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

Merge branch 'develop' into feature/AASequence_refactoring

215864c5f62063543865cd9a9f00ec4cb8aca0ce authored over 10 years ago by Timo Sachsenberg <[email protected]>

[FEATURE,PARAM] reworked parameter handling, added internal feature detection (not yet finished)

5af924407f57190da4d3ecc754d72843bee78ce0 authored over 10 years ago by Hendrik Weisser <[email protected]>

[FEATURE,FIX]: Small changes for RTNormalizer

573b75203718507d103bb0c6b2040dc90985366c authored over 10 years ago by George Rosenberger <[email protected]>

[API] added new FilterResult data structure

064bc452ddb82bd926c095b660f4822917fe4a16 authored over 10 years ago by lars20070 <[email protected]>

[API] added new FilterResultPeak data structure

ba32b15e4db340bd21d5c2c7c7e26e6b54b2d722 authored over 10 years ago by lars20070 <[email protected]>

[API] extended FilterResultRaw API

0798bc25bfae9ec79e2a61f05e3faeb4a42c425e authored over 10 years ago by lars20070 <[email protected]>

[API, INTERNAL] new FilterResultRaw data structure

597fcdf449f2accd197a2e10ef92b3d730bce1e0 authored over 10 years ago by lars20070 <[email protected]>

[INTERNAL] MassPattern and PeakPattern lists generated

c74f7e6299054a48c32d2bc86c74c20774521b07 authored over 10 years ago by lars20070 <[email protected]>

Merge pull request #801 from cbielow/interface_RTPredict

RTPredict: fixed order of parameters and doc

880d2e5779777a5b7a2359cc96724978badc4763 authored over 10 years ago by Hannes Roest <[email protected]>

RTPredict: fixed order of parameters and doc

40994e275d8eab2a0aede412fd5a91f98f710887 authored over 10 years ago by Chris Bielow <[email protected]>

[API] extended PeakPattern

d22711667f7d6f9f7d0beba580ad2706d49eadb7 authored over 10 years ago by lars20070 <[email protected]>

Undo changes for MyriMatchAdapter in branch fix-msgfplusadapter

modified: ../src/topp/MyriMatchAdapter.cpp

19d1d9ceb9fce39730ec7161de901f5e99f4b6f5 authored over 10 years ago by Petra Gutenbrunner <[email protected]>

Merge branch 'fix-msgfplusadapter' of https://github.com/PetraGutenbrunner/OpenMS into fix-msgfplusadapter

fadaee8adf7dc57171ce7319979a43e7257cd53f authored over 10 years ago by Petra Gutenbrunner <[email protected]>

[BUILD] add PeakPattern to make files

08fd84a2e86d8c8e146429ff1fef9e4f95d12e18 authored over 10 years ago by lars20070 <[email protected]>

[API] new PeakPattern data structure

ffb700a885fa1b5439b58e0c306e475d13969936 authored over 10 years ago by lars20070 <[email protected]>

[MSGFPlusAdapter extension]

- added input parameters for the search
- replaced the static parameter values with the input pa...

fcd50a14f3bac11dc6730c728da3ec279cd3f047 authored over 10 years ago by Petra Gutenbrunner <[email protected]>

[INTERNAL] added section for testing peak picking

2793a5eb607e0e005160fbfe21dfe40030214d8f authored over 10 years ago by lars20070 <[email protected]>

[DOC] add/clarify documentation

bf8021ebb602c6d0eed0e9cda8ec5667e47e105a authored over 10 years ago by Hannes Roest <[email protected]>

[CLI] cleanup, simplify CLI

f6fad7d9f19d317dcb500d716e4acbd46880f5f1 authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] pyOpenMS fixes

06830d9f8a6f6b6640cd99b07ceb535afeee5ba6 authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] addendum to 3765a363c5a9f47b621ec58c6fd62115d11b4a91, removed OpenMS_DB.sql from File_test

7a44093e51eb635f1df924b3199394a4504cacb6 authored over 10 years ago by Stephan Aiche <[email protected]>

[INTERNAL] DoubleReal from FeatureSetFinder removed

66873fbcdcb1393ae82965aa3a65e2f5eeab8e49 authored over 10 years ago by lars20070 <[email protected]>

make files added

1bb67d21b373220657ffa91a82cc6a150e91a8da authored over 10 years ago by lars20070 <[email protected]>

remove make files before merge

ff381880f06ff488582c7d4a4e2c0d853625ba39 authored over 10 years ago by lars20070 <[email protected]>

[TEST] python wrappers for SplinePackage and SplineSpectrum added

c7c7aa02ec145713cc1aa0eb3aad6ea2327f37d3 authored over 10 years ago by lars20070 <[email protected]>

[API] SplinePackage simplified

f21ebc8bc50ba8a9c3df923139e4bd55e02f39d1 authored over 10 years ago by lars20070 <[email protected]>

[TEST] TOPP tool test for FeatureSetFinder added

198ad4ed6b9e1384d57f3ac2035705c444047878 authored over 10 years ago by lars20070 <[email protected]>

[TEST] unit tests for SplinePackage and SplineSpectrum added

72ce63e4d440cb677b287551a87583d60b200802 authored over 10 years ago by lars20070 <[email protected]>

[INTERNAL] old functionality from FeatureSetFinder removed

69bc74aa9f476d76f0e842fdf64fc180f9343276 authored over 10 years ago by lars20070 <[email protected]>

[API,COMMENT] minor interface changes

c0165bb63dda96b3132e29cf9b46391efd170db5 authored over 10 years ago by lars20070 <[email protected]>

extended interface

5e2384a8a8c3b41612cc9bca30d2860bfae93d68 authored over 10 years ago by lars20070 <[email protected]>

simplified SplinePackage data structure

d96124596d5d5fb279e83c7b20ea015499a6695e authored over 10 years ago by lars20070 <[email protected]>

[FIX] amend to #765 feature/db_removal. Removed 2 additional files.

3765a363c5a9f47b621ec58c6fd62115d11b4a91 authored over 10 years ago by Timo Sachsenberg <[email protected]>

[NOP] cleanup, code formatting

297cb220bf17e2ffa048cc0cf6df1f0f357058cd authored over 10 years ago by Hannes Roest <[email protected]>

[PYOPENMS] adopt Python bindings

0302b8c2ffb36f6e8059dda373bc3ba39f293eda authored over 10 years ago by Hannes Roest <[email protected]>

[TEST] add topp tests for new CLI

a6df3b29b693b7a682ec45384f31f65d953cea54 authored over 10 years ago by Hannes Roest <[email protected]>

[TODO] add todo comments

6493912c178ba572f3d5eb9064497f3f6df9be6d authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] adopt UI, code cleanup

- rename functions (Coding conventions)
- adopt UI to be clearer about which method is used for ...

16ecfc191fb3b3e6b4bcacfef90f06496e2cbb1e authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] adopt OpenSwathWorkflow

- remove duplicated code
- adopt test (different UIDs)

4d24a86e2ea0ab68bf5da652540d081ea1de5e0d authored over 10 years ago by Hannes Roest <[email protected]>

[NOP] migrate helper functions to OpenSwathHelper

a113c595b24c1adea980439eb0a5ec8441d82277 authored over 10 years ago by Hannes Roest <[email protected]>

Merge branch 'develop' into feature/custom_iRT

Conflicts:
src/topp/OpenSwathRTNormalizer.cpp

b277dac07283846c322c2a338d61a8151e7764a3 authored over 10 years ago by Hannes Roest <[email protected]>

Merge pull request #799 from timosachsenberg/doc/migratedoc

[DOC] removed migrated pages from doxygen. replaced by link to wiki

70b07db5c18b610b8b716cb1a892e6095e13232e authored over 10 years ago by Stephan Aiche <[email protected]>

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

b445e13ebc4a84811a10d21fa3718e24debb3f96 authored over 10 years ago by Hendrik Weisser <[email protected]>

[PARAM] added flag 'all_features' to FeatureFinderIdentification (return all features found by OpenSWATH per peptide ID, instead of best one only)

2c164ca7b9aa3e02d6f044eec7c267ab1a69b270 authored over 10 years ago by Hendrik Weisser <[email protected]>

[DOC] removed migrated pages from doxygen. replaced by link to wiki

61128f57778d1de637dec877f90958944559dcb4 authored over 10 years ago by Timo Sachsenberg <[email protected]>

[FEATURE,TEST]: CiRT features and tests added to MRMRTNormalizer and OpenSwathRTNormalizer

323c8ee6ce1e89dda1b40981e88daa417c3a095d authored over 10 years ago by George Rosenberger <[email protected]>

Merge pull request #798 from hroest/fix/pyOpenMS_testfix

Fix/py open ms testfix

ff6d9a981cec628187dee33aab96111f5112cab3 authored over 10 years ago by Hannes Roest <[email protected]>

[FEATURE,PYOPENMS] adopt MSChromatogram after MSSpectrum (#754)

adopt MSChromatogram after the changes in
97e6477e3d2b57881e651d17fc0bac7675bfddd5 to MSSpectrum

cf9ee565498166b373115f46c9c8f25269d5f54e authored over 10 years ago by Hannes Roest <[email protected]>

[TEST,PYOPENMS] fix test after #754

5438bbe083e8583a6aa4765b50d30f3e308b7488 authored over 10 years ago by Hannes Roest <[email protected]>

destructors changed

0ccd5381f5b446440f64f0dbe700baeca48745b9 authored over 10 years ago by lars20070 <[email protected]>

Merge branch 'feature/AASequence_refactoring' of https://github.com/timosachsenberg/OpenMS into test-msgfadapter

22d43801f35a9695b5b6c5dac5577e05de528ec6 authored over 10 years ago by Petra Gutenbrunner <[email protected]>

Renamed the Adaper to MSGFPlusAdapter

Extended the parameter definition
Added the adapter to de make files

modified: ../doc/doxygen/...

5149d6d28dffd7f944b112f03e6561228671eb69 authored over 10 years ago by Petra Gutenbrunner <[email protected]>

destructors added

cd2fde75fa7582ebadd1b84d73cca8d09cdad132 authored over 10 years ago by lars20070 <[email protected]>

destructors added

b46bad7bbe8a6f6c58f8770f9875984a51de1127 authored over 10 years ago by lars20070 <[email protected]>

Merge pull request #797 from aiche/fix/remove-last-traces-of-SILAC

[NOP,DOC] removed all remaining references to FeatureFinderRaw and SILAC...

cdc36b86f7c0f6684091afbd46695c8207ed216e authored over 10 years ago by Stephan Aiche <[email protected]>

[NOP,DOC] removed all remaining references to FeatureFinderRaw and SILACAnalyzer

67fde794bbc1831dbb4e1c7d5220efc2542ccb5c authored over 10 years ago by Stephan Aiche <[email protected]>

[FIX] corrected comment in test

3358465e8da00f7031e8d2833bc4278377c6470d authored over 10 years ago by Timo Sachsenberg <[email protected]>

[FEATURE] N-terminal integer mass tags in AASequence

c9fe656476309ce883ed36d5bb48de68a63fac6b authored over 10 years ago by Timo Sachsenberg <[email protected]>

[DOC] added FidoAdapter to TOPP docu page (and removed broken links to SILACAnalyzer/FeatureFinderRaw)

8e111e8a17b4ba6a9f1f144d61e750169ca5b073 authored over 10 years ago by Hendrik Weisser <[email protected]>

[FEATURE,DOC] completed implementation of Fido adapter, added documentation

d46f2627c4a8623a5d9d8feb010428c53c8a519e authored over 10 years ago by Hendrik Weisser <[email protected]>

[FEATURE] added support for mass tags at N-term

e7d47dbeca026909c46012efe1ac5f15f2e1ea2e authored over 10 years ago by Timo Sachsenberg <[email protected]>

destructors added

ae48e036186173c178db5790da9f4f2a7cc28805 authored over 10 years ago by lars20070 <[email protected]>

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

dc205380b7422c1149be58c827cf799c236ff31f authored over 10 years ago by Hendrik Weisser <[email protected]>

[FIX] fixed clang compiler warnings

367959f552cbc385f0acb45ee6803bc48caf1228 authored over 10 years ago by Hendrik Weisser <[email protected]>

Merge branch 'develop' into feature/AASequence_refactoring

1437fafb5ccfb03a07e3c326cfbd31ec540ea32d authored over 10 years ago by Timo Sachsenberg <[email protected]>

[FIX] removed isValid and sequence_string_ from AASequence

0950fb9334d8f0a3aaed8a63ae42d0edb9ed1654 authored over 10 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #794 from cbielow/WrapR

Generic Wrapping of R scripts using GenericWrapper

20ea997bd7cc6237c77b3fa9a09e75870a7755a1 authored over 10 years ago by cbielow <[email protected]>

Merge branch 'develop' into feature/AASequence_refactoring

4312a527cbda593db598c8058641073c8859225e authored over 10 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #777 from cbielow/SysInfoMem

Memory profiling class for all three platforms

39ff415516a892a60604cbf271d79c7a4b96cf03 authored over 10 years ago by cbielow <[email protected]>

minor line endings and message fix

3508a6f27c807c863dc2ca5602c7c3ab6223c3ed authored over 10 years ago by Chris Bielow <[email protected]>

[TEST] read mzML to enforce allocation of memory

d4a1a743624ef6323f0bc8799ddc5b546555f335 authored over 10 years ago by Stephan Aiche <[email protected]>

[INTERNAL] some cleanups of mac memory consumption

* added memory info to mzML reading in FileInfo

b40b9c34a541c750797a3b06e252824783c66490 authored over 10 years ago by Stephan Aiche <[email protected]>

fixed typo@

b5349e1545629f89b722ba055e087ba03a7d1974 authored over 10 years ago by Chris Bielow <[email protected]>

fixed/added some info memory info for FileInfo

657f6be12ca0f95c34efc0389f203bdf6c1dad43 authored over 10 years ago by Chris Bielow <[email protected]>

a memory query class -- cross platform (hopefully)

cc14c0029993e1ac6dbb865d6004b6427989a6e6 authored over 10 years ago by Chris Bielow <[email protected]>

Merge branch 'develop' into feature/AASequence_refactoring

d727d70717d682b6f43c6defa4efb1115ecf1655 authored over 10 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #786 from aiche/feature/lib-macro

[FEATURE] added openms_add_library function

605d1f5509678d6fcf438c6d6a5f7123fc0a1f43 authored over 10 years ago by Stephan Aiche <[email protected]>

optimized SplineSpectrum data structure

5bf2a2246532ce7d312c797dc66be0ada25f9b42 authored over 10 years ago by lars20070 <[email protected]>

fixed TOPPAS edge crash when connecting Input and Merger node; finished Example TOPPAS pipeline and R script

27190b90dc3912f3efbc052586ad138a2248ed41 authored over 10 years ago by unknown <[email protected]>

[NOP,BUILD] removed OpenBuildSystem prefix from cmake scripts

* fixed last change date generation in knime package generation
* re-added targets target
* a...

fd9b81896183e5ec20182214c483c6ec56ef84eb authored over 10 years ago by Stephan Aiche <[email protected]>

[FIX] fixed test error introduced via merge

607121223275ba9638b349024e5acdce5df5787f authored over 10 years ago by Timo Sachsenberg <[email protected]>

Merge branch 'develop' into feature/AASequence_refactoring

Conflicts:
src/tests/class_tests/openms/source/IdXMLFile_test.cpp
src/tests/class_tests/openms...

b2867c8a40b2416b440243d677e07a3b259d23ae authored over 10 years ago by Timo Sachsenberg <[email protected]>

optimized SplineSpectrum data structure

a619bd29bef95632516bc039dba4267e9aa51ede authored over 10 years ago by lars20070 <[email protected]>

[NOP] added missing author

3b2d70604d3d86d2da796fb89c54ddef682da9da authored over 10 years ago by Stephan Aiche <[email protected]>

[NOP] removed obsolete file from cmake folder

8c4e5f28b1fdb8516f1a32fd27438924aea3b42a authored over 10 years ago by Stephan Aiche <[email protected]>

[FIX] AASequence::fromString now throws a ParseError instead of just

setting valid to false

48b241509ca2cdd898820c0b3ae227347dcaba47 authored over 10 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #790 from cbielow/fix_pepRTMZ2

Remove 'RT' and 'MZ' metavalues from PeptideIdentification

a83b3ecb1440bbe3e3f4d5fcde72cdf2300873b2 authored over 10 years ago by cbielow <[email protected]>

fixed tabs

28a96aa00c338a8a3effded553b5f93874a108c5 authored over 10 years ago by Chris Bielow <[email protected]>

Merge branch 'develop' into feature/AASequence_refactoring

8e0d7247ff34c7511e45c0198295d019e67ae57e authored over 10 years ago by Timo Sachsenberg <[email protected]>

Merge branch 'develop' into feature/lib-macro

Conflicts:
src/openms/CMakeLists.txt

04be2b9697d857e5517396b02e82e929898138ff authored over 10 years ago by Stephan Aiche <[email protected]>

[FIX] removed obsolete comments. moved fromString to cpp

e56ae56f119cc3d34f997471040581af6530702a authored over 10 years ago by Timo Sachsenberg <[email protected]>

[FEATURE] updated AASequence pxd to reflect interface changes

10df9fd82ff15e632e336dc6a5402d94d46a4186 authored over 10 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #780 from hroest/feature/OpenSwathWindowEstimation

[FIX] fix Swath window estimation

d64ce61ea549c0b8b1dda1fa70cbfd5d7835ea89 authored over 10 years ago by Hannes Roest <[email protected]>

Merge pull request #787 from aiche/feature/pyopenms-fixes

[FEATURE,BUILD] move pyOpenMS to src

208cff37c19d6285fdafe9d07bbc03b028e82fca authored over 10 years ago by Hannes Roest <[email protected]>

Merge branch 'develop' into feature/AASequence_refactoring

36ffb16ddae3f862ed6172bec695a3f54e4559e3 authored over 10 years ago by Timo Sachsenberg <[email protected]>

Merge branch 'develop' into feature/AASequence_refactoring

Conflicts:
src/openms/include/OpenMS/CHEMISTRY/AASequence.h
src/openms/include/OpenMS/FORMAT/D...

fbf018769f2f730d11170597f644650c410b5046 authored over 10 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #791 from timosachsenberg/fix/VS2013

[FIX] forgot writtenDigits fixes in tests VS2013

f8ad79cfe8d1743daf1976591bd834e131994d43 authored over 10 years ago by timosachsenberg <[email protected]>

[BUILD,NOP] some final cleanups of comments and macro names

efb572bfd235106bc9e9f790d45bd5f4a5ae4e58 authored over 10 years ago by Stephan Aiche <[email protected]>

Merge branch 'develop' into feature/lib-macro

Conflicts:
CMakeLists.txt
cmake/OpenMSConfig.cmake.in
src/openms_gui/include/OpenMS/VISUAL/DI...

6a7473736d965c5e2a39782973e88b8467e97702 authored over 10 years ago by Stephan Aiche <[email protected]>

[FIX] forgot writtenDigits fixes in tests

4ebfabb42a8d786c9473a183addad1d1d9680230 authored over 10 years ago by Timo Sachsenberg <[email protected]>