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

Merge pull request #1037 from hroest/fix/TraMLLoadStore

Fix/ TraML load/store

8c9446ad8701a5a232314df06378d34fb330b8f4 authored about 10 years ago by Hannes Roest <[email protected]>

[API] now passing const references

e981ad7e103cc65ece685d4cb9b5dda1e518f8d2 authored about 10 years ago by lars20070 <[email protected]>

[API] virtual destructor used

7ba422434470776a8b6b7c61280365e9071756ff authored about 10 years ago by lars20070 <[email protected]>

[API] free pointer in destructor

527f65a4e109c2cd1c47b1778d6db7bb8f8bdd68 authored about 10 years ago by lars20070 <[email protected]>

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

aa3d90fb27189ecbae99d3490e31927659b142e9 authored about 10 years ago by Hendrik Weisser <[email protected]>

[TEST] PeakWidthEstimator class test added

1733fada6007e222a57a92f292cb26c183bebff4 authored about 10 years ago by lars20070 <[email protected]>

[API] removes PeakWidthEstimator_ from MultiplexClustering

f5179364efffdb2c0d02899c3b5e722875e318ab authored about 10 years ago by lars20070 <[email protected]>

[FIX] improve set_peaks documentation

- write message what went wrong in assertion code
- fix typo
- reserve space for new data (for s...

97422385b9723967dfa0c6851e08abd76fe3f88d authored about 10 years ago by Hannes Roest <[email protected]>

[API,INTERNAL] new implementation of PeakWidthEstimator

174cffc4bd54b8f52227b7e4437ed56b95b2386e authored about 10 years ago by lars20070 <[email protected]>

[TEST,PYOPENMS] add test

38b4cd53558d236be35fc5b0c811c5e8dead19b2 authored about 10 years ago by Hannes Roest <[email protected]>

[NOP] rearrange pychecker ignore

a093031f90007505bb9aa6d59daa3103f742676d authored about 10 years ago by Hannes Roest <[email protected]>

pxd files

34e807cbbccbaa07c230ce3d8b416a4c6668219d authored about 10 years ago by Hannes Roest <[email protected]>

[FIX] add inequality operator

213573384dccf5f6aa3b291c77db3a626ecd5fae authored about 10 years ago by Hannes Roest <[email protected]>

[FIX,PYOPENMS] add operators to TargetedExperiment

4bf21eed4ace82384bf151ad74f422b187119b14 authored about 10 years ago by Hannes Roest <[email protected]>

[FIX] ensure valid TraML file is written by not outputting a double equal to numeric limits

35639f1ef04e02be44489142776048f1a3958291 authored about 10 years ago by Hannes Roest <[email protected]>

[FIX] added missing export macros and moved some more code from headers to cpp

d04a9d2150d3cd9ceac4a89063cd96da93430b36 authored about 10 years ago by Stephan Aiche <[email protected]>

[INTERNAL] moved TOPPBase code to cpp file

9c9674bf5f8b0ea348d60387ed8da1b736f3f464 authored about 10 years ago by Stephan Aiche <[email protected]>

[INTERNAL] moved IDMapper code to cpp file

a214dffc825dc09bcc936e08deeded6f24036526 authored about 10 years ago by Stephan Aiche <[email protected]>

[INTERNAL] moved FileHandler code to cpp file

1204130716095176fded0f6457156ef2632e1d86 authored about 10 years ago by Stephan Aiche <[email protected]>

[INTERNAL] moved ConversionHelper code to cpp file

9acc9b4a0ed74e69766cc4eb87e26af6af97f40b authored about 10 years ago by Stephan Aiche <[email protected]>

[INTERNAL] moved FeatureMap code to cpp file

1271f064ee6189921b1cd1e7b9ae791806572776 authored about 10 years ago by Stephan Aiche <[email protected]>

[FEATURE,API] removed template argument from FeatureMap

66d120a072c064d0fd781adcd147e7a7a556012d authored about 10 years ago by Stephan Aiche <[email protected]>

[INTERNAL] B-spline wavelength adjusted

0b0a7cdd6854e0ccb834a28b75cb77c86d4f1451 authored about 10 years ago by lars20070 <[email protected]>

[API,INTERNAL] replace linear fit by B-spline in peak width estimation

8848672d3a9d436ec504694f27260e8e2780046d authored about 10 years ago by lars20070 <[email protected]>

Merge pull request #1029 from aiche/feature/remove-public-vector-inheritance

[FIX-#184] remove public vector/map inheritance

4d2ae8e09301b950f9ca40947ae61259188fecb8 authored about 10 years ago by Hannes Roest <[email protected]>

[TEST] add test for TraML file

- TraMLFile should be able to store a (valid) minimal example of a TraML
file and read it again.

855b54d8f3530bbc0b83f803f4e1cfa774162d92 authored about 10 years ago by Hannes Roest <[email protected]>

[NOP] switch pyOpenMS version to 1.12

e817cb230e5eb60a818cd77ed2aa546cbdfc2714 authored about 10 years ago by Hannes Roest <[email protected]>

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

072bd9e2e1cb3bd07f1195126cbd6423445b3825 authored about 10 years ago by Hendrik Weisser <[email protected]>

[FIX,PARAM] use Java memory setting (parameter 'java_memory_size') also for MzIDToTsv tool

e83d9efa8621a181a2694697bb6ee8146cf1fb5d authored about 10 years ago by Hendrik Weisser <[email protected]>

Merge pull request #1026 from lars20070/fix/SplineSpectrum2

additional example in SplineSpectrum test

fc50dcd22df1ffa8bf338494dba896f746ab9771 authored about 10 years ago by Hannes Roest <[email protected]>

Merge pull request #1032 from lars20070/fix/PeakPickerHiRes

fixes peak boundaries in PeakPickerHiRes (resolves #1022)

4bac619bf01bb0f5cf0abecc36ae0b0a0d377adf authored about 10 years ago by Hannes Roest <[email protected]>

[TEST] PeakPickerHiRes class test fixed

8da69ead25b3c2c0705725d1f86fc7d6ea8eeab1 authored about 10 years ago by lars20070 <[email protected]>

[TEST] PeakPickerIterative test fixed

c0f7748c42f7940040490d89c1ad32c9c31e0d03 authored about 10 years ago by lars20070 <[email protected]>

[TEST] PeakPickerIterative test fixed

d79c04f0945e0a87d5c44dfdf1ec17fccd058030 authored about 10 years ago by lars20070 <[email protected]>

[API] additional parameter defining a large m/z gap

9dd4729e910c510bd98259e57d2f66a89ca542d1 authored about 10 years ago by lars20070 <[email protected]>

[API] additional parameter defining a large m/z gap

26054a30a7c5ddd710615c81d0045628d45740b5 authored about 10 years ago by lars20070 <[email protected]>

Merge pull request #1024 from lars20070/fix/FeatureFinderMultiplex4

[TOPP,FEATURE] sorting mass shifts in FeatureFinderMultiplex

1f2a6cc88c1343ec7666c943929cf7b52a66451b authored about 10 years ago by Stephan Aiche <[email protected]>

[TEST] LowMemPeakPickerHiRes TOPP test fixed

d48c1da54e056a8ade02ebb23bd12a6f302962b4 authored about 10 years ago by lars20070 <[email protected]>

[TEST] LowMemPeakPickerHiRes TOPP test fixed

51595181331563a64a5656e4fe85c557d6ddc5bf authored about 10 years ago by lars20070 <[email protected]>

[TEST] PeakPickerIterative test fixed

07145bb9fcbbb27942159c655ac309630fa5b098 authored about 10 years ago by lars20070 <[email protected]>

[TEST] PeakPickerHiRes TOPP test fixed

f5d181809bdb013313c49a0b9743c30cb36d53da authored about 10 years ago by lars20070 <[email protected]>

[TEST] PeakPickerMRM class test fixed

65018c24a2b250e7bddb45b854dddf8f8d934a60 authored about 10 years ago by lars20070 <[email protected]>

[TEST] PeakWidthEstimator class test fixed

afbcb0df0977b2acba9960d69c5a429c8e6804a7 authored about 10 years ago by lars20070 <[email protected]>

[TEST] PeakPickerHiRes class test fixed

32d1c95910f72737aab35145bb74602420d88f6b authored about 10 years ago by lars20070 <[email protected]>

[FIX] warning/error in BinnedSpectrum.cpp

0e4c7ca13ff4eb4ec8448fc60bde25bb7d019fb2 authored about 10 years ago by Stephan Aiche <[email protected]>

[PYOPENMS,API] switched from pair<> to simple struct in SimTypes to support python wrapping

* additional cleanup of the BinnedSpectrum pad

f5410d40e3975a83f0476af54ca90d1874417446 authored about 10 years ago by Stephan Aiche <[email protected]>

[BUILD] fixes RPATH warning on osx

876a3629cca21b73b31ce26dd628c2309fc3a24c authored about 10 years ago by Stephan Aiche <[email protected]>

[TEST] test fixes

114fe8f93831799a98afcabe95477ac88bcedf57 authored about 10 years ago by Stephan Aiche <[email protected]>

[COMMENT] typo

5a832a997d78313a3eff3c165a330aae42ed8947 authored about 10 years ago by lars20070 <[email protected]>

[NOP] additional uncrustify run

1d12cfa065dd937489e053657ac61fdf762accbc authored about 10 years ago by Stephan Aiche <[email protected]>

[FIX] fixes windows compile issues after removing public inheritance

* BinnedSpectrum now has a spectrum as member instead of deriving from MSSpectrum<>

b023e76059e5427e988028ba530ef86a2469f4ad authored about 10 years ago by Stephan Aiche <[email protected]>

[FIX] fixes gcc warning/error for unreachable code

2dff9457c2fd2f07dcd0345c152604382ca03187 authored about 10 years ago by Stephan Aiche <[email protected]>

[INTERNAL] default parameter changed

aa6ccfe4a3ecabf7318fb5bd69cd44de19033165 authored about 10 years ago by lars20070 <[email protected]>

[TEST] peak boundaries tested on orbitrap data

44d23e436930a013b80f7113425a959622ba1ee1 authored about 10 years ago by lars20070 <[email protected]>

[PYOPENMS] adapted api changes in pxds

9db145e2ee3c213649747262a22b6d7512bd35fd authored about 10 years ago by Stephan Aiche <[email protected]>

[NOP] automatic uncrustify run on changed files

bc692aa57d2dd3e5bebfe5e224b4ba84e26058d7 authored about 10 years ago by Stephan Aiche <[email protected]>

[INTERNAL] IDPosteriorErrorProbability code clean-up (primarily iterators)

17f9165c57b7643b9ab9a8f6fc8f2be61d5c21a8 authored about 10 years ago by Hendrik Weisser <[email protected]>

[TEST] class test extended

b9b0b1b743e7cff274b075b63fb73c62ddf4c3a5 authored about 10 years ago by lars20070 <[email protected]>

[TEST] class test now detects correct peak boundaries

19d3856dcda40ce7977ed3e18438814f663a3c09 authored about 10 years ago by lars20070 <[email protected]>

[API] new parameter for missing data points added

abb2c9a15fe364c0348b75e76ea25b0f7446e34e authored about 10 years ago by lars20070 <[email protected]>

[INTERNAL,API] removed public inheritance from Map and replaced it with private inheritance

f1d4050e7ea7175e33f336d578520fb39e8f348a authored about 10 years ago by Stephan Aiche <[email protected]>

[FIX] fixes static loading issue in ProgressLogger

1e15671f69e6f8ad9dd17a65a2cc6406bed3c091 authored about 10 years ago by Stephan Aiche <[email protected]>

[INTERNAL,API] removed public inheritance from TextFile and replaced it wit a member

* moved implementation for KroenikFile to cpp and removed template argument

ce95e03cc44a5a25c7ceee53786d46df0662acee authored about 10 years ago by Stephan Aiche <[email protected]>

[INTERNAL,API] removed public inheritance from std::vector for spectrum and chromatogram

e6bada724fed6b372c877e31033f6e56442f1c69 authored about 10 years ago by Stephan Aiche <[email protected]>

[INTERNAL,API] removed public inheritance from AcquisitionInfo

2219311e7b83eaa415ed978d64449c53b1c3bb41 authored about 10 years ago by Stephan Aiche <[email protected]>

[API,INTERNAL] moved SimTypes typedefs into a namespace, replaced Sample* with typedefs

27fd9390b400f31407cadaa5589a916444dafb50 authored about 10 years ago by Stephan Aiche <[email protected]>

[API] new parameter for missing data points added

143137319246fedbb6655e81d85029b56f288150 authored about 10 years ago by lars20070 <[email protected]>

[INTERNAL,TEST] number of missing data points now variable, spacing_difference now defines maximal allowed difference

b3c7cd4efbe5d43b925c4dbe58b2eafd3eee02a3 authored about 10 years ago by lars20070 <[email protected]>

[INTERNAL] single missing data point allowed

82188445024256fd563e4c11ec84e0487adeab8d authored about 10 years ago by lars20070 <[email protected]>

[FIX,TEST] fixed FidoAdapter tests

b45cb23fe7bfd60dafcb99c79198ccd8e30b6a58 authored about 10 years ago by Hendrik Weisser <[email protected]>

[INTERNAL] removed unnecessary distinction between Windows/UNIX

5a6c457b5eef6af8b036a742550bf9477be0cc8c authored about 10 years ago by Hendrik Weisser <[email protected]>

[TEST] simulated data added to PeakPickerHiRes_test

8eaca4a34c62485bf09e1febd270311bead0e90f authored about 10 years ago by lars20070 <[email protected]>

[DOC] updated documentation

4ecf028273b7cb8d2a676d397b96ef0881f4dab3 authored about 10 years ago by Hendrik Weisser <[email protected]>

[TEST,BUILD] added/revised tests for FidoAdapter

9bf2afd1c87d6f175ab13b6bc6c422ddce3c73d7 authored about 10 years ago by Hendrik Weisser <[email protected]>

[FEATURE] improved behavior for input files containing multiple ID runs

d44230ac6440652ddbc84d421a3a1f781cc6c40b authored about 10 years ago by Hendrik Weisser <[email protected]>

Merge pull request #1025 from hroest/fix/checker_fixes

[FIX] checker fixes

6146a072b337e899ccb98b39e986421ed26ff602 authored about 10 years ago by Stephan Aiche <[email protected]>

[TEST] added a test demonstrating the limits of the interpolation

a35df29c78a3dbe7841113e5d82783042e2aa7ce authored about 10 years ago by lars20070 <[email protected]>

[NOP] licence fixes

7b032d70c3cf70dc1619473ad5a21dc09a6ab753 authored about 10 years ago by Hannes Roest <[email protected]>

[FIX] coding convention fix

1d84bd27ca8f9c827e66297ff5b93bfb7b08190f authored about 10 years ago by Hannes Roest <[email protected]>

[INTERNAL] generateMaps() restructured

356670d47e90d668b5c53c6b775f46350ae64173 authored about 10 years ago by lars20070 <[email protected]>

[INTERNAL] sort mass shift list

00147abaf83cccc866ae1d35276038c7f0563fd7 authored about 10 years ago by lars20070 <[email protected]>

Merge pull request #1021 from hroest/feature/pyOpenMS_fixesAndWraps

Feature/py open ms fixes and wraps

d8a004b59593b9bedb5aacc9e30d1c09981d6cbe authored about 10 years ago by Hannes Roest <[email protected]>

[FIX] remove mutable access functions without implementations

f02106a6c589b81e74e04e44654affb49502327c authored about 10 years ago by Hannes Roest <[email protected]>

[FEATURE] wrap additional functions (raw pointers)

07589777a60ebb6cd8bde0e724f2b80752b8e078 authored about 10 years ago by Hannes Roest <[email protected]>

[FEATURE] add additional wrappers

312f805a44adb268b992d3e79361554cf72605cb authored about 10 years ago by Hannes Roest <[email protected]>

[FIX] fixes win32 compile issue with missing OPENMS_DLLAPI

ddd42bcf963e2b1863975b1e94538fd8acb1b64d authored about 10 years ago by Stephan Aiche <[email protected]>

Merge pull request #1019 from aiche/fix/eol-unitybuild

[FIX] fixed unitybuild problem on win32 with eol-bsplines

6ed228d13a0b1da7f10e41cd63169ec88a0b1bbb authored about 10 years ago by Stephan Aiche <[email protected]>

[NOP] addendum to c2686c754a0a7bbd7b1192182ba87d5ef4c014ce; GUIProgressLogger was missing

341f4ce4ea3abd4ace6ce7116f8423ef186eb65b authored about 10 years ago by Stephan Aiche <[email protected]>

Merge pull request #1020 from hroest/fix/licence_header

b6e3f1a1cf3ed394b9259ddc2a7aa349e92f193f authored about 10 years ago by Stephan Aiche <[email protected]>

[FIX] re-added accidentally removed std::endl

b058b67eb4a86b7c0f91a73cb69e9c58142d23e2 authored about 10 years ago by Stephan Aiche <[email protected]>

[FIX] fixed test failure in ParamXMLFile

314392b87dfe66241cf132fc4eaeebb0a38c90b8 authored about 10 years ago by Stephan Aiche <[email protected]>

[FIX] fixed compile issue in FeatureFinderAlgorithmPickedHelperStructs

73629c2b1313fc7b859df87a1cbe36699283a8a2 authored about 10 years ago by Stephan Aiche <[email protected]>

[FIX] removed public inheritance from FFAlgoPickedHelperStructs::MassTraces

see #184

69f58ce40ce65580132a912d1f1edbe4f2324d10 authored about 10 years ago by Stephan Aiche <[email protected]>

[FIX,PARAM] fixed processing of files with multiple ID runs; added parameter 'separate_runs' for such cases

4b5c8f5919076ac57ee9014e36282dea5a9cd372 authored about 10 years ago by Hendrik Weisser <[email protected]>

[INTERNAL] removed all occurrences of using namespace OpenMS from OpenMS

401071224b40d9abef9c4f590dd695090eda1707 authored about 10 years ago by Stephan Aiche <[email protected]>

Merge pull request #1009 from lars20070/fix/methylSILAC2

update unimod.xml with newest version from unimod.org

e115683a7596d73e23d90c7c8096a56bcca6c415 authored about 10 years ago by Hannes Roest <[email protected]>

Merge pull request #1006 from aiche/feature/gui-less-progress-logger

[FEATURE] enable gui less OpenMS

63557e70ff2e7a470b8de8dab88c4ca3f8556533 authored about 10 years ago by Hannes Roest <[email protected]>

c2686c754a0a7bbd7b1192182ba87d5ef4c014ce authored about 10 years ago by Hannes Roest <[email protected]>

[PYOPENMS,NOP] fixes, comments

0663c80713b7b133ad9e6dc5dc11f59429ba6d6f authored about 10 years ago by Hannes Roest <[email protected]>

[NOP] cleanup

1dcc625b7d6b7fbc9797d4a0c645bcf8a6c4829f authored about 10 years ago by Hannes Roest <[email protected]>