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

[FEATURE] simple sequence tagger

aedaaf2b2138df3793655aed3c0e1b03da407fec authored almost 6 years ago by timosachsenberg <[email protected]>

check whether any peptide intensity is -1 (and not just the first one)

7fe201e030fc4b2b2844ca76891e38096266b03d authored almost 6 years ago by lars20070 <[email protected]>

Merge pull request #3842 from biosustain/feature/MRMFeatureSelector

[FEATURE] MRMFeatureSelector and MRMFeatureScheduler

8a2b48cac086374e582b132f6abf604c8c137939 authored almost 6 years ago by Timo Sachsenberg <[email protected]>

Update common-cmake-parameters.doxygen

d2864d4c6f201529a4a6a8ea9533ba15deb42125 authored almost 6 years ago by Chris Bielow <[email protected]>

Merge pull request #3931 from cbielow/custom_cxx

[FEATURE] custom CXX flags via CMake

0aa939543365a208f47caebc7f4e04aada576777 authored almost 6 years ago by Chris Bielow <[email protected]>

Merge pull request #3930 from lars20070/feature/NumericMassShifts

numeric mass shifts for FeatureFinderMultiplex

593a62d6f07c13310cd41504af5048b0bbcbdf03 authored almost 6 years ago by Timo Sachsenberg <[email protected]>

chore: change filename to data file

fea4b7a01e5cf8cf822dffe647ce0a21cafb1fb4 authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

chore: reduce test data file size

66552ad83527bbef920abb7de9a9b23e9e018bd4 authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

chore: remove debugging info from coinor

e19872b8e93333ea3d61f4a25bb6376dd49fb056 authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

remove debug methods from pxd

70e3494352ea00564f35f1d00d3775623e9bce27 authored almost 6 years ago by lars20070 <[email protected]>

Lower filtration thresholds and source code clean up (make some functions..)

05eb4cc3d7d3584e0a38082f38b652875efb2b75 authored almost 6 years ago by kyowonjeong <[email protected]>

Update String_test.cpp

31be18f8eca8ce5db9f576e4cc9c697bb2d8a736 authored almost 6 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #3937 from OpenMS/jpfeuffer-patch-1

[FIX] ASan error

9bf3075230f465ad6d0176441e94b9b7fa41a0b2 authored almost 6 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #3935 from cbielow/develop

[FIX] Fix IonizationSim_test

e1fab3acabc4af05691aa45f05a4980f58c470ab authored almost 6 years ago by Timo Sachsenberg <[email protected]>

test: linear score weights

bd58997c3aaa63af972a103c2920fc1dd14841b8 authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

[FIX] ASan error.

From cppreference:
Hexadecimal escape sequences have no length limit and terminate at the first...

104dbdd5d775e6d7347d2d8fd45fbf0439a2e198 authored almost 6 years ago by jpfeuffer <[email protected]>

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

e402fb92c8fb7fc6f382bccd8227f9f6c4c87996 authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

update pxd

d60b5ae3599046b28a24959b56dfb41685a58f14 authored almost 6 years ago by lars20070 <[email protected]>

score threshold bug fixed..

44b5aa2ef946039cd55b5488f1ce7dcf8efd5395 authored almost 6 years ago by kyowonjeong <[email protected]>

[TEST] added tool test for FeatureFinderIdentification with 'model:each_trace' option

2b883f13f339ae2b0665b036d23b4ab727fb28ee authored almost 6 years ago by Hendrik Weisser <[email protected]>

merge develop

18dae23fdc645c994efaef65b6ad4d9f66247997 authored almost 6 years ago by Chris Bielow <[email protected]>

fix IonizationSim test

7f2ad5aab37eb89fe5da35adb705969b230954a3 authored almost 6 years ago by Chris Bielow <[email protected]>

Merge pull request #3933 from cbielow/develop

[FIX] PI: Report Progress correctly

54401dbab09839bf8e1ebf419f029a8961edbc73 authored almost 6 years ago by Timo Sachsenberg <[email protected]>

merge develop

035863ca2368dd79eb09ad625f8f002687961c0e authored almost 6 years ago by Chris Bielow <[email protected]>

score threshold bug fixed..

0194b306fd6c45379e6855317b76dd3e8738d2d3 authored almost 6 years ago by kyowonjeong <[email protected]>

Revert "[FEATURE] faster FASTA reading & AC"

This reverts commit afb6344b89c15491839acefd5d0bb9ee3e72b981.

f65fbecb9196096d3d34a4e195275e63cb34a00c authored almost 6 years ago by Chris Bielow <[email protected]>

PeptideIndexer fix ProgressReport for large DBs

2338fe8f3bca4cc6b660c4fa7e95affd994689db authored almost 6 years ago by Chris Bielow <[email protected]>

[FEATURE] faster FASTA reading & AC

afb6344b89c15491839acefd5d0bb9ee3e72b981 authored almost 6 years ago by Chris Bielow <[email protected]>

[API] pass output stream to debug method

0e981ce83bce6daca04615c36a8915567d357044 authored almost 6 years ago by lars20070 <[email protected]>

custom CXX flags via CMake

bc1f60ccce52bff23254ef13d23cf7de87d31452 authored almost 6 years ago by Chris Bielow <[email protected]>

reduce scope of variable, simplify ini file

146086b6f79ef9950cfc786886fc23f2e09dfdbe authored almost 6 years ago by lars20070 <[email protected]>

switch off debug mode

6a28fd797703817a5f29882b10ae56702b9f1c91 authored almost 6 years ago by lars20070 <[email protected]>

remove debug code, add TOPP test

ee83b2b3a338bfe05c21b1629a45bf6d72f0321d authored almost 6 years ago by lars20070 <[email protected]>

isotope grouping done isotope scoring is not done...

e1dabe77c6565aac5ca4033fc4251de644f06c39 authored almost 6 years ago by kyowonjeong <[email protected]>

change debug output

7cbd579bede8752dd858419478f287b789590654 authored almost 6 years ago by lars20070 <[email protected]>

merge develop

82f1da5a8ede70e56687509a6e7d719ee7e1e690 authored almost 6 years ago by lars20070 <[email protected]>

fit into other labelling schemes

2bf6527108b50b7cef975623190c8d4d6446548f authored almost 6 years ago by lars20070 <[email protected]>

Merge pull request #3927 from lars20070/fix/CloseTripletDetection

FeatureFinderMultiplex - fix for overlapping, unresolved peptide features

a05fa203dd7cb56fee797cc77203a5c2c3afe21a authored almost 6 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #3918 from oliveralka/fix/add_scores_LuciPhorAdapter

[ADD] additional scores to LuciPhorAdapter ouptut

3f454423013a17d279d1c9dcb604184a6c4a04d8 authored almost 6 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #3928 from enetz/feature/OPXL_memory_usage

[FEATURE] OpenPepXL: more efficient memory usage

4fed5a636932c7b2279ae60c99bd1d2a05c93b0d authored almost 6 years ago by Timo Sachsenberg <[email protected]>

construct delta_masses_list_

5c80c15ad302a420fb368fc1c55e4e5057fc50ea authored almost 6 years ago by lars20070 <[email protected]>

extend the three label master maps

2a4813f57f6d2b728fef7702a2123e444f2580e1 authored almost 6 years ago by lars20070 <[email protected]>

[PYOPENMS, FIX] fixed python bindings for ProteinProteinCrossLink

5fd690555d35064ac23a06b0425b43a54552bdf4 authored almost 6 years ago by enetz <[email protected]>

[FEATURE,PARAM] added (advanced) option to FeatureFinderIdentification to fit a model to each individual mass trace of a feature

2381ccd55b03003d534429cd0b4692a566f9dd6e authored almost 6 years ago by Hendrik Weisser <[email protected]>

Merge pull request #3926 from oliveralka/fix/SCMzTabWriter_travis

[TEST] FIX SiriusAdapter travis

fa33ce8a45f21f80ea953b8b8ca5b3c1bb85930e authored almost 6 years ago by Timo Sachsenberg <[email protected]>

[TEST] new class test for fix

da661fa6d6266b94168d520b26e8ff9058aa785d authored almost 6 years ago by lars20070 <[email protected]>

[INTERNAL] check that fc corrections for triplets and higher are allowed

4c6d090ffaf48b21637a6061bbc174c503b067dc authored almost 6 years ago by lars20070 <[email protected]>

Merge pull request #3919 from oliveralka/fix/CometAdapter

[FIX] CometAdapter terminal modification

e3841efb9b6607cfa26df9daaabd6054bd08df71 authored almost 6 years ago by jpfeuffer <[email protected]>

Merge pull request #3911 from Leon-Bichmann/fix/maracluster_exe

Fix MaRaClusterAdapter Exectuable Check Fail in KNIME

5fa6b939144a3f1e44e9a8d07ce93019f47e3833 authored almost 6 years ago by jpfeuffer <[email protected]>

[FEATURE,PARAM] added support for cDNA input to RNADigestor util

c0286642c588f0eb9da28692fb48b3f444a3d843 authored almost 6 years ago by Hendrik Weisser <[email protected]>

[FIX] SpectrumLoopUp - last match

f9868ac063d9ad2de9d93e0ea870b62c91d9c4dd authored almost 6 years ago by oliveralka <[email protected]>

fix logical bug in filterPeakPositions_()

0600002636d2a7222d5212f853992ec1a02e5da1 authored almost 6 years ago by lars20070 <[email protected]>

Merge pull request #3924 from hroest/fix/readme

[FIX] readme links to docu

957151f430faa31ba3ff1b93e48b2bf6fff05df7 authored almost 6 years ago by Timo Sachsenberg <[email protected]>

Update TOPPBase.cpp

f17bee3dc0e80f1392f6ef16a460f2efdfed5dd8 authored almost 6 years ago by jpfeuffer <[email protected]>

[INTERNAL] if the zeroth peak part of the pattern, do not abort

e77805fa8b65ff022db07c1336cd9908a6eb129e authored almost 6 years ago by lars20070 <[email protected]>

[API] checkForSignificantPeak_() now returns the peak index and not just a boolean

fdfd99eb56680492bd2f76de44e34eec47e5c4a7 authored almost 6 years ago by lars20070 <[email protected]>

order in peak filtering changed, no peak can appear multiple times in satellite set

6806ab7ed4f301fb62230cc3620497d358ba24fb authored almost 6 years ago by lars20070 <[email protected]>

add checkSatellite() method

1c33ef76c440133e9812a10caf254c458d5030e7 authored almost 6 years ago by lars20070 <[email protected]>

Update README.md

0c230fe27016125bbccf460a3064f9e18b8016ba authored almost 6 years ago by Hannes Roest <[email protected]>

[FIX] readme links to docu

f4f3a173969c6c6845319acef7a54605dba96128 authored almost 6 years ago by Hannes Roest <[email protected]>

optimal_threshold test

76867117414c0a001044f9875fa7413597851095 authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

[FIX] OPXL: changed parallel loop variable types to SignedSize

This is compatible with more OpenMP versions.
Should fix windows builds.

745b63991a25e19880343869cc57d3478bc267c1 authored almost 6 years ago by enetz <[email protected]>

[FEATURE] OPXL: reduced memory usage by moving parallel for-loop

b2d4075162fb2237992e0e020565b2af81d99f8e authored almost 6 years ago by enetz <[email protected]>

[FEATURE] OPXL: parallellized enumeration of candidates for each spectrum

2e1bfa5351bfca0cbe679bc9f9a0c5ad98aee7a7 authored almost 6 years ago by enetz <[email protected]>

[FEATURE] OPXLLF: reduced memory usage by moving the parallel loop

previously the parallelized loop was looping over the spectra.
The list of candidates and result...

5a2dada70c6eeabd728039298cce7cfa09b1f97b authored almost 6 years ago by enetz <[email protected]>

[FIX] OPXLDataStructs: initialization of pointers, just to be sure

7a1011de8d3e73ec877237e89052c197766ecead authored almost 6 years ago by enetz <[email protected]>

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

574c2d8e13de5289acc36937fa403562dfbe7628 authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

clean up debug output, write to std::cout instead of LOG_DEBUG

f3ef3488f7093228ade7c6d5ac8dff3ad90d4239 authored almost 6 years ago by lars20070 <[email protected]>

isotope basic filtering enabled.

Isotope env grouping is to be done.

dfc5e1cb9bb427d8a4b940f8e8c31ae3c51c6d63 authored almost 6 years ago by kyowonjeong <[email protected]>

Merge remote-tracking branch 'origin/develop' into fix/CometAdapter

4324fc9d60e6a6df880fc5de1095ea362f5b67c8 authored almost 6 years ago by oliveralka <[email protected]>

Merge pull request #3922 from hroest/fix/fix_travis

[FIX] fix travis error

767e8829bb9263d12b066ca5fde40e6b74d4177a authored almost 6 years ago by Hannes Roest <[email protected]>

revert

76e76980c70420ac1d24c243aecaec9b4f4bd38b authored almost 6 years ago by Hannes Roest <[email protected]>

[TEST] fix test

8b97a5ad6d21e5d0cabfb0f8f38f51bde4b92b34 authored almost 6 years ago by Hannes Roest <[email protected]>

[FIX] fix travis error

75bcbb86f8a15068ba6a01424f1ef775a9ed934a authored almost 6 years ago by Hannes Roest <[email protected]>

[TEST] adapted tests to the use of pointers in OPXL

3cf298fb4b319be06e383b9d182c757f218c5409 authored almost 6 years ago by enetz <[email protected]>

[FEATURE] OPXL: improved memory efficiency by using pointers

Enumeration of candidates of peptide pairs now points to the list of single peptides instead of ...

623495cb56986d773f76b614db7dc793864fe48e authored almost 6 years ago by enetz <[email protected]>

[FEATURE] use String

4b072db7b0c78fdc6b0e61c5910dd36297d87a67 authored almost 6 years ago by Hannes Roest <[email protected]>

[TEST] test fixes

d989a789b60571966495f7e17987e546c42840b6 authored almost 6 years ago by Hannes Roest <[email protected]>

[FIX] string fixes

6e8f35e3cd6a3c74b532db18aab72c0c13848a72 authored almost 6 years ago by Hannes Roest <[email protected]>

[TEST] fix unit tests

f854137f24ba0dc3ce9e419b5f3ea8bf176deb4e authored almost 6 years ago by Hannes Roest <[email protected]>

Merge branch 'develop' into feature/pyopenms_string

15a9f23fe347feb68314744b4d8e985b48bd65f2 authored almost 6 years ago by Hannes Roest <[email protected]>

[FIX] style

d46493605e5558a451fff83227850a1e2cb1d6d7 authored almost 6 years ago by oliveralka <[email protected]>

[FIX] extract modification

5966b9082724ed47de14c10046d9716f58ca1007 authored almost 6 years ago by oliveralka <[email protected]>

Merge pull request #3916 from cbielow/perf

FuzzDiff Performance improvements

2712ff8926259719b02891ff3f69f5a385f66f29 authored almost 6 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #3917 from hroest/feature/ustring

Storing Unicode in OpenMS::String

a044f45a593311eac748f908420764a243b21772 authored almost 6 years ago by Timo Sachsenberg <[email protected]>

[FIX] columns

a49816ea9a1e3b9ad8a68ed9121686f9252cb1e3 authored almost 6 years ago by oliveralka <[email protected]>

[ADD] scores

114909bb79e16794980a0b8ddf2f26d494c4971a authored almost 6 years ago by oliveralka <[email protected]>

[TEST] add test for Unicode

8e0eaf323d47d7a56c5e0634a9e05d28777f34f2 authored almost 6 years ago by Hannes Roest <[email protected]>

[TEST] test unicode strings in Python

45235a4e798d06371bcc94f027d4a466dfa5c7df authored almost 6 years ago by Hannes Roest <[email protected]>

[FIX] Python3 fixes

4beddabad0dde6237ac241777939bf891868f165 authored almost 6 years ago by Hannes Roest <[email protected]>

ExternalProgramError

9408952b7965cf259f149cc39bd6a1d379ef8324 authored almost 6 years ago by Leon Bichmann <[email protected]>

[NOP] cosmetics

57a206d926c9ab7a3a0720a535af3be61f7293ce authored almost 6 years ago by Hannes Roest <[email protected]>

[FEATURE] properly handle zero bytes in Python

also copy zero bytes into byte array in Python

a8a837b4354445eefaa7ef8c3eb542a45b17fd50 authored almost 6 years ago by Hannes Roest <[email protected]>

[FIX] conversion fix for zero-bytes

076c71f7867e56e17c989cdf1f30599b8f510cf5 authored almost 6 years ago by Hannes Roest <[email protected]>

[FEATURE] Unicode strings

allows toString to also parse unicode strings that contain zero bytes
(instead of simply truncat...

08baf6663f4eb6f09fe33cd273cb9c13d61cbaa6 authored almost 6 years ago by Hannes Roest <[email protected]>

[FEATURE] properly handle zero bytes in Python

also copy zero bytes into byte array in Python

1a803bdda6f28c18d2868ba9ca8eead3fa6b76e0 authored almost 6 years ago by Hannes Roest <[email protected]>

[FEATURE] Unicode strings

allows toString to also parse unicode strings that contain zero bytes
(instead of simply truncat...

22b3f729be81707e2efb115851f9b288fab0b2bc authored almost 6 years ago by Hannes Roest <[email protected]>

[FEATURE] return str / bytes depending on encoding

When decoding with UTF8 fails, then return a byte array

55a7e3764fff917606ffcd861376e03301c669c8 authored almost 6 years ago by Hannes Roest <[email protected]>

[DOC] internal

56a780b5e08b5b32848df17eb192ec8f8cf90a34 authored almost 6 years ago by Chris Bielow <[email protected]>

[FIX] reduce time for StopWatch test

[DOC] start() does mean restart()

05932b93b1c4175c1806ac219a0a3780825f286f authored almost 6 years ago by Chris Bielow <[email protected]>