Ecosyste.ms: OpenCollective

An open API service for software projects hosted on Open Collective.

github.com/OpenMS/OpenMS

The codebase of the OpenMS project
https://github.com/OpenMS/OpenMS

[FIX,BUILD] addendum to [10250], accidentally fixed the DISABLE_OPENSWATH value to OFF

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10251 6adb6e08-d915-0410-...

a21db33af2e30c907aa552277eb6521aa8e180c5 authored about 12 years ago by Stephan Aiche <[email protected]>
[BUILD] added DISABLE_OPENSWATH flag to build system to disable building OpenSWATH lib and related parts of OpenMS

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10250 6adb6e08-d915-0410-...

fef04becc473f557f2ea108ace969b911e63645f authored about 12 years ago by Stephan Aiche <[email protected]>
[FIX] fix wrong file path of testfile

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10249 6adb6e08-d915-0410-...

f035ea98fd1780342127c0d7f4b6fc5e211535fd authored about 12 years ago by Hannes Roest <[email protected]>
[FIX] changes to make OpenMP 2.5 work with OpenSWATH

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10248 6adb6e08-d915-0410-...

bcdeb0f1ee1fd836542df30fd9606457864ba756 authored about 12 years ago by Hannes Roest <[email protected]>
[FEATURE] OpenSWATH add data processing to OpenSwath Analyzer and ChromatogramExtractor

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10247 6adb6e08-d915-0410-...

91b8ac8871d8bd1fe7fdd52c26ca4dcf9e42b5eb authored about 12 years ago by Hannes Roest <[email protected]>
[FIX-#433] also add dataprocessing to all chromatograms in MSExperiment

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10246 6adb6e08-d915-0410-...

2570436b212209f8e2eaf138b098b13f23c46e16 authored about 12 years ago by Hannes Roest <[email protected]>
[INTERNAL,FIX-#369] reenabled parsing of FASTA files using seqan

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10245 6adb6e08-d915-0410-...

77aa14f432514b6646b0a2b99dba26777c498116 authored about 12 years ago by Stephan Aiche <[email protected]>
[FIX] PepNovoAdapter fix for linux (cannot parse -inf as double)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10243 6adb6e08-d915-0410-...

747ce78921c97e89071d1feb3cd8977f41616e9f authored about 12 years ago by Chris Bielow <[email protected]>
[FIX] fixed and annotated some OpenMP compile errors (mind 2.5!, not all have 3.0)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10242 6adb6e08-d915-0410-...

11aba9f43852e13bcb21efbd3e1e68f57fd5497a authored about 12 years ago by Chris Bielow <[email protected]>
[TEST] added test for OpenSwathConfidenceScoring

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10241 6adb6e08-d915-0410-...

4368f08d3360ae2fa53e56e3250df3e82026d3b4 authored about 12 years ago by Hendrik Weisser <[email protected]>
[IO] made 'trafo' parameter optional

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10240 6adb6e08-d915-0410-...

7a710e043705c6cc57a8c70a734c4062cc0b6ffb authored about 12 years ago by Hendrik Weisser <[email protected]>
[NOP] some minor code style updates regarding spaces between code and comments

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10239 6adb6e08-d915-0410-...

68e7ec903453c6349989b2da1f12b55e0ecd2d30 authored about 12 years ago by Stephan Aiche <[email protected]>
[FIX] fixed erroneous commit in rev. 10235

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10238 6adb6e08-d915-0410-...

6c01c00c99b0461ffdb4da1984d1233e40d4277a authored about 12 years ago by Hendrik Weisser <[email protected]>
added OpenSwathRewriteToFeatureXML and commented out missing files in source/APPLICATIONS/UTILS/executables.cmake

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10237 6adb6e08-d915-0410-...

1f2721da9f74fbc24b6bda5a166083b5e77b59b5 authored about 12 years ago by George Rosenberger <[email protected]>
[INTERNAL,FIX] fix MS compile error, change and sort includes

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10236 6adb6e08-d915-0410-...

bb21321eadb31c87d02466c699fafad4c16143af authored about 12 years ago by Hannes Roest <[email protected]>
[FEATURE] added new tool for scoring of OpenSwath results (docu integration and test still missing)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10235 6adb6e08-d915-0410-...

903fff62a369b3e4878c8721c3f6204e7ad7183a authored about 12 years ago by Hendrik Weisser <[email protected]>
[NOP] moved docu to top, adjusted page name

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10234 6adb6e08-d915-0410-...

010aa659c6825677039c3baa83123ee3caf14047 authored about 12 years ago by Hendrik Weisser <[email protected]>
[FIX,NOP] fixed #335 by disabling ALL log_ output if debug was not set to true; removed whitespaces from LICENSE file

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10233 6adb6e08-d915-0410-...

c03f022b625b7d1b9f236da90ac1e200fa849456 authored about 12 years ago by Stephan Aiche <[email protected]>
OpenSwathRTNormalizer: fixed bug to disable rt_score, renamed classes and internal names for other OpenSwath tools, added George Rosenberger to authors

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10232 6adb6e08-d915-0410-...

2b1ad41e218b290eabda8f5dc91fe9b980d2c419 authored about 12 years ago by George Rosenberger <[email protected]>
[INTERNAL] code cleanup, move code to C file

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10231 6adb6e08-d915-0410-...

4e8c3d995771cffec7f57eb4dfdb15a6b509d359 authored about 12 years ago by Hannes Roest <[email protected]>
[FIX] OpenSWATH : set linear model in RTNormalizer by default (instead of none)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10230 6adb6e08-d915-0410-...

72ce53726cd49d90e88fdfe748e51be9e273c33f authored about 12 years ago by Hannes Roest <[email protected]>
[FIX] OpenSWATH : compiler fixes

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10229 6adb6e08-d915-0410-...

9f3eb01c5869ffce2a32615773110e65dc7e13cf authored about 12 years ago by Hannes Roest <[email protected]>
[TEST-FIX] OpenSWATH : fixed Swath Tests

Author: Witold <[email protected]>

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/...

83e3c0b854a058faf6e131dce59bce8947119480 authored about 12 years ago by Hannes Roest <[email protected]>
[INTERNAL] OpenSWATH : changes to OpenSwath::Spectrum interface

Author: Witold <[email protected]>

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/...

17c4a6b5bd2f605b97eb31952b809b8ae7fd843e authored about 12 years ago by Hannes Roest <[email protected]>
[TEST] OpenSWATH : Add tests for SpectrumHelpers, StatsHelpers, DIAScoring, DataAccess

original commit messages
* test for SpectrumHelpers and DiaScoring done
* [TEST] StatsHelpers_t...

3cb06b9f9c56379665e9a8a5ef4e8f1c51d85574 authored about 12 years ago by Hannes Roest <[email protected]>
[NOP] fix compile warning: mock object does not use the parameter

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10225 6adb6e08-d915-0410-...

807a8b490907d87e71e15308a28dd168400a77e6 authored about 12 years ago by Hannes Roest <[email protected]>
[BUILD] when searching X! TANDEM executable search also for tandem.exe (executable name on linux)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10224 6adb6e08-d915-0410-...

fd9ffba0e887ed9b45e46ab9286ad33759a17efa authored about 12 years ago by Stephan Aiche <[email protected]>
[NOP] changed code formatter options again; using 'T& x' and 'T* x' now (and in perpetuity)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10223 6adb6e08-d915-0410-...

87e2b541c2394d27941df1bf554f9af2b208eecb authored about 12 years ago by Hendrik Weisser <[email protected]>
[NOP] uncrustify, fix cpplint warnings (add explicit to constr)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10222 6adb6e08-d915-0410-...

2560480c201ea6fb47be2ecb98e63180e61bcafc authored about 12 years ago by Hannes Roest <[email protected]>
[FIX] OpenSWATH : fix unsigned integer comp. warning

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10221 6adb6e08-d915-0410-...

e8895fce980f6615a888f5f90bb76b0e44a5fdea authored about 12 years ago by Hannes Roest <[email protected]>
[FIX] OpenSWATH fix compiler problems (and test hopefully)

* fabs -> abs for ints
* change mock object to not divide by RT any more (could by zero)

git-sv...

a137dfcdebcd238e8684b3e3b8dd3976c46d2231 authored about 12 years ago by Hannes Roest <[email protected]>
[FIX] PepNovoAdapter now writes idXML which is parsable again (before a rounding error created a too large doubleReal, which cannot be parsed from String to DoubleReal when reading from file)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10219 6adb6e08-d915-0410-...

6aa1fa62997303858a34c0d3d7adc69d002f605a authored about 12 years ago by Chris Bielow <[email protected]>
[NOP] addapted uncrustify.cfg to discussions on mailing list; 'T & x' is now 'T &x'

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10218 6adb6e08-d915-0410-...

471f9659c8921aa9779e01353665d6b9ebce6ecc authored about 12 years ago by Stephan Aiche <[email protected]>
[NOP] OpenSWATH : removed code (will be moved to seperate tool)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10213 6adb6e08-d915-0410-...

ec9b95a1d554d3a8c2e18a3bc034c24da50002ed authored about 12 years ago by Hannes Roest <[email protected]>
[INTERNAL] OpenSWATH : numerical adaptation for MRMRTNormalizer

Author: George Rosenberger <[email protected]>

git-svn-id: https://open-ms.svn.sourcefo...

4a48cd4caad5966f0f705b1adeb1b79374813d51 authored about 12 years ago by Hannes Roest <[email protected]>
[INTERNAL] OpenSWATH : removing namespace std from MRMRTNormalizer.C

Author: George Rosenberger <[email protected]>

git-svn-id: https://open-ms.svn.s...

40b65c3707906a5cad907e8e1b95f43d67924994 authored about 12 years ago by Hannes Roest <[email protected]>
[INTERNAL] OpenSWATH : Comments for MRMRTNormalizer

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10210 6adb6e08-d915-0410-...

08e3087991137deb0cd23817182a0263b49da7b5 authored about 12 years ago by Hannes Roest <[email protected]>
[FEATURE] OpenSWATH : add up Spectra at peak apex

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10209 6adb6e08-d915-0410-...

bd330e3e2e18733118f89f151264767fa3ababe7 authored about 12 years ago by Hannes Roest <[email protected]>
[TEST] OpenSWATH : adding SpectrumHelpersTest

Author: Witold <[email protected]>

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/...

f7f26980df61354dce4c6f16e0903e2823d985b5 authored about 12 years ago by Hannes Roest <[email protected]>
[INTERNAL] OpenSWATH : renamed test files

Author: Witold <[email protected]>

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/...

1bc6145591b4674a23289ca790ec9e6d431d2dd7 authored about 12 years ago by Hannes Roest <[email protected]>
[FEATURE] OpenSWATH : Background Subtraction of peaks

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10206 6adb6e08-d915-0410-...

099ebe581d44015d924c5aa33973dcada6133fe7 authored about 12 years ago by Hannes Roest <[email protected]>
[INTERNAL] OpenSWATH : add update members to MRMFeatureFinderScoring

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10205 6adb6e08-d915-0410-...

9d71ad2d7996ed7cc6fb58d87f6088e1677d226e authored about 12 years ago by Hannes Roest <[email protected]>
[INTERNAL] OpenSWATH : file rename DiaPrescoring to DIA prescoring

Author: Witold <[email protected]>

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/...

ecfb90e81468c5ec82426fa1e35d816b87176ea9 authored about 12 years ago by Hannes Roest <[email protected]>
[INTERNAL] OpenSWATH : added documentation to DIAHelper methods

Author: Witold <[email protected]>

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/...

1af65f9e27f3dfe6b8a10597c432a47ef16e37ec authored about 12 years ago by Hannes Roest <[email protected]>
[INTERNAL] OpenSWATH : file rename from OpenMS helper to DIAHelper

Author: Witold <[email protected]>

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/...

09936580e2999641a6d66e71dfa07ace6b2ef4f4 authored about 12 years ago by Hannes Roest <[email protected]>
[DOC] OpenSWATH : added documentation, moved methods to .C file

Author: Witold <[email protected]>

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/...

83cd6401c2eb3e779a614c48632070de23be02eb authored about 12 years ago by Hannes Roest <[email protected]>
[API] OpenSWATH : rework param handling of OpenSwathAnalyzer

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10200 6adb6e08-d915-0410-...

1e574de35184ff821181a82574106b6907b6bd5f authored about 12 years ago by Hannes Roest <[email protected]>
[NOP] OpenSWATH : change author statements back as discussed

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10199 6adb6e08-d915-0410-...

dad6b787c77ca70a1d303790bdbebb63be1940b8 authored about 12 years ago by Hannes Roest <[email protected]>
[INTERNAL] OpenSWATH : Namespace cleanup

OpenMS for everything in libOpenMS, OpenSwath for everything in libOpenSwathAlgo

git-svn-id: ht...

911308ce984953dfe7e763d354f6c0f173dd6887 authored about 12 years ago by Hannes Roest <[email protected]>
[DOC] OpenSWATH : added documentation

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10197 6adb6e08-d915-0410-...

0718847e0d79e2758e3d07e3c1e677cb31e5a77a authored about 12 years ago by Hannes Roest <[email protected]>
[FIX] OpenSWATH : fixing test after moving factory method

Author: Witold <[email protected]>

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/...

909c46ffe972f24c0d96c4be7864270575ee3f14 authored about 12 years ago by Hannes Roest <[email protected]>
[INTERNAL] OpenSWATH : code move, Author statement changed

SimpleOpenMSSpectrumAccessFactory restored

Author: Witold <[email protected]>

git-svn-id: ...

772282bc34382284c580b77536acda2999fcad48 authored about 12 years ago by Hannes Roest <[email protected]>
[INTERNAL] OpenSWATH : change Author statements

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10194 6adb6e08-d915-0410-...

1d42f3a9124465b5b6f7548b8439546b49c6dd01 authored about 12 years ago by Hannes Roest <[email protected]>
[INTERNAL] OpenSWATH : re-organization, code move

* reorganised stats functions into StatsHelpers.C
* Reorganized DIAHelpers
* cleaned DiaScoring
...

b3e0e7983e3b57d30b2a16749dba7775b67a7bd1 authored about 12 years ago by Hannes Roest <[email protected]>
[FEATURE] OpenSWATH : added OpenSwathDIAPreScoring.C

Author: Witold <[email protected]>

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/...

15764145f9d77d4c7b5c6d49eff7cc01629a97b3 authored about 12 years ago by Hannes Roest <[email protected]>
[FEATURE] OpenSWATH : use C12-C13 massdiff for isotope differences

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10191 6adb6e08-d915-0410-...

b7afb26954501f662c04a80f2391c459d1c2ff1b authored about 12 years ago by Hannes Roest <[email protected]>
[FEATURE] OpenSWATH : add possibility to specify the product charge state in TraML

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10190 6adb6e08-d915-0410-...

ba1171acf06e6f9aac5f5d6da5a2e9aff5de8316 authored about 12 years ago by Hannes Roest <[email protected]>
[BUILD] OpenSWATH : make separate build for OpenSwathAlgo lib

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10189 6adb6e08-d915-0410-...

47ebaaa17ee529626961012986149c995eb2aa10 authored about 12 years ago by Hannes Roest <[email protected]>
[FIX] OpenSWATH : use std::distance, add comments

change comments: add TODOs, assign TODOs

git-svn-id: https://open-ms.svn.sourceforge.net/svnroo...

208f905645cb3c87642a13b646bd36df15d1d614 authored about 12 years ago by Hannes Roest <[email protected]>
[INTERNAL] OpenSWATH : cleanup, renames, comments, change Author statements

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10187 6adb6e08-d915-0410-...

a116472ecc95a08571fb1f65ded434319dd301b3 authored about 12 years ago by Hannes Roest <[email protected]>
[NOP] OpenSWATH : add DLLAPI, clean up, add TODOs

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10186 6adb6e08-d915-0410-...

3ba1a9615ad48186b736548e7d01ef64c0415be9 authored about 12 years ago by Hannes Roest <[email protected]>
[FEATURE] OpenSWATH : use cached mzML as input to OpenSwathAnalyzer

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10185 6adb6e08-d915-0410-...

7b14207d7090ed00e4bc89f779b0d1099bab1fa9 authored about 12 years ago by Hannes Roest <[email protected]>
[TEST] OpenSWATH : Additional tests for MRMRTNormalizer + fix for rm_outlier

Author: George Rosenberger <[email protected]>

git-svn-id: https://open-ms.svn.s...

15805148b792255cad9c9e4a9277d07282c00242 authored about 12 years ago by Hannes Roest <[email protected]>
[FIX] OpenSWATH : Chauvenet fixed & tested

Author: George Rosenberger <[email protected]>

git-svn-id: https://open-ms.svn.s...

3883bc4dbba72a30e623293e3280992598195ade authored about 12 years ago by Hannes Roest <[email protected]>
[INTERNAL] OpenSWATH : renamed DiaPrescoring.C

Author: Witold <[email protected]>

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/...

e6f1632830d55b5c9dcd23b3dbf9a69733c64d7d authored about 12 years ago by Hannes Roest <[email protected]>
[NOP] OpenSWATH : licence change, comment

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10181 6adb6e08-d915-0410-...

fe772e1d934a6b7827f578735f038c0563d6af31 authored about 12 years ago by Hannes Roest <[email protected]>
[INTERNAL] OpenSWATH : moved DiaScoring fix includes

Author: Witold <[email protected]>

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/...

dd07c84ae3f80283e6e5df21235effbb4294d240 authored about 12 years ago by Hannes Roest <[email protected]>
[INTERNAL] OpenSWATH : still fixing - should work now

Author: Witold <[email protected]>

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/...

e1428f9d99436bc2ff76e2b431d41c67247dccc4 authored about 12 years ago by Hannes Roest <[email protected]>
[BUILD] OpenSWATH : fixing cmake

Author: Witold <[email protected]>

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/...

2e1a24473c84947e8b305c2c67f5d73128fda603 authored about 12 years ago by Hannes Roest <[email protected]>
[BUILD] OpenSWATH : cmake source.cmake include OPENSWATHALGO

Author: Witold <[email protected]>

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/...

a2827062b9676dc916c604feb700342ec9c22cdc authored about 12 years ago by Hannes Roest <[email protected]>
[INTERNAL] OpenSWATH : moved DIAHelpers.h

Author: Witold <[email protected]>

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/...

93284bba14c67c58bf22d8d7de323d6bff5b36f7 authored about 12 years ago by Hannes Roest <[email protected]>
[FIX] OpenSWATH : add forgotten files for OpenSwathDecoyGenerator

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10175 6adb6e08-d915-0410-...

fe6f52fa45b52f86dd033d04c298909635d074c6 authored about 12 years ago by Hannes Roest <[email protected]>
[BUILD] OpenSWATH : moved OpenSwath library in cmake

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10174 6adb6e08-d915-0410-...

2b6ee368a5eba2a4ac859ffc6c6b3ffde83e6361 authored about 12 years ago by Hannes Roest <[email protected]>
[FEATURE] OpenSWATH : MRMRTNormalizer new chauvenet

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10173 6adb6e08-d915-0410-...

d912e257c3c23b4ab2f7ffb5ab6032fff1b861e1 authored about 12 years ago by Hannes Roest <[email protected]>
[INTERNAL] OpenSWATH : extract method, remove dead code

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10172 6adb6e08-d915-0410-...

0e5baa607d578093a0cf8aa3dd622e7894d48c0a authored about 12 years ago by Hannes Roest <[email protected]>
[NOP] OpenSWATH : run uncrustify, fix compiler warnings

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10171 6adb6e08-d915-0410-...

da7338c84a70ebd35df43b8acf23de5b6be92879 authored about 12 years ago by Hannes Roest <[email protected]>
[INTERNAL] OpenSWATH : rename, code move, fix of include guards

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10170 6adb6e08-d915-0410-...

d6468c0e64729afffcc464504aef0c6973ce5966 authored about 12 years ago by Hannes Roest <[email protected]>
[FEATURE] OpenSWATH : added OpenSwathRTNormalizer

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10169 6adb6e08-d915-0410-...

18fd7201f79af9ef9050d4be313b540866054c52 authored about 12 years ago by Hannes Roest <[email protected]>
[TEST] OpenSWATH : add TOPP tests for OpenSwathAnalyzer

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10168 6adb6e08-d915-0410-...

ca07f228e53587c1b58f10d1475a7b410322a6a9 authored about 12 years ago by Hannes Roest <[email protected]>
[TEST] OpenSWATH : switch from boost_unit tests to OpenMS framework

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10167 6adb6e08-d915-0410-...

f96f55e27a50027d240b2307c93196cd149788b8 authored about 12 years ago by Hannes Roest <[email protected]>
[FEATURE] OpenSWATH : added OpenSwathAnalyzer, the main Tool

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10166 6adb6e08-d915-0410-...

818c130c698d304b1fd1816ea1c7a6a0cc80cf65 authored about 12 years ago by Hannes Roest <[email protected]>
[FEATURE] OpenSWATH : add class MRMFeatureFinderScoring and 2 tests

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10165 6adb6e08-d915-0410-...

34452ed60c8b715dac66eefdc6f265eb97ec2a4f authored about 12 years ago by Hannes Roest <[email protected]>
[FEATURE] OpenSWATH : add data access methods implementing OSW Interfafces

Add a set of classes that implement the OpenSWATH interfaces using
OpenMS. The following classes...

282959076647be6f01ae2e41e45698fe6a9731be authored about 12 years ago by Hannes Roest <[email protected]>
[FEATURE] OpenSWATH : DIA (data independent acquisition) scoring functions added

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10163 6adb6e08-d915-0410-...

3d47f4756d23194022a3399c18eafdfec93bc321 authored about 12 years ago by Hannes Roest <[email protected]>
[FEATURE] OpenSWATH : OpenMS helper for OpenSwath (OSW)

Helper for isotope handling, AASequence handling etc

git-svn-id: https://open-ms.svn.sourceforg...

bec72ee3b9ddd4024bc71a2b45df5a18bff2e69c authored about 12 years ago by Hannes Roest <[email protected]>
[NOP] OpenSWATH : licence change/addition and coding style

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10161 6adb6e08-d915-0410-...

1e1e28577d9494aacc13af58460e4d91b6a8a35b authored about 12 years ago by Hannes Roest <[email protected]>
[FEATURE] OpenSWATH : scoring based on Emg model added

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10160 6adb6e08-d915-0410-...

235bb015d0e2eb24c5a4e8733c1643f90091fb97 authored about 12 years ago by Hannes Roest <[email protected]>
[BUILD] OpenSWATH : build system changes, move tests

* use the OpenMS folders for lib and TEST
* cleanup cmake files
* move tests to TESTS/OPENSWATH
...

77f5fa4e80fe226f2312d14ac541d90e9c7f79c4 authored about 12 years ago by Hannes Roest <[email protected]>
[FEATURE] OpenSWATH : add TransitionGroupPicker

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10158 6adb6e08-d915-0410-...

2e1a05b1d82052f7370d42c12824d59dd9189979 authored about 12 years ago by Hannes Roest <[email protected]>
[FEATURE] OpenSWATH : adding OpenSwathLib

Author: Witold <[email protected]>

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/...

ad8c679844a83efbae99950cdf3f03f3756c877c authored about 12 years ago by Hannes Roest <[email protected]>
[FEATURE] OpenSWATH : added OPENSWATHALGO

Author: Witold <[email protected]>

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/...

5fdebfd092808330637b6fcfbd152082f48a2df4 authored about 12 years ago by Hannes Roest <[email protected]>
[FIX] OpenSWATH : MRMDecoyGenerator fixed restriction of transitions

Author: George Rosenberger <[email protected]>

git-svn-id: https://open-ms.svn.s...

edcd7cb996967c98b72341056d09f1486f477486 authored about 12 years ago by Hannes Roest <[email protected]>
[FEATURE] OpenSWATH : add a resampling algorithm for aligned data

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10154 6adb6e08-d915-0410-...

3f6fc2fcc3308cd91f12a14f1662cef06d7370b0 authored about 12 years ago by Hannes Roest <[email protected]>
[FEATURE] OpenSWATH : add OpenSwath Chromatogram Extraction

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10153 6adb6e08-d915-0410-...

a7c6669cbfc707ea8404e9d3aae3f44c4d2acd5c authored about 12 years ago by Hannes Roest <[email protected]>
[FEATURE] OpenSWATH : add FeatureXML to TSV converter

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10152 6adb6e08-d915-0410-...

658a2fbc20587145a8fbce16875696ad07c30378 authored about 12 years ago by Hannes Roest <[email protected]>
[FEATURE] OpenSWATH : add MRMMapper to UTILS

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10151 6adb6e08-d915-0410-...

33bea36887d913076371a16e356b540db014fa33 authored about 12 years ago by Hannes Roest <[email protected]>
[FEATURE] OpenSWATH : add UTIL to convert TraML / TSV files

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10150 6adb6e08-d915-0410-...

1dc17fc388ff1883624dcb1db839d93314c58e60 authored about 12 years ago by Hannes Roest <[email protected]>
[NOP] OpenSWATH : copy to UTILS, add comments, licence change

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10149 6adb6e08-d915-0410-...

b0dd8836d9533f3ab1db05d70f5af9fce85c42f1 authored about 12 years ago by Hannes Roest <[email protected]>
[FIX] OpenSWATH : MRMDecoyGenerator fix

* Proton Hack reversed
* Tests optimized

Author: George Rosenberger <[email protected]...

2ccf323fc2869d39573c541958cda16e82a988dd authored about 12 years ago by Hannes Roest <[email protected]>
[FIX] OpenSWATH: cleanup shufflePeptide, use single RNG now

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10147 6adb6e08-d915-0410-...

53bf7d2a3e3da8db7df79e8328981c78ad18fb8d authored about 12 years ago by Hannes Roest <[email protected]>