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

[FIX] fix data access for cached ion mobility spectra

54541966502058024567333165c5d6b145337428 authored almost 6 years ago by Hannes Roest <[email protected]>

[FEATURE] ion mobility array in OpenSwath data

8660ea2e4491f3e8b0b6991630e763879dc941be authored almost 6 years ago by Hannes Roest <[email protected]>

Merge remote-tracking branch 'origin/fix/SiriusAdapter_20181204' into refactor/AssayGeneratorMetabo

35e68f227d29e83906b944d5acf40e1650fe80ae authored almost 6 years ago by oliveralka <[email protected]>

[FIX] test, charge in precursor isotope extraction

36c4d26ad8686b4994cc13b9c893b0aeb4887420 authored almost 6 years ago by oliveralka <[email protected]>

[FEATURE] add unit for drift time

9fce5ab3744ae78656747bddf9f768a540474304 authored almost 6 years ago by Hannes Roest <[email protected]>

[FEATURE] store unit during conversion

8e13b678b537c4aee0e4ce0eeec40886d20c04e6 authored almost 6 years ago by Hannes Roest <[email protected]>

[TEST] test the new features

f6e8c29c3c0f1fef5e641f6e267afbd677ebf588 authored almost 6 years ago by Hannes Roest <[email protected]>

[FEATURE] read ion mobility unit

1660c932fb2be6c845fe77fd8d5d815384ab4c88 authored almost 6 years ago by Hannes Roest <[email protected]>

[OBO] update obo file

3a09f2274667985a6541bbf23ebcd5ecec35cc94 authored almost 6 years ago by Hannes Roest <[email protected]>

[FEATURE] OpenPepXL: output of currently processed file

makes it easier to assign logs to specific input files for automated workflows

a6704f2e5490d504ece8e1069a7c6e7ab2e3cf24 authored almost 6 years ago by enetz <[email protected]>

Merge remote-tracking branch 'origin/fix/SiriusAdapter_20181204' into refactor/AssayGeneratorMetabo

4a1c5bb4f6f4737dd921e20b0d0924f4227138df authored almost 6 years ago by oliveralka <[email protected]>

[INTERNAL] use const reference in Residue::residueTypeToIonLetter

883524fa6dddefb4d10d742fa1dbea5a8545044d authored almost 6 years ago by enetz <[email protected]>

[FIX] rm cout

e88e7eaff777f7fa522b89a525afaddb5dfcf259 authored almost 6 years ago by oliveralka <[email protected]>

Merge remote-tracking branch 'origin/fix/SiriusAdapter_20181204' into refactor/AssayGeneratorMetabo

24fe5adf58735bad59c72a4be23ba8ea774ca625 authored almost 6 years ago by oliveralka <[email protected]>

[ADD] adducts, exclude_ms2_precursor, use_exact_mass,

filter_known_unkowns

cfc0e0272acbc4c06416516bdbf23652127f14e3 authored almost 6 years ago by oliveralka <[email protected]>

Merge remote-tracking branch 'enetz/feature/OPXL_speedup_by_simplification' into feature/RNPxl_logReg

31a0b5fa1d1a6336c9fe3f8aaf7532c7ed1c7822 authored almost 6 years ago by timosachsenberg <[email protected]>

[FIX] move early out before partial loss generation to speed up search

c1a7b4ec352c6add12a33aee850636582089c8a4 authored almost 6 years ago by timosachsenberg <[email protected]>

Merge pull request #3892 from lars20070/fix/labels

ini params correctly passed to FeatureFinderMultiplex algorithm

e1a181fb7216e9a4f786790c90cd258776a9ffe5 authored almost 6 years ago by Eugen Netz <[email protected]>

[FIX] shorten if statement

e62dbf4cc93d3751497cf6a75481c3d5caf7c534 authored almost 6 years ago by oliveralka <[email protected]>

[FIX]

cbfd0a4330e13f3997ec1205ebf0cfba9179b124 authored almost 6 years ago by oliveralka <[email protected]>

[PYOPENMS] added python bindings for class SimpleTSGXLMS

d0ee5703d66a90578438b3d7634d436c76ec02c7 authored almost 6 years ago by enetz <[email protected]>

[PYOPENMS] added python binding for new function

in OPXLSpectrumProcessingAlgorithms

37f5b9ff9a3a5c457d3d87073f7fe4bc63d85f25 authored almost 6 years ago by enetz <[email protected]>

[INTERNAL] removed residueTypeToIonLetter from SimpleTSGXLMS

aae661feefce98b82e58a98d0d222bf1a464ff06 authored almost 6 years ago by enetz <[email protected]>

[PYOPENMS] added Residue::residueTypeToIonLetter python binding

05e47541ee6675d143853d87cc35b7ac9e5829c6 authored almost 6 years ago by enetz <[email protected]>

[INTERNAL] removed low dash from a public function

f785dc688f44904842318b1f8d429f98d4f96250 authored almost 6 years ago by enetz <[email protected]>

[TEST] SimpleTSGXLMS_test: added commented out benchmark for sorting

daccd0574b01bf6f1e50d6eab604c44c68bbd38c authored almost 6 years ago by enetz <[email protected]>

[NOP] removed whitespace

cd5964fb1a7c542f2798c857d088b036bc3437e0 authored almost 6 years ago by enetz <[email protected]>

[FIX] OpenPepXL: synchronized terminal output

All progress reported to the terminal is now written out within on critical section.
Avoids a co...

d03c5ef748aedb3761be4ec2cafb318b86048a80 authored almost 6 years ago by enetz <[email protected]>

[FEATURE] more efficient neutral losses in TheoreticalSpectrumGeneratorXLMS

5d7a4839de209d713a022348af311613fb90f588 authored almost 6 years ago by enetz <[email protected]>

[INTERNAL] removed residueTypeToIonLetter from TSG

TheoreticalSpectrumGenerator now uses residueTypeToIonLetter in the Residue class

63232f7eb48144cff1bdac821c1b8c14c0002b77 authored almost 6 years ago by enetz <[email protected]>

[INTERNAL] added residueTypeToIonLetter function to Residue class

3f19b9e1bd0c4fbc923cbafe50058318f40eaf2d authored almost 6 years ago by enetz <[email protected]>

[INTERNAL] update member label_mass_shift_ from ini params

7ec4a3cc1370d700ad894be0453907bdeb4cd86f authored almost 6 years ago by lars20070 <[email protected]>

Merge pull request #3888 from lars20070/feature/ImprovedPeptideIntensities

improve peptide intensities in FeatureFinderMultiplex

3079bca9f6591f6b036e6e0b3612ddddcee40190 authored almost 6 years ago by Timo Sachsenberg <[email protected]>

[FIX] revert style to open form

f7e0e87d32bd0b5cf09f5888c0f9581c59f4ae6b authored almost 6 years ago by oliveralka <[email protected]>

Merge branch 'develop' into poshul/hendrikweisser-rna-ms2-id

cf989faf0acb11de54b8880f2eba3ef8f2dde280 authored almost 6 years ago by Samuel W <[email protected]>

Merge branch 'poshul/hendrikweisser-rna-ms2-id' of ssh://github.com/poshul/OpenMS into poshul/hendrikweisser-rna-ms2-id

dc38fe4b259415fdcace7b270bb6bb2d61915789 authored almost 6 years ago by poshul <[email protected]>

[fix] fixed pxd for NASequence (thanks Hroest) and fixed typo in Ribonucleotide.pxd

21ced642b9cf57a0c9365d8e1d562849cc4a3302 authored almost 6 years ago by poshul <[email protected]>

Merge branch 'develop' into feature/MRMFeatureSelector

f331f20f3926fd1cc4d8e848ec9524afa0816527 authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

style: use const, avoid pointers, fix indentation, pt.2

d12445db568823cdadaa584451b5b3430b309150 authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

[TEST] fix tests

36edf4e06735484f9948ef521ddf7d5a0026ffbe authored almost 6 years ago by lars20070 <[email protected]>

[API] improve peptide intensities (trapezoid areas under chromatograms + linear regressions)

86c4a02e2559d63baf13325029b69b148c3ef938 authored almost 6 years ago by lars20070 <[email protected]>

Merge remote-tracking branch 'origin/fix/SiriusAdapter_20181204' into refactor/AssayGeneratorMetabo

175ec454ba7f5ca2188987450e14b9c0f7c1ce17 authored almost 6 years ago by oliveralka <[email protected]>

Merge remote-tracking branch 'origin/develop' into refactor/AssayGeneratorMetabo

8b9a9dd8b704a2f293f6fcfd0c0301cf4b8588be authored almost 6 years ago by oliveralka <[email protected]>

[ADD] SiriusAdapter integration

d46b0590778ff5d5165b4ef8e2ca638708479261 authored almost 6 years ago by oliveralka <[email protected]>

Merge remote-tracking branch 'JeeH-K/feature/TDdeconv' into feature/TDdeconv

# Conflicts:
# src/utils/TopDownOnlineDeconv.cpp

8f62bbbaf713d3545561b64d631f9a7878088a1a authored almost 6 years ago by kyowonjeong <[email protected]>

mass trace test parameter testing

d4d1a7239870d7c9c4565d4cbab0c507b6563f02 authored almost 6 years ago by kyowonjeong <[email protected]>

Add sorting

43300366d8fd8a9339bdb60819be0600cf20804b authored almost 6 years ago by JeeK <[email protected]>

[TEST] updated OPXL test to reduced output

da76bd99b3b699831ad7e80d4ce95c8a79ced5c0 authored almost 6 years ago by enetz <[email protected]>

[FEATURE] OpenPepXL: drop really bad matches earlier

improves runtime and output by dropping matches, that one would not trust anyway, earlier

9c107f1743cec40b1a5e99874fb8cada08a11570 authored almost 6 years ago by enetz <[email protected]>

style: avoid using pointers, enforce const where possible

3a4e7c308490e6d2ab3fa53beb9806c3f0d1bffe authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

[DOC] improved documentation for SimpleTSGXLMS

a7d2da9aad74c31f9b6c1d3188404df0888ee781 authored almost 6 years ago by enetz <[email protected]>

mass trace test parameter testing

607c5889aa2789e4e7a7aa4c518c0939ffc26ad8 authored almost 6 years ago by kyowonjeong <[email protected]>

[TEST] updated OPXLAlgorithm test

1105cf51e400b0d776399ab87392d4d93b78bf7a authored almost 6 years ago by enetz <[email protected]>

Add TopDownOnlineDeconvolution class

ad250c93125855714b533546990a8044f25749b5 authored almost 6 years ago by JeeK <[email protected]>

Merge pull request #3884 from hroest/feature/osw_debug

Feature/osw debug

9088c38f71bc98207bba4a6e1fb44477dc798b66 authored almost 6 years ago by Timo Sachsenberg <[email protected]>

[FEATURE] OpenPepXL using SimpleTSGXLMS

9400ac1e378d8a58d4e7cac4f405610b04573a70 authored almost 6 years ago by enetz <[email protected]>

[TEST, COMMENT] removed unnecessary comment

0ff85a1c0cf6beba6ff702a93a05557b2584d088 authored almost 6 years ago by enetz <[email protected]>

[INTERNAL] removed unused code

4b38007239828fd7f89e373df5225e210e7ea170 authored almost 6 years ago by enetz <[email protected]>

[TEST] updated test file by removing nonexistent parameters

e62145e73d2d111daaf7fbb499f54975ea370b37 authored almost 6 years ago by enetz <[email protected]>

[FIX, PARAM] OPXLLF: removed the unused prescoring and other unused code

9e155b470f031972742345fa531ac0b5c51e69b0 authored almost 6 years ago by enetz <[email protected]>

[FIX] removed unused variables

24c402300b77744486d23aec4369359b5a3d6c1c authored almost 6 years ago by enetz <[email protected]>

[FEATURE] Residue: faster getMonoWeight() with precalculated weights

952a197ec9e306f33aea8ab3d8dd3446032cd1b3 authored almost 6 years ago by enetz <[email protected]>

[FIX] sytle

477a9581f5972771e6ea1d4dbee347c1d2d3e1ad authored almost 6 years ago by oliveralka <[email protected]>

[FIX] else if

da28b790c25eb385f8a5c434e2c0fe548d5babac authored almost 6 years ago by oliveralka <[email protected]>

[FIX] style

1adb813158f610afc7939e9ba78e63b295bfbc2a authored almost 6 years ago by oliveralka <[email protected]>

[FIX] add suggestions

fccea5f2d8613c666041ef31377481ce1787b1ae authored almost 6 years ago by oliveralka <[email protected]>

[FIX] minor code improvements with auto

4810f41a358cb485492c71b91e327d11caf72382 authored almost 6 years ago by Hannes Roest <[email protected]>

[DOC] add docu

b6ff5dd60eb5be356712cd07a98e9d25f4e52135 authored almost 6 years ago by Hannes Roest <[email protected]>

[FIX] OPXLLF: using correct params for SimpleTSGXLMS

0534d8ac2a5f7a1d8f5f558e756e149c68bb9853 authored almost 6 years ago by enetz <[email protected]>

[FEATURE] SimpleTSGXLMS: faster and simpler neutral loss generation

89e9c7d110f3b15247e64dd14b52e09e21dd6893 authored almost 6 years ago by enetz <[email protected]>

[TEST] remove hotfix

bbcb763ecc70af68ebfef0800910c89b3c356764 authored almost 6 years ago by Hannes Roest <[email protected]>

[FIX] fix for input files without UniMod

- fixes #3764
- allows user to provide input files without UniMod modifications

08d7006ce7014e392aca79dfa0ca302acde61e3f authored almost 6 years ago by Hannes Roest <[email protected]>

[FIX] precondition fix

a43271cbe7f726afa23216a43b242c69a5b8de67 authored almost 6 years ago by Hannes Roest <[email protected]>

[FEATURE] OpenPepXLLF using SimplePeak spectra as theoretical spectra

cdb5420abc040286ca3b94de0363e9042447f6d3 authored almost 6 years ago by enetz <[email protected]>

[FEATURE] added simpler alignment function using SimplePeaks

ce304bcfaecb230e1c9009ceb24b30f4bc4fbfe1 authored almost 6 years ago by enetz <[email protected]>

[FIX] added matchOddsScore for SimplePeak spectra

3e668145cdc5b688607f3f306af23203c531d074 authored almost 6 years ago by enetz <[email protected]>

[FEATURE] SimpleTSGXLMS using SimplePeak for simplification and speedup

31ea8edaa1c3a453e6064614eb14548df3434aef authored almost 6 years ago by enetz <[email protected]>

Merge pull request #3882 from OpenMS/hroest-patch-1

Fixes #3764

e5c775cb55d2b95a8f037accaf9c82c3b39e92f0 authored almost 6 years ago by Timo Sachsenberg <[email protected]>

[FIX] const, negative mode feature_only

bb77b66bb990dc062c8968d5eb14b66dfd4f2b6b authored almost 6 years ago by oliveralka <[email protected]>

[FEATURE] OpenPepXL: major speedup by simplifying loss mass generation

0652dcdfb67cf1b8d3016158d25347265cfd6537 authored almost 6 years ago by enetz <[email protected]>

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

7b1df0cd62c488577323d143448da2cdaf88fbb4 authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

Fixes #3764

Hot fix for debug mode.

24cd3733664eb78cf003bbf7700176568ec73715 authored almost 6 years ago by Hannes Roest <[email protected]>

[FIX] corrected struct definition

fcb30f7dc7189bbf8ba332ed37c5207459dd0cc3 authored almost 6 years ago by enetz <[email protected]>

[FEATURE] SimplePeak struct for SimpleTSGXLMS

c461bcbb539204827e1d7841b9d2ac04c30d06d9 authored almost 6 years ago by enetz <[email protected]>

Merge pull request #3879 from biosustain/fix/LPWrapper_mem_leak

fix: LPWrapper destructor frees ctor's allocated memory

30b21c52c71472563257a551ae31136826ae2dab authored almost 6 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #3880 from OpenMS/revert-3808-jpfeuffer-patch-1

Revert "[FIX] Error in OpenSwathWorkflow_21 in debug mode"

85d7d07932b47fc2eb5181fdc71c457d5767c244 authored almost 6 years ago by Hannes Roest <[email protected]>

Revert "[FIX] Error in OpenSwathWorkflow_21 in debug mode"

7b91a9cf8b4822659dee4aebab5e739c917ab20e authored almost 6 years ago by Hannes Roest <[email protected]>

[TEST] updated OPXLLF tests after alignment fix and improved filtering

0f2a0319e8953b8b2cfc4ca20a8f1dce5e8fac15 authored almost 6 years ago by enetz <[email protected]>

[FEATURE] OpenPepXL: using SimpleTSGXLMS for speedup

reduced total tool runtime by a factor of about 2.5

caef625315fe507dd1fe9a46d6ee4fdd3e99f1bb authored almost 6 years ago by enetz <[email protected]>

[COMMENT, DOC] fixed spelling error

31316a000fa1c81205d78ae4376e063e95b68448 authored almost 6 years ago by enetz <[email protected]>

fix: LPWrapper destructor frees ctor's allocated memory

3efcefd1bf16dcf70ac69b64fed2d9d84a07380b authored almost 6 years ago by Pasquale Domenico Colaianni <[email protected]>

[TEST, FIX] fixed SimpleTSGXLMS_test

9a55eb53c63bfbaa1bffbff3009b73cacbce429d authored almost 6 years ago by enetz <[email protected]>

[FIX] fixed test executable name of SimpleTSGXLMS

5da05e7e550da245157a6e5eee8f6f047e98f80e authored almost 6 years ago by enetz <[email protected]>

[FEATURE] TSGXLMS: separate parameters for string annotations and charges

96cc28fef98acb1a12fa9b1520d929599811ae08 authored almost 6 years ago by enetz <[email protected]>

[FEATURE] prototype of a simpler, faster TSG for OpenPepXL

94350d546b9bef0254ac800b7e787292a966b9e3 authored almost 6 years ago by enetz <[email protected]>

Merge pull request #3851 from OpenMS/fix/mascot_query

[FIX] replace hostname in mascot query

57aacc09a393b2f309300abf76665a4552c809ee authored almost 6 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #3808 from OpenMS/jpfeuffer-patch-1

[FIX] Error in OpenSwathWorkflow_21 in debug mode

79e3d85b77f1f733e65c2c611cd8d51aa29aafae authored almost 6 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #3877 from oliveralka/feature/SiriusAdapter_output

[REFACTOR] SiriusAdapter

ca59a2d5ee6c221b1f7121aaf28b89c313543339 authored almost 6 years ago by Timo Sachsenberg <[email protected]>

Update AUTHORS

94855e210000c36be52b59dfd11c36bad8c90198 authored almost 6 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #3875 from enetz/fix/xfdr_labeled

OpenPepXL stability and applicability improvements

ed99186ea18eb6b013824cf394db77277bd2fc07 authored almost 6 years ago by Timo Sachsenberg <[email protected]>