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

Parameditor rewritten by QtCreator...

90bcd1fffc0815c5aa15098ec4264c5a75d6e1e9 authored over 4 years ago by Chris Bielow <[email protected]>

looked up wrong meta data

3124db0923c5334ca00c59dd335c1a52882906e2 authored over 4 years ago by timosachsenberg <[email protected]>

let PeptideIndexer query original search engine

00f82667f102941d153ee4b2020e6d8c684d2dcf authored over 4 years ago by timosachsenberg <[email protected]>

[FIX] Add BOOST_ALL_NO_LIB to Superhirn tests (#4749)

* Add BOOST_ALL_NO_LIB to Superhirn tests

* Update CMakeLists.txt

cfbac237d4ea7df25f38416101a6bf00f9698311 authored over 4 years ago by jpfeuffer <[email protected]>

Deepcode comment fix

d0dde2eee2aca528c0b31c2dd0cb8a5564682aa1 authored over 4 years ago by Michał Startek <[email protected]>

Deepcode comment for false positive memleak error

6ec7b18480cb1f8556ed11cf55aa16498abc0b09 authored over 4 years ago by Michał Startek <[email protected]>

Add some nullptr checks in non-speed-critical code paths

80fded0a7ca885c3db3bd49c58ddee45e1190055 authored over 4 years ago by Michał Startek <[email protected]>

MSVC compile fixes

1766e76d807b3bc90298d4dff7f7e413718f795b authored over 4 years ago by Michał Startek <[email protected]>

moved getOriginalSearchEngineName to ProteinIdentification

9572f708c75cdd3e27455a2977a25a2955be0952 authored over 4 years ago by timosachsenberg <[email protected]>

Sync up with IsoSpec (minor fixes)

90ff91977fb3c7c918a1fe7ba707dccbfe48917c authored over 4 years ago by Michał Startek <[email protected]>

explicitly check for nullptr

626c021c64a187d0df2873047fcae264279a9e96 authored over 4 years ago by Anton Kriese <[email protected]>

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

Conflicts:
src/tests/topp/MzTabExporter_1_output.mzTab
src/tests/topp/MzTabExporter_2_output.m...

b28eecff23cb317a19193d0347f7cc23f4adfe4d authored over 4 years ago by timosachsenberg <[email protected]>

Update pyopenms-wheels.yml

6a44b9d7eb16ac79dc5478696f62a7952aa05a29 authored over 4 years ago by jpfeuffer <[email protected]>

Merge pull request #4737 from jpfeuffer/fix/scoreCheckSwitchPLFQ

[FIX] PLFQ check score types again after reloading IDs.

eaa3117cfa3416fee2b0476e29c91cf5345983b4 authored over 4 years ago by jpfeuffer <[email protected]>

changed PRT optional column to indicate details, single or group

information

f3e1a7c770a7556fc647c75fce19673e099d5c7c authored over 4 years ago by timosachsenberg <[email protected]>

Fibonacci heap (#4721)

* Elimination of unnecessary map-copy-work

Co-authored-by: taranehstrunk <[email protected]>
...

fe8b9e3a9ade4c456b0110da007eb81f786c8da6 authored over 4 years ago by Felix-Droop <[email protected]>

safer parse of MC in mzIdentML.

ad0f75823a53d8047c232a69f11eec300183cdec authored over 4 years ago by Julianus Pfeuffer <[email protected]>

update consensusMap protein references

3c66dead9fb3653ba0a3fe81b1415e4c23db5c44 authored over 4 years ago by timosachsenberg <[email protected]>

Merge pull request #4748 from dmccloskey/fix/EMGDerivatives

fix: vector out of bounds in EMG derivative calculations

2cb5a8ab02439a9fcf7f4083fdfb0c09a2b1c8a2 authored over 4 years ago by Timo Sachsenberg <[email protected]>

small fixes and test fixes

a321b7dce02ae934de49ad1621b4b2e932bc7a9e authored over 4 years ago by Julianus Pfeuffer <[email protected]>

fix: vector out of bounds in EMG derivative calculations

d3d3bd9b25fd3df72421a14b6d2c19d58e0fb6c3 authored over 4 years ago by Douglas McCloskey <[email protected]>

update peptide evidences

c3539522f3b47b0d2fd61c3d963b7c6873a96fee authored over 4 years ago by timosachsenberg <[email protected]>

forgot one

e17df635216c271918b752ca538f7d2ed3cbb90e authored over 4 years ago by Julianus Pfeuffer <[email protected]>

Merge pull request #4744 from nateglasser/isodist_constaccess

Add a missing const operator[] for IsotopeDistribution

75c4823467a54dd8f4fa1e95f311416b0ba3b32a authored over 4 years ago by Timo Sachsenberg <[email protected]>

Update IsotopeDistribution.h

bc43f57d600f602d2adf26bd6d44352ccd99a941 authored over 4 years ago by Timo Sachsenberg <[email protected]>

count PSMs over all charge states and fractions

c4ac6ecd2d084a35ea3af07ee8f72e8a5e92711a authored over 4 years ago by timosachsenberg <[email protected]>

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

Conflicts:
src/openms/source/ANALYSIS/QUANTITATION/PeptideAndProteinQuant.cpp

d643eb6f57114196b2e752c3af3958a53cf451d9 authored over 4 years ago by timosachsenberg <[email protected]>

added distinct peptides

009ad51d6ae2e2ace23dca8b6f595a07ea089708 authored over 4 years ago by timosachsenberg <[email protected]>

update pyOpenMS

485ca0d545ec2a57bd78e910640571da201689f8 authored over 4 years ago by Timo Sachsenberg <[email protected]>

Added a missing const operator[] overload for IsotopeDistribution. Allows a const IsotopeDistribution& to be passed to functions and have its individual peaks accessed.

31ec6f498ca408088e67fc637189d48b87085b61 authored over 4 years ago by Nate Glasser <[email protected]>

last test fixes?

896dd442a5a0eafed984c3a003aa740a143f02df authored over 4 years ago by Julianus Pfeuffer <[email protected]>

Merge pull request #4742 from OpenMS/fix/cometTermModWithOrigin

[FIX] term. mods with specific origin in Comet

4a80f227e22f4eb5d5febded8fcc71c8f9db13a4 authored over 4 years ago by Timo Sachsenberg <[email protected]>

Update PeptideAndProteinQuant.cpp

a7b20d72cb05da24cd69c8e98fc73a022d88fbae authored over 4 years ago by Timo Sachsenberg <[email protected]>

chars

5bc7398290bd5c34e1bb849ec558914be79b87ea authored over 4 years ago by jpfeuffer <[email protected]>

[FIX] term. mods with specific origin in Comet

8747e47a008077716c70ab43096947ae92dde0a9 authored over 4 years ago by jpfeuffer <[email protected]>

use enums values instead of numbers

f02c1bb2ba885c09e671d6be12581eac14bd184a authored over 4 years ago by Julianus Pfeuffer <[email protected]>

add SIZE_OF again

37c765a2d18984ff0c1dea3bf293fce199ad6595 authored over 4 years ago by Julianus Pfeuffer <[email protected]>

moved spectral counting before filtering

682b7e5e9df60c12cff350e91162ac07e8064cf8 authored over 4 years ago by timosachsenberg <[email protected]>

small fixes and test fixes

d5bef2f1701c04c17c3851883b4ae3cf3acc24e8 authored over 4 years ago by Julianus Pfeuffer <[email protected]>

fix compilation errors and pyopenms enums

018c0cc0ce8124aefb14dde38c1437922a20aba1 authored over 4 years ago by Julianus Pfeuffer <[email protected]>

fix compilation in plfq

1156244d92ae3e6877f5dae69bfaf64b813b9068 authored over 4 years ago by Julianus Pfeuffer <[email protected]>

clang-tidy

cb84606e8c02d313058564400b8984b28601f905 authored over 4 years ago by Julianus Pfeuffer <[email protected]>

better defaulting in PepIdxer

c80d1bad5c55d16d76a60b0a593dcad13dd9558a authored over 4 years ago by Julianus Pfeuffer <[email protected]>

refactored to EnzymaticDigestion. Rename.

Make Pepidxr read the new data.

97795f5f9f541be3bc28212f7bf95d00f152b12a authored over 4 years ago by Julianus Pfeuffer <[email protected]>

Add support for msgf, comet, sse

41d573011b14a3bee6c290b566e85a0af94077b5 authored over 4 years ago by Julianus Pfeuffer <[email protected]>

check score types again after reloading IDs.

Add trypticity to search engine parameters.

4d4ef19b3b015d43bb581fe53d9d08603d44237e authored over 4 years ago by Julianus Pfeuffer <[email protected]>

minor beauty changes

f45433a53b9ef8f6a60be944b0a722398e6ec492 authored over 4 years ago by Anton Kriese <[email protected]>

Don't use [[maybe_unused]] when if constexpr is unavailable

676d06d3871e52531f5a6377e99991cdb84736bb authored over 4 years ago by Michał Startek <[email protected]>

go back to const member functions by making cahced_terms_ mutable

8ef988246459c428b66c14cdc9582d391c065e0b authored over 4 years ago by Anton Kriese <[email protected]>

Sync IsoSpec sources with 879f47b6b0eabde21f07fc01f2d2fb6f8aa0452c

9eea8208d23eec9bdeb1076bd4e1847914345275 authored over 4 years ago by Michał Startek <[email protected]>

add function description

dcefe64edad63334bd55cf426a6e3fecf312b107 authored over 4 years ago by Anton Kriese <[email protected]>

make cached_terms a member of MzMLHandler

9fde6b0772931a74e564a7e665396a072f7ea70c authored over 4 years ago by Anton Kriese <[email protected]>

Update IDScoreSwitcherAlgorithm.h

c4d1e5e82e6256bf08ba2c694518c32d4d8cd95b authored over 4 years ago by jpfeuffer <[email protected]>

Merge branch 'test_branch_1_1' into getchildterms

948605b945090da92667107f303aab7344a5d2bc authored over 4 years ago by Anton Kriese <[email protected]>

Merge pull request #4723 from Waschi97/feature/TempDirClass

temporary directory class

572b8aed064b8656a1fd6d1a7c8c584b8afe2b19 authored over 4 years ago by TomW <[email protected]>

Readability

95fd174b35313e970beb85e091050da219a35e4a authored over 4 years ago by Michał Startek <[email protected]>

Style fixes

72d5599624a06f60f6bec3ff56a64fc297352c63 authored over 4 years ago by Michał Startek <[email protected]>

Remove obsolete file

4f867f3264f0665b6d13e6fd9fc340ebda4b6dc1 authored over 4 years ago by Michał Startek <[email protected]>

fixed initialization order

67ae2f63e1f3713378bab80a97db901f974bcda5 authored over 4 years ago by Tom Waschischeck <[email protected]>

Add missing files

a645bad3c94da204c68782e1f25bf9aae8a0c38b authored over 4 years ago by Michał Startek <[email protected]>

style fix

6c39eee8e24f9a04615557d5c3d7a1fe2b1961ed authored over 4 years ago by timosachsenberg <[email protected]>

fixed test

8148b0d21b3d43a9ae6eeaed858fbe68d372e244 authored over 4 years ago by timosachsenberg <[email protected]>

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

5c4509a83fa52f3ea9c7a1714591f6b5a22b609f authored over 4 years ago by timosachsenberg <[email protected]>

extended spectral counting code

1e155b2d0afc0a48dea070408a38147191c1f94a authored over 4 years ago by timosachsenberg <[email protected]>

Update tests now that do_p_trim is default in FixedEnvelope

f192b0c89cc3faca2a6d4c67b2fdaecc5401ff2b authored over 4 years ago by Michał Startek <[email protected]>

Doing p_trim by default seems to be the more user-friendly option. This changes behaviour of one test.

6447e9fb2cba7f8e581250d328d77e389357cd38 authored over 4 years ago by Michał Startek <[email protected]>

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

merge to fix compile error

340d83796ec10a3c932cea03e05ba7e979821d71 authored over 4 years ago by Tom Waschischeck <[email protected]>

Probabilities are calculated differently now. Mathematically it's equal, but we make diffrent rounding errors now, and as a result, output size differs by 1 configuration.

0ff6a8ceb71ad8849052cd4481ddbf21d176b124 authored over 4 years ago by Michał Startek <[email protected]>

Copy quickselect algotithm from IsoSpec to operate in-place on OMS structures (like vector of Peak1D)

c09b2a493f7c29d4ae2f4b7f83415d88bc82ba7b authored over 4 years ago by Michał Startek <[email protected]>

CodeFactor issue

3eb7c586e8516aede419d2c36e6c07f6a828d93f authored over 4 years ago by Tom Waschischeck <[email protected]>

working_directory with TempDir object

1080af20be8c40150fa6dbca9414458643617e80 authored over 4 years ago by Tom Waschischeck <[email protected]>

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

d1b7cfa83f6bcf034e115d4f4482453696203b66 authored over 4 years ago by timosachsenberg <[email protected]>

nitpick changes, removed removeTempDir_() from CruxAdapter

af72bbac39eaf387337bc0104c28e506ef753d89 authored over 4 years ago by Tom Waschischeck <[email protected]>

Update CMakeLists.txt

a24cf1873e6c16adbd822f2d6127ecc5305e9af6 authored over 4 years ago by Timo Sachsenberg <[email protected]>

[FEATURE] add spectral counting to mzTab file

53c505f803acf9973c7ff935914032ebccc9c2ca authored over 4 years ago by timosachsenberg <[email protected]>

fixed indention

ce81c637699f42ee562a3cf2b4b8a15b0b8fafdb authored over 4 years ago by Tom Waschischeck <[email protected]>

PR changes

ec57f9784d691081fd350e38257f3292ed5df6bb authored over 4 years ago by Tom Waschischeck <[email protected]>

Merge pull request #4718 from Waschi97/DOC/win_install_update

Update of the Windows building guide

8be3ba98d4e77c2429b7faa0acb13825c18c24a0 authored over 4 years ago by jpfeuffer <[email protected]>

first part of spec counting. TODO: exp. design in consensus missing,

export

4523446424eac5dd08bf3fac0c772be2f4a56973 authored over 4 years ago by timosachsenberg <[email protected]>

Merge pull request #4720 from jpfeuffer/fix/mzTabMTD

[Fix] repeating secondary search engine settings in mzTab MTD section.

08df76f89272dac4656e9eda69cc6c1c0c7b812d authored over 4 years ago by jpfeuffer <[email protected]>

emplaces

20ba268f4a175e6fdabba9704cc03cb25a529a87 authored over 4 years ago by Julianus Pfeuffer <[email protected]>

remove templates from make_pair

5ac76a24b656a2dc5fb5831e4ac50e247e4d47d0 authored over 4 years ago by Julianus Pfeuffer <[email protected]>

upgrade pip on win for pyopenms wheels

2ab05eab4f4759793b5db1959983eef288b71559 authored over 4 years ago by jpfeuffer <[email protected]>

review comments. make protein inference software unique.

bb7e7b6c647c7b8f9e7d9d6af1fd06157b834747 authored over 4 years ago by Julianus Pfeuffer <[email protected]>

removed blank line

8bcd9fd87ae52f4891d6eb003617c34f89090a94 authored over 4 years ago by Tom Waschischeck <[email protected]>

added a test for TempDir class

17f70bf6729ebc046f5f28e4f923d36a27046677 authored over 4 years ago by Tom Waschischeck <[email protected]>

removed some comments

ffdd06f4521159ec4053612cfb071050ead8891b authored over 4 years ago by Tom Waschischeck <[email protected]>

removed temporary directory functions from TOPPBase, changed usage in tools and utils

f809a00b8f31dcbce4c3bf7ce2f0afecbbeb1747 authored over 4 years ago by Tom Waschischeck <[email protected]>

temporary directory class in File.h/File.cpp

b80b7dd51225ab44a19bc450c300311d86fac733 authored over 4 years ago by Tom Waschischeck <[email protected]>

qScore added

fcde29df21dadb129c162c0d57c6c468e7e6a2b5 authored over 4 years ago by kyowonjeong <[email protected]>

forgot QC test

29b345454e30f72db198e6c1f5b33b41c1ea652a authored over 4 years ago by Julianus Pfeuffer <[email protected]>

forgot

9cd29dc3d5fea9295df495463a9297c6f8df488b authored over 4 years ago by Julianus Pfeuffer <[email protected]>

Fix and refactor writing of search engine metadata.

be5fdced6c47d1ef7c2a72f288a4330375070180 authored over 4 years ago by Julianus Pfeuffer <[email protected]>

Unique_ptr does not carry an overhead these days and is better than raw

807ba65dfb54f0b1444194e4d27c2b5cdc21c793 authored over 4 years ago by Michał Startek <[email protected]>

< &rt; instead of < >

9f6c60932d05e41e139fc788f178abac4ce8ef39 authored over 4 years ago by Tom Waschischeck <[email protected]>

Tests compile fixes

1156a2d3c74b3ade24028f3475ae2fda0de97635 authored over 4 years ago by Michał Startek <[email protected]>

Initial integration for IsoSpec API changes

f4f7d84bb0b49ad905af1e5cc0d88719b2a0cb13 authored over 4 years ago by Michał Startek <[email protected]>

Little fix in IDScoreSwitcherAlgo. Added test.

Fixes repeating secondary search engine settings in mzTab MTD section.

a364138cb777235200db7e45fe3fcce8c8a62448 authored over 4 years ago by Julianus Pfeuffer <[email protected]>

fixed typo

e180e4bc313434587691a35499670fddf300ba4a authored over 4 years ago by Tom Waschischeck <[email protected]>

Rest of IsoSpec v2.1.0b1 import

3c436e0b57075bcafabc7c17d9d717e29ce6eb0e authored over 4 years ago by Michał Startek <[email protected]>