Ecosyste.ms: OpenCollective
An open API service for software projects hosted on Open Collective.
github.com/OpenMS/OpenMS
The codebase of the OpenMS project
https://github.com/OpenMS/OpenMS
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]>- 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]>
- cleanup
- add documentation
- do more work in constructor of SpectrumAccessOpenMSCached, store...
- Since some implementations might actually change internally thus not
be really constant, rem...
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]>
* custom code is only used when stream_extraction_bug is found
* additionally re-formated Fuzz...
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]>
* was included via MRMFeatureFinderScoring.h, after removal there [11951] it had to be
expli...
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]>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]>
* merged from head commit [11917]
* in 2.8.12 the signature of qt4_extract_options() macro cha...
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]>- 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]>
- create new internal class MzMLHandlerHelper which contains helper
functions that are called ...
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]>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]>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]>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]>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]>
- make processSpectrum_ and processChromatogram_ both private pure
virtual functions which der...
- fix regression introduced in r11839
- check for array type _outside_ of loop makes the code mu...
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]>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]>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]>- 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]>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]>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]>
- the IndexedMzMLFileLoader can read and write IndexedMzML files using
the familiar interface ...
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]>
- add openFile to IndexedMzMLFile and OnDiscMSExperiment to allow for
later opening of a file ...
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]>
unique id is now generated at a different point in the program, thus the
test output is slightly...
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]>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]>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]>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]>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]>
- remove the cached_data dataprocessing flag because otherwise even
non-cached data on disk wo...
- add maximal Z-Score parameter that controls how much the left/right
border can deviate
- cal...
- 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]>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]>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]>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]>* 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]>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]>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]>* 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 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]>
* in 2.8.12 the signature of qt4_extract_options() macro changed which we need to adopt
depe...
- using the spellchecker and exclusion list in tools/spellcheck
- run on all header files and el...
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]> * 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]>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]>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]>
- The TEST_REAL_SIMILAR macro uses writtenDigits which does not have a
template specialization...
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]>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]>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]>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]>
- fix file path
- fix include statement of C++ source code that changed
- make clear what a new ...
- source code is formatted by individual spans in doxygen-generated
html-documentation:
- If t...
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]>- 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]>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]>* 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]> The fix prevents TOPPAS from not being responsive on large inputs from cmd (e.g. from XTandem).
...
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]>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]>
- change unsigned to signed loop variable
- replace continue statements with if statements
git-...
6a3959dcc99d473d009149e9666e42b528d6e57b authored almost 11 years ago by Hannes Roest <[email protected]>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]>
- 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]>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]>- 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]>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]>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]>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]>
- 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]>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] make function extern
- [NOP] rename function names and variables to fix checker var...
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]>
- Change numpress licece to 3 clause BSD (is now dual licence)
- Add Johan Teleman and Witold Wo...
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]>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]>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]>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]>
- ignore doxygen stuff:
- ignore parameter list (ofen variable names)
- ignore exception nam...
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]>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]>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]>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]>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]>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]>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]>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]>
- OpenSwathDataAccessHelper::convertTargetedPeptide is now used to
determine the output peptid...
- add createPeptideReferenceMap_ function for easy lookup of peptides
- add typedef in TargetedE...
- if the raw spectral data should not be appended to the spectra list,
we can skip several ste...
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]>* 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]>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]>