added scannumber to metainfo of PeptideIdentification

50f629d49242e178f783a4519f134a86689422be authored about 10 years ago by mwalzer <[email protected]>

[FEATURE] added mzid support via DOM parsing

- starting with read functionality on handler level
- new branch(!), after merge/rebase nightmare...

c37182eba4956d9d63901c6caa0bb06cb1047e67 authored about 10 years ago by mwalzer <[email protected]>

[FIX] fixed proteinhit reading

02908d0eb6013ffe7304a30b2a5d122fb99eb107 authored about 10 years ago by mwalzer <[email protected]>

Merge pull request #945 from hroest/feature/pyopenms_wrap

[FEATURE] pyopenms wrap improved

f41e39b58098dce006f162e947eb26fa5bbbb19d authored about 10 years ago by Stephan Aiche <[email protected]>

[TEST] pyOpenMS tests

7ba8a19aa362c50c4df9db898ba318bf71499ce3 authored about 10 years ago by Hannes Roest <[email protected]>

[PYOPENMS] wrap additional classes and functions

2afb972baa303fa79f07efc69f9e12ce582ac266 authored about 10 years ago by Hannes Roest <[email protected]>

[PYOPENMS] add additional functions

c1a044b3a38e417adcce251204c8225f0dcea33a authored about 10 years ago by Hannes Roest <[email protected]>

[PYOPENMS] wrap additional classes

36fa7f3fdc711c279396c4e2d2a42b2357421252 authored about 10 years ago by Hannes Roest <[email protected]>

[BUILD] fix extension checker

75eefe01fb4c5519b7c98ef034630cbff8a7ab92 authored about 10 years ago by Hannes Roest <[email protected]>

Merge pull request #944 from hroest/fix/pyopenms_parser_fix

[FIX,TOOLS] pyopenms parser fix

a39a2069eee54724cbfc29c4d56b63777b5b491d authored about 10 years ago by Stephan Aiche <[email protected]>

[FIX] fix crash

775787d20c517e585fd02771af32361da417d705 authored about 10 years ago by Hannes Roest <[email protected]>