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

Merge remote-tracking branch 'remotes/upstream/develop' into feature/cXMLProtGroups

# Conflicts:
# src/utils/ProteomicsLFQ.cpp

7898da8706aea59d01900a661d057b880397fd33 authored over 4 years ago by Julianus Pfeuffer <[email protected]>

merge develop

49d3475dfdc151f363b887b8f3e265703c7d1fee authored over 4 years ago by Julianus Pfeuffer <[email protected]>

[NOP] added additional checks to prevent wrong order of input files (#4646)

* [NOP] added additional checks to prevent wrong order of input files

* Update ProteomicsLFQ....

26e303734412ac2c0fe45fcb000ac9bd6e6177a6 authored over 4 years ago by Timo Sachsenberg <[email protected]>

Amonia loss added in MS2

17abc34264945d0fecc08cb39e46cb02767bf463 authored over 4 years ago by kyowonjeong <[email protected]>

forgot a test file

3a82b6af26d014d9e95aa6346e399f559a8e5438 authored over 4 years ago by Julianus Pfeuffer <[email protected]>

- ignore software line in mztab test

- use mutable ref to append proteins

81c98d49a0158a1f50a08faf614770510346a3f4 authored over 4 years ago by Julianus Pfeuffer <[email protected]>

- reset Protein scores before inference

- fix handling of proteins without PSMs in features
- make writing of mztab protein header safer ...

09577076d0546c0267be4c4bdada7dcdc8d76b1b authored over 4 years ago by Julianus Pfeuffer <[email protected]>

fix, docs: misc style changes and docstrings

0c7004c53e131aa4e6b5262a2ca0625ae2a19ab7 authored over 4 years ago by Douglas McCloskey <[email protected]>

Amonia loss added in MS2

b4a65b9291948bf35be0a215f1ce38f7a25cfefe authored over 4 years ago by kyowonjeong <[email protected]>

[FIX] add fall-back if alignment not possible (#4644)

* [FIX] add fall-back if alignment not possible

* Update ProteomicsLFQ.cpp

9dbbeb3e0dfbae699e43d2670b6194cdf8c4fbb8 authored over 4 years ago by Timo Sachsenberg <[email protected]>

MS2 mass2 optimized!!!

MS1 std works great (15 spectra overlap)

1af335a19a805ac19bd33b6d523af29eb2bf0de9 authored over 4 years ago by kyowonjeong <[email protected]>

fixes #4642, amends #4610 (#4645)

c6aeba94b3bd26b06e33ae1bc40c68b553a76e1b authored over 4 years ago by Chris Bielow <[email protected]>

fix: linting...

56ca5e1f56b1aa52cdcd450ee84690318acdb817 authored over 4 years ago by Douglas McCloskey <[email protected]>

Merge branch 'develop' into id-file-format

ab59ebf875b19c99310160d3fa6066cc27bf217f authored over 4 years ago by Timo Sachsenberg <[email protected]>

fix: manually checkout out previous contrib branch

f95b73554b7ee55163fd6af421171c36855461d7 authored over 4 years ago by Douglas McCloskey <[email protected]>

fix: init contrib

fdf74d5f45f62dc9d77f75030b63660d5d1d44cc authored over 4 years ago by Douglas McCloskey <[email protected]>

fix: linting errors

767d477ddf68cc401bbf64d39aa54a9ff9e15d47 authored over 4 years ago by Douglas McCloskey <[email protected]>

Linear regression trial 1

0dadf754d6bcaf3ab27e0063edb5288ea4fc4cf6 authored over 4 years ago by kyowonjeong <[email protected]>

Linear regression trial 1

bbab96ac390e4a9e8350a18976468f49d69c6112 authored over 4 years ago by kyowonjeong <[email protected]>

[FIX] test presence of files in input file lists (#4643)

* [FIX] test presence of files in input file lists

* add skipexists check to Input file lists

40f33a866798f9eaa86849864f70bdb0cf507592 authored over 4 years ago by Timo Sachsenberg <[email protected]>

[FIX] more sanity checks in ProteomicsLFQ

7f2b7875b85e43c8727e529e8f3f720640a43cfe authored over 4 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #4628 from hendrikweisser/mapalignerident-force

MapAlignerIdentification: option to use "identity" transformation when data is missing

e537b4410223a29be6661bd52474bf39d780d08b authored over 4 years ago by jpfeuffer <[email protected]>

Merge branch 'develop' into id-file-format

501f67d7d536dc9f3583bd976d881d5bb1930e2a authored over 4 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #4640 from OpenMS/updateCometNonWin

Update Comet on non-Win in THIRDPARTY to match bugfix version.

82d5e406d04ada29d7ffde334d722c72f0281faa authored over 4 years ago by jpfeuffer <[email protected]>

MassCalculator: output is csv (#4562)

* MassCalculator: output is csv

* MassCalculator: set input type to tsv

* MassCalculator: ...

9dbd68be524bf7781dd253a2a12b9fdb476941de authored over 4 years ago by M Bernt <[email protected]>

next try

038f88752cb863ec2478fc8c3c2361096e72e8a6 authored over 4 years ago by jpfeuffer <[email protected]>

Overlap count bug fixed..

8ecff460d365c35d37abc25afb0bce0ba110b17a authored over 4 years ago by kyowonjeong <[email protected]>

STD 6 protein works perfect... MS2 great before complex dataset test..

c589a102c4536f1e9b6ef0ff1a9417abef31e395 authored over 4 years ago by kyowonjeong <[email protected]>

Update Comet on non-Win in THIRDPARTY to match bugfix version.

20934d4e2ae478d911ef67e18783405cd4ed2a06 authored over 4 years ago by jpfeuffer <[email protected]>

Merge pull request #4610 from cbielow/feat_QC_labeled

support QC of labeled experiments (iTRAQ/TMT)

9c6c486be250e2b743bd0939db0cc33586866a03 authored over 4 years ago by Chris Bielow <[email protected]>

unordered map bug fixed

23cbe96f02c278b9731922ffff8478718a38b135 authored over 4 years ago by kyowonjeong <[email protected]>

fix: == to = and odd issue with macro in test

040a80673bbb1f2b56a4c840b2437ffe5d4da6ce authored over 4 years ago by Douglas McCloskey <[email protected]>

fix: removed C++14 auto argument in lambda

6c82f4a062a21355748f97368f372f03474cbc34 authored over 4 years ago by Douglas McCloskey <[email protected]>

Memory leak resolved

283509440748b6620064c6c283a2eed65da91e14 authored over 4 years ago by kyowonjeong <[email protected]>

Memory leak resolved

fb19a79818546ffed262e756eb647d0c73c635ad authored over 4 years ago by kyowonjeong <[email protected]>

Memory leak resolved

5aed0953110b91282b22d7c32e6bcfb24b881157 authored over 4 years ago by kyowonjeong <[email protected]>

fix, tests: added comparator to MRMFeatureQC, fixed a few bugs in store, and added tests for MRMFeatureQCFile::store

d8baf25d1fb1da361fffcceb0dff8a31102f95c9 authored over 4 years ago by Douglas McCloskey <[email protected]>

wip: adding in comparators to structs in MRMFeatureQC

226be3f9cfeb03c99910201b2a59b5e7bc078789 authored over 4 years ago by Douglas McCloskey <[email protected]>

feat: MRMFeatureQCFile::store without unit tests

2856eeba7c3eed96d7bf5da99418ffe9e4b6458d authored over 4 years ago by Douglas McCloskey <[email protected]>

[FIX] limit double precision to 17 digits during write (#4636)

* [FIX] limit double precision to 17 digits during write

* little fix

* revert only real s...

366944c4ae238bd1a309cb724e58e5936ebe8b6e authored over 4 years ago by jpfeuffer <[email protected]>

feat, test: filterFeatureMapBackgroundIntensity

1f8f1dbb52299e463e642721292bbcd792e8ae4b authored over 4 years ago by Douglas McCloskey <[email protected]>

feat, tests: FilterFeatureMapPercRSD

3733054e94b9cca57f1977dc50852b4e013fc9ce authored over 4 years ago by Douglas McCloskey <[email protected]>

feat, tests: options for how to estimateDefaultQCValues and associated tests

099f230334d1b7063465e3ae3a3391b57ee2f8fc authored over 4 years ago by Douglas McCloskey <[email protected]>

fix, tests: changed the behavior of EstimateDefaultQCs so that the minimum and maximum ranges are determined by the samples and not the template. Will also add a parameter to the arguments to allow for updating instead of overwritting

b3ced34234a4e83dffe662a73d50e6cc5fb39a31 authored over 4 years ago by Douglas McCloskey <[email protected]>

tests: accumulateFilterValues

183aabd5ca968651be8db4f57dc8289067a79635 authored over 4 years ago by Douglas McCloskey <[email protected]>

WIP: accumulateFilterValues test

af092b8082304cb3655ae25c2289f0837155ab51 authored over 4 years ago by Douglas McCloskey <[email protected]>

WIP: EstimateBackgroundInterferences test

9b51739974d709845229ac0056c69d4b9205f266 authored over 4 years ago by Douglas McCloskey <[email protected]>

fix, tests: calculateFilterValuesVar and calculateFilterValuesPercRSD

f33224acefca6861b170153841fc74809cb22f56 authored over 4 years ago by Douglas McCloskey <[email protected]>

H2o add

d9d5d11e893b1c600d7484b5fea3a86f7724fa3e authored over 4 years ago by kyowonjeong <[email protected]>

H2o add

6b83c2b20dc3b18ca5bf88e15e439e9effdf96c0 authored over 4 years ago by kyowonjeong <[email protected]>

fix, tests: calculateFilterValuesMean

cbb86707f4cd011b7e01860dc699afcf5e7b865f authored over 4 years ago by Douglas McCloskey <[email protected]>

tests: zeroFilterValues

aab3d7cb76659ae80588d0611598ddb9a33b9faf authored over 4 years ago by Douglas McCloskey <[email protected]>

tests: setMetaValue

08802f1f2a926b2443a3e256bfe94ccad852add6 authored over 4 years ago by Douglas McCloskey <[email protected]>

feat: EstimateBAckgroundInterferences without unit tests

d77d33cb1012305502f24a41cb74fc6312dcefd5 authored over 4 years ago by Douglas McCloskey <[email protected]>

feat: EstimatePercRSD with submethods without unit tests

ed22cc8442d41ab47a5b0b50d5a70fdd6f8b8635 authored over 4 years ago by Douglas McCloskey <[email protected]>

Total SNR introduced..

e36685cf1e7438b7879735b611076df2e8a97d20 authored over 4 years ago by kyowonjeong <[email protected]>

MS1 deconv bug fixed (STD dataset) MS2 .. still goes on..

bd79af9c66959872175d798b786c91142a23860d authored over 4 years ago by kyowonjeong <[email protected]>

Fix/lf qfixrequant (#4633)

* [TEST] test stub to reproduce failing plfq if requant is enabled

* [FIX] requantification
...

ead8f6ff000b2d09c194edd2ce2b1360d1a8a958 authored over 4 years ago by Timo Sachsenberg <[email protected]>

WIP: EstimatePercRSD; todo: refactor into smaller methods that can each be unit tests

999c2a66afd1c70639642066051e31a8e77765fa authored over 4 years ago by Douglas McCloskey <[email protected]>

fix: failing build/tests

1c4d0434febe062a1e71fce557084ae550492286 authored over 4 years ago by Douglas McCloskey <[email protected]>

feat: TransferLLoQandULOQToCalcConcBounds without tests

2b16be624d8223f7580e5a0658935659df61712e authored over 4 years ago by Douglas McCloskey <[email protected]>

tests: tests for helper methods updateRange and updateMetaValue

b8732c6bfbbf9a10d769d0bdb5d26eabf011c0e2 authored over 4 years ago by Douglas McCloskey <[email protected]>

feat: EstimateDefaultMRMFeatureQCValues without tests

6e8181be66b5b7fa36e55565b4725c8a431fd67c authored over 4 years ago by Douglas McCloskey <[email protected]>

fix, feat, doc: removed previously added members to MRMFeatureQC as they were not needed and introduced docstrings and method signatures to MRMFeatureFilter

f37f72dc24474aada6128501adb9ea47b25e25e9 authored over 4 years ago by Douglas McCloskey <[email protected]>

fix: removed potential future QCML features as there appears to be no interest in moving in supporting QCML with MRMFeatureFilter

b0d99021486f91c1f47d8ac5dd3382977e498106 authored over 4 years ago by Douglas McCloskey <[email protected]>

feat: added new members to MRMFeatureQC in preparation for new methods to filter on new members in MRMFeatureFilter

57da84b665a5ab484e87f032cebb760d47f25b65 authored over 4 years ago by Douglas McCloskey <[email protected]>

fix: small cleanup of MRMFeatureQC header/cpp files

ba4a57e3a014dbf6879da10beb11ebdcce27ae33 authored over 4 years ago by Douglas McCloskey <[email protected]>

ms2 debugging2

89f66cf03ad5542dbd672bb500fb1a33a6613706 authored over 4 years ago by kyowonjeong <[email protected]>

ms2 debugging2

3c00a9f2e59a2f5f2e7e917ff858649e439395c1 authored over 4 years ago by kyowonjeong <[email protected]>

ms2 debugging2

8310148f80962ae81b02fba0505a0c7dee7a25d9 authored over 4 years ago by kyowonjeong <[email protected]>

ms2 debugging

d32491e183c55f0c7334ac0a7651f112beb39465 authored over 4 years ago by kyowonjeong <[email protected]>

[FIX] wrap changed static method in TransformationModelLowess (#4631)

* wrap static method in TransformationModelLowess

* Update TransformationModelLowess.pxd

I...

25c468e571e62c6a5d54a20a39d8a7b2dd110b3f authored over 4 years ago by jpfeuffer <[email protected]>

[FIX] Do not fill spectrum data and check all spectra for centroided in... (#4634)

* [FIX] Do not fill spectrum data and check all spectra for centroided in Comet

* Update Come...

3ec3c246b554dd3f633ba7462f66aea93325102d authored over 4 years ago by jpfeuffer <[email protected]>

Spec deconv output per MS level

8b6078293ee21190509066e1d38176530f229a48 authored over 4 years ago by kyowonjeong <[email protected]>

[API] IdentificationData: moved/extended function for picking a score type; simplified function for finding score type by name

8929c83b311705e7683e68b4aaaae75e11050d83 authored over 4 years ago by Hendrik Weisser <[email protected]>

Spec deconv output per MS level

acc4b6e04d2ab2856d4df62fa7e39d99c289c02f authored over 4 years ago by kyowonjeong <[email protected]>

[INTERNAL] remove silent filtering of decoy hits in FeatureFinderIdentification

185db9989ee1225ab1a0c6a80615b7f533d0185f authored over 4 years ago by Hendrik Weisser <[email protected]>

Spec deconv output per MS level

46115cce5bfeae27b05a9c5132a40506439d568c authored over 4 years ago by kyowonjeong <[email protected]>

Merge pull request #4618 from poshul/file_name_fix

File name fix

c939941cb9fb2135d8d8b0de4ebec4fb99ccbc99 authored over 4 years ago by Timo Sachsenberg <[email protected]>

[INTERNAL] minor code clean-up (FeatureFinderIdentificationAlgorithm)

b688284bac1c44648918ce37365e3891dd61f562 authored over 4 years ago by Hendrik Weisser <[email protected]>

update windows and linux comet (mac still missing)

f6528c95c553e9a0ec7013556f8c747f5ca6861a authored over 4 years ago by Timo Sachsenberg <[email protected]>

Spec deconv output per MS level

7ae2cdb8782837175efd7aaf632c7975388d71d9 authored over 4 years ago by kyowonjeong <[email protected]>

Merge branch 'mapalignerident-force' into idfile-integration

7ba9f6a121595a4e823788f80cc109453a2cb353 authored over 4 years ago by Hendrik Weisser <[email protected]>

TopFC output done

853ac873fc9a092d9366eeb367183a71222902fc authored over 4 years ago by kyowonjeong <[email protected]>

Merge pull request #4623 from OpenMS/doc/ed

[DOC] extended documentation of experimental design

68e9486941a0b6f86b8ffa4bf5f9265395088bc6 authored over 4 years ago by Timo Sachsenberg <[email protected]>

Update Spectrum1DWidget.cpp

320917e2c1c36431820b2ae335c9595834a17afa authored over 4 years ago by Timo Sachsenberg <[email protected]>

Update ProteomicsLFQ.cpp

378d725b495a2590b01d88fc9e87b1decf0162a8 authored over 4 years ago by Timo Sachsenberg <[email protected]>

TopFC output done

6874221ee2300f4226c6c992323fdcf413de4f11 authored over 4 years ago by kyowonjeong <[email protected]>

Update ProteomicsLFQ.cpp

dfa091ae1c158bd1d937710dce09a12f54210881 authored over 4 years ago by Timo Sachsenberg <[email protected]>

Update ProteomicsLFQ.cpp

a1e2ea79ba1091e0d34dff91640dd3c79c08a51e authored over 4 years ago by Timo Sachsenberg <[email protected]>

Update ProteomicsLFQ.cpp

f4c42d816270dccd14e125cc0b73e4e6b2b88fff authored over 4 years ago by Timo Sachsenberg <[email protected]>

Update ProteomicsLFQ.cpp

65f4a897d6c7ca965ee6e6177e4f8c1371a0bb50 authored over 4 years ago by Timo Sachsenberg <[email protected]>

Update ProteomicsLFQ.cpp

b81ef68525a14e0c7421d83edbcd90c28e1e8d71 authored over 4 years ago by Timo Sachsenberg <[email protected]>

[DOC] experimental design small grammar/spelling fixes

dd57a1a6b0a9d9b5a285e0f45bd4dfb1ce6095f9 authored over 4 years ago by jpfeuffer <[email protected]>

[FIX] use proper way to rethrow exception in MapAlignerIdentification

52b0efde32d84397dfebd8f8460783dd103ad2c3 authored over 4 years ago by Hendrik Weisser <[email protected]>

[TEST] added test case for MapAlignerIdentification with 'force' option

d6a3db7d3e900b81134fda3214b4e743dd9682a9 authored over 4 years ago by Hendrik Weisser <[email protected]>

Merge branch 'develop' into file_name_fix

3f680d5e1693de00b05dd8d4276a9edde7942692 authored over 4 years ago by Timo Sachsenberg <[email protected]>

[FIX] fix segfault in MapAlignerIdentification ('force'/missing data fallback)

e7fd23c324710822c6f242ef72f146534af73fee authored over 4 years ago by Hendrik Weisser <[email protected]>

[fix] changed type of sel_filter

d2ed1ea6396bace8d47f9946e935ddd8c08a1f03 authored over 4 years ago by Samuel Wein <[email protected]>

[FIX,TEST] fixed single table design.

318fe680e78d3ac16d820bc4dda260810c20ba72 authored over 4 years ago by timosachsenberg <[email protected]>