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

[INTERNAL] averagine filter extended

ed8fc18d38988ecc9a54673d50bbe7768bd4a9c4 authored over 10 years ago by lars20070 <[email protected]>

[INTERNAL] removed camels

9d101d9d0e5167e6527314df44b8b0196057aca4 authored over 10 years ago by lars20070 <[email protected]>

[NOP] code formatting

9664ab42f47b32d16122bae78e78ac95c96421e0 authored over 10 years ago by Hendrik Weisser <[email protected]>

[PARAM,DOC] changed some parameter defaults and improved parameter documentation for FeatureFinderIdentification

e372530bbf1a350ee1c85f1905e4e5440ce70c3b authored over 10 years ago by Hendrik Weisser <[email protected]>

[INTERNAL] peptide similarity filter finished

a1786ed11a5c836c945048825603d48215fd1234 authored over 10 years ago by lars20070 <[email protected]>

[INTERNAL] minor changes

fa0adf7369e28b513adf616ab5567fedbfdc160a authored over 10 years ago by lars20070 <[email protected]>

[FIX] work-around for OpenSWATH: include all protein accessions (not just one) of quantified peptides in output

4277bc3afe371e039bad1f4910450b48ed59ab07 authored over 10 years ago by Hendrik Weisser <[email protected]>

[INTERNAL] peptide similarity filter extended

867c147f5d77771295715a5bb37b14aa101f611c authored over 10 years ago by lars20070 <[email protected]>

Merge remote-tracking branch 'upstream/develop' into feature/MultiplexFiltering2

a5334838fd9a874fdeefbbb4e4f40ba8f7848ca6 authored over 10 years ago by lars20070 <[email protected]>

[API] methods for peptide similarity filter and averagine similarity filter added

b382fdf15145244812d0f9e7f102c1acbc150e7d authored over 10 years ago by lars20070 <[email protected]>

Merge pull request #854 from PetraGutenbrunner/fix-consensusid

[FIX] ConsensusID doesn't sort peptide hits before processing (idXML)

5448e53f8a7381f8bb4bef63fdd83f446f282574 authored over 10 years ago by Hannes Roest <[email protected]>

some benchmarking

79f68263f0cc9fbb191cd628b5c7158308319193 authored over 10 years ago by Timo Sachsenberg <[email protected]>

[FIX] ~40x speedup for constructions of unmodified AASequence

d59892d86907420e7aeff146ab8bfbcf64ccd890 authored over 10 years ago by Timo Sachsenberg <[email protected]>

[FEATURE] use protein group probabilities as scores in ProteinQuantifier output when available

2f0352a63090c22967f27f86adf428b5677fded3 authored over 10 years ago by Hendrik Weisser <[email protected]>

[FIX] corrected listing of relevant parameters in ProteinQuantifier output

e8b4f4410506c5b9ca6f8042bf7b608d1579c3fe authored over 10 years ago by Hendrik Weisser <[email protected]>

[API] peptide similarity filter added

a969a3d2085e3e955d0e88953d5ef24577f9b91d authored over 10 years ago by lars20070 <[email protected]>

[PARAM,DOC] renamed 'protxml' parameter of ProteinQuantifier to 'protein_groups' to signify more general usage

d8d675e0c3f4ed70efa7a3dd40625c16a8ae47d1 authored over 10 years ago by Hendrik Weisser <[email protected]>

Merge pull request #857 from hroest/fix/pyOpenMS_fix

Fix/py open ms fix

a4477ded8dd3e721a18a5701dba7b17c5a80909b authored over 10 years ago by Hannes Roest <[email protected]>

Merge pull request #856 from aiche/feature/knime-package-generation

[FEATURE] KNIME package generation updates

7464c9290df1565f37a6c9e6515cc80083e5b6bd authored over 10 years ago by Stephan Aiche <[email protected]>

[FIX,PYOPENMS] wrap one more function

33db8ae0de682f49196109b3e8f439600ea6ca88 authored over 10 years ago by Hannes Roest <[email protected]>

[FIX,PYOPENMS] fix pyOpenMS after #814

67dd66802e39833b1f6d0e14d8320b4aa37d9d7d authored over 10 years ago by Hannes Roest <[email protected]>

Merge pull request #844 from lars20070/feature/fix_SplineSpectrum

[FIX] evaluation at m/z in first package now possible

3b6ff6b0e6f059908ef946e535767f9a9951ff79 authored over 10 years ago by Hannes Roest <[email protected]>

[API] zeroth peak veto filter added

fed5d9fc9cd71744ea6ad2f133118292b607cd1f authored over 10 years ago by lars20070 <[email protected]>

[BUILD] added libSuperHirn to KNIME package and fixed permissions of qt-find script

8794bc8e97f61d28656fc2ec6d617c4adf19e545 authored over 10 years ago by Stephan Aiche <[email protected]>

[API] non-local intensity filter added

8022ab8559d47f7c19247e0c958a8a9d81cf077c authored over 10 years ago by lars20070 <[email protected]>

Merge branch 'develop' into FidoAdapter

Conflicts:
src/topp/PeptideIndexer.cpp

354b2b7e71cd5b657dd7573b32a503bab6a6fa6f authored over 10 years ago by Hendrik Weisser <[email protected]>

[NOP,BUILD] fixed lnx knime package preparation (see r12130)

3086c6a81858dd09b6df89a4bd88e95d5611108f authored over 10 years ago by Stephan Aiche <[email protected]>

[NOP] removed IDEvaluator from KNIME package as it requires an X server (see r12129)

dbce7da387b92e71282635ff8b87a317c965b21b authored over 10 years ago by Stephan Aiche <[email protected]>

[NOP] added FuzzyDiff to knime package to enable testing (see r12128)

2b0fa51ef26af06827369ca9a1dff25f348ff867 authored over 10 years ago by Stephan Aiche <[email protected]>

Merge pull request #855 from PetraGutenbrunner/fix-falsediscoveryrate

[FIX] FalseDiscoveryRate "target+decoy" hits should be considered as targets

5d6963b647d800ad93feb9a4ccb34dffcb0589b5 authored over 10 years ago by Hannes Roest <[email protected]>

[TEST] tests fixed

fadcca72d75692d3ed4dbee984db0d61648ce48e authored over 10 years ago by lars20070 <[email protected]>

[INTERNAL] minor changes

972aa976b8316484f3a9c280ce71fe6a59c0d701 authored over 10 years ago by lars20070 <[email protected]>

[INTERNAL] mono-isotopic peak intensity filter finished

6b078d458c95849d000b4209962071388c8148e7 authored over 10 years ago by lars20070 <[email protected]>

[FIX #853] tests

added specific target+decoy class_tests

../src/tests/class_tests/openms/source/FalseDiscovery...

93a34a7959275cb7f2fb7f1a16cfff098501af08 authored over 10 years ago by Petra Gutenbrunner <[email protected]>

[API] intensity cutoff parameter added

4f3a99503bdb265f6c155c8b3d20a32f09d32bb8 authored over 10 years ago by lars20070 <[email protected]>

[TEST] tests fixed

c9ccda42a4dd1f9160c5a4b6ff91843d0976f411 authored over 10 years ago by lars20070 <[email protected]>

[TEST] tests fixed

75518949f8f76204f643804fa6f521defdc2445e authored over 10 years ago by lars20070 <[email protected]>

[TEST] tests fixed

fcde0c65895f5ba5c0ceb028cf64e74dc9100e40 authored over 10 years ago by lars20070 <[email protected]>

[API] blunt intensity filter started

bdb11da1116215ff07f99c2fabbbfdb6db496dc3 authored over 10 years ago by lars20070 <[email protected]>

[INTERNAL] position and blacklist filter debug code added

073efaea3e9f4d086cdac8cfadb30df49b5e13d5 authored over 10 years ago by lars20070 <[email protected]>

[INTERNAL] position and blacklist filter finished

5f769dcdb23429e901ccd5f3aded0217b7bfe503 authored over 10 years ago by lars20070 <[email protected]>

[INTERNAL] peak registry and blacklist initialised

9f77eab7066c98a1d66cee7f5ed6810140b999b2 authored over 10 years ago by lars20070 <[email protected]>

[INTERNAL] iterators modified

0253bb33073a1c5d8cd15dfa52a400c05d0a9a79 authored over 10 years ago by lars20070 <[email protected]>

[INTERNAL] further code for initialisation

632fded744b2125025f6ad48f3b79c930484c0fc authored over 10 years ago by lars20070 <[email protected]>

[INTERNAL] peak registry and blacklist initialised

0e6fd65a451609bd618f244cb719ac6fdeb6cd7a authored over 10 years ago by lars20070 <[email protected]>

[API] Navigator and BlackList structs added

031d4f44483580a9dd218e7d2497ac36dde71a5a authored over 10 years ago by lars20070 <[email protected]>

[API] peaks per peptide minimum added

f1efaf4063197e184043ccb53cc3ab4a064f7ee0 authored over 10 years ago by lars20070 <[email protected]>

[INTERNAL] iteration over RT and m/z sorted

6d646e8fd50b92bcd06c2da083ecc156ec1e9523 authored over 10 years ago by lars20070 <[email protected]>

[DOC] some parameter documentation

8ba0cded289afb335db59488e48967ae2cc3a185 authored over 10 years ago by lars20070 <[email protected]>

[API,DOC] minor changes

816097ea2ce009fe167c802f5af0fdc726d16fa6 authored over 10 years ago by lars20070 <[email protected]>

Merge pull request #814 from grosenberger/SpectraST

[FEATURE] ConvertTSVToTraML: Support for SpectraST MRM Transition Lists

cde39b4755508eee112f295fe589a83672269532 authored over 10 years ago by Hannes Roest <[email protected]>

[API] peak boundaries added

eca95628a217075e3b99ce38ce75985896817917 authored over 10 years ago by lars20070 <[email protected]>

[API] MultiplexFiltering class added

276e426ff14295123150742ef211a1a641ae893c authored over 10 years ago by lars20070 <[email protected]>

[API] filter result classes added

197087c653001619b1e5a1742214c42136bfcaca authored over 10 years ago by lars20070 <[email protected]>

[API] PeakPattern class added

47715476cf6cec51d7dd61cd0cf08ff4584829c2 authored over 10 years ago by lars20070 <[email protected]>

[TEST] SplineSpectrum test fixed

30b4305ec482b18d325a5bfab4b8140028ae9f70 authored over 10 years ago by lars20070 <[email protected]>

Merge branch 'develop' into fix-consensusid

064d545aaf0a2e0bc938748890deb10e1721fa44 authored over 10 years ago by Petra Gutenbrunner <[email protected]>

[FIX #853] "target+decoy" as targets

If a hit is a target+decoy then it will be considered as target.

modified: ../src/openms/sour...

ff18c87a002da3a86c70bb87f9e9908beae54359 authored over 10 years ago by Petra Gutenbrunner <[email protected]>

Added .mrm to knime MIME types

0a21f19f60d8e6c97281ff4593d7fed3eb8e349f authored over 10 years ago by George Rosenberger <[email protected]>

Merge pull request #850 from timosachsenberg/feature/XTandemSledgehammerSupport

[FEATURE] modified tests to reflect X!Tandem SLEDGEHAMMER as default

5a220c85c426d585ae8a5b6d26d0d0e427beeb3f authored over 10 years ago by Stephan Aiche <[email protected]>

Merge pull request #851 from hendrikweisser/fix-mascot-identifier

Fix and tests for a bug in reading Mascot XML files

b98e315260dce880e87e4da874106996300c5616 authored over 10 years ago by Hannes Roest <[email protected]>

[TEST] optimised SplineSpectrum test

e9530eae28c9104185c9d27e982fecbe98b67eff authored over 10 years ago by lars20070 <[email protected]>

[TEST] optimised SplineSpectrum test

2e397ff5f5bfbc70d491dfcd49d09b0c2484aca2 authored over 10 years ago by lars20070 <[email protected]>

[INTERNAL] condition removed

889f8bbbd85ec40e340ad0759ec06ea425e19fdd authored over 10 years ago by lars20070 <[email protected]>

Merge pull request #852 from hroest/fix/WindowsFix

[FIX] fix windows compile error (redefinition; different linkage)

200d5dfaed7e0894472d7ff645eb5d371e2cce40 authored over 10 years ago by Stephan Aiche <[email protected]>

[FIX] fix windows compile error

- windows complains about "redefinition; different linkage" which should
be fixed if declarati...

32b5dd1177ae58815d53d37d1dd92de153af186b authored over 10 years ago by Hannes Roest <[email protected]>

[NOP] retrigger build

43e34b8968666f4baa21513e0ad0f3738e641441 authored over 10 years ago by timosachsenberg <[email protected]>

[TEST] added tests for Mascot XML reading bug fixed in commit dda851f05309eb130552678834cfa6420cd94f8e

5248330bfd8ddc8128db64ee6be5dc94573060f7 authored over 10 years ago by Hendrik Weisser <[email protected]>

[FIX] fixed bug that lead to omission of 'unassigned peptides' when converting Mascot results to idXML (introduced in commit 1e532159ad27d2651d2e9bfe89de80c5ecc5eee3)

dda851f05309eb130552678834cfa6420cd94f8e authored over 10 years ago by Hendrik Weisser <[email protected]>

[FEATURE] modified tests to reflect X!Tandem SLEDGEHAMMER as default

x!tandem version

0a320689d1318d4945b5f33e14e5e88d769e7020 authored over 10 years ago by Timo Sachsenberg <[email protected]>

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

81de74c6aad20709995ceebd90db8f13f2822614 authored over 10 years ago by lars20070 <[email protected]>

Merge pull request #847 from lars20070/feature/PeakPickerHiRes_boundaries

peak boundaries and new cubic splines for PeakPickerHiRes

f3fb0c23bb8ea21acc969af63da87bda2903c726 authored over 10 years ago by Hannes Roest <[email protected]>

[TEST] SplineSpectrum test further extended

8a77d1941e1da3a1702ef52b9ae1fc4c5abf9b24 authored over 10 years ago by lars20070 <[email protected]>

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

9f9018bcebce5cb7d7f27615ba17fe20f232675f authored over 10 years ago by lars20070 <[email protected]>

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

4ecba48b65124a814fa5e927d31668ef3e98de13 authored over 10 years ago by lars20070 <[email protected]>

[TEST] SplineSpectrum test extended

20333835955f23b3e7c8db9b0db97f0b7a651cad authored over 10 years ago by lars20070 <[email protected]>

Merge pull request #846 from hroest/fix/fixesFrom822

Fix/fixes from822

0f4b5d71618c1b3bf407bfb6903817a08c6a0b2b authored over 10 years ago by Hannes Roest <[email protected]>

[TEST] test for peak boundaries added

3eb8a6578e7af77b055ae91cd0086103018a8411 authored over 10 years ago by lars20070 <[email protected]>

[TEST] TOPP tests fixed

9914ad127fd0a0cba8dc57872c5f6252a3decea9 authored over 10 years ago by lars20070 <[email protected]>

[TEST] class tests fixed

56ba71535f12bae8be8d33e4f1d30263d726f224 authored over 10 years ago by lars20070 <[email protected]>

[API,INTERNAL] peak boundary structures added, Eigen splines replaced by CubicSplines2d

3f85fa91c63e6ed7afa85e797bb45e84a8c10a8d authored over 10 years ago by lars20070 <[email protected]>

[FIX] fix sorting for quantile computation

8d5ec3a439ce81d7737d3d94644b362dd3f966d3 authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] at least initialized all members, in the proper order

34d09aba9e553172c86467627531b5d92cae57c4 authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] remember whether RT was set or not

16eb4e7a2d03b7095e98bad22a57efa33062ef75 authored over 10 years ago by Hannes Roest <[email protected]>

[FEATURE] replace String classes with StringUtils

018cc2551dc595ffb4ddff743c074cc12afbd576 authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] sane input validation for CompressedInputSource

3da4ecf61e685ef92408084a137b6bf4426c91ab authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] remove dead code, as discussed in #822

57f359c687eab3fa3ec8fe032a97ab0d4cfe89f1 authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] fix bug, as discussed in #822

27a052efc2579e38adb6eb5b08ee74ab078dcfde authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] simplify code, as discussed in #822

fd49a8dfe786db9ed9af205f84f8a258e6ca5eee authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] as discussed in #822

4765434b9a806b05eb00608e9bf58d0b8ef0bb0c authored over 10 years ago by Hannes Roest <[email protected]>

Merge pull request #833 from hroest/feature/visibilityHidden

Feature/visibility hidden

f1bc656b15c5e1da9af7269f0e788fd26ce7cffb authored over 10 years ago by Hannes Roest <[email protected]>

Merge branch 'develop' into feature/visibilityHidden

Conflicts:
cmake/compiler_flags.cmake

f81dc359f1766321218f4b939ffe1b9c3e7e5531 authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] evaluation at m/z in first package now possible

99645175f8c1f4e276e8a2bd1db30cd7b0a2fee2 authored over 10 years ago by lars20070 <[email protected]>

Merge pull request #843 from aiche/fix/win-debug-mode-fixes

[FIX] fixes tests failing win debug mode

5a27b794a1f256b9d83055fa345818888ce3832e authored over 10 years ago by Hannes Roest <[email protected]>

Merge pull request #842 from hroest/fix/fixCachedMzML

[FIX] fix dereference of iterator

dfbeb2020304fa8003437897800b4ccbe5a00e9b authored over 10 years ago by Hannes Roest <[email protected]>

Merge pull request #5 from aiche/hroest-fix/fixCachedMzML

[FIX] fixed reading of empty spectra

0f046ddaf1edd035d16f56088959af3df9eef13c authored over 10 years ago by Hannes Roest <[email protected]>

Merge pull request #841 from OpenMS/feature/EnableWerror

[BUILD] disable -Werror by default

b889e6763a7c498f16538277bc71e2726b73a538 authored over 10 years ago by Stephan Aiche <[email protected]>

[FIX] fixed UniqueIdGenerator_test, derefenced end() iterator

2392638c808d935a2cfd27e27a01e3b8a064a1d0 authored over 10 years ago by Stephan Aiche <[email protected]>

[FIX] fixed access to non-existing elements during median computation

16a0de9aceb33516acf381be9ac132cf18615f1e authored over 10 years ago by Stephan Aiche <[email protected]>

[NOP] fixed indentation

c47674ccacad35900581027d333687eb282b20ee authored over 10 years ago by Stephan Aiche <[email protected]>