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

[FIX] use 'sigma' instead of 'sigmasquare' in model fitting, to avoid negative estimates for 'sigmasquare'

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@12074 6adb6e08-d915-0410-...

de3e9c3053e7c12554abb5fdc9adf0e37f92192c authored almost 11 years ago by Hendrik Weisser <[email protected]>

[FEATURE] add multiple new files to pyOpenMS

- provide separate names for OpenSwath Interfaces and OpenMS Interfaces
- wrap MSDataWritingCons...

ba8d35935dc39c266432d6d9d09be6b402b40ed4 authored almost 11 years ago by Hannes Roest <[email protected]>

[FEATURE] add option to validate any XML

- adopt SemanticValidator and XMLValidator to also allow a generic .xml
file for validation
- ...

c72c267a5ba2e8d5503cccb82c734de5291eb00e authored almost 11 years ago by Hannes Roest <[email protected]>

[INTERNAL] fixes suggested by cppcheck

- cppcheck fixes
- build fixes (forgotten OPENMS_DLLAPI)

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

50b17278c61682a690d3470bdd3ac9b2afd69058 authored almost 11 years ago by Hannes Roest <[email protected]>

[FIX] compile error introduced in r12040

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@12070 6adb6e08-d915-0410-...

4643805d9f86db316dd9a6e49b00a10758f8c2a8 authored almost 11 years ago by Chris Bielow <[email protected]>

[NOP] updated comment to reflect change in r12063

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@12069 6adb6e08-d915-0410-...

7e1c42ffb940d4fcebb0a2314d03b202dc762a0a authored almost 11 years ago by Hendrik Weisser <[email protected]>

[INTERNAL] fix checker warnings

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@12066 6adb6e08-d915-0410-...

18c86da3231b37b0a72e2260e7ee4dab2e76af08 authored almost 11 years ago by Hannes Roest <[email protected]>

[FIX] MetaboliteSpectralDB.mzML removed from repository; for now, this renders MetaboliteSpectralMatcher non-functional

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@12065 6adb6e08-d915-0410-...

20fc33eacddb9014fccae863dbe45c4155650be8 authored almost 11 years ago by Erhan Kenar <[email protected]>

[FIX] new parameter defaults for MyriMatch-Adapter, since current versions of MyriMatch complain about certain parameter combinations

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@12064 6adb6e08-d915-0410-...

46c8b59193b8a1e7138c0d9fad1368ff9758fda5 authored almost 11 years ago by Chris Bielow <[email protected]>

[FIX] Windows compile error: templates belong into Header files....

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@12063 6adb6e08-d915-0410-...

9db0e014087b9d3b4a7568f93f69529f245667b4 authored almost 11 years ago by Chris Bielow <[email protected]>

[INTERNAL] Refactor MRMFeatureFinderScoring

- move code to OpenSwathScoring
- add documentation

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

aafd5880afbf3d1590ac465de96e08b12b2c75df authored almost 11 years ago by Hannes Roest <[email protected]>

[TEST] add test for OpenSwathWorkflow

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@12061 6adb6e08-d915-0410-...

d45aeca5c4cb0d12ca8d563d70ced66b4539624e authored almost 11 years ago by Hannes Roest <[email protected]>

[FIX-#639] forgotten changes

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@12060 6adb6e08-d915-0410-...

5e2a4b4e48bde1b52784e8f57aa4f782c44f24c4 authored almost 11 years ago by Hannes Roest <[email protected]>

[TEST-#639] fix tests after code changes

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@12059 6adb6e08-d915-0410-...

b9b3fc0d7f71f0f8ee3c051e46a8e75f015ee664 authored almost 11 years ago by Hannes Roest <[email protected]>

[FIX-#639] fix MzXMLHandler: interprets IsolationWindow wrongly

- the windowWideness parameter in mzXML gets converted to the CV Terms
1000827-29 in a way tha...

e7e5e659350861667785fd0a0609d85604e0c09c authored almost 11 years ago by Hannes Roest <[email protected]>

[NOP] cleanup for checker script

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@12057 6adb6e08-d915-0410-...

da0fc7dd23678d0299555cee6bc5be36b33e1359 authored almost 11 years ago by Hannes Roest <[email protected]>

[FIX,PYOPENMS] fix pyOpenMS - ModificationDefinitionsSet (removed method)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@12056 6adb6e08-d915-0410-...

d75b2b81dbbc46094258f7133fb979fe1643613b authored almost 11 years ago by Hannes Roest <[email protected]>

[FIX] update DataValue to work with pyOpenMS again

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@12055 6adb6e08-d915-0410-...

bc3991fe01efc09e90f6b152b176826bf52442a6 authored almost 11 years ago by Hannes Roest <[email protected]>

[FIX,PYOPENMS] fix pyOpenMS after removal of lists

- replace StringList, DoubleList and IntList with their
std::vector equivalents

git-svn-id: h...

1130da957f1a075b7e67e3e515b1b730081af36f authored almost 11 years ago by Hannes Roest <[email protected]>

[FIX] fixed win32 compile issues introduced with ListUtils replacing StringList::create

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@12052 6adb6e08-d915-0410-...

ddaaf9ea6d63bfb9fe793a4285f37a48ec4241a7 authored almost 11 years ago by Stephan Aiche <[email protected]>

[FIX] don't subtract baseline from mass traces; use new function name 'TraceFitter::getArea' (r12050)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@12051 6adb6e08-d915-0410-...

4cdf728f70489b7947a9ac3b1b8acc0bff7042d8 authored almost 11 years ago by Hendrik Weisser <[email protected]>

[API] renamed function to make clear what it does: TraceFitter::getFeatureIntensityContribution -> getArea

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@12050 6adb6e08-d915-0410-...

653f99698ae85196e157447e283e0c7263298bdf authored almost 11 years ago by Hendrik Weisser <[email protected]>

[FIX-#618] fix spelling errors across OpenMS header files

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@12049 6adb6e08-d915-0410-...

3591e338c31c55fe7a12ec324608db549cb64794 authored almost 11 years ago by Hannes Roest <[email protected]>

[TEST] add two tests

- add test for MSDataCachedConsumer
- add test for MSDataTransformingConsumer

git-svn-id: https...

4611c97b3f9ac1f6be6335b2d2bb253bd0911e6d authored almost 11 years ago by Hannes Roest <[email protected]>

[NOP,INTERNAL] cleanup for checker

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@12047 6adb6e08-d915-0410-...

96c5e85d63d3c677c19f9319c32348d12e3c9b6b authored almost 11 years ago by Hannes Roest <[email protected]>

[FEATURE-#637] XML parsing: optimize also for decoder

- switch in MzMLSpectrumDecoder to StringManager to get access to faster
parsing as well

git-...

69a7c8454f426fcda26ec9816315c6dba8d8a15d authored almost 11 years ago by Hannes Roest <[email protected]>

[FEATURE-#637] XML parsing: optimize ASCII (base64) parsing

- provide new implementation for conversion in StringManager (only ASCII
strings will be conve...

765b54c638771c4de3ca7a203136a32392f353a9 authored almost 11 years ago by Hannes Roest <[email protected]>

[INTERNAL] removed wrapper and replaced it with template specialisation of create

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@12044 6adb6e08-d915-0410-...

c3a9304f70acfee1f8a87443173c13a433950b83 authored almost 11 years ago by Stephan Aiche <[email protected]>

[INTERNAL,NOP,TEST] added missing C file and moved _create functions to OpenMS::Internal namespace

* fixed checker warnings in StringListUtils_test
* fixed some spelling errors
* updated and e...

f3e2f9c33815450a3c9c5a381ead1fcb846ceb20 authored almost 11 years ago by Stephan Aiche <[email protected]>

[API,INTERNAL] renamed StringList file to StringListUtils

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@12042 6adb6e08-d915-0410-...

ba006770f75562df1cfc16d8fbd9063679f7324b authored almost 11 years ago by Stephan Aiche <[email protected]>

[INTERNAL] moved typedefs from Types.h to ListUtils.h

* some code cleanups

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@12...

ff2c717e9eca7ad360382e19192133c18c19ec23 authored almost 11 years ago by Stephan Aiche <[email protected]>

[INTERNAL,API] replaced static member of StringList with ListUtils functions and made StringList

* StringList member functions are now static utils methods
* replaced StringList class with ty...

9e1468bf972015ff2464f4d586713236d80fd414 authored almost 11 years ago by Stephan Aiche <[email protected]>

[INTERNAL,API] replaced DoubleList’s contains and create with the ListUtils version and replaced DoubleList class with std::vector typedef

* switched part of StringList code also to ListUtils

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

a1f2f38da80c88c7a65326f3c288c85be3867fe9 authored almost 11 years ago by Stephan Aiche <[email protected]>

[INTERNAL,API] replaced IntList’s contains and create with the ListUtils version and replaced IntList class with std::vector typedef

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@12038 6adb6e08-d915-0410-...

df9ea4047b2644730475aa67ceb0f62b87d3d523 authored almost 11 years ago by Stephan Aiche <[email protected]>

[FEATURE,TEST] added ListUtils class that bundles the functionality of IntList, StringList, and DoubleList

* currently supported are create, contains, and concatenate

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

3435981a737c3785b3e35fa9946ef235d0276409 authored almost 11 years ago by Stephan Aiche <[email protected]>

[INTERNAL] refactoring code

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@12036 6adb6e08-d915-0410-...

5812448afe89ab998641bf8cac7979d6d475c0ca authored almost 11 years ago by Hannes Roest <[email protected]>

[TEST] TSV to TraML: added tests

- test the different interpretations of the retention time

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

06015cf82d436a1d32c6094031abdd664be531ed authored almost 11 years ago by Hannes Roest <[email protected]>

[FEATURE] TSV to TraML: allow to specify how the RT is interpreted

- the retention time given in the CSV file can mean different things and
its interpretation ca...

e22295f9bead58dabc26dc8ebc81a497e6d729f2 authored almost 11 years ago by Hannes Roest <[email protected]>

[FIX] enable consistent ordering of the Swath Maps

- maintain the same ordering as the input files even in a parallel
environment

git-svn-id: ht...

1919a1145d37c16cc789ea4bda24d0eb8953d53b authored almost 11 years ago by Hannes Roest <[email protected]>

[FIX] fixes errors introduced in [12029]; the moc problem seems to affect only mac os x

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@12032 6adb6e08-d915-0410-...

9fa28a2cbe8dccbb4cf68e0543b0e1a6940c80e6 authored almost 11 years ago by Stephan Aiche <[email protected]>

[DOC] update documentation, allow additional header

- update documentation about input file for TraML conversion
- allow CollisionEnergy as well as ...

77ff2bcdd34684702b1d6eeaae8ed2bb0e592f05 authored almost 11 years ago by Hannes Roest <[email protected]>

[FIX] added missing file restrictions to AccurateMassSearch

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@12030 6adb6e08-d915-0410-...

dc9575f351ed67004b31a505c9cd4bdffc78ff38 authored almost 11 years ago by Stephan Aiche <[email protected]>

[FIX,BUILD] workaround for a bug in qt’s moc compiler

* see https://bugreports.qt-project.org/browse/QTBUG-22829 for details on the bug
* affects bo...

c908820cd50a7156461da5c0346cfd7a0e854f4f authored almost 11 years ago by Stephan Aiche <[email protected]>

[FIX,INTERNAL] added missing MetaboliteSpectralMatcher to tool handler

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@12028 6adb6e08-d915-0410-...

4acbdf5c3edf55c171c941e9b55ddc6e0d6c49bd authored almost 11 years ago by Stephan Aiche <[email protected]>

[FIX] Fixed some minor bugs in MetaboliteSpectralMatcher

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@12027 6adb6e08-d915-0410-...

49027f11e6d1e13984d6b000f6f7352e8962d5f5 authored almost 11 years ago by Erhan Kenar <[email protected]>

[FIX,TEST] more accurate calculation of peak area

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@12026 6adb6e08-d915-0410-...

eca6bcc7d22b84b691015cd8f2e13419d27c3f65 authored almost 11 years ago by Hendrik Weisser <[email protected]>

[FEATURE] MetaboliteSpectralMatcher now with MzTab export; MetaboliteSpectralDB.mzML was overhauled (now contains ~28.000 fragment spectra)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@12025 6adb6e08-d915-0410-...

1d71712e982478c668e22a36594d6e81e4650237 authored almost 11 years ago by Erhan Kenar <[email protected]>

[NOP] added explanatory comment

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@12024 6adb6e08-d915-0410-...

207a2f394e708c592c5c1ece41e40c1d4bdc1537 authored almost 11 years ago by Hendrik Weisser <[email protected]>

[FEATURE,PARAM] added option to fit elution models (Gauss or EGH) to features - but not yet used for quantification/scoring

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@12023 6adb6e08-d915-0410-...

3259ecfa478d8fd1debf1c90844af6bfeac0d8ce authored almost 11 years ago by Hendrik Weisser <[email protected]>

[FIX] actually read the parameters that are passed

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@12022 6adb6e08-d915-0410-...

82777dd263d6c440a0a9481e93444c51cce789bc authored almost 11 years ago by Hendrik Weisser <[email protected]>

[FEATURE,PARAM,TEST] added option for weighted fitting (according to theoretical intensities of mass traces)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@12021 6adb6e08-d915-0410-...

e6578ee7aae5be86f0bcb7360bfc9f75b96bd0a1 authored almost 11 years ago by Hendrik Weisser <[email protected]>

[FIX] appendium to r11994: open file in binary mode

- opens files in binary mode to avoid unwanted line ending conversions
- potentially fix the Ind...

e2f948ff6b58d8c4795650805f4564228da2f88c authored almost 11 years ago by Hannes Roest <[email protected]>

[INTERNAL] cleanup code, change int to size_t

cleanup code and comments, change positive integer swath_nr into size_t

git-svn-id: https://ope...

6640db2f954628e8ef836e5af5d4452a819eb46d authored almost 11 years ago by Hannes Roest <[email protected]>

[DOC] updated and expanded Linux install doc

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@12018 6adb6e08-d915-0410-...

f55ddf9482abe16a6661ee68ed76d957e7ac97bd authored almost 11 years ago by Hannes Roest <[email protected]>

[TEST] fix Python test

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@12017 6adb6e08-d915-0410-...

a56a2b904160f862b6b9d701e4bf59b5477a1ddf authored almost 11 years ago by Hannes Roest <[email protected]>

[DEBUG] increase debug message verbosity

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@12016 6adb6e08-d915-0410-...

8f8da5f722ef68b2f9da05ce03d05c1d1898e58f authored almost 11 years ago by Hannes Roest <[email protected]>

[NOP] fix compiler warning

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@12015 6adb6e08-d915-0410-...

b3b2e12dfa2cca39d15fb97c95325dcf8f0ee874 authored almost 11 years ago by Hannes Roest <[email protected]>

[NOP] added two .desktop files (for Linux desktop)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@12014 6adb6e08-d915-0410-...

8de4649b7fe31e793324a73da8a5a65abf5e0341 authored almost 11 years ago by Hannes Roest <[email protected]>

[NOP] coding style fixes

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@12013 6adb6e08-d915-0410-...

b6b4a5dc1dbaa33845f2cbc19ea93b7f62615d54 authored almost 11 years ago by Hendrik Weisser <[email protected]>

[FIX] added missing tools to ToolHandler

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@12012 6adb6e08-d915-0410-...

947a4a54bccfd9443366e45dbfa24ab01cfda08b authored almost 11 years ago by Stephan Aiche <[email protected]>

[BUILD] try to fix build

- Win8 VS12 complained about overloaded + operator, try to use
OpenMS::String to reduce ambigu...

d4b25b37c0d1a0ab7edbf35f7e89d1394f040c16 authored almost 11 years ago by Hannes Roest <[email protected]>

[DEBUG] increase debug message verbosity

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@12010 6adb6e08-d915-0410-...

69801793a0881a9a661eebfa1469919c59f5b302 authored almost 11 years ago by Hannes Roest <[email protected]>

[TEST] reduce the workload of the SwathFile_test

we had timeouts of this test on the build servers, therefore try to
reduce the workload a bit an...

f73cdd464fbfe75f5b8b113a5366524a5ea8a9f9 authored almost 11 years ago by Hannes Roest <[email protected]>

[FEATURE] Add an option to FileInfo to check indexedmzML

- using the -i flag, the FileInfo executable will check whether a given
mzML contains valid in...

ff115f5ae11b5130af5af16e01c9f785552f9604 authored almost 11 years ago by Hannes Roest <[email protected]>

[INTERNAL,TEST] internal cleanup of MzMLSpectrumDecoder

- throw meaningful errors when encountering faulty input
- test different types of spectrum tags...

200ffb82ecd4c8cfdb07e2389073c09e9e6e28ab authored almost 11 years ago by Hannes Roest <[email protected]>

[TEST] change full spectra comparison (for easier debugging)

- testing TEST_EQUAL(spectrum == spectrum, true) produces less debug
output

git-svn-id: https...

cf2391ed9eb5dc7555c6e9c08727f0f68c08b4c4 authored almost 11 years ago by Hannes Roest <[email protected]>

[FIX] read defaultArrayLength in MzMLDecoder

- read the expected defaultArrayLength in the MzMLSpectrumDecoder to
prevent a warning in MzML...

5c3dc27a17f707cd6bf7256d6b9446a0b8709aa8 authored almost 11 years ago by Hannes Roest <[email protected]>

[DOC,API] improve doc, add const-correctness

- documentation improvement
- improved error reporting for IndexedMzMLDecode
- add const-correct...

7258db2ce3a409a358989cee1fe79ed1d9241344 authored almost 11 years ago by Hannes Roest <[email protected]>

[FIX] fix Python bindings

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@12003 6adb6e08-d915-0410-...

43f989c4eaefc4cd123289575fcf149bfebad6f9 authored almost 11 years ago by Hannes Roest <[email protected]>

[TEST] IndexedMzMLFileLoader_test: also check loading success

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@12002 6adb6e08-d915-0410-...

b5360404ddfd729a2a3fc90a465ee99f801ac635 authored almost 11 years ago by Hannes Roest <[email protected]>

[FIX] write the mzML index in the OpenSwathWorkflow

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@12001 6adb6e08-d915-0410-...

84fd3d5a853269cca4363651c8b4fef9cf4dc306 authored almost 11 years ago by Hannes Roest <[email protected]>

[FEATURE] MRMRTNormalizer: choose whether to use Chauvenets criterion

- allow to not use Chauvenets criterion, thus forcing the removal of
datapoints until the best...

c22cbbcc72f6c833a453cd6d73540485db891385 authored almost 11 years ago by Hannes Roest <[email protected]>

[FEATURE] (Re)added MetaboliteSpectralMatcher tool for further development

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11998 6adb6e08-d915-0410-...

6d84945d11335bcce3122050d95b6d18a90ebb0b authored almost 11 years ago by Erhan Kenar <[email protected]>

[NOP,FIX] fixed whitespace and a comment

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11997 6adb6e08-d915-0410-...

9e7e1a2adf422ebdb131d9ad4a0ecc2b5fb23c20 authored almost 11 years ago by Hendrik Weisser <[email protected]>

[FIX,DOC] small fix of parameter documentation

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11995 6adb6e08-d915-0410-...

c93b5630763590e9d4093daa648638b4f95e66c7 authored almost 11 years ago by Hendrik Weisser <[email protected]>

[FIX] XMLFile now opens files in binary mode to avoid unwanted line ending conversions

* indexed mzml file tests failed due to line ending conversions on win32 systems
* some doc cl...

636ac27917e61bc58086bdbc40d545e8a6b0de62 authored almost 11 years ago by Stephan Aiche <[email protected]>

[FIX]XTandemInfile_test_write.xml now reflects that cleavage site is written by default.

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11992 6adb6e08-d915-0410-...

446e401b1200fa457dddd0153e1adac5b42da2bc authored almost 11 years ago by Mathias Walzer <[email protected]>

[FIX] corrected qcml cv file (imports, remarks, ...)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11991 6adb6e08-d915-0410-...

497da7eb37fde0ee6bbb73304c430b7fcf1bd774 authored almost 11 years ago by Mathias Walzer <[email protected]>

[NOP] removed svn:executable property on share files

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11990 6adb6e08-d915-0410-...

f8aea293960d11689e31f74ec50761cd97630af2 authored almost 11 years ago by Stephan Aiche <[email protected]>

[FIX] fixed issue with wrong protein accessions when using 'add_to' option

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11989 6adb6e08-d915-0410-...

bdd12ac2d33b44752eb2044aec956ce4f6b12ee3 authored almost 11 years ago by Hendrik Weisser <[email protected]>

[FIX] second attempt to fix Visual Studio compile bug (see r11851, thanks to Hannes for suggestion)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11988 6adb6e08-d915-0410-...

5ddd44b937765a76c0ebf7e08c87250ee0b2db30 authored almost 11 years ago by Hendrik Weisser <[email protected]>

[FEATURE] added support for Jiri's SimTandem

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11987 6adb6e08-d915-0410...

796146bf6ab59f6771013cd86e70c55b1ecd9dab authored almost 11 years ago by Timo Sachsenberg <[email protected]>

[NOP,FIX] fixed a lot of cppling issues; mostly explicit c'tor

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11986 6adb6e08-d915-0410-...

ca826521f02512a7cf1dd387c202116c2b6a3e9e authored almost 11 years ago by Stephan Aiche <[email protected]>

[MERGE] merging changes from released 1.11.1 branch into trunk

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11985 6adb6e08-d915-0410-...

b10b9368f63ebf7cb7d169af2b969a0719b29ac1 authored almost 11 years ago by Stephan Aiche <[email protected]>

[FIX] fixes compile issue introduced in [11982]

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11984 6adb6e08-d915-0410...

dc48c65af5b32459e50ce463f5674142f1c6911c authored almost 11 years ago by Stephan Aiche <[email protected]>

[FIX] Workflow: fix tsv header, make more readable

- fix vat to var
- make the header writing more readable

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

fb4bea0c642ca2d566c59ab8ab5abcd7a633a8e7 authored almost 11 years ago by Hannes Roest <[email protected]>

[FIX] fix empty chromatogram issue

- empty chromatograms would create very bad scores and lead to an
exception in the RT normaliz...

3843f2fca501165b81abcd05c8466ec0f36fddaa authored almost 11 years ago by Hannes Roest <[email protected]>

[NOP] increase debug output

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11981 6adb6e08-d915-0410-...

f6442e17fd30344afded5d5ea3a20d2831f1ec36 authored almost 11 years ago by Hannes Roest <[email protected]>

[BUILD-#635] add option to specify doc path for cmake

- make it possible to configure a separate path for the documentation
- patch suggested by Filip...

e27416282bf54a8ead466d6cc3e642d6a5b4898d authored almost 11 years ago by Hannes Roest <[email protected]>

[FIX-#634] fixed cleavage site setting ignorance

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11979 6adb6e08-d915-0410-...

da7c9986cd257a1fb68c32a052d3e1e0f5c274c9 authored almost 11 years ago by Mathias Walzer <[email protected]>

[FIX-#633] ConsoleUtils::breakStrings_ checks for ' ' before calling String::suffix()

* updated changelog accordingly

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

6a515dd1e23882ec60578a289920bf46ca4f525d authored almost 11 years ago by Stephan Aiche <[email protected]>

[DOC] fix typos

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11975 6adb6e08-d915-0410-...

9ebd0d44c444aff605d9e5720615b87f41c0188b authored almost 11 years ago by Hannes Roest <[email protected]>

[FEATURE,IO] also write out elution model score, simplify CLI

- fix use_elution_model_score to be passed directly on the command line
- fix recalculate_peaks_...

fb036a5796f8a744a3753035231dd2dc65753f6d authored almost 11 years ago by Hannes Roest <[email protected]>

[NOP] fix compiler warning (endif stands by itself)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11973 6adb6e08-d915-0410-...

5832ed91558ad70dc9f466e7259a76140121a2fa authored almost 11 years ago by Hannes Roest <[email protected]>

[NOP] added 1.11.1 release also to CHANGELOG in trunk

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11972 6adb6e08-d915-0410...

112f8c9a18a06a5da621c6cdf922deb24062e11e authored almost 11 years ago by Johannes Veit <[email protected]>

[NOP] updated changelog in 1.11.1 branch

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11.1@11971 6a...

ecc5e1305ef5b93cd09bb2cbd1f3809f7ff6355c authored almost 11 years ago by Johannes Veit <[email protected]>

[FIX,BUILD,NOP] Merged 11843:11844 from trunk to release 1.11.1 branch

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11.1@11970 6a...

357c298009bda162162a7551eb30646a20e58076 authored almost 11 years ago by Johannes Veit <[email protected]>

[FIX] Merged 11791:11792 from trunk to release 1.11.1 branch

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11.1@11969 6a...

b2e652b4a8d2c988b9dcb197e4c7f4c324842b1f authored almost 11 years ago by Johannes Veit <[email protected]>

[FIX-#609] Merged 11757:11758 from trunk to release 1.11.1 branch

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11.1@11968 6a...

4257e0dd03accf5bfe5690e1196924296dabb25a authored almost 11 years ago by Johannes Veit <[email protected]>

[FIX-#614,TEST] Merged 11873:11874 from trunk to release 1.11.1 branch

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11.1@11967 6a...

0b1a7a1d11e9164ea0daaabce10606822700afc7 authored almost 11 years ago by Johannes Veit <[email protected]>