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

[FIX] fixed windows compile error due to map::at method usage and fixed some signed/unsigned warnings

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10385 6adb6...

8a0e288307431a548c787a237108520975142315 authored almost 12 years ago by Stephan Aiche <[email protected]>

[FIX-#475] adapted TOPPBase::writeCTD_ method to recent changes in CTD schema

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10384 6adb6...

0e57ed5bfe6ecdf20ab2c78288b794819aeba31b authored almost 12 years ago by Stephan Aiche <[email protected]>

[FIX] fixed parameter problems in CVInspector and SemanticValidator introduced in [10355] and [10354] and added analysisXML file type

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10382 6adb6...

5fecb7e186a2cf3ffd17e79963ed9d514f5bee0a authored almost 12 years ago by Stephan Aiche <[email protected]>

[FIX] docs did not build because Param::load() does not exist anymore

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10381 6adb...

82601078fe451a324ccf81db7e4bf1707d34cba5 authored almost 12 years ago by Johannes Veit <[email protected]>

[FIX,NOP] fixed #477, improved error message

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10380 6adb...

b7a2bed789f620d9fef389083c920ce0f9432aba authored almost 12 years ago by Johannes Veit <[email protected]>

[FIX] fixed wrong include

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10379 6adb6...

d8e482ca900d8d024bebe94760f14ce98b9079fe authored almost 12 years ago by Stephan Aiche <[email protected]>

[FIX-#476,FEATURE] paramXML now reads and stores file restrictions in the supported_formats field (see #476 for details) but can still read file restrictions from the restrictions field

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10378 6adb6...

b64ed764007a38a20c77f10dfa81049f45905b09 authored almost 12 years ago by Stephan Aiche <[email protected]>

[FIX-#474] updated paramXML version to 1.4

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10377 6adb6...

2096540331101b6fa6a7ce08493c3de6ac7a4f4b authored almost 12 years ago by Stephan Aiche <[email protected]>

[NOP] added Param_1_4 schema

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10376 6adb6...

5096acc523906aa622a21a82931db977bace5ac1 authored almost 12 years ago by Stephan Aiche <[email protected]>

[NOP] removed svn:executable property from README and cmake files

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10373 6adb6...

c1f9c89b27a5e1f257e2ee9c4345668c9655b8a2 authored almost 12 years ago by Stephan Aiche <[email protected]>

[NOP] fixed spelling errors found by Filippo/lintian

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10372 6adb6...

9a1ec6142724008895e9c08b255fe7d7b866113f authored almost 12 years ago by Stephan Aiche <[email protected]>

[FIX] svn diff/patch accidently duplicated the content of the new ParamXMLFile(.h|.C|_test.C) files

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10371 6adb6...

3d7e6b39a4c8689f3355700246d178a168579f42 authored almost 12 years ago by Stephan Aiche <[email protected]>

[INTERNAL,API] moved paramXML loading code from Param class into separate class ParamXMLFile

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10370 6adb6...

3f159964125fc5c7a547238ab39e91299eead0ff authored almost 12 years ago by Stephan Aiche <[email protected]>

branch for 1.10 release

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10369 6adb...

39fb79fe598d472c7c50bd88e81982c166cc8c39 authored almost 12 years ago by Timo Sachsenberg <[email protected]>

[FIX] addendum to [10366]; fixed wrong case of file ending pattern

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10368 6adb6e08-d915-0410-...

dde9ce9777647214f0dce751642f29d29948e6fa authored almost 12 years ago by Stephan Aiche <[email protected]>

[FIX,INTERNAL,TEST] Fixed exclusion of similar assays in OpenSwathDecoyGenerator

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10367 6adb6e08-d915-0410-...

0a6da6cbc98c1aaa988b8c8097c2da3863199f8a authored almost 12 years ago by George Rosenberger <[email protected]>

[FIX, INTERNAL] fixed missing simple type error

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10366 6adb6e08-d915-0410-...

adad5c80d1367e24fd62a2d48320dc07e551740a authored almost 12 years ago by Timo Sachsenberg <[email protected]>

[FIX] fixed missing OPENMS_DLLAPI in FileTypes and inconsistent Maintainer infos

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10365 6adb6e08-d915-0410-...

57c4d558bb3591b0e9dd4790e48b774ce67889b8 authored almost 12 years ago by Stephan Aiche <[email protected]>

[FIX] another attempt to fix the FFMetabo tests

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10364 6adb6e08-d915-0410-...

801aefa18389b78476f0ff46b92814469b292dce authored almost 12 years ago by Stephan Aiche <[email protected]>

[FIX, INTERNAL] style corrections

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10363 6adb6e08-d915-0410-...

c671556658a1a23d21c4d25f8a8dc5f24c0e2fd0 authored almost 12 years ago by Timo Sachsenberg <[email protected]>

[FIX,TEST] applied according changes to wsdl test file from rev10355

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10362 6adb6e08-d915-0410-...

080cf530895b1b389e5917a00669281f9efebc61 authored almost 12 years ago by Mathias Walzer <[email protected]>

[FIX] reapplied [10356] fixing the CTD issues of FileInfo

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10361 6adb6e08-d915-0410-...

b8489bd5edef20ebdd45906461970aa9b16e156a authored almost 12 years ago by Stephan Aiche <[email protected]>

[FIX,INTERNAL] moved nameToType/typeToName code into FileTypes class to prevent additions of file types without extension of the name array

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10360 6adb6e08-d915-0410-...

18527fb4e6ee2a0bfb656ed7981d5b79060b1649 authored almost 12 years ago by Stephan Aiche <[email protected]>

[FIX, INTERNAL] some output type corrections

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10359 6adb6e08-d915-0410-...

86e5869c4d34d9dc322051a0e69d82c5d8154364 authored almost 12 years ago by Timo Sachsenberg <[email protected]>

[FIX, INTERNAL] added tool output to some TOPP tools

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10358 6adb6e08-d915-0410-...

db1809535c2b558e240f98823671bbaafd58f65f authored almost 12 years ago by Timo Sachsenberg <[email protected]>

[FEATURE] added experimental RNPxl tool

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10357 6adb6e08-d915-0410-...

23c7009245ea844dd1c375382ab18d6f44d12a20 authored almost 12 years ago by Timo Sachsenberg <[email protected]>

[FIX,INTERNAL]Reverting previous commit for FileInfo - going back [CTD issue unresolved].

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10356 6adb6e08-d915-0410-...

06408eae840f7718b5f76bc7d695f9781081f864 authored almost 12 years ago by Mathias Walzer <[email protected]>

[FIX,INTERNAL] edited TOPPTools setValidFormats to support valid CTDs

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10355 6adb6e08-d915-0410-...

3d62dc3e15e47c714992a053819c565ba2e8644d authored almost 12 years ago by Mathias Walzer <[email protected]>

[FIX] Added supported file formats to input/output parameters for better compatibility with CTDs

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10354 6adb6e08-d915-0410-...

54411e2e7e227819a026177de61c266fae427984 authored almost 12 years ago by Erhan Kenar <[email protected]>

[FIX, INTERNAL] added output options to tools

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10353 6adb6e08-d915-0410-...

43fbc9540dd2ef45b1582d2242466e36829cd5fa authored almost 12 years ago by Timo Sachsenberg <[email protected]>

[FIX, INTERNAL] added output options to tools

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10352 6adb6e08-d915-0410-...

f2f15506c5944c495b9c34849ccc774820b0a9a4 authored almost 12 years ago by Timo Sachsenberg <[email protected]>

[FIX, INTERNAL] added output file type to tools

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10351 6adb6e08-d915-0410-...

95962c57a6f085d1b460c2ecb772992e968b77ce authored almost 12 years ago by Timo Sachsenberg <[email protected]>

[FIX] added setValidFormat_ to input and output parameters

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10350 6adb6e08-d915-0410-...

68dc6cfb8d1a1bdc01a7542c8328fbd2f619156f authored almost 12 years ago by Timo Sachsenberg <[email protected]>

[FIX] Fixed FeatureFindingMetabo_test / CTest for TOPP_FeatureFinderMetabo_1_out

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10349 6adb6e08-d915-0410-...

43a6233e1972b5776aeff3fdd2740e91fba1854d authored almost 12 years ago by Erhan Kenar <[email protected]>

[FIX] FeatureFindingMetabo_test fixed... again...

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10348 6adb6e08-d915-0410-...

d57da6e6f8a0fe0f55bff6dc9e0ab8f1883a5ad5 authored almost 12 years ago by Erhan Kenar <[email protected]>

[CONTRIB,BUILD] updated required SeqAn version to 1.4.0 to reflect changes made in [10307]

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10347 6adb6e08-d915-0410-...

b70bf3f0364c990fd9f39af2dcbf8f5f85266c2f authored almost 12 years ago by Stephan Aiche <[email protected]>

[FIX] Ticket #468 fixed for Mascot2.2 with Content-Dispositions correct name entry. Until testing with other Versions I will not close ticket..

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10345 6adb6e08-d915-0410-...

52e83cfd440f73f68077f5200f755985573c0da1 authored about 12 years ago by Mathias Walzer <[email protected]>

[INTERNAL] fixed Superhirn (and some more) header-guards to appease the checker

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10344 6adb6e08-d915-0410-...

becc625687dd10182defb84e792302c6c9f02dea authored about 12 years ago by Stephan Aiche <[email protected]>

[FIX] memory leak in FFmetabo

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10343 6adb6e08-d915-0410-...

8aa7679a579240f49da1710c2923e26b12738b5b authored about 12 years ago by Timo Sachsenberg <[email protected]>

[NOP,FIX] fixed missing svn Ids for tests

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10342 6adb6e08-d915-0410-...

44a3be3c271dfc9fc1bc39a57b7f59ccbae45ccb authored about 12 years ago by Stephan Aiche <[email protected]>

[INTERNAL,FIX] fixed minor stuff in checker related to [10337]

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10341 6adb6e08-d915-0410-...

6a5bbea04a7f4d2d221faf1d5899cef44788a496 authored about 12 years ago by Stephan Aiche <[email protected]>

[INTERNAL] fixed a warning

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10340 6adb6e08-d915-0410-...

a557ffd7fb5090186f7527673906d8057599199b authored about 12 years ago by Chris Bielow <[email protected]>

[FIX-#469] proper escaping of paths with spaces during INI-save (using QProcess, since system() is a beast, e.g. the first argument WITHIN THE STRING needs to be the executable,

all following arguments must be quoted as a whole as well as indivudueally: "\"/some path/myexe\"...

c15b39e43c25553b129e37b382f1a6d377b4038f authored about 12 years ago by Chris Bielow <[email protected]>

[FIX] corrected parameter handling in IDFilter for readout so upper bound only length filtering is possible.

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10338 6adb6e08-d915-0410-...

eb0d2c9542bbb47ef43854f8f952d8980fd3ef3f authored about 12 years ago by Mathias Walzer <[email protected]>

[INTERNAL] checker now reports data in a format that can be utilized by ctest to be submitted to cdash

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10337 6adb6e08-d915-0410-...

df96c6c5f31f1965ee973cf4454d9fa2701c4395 authored about 12 years ago by Stephan Aiche <[email protected]>

[API,FEATURE] added two sided length filtering capabilities for IDFilter.filterIdentificationsByLength(...). Accordingly, there is a new TOPPTool parameter IDFilter.max_length.

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10336 6adb6e08-d915-0410-...

ee43bbf7059beb9c99bc022a53bb54e4fdf3b324 authored about 12 years ago by Mathias Walzer <[email protected]>

[INTERNAL] fix warnings by checker script

Remove OpenSWATH from tests checker since it cannot find the tests

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

2ca1a2bb3e7a2bb786c166cce43e9ecf096820e8 authored about 12 years ago by Hannes Roest <[email protected]>

[NOP] fixed last style errors and moved explicit constructor warning to level 4

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10334 6adb6e08-d915-0410-...

6bec0e62424dba35c8d3091f4a65bd1d0c89eaed authored about 12 years ago by Timo Sachsenberg <[email protected]>

[FIX] Minor bug fixes; cleanup of old code

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10333 6adb6e08-d915-0410-...

5e2a010f63f278686d535a39d0f3ead5c28a5c44 authored about 12 years ago by Erhan Kenar <[email protected]>

[FIX] fix fabs bug

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10332 6adb6e08-d915-0410-...

1179a87cb63099ad3eae9b624ece7a06cd3e1284 authored about 12 years ago by Hannes Roest <[email protected]>

[FIX] Fix several bugs (SuperHirn / OpenSWATH)

* fix compilation warning for SuperHirn file inclusion
* fix ChromatogramExtractor : check for i...

7029d0bfee87e1095437636397a91432fca2dbe1 authored about 12 years ago by Hannes Roest <[email protected]>

[FIXED, #390] scan list and identification list should be cleared now

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10330 6adb6e08-d915-0410-...

0d25046012ed1b2e31ac160160485a18969ff575 authored about 12 years ago by Timo Sachsenberg <[email protected]>

[DOC] Added some documentation to the 'enzyme' section of the ID engine adaptors

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10329 6adb6e08-d915-0410-...

5e52aa7332018ac869bca70131dfb9d3dc548252 authored about 12 years ago by Mathias Walzer <[email protected]>

[FEATURE] add ion type annotation for non b,y, ions to identification view

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10328 6adb6e08-d915-0410-...

ce6389e12ee36af1122c775110f85fd5debd31a7 authored about 12 years ago by Timo Sachsenberg <[email protected]>

[FEATURE] specify maximum number of charge for charge ladder generation in identification view

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10327 6adb6e08-d915-0410-...

603b6a96744608d83756f2e9831abe3d1245cf98 authored about 12 years ago by Timo Sachsenberg <[email protected]>

[NOP] renamed some XL modifications

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10326 6adb6e08-d915-0410-...

3f23ddd87bede17809aa3b1d71f600247294e465 authored about 12 years ago by Timo Sachsenberg <[email protected]>

OpenSwathDecoyGenerator: new options for exclusion of decoys

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10325 6adb6e08-d915-0410-...

756871834c1e1efdc0997e2eaf85f92389b72bca authored about 12 years ago by George Rosenberger <[email protected]>

MRMDecoy.C: fix seed bug for shuffle method

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10322 6adb6e08-d915-0410-...

2dbf730163fa6e6481b1e52f289fa197c1ee78ec authored about 12 years ago by George Rosenberger <[email protected]>

[FIX] Various fixes of errors in OpenSWATH

* require at least 2 datapoints for the EMG fitter
* pass array by reference
* fix find() for ST...

df960662e9c243ededbb41e7b0c3d9bbe568083a authored about 12 years ago by Hannes Roest <[email protected]>

[FIX] Removed bug in collision check for overlapping feature hypotheses; should also help with the failing tests under certain compiler/platform settings

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10315 6adb6e08-d915-0410-...

28f41f2d0d888748baf566475fa96a32280511a0 authored about 12 years ago by Erhan Kenar <[email protected]>

[NOP] added OMSSA, XTandem and MyriMatch licenses to License.txt

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10309 6adb6e08-d915-0410-...

7b5d288fc17bbc2265813cfe67fa012dfc42fbfd authored about 12 years ago by Timo Sachsenberg <[email protected]>

[FIX]added generic wrapper nodes Rscript used in QC, adapted SCRIPTS accordingly

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10308 6adb6e08-d915-0410-...

fb0c2696229958d314856e5368d920dadc69b7bf authored about 12 years ago by Mathias Walzer <[email protected]>

[FIX] fix runtime error (SN parameters need to be larger than zero)

* [BUILD] add new path for OpenSWATH

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

7efefd751a3e8286eec2a7b3f7f080ed6feee9f0 authored about 12 years ago by Hannes Roest <[email protected]>

[INTERNAL,FIX] fixed win32 build of OpenSWATH by moving code to C files and many more minor and major code fixes

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10304 6adb6e08-d915-0410-...

4501fa99a399a2ea52fcf1b09262fd1dad3d7c21 authored about 12 years ago by Stephan Aiche <[email protected]>

[FIX] compile bug

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10303 6adb6e08-d915-0410...

132a546cd4cd9417856b77b3186498b258c098f5 authored about 12 years ago by Timo Sachsenberg <[email protected]>

[BUILD] try to fix Windows build again by using more DLL exports

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10302 6adb6e08-d915-0410-...

5f7a4efd35bd97673c86202199155e3969ca9718 authored about 12 years ago by Hannes Roest <[email protected]>

[TEST] added PSProteinInference test

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10301 6adb6e08-d915-0410-...

d3c673c76a97e691709cb638a4bd92f6960b4d91 authored about 12 years ago by Alexandra Zerck <[email protected]>

[INTERNAL] remove _define private public_ statements

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10300 6adb6e08-d915-0410-...

44582407f67f06607dabcad7bfec04a5f0e02a78 authored about 12 years ago by Hannes Roest <[email protected]>

[FEATURE] added some cross linking relevant modifications

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10299 6adb6e08-d915-0410-...

a1ce7f5727a2bf9c22b20da6e2450fe033496dae authored about 12 years ago by Timo Sachsenberg <[email protected]>

[FEATURE] added Pyrrolysine (Pyr, O) to natural AAs to prevent crash of search engines if O is contained in AA sequence

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10298 6adb6e08-d915-0410-...

cfbc86b9a8a2454d48a13337992f8ce389140236 authored about 12 years ago by Timo Sachsenberg <[email protected]>

[FIX] compile error due to missing include

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10297 6adb6e08-d915-0410-...

5533bc9731737825370205d8e7ed0958bf2afe6e authored about 12 years ago by Timo Sachsenberg <[email protected]>

[BUILD] VC copy build OpenSwathAlgo(d).dll to TEST directory

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10296 6adb6e08-d915-0410-...

e63d16c791156afba78ba5bf7fbbb88476511109 authored about 12 years ago by Stephan Aiche <[email protected]>

[INTERNAL] remove unnecessary parameter

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10295 6adb6e08-d915-0410-...

683e64aac219a03773a1e6d03fdc7eacaac0bb29 authored about 12 years ago by Hannes Roest <[email protected]>

[FIX] fixed whitelist of OMSSA adapter test diff and updated idXML files (again) to new output

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10294 6adb6e08-d915-0410-...

e071dc291206b44fb877dc48d303cb61e3c236c6 authored about 12 years ago by Stephan Aiche <[email protected]>

[FEATURE] support (for restrictions) for .csv and .txt file endings in TOPP tools

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10293 6adb6e08-d915-0410-...

3f33b92318b81fa0f3febbbca4d22f869b1488ff authored about 12 years ago by Chris Bielow <[email protected]>

[FEATURE] PepNovoOutfile can now also infer RT and m/z from title

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10292 6adb6e08-d915-0410-...

9363e5d4fc4702740aefe1e279326b5853f19e28 authored about 12 years ago by Chris Bielow <[email protected]>

[FIX] replaced uint32_t with UInt since VS is missing the stdint.h types

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10291 6adb6e08-d915-0410-...

02531240f35a8f3da6e852874f36d2f07dc0e6ba authored about 12 years ago by Stephan Aiche <[email protected]>

[FIX, TEST] PepNovoAdapter did not annotate Ids with MZ+RT and the naming of a metavalue (containing the original PepNovo score) was wrong

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10290 6adb6e08-d915-0410...

28384d767ed0f35d9fedf857bc6e2257eb63f445 authored about 12 years ago by Chris Bielow <[email protected]>

[INTERNAL,FIX-#466] removed unused code from IdXML writer (addendum to [10288])

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10289 6adb6e08-d915-0410-...

e56503d8b5bda6d7d43fc2572cfeb81079c219d7 authored about 12 years ago by Stephan Aiche <[email protected]>

[FIX-#466] added link to xsl file on the openms server instead of local file reference and adapted test files accordingly

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10288 6adb6e08-d915-0410-...

000d802f2bc97813bf641f4832dd7c479ef34891 authored about 12 years ago by Stephan Aiche <[email protected]>

[NOP] reformated comment since the checker-script had a problem with the contained ^S

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10287 6adb6e08-d915-0410-...

80aa73cc59d24b977ad8cbd4e7f3da2369d8ce7d authored about 12 years ago by Stephan Aiche <[email protected]>

[INTERNAL] remove template nesting in OpenSWATH

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10286 6adb6e08-d915-0410-...

2ca3ed023c3a0c8ab8bebd10d71fe52e13a51448 authored about 12 years ago by Hannes Roest <[email protected]>

[INTERNAL] fix template param name (do not name templates like classes)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10285 6adb6e08-d915-0410-...

912c72086fce34ccd13202c1696ffd6985802e97 authored about 12 years ago by Hannes Roest <[email protected]>

[INTERNAL] added two more default MRMTransitionGroup

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10284 6adb6e08-d915-0410-...

5002b933ea7b8e914e4d37f37cf46eb8e5923b6a authored about 12 years ago by Hannes Roest <[email protected]>

[TEST] Rework how test data is generated for EmgScoring and MRMFeatureScoring tests

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10283 6adb6e08-d915-0410-...

708c16527249542991caf7ddaa9e02e3c3caef38 authored about 12 years ago by Hannes Roest <[email protected]>

[INTERNAL] rename internal variable and functions, various checker errors

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10282 6adb6e08-d915-0410-...

66debec8a5d738f70a1a0b1ac7f83aad692658c2 authored about 12 years ago by Hannes Roest <[email protected]>

[NOP] fix checker errors in OpenSwath (doxygen errors, licence file, header guards)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10281 6adb6e08-d915-0410-...

83c3829baadaa5d47d385dc22ec639aba7c4cdfb authored about 12 years ago by Hannes Roest <[email protected]>

[INTERNAL] add default MRMTransitionGroup (to fix Windows compilation)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10280 6adb6e08-d915-0410-...

ec18ab32adabe3e80add6bc08dfd4fab417306e5 authored about 12 years ago by Hannes Roest <[email protected]>

[BUILD,FIX] fixed building OpenSWATHALGO lib on windows, some dll linkage issues remain

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10279 6adb6e08-d915-0410-...

bf59b0a9dcbb0ad3f0c5c48d9cda1dc1eaf1f2b1 authored about 12 years ago by Stephan Aiche <[email protected]>

[INTERNAL] fixed Windows template compile (do not name template typenames like real classes)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10278 6adb6e08-d915-0410-...

796be262bc978584e61ca798dd5495b4dd65314b authored about 12 years ago by Chris Bielow <[email protected]>

[NOP] removed tab settings check and added license header check to checker script

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10277 6adb6e08-d915-0410-...

be49715f8023e68279f0f49e0314318efcf13bfa authored about 12 years ago by Stephan Aiche <[email protected]>

MRMRTNormalizer: fixed fabs bug and test

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10276 6adb6e08-d915-0410-...

18f1168e967b8a1595e3f853b4ebb856020a3eb8 authored about 12 years ago by George Rosenberger <[email protected]>

[FIX] made QCExporter more awesome

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10275 6adb6e08-d915-0410-...

309edae65e0a6503e6c497ba539797cf7b774927 authored about 12 years ago by Mathias Walzer <[email protected]>

[FIX] fixed QCCalculator and subsequently changed the qc scripts

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10259 6adb6e08-d915-0410-...

fa05515f1d53e9112abf272d820ed3339792da8e authored about 12 years ago by Mathias Walzer <[email protected]>

[FIX] Windows compile errors fixed (all tests compile now using VS11)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10258 6adb6e08-d915-0410-...

6f275bae3d6d26bb6911d8ad7c146d4b59f4fc85 authored about 12 years ago by Chris Bielow <[email protected]>

[INTERNAL] Windows compile errors fixed

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10257 6adb6e08-d915-0410-...

cc8ec2702ba65bbc41c64cb1dd23d1b81c315649 authored about 12 years ago by Chris Bielow <[email protected]>

[INTERNAL] fixed compile errors of MRMFeature (use [], not .at() for maps)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10256 6adb6e08-d915-0410-...

ec350d3c1adddf63b897d743cb771254183f4e81 authored about 12 years ago by Chris Bielow <[email protected]>

[FIX,BUILD] made DISABLE_OPENSWATH also available in nightly builds

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10255 6adb6e08-d915-0410-...

76d8c7d007e7c2f408797b017cba6e5c3f0d6cb0 authored about 12 years ago by Stephan Aiche <[email protected]>

[DOC] OMSSAAdapter doc improved

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10254 6adb6e08-d915-0410-...

2b8c74bd07ea713ea8c5cc893a2dc82b0d11882a authored about 12 years ago by Chris Bielow <[email protected]>

[INTERNAL] got MRMMapper to compile on windows

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10253 6adb6e08-d915-0410-...

311f7fceedf33f70ee0e4f01d8c18c31e37231d0 authored about 12 years ago by Chris Bielow <[email protected]>