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

[BUILD,DOC] doc improvements to Python checker

370c7d2cb2510a574b628060a21d6de66ed3e449 authored about 10 years ago by Hannes Roest <[email protected]>

[BUILD,FIX] adopt Python extension with new Path

- use new path starting with ./src in Python extension checker

ba23d34b67d78aa4a544be2f4dc0abcaef1b8cdb authored about 10 years ago by Hannes Roest <[email protected]>

[FIX] fix pxd map of Python extension checker

bbefd2c1036e0a414d0fe7a950e886ce23f35057 authored about 10 years ago by Hannes Roest <[email protected]>

[BUILD,NOP] extract method

603a2ff62f43c1853fbfe4ed159b193e79688fa1 authored about 10 years ago by Hannes Roest <[email protected]>

[API] legacy code removed

dde4bdcd253442497c2a61c19d535bef5b629bff authored about 10 years ago by lars20070 <[email protected]>

Merge branch 'feature/MZID' of https://github.com/mwalzer/OpenMS into

feature/MZID
Resolved Conflicts:
src/openms/source/FORMAT/HANDLERS/MzIdentMLHandler.cpp

4c0fe2d260b74d9affe9f231b238239e823c2921 authored about 10 years ago by mwalzer <[email protected]>

Merge pull request #943 from hroest/fix/pyopenms_fix

[FIX,PYOPENMS] fix pyOpenMS after #889

079486f8489030069b7c2abc820087c64c4d9be5 authored about 10 years ago by Hannes Roest <[email protected]>

[FIX,PYOPENMS] fix pyOpenMS after #889

1d8d64d96803bfb6ad7f63918f1e558b1fa2a06c authored about 10 years ago by Hannes Roest <[email protected]>

[FIX] fixed SpectrumID write for mzid with MetaValue spectrum_reference

-
this will be empty if read from idxml (not captured there at all, yuk!)
then set to MZ:...@RT:....

2769f7f87093369781cfe19a660d33ed5cffbfd0 authored about 10 years ago by mwalzer <[email protected]>

[FIX] fixed SpectraData write for mzid with MetaValue spectra_data -

this will be empty if read from idxml (not captured there at all, yuk!)
then set to UNKNOWN in mzid

8ee13fa956582992c30ff219183cdd4cf1f9b2e1 authored about 10 years ago by mwalzer <[email protected]>

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

772e9494c5b55bd550d7852fc9cc53f1ba1076b2 authored about 10 years ago by lars20070 <[email protected]>

Merge pull request #940 from lars20070/fix/MultiplexClustering

coding convention violations in MultiplexClustering fixed

fdb579bd21f9c4c045ea95be327da4cc5b51708e authored about 10 years ago by Hannes Roest <[email protected]>

[API] variables renamed

760b3675df116a9c78901b7a4e4e334f3b6cdf32 authored about 10 years ago by lars20070 <[email protected]>

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

95f4125e215c188621337a548e2f5846548b4ab5 authored about 10 years ago by lars20070 <[email protected]>

[TEST] casting corrected

3376c040965a5dabedb7dac8c5c5ac5ae4de4117 authored about 10 years ago by lars20070 <[email protected]>

[API] coding conventions fixed

be520c7be033a588c35e9429b8788da9dc0a023d authored about 10 years ago by lars20070 <[email protected]>

[TEST] add test output

cff2e04871d8cb7b78c0a53369c7a690d2da2b99 authored about 10 years ago by Hannes Roest <[email protected]>

[FEATURE] add isotope fullscan MS1 scoring

- [DOC] docu, nop

533678fd5b10b954739ad9e5c9e30ec1c687bf53 authored about 10 years ago by Hannes Roest <[email protected]>

[NOP] typo

fcc6b757fd1957dfde6bb429b6ad8a747fc46ad9 authored about 10 years ago by Hannes Roest <[email protected]>

[FIX] replace max_ppm_diff with real parameter

4c57a5fa46f9261de4cd6389c31899f2e6b71909 authored about 10 years ago by Hannes Roest <[email protected]>

[FATURE] add precursor isotope score

fe60e3ba1afcabcfa22794076438474ab320b795 authored about 10 years ago by Hannes Roest <[email protected]>

[NOP,INTERNAL] change variable name, fix pointer by reference, docu

b378fe007ebfc81faa5cba1d44515bf3323d13b1 authored about 10 years ago by Hannes Roest <[email protected]>

Merge pull request #939 from hroest/fix/build_error

[FIX] fix MSVC compile error (log() ambiguous on integer types)

add2cd526333cd6f761976b9b094cc05058f3b14 authored about 10 years ago by Stephan Aiche <[email protected]>

[FIX] fix compile error

- resolve overloaded call to log function
- fix MSVS error

2a3085a3e09174dac80d78eae8cdc62e81853e07 authored about 10 years ago by Hannes Roest <[email protected]>

Merge pull request #889 from lars20070/feature/MultiplexClustering2

[FEATURE] FeatureFinderMultiplex algorithm based on multiplex clustering

6fc6c64e30db171f2df6f97effa0f591cbe8e9a4 authored about 10 years ago by Stephan Aiche <[email protected]>

[FIX] fixed mzid searchdatabase read/write

8d1850499ef7b9d83ed6b0c03e1ca7a49cba6a91 authored about 10 years ago by mwalzer <[email protected]>

[API] some includes removed

3be664b11032bab3732877c6a564038e6d639cf0 authored about 10 years ago by lars20070 <[email protected]>

[API] MinimumDistance implementation moved to cpp

787259b7b6a39eed3c16e3b7a13ab06f24f0ba67 authored about 10 years ago by lars20070 <[email protected]>

[API] featureXML output added

bd745a049d6dc80d08f968124235a0d0475a9044 authored about 10 years ago by lars20070 <[email protected]>

[FIX] fix bug

e350482199c349e11a5d0bf0467d8a43721aa33d authored about 10 years ago by Hannes Roest <[email protected]>

[FIX] disable cppcheck for DIAScoring.cpp

- running cppcheck on DIAScoring.cpp triggers a bug in cppcheck (which
is unrelated to the cod...

abff2bd8ef8a5d507649fb573e93e6804256540f authored about 10 years ago by Hannes Roest <[email protected]>

[NOP] cpplint fix

f9f9e2779df5dfba9a143dff3657eb6edd39e081 authored about 10 years ago by Hannes Roest <[email protected]>

[FIX] check return value of window integration

59baa55eb1e61b9cb6dfa015ec6700bee81c8b82 authored about 10 years ago by Hannes Roest <[email protected]>

[INTERNAL] Refactor: Method Extraction

54d5c02a0df8faa79a005a3251fc66dc65e55e4f authored about 10 years ago by Hannes Roest <[email protected]>

[NOP] add to test

047df3516b551e5245446ae378eeb87019d5ba25 authored about 10 years ago by Hannes Roest <[email protected]>

[TEST] adapt all test outfiles

964a315a27154ad8f10aaab094aff99265491792 authored about 10 years ago by Hannes Roest <[email protected]>

[INTERNAL] corrected intensities written consensuses

2ac96a71c3decc0858c84d0704362929e26721d7 authored about 10 years ago by lars20070 <[email protected]>

[API] FeatureMap added

de240c0c02055d16f4bf09671dd2adcb059acdfb authored about 10 years ago by lars20070 <[email protected]>

[INTERNALK] peptide intensities corrected

5d06df5e3546180d8ce6fefb1c7167b03a76e66e authored about 10 years ago by lars20070 <[email protected]>

[FIX,TEST] fix tests

de86fa8781f508247ce9b337b907866eb8d91c3d authored about 10 years ago by Hannes Roest <[email protected]>

[FEATURE] OpenSWATH: implement precursor scores in workflow

954f2c9465648163ccddd03ccc1a877fbea12455 authored about 10 years ago by Hannes Roest <[email protected]>

[FEATURE] OpenSWATH: Add the precursor scores to the output

f1943e8f767ca5e95cfe6027356bb4ab77806446 authored about 10 years ago by Hannes Roest <[email protected]>

[TEST] MS1 test for MRMTransitionGroupPicker

c2b4e85fd2a7f1cc129aa63e857b830e87fbe47b authored about 10 years ago by Hannes Roest <[email protected]>

[FEATURE] add capability to find features in the MS1 trace

- add capability to find features in the MS1 trace to the
MRMTransitionGroupPicker
- the class...

c4ee900d7e9ffc998bf8aeca830fabe032ad5fb5 authored about 10 years ago by Hannes Roest <[email protected]>

[FEATURE] SpectrumAccess: add light clone operator to interface

- add light clone operator to SpectrumAccess Interface

81806bb4cdd3f2fd0e0f08477e33ef6d6ad98374 authored about 10 years ago by Hannes Roest <[email protected]>

[FEATURE] SpectrumAccess: add light clone operator

- add lightClone() call to OpenMS Spectrum access which provides a safe
way to handle multiple...

50103209c956e7f52e58123a89197f1eaccc489a authored about 10 years ago by Hannes Roest <[email protected]>

[FEATURE] add option for precursor scores to MRMFeatureFinder

21d0053dc5a25da82cc8eaaac38932ae4a18e3ee authored about 10 years ago by Hannes Roest <[email protected]>

[FIX] DIAScoring: add return value if no signal was found

1079e3b426294a7461834c09df68b3f77f94c223 authored about 10 years ago by Hannes Roest <[email protected]>

[FIX] DIAScoring: fix case where no signal was found

0c4794cfebd185bce8b9fefc5743378555b2f2ab authored about 10 years ago by Hannes Roest <[email protected]>

[FEATURE] add precursor scoring to OpenSWATH

9c792c70d69534b7446e4dfda6bd959a1cbad1db authored about 10 years ago by Hannes Roest <[email protected]>

[INTERNAL] reorganize test

0c40e0fd8a023e1e8603b11bf7861341f36fbd3b authored about 10 years ago by Hannes Roest <[email protected]>

[INTERNAL] reorganize test

cef45b02bcd852d368283f665f416f922305e5e7 authored about 10 years ago by Hannes Roest <[email protected]>

[FEATURE] MS1 massdiff score

322c1b1a3bc28f5d3f21d13cb13a94a59ae8a31e authored about 10 years ago by Hannes Roest <[email protected]>

[FEATURE] get list of available precursor traces

4146a6ea09fb708145a6af8ba409d58d8c4dcc5a authored about 10 years ago by Hannes Roest <[email protected]>

[FEATURE] add MS1 chromatogram to mrm feature interface

eb9991e2e5939754d574fb28baf813f0dab158be authored about 10 years ago by Hannes Roest <[email protected]>

[FEATURE] add precursor chromatograms to MRMFeature

- allow storage of features found in the precursor chromatograms
- test new functions

6b71350c9790cc0b1ceb2e9afd323bef690d2a89 authored about 10 years ago by Hannes Roest <[email protected]>

[FEATURE] add precursor chromatograms to transition group

- allow storage of precursor chromatograms (monoisotopic, isotopic
patterns) to be stored in t...

bf511875ff23a3b91449110ef8d945bc912d4390 authored about 10 years ago by Hannes Roest <[email protected]>

[FIX] fixed correct number of peptideevidences

1cc39101203a91992e6932962c3d421a07456baf authored about 10 years ago by mwalzer <[email protected]>

Merge pull request #895 from timosachsenberg/feature/SimpleSearchEngine_clean

[FEATURE] simple search engine for benchmarking of internal data structures

ab12673430c5eda2b62b6bef2a09fb058ac2365a authored about 10 years ago by Timo Sachsenberg <[email protected]>

[FIX] added generic fragmentation table entry in mzid

3778cfa0261c980153178dca2bc51b5fe4d58557 authored about 10 years ago by mwalzer <[email protected]>

[API] linear regression through origin added

e42eb7b4cac4f6154ad777e898b50066516e45d0 authored about 10 years ago by lars20070 <[email protected]>

[FIX] added relative and absolute tolerance to fuzzy comparison

17143148cf58ac26b40b3ab9a1863f45d65d8679 authored about 10 years ago by Timo Sachsenberg <[email protected]>

[FIX] fixed the 'variable' consumption of xslt files for a QcML file. Now expects a valid standalone xslt (i.e. with a xml preamble in the first line, stylesheet starting in the second line).

bb9609f9d2e3a5c045753ba767cbdef204e6d34d authored about 10 years ago by mwalzer <[email protected]>

[FEATURE] faster mass calculations without intermediate formulas,

adapted tests

e572bedda6e92c00e0a3d6a46b42222fd9b5d67e authored about 10 years ago by Timo Sachsenberg <[email protected]>

[FIX] some AASequence cleanup that possible prevents some reallocation

overhead

a237289f545cdfabf6a52075d9023a9704c62d5f authored about 10 years ago by Timo Sachsenberg <[email protected]>

[FIX] changed operator< of AASequence to compare N-term before sequence

848907563356d845f7aa21667cc94a36d78c47b2 authored about 10 years ago by Timo Sachsenberg <[email protected]>

[NOP] restructured search engine

937d8e5f397b931b1ac38f81d59215729e878d97 authored about 10 years ago by Timo Sachsenberg <[email protected]>

[NOP] moved searchengine test to topp tests

3dc842afe736de440a8d8d6601671bcb70dae200 authored about 10 years ago by Timo Sachsenberg <[email protected]>

[FIX] restructuring, less memory consumption

98af9e0d7154426230eaf6862b078c7239a0f77d authored about 10 years ago by Timo Sachsenberg <[email protected]>

[TEST] extended AASequence test

[TESTS] adapted tests to AASequence ordering and expanded AASequence
test

fdbab3158f4ab6e0ceaf02539d640d2888380063 authored about 10 years ago by Timo Sachsenberg <[email protected]>

[FIX] correct handling of operator==

03d0316f2e4ff4acd333487c767aef7207f96e9a authored about 10 years ago by Timo Sachsenberg <[email protected]>

[FEATURE] multi-threaded search

e75c8ade5da093b83e545c235759dc77dd7a366f authored about 10 years ago by Timo Sachsenberg <[email protected]>

[FIX] fixed bug in deisotoping

58c78776ba757b12dc3dceee6f48b65c1593dfc1 authored about 10 years ago by Timo Sachsenberg <[email protected]>

[FIX] minor const fixes

f92320c002bc37b9657b1f06bc1840b336eef92b authored about 10 years ago by Timo Sachsenberg <[email protected]>

[FEATURE] new small testfile

cda1cb745c5d3cc82743392df4858cfec61ed992 authored about 10 years ago by Timo Sachsenberg <[email protected]>

[FEATURE] speedup and restructurin speedup and restructuring

d3abb2b620ee30b4bff7b271f02ba87ab8ee97a7 authored about 10 years ago by Timo Sachsenberg <[email protected]>

[FIX] resolved merge issues

aa17eb569de4405abc816632acfc2fe62ffa1813 authored about 10 years ago by Timo Sachsenberg <[email protected]>

[FIX] fixed usage of RT and MZ

141fe49ec82d0d34a08c41d54a765bced8a15682 authored about 10 years ago by Timo Sachsenberg <[email protected]>

[FEATURE] multi threaded

17c30a6f06ed52180fbebe5565a802d9428dd546 authored about 10 years ago by Timo Sachsenberg <[email protected]>

[FEATURE] minor edits

410a1dea08036b077ee96cb95738ebc035e1fef2 authored about 10 years ago by Timo Sachsenberg <[email protected]>

[FEATURE] initial commit of simple search engine

44a5c0a37f54ae8fc1eb0a85cbe96e5eaa3de139 authored about 10 years ago by Timo Sachsenberg <[email protected]>

[FIX] some minor updates

09bc656052107b124cac71493e9b053d09045d45 authored about 10 years ago by Timo Sachsenberg <[email protected]>

[NOP] SimpleSearchEngine

a9eb2a010b79532fa1dec4ca6867e7b278862b7b authored about 10 years ago by Timo Sachsenberg <[email protected]>

[TEST] test adjusted for API change

de99590a85dd66d1da0a3c450f3b586b71deaf56 authored about 10 years ago by lars20070 <[email protected]>

[TEST] test adjusted for API change

6225d836bdf320b66c42bd707e6f5552a26623f6 authored about 10 years ago by lars20070 <[email protected]>

Merge remote-tracking branch 'upstream/develop' into feature/MultiplexClustering2

71f7a99bc2e4f4ec06180338f27e4758070013ab authored about 10 years ago by lars20070 <[email protected]>

[INTERNAL] MultiplexFiltering fixes

04d3cad319d812c3b58b7261f3ebd0ada373d9a6 authored about 10 years ago by lars20070 <[email protected]>

Merge pull request #930 from lars20070/fix/MultiplexFiltering

[FIX] added check for missing peaks to MultiplexFiltering

7c408ddb23d2f61400db919deb0f37ccf7fdc62f authored about 10 years ago by Stephan Aiche <[email protected]>

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

3dfafd46edbf5d0dcea1ac8612b63a0e32ab50a8 authored about 10 years ago by lars20070 <[email protected]>

Merge pull request #931 from lars20070/fix/CubicSpline

[FIX] fixes evaluation of CubicSplines2d at last node

befbcf199b10f0c645785221947c8beb355db27d authored about 10 years ago by Stephan Aiche <[email protected]>

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

cbe8f7d21eaf14680b8ebd211308c846424f5fe2 authored about 10 years ago by lars20070 <[email protected]>

[INTERNAL] debug output fixed

a66b31951a85f08b550834e5aa296f37a2137f83 authored about 10 years ago by lars20070 <[email protected]>

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

9bdfda1d77a8f40cb4ef1077b27d557306b59f5a authored about 10 years ago by lars20070 <[email protected]>

[TEST] test for boundary conditions added

0ba0381f4107212255e47a22f7f1e25aa1180947 authored about 10 years ago by lars20070 <[email protected]>

[FIX] mzid AdditionalSearchParams are written, redundant pepevidence

fixed, broke spectrumidentificationresult - see FIXMEs

ad539a91f7b4f487e3578300e09606f994bf2bc5 authored about 10 years ago by mwalzer <[email protected]>

Merge pull request #884 from liangoaix/pepXMl

[FIX] Convert XTandem search results into .pepXML by IDFileConverter

ed64f8c78c60901f959ccbbb906ba9ebc53226b6 authored about 10 years ago by Stephan Aiche <[email protected]>

[NOP] minor change

b737bdf86a76076fd4bb06609a4de4d32a42518d authored about 10 years ago by lars20070 <[email protected]>

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

5cca91e25bf8fe690757e14c97e3d6ea2062b78e authored about 10 years ago by lars20070 <[email protected]>

[TEST] smaller x interval for only 10 nodes

09bd58da7067d1de73e59b3c119c469eff47445f authored about 10 years ago by lars20070 <[email protected]>

[TEST] relative tolerance added

fa2074cf4a345c2311ccd3cf57a609f37db96ad5 authored about 10 years ago by lars20070 <[email protected]>