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

[FEATURE] add minimal peak width to peak picker

- peaks below the minimal width are not reported upon

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

65a5009db3636474736fff1e6596f4e7927c6675 authored over 11 years ago by Hannes Roest <[email protected]>

[INTERNAL] extract class PeakPickerMRM

- extract the MRM PeakPicker and leave as standalone class

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

0f6fe6132dc22e1add6fdf35f51713c8c85bcbc2 authored over 11 years ago by Hannes Roest <[email protected]>

[FEATURE] add option to detect and remove overlapping peaks during the peakpicking process

- add removeOverlappingPeaks_ which checks for overlapping peaks and
corrects them
- allow adj...

0ac6e9044e2de14b2c472d5c48deef8dfbd06a43 authored over 11 years ago by Hannes Roest <[email protected]>

[INTERNAL] MRMFeatureFinderScoring simplify

- remove ITransitionGroup from FeatureFinder (not necessary any more)
and all other classes us...

ffdab692f5af4da494069e875f09d190a8b04180 authored over 11 years ago by Hannes Roest <[email protected]>

[INTERNAL] MRMFeatureFinderScoring refactoring

Rework how the scoring is done:

- Use simple struct to hold scoring
- Create class SwathScorer ...

90272d7ba4b3a0cfeb8cd45316788334283b4fe0 authored over 11 years ago by Hannes Roest <[email protected]>

[TEST] add test for OpenSwathAnalyzer with trafoXML

- we have not tested using a trafoXML file so far, do this before
refactoring

git-svn-id: htt...

69bd6168a2d315742602ddba5f7b9a4e8ca34edb authored over 11 years ago by Hannes Roest <[email protected]>

[FEATURE,DOC,INTERNAL] OpenSwath::Scoring add functions

- rename methods in scoring
- add documentation
- add new functions for RootMeanSquareDeviation ...

f0932d83925cea10b4da3a8e47510335e0b3a633 authored over 11 years ago by Hannes Roest <[email protected]>

[DOC] improve documentation

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11493 6adb6e08-d915-0410-...

205d807f5d71db1c9fbc9ffd7490a05c8ba3a79d authored over 11 years ago by Hannes Roest <[email protected]>

[FIX] fixed erroneous iteration condition in QTClusterFinder leading to win32 test errors

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11492 6adb6...

53048d70f5e374479feb49c92db0424b5cf764a4 authored over 11 years ago by Stephan Aiche <[email protected]>

[FIX] added PeakPickerRapid to tool handler and made it a real util.

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11491 6adb...

8f18fe58e5b3070dcba7d56de343bc0a65d81657 authored over 11 years ago by Stephan Aiche <[email protected]>

added missing include

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11489 6adb6e08-d915-0410-...

c82df1f84571ed7bc9f482a53f02d8a60f63ea8a authored over 11 years ago by Christian <[email protected]>

[BUILD,FIX] updated xerces dll reference in knime package generation

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11486 6adb6...

a580282cb0f21d32e158fbc023ff226d1c5d2bfa authored over 11 years ago by Stephan Aiche <[email protected]>

[FIX] Added check to MassTraceExtractor/FeatureFinderMetabo tools if input spectra are sorted by m/z

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11485 6adb6...

469cd74382b085707e9f696ca2a241489dc8a8a9 authored over 11 years ago by Erhan Kenar <[email protected]>

[FIX] create better interface to write consensusXML

- user can now specify dirctly whether a featureXML or consensusXML
should be written (fixes r...

0013fecdc678256d84dc9ad4469035b564117a09 authored over 11 years ago by Hannes Roest <[email protected]>

[TEST,FIX] fix tests for ConfidenceScoring

- throw correct exceptions in the code if mapping was not successful
- test that the correct exc...

20ebae94ecfee8e7f13d2b5bd73d74bc2e5736d4 authored over 11 years ago by Hannes Roest <[email protected]>

[NOP,BUILD] added missing svn:keywords and some missing header to sources.cmake in ANALYSIS/OPENSWATH/

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11482 6adb6...

55feb98fc35627b5b82fab54dee08fb200d667f6 authored over 11 years ago by Stephan Aiche <[email protected]>

[FIX, DOC, API] renamed FeatureMap::swap_features_only to fit conventions and added RangeManager swap (for consistency)

* some missing/fixing tests for VersionInfo, EnzymaticDigestion, FeatureXMLFile

git-svn-id: htt...

169915dbb2e240b9b9e8f36a8bdae0d983cb9ce8 authored over 11 years ago by Chris Bielow <[email protected]>

[NOP] some style fixes

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11479 6adb6...

96ad18a96648fe5757d62d54d2e371d16443a379 authored over 11 years ago by Timo Sachsenberg <[email protected]>

[FIX] handling of last window in WindowMower

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11478 6adb6...

0cf4571ba18df7ddf283a72d8b33f80b84db245c authored over 11 years ago by Timo Sachsenberg <[email protected]>

[FIX,BUILD] fix pyOpenMS build after rename in r11463

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11477 6adb6...

9e1d8fbf79b9c977e3a1c057ddcf2aabb3f8b4c3 authored over 11 years ago by Hannes Roest <[email protected]>

[NOP] replaced tabs with spaces

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11476 6adb6...

c40b7549c86eeb877295fb87724b9ee8172d2ca8 authored over 11 years ago by Hendrik Weisser <[email protected]>

[NOP] replaced tabs with spaces

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11475 6adb6...

2cfaf2693a9c7f09ce05d1d6bf79bd0e98c9c6e9 authored over 11 years ago by Hendrik Weisser <[email protected]>

[FIX] fixed excessive error messages about ambiguously defined modifications

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11474 6adb6...

d4434e7a4fe9f9330c0c59234e43f2c529db8b59 authored over 11 years ago by Hendrik Weisser <[email protected]>

[NOP] official OpenMS 1.11 release branch

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11472 6adb...

735aeca5f502fe7e950a2a478aa5b8b1e6d998e4 authored over 11 years ago by Stephan Aiche <[email protected]>

[FIX] windows compile error

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11471 6adb6e08-d915-0410-...

ab42ca5bee7c7e207078f00075389c7b4d3353aa authored over 11 years ago by Chris Bielow <[email protected]>

[TEST] improved tests for spectral counting (rev. 11467)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11470 6adb6e08-d915-0410-...

6735f066f7e7c9cbcd580bda5d8f2c4b90fb965d authored over 11 years ago by Hendrik Weisser <[email protected]>

corrected indentation

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11469 6adb6e08-d915-0410-...

f1c61a4c469970d0bffffedf0d601608f08da0e8 authored over 11 years ago by Mathias Walzer <[email protected]>

fixed license header

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11468 6adb6e08-d915-0410-...

538bab3270f2e0eb6086e824bd1864196494750a authored over 11 years ago by Mathias Walzer <[email protected]>

[FEATURE,IO,TEST,DOC] added functionality for spectral counting (given idXML input) to ProteinQuantifier

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11467 6adb6e08-d915-0410-...

c7749f17df94d49e01fb1ccc0dffb6ed22353248 authored over 11 years ago by Hendrik Weisser <[email protected]>

[LOG] removed annoying debug output

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11466 6adb6e08-d915-0410-...

e406498660268f277961ef9818719ea2af2b1db0 authored over 11 years ago by Hendrik Weisser <[email protected]>

[FIX] Refactoring code in AccurateMassSearchEngine

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11465 6adb6e08-d915-0410-...

40ce5d51ded442ef484142a236c81492e778daa0 authored over 11 years ago by Erhan Kenar <[email protected]>

[FIX] Refactoring code in AccurateMassSearchEngine

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11464 6adb6e08-d915-0410-...

eb29e5a145156865f8e1f0e6f5c20b399805b1d8 authored over 11 years ago by Erhan Kenar <[email protected]>

restructured QCtools - not extensively tested yet

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11463 6adb6e08-d915-0410-...

bda642b5773fd3ec62242db4bfdfe1bb69a2809b authored over 11 years ago by Mathias Walzer <[email protected]>

[FIX-#556] fixed bug which prevents storing of ParamEditor values if the last param edited was anything other than a simple QLineEdit (i.e. a dropdown, file selection dialog)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11462 6adb6e08-d915-0410-...

4fa59255383ec1c104eef3fa5630a7552f1e67f0 authored over 11 years ago by Chris Bielow <[email protected]>

[TEST] add ConfidenceScoring test

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11459 6adb6e08-d915-0410-...

4e09101ef6f66e6738e8b8faee5cf6c9552bae9a authored over 11 years ago by Hannes Roest <[email protected]>

[NOP] changes to license / maintainers

- updated copyright/license header to 2013
- consistent maintainers
- guards

git-svn-id: https:...

559177518a3293b5401f12cbe40a6ea01134a6fd authored over 11 years ago by Hannes Roest <[email protected]>

[FIX-554] amend to r11438

Do not load the reference map twice but store the important information
temporary and later add ...

2f71e170e5215ab74914e44fa745b3ae68314a31 authored over 11 years ago by Hannes Roest <[email protected]>

[FIX-554] FeatureFinderUnlinkedQT Performance increase

significant speedup of 5x to 8x was observed by implementing

- a lookup table which contains th...

880edcfb387348deb1c43fe5e385d2d0431c3bbc authored over 11 years ago by Hannes Roest <[email protected]>

[FIX-554] FeatureFinderUnlinkedQT Performance increase

the clustering shows performance benefits with this change:

- instead of sorting the list each ...

3c206076375ffeebc544fb9ffc7522e7b4f2c9ba authored over 11 years ago by Hannes Roest <[email protected]>

[INTERNAL] add comments

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11453 6adb6e08-d915-0410-...

12f6711ae80018c0719241a9022eb84a2b4f2b03 authored over 11 years ago by Hannes Roest <[email protected]>

[FIX] Results reporting was faulty if the input featureXML originated from other sources than FeatureFinderMetabo.

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11452 6adb6e08-d915-0410-...

05ce4953ba1f565b8f958d28b30676804d2dc896 authored over 11 years ago by Erhan Kenar <[email protected]>

[FEATURE] Added MetaboliteSpectralMatcher to ANALYIS/ID

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11451 6adb6e08-d915-0410-...

89be6f74c37424009957d93d214074c0be8cee85 authored over 11 years ago by Erhan Kenar <[email protected]>

[NOP] Whitespace changes to fix cpplint warnings

- replace all tabs with spaces
- add space between if/for and bracket

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

5641425d8be9eebb21328e98a0ac4d53fe56de89 authored over 11 years ago by Hannes Roest <[email protected]>

[IO] turned 'mz_file' into an 'input file' parameter to ease use of IDFileConverter in TOPPAS

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11449 6adb6e08-d915-0410-...

980e65f1c4ceca8de3a49f90e2976f8ff85edb38 authored over 11 years ago by Hendrik Weisser <[email protected]>

[FORMAT,TEST] enable parsing of pepXML files exported from Mascot

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11448 6adb6e08-d915-0410-...

1cbbc62ecbf11f41885569f27224da970e064358 authored over 11 years ago by Hendrik Weisser <[email protected]>

[BUILD] made boost's search for static-only libs optional to support linking against shared libs on windows systems

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11447 6adb6e08-d915-0410-...

35abbe5068af3cefb20eacc462053d1e102192ab authored over 11 years ago by Stephan Aiche <[email protected]>

[TEST] set regex parameter in .ini file to avoid CMake warning (reported by Hannes)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11446 6adb6e08-d915-0410-...

da64c12328276b66acac0e09f6beffd47d7e7e7c authored over 11 years ago by Hendrik Weisser <[email protected]>

[FEATURE] allow MassTraceExtractor to write out full MassTraces into consensusXML

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11444 6adb6e08-d915-0410-...

2c74153ea6b35404af6dc25af6d577b8b18bf4f6 authored over 11 years ago by Hannes Roest <[email protected]>

[INTERNAL] CachedMzML

- allow inheritance
- const-correctness for writeSpectrum_

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

4b75c137e930dd2ee7eef971324a941f662bd961 authored over 11 years ago by Hannes Roest <[email protected]>

[INTERNAL] separate MzML Handler writeTo into individual functions

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11440 6adb6e08-d915-0410-...

7227c22f24054b27ab4c37fdb38d212cc2a19723 authored over 11 years ago by Hannes Roest <[email protected]>

[INTERNAL] Provide the same reserve interface for Spectra/Chromatograms

- The user can now specify in which vector he wants to reserve space
- calling reserve() on the ...

be27b9876c4f32fb5e0fbe8266daecc5ad682283 authored over 11 years ago by Hannes Roest <[email protected]>

[FIX-XXX] Decrease memory footprint of FeatureLinkerUnlabeled

apply the same improvements made to MapAlignerPoseClustering in r9805
also to FeatureLinkerUnlab...

c5daad7b98dc4eb722cabd6ddc19a13bf9e0a016 authored over 11 years ago by Hannes Roest <[email protected]>

[BUILD] extended search names for libsvm for upcoming changes of contrib libsvm

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11437 6adb6e08-d915-0410-...

7fac3ae762eb77c865aef939ff2dd4759a0d4d55 authored over 11 years ago by Stephan Aiche <[email protected]>

[REVERT] revert 11435, un-revert 11434 (contrib needs to be rebuilt\!)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11436 6adb6e08-d915-0410-...

7e345aae34e05f1ce5b4458801d62775bb7e7360 authored over 11 years ago by Hendrik Weisser <[email protected]>

[REVERT] revert 11434

patch breaks build on all test machines

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

d68aebb267d0bba6e4f1bca58ebff5ccd39fdc30 authored over 11 years ago by Hannes Roest <[email protected]>

[FIX-#549,BUILD,PARAM,TEST,DOC] more general solution for extracting RTs from Mascot XML files based on regular expressions, with tests and improved documentation

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11434 6adb6e08-d915-0410-...

acddcdf211225c6c230c8e5cb400549ccd73906f authored over 11 years ago by Hendrik Weisser <[email protected]>

[FIX] Added upper bound for mass trace length as a parameter for mass trace detection

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11433 6adb6e08-d915-0410-...

4aa78cd6163303943222cd9e7e03e923fa3d4838 authored over 11 years ago by Erhan Kenar <[email protected]>

[FIX-#553] fixed TOPPView's Apply TOPP tool functionality

* TOPPView now uses the File::findExecutable method to find the correct TOPP executable
* QPr...

a07d2bf6a53ce00b79a884f8a163cb6ea9a88d18 authored over 11 years ago by Stephan Aiche <[email protected]>

[NOP] change licence statement to BSD in GUI

- remove old licence from ./source

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

c27e73dd2b7166d9377eb0ebbed597f1087ea0e7 authored over 11 years ago by Hannes Roest <[email protected]>

[INTERNAL,FIX-#517] move pick function to header

- since it is a templated function, it should reside in the header file

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

517c3874d429225cd673f3877f89fb959f6bb73f authored over 11 years ago by Hannes Roest <[email protected]>

[NOP] fix typos in CMAKE files

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11429 6adb6e08-d915-0410-...

13bd283aab1c505f61a80eb3ce32aec34acf7d39 authored over 11 years ago by Hannes Roest <[email protected]>

[BUILD-#552] add pyOpenMS to the default target (if it is enabled)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11428 6adb6e08-d915-0410-...

a6e809681e6a1ba8aac0038d239f736e23a78975 authored over 11 years ago by Hannes Roest <[email protected]>

[INTERNAL,FIX-517] removed not implemented functions from API

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11427 6adb6e08-d915-0410-...

707b0530f21e9e4ff6e67691e2bfa22b73e25079 authored over 11 years ago by Hannes Roest <[email protected]>

[FIX] fixed false slot connection of TOPP tool exec in TOPPView

The slot must be created before the start method is called. used to be after.

git-svn-id: http...

9e1f8fde62b2f4accd23f02a8325b1c7e2f03f36 authored over 11 years ago by Christian <[email protected]>

[FIX] removed unnecessary if(test_mode_) code from FileMerger, FileConverter, and PrecursorMassCorrector as we can handle the file location in the TOPP test using FuzzyDiff's -whitelist

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11425 6adb6e08-d915-0410-...

52ce6f30feee56acb9cf476bc18229b717e58c10 authored over 11 years ago by Stephan Aiche <[email protected]>

[INTERNAL] check for errors in the spectrum before appending

- Remove call to getSpectra() since this code does not really need to
access a full spectrum l...

2854781a1f0698440ed8c5510512136d021312ab authored over 11 years ago by Hannes Roest <[email protected]>

[INTERNAL] Partial revert of r11400 (affecting FIX-#420)

- currently some tests trigger this exception -> we first need to
investigate the root cause o...

b4e9ac0d0f68bf87444786b6eb36ef747d9d2d9b authored over 11 years ago by Hannes Roest <[email protected]>

[DOC] fixed some grammar issue

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11422 6adb6e08-d915-0410-...

a431ee6a3808f35c20de42f9e0567b4f205c2608 authored over 11 years ago by Chris Bielow <[email protected]>

[NOP,FIX] added missing svn keyword to FileHandler_test

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11421 6adb6e08-d915-0410-...

0dec54a50bd4ba16570e0f5f392f02d33edcee3f authored over 11 years ago by Stephan Aiche <[email protected]>

[FIX] fixed checker problem in FileHander_test

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11420 6adb6e08-d915-0410-...

b31db7535ec8057a5f69c7f2ceb7ca12f3f032c1 authored over 11 years ago by Stephan Aiche <[email protected]>

[FIX-549,TEST] fixed extraction of RT info for Mascot results, added test case

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11419 6adb6e08-d915-0410-...

62de8e1d77761897e58f9750f216e5c3e92542c6 authored over 11 years ago by Hendrik Weisser <[email protected]>

[FIX] removed tutorial tests from style test mode and fixed some cpplint issues (mostly tabs)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11418 6adb6e08-d915-0410-...

f24b52f3c24cea7cd877eb9ee05c4af733642839 authored over 11 years ago by Stephan Aiche <[email protected]>

[FIX-#549] (partial fix) better error message in TOPPView for idXML without RTs

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11417 6adb6e08-d915-0410-...

b2fd1752f0465172479d8d5e26aa637c010bf3c6 authored over 11 years ago by Hendrik Weisser <[email protected]>

[DOC,FIX-#550] fixed documentation in several TOPP tools w.r.t. to doxygen 1.8

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11416 6adb6e08-d915-0410-...

cd66cba00b2f4c321355cefc1157aced985284b9 authored over 11 years ago by Stephan Aiche <[email protected]>

[FIX] corrected error message

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11415 6adb6e08-d915-0410-...

f951cccc633c073659657a8d762eca29939be035 authored over 11 years ago by Hendrik Weisser <[email protected]>

[FIX, TEST] PrecursorMassCorrector fixed

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11414 6adb6e08-d915-0410-...

457edc89ac868f4c520f9b6fbd5ed31ccd9bda33 authored over 11 years ago by Chris Bielow <[email protected]>

[FIX] fixed clang compile error introduced in [11403] due to missing typename

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11413 6adb6e08-d915-0410-...

141e54803ab0d0595b759de3a0a94c73fe67e57d authored over 11 years ago by Stephan Aiche <[email protected]>

[FIX-#309] FileHandler now computes SHA-1 hashes of the source file when loading experiments

* adapted test files to SHA1 hashes
* uncrustified FileHandler/SourceFile
* made myself maint...

d0c7c3fff30243403082c975d28cb01a4de79ae4 authored over 11 years ago by Stephan Aiche <[email protected]>

[FIX] switched to Constants::PI instead of M_PI to avoid redefinition warning

* uncrustified PeackPickerRapid.(h|C) to ensure compliance with style guide

git-svn-id: https:...

62a05b5f8fb16f9d974e5782025497e1dc159bf1 authored over 11 years ago by Stephan Aiche <[email protected]>

[BUILD] made tutorial tests cmake <= 2.8.4 comaptible

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11410 6adb6e08-d915-0410-...

dbd4b4d8bc3a1bc6e5325bba5fd8ee472645b596 authored over 11 years ago by Stephan Aiche <[email protected]>

[FIX] amend r11400: rename "isValid"

pyOpenMS cannot handle inherited and overloaded functions, thus it is
easer to not have an overl...

550ff8975767e522afc762fb43f8a1925b196cd8 authored over 11 years ago by Hannes Roest <[email protected]>

[FIX] amend to r11392

- also fix pyOpenMS with the new WindowMower

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

be4e6354af9649976c16232fbe2b0d4c6c46686f authored over 11 years ago by Hannes Roest <[email protected]>

[FIX-#184] ConsensusMap: remove unused functions from the interface

- remove front() -> replace with begin()
- remove insert / erase

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

c6c056ff3a17055f62b8c5cb7fa0b9c5be463241 authored over 11 years ago by Hannes Roest <[email protected]>

[FIX-#184] ConsensusMap: private inheritance from std::vector

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11406 6adb6e08-d915-0410-...

3a35c27d96d0342bf078b8a6526b9db778d6a0af authored over 11 years ago by Hannes Roest <[email protected]>

[FIX-#184] FeatureMap: replace front() with begin()

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11405 6adb6e08-d915-0410-...

50a2f9d0f704643528bd91e50efcc507f79c19f2 authored over 11 years ago by Hannes Roest <[email protected]>

[FIX-#184] Feature Map: remove unused functions from the interface

- remove unused insert
- replace rbegin with back()

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

4045d406ef7387c820d94de438087d441fed9b58 authored over 11 years ago by Hannes Roest <[email protected]>

[FIX-#184] FeatureMap: private inheritance from std::vector

- Replace public with private inheritance
- Expose full interface of std::vector through "using"...

86bb770b523a388e01610286661220a5473bd419 authored over 11 years ago by Hannes Roest <[email protected]>

[FIX] amendment to r11400

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11402 6adb6e08-d915-0410-...

43df9731bb2dea54301fb0ca7352eaa60366ddcc authored over 11 years ago by Chris Bielow <[email protected]>

[FIX-#484] all source files in MSExperiment are now written to mzML.

Upon loading a file, this very file is listed as source file, thus writing it out again will prod...

e35630dc9fa7bd1002216b0fa3ed659dd89a6d26 authored over 11 years ago by Chris Bielow <[email protected]>

[FIX-#420] currently, loading a consensusXML file which contains incomplete map information only produces a warning, since otherwise we would not be able to load old files

however, this might now produce an exception during storing, when the consensuXML file is just ch...

79ee9dea9aac263ff229306836564d3ca896b08f authored over 11 years ago by Chris Bielow <[email protected]>

[FIX] more warnings

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11399 6adb6e08-d915-0410-...

208c8271e902c40c2a1d61148406523825f6553c authored over 11 years ago by Chris Bielow <[email protected]>

[FIX] some compiler warnings

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11398 6adb6e08-d915-0410-...

457aa5bc0f83cf4f8b54ffebb4da72c1ee0287bd authored over 11 years ago by Chris Bielow <[email protected]>

[TEST] fixed test on windows (undifined M_PI), cleaned up code and added documentation

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11397 6adb6e08-d915-0410-...

ce5177ab2cf616e479b41aab780050b0d0bd9d07 authored over 11 years ago by Timo Sachsenberg <[email protected]>

[TEST,DOC,BUILD] Moved examples out of the source tree into doc

* restructured the build system of the code examples
* added tests for all non-GUI examples

...

ae6d90bc6bf4ea8c2d86c9ec5ace2f65befa96a7 authored over 11 years ago by Stephan Aiche <[email protected]>

[TEST] added test for alternative WindowMower

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11395 6adb6e08-d915-0410-...

4afdab8ae72c629954a2f1e5a0ae67ae2024ff1f authored over 11 years ago by Timo Sachsenberg <[email protected]>

[FIX] enforce sorting of spectrum in WindowMower

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11394 6adb6e08-d915-0410-...

a467a7571261a099a546b4e73a652f892f3e9971 authored over 11 years ago by Timo Sachsenberg <[email protected]>

[FIX] Small parameter fix in WindowMower

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11393 6adb6e08-d915-0410-...

6debf26ac1a2b12962d683116947accd7b50fa7d authored over 11 years ago by Erhan Kenar <[email protected]>

[FEATURE] faster version of WindowMower with jumping window

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11392 6adb6e08-d915-0410-...

4ed17d3adbdeb13494f41db09bc46f5e5e1c69a8 authored over 11 years ago by Timo Sachsenberg <[email protected]>

[DOC] added IsobaricAnalyzer to TOPP docu page

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11391 6adb6e08-d915-0410-...

3658ae0e1777376615ef450c1a23261fbcba6a2d authored over 11 years ago by Stephan Aiche <[email protected]>

[NOP] fix warnings from cppcheck

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11390 6adb6e08-d915-0410-...

c9b8b4eed5086e10b95e5e7fc4efa35b73ab1d0d authored over 11 years ago by Hannes Roest <[email protected]>