github.com/OpenMS/OpenMS-1 commits | Ecosyste.ms: OpenCollective

start and end position of peptide extracted

67af40af5c744637d628883689f3c4b70c2d197c authored over 3 years ago by Dhanmoni Nath <[email protected]>

protein sequence, accessions, peptide start, end, seq extracted and send to JS using QJsonDocument

d599f8ed36fd5833bca0f82b62228e8e15cf90c2 authored over 3 years ago by Dhanmoni Nath <[email protected]>

add peptide/protein identifications

7a0fff1f863a3207f7fe008e5f1bc7a93f19ba0b authored over 3 years ago by axelwalter <[email protected]>

new window appears on sequence clicked, and shows sequence inside html page

920247410e7e82d2ea2a67b5c8dfd0467f62ff42 authored over 3 years ago by Dhanmoni Nath <[email protected]>

Merge pull request #5385 from poshul/feature_moveconfig

[fix] updated the config storage path for linux

7b74d2c002aaf14c5bbfcc430ded009dc32cfb85 authored over 3 years ago by Samuel Wein <[email protected]>

[fix] fixed variable scoping goof.

0ff0d38c0bf440348fbfe41f0e258d13ceaeed0f authored over 3 years ago by Samuel Wein <[email protected]>

[fix] address reviewer comments

0b0216b4935375fea7ba1562decbf36b1e41fe5a authored over 3 years ago by Samuel Wein <[email protected]>

[fix] added support for explicitly specified XDG_CONFIG_HOME parameters

c5b7a32390ac358d3111f671e5893994ed2ebd7c authored over 3 years ago by Samuel Wein <[email protected]>

[fix] Added some additional logic to determine platform for tool names

34406e445f0057dc438e8aa8cb6899bf96839ea0 authored over 3 years ago by Samuel Wein <[email protected]>

merge TopFD output format checkboxes into one

2d6170ea59b098c2473a82a45f165fe998efe21d authored over 3 years ago by JeeH-K <[email protected]>

rename variables

59cb28de0bf3e81aaafcebe1a601fbc4919eaa95 authored over 3 years ago by axelwalter <[email protected]>

add RT shift mean and update qc-cv

6a32c1009e2d72f73b479c459a8bfb1ad927b692 authored over 3 years ago by axelwalter <[email protected]>

Merge pull request #5383 from cbielow/test_opt

Fix class test macro

66e8b4ebd8755193529b18a249440cc0dc50c54f authored over 3 years ago by Chris Bielow <[email protected]>

more fixes for CI

a6836d9a7762b03df29a2091df541b7d11daf546 authored over 3 years ago by bielow <[email protected]>

make exception for Windows (in a VM)

800313c0cbfcb8144e11c28f289d0c6994be828f authored over 3 years ago by bielow <[email protected]>

Merge pull request #5341 from bertrandboudaud/feature/TargetedSpectraExtractor_storeSpectra_for_pr

Feature/targeted spectra extractor store spectra for pr

47f08c48322b25e43d005616e3366e4265fea5d8 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

some stopwatch debug stuff

b9f85a5b8d6346e28cea4e8631bd87b4872c64c8 authored over 3 years ago by bielow <[email protected]>

open new widget with sequence data when clicked on sequence of a row

000c9bcfe61b907d248dce0fb577296d7a09f6f0 authored over 3 years ago by Dhanmoni Nath <[email protected]>

aggressive fix

4c59eaaa99127183749c4dffdb32c4ba027b529a authored over 3 years ago by bielow <[email protected]>

open uniprot site on browser on accession clicked feature added

8e0aefc46ad8ddfa7ad9e1a689e0a1ef5cb86b6d authored over 3 years ago by Dhanmoni Nath <[email protected]>

attempt to fix StopWatch test

962645766f205aaf2a6c8eb8ea2df1d481fd9813 authored over 3 years ago by bielow <[email protected]>

fix test

9976d5a8b57c38983820a49b8f44d961b197f33f authored over 3 years ago by bielow <[email protected]>

Merge pull request #5386 from jpfeuffer/gnpsexport

[FEATURE] Rebased GNPSExport

4557880c2bf22327059549edf467c782ce9b590c authored over 3 years ago by Julianus Pfeuffer <[email protected]>

correct tool registry

1adcbe89c9f696139ac97b4324af33743e08dbb6 authored over 3 years ago by jpfeuffer <[email protected]>

[GNPSExport] Refactor code and address integration test errors

Deduped code between export types and simplified topp unit tests.
Also addressed Travis integrat...

3d6a336c34e8e3185dbe9fd16a43dc268ac190a1 authored over 3 years ago by Abinesh Sarvepalli <[email protected]>

upd GNPSExport test suite

c0865fe2011c50514b1b8673f8c1550cc99a7a8b authored over 3 years ago by Abi Sarvepalli <[email protected]>

Addressed PR 4761 to OpenMS/openms

https://github.com/openms/openms/pull/4761

Added...
- Technical documentation to method headers
...

59c43b3dd1cc73678a54de61d8bc9bf569c94aa6 authored over 3 years ago by Abinesh Sarvepalli <[email protected]>

upd test suite ini files

1e98c211d76c7b80164e1d448b848c034d562b42 authored over 3 years ago by Abi Sarvepalli <[email protected]>

fix: trailing whitespaces and extra blank lines

12aee8d4ab777e2f17595e944e8a2559e4cf7c7d authored over 3 years ago by Abinesh Sarvepalli <[email protected]>

upd GNPSExport mem management

f641f7e5e08ee735674d67bf0b3681386c975405 authored over 3 years ago by Abi Sarvepalli <[email protected]>

- added module citation

- fix binning first mz value
- use c++11 for ranging

added large test to GNPSExport module test ...

aa4333702368373d2a43fa6b18c1aa486072295d authored over 3 years ago by Abi Sarvepalli <[email protected]>

fix/upd GNPSExport mem reading mzml files

8c672737c650dbfa41b463dc9503b858e1d50e18 authored over 3 years ago by Abi Sarvepalli <[email protected]>

close output stream

5367d47bb24093d8fbf32f83547ada385555911f authored over 3 years ago by Abi Sarvepalli <[email protected]>

fix travis lint issues

c2ef1249f30a49cf94fba5628210ea28b2e59fa2 authored over 3 years ago by Abi Sarvepalli <[email protected]>

prefix ++ for non-primitive types

00df465bfec0419bd23200c6dbacfb81f54903f5 authored over 3 years ago by Abi Sarvepalli <[email protected]>

fix tool description

eb791aec4f21f9741e68248a485beb8ef30b7ca9 authored over 3 years ago by Abi Sarvepalli <[email protected]>

- edit doxygen info

- remove repetitve spawn of MzMLFile objs
- opt loading MSExperiments from mzml module arg

515ce441f1f9cbef4e4b94fc6826b7211580b799 authored over 3 years ago by Abi Sarvepalli <[email protected]>

refactor getSpectrumAtIndex -> getSpectraAtIndex

5e8815f557e982aa06992f69b113a725365e6d97 authored over 3 years ago by Abi Sarvepalli <[email protected]>

remove large test case

97b93b7c415a14d06e7694a7e9eff6639d649637 authored over 3 years ago by Abi Sarvepalli <[email protected]>

refactor write to file as method

bea1e5d463949e27ae8f0394110bdde6aabb5b1d authored over 3 years ago by Abi Sarvepalli <[email protected]>

use emplace_back to prevent creating duplicate structs

23ed6cb53e1179aa66dc304e21a6e991afebf456 authored over 3 years ago by Abi Sarvepalli <[email protected]>

fixed output errors:

- prefix "e_" when specifying consensusElement feature id
- change feature_charge to int
- clamp ...

edf8a05c2123d134e8064513e7612b6e8dac0030 authored over 3 years ago by Abi Sarvepalli <[email protected]>

[fix] pass ms2_block to write method by reference rather than value

bd46c1ed479ba6f8da087354702d45701898cd95 authored over 3 years ago by Abi Sarvepalli <[email protected]>

fix documentation; updated generateMSMSSpectrumBins_ with overloaded method accepting MSSpectrum

Signed-off-by: Abinesh Sarvepalli <[email protected]>

dd8eda367678dc67c40044cde85245a290407af4 authored over 3 years ago by Abinesh Sarvepalli <[email protected]>

upd test suite

3d146a0101296d29ef1eb737f319e4a639d4616f authored over 3 years ago by Abi Sarvepalli <[email protected]>

updated GNPSExport module

2129705a4e8eaf9ef8dbd9e63f9f0aa340a44c8a authored over 3 years ago by Abi Sarvepalli <[email protected]>

pass args by value into sort helper funcs

eb75504fd98773303e7c3a902cbe62fd6107fd6a authored over 3 years ago by Abi Sarvepalli <[email protected]>

add small result struct to DetectedCompounds

75b13cf25a537381af4df42e53e7bf3d3434b881 authored over 3 years ago by axelwalter <[email protected]>

adding missed file

6e7ba5757bb2c3ce1f3152b63255a48880c202e1 authored over 3 years ago by JeeH-K <[email protected]>

added output format checkboxes and changed wizard name

8a53f6303b9ea5df6bf7681b667a809081a47500 authored over 3 years ago by JeeH-K <[email protected]>

fix TIC relative intensity calculation

d4fe4e6c31acc328c329f2332d18671da40fbb0f authored over 3 years ago by axelwalter <[email protected]>

add detected compound QC metric

bd196a923ee2e4e01cab4bb2fc30dcf1706ecd40 authored over 3 years ago by axelwalter <[email protected]>

Update CHANGELOG

ad30d3e0d6a62990b9b18c285e2faabafe43d6d7 authored over 3 years ago by Samuel Wein <[email protected]>

[fix] updated the config storage path for linux

21f6614d2fff43428da1698d8c2f078797a44c52 authored over 3 years ago by Samuel Wein <[email protected]>

noop

4c638b548103b89bf875352dd0f2fb9c10ee0282 authored over 3 years ago by bielow <[email protected]>

fix test condition

9ad04f96d2daed0d5615dae6f892ecc38ec51571 authored over 3 years ago by bielow <[email protected]>

remove test -- its unclear why it should fire

df9fed30bd8195fed68506a51935ee0833ba413a authored over 3 years ago by bielow <[email protected]>

fixed parameter handling

e86109d47925c87094fe17a1bab7651219384289 authored over 3 years ago by JeeH-K <[email protected]>

Merge pull request #5384 from OpenMS/jpfeuffer-patch-1

[FIX] segfault in NeedlemanWunsch

64802a57fd97acf6b784cc9abc0803b7e002b31b authored over 3 years ago by Julianus Pfeuffer <[email protected]>

[FIX] segfault in NeedlemanWunsch

breaks nightlies

2d62314275156894874aa299e00b7295427fd205 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

setting FLASHDeconvWizard (parameter part not done)

4b287605606e58caf8c9e5f615c3f2cec272d8df authored over 3 years ago by JeeH-K <[email protected]>

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

1ed19762c8f67571f928774192bfbc4854c3239e authored over 3 years ago by bielow <[email protected]>

fix ABORT_IF's unexpected behaviour

ec11b43cf6ab1e1fbaebead6ff7a4308a266b648 authored over 3 years ago by bielow <[email protected]>

Merge pull request #5381 from cbielow/fix_static_initsegfault

fix segfault when starting any executable

60ebf3d7f27ee475fc93a861b19f8bdd69aee3b1 authored over 3 years ago by Chris Bielow <[email protected]>

* removed unused mz_right_lim and mz_left_lim

* using Logging mechanisms instead of std::cout
* use if (! x.empty()) instead of if (x.size())

e3877cf1d2bb4178d9631b957b8713cd17f58f84 authored over 3 years ago by Bertrand Boudaud <[email protected]>

fix segfault when starting any executable which was linked with

which results in
Program received signal SIGSEGV, Segmentation fault.
0x00007ffff7893f00 in xerce...

f29631567ac45adf083162faa3e2709451449714 authored over 3 years ago by bielow <[email protected]>

massively reduce build time (#5377)

* massively reduce build time by removing includes from ClassTest.h

* fix linux compile error...

f0f3b9411164256e8a9a266faaea757d547cdfe0 authored over 3 years ago by Chris Bielow <[email protected]>

support for IM data conversion (#5375)

* support for IM data conversion

* fixed tests

* fix

* extend test

* fix fallthrough...

9810f53ea6715d9d4b957cb4bdbd8cc57ae6fe86 authored over 3 years ago by Chris Bielow <[email protected]>

add complete TIC and MS2 TIC for mzqc

d90aad291b9d5e7df88b97be8662dbd9b11357f5 authored over 3 years ago by axelwalter <[email protected]>

review comments

02b63b76d2bdb7152c9d45eaf89cf084ca05f099 authored over 3 years ago by bielow <[email protected]>

fix linter errors

55257ea188541e4f05a3cb0dba45475015a6f7e1 authored over 3 years ago by bielow <[email protected]>

fix linux compile error

68b2f43c1fd548da170fbc4a866c883b58d959ff authored over 3 years ago by bielow <[email protected]>

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

89e74fe9fa1e4453a1e82a283be4359b290e6cef authored over 3 years ago by bielow <[email protected]>

massively reduce build time by removing includes from ClassTest.h

bbe0beded94bae282d88ff59b42afe4c99b511c4 authored over 3 years ago by bielow <[email protected]>

add ms_level parameter to MSExperiment::getTIC()

45a392709653428fbc329784672d62784c032bb9 authored over 3 years ago by axelwalter <[email protected]>

Fixed mergeFeatures unit test

2e8c746169f0f09eee2b39bd5df33c2c83dbd5ad authored over 3 years ago by Bertrand Boudaud <[email protected]>

Merge pull request #5351 from singjc/fix/ipf_peptidoform_gen

Fix/ipf peptidoform gen

ad726f579de423c20852c871ae572df933f06a55 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

[FIX] Adjust braces on multiline if-else statements to match consistent code style

e9d599894eb394994e0a334b03e3fc826c7fb28a authored over 3 years ago by Justin Sing <[email protected]>

Merge pull request #5374 from OpenMS/py_nightly_test

[TEST] PyOpenMS Nightly Linux failing

4389ed7dec33354c15852c62dcab52e74d8f830e authored over 3 years ago by Julianus Pfeuffer <[email protected]>

reformat patch

908bc0c756fb6cc8c95da1b534a98a8d89481e04 authored over 3 years ago by oliveralka <[email protected]>

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

a42d77e5b62166ba6ed4ec6acfeba071695f0c7a authored over 3 years ago by oliveralka <[email protected]>

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

b54873efd15dc1dfeb93997ad128b83ec270440d authored over 3 years ago by oliveralka <[email protected]>

format

c68a8790584df28f857399219539a6c0b864af46 authored over 3 years ago by oliveralka <[email protected]>

test1

d86531571420d6b4e510b324b4af89301e9eb519 authored over 3 years ago by oliveralka <[email protected]>

test

3e9071285202f478f9e457358343acf53dd76353 authored over 3 years ago by oliveralka <[email protected]>

Disallow IL_equiv with enzymes that potentially distinguish them. (#5368)

25e5034768f8fa897edc695fd03cfc5903dc2594 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

make getOpenMSDataPath thread-safe (#5372)

* make getOpenMSDataPath thread-safe

* Update File.cpp

6365587b5ee42d1dea730c9619df679c16a199c5 authored over 3 years ago by Timo Sachsenberg <[email protected]>

Update src/openms/include/OpenMS/ANALYSIS/OPENSWATH/TargetedSpectraExtractor.h

Co-authored-by: Timo Sachsenberg <[email protected]>

6a00f8ec1145f2ed226db556c0b6e8b40780da06 authored over 3 years ago by bertrandboudaud <[email protected]>

add missing meta data to FFMultiplex output (#5371)

* add missing meta data to FFMultiplex output

* Apply suggestions from code review

* set c...

1645a2233380df34d69fe7388c3c6b935adbfeca authored over 3 years ago by Lars Nilse <[email protected]>

Add option for compile time tracing (#5364)

383408f0555372116a72385d962632688af8e6a5 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

remove superhirn (#5369)

* remove superhirn

* remove also algo

68cc62d87b8716bb051909f26082291ab182a591 authored over 3 years ago by Timo Sachsenberg <[email protected]>

insert Element.xml info into ElementDB file (#5279)

* insert Element.xml info into ElementDB file

* changed String, Map to std::string, std::map;...

c096c1185f8c9fb21b3c1695bfd445760913f682 authored over 3 years ago by JangJang3 <[email protected]>

only considering the 1st identifier in organizeMapWithSameIdentifier

f7d28e0495f2a3af7d1c487b86c2275f117472ff authored over 3 years ago by Bertrand Boudaud <[email protected]>

moved include

8700e2397b05886ccd7a3242235ea36b779176c6 authored over 3 years ago by Timo Sachsenberg <[email protected]>

update toppas workflow in share

26acfb33e41d5b1e170e036b24d27a3f433f58b1 authored over 3 years ago by timosachsenberg <[email protected]>

Merge pull request #5363 from OpenMS/add/openms_ci_thirdparty_tests

[TEST] openms-ci THIRDPARTY tests

5934031ea4e8f3dc8d5d5c27a538c38a3cd8c417 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Merge branch 'feature/TargetedSpectraExtractor_storeSpectra_for_pr' of https://github.com/bertrandboudaud/OpenMS into feature/TargetedSpectraExtractor_storeSpectra_for_pr

da8e0abfd6a05585bc200100a9396e8e32cbde5c authored over 3 years ago by Bertrand Boudaud <[email protected]>

added max_precursor_mass_threashold_ parameter

1a835957af4570aa94a608fddbcd81f8b0e6c628 authored over 3 years ago by Bertrand Boudaud <[email protected]>

added and apply AMSE parameters

cf4faa84a0992b7c3d3e25a94f1254ea8d45159b authored over 3 years ago by Bertrand Boudaud <[email protected]>

switch to loop

ca19c1c514282a17042699a2eedb1bfadbcdb552 authored over 3 years ago by oliveralka <[email protected]>