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

[INTERNAL] throw OpenMS exceptions in CachedmzML

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11966 6adb6e08-d915-0410-...

3f710c5ef8e4a56ac891b5d6e8a4625e90f80fe7 authored almost 11 years ago by Hannes Roest <[email protected]>

[FIX] bugfix

- ensure that file gets properly closed and flushed

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

c011494ea9ce275054556c041778d17ed7cb10aa authored almost 11 years ago by Hannes Roest <[email protected]>

[INTERNAL] cleanup SpectrumAccessOpenMSCached and CachedmzML

- cleanup
- add documentation
- do more work in constructor of SpectrumAccessOpenMSCached, store...

26c22f3a61cacd1110727de7a90cfc838f5bac85 authored almost 11 years ago by Hannes Roest <[email protected]>

[API,DOC] remove const for Spectra/Chromatogram access

- Since some implementations might actually change internally thus not
be really constant, rem...

ec13901c2db180e60b41f71719d18f7b2a0070f4 authored almost 11 years ago by Hannes Roest <[email protected]>

[FEATURE,PYOPENMS] wrap IndexedMzML

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11962 6adb6e08-d915-0410-...

3424ca98806699ace80ff2c42bb00a5d0d54d94d authored almost 11 years ago by Hannes Roest <[email protected]>

[INTERNAL-#623] added custom stream extraction code for doubles

* custom code is only used when stream_extraction_bug is found
* additionally re-formated Fuzz...

6010f8900b1b928368a260ec36bc141217129c58 authored almost 11 years ago by Stephan Aiche <[email protected]>

[BUILD-#623] let cmake detect if the current compiler has the stream extraction bug

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11960 6adb6e08-d915-0410-...

f1917217cd48af09716ce9a3c7a3e5fd0aaf73d9 authored almost 11 years ago by Stephan Aiche <[email protected]>

[FIX] adds missing header to MRMFeatureFinderScoring_test

* was included via MRMFeatureFinderScoring.h, after removal there [11951] it had to be
expli...

3f367fde68f973490f32b3576336f74c7e1a6c8a authored almost 11 years ago by Stephan Aiche <[email protected]>

[BUILD,FIX-#630] fixed knime mime types

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11.1@11958 6ad...

ddf93dacab54f5ab85164aa4c599228725215e57 authored almost 11 years ago by Stephan Aiche <[email protected]>

[NOP,RESOURCES] updated bug-fix branch version to 1.11.1

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11.1@11957 6ad...

fdb08a5b43719860e9092184410c4a57edaed2c4 authored almost 11 years ago by Stephan Aiche <[email protected]>

[FIX-#629] fixed cmake 2.8.12 related issue in OpenMS' qt_wrap_ui macro

* merged from head commit [11917]
* in 2.8.12 the signature of qt4_extract_options() macro cha...

f83d6f683c18b07c20d275482d90dbe6609b5c4a authored almost 11 years ago by Stephan Aiche <[email protected]>

[FIX] fix after r11951

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11955 6adb6e08-d915-0410-...

20b9f534d47fc92535129c85ca5121afb82e8fec authored almost 11 years ago by Hannes Roest <[email protected]>

[INTERNAL] refactor mzMLDecoder

- use MzMLHandlerHelper to reduce code duplication and offload some work

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

7dfabfa78a64bf732358efc08d481f35b6493bf2 authored almost 11 years ago by Hannes Roest <[email protected]>

[INTERNAL] refactor mzMLHandler

- create new internal class MzMLHandlerHelper which contains helper
functions that are called ...

19d1a06c6751d1ccd54d47e5d2446d3a2ce45f2b authored almost 11 years ago by Hannes Roest <[email protected]>

[DOC] update documentation in indexed mzML sources

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11952 6adb6e08-d915-0410-...

3ab1d0f3def2e2572ac746777ec5893cd20a6540 authored almost 11 years ago by Hannes Roest <[email protected]>

[INTERNAL] remove some header dependencies

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11951 6adb6e08-d915-0410-...

9c67c0185edaf4701c0f8c54da98582f2d7e8c34 authored almost 11 years ago by Hannes Roest <[email protected]>

[API] provide easy-access to spectra and chromatograms

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11950 6adb6e08-d915-0410-...

ac770aa74cda470b2345218a60dc335484ac02c1 authored almost 11 years ago by Hannes Roest <[email protected]>

[API] also allow MzMLHandler to return its options

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11949 6adb6e08-d915-0410-...

6bcf798568f6150a286fda50499e9369bc45a1e2 authored almost 11 years ago by Hannes Roest <[email protected]>

[DOC] documentation about how to use consumers

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11948 6adb6e08-d915-0410-...

689b439c4bb9811276def46f582f4e92f1fd2204 authored almost 11 years ago by Hannes Roest <[email protected]>

[DOC,INTERNAL] add documentation, use template method pattern

- make processSpectrum_ and processChromatogram_ both private pure
virtual functions which der...

b13facb7f2b4845cb731c89f0175e8cc0e4fc4e8 authored almost 11 years ago by Hannes Roest <[email protected]>

[FIX-#628] fix speed regression in writing mzML

- fix regression introduced in r11839
- check for array type _outside_ of loop makes the code mu...

e32c7ac12ec2b94228d9650ef1c8ac80dbf8122d authored almost 11 years ago by Hannes Roest <[email protected]>

[DOC] small typo fixes

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11945 6adb6e08-d915-0410-...

5be7b39c09f099071ad61409f7b3bc9850df12f2 authored almost 11 years ago by Chris Bielow <[email protected]>

[FEATURE] show ppm error in TOPPView when measuring distances between peaks, features etc

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11944 6adb6e08-d915-0410-...

eaab03f3f3fa6d457fda7a9cfff40f75470506fe authored almost 11 years ago by Chris Bielow <[email protected]>

[FIX-#625,TEST,FEATURE] work-around for libc++ newline problem; added better newline indicator 'nl', adapted TextExporter to use it, added test case; improved code formatting

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11943 6adb6e08-d915-0410-...

5d5c4ad9c712659114d755e58d504be5934a8b33 authored almost 11 years ago by Hendrik Weisser <[email protected]>

[DOC] add documentation about indexedMzML File I/O and MSDataConsumers

- add Indexed MzML File

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

0e6e102677f93b3cca144ab44d8e3327188c7253 authored almost 11 years ago by Hannes Roest <[email protected]>

[FIX,DOC] docfix and cleanup

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11941 6adb6e08-d915-0410-...

808e98731dfd8a4eaeff3247065d534d27d6133f authored almost 11 years ago by Hannes Roest <[email protected]>

[DOC] update README with information how to start contributing and building OpenMS

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11940 6adb6e08-d915-0410-...

672333e5f12e32068f3f83483dcf83f63ea8a439 authored almost 11 years ago by Hannes Roest <[email protected]>

[FEATURE] add a class to load/store IndexedMzML files

- the IndexedMzMLFileLoader can read and write IndexedMzML files using
the familiar interface ...

b19fba9301c5bb3b3757e7a4a90d98bd828d097c authored almost 11 years ago by Hannes Roest <[email protected]>

[FIX] fix MSChromatogram ostream overload

adapted from MSSpectrum (current version failed to compile)

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

272c8b7f07a01d6e4ae670523b34cdff719bae14 authored almost 11 years ago by Hannes Roest <[email protected]>

[API] add openFile function

- add openFile to IndexedMzMLFile and OnDiscMSExperiment to allow for
later opening of a file ...

47f580f8051d9dc620b61e3714e812d8ad7e87d1 authored almost 11 years ago by Hannes Roest <[email protected]>

[API] make setExperimentalSettings accept a const ExperimentalSettings

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11936 6adb6e08-d915-0410-...

2e8e736ba51818b0c19bb200b6a818b67631b375 authored almost 11 years ago by Hannes Roest <[email protected]>

[TEST] fix tests after r11928 and r11929

unique id is now generated at a different point in the program, thus the
test output is slightly...

0bd502035fc0f7f3a3348420629efeb735dcad4c authored almost 11 years ago by Hannes Roest <[email protected]>

[FIX-#618] fix spelling errors in the documentation

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11934 6adb6e08-d915-0410-...

4b6f5c36b16ea67618fccc2b201725e5b96b3d58 authored almost 11 years ago by Hannes Roest <[email protected]>

[REVERT] revert from r11916

this patch was mistakenly included in the spellcheck commit

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

21c5d0012a504d21446656f7a0610c245c32a912 authored almost 11 years ago by Hannes Roest <[email protected]>

[FEATURE] allow to specify extra range for chromatogram extraction

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11932 6adb6e08-d915-0410-...

ae2091e6a3e9ce68ef78378cf696b519f1c659c2 authored almost 11 years ago by Hannes Roest <[email protected]>

[FIX] optimize parameters for SWATH-MS

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11931 6adb6e08-d915-0410-...

06cd014c019ae335fe15a25a3fd4dcb2872291aa authored almost 11 years ago by Hannes Roest <[email protected]>

[FEATURE] remove completely overlapping features

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11930 6adb6e08-d915-0410-...

132191383d579ea3a9c7e73d28796352277e02ce authored almost 11 years ago by Hannes Roest <[email protected]>

[FIX] fix extractor output when extracting from cached files

- remove the cached_data dataprocessing flag because otherwise even
non-cached data on disk wo...

f2e993f34654224ed417570e76a6a2e18661f692 authored almost 11 years ago by Hannes Roest <[email protected]>

[FEATURE] add parameter that controls left/right deviation

- add maximal Z-Score parameter that controls how much the left/right
border can deviate
- cal...

5265a90d4ce9faeb49b06380d42d34c738167065 authored almost 11 years ago by Hannes Roest <[email protected]>

[FEATURE] better estimate size of chromatograms

- need to estimate the size of the output chromatograms so that the mzML
will be consistent

g...

08674825b1fd0f8e4ed74437e0abbbd512e1900a authored almost 11 years ago by Hannes Roest <[email protected]>

[INTERNAL] clearer

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11926 6adb6e08-d915-0410-...

5d07944db301bff881286d7db1de1f847f4a2858 authored almost 11 years ago by Hannes Roest <[email protected]>

[INTERNAL] adopt to OpenMS conventions

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11925 6adb6e08-d915-0410-...

8296c43dcf834155b52abfc2812b60fed329cd20 authored almost 11 years ago by Hannes Roest <[email protected]>

[FIX] speedup of writing idXML by re-write of writeXMLEscape() -- Xerces requires a lot of data conversion to do this

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11924 6adb6e08-d915-0410-...

bcb86ea8d306831e0570a2cadbb4ae289396dd8f authored almost 11 years ago by Chris Bielow <[email protected]>

[FIX] minor cleanup of idXML file

* give IDFileConverter a basic loading and storing timer

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

087780aabf0e2a87b54dc50fa264279f99c6e68d authored almost 11 years ago by Chris Bielow <[email protected]>

[FIX] test for FF-Metabo

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11922 6adb6e08-d915-0410-...

fd9ab29866bc8045f18bb74c03bae5e23bf4deb4 authored almost 11 years ago by Chris Bielow <[email protected]>

[RESOURCE,INTERNAL] updated OpenMS head revision to 1.12

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11920 6adb6e08-d915-041...

2740458c57686113541930c49cb335869f372da3 authored almost 11 years ago by Stephan Aiche <[email protected]>

[TEST] added missing topp test dependencies for PeakPickerIterative tests

* also renamed the tests to be conform with the remaining topp tests

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

2f1bdc4895609fa4093515034632fd32d368289d authored almost 11 years ago by Stephan Aiche <[email protected]>

[TEST] added test documenting the libc++ issue reported in #623

* test is expected to fail when compiled with libc++

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

5e3ff05b16aa23d325fd18d93fcd397f3fc0df6c authored almost 11 years ago by Stephan Aiche <[email protected]>

[FIX] fixed cmake 2.8.12 related issue in OpenMS' qt_wrap_ui macro

* in 2.8.12 the signature of qt4_extract_options() macro changed which we need to adopt
depe...

337e92230424028a74eb13c0296067288362f427 authored almost 11 years ago by Stephan Aiche <[email protected]>

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

- using the spellchecker and exclusion list in tools/spellcheck
- run on all header files and el...

ea32a57f479c16880320d982857e400b7513d5bf authored almost 11 years ago by Hannes Roest <[email protected]>

[FIX] compile error

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11915 6adb6e08-d915-0410-...

b5a94c1bab86d1c0bb7eda5f1e2e93e5c1d6ecd7 authored almost 11 years ago by Chris Bielow <[email protected]>

[FEATURE/FIX] * AccurateMassSearch: expose file parameters as such (not as string)

* some stats on results
* minor fixes

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

938f5156f984a08e1ef6a988e8d7ac86395ad984 authored almost 11 years ago by Chris Bielow <[email protected]>

[DOC] internal annotation in MzMLHandler (info: since last week proteowizard writes this CV term at correct position, so we can read it).

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11913 6adb6e08-d915-0410-...

29aee04613aa0e8333f035195c76596366915806 authored almost 11 years ago by Chris Bielow <[email protected]>

[FIX] FileInfo::find() should return failure on empty string

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11912 6adb6e08-d915-0410-...

a4f2612b00e3c5b9f384b378c3334aa206b659fc authored almost 11 years ago by Chris Bielow <[email protected]>

[FIX,BUILD] MSVS fix for TEST_REAL_SIMILAR macro

- The TEST_REAL_SIMILAR macro uses writtenDigits which does not have a
template specialization...

d3f74f85ab05aa88ef6669f79bd2c947aa1b2f66 authored almost 11 years ago by Hannes Roest <[email protected]>

qc-cv.obo again synced with google code repository

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11910 6adb6e08-d915-0410-...

5224c255eaf40f23381e776ee5f5dadb32738ad8 authored almost 11 years ago by Mathias Walzer <[email protected]>

added paranoidal bracketing in dppm calc formula

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11909 6adb6e08-d915-0410-...

d4cc0b88335a8faa87229df9d945b2c17c4cc238 authored almost 11 years ago by Mathias Walzer <[email protected]>

synced qc-cv.obo with google code repository

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11908 6adb6e08-d915-0410-...

ab5b7c9767b753ba863c06ccc25592c078e31722 authored almost 11 years ago by Mathias Walzer <[email protected]>

[FIX,BUILD] MSVS fix (remove OPENMS_DLLAPI)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11907 6adb6e08-d915-0410-...

e6ac6b8f47aa40f630c62c123cf414d47bedf988 authored almost 11 years ago by Hannes Roest <[email protected]>

[DOC,FIX] various fixes in the documentation

- fix file path
- fix include statement of C++ source code that changed
- make clear what a new ...

cfb88e8421eae0bd05046e26d298e122d202d3d8 authored almost 11 years ago by Hannes Roest <[email protected]>

[DOC,FIX] fix source code formatting in documentation

- source code is formatted by individual spans in doxygen-generated
html-documentation:
- If t...

79125675f49824cbd94d73781b201b156a8f8c85 authored almost 11 years ago by Hannes Roest <[email protected]>

[DOC,FIX-#618] fix spelling errors in the documentation

check whole ./doc/doxygen folder and fix spelling mistakes

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

8e2fc9ab847f0427acd5337f62c178531ad7949b authored almost 11 years ago by Hannes Roest <[email protected]>

[TOOLS] add list of correct words for ./doc (#618)

- also update README file

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

e81321e81e2d5673df61d25cfb8d28477230e751 authored almost 11 years ago by Hannes Roest <[email protected]>

[FIX] addendum to [11901]; fixed compile issue and renormalized line endings

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11902 6adb6e08-d915-0410-...

b94c62fad2e2a53178c65afc0c57e50e3a101d3c authored almost 11 years ago by Stephan Aiche <[email protected]>

[FEATURE, FIX] fixes for AccurateMassSearch (handle negative ion mode), automatic polarity detection, allow dynamic mass calculation from DB (mass not required to be given in DB), many smaller fixes (loading DB etc)

* FF-Metabo will write ion mode of raw data to allow auto-detection in AccurateMassSearch

git-s...

8c9c1395329e38423752369db0477e2d0d1d5a96 authored almost 11 years ago by Chris Bielow <[email protected]>

[FEATURE] actually enable changes introduced in [11884].

The fix prevents TOPPAS from not being responsive on large inputs from cmd (e.g. from XTandem).
...

6918d23b4ad2d01af35b7d8113379482af490b93 authored almost 11 years ago by Chris Bielow <[email protected]>

[NOP] fix checker warnings

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11899 6adb6e08-d915-0410-...

4caef80995ab071c0db1571074299453c375fa19 authored almost 11 years ago by Hannes Roest <[email protected]>

[FIX] fix error in TSV header (extra t)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11898 6adb6e08-d915-0410-...

b7442b56f9430236d47c0f91c646a19f15d2fc65 authored almost 11 years ago by Hannes Roest <[email protected]>

[FIX] fix for OpenMP 2.0 (signed loop variable)

- change unsigned to signed loop variable
- replace continue statements with if statements

git-...

6a3959dcc99d473d009149e9666e42b528d6e57b authored almost 11 years ago by Hannes Roest <[email protected]>

[FIX] fixed test error introduced in [11878]

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11896 6adb6e08-d915-0410-...

788e0932eab3ac18c8237b786d857840f7cbe486 authored almost 11 years ago by Stephan Aiche <[email protected]>

[FIX] fix for OpenMP 2.0 (signed loop variable)

- change unsigned to signed loop variable
- also include OpenMP header

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

3826f6d1a245c414ab17fe1e6190536ccd72aa77 authored almost 11 years ago by Hannes Roest <[email protected]>

added two more qp to QCCalculator

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11894 6adb6e08-d915-0410-...

368300918f7d0fc66494075a7cc982f8d23243e6 authored almost 11 years ago by Mathias Walzer <[email protected]>

[FEATURE] OpenSWATH Workflow UTIL

- a tool to run the complete OpenSwath Workflow from a single binary

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

206f30c60a13df2749a835c432ebd9e31cab5719 authored almost 11 years ago by Hannes Roest <[email protected]>

[NOOP] code cleanup

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11892 6adb6e08-d915-0410-...

ef384cf3cf94eb0556eddfb154578505d739279c authored almost 11 years ago by Hannes Roest <[email protected]>

[TEST] add test for SwathFileConsumer

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11891 6adb6e08-d915-0410-...

8999ebfbda70acae0d03f1f17b1b0c0cd2ca2854 authored almost 11 years ago by Hannes Roest <[email protected]>

[TEST] add test for SwathFile

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11890 6adb6e08-d915-0410-...

74ec8ac210387ff4406cc55051e29561a21f586c authored almost 11 years ago by Hannes Roest <[email protected]>

[FEATURE] Create SwathFile and SwathFileConsumer

- two classes designed to read a file produced by a DIA (SWATH) enabled
MS instrument

git-svn...

a9c064c3a0e5abb88e08d7ba22f54149a61a5b15 authored almost 11 years ago by Hannes Roest <[email protected]>

[INTERNAL] only copy those peptides and proteins that are used in the relevant SWATH

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11888 6adb6e08-d915-0410-...

9c60b55a6267f650af5717f5fbc80f6a6f6a921c authored almost 11 years ago by Hannes Roest <[email protected]>

[INTERNAL] small fixes, fixes checker warnings

- [INTERNAL] make function extern
- [NOP] rename function names and variables to fix checker var...

ca9a12bdab6446c0c1f74a4f13e0ba934aa53f70 authored almost 11 years ago by Hannes Roest <[email protected]>

[FIX] fixed problem with adaptive RT windows and some GCC warnings

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11886 6adb6e08-d915-0410-...

d500fb9b77390e1936023477cf3e3c436af8d2ed authored almost 11 years ago by Hendrik Weisser <[email protected]>

[NOOP] Change Numpress licence, add to AUTHOR list

- Change numpress licece to 3 clause BSD (is now dual licence)
- Add Johan Teleman and Witold Wo...

eb62b5c5c86d9b0af18aa3e4c8b59ae8da39454b authored almost 11 years ago by Hannes Roest <[email protected]>

[FEATURE] limit TOPPAS log output to 10 million characters and trim otherwise. Avoids excessive memory usage for very talkative tools or big pipelines ...

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11884 6adb6e08-d915-0410-...

30468a8f66b8c40216aabc1fcf3326913a145f03 authored almost 11 years ago by Chris Bielow <[email protected]>

changed the qcML stylesheet to some better looks

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11883 6adb6e08-d915-0410-...

06291c91dbdb928667c2abf24ac473b4b21abc21 authored almost 11 years ago by Mathias Walzer <[email protected]>

added some features to QCCalculator

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11882 6adb6e08-d915-0410-...

79c02dd1b2891a7d610baa3e291af15b3a51b6cf authored almost 11 years ago by Mathias Walzer <[email protected]>

[TOOLS] add list of correct words (#618)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11881 6adb6e08-d915-0410-...

185910354712150c3db627e973b8d48393ae9cde authored almost 11 years ago by Hannes Roest <[email protected]>

[TOOLS] OpenMS adaptation to the spellchecker (#618)

- ignore doxygen stuff:
- ignore parameter list (ofen variable names)
- ignore exception nam...

02aef01cec552f9a5011a9dfa7dd9a47aa970b63 authored almost 11 years ago by Hannes Roest <[email protected]>

[TOOLS] Linux Kernel spellcheckers (#618)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11879 6adb6e08-d915-0410-...

28c5d2d91cc30c0fa9f381dbedd167c6e8b9fa10 authored almost 11 years ago by Hannes Roest <[email protected]>

[INTERNAL,FIX-#618] Typo in variable name and TOPPTool

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11878 6adb6e08-d915-0410-...

2b4d56691f5447f9e195eabee7fc1cfaa1686ec5 authored almost 11 years ago by Hannes Roest <[email protected]>

[FIX] TOPPAS filename creation fixed

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11877 6adb6e08-d915-0410-...

aabe7c8456b3e00bd78da0b9dc22faa36aca8b90 authored about 11 years ago by Chris Bielow <[email protected]>

[FEATURE,IO,DOC] added option to generate idXML file containing ground-truth IDs from simulated MS2; some param doc and coding standards improvements

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11876 6adb6e08-d915-0410-...

0fc7df61b552991cc1dbe9f6945789e3e23c57fa authored about 11 years ago by Hendrik Weisser <[email protected]>

[PARAM,FEATURE] added option to specify m/z window in ppm (instead of Th)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11875 6adb6e08-d915-0410-...

e566e529b479c8f6aafab4728498131cc4998393 authored about 11 years ago by Hendrik Weisser <[email protected]>

[FIX-614,TEST] check for non-standard amino acids when using cleavage model (otherwise crash); added test case; some code clean-up

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11874 6adb6e08-d915-0410-...

098a517861c09ed7bd857943c50839c5e2b93c16 authored about 11 years ago by Hendrik Weisser <[email protected]>

[FEATURE] show neutral loss offset in TOPPView's spectra list (in precursor column) for constant neutral loss scans

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11873 6adb6e08-d915-0410-...

48287feca262bc3a9a70874e064501feb817b456 authored about 11 years ago by Chris Bielow <[email protected]>

[TEST] fix test after r11854

the extra space was there from the beginning, now it is removed

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

a61662cdc176f730416d7d53a4694e9d33d6668e authored about 11 years ago by Hannes Roest <[email protected]>

[TEST] fix test after r11857

- OpenSwathDataAccessHelper::convertTargetedPeptide is now used to
determine the output peptid...

2137097471308195b51801d3ec598a35d1c0a51e authored about 11 years ago by Hannes Roest <[email protected]>

[INTERNAL,API] refactoring in ChromatogramExtractor

- add createPeptideReferenceMap_ function for easy lookup of peptides
- add typedef in TargetedE...

0b7a2acaf0037e3f0f115ab2c69e83c53042f40b authored about 11 years ago by Hannes Roest <[email protected]>

[INTERNAL] optimize performance of mzXMLHandler if FillData is false

- if the raw spectral data should not be appended to the spectra list,
we can skip several ste...

62775a50f7e2fa0048c9ce584402dd4f877e34da authored about 11 years ago by Hannes Roest <[email protected]>

[NOP] space/formatting

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11868 6adb6e08-d915-0410-...

96b2369b79ae0f9b2af2057a150f044ad09a0af9 authored about 11 years ago by Chris Bielow <[email protected]>

[FIX] * cleanup of TOPPASToolVertex

* re-enabled filename heuristic

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

82dc54c199c59c014332828c1ef2c8eb6e77f060 authored about 11 years ago by Chris Bielow <[email protected]>

[FEATURE] enable LOG_DEBUG for TOPPAS by --debug flag

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11866 6adb6e08-d915-0410-...

69bc7bc1dbffb74f06d863ce2f908870231f5e7d authored about 11 years ago by Chris Bielow <[email protected]>