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

[NOP] fixed comment

3cbcf674e6abea5fc5b5e8ed9400c32ae9fbe0bb authored over 10 years ago by Stephan Aiche <[email protected]>

Merge pull request #773 from OpenMS/fix/pyOpenMS_fix

[BUILD,PYOPENMS] fix pyOpenMS build

83927bc24b528b140471da886fef5066beb0b7a6 authored over 10 years ago by Hannes Roest <[email protected]>

[BUILD,PYOPENMS] fix pyOpenMS build

- move overloaded functions into a class (pyOpenMS currently cannot deal
with overloaded globa...

e08094403f0bf2abe729e66a45cd57eae5d41aa2 authored over 10 years ago by Hannes Roest <[email protected]>

[NOP] corrected comment in SuperHirn's CMakeLists.txt

f8d4dad1e700c4cc5f6e6e040e09ed20604635c8 authored over 10 years ago by Stephan Aiche <[email protected]>

[BUILD] adapted pyOpenMS build to libSuperHirn

4ab4851dc5fbebd2b944d9ff96f6d4ce9578063f authored over 10 years ago by Stephan Aiche <[email protected]>

[FIX] fixed compile issue with unity build due to duplicated/wrong header guards

213524e0eac75e07a2755ce1771142519367c123 authored over 10 years ago by Stephan Aiche <[email protected]>

Merge branch 'develop' into feature/libsuperhirn

Conflicts:
src/superhirn/include/OpenMS/TRANSFORMATIONS/FEATUREFINDER/SUPERHIRN/LCElutionPeak.h...

9759e5f1c838e98b88ee91b74164c9501f7c7ccb authored over 10 years ago by Stephan Aiche <[email protected]>

Merge pull request #768 from mcmenace/warningfix

[FIX] fixed warnings in CONCEPTS

260deb9e123ba171bbe7f4696c0e0ac700aa8e77 authored over 10 years ago by timosachsenberg <[email protected]>

Merge pull request #771 from jleclaire/new_Warnings

[NOP] Shadow warnings

bd684ca34ee9ea485ccce3f5d5ca2d850184ccb2 authored over 10 years ago by timosachsenberg <[email protected]>

Merge pull request #756 from cbielow/unityBuild

[FEATURE,BUILD] Support unity builds in OpenMS to increase win compile performance

58adc289c7cb3781fca661913b8074c7675e5566 authored over 10 years ago by Stephan Aiche <[email protected]>

[BUILD,INTERNAL] fixed win linker error when linking libSuperHirn

* some more cleanups of SuperHirn code

82aa0dbe56b95c20c744881973595642d4d86d49 authored over 10 years ago by Stephan Aiche <[email protected]>

Merge pull request #770 from mcmenace/streamfix_stephan

[FIX] fixed some clang warnings in stream manipulation

9d766bf9041be56dcd81b5bfce402ddbe56d709f authored over 10 years ago by Stephan Aiche <[email protected]>

fixed some overoptimizations which prevent compilation in non-unity mode

e6d21f5fef55ffe2dedf022317572a8b65c8679a authored over 10 years ago by Chris Bielow <[email protected]>

[FIX] fixed typo in include

30ab3cf3d582302d53e4aa5ee0442afd100f61a8 authored over 10 years ago by Stephan Aiche <[email protected]>

[FIX] fixed windows linker error in ConversionHelper::convert

53f7549e76da1033ee4be6afcbe4901d809e233d authored over 10 years ago by Stephan Aiche <[email protected]>

[FIX] shadow warning

ad0a074725a11a290932ebf439a3446b25618834 authored over 10 years ago by Jenny <jenny@jenny-Latitude-E4300.(none)>

[FIX] fixed shadow warning

5500e76b90b776bd23daa41cf33704dc31133dee authored over 10 years ago by Jenny <jenny@jenny-Latitude-E4300.(none)>

[FIX] fixed a large number of minor issues in libSuperHirn

0ef1265282271ef998046922c134492d48938d51 authored over 10 years ago by Stephan Aiche <[email protected]>

[FIX] fixed windows linker error in ConversionHelper::convert

96d191d67b7ecbb28534297b480df8f421c8a6fa authored over 10 years ago by Stephan Aiche <[email protected]>

fixed some clang warnings

Conflicts:
src/openms/include/OpenMS/KERNEL/PeakIndex.h

5cabb10dc059475d0c09ca9e4865cc7e31a1b69f authored over 10 years ago by Stephan Aiche <[email protected]>

Merge branch 'MSGF+-Adapter' of https://github.com/mwalzer/OpenMS into test-msgfadapter

24cbf4b0010a6b84c501c1ce9041b08e6e50c9c3 authored over 10 years ago by Petra Gutenbrunner <[email protected]>

[FIX] fixed warnings in CONCEPTS

512c664aeaaf093059d5e22ff4c29b30addc6e30 authored over 10 years ago by Christian Ehrlich <[email protected]>

[FIX] fixed wrong reference to test data folder in superhirn tests

* made CF_OPENMS_TEST_DATA_PATH "private" to avoid interference with other parts of the build s...

ba015a45e6e9f122b25b82462944ec6c9b9e3033 authored over 10 years ago by Stephan Aiche <[email protected]>

[FIX] fixed linux build

149d1d95aaa114e2cd0268fc0c3247085d8ffa1b authored over 10 years ago by Stephan Aiche <[email protected]>

[FIX] added missing include

bf199281100a3278e922e32cd5ab82178c5f988e authored over 10 years ago by Stephan Aiche <[email protected]>

[DOC,BUILD] added superhirn documentation to the doxygen system

* revised generation of doxygen search paths (now macro based and customisable by the individua...

73e3265e6abc5f4b5fe48028e24e2739df88bdd7 authored over 10 years ago by Stephan Aiche <[email protected]>

[BUILD,INTERNAL] moved superhirn code to separate lib

28a96051d82868051cc22859471ff0b64ea537fa authored over 10 years ago by Stephan Aiche <[email protected]>

[BUILD] moved all SH tests to separate test project

e64fbe200b62940ac04cdc09a46c2e97ce4a49e4 authored over 10 years ago by Stephan Aiche <[email protected]>

Merge pull request #760 from hroest/feature/spellcheck

[FIX-#618] fix spelling errors in headers

d4964614d954c4878b1310817c2f4af5ec334811 authored over 10 years ago by Hannes Roest <[email protected]>

Merge pull request #761 from hroest/feature/headerFixes

[FEATURE] moved ConsensusMap::convert into separate class to reduce coupling

68274e69864c85d1538191aee8ed689b042b948d authored over 10 years ago by Stephan Aiche <[email protected]>

[FIX-#618] fix spelling errors in headers

21cc7ec8b4115ec90e32da6f23d6939259ca860f authored over 10 years ago by Hannes Roest <[email protected]>

[FEATURE] move conversion of ConsensusMap to own class

- put conversion of ConsensusMap into helper class

60a2c97dd183a5fc1a047931f8f693eeb7bccecf authored over 10 years ago by Hannes Roest <[email protected]>

[FEATURE] forward declaration of Matrix

d5f2be3d0eb7814ee8abea903dc55d8c6ba302b9 authored over 10 years ago by Hannes Roest <[email protected]>

[BUILD,DOC] fixed some minor issues introduced with the GSL merge

cf34e8b8c3b1902c4fae24989f2acfd3c9ea5e31 authored over 10 years ago by Stephan Aiche <[email protected]>

unity build for GUI

3165f0450fe9dd4ad5395e6080570af7dd1a6328 authored over 10 years ago by Chris Bielow <[email protected]>

Merge pull request #651 from mcmenace/develop

[INTERNAL,API,FEATURE] removal of the GSL

1262e3d8523cce6cba17cc880062df50b672ddc1 authored over 10 years ago by Stephan Aiche <[email protected]>

fixes for linux and VS2013

b5a9d7a65171b0a728455646abed394818f0d2e3 authored over 10 years ago by Chris Bielow <[email protected]>

merge develop

24b922ed9502b3676a2f59ea653d16c62bc72e32 authored over 10 years ago by Chris Bielow <[email protected]>

fix attempt by omitting offending include

bbb6901a3376c7bff7dc37c3c15641ecf004a7b3 authored over 10 years ago by Chris Bielow <[email protected]>

enable unity build on OpenMS lib (this required some fixes for unclean variable names and solution for ambiguous classes (std::set vs seqan::set), compilation time on Windows is reduced to <10% (5min vs 45min) on Ultrabook

27c659b3be04faa0917da3eff67f6a1d53fdab49 authored over 10 years ago by Chris Bielow <[email protected]>

Merge pull request #755 from kreinert/shadowwarning

[FIX] fixed shadow warning

45455356482ce5ab35e32e445609b291ec78a6d6 authored over 10 years ago by Knut Reinert <[email protected]>

[FIX] fixed shadow warning

9a621615b98847bef5603bf5a05d615002ff3776 authored over 10 years ago by Knut Reinert <[email protected]>

[PYOPENMS] changed extra methods on MSSpectrum

get_peaks and set_peaks now return and receive different
precisions for mz and ii, so th...

97e6477e3d2b57881e651d17fc0bac7675bfddd5 authored over 10 years ago by Uwe Schmitt <[email protected]>

fixed shadow warning

de66185011803f7082e97f97e3f0640884dde9e0 authored over 10 years ago by Knut Reinert <[email protected]>

Merge branch 'fix-myrimatchadapter' into develop

7b58ce5fd34ba44a1f826d0069541d2c23ce1a3b authored over 10 years ago by Petra Gutenbrunner <[email protected]>

Merge pull request #752 from uweschmitt/feature/track_peptide_identifcation_base_name

[FIX] fixed missing adaption PeptideIdentification::empty()

03c649d3b09a56e77ab5d563fb1dc05220dd8a75 authored over 10 years ago by Hannes Roest <[email protected]>

[BUG-FIX #753] MyrimatchAdapter

process.start doesn't call the myrimatch. Replaced process.start with process.execute to fix the...

797a018b0db89e31866621a6bd72c48f022265de authored over 10 years ago by Petra Gutenbrunner <[email protected]>

[NOP] adapted formatting

a64f943c8dd138f077f094112a5e3c3dfa8eb6a9 authored over 10 years ago by Uwe Schmitt <[email protected]>

[FIX,TEST] adapted test for PeptideIdentifaction::empty

eb4369af1440c8062badf26cba30d4854d073067 authored over 10 years ago by Uwe Schmitt <[email protected]>

Merge branch 'develop' into feature/track_peptide_identifcation_base_name

7596ac2fa69cf8bf0a3199edb164fae7c984451f authored over 10 years ago by Uwe Schmitt <[email protected]>

[FIX] fixed missing adaption PeptideIdentification::empty()

last commit 8c2f86 missed apdation of method 'emtpy()'
to new introduced attribute base_...

8be6427a6d2e48e555c0ab0af6f2adf36bbdd7dc authored over 10 years ago by Uwe Schmitt <[email protected]>

new data structures for spectrum spline interpolation

bdefb601037c5ea7f9d17fe797c358b82d0c1216 authored over 10 years ago by lars20070 <[email protected]>

Merge pull request #751 from uweschmitt/feature/track_peptide_identifcation_base_name

[FEATURE] track base name when reading pep.xml files

1ecef0eb3603667e42b46bbe149aac4b7440a7e8 authored over 10 years ago by Hannes Roest <[email protected]>

[FEATURE] track base name when reading pep.xml files

PeptideIdentifcation has a new attribute base_name_ including the
corresponding accessor...

8c2f86282d433d5e25f886760083d8fe74bd856f authored over 10 years ago by Uwe Schmitt <[email protected]>

Merge pull request #747 from cbielow/search_stats

Speedup OMSSA-XML parsing and some stats for OMSSA&XTandem

15771241f26dfc971cc33a0afcd25e03c8cb7a95 authored over 10 years ago by Hannes Roest <[email protected]>

[PYOPENMS,FIX] fixed streampos->long conversion

83809e5fe81e93c7c5810b4ebb61af6844c49c35 authored over 10 years ago by Uwe Schmitt <[email protected]>

fixed real-doublereal issue

c8a12f1e16eb8732a780e5af4363a61479cbb7e2 authored over 10 years ago by Chris Bielow <[email protected]>

Merge remote-tracking branch 'origin/develop' into gsl-removal

Conflicts:
src/openms/source/TRANSFORMATIONS/RAW2PEAK/OptimizePick.cpp

57958993581d8a13a35d8d8b97d92ee1b86c06c5 authored over 10 years ago by Hans-Christian Ehrlich <[email protected]>

fixed copy&paste error; some minor optimizations

55409d9278962ce4caceff18b94106d759a8b153 authored over 10 years ago by Chris Bielow <[email protected]>

[FIX] fixed compilation error on vs2013

fb5a17b5e0f46c293007079ae89982b137de0ae8 authored over 10 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #734 from OpenMS/feature/more_pyopenms_improvements

Feature/more pyopenms improvements

e1af900a899ef422fc60de5e7c76712a1179ca4a authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] fixed MRMDecoy.pxd

68b082e42e9da3531e618b95156483019f645c35 authored over 10 years ago by Uwe Schmitt <[email protected]>

[BUILD] use consistent file names for test files

810cffb45ea5411a325a3ec3880740e7384ad462 authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] fixes for Python 2.6

924af0eb8dc7d7d97ad34bc998feeda5c6e8e920 authored over 10 years ago by Hannes Roest <[email protected]>

[PYOPENMS, FIX] fixed import path in pxds/RichPeak1D.pxd

ade326fc262f7d8706b64c749c322cdcfc113db0 authored over 10 years ago by Uwe Schmitt <[email protected]>

[PYOPENMS] better error message for MzMLFile.transform

059b882c48f11ef17a0c723a3cce16b8cb3761e7 authored over 10 years ago by Uwe Schmitt <[email protected]>

[PYOPENMS,FIX] added missing test_MzMlDecoder.py to pyopenms.cmake

Conflicts:

pyOpenMS/pyopenms.cmake

0121dc835db61df11d1a1cc011919c6d7d898332 authored over 10 years ago by Uwe Schmitt <[email protected]>

[PYOPENMS] added conversion streampos -> Python long

90069790484f3efcbf39a312d019f9f2030e1b91 authored over 10 years ago by Uwe Schmitt <[email protected]>

[FIX] missing include

4385eda094578f5c7e01b5c3a2b45a737ccac09c authored over 10 years ago by Hannes Roest <[email protected]>

[PYOPENMS,FIX] fixed wrapping of IndexedMzMLDecoder

Conflicts:

pyOpenMS/pxds/IndexedMzMLDecoder.pxd

1481d91d58a1f57435d4264c56c5f47ae5d62460 authored over 10 years ago by Uwe Schmitt <[email protected]>

Merge pull request #743 from timosachsenberg/feature/vs2013_compile_fix

[FIX] fixed compilation error on vs2013

bc15778499ca7fd56bde189ce721216613ceb59a authored over 10 years ago by Hannes Roest <[email protected]>

OMSSA-xml parsing speed +20%; some statistics after OMSSA & XTandem finished search (#identified spectra); some cleanup

d53e8de3041d6c15005195b0b3f0926ae625f915 authored over 10 years ago by Chris Bielow <[email protected]>

Merge pull request #741 from cbielow/proteinresolver_mem

[FIX] ProteinResolver switch from recursive to iterative to avoid stack overflow

59653288ecefccc882cd1e1ad4323fcbc6b30e0a authored over 10 years ago by Stephan Aiche <[email protected]>

[FIX #740] Fixed bug in IDPosteriorErrorProbability.cpp

Codereview: replace tabs with spaces, changed comments

modified: ../src/topp/IDPosteriorError...

d468c85c60dfadb6c9e299544d237f0bacd473cc authored over 10 years ago by Petra Gutenbrunner <[email protected]>

Merge pull request #742 from cbielow/svn_clean

[DOC] removed svn occurrences from documentation

01e8b273d2f5efc98100eae3047605931f00e073 authored over 10 years ago by Stephan Aiche <[email protected]>

[INTERNAL] resolved merge conflicts

ef9e6684be4959f909d7b364fd521ce395e3976a authored over 10 years ago by Hans-Christian Ehrlich <[email protected]>

minor fix

2c65b79f53d8451bad26e180fe49e108bebc0c02 authored over 10 years ago by Chris Bielow <[email protected]>

more cleanup

0130363cd849b3ff121f08f26957151dfc3d176a authored over 10 years ago by Chris Bielow <[email protected]>

removed sourceforge and 'svn' references where possible; in addition, we should redirect http://open-ms.sourceforge.net/schemas to github (using Wordpress interface)

0e1e5e2a3ecf7d2daec1f702de3346bc853c0d19 authored over 10 years ago by Chris Bielow <[email protected]>

[TEST #740] testing changes of bugfix for IDPosteriorErrorProbability

Extended ...Mascot_input, ...Mascot_input2 with PeptideIdentification. It includes a PeptideHit ...

dfb9e87b737a26432d77f53434f00a77a07c1240 authored over 10 years ago by Petra Gutenbrunner <[email protected]>

proper status message, small fix

08c892afaf5087140680c1d42165dd49849b6278 authored over 10 years ago by Chris Bielow <[email protected]>

replace recursive connected components in ProteinResolver with Queue to avoid stack overflow which occurs even for medium sized tasks

a95b8ad12b8e7e2c2e87e1694922bc6636003054 authored over 10 years ago by Chris Bielow <[email protected]>

[FIX-#740] Fixed bug in IDPosteriorErrorProbability.cpp

Peptide with score 0 (e-value 10^99) will be ignored in the model testing and fitting. If the sc...

6b6b0a3523f0bc26e73d8968e29dffee56183d50 authored over 10 years ago by Petra Gutenbrunner <[email protected]>

Merge pull request #739 from timosachsenberg/feature/uids_fileconverter

Feature/uids fileconverter

d5099bf32764d935246cf9e22ee6c337699aab7e authored over 10 years ago by Hannes Roest <[email protected]>

[FEATURE] added option to keep, ensure or reassign UIDs during conversion

[NOP] removed debug code

[NOP] fixed style

7b98e591808e96698c6c17d832131f83b6a51608 authored over 10 years ago by Timo Sachsenberg <[email protected]>

[FIX] fixed win compile issue introduced in #721

ec7bbfbed11a7da757def9c21f3313c052dd5e10 authored over 10 years ago by Stephan Aiche <[email protected]>

Merge pull request #737 from aiche/feature/fix-736

[FIX] several minor fixes

800306f10adbafa673c08865a7cea3d89708b570 authored over 10 years ago by Hannes Roest <[email protected]>

Merge pull request #711 from aiche/feature/fix-install-target

[FEATURE,BUILD] fix install target

850992123abb223e8d88cf8981173b9b03d0b0bb authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] fixed SVMData win compile issue introduced in #721

ce148193261c20a3307e94acf5c95aa120a4297c authored over 10 years ago by Stephan Aiche <[email protected]>

[FIX] fixed compile issue in TOPPDocumenter (introduced in #721)

3db001fd7a5cba869f3fbd19340859c1b3c681c8 authored over 10 years ago by Stephan Aiche <[email protected]>

[NOP,DOC] fixed some checker warnings introduced with #721

1680fd367a28590c7f989cc139695d75eef55022 authored over 10 years ago by Stephan Aiche <[email protected]>

[NOP] renamed PrecissionWrapper -> PrecisionWrapper

08660e563c9b52d825c0e53f20a1aec733a0be53 authored over 10 years ago by Stephan Aiche <[email protected]>

[NOP] added missing new-line at end of file

6589a234bce9ed6b1ba498a8baca453f9e8e1213 authored over 10 years ago by Stephan Aiche <[email protected]>

[NOP,DOC] fixed minor documentation issue and updated FAQ

f58bc2a3902b27162bf02637ed52360d0816a80b authored over 10 years ago by Stephan Aiche <[email protected]>

Update feature/fix-install-target with recent changes from develop

3249dc4f8f5f7523e4e6059b4b315d9d150aa77d authored over 10 years ago by Stephan Aiche <[email protected]>

Merge pull request #735 from aiche/feature/clang-warning-level

[FEATURE] clang warning level

6f0715e196db4e966429ddb3ddc0b6c033b0837b authored over 10 years ago by Hannes Roest <[email protected]>

Merge pull request #726 from cbielow/IDPEP++

IDPosteriorErrorProbability fixes

cb7e83044227bd3d4527f6523f199d65d1095020 authored over 10 years ago by Stephan Aiche <[email protected]>

[FIX] amend previous commit

7054c8f8c648ea7e34cd16450fdb78ccd697feb7 authored over 10 years ago by Hannes Roest <[email protected]>

[FIX,NOP] fixed all the -Wextra-semi warnings reported by clang

d2df2428a8028bb297a0f7340fd66021cd1dbcaa authored over 10 years ago by Stephan Aiche <[email protected]>

added missing include

925ad59e45e2a84058a8202cf702ce032a63b5b6 authored over 10 years ago by Chris Bielow <[email protected]>