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

[API,TEST] Fixed MassTrace_test and MassTraceDetection_test to reflect changes to MassTrace/MassTraceDetecion API

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9931 6adb6e08-d915-0410-9...

b7708d1dd294d6c9fbf2c67b01ca6f0827b0fbe3 authored about 12 years ago by Erhan Kenar <[email protected]>

[FIX] Readjusted the mass error model of feature assembly

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9929 6adb6e08-d915-0410-9...

1828115f4c23786903509dc06ef6079885535486 authored about 12 years ago by Erhan Kenar <[email protected]>

[FEATURE] FeatureFinderMetabo now supports the Averagine model for feature finding on proteomics datasets; see isotope_model parameter under the Advanced Parameters section.

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9928 6adb6e08-d915-0410-9...

836e845644f998f70f025e0d4c9f9e6fbdc7e895 authored about 12 years ago by Erhan Kenar <[email protected]>

[FIX] Several bugfixes enhancing numeric stability of MassTraceDetection, ElutionPeakDetection, and FeatureFindingMetabo

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9927 6adb6e08-d915-0410-9...

d025b247f17f85be7065d7b8158e2b1d902f1cf2 authored about 12 years ago by Erhan Kenar <[email protected]>

FeatureFindingMetabo.C: Minor bugfixes

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9925 6adb6e08-d915-0410-9...

890917fb8a7a360cc8b04874599176c5f218ed19 authored about 12 years ago by Erhan Kenar <[email protected]>

FeatureFinderMetabo: re-integrated the chrom_fwhm parameter; FeatureFindingMetabo.C: scoreRT method depends on chrom_fwhm parameter

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9922 6adb6e08-d915-0410-9...

593b60f9ae84f7c74795fad36b5712680b546fb5 authored about 12 years ago by Erhan Kenar <[email protected]>

[FIX] UTILS/ImageCreator will not crash late and ungraceful anymore when invalid image suffix is given.

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9921 6adb6e08-d915-0410-9...

39efb91ab99e88beab0bec41877c3fdb30c614a3 authored about 12 years ago by Chris Bielow <[email protected]>

[FIX, FEATURE] * TOPP/Digestor had a "enzyme" parameter with no influence; now fixed to either Trypsin or none, and doing the right thing

* TOPP/Digestor now prints some stats of how many peptides were created and did pass length fil...

461421e90f5a9da5fddc3c3e2ee4c56dd499df29 authored about 12 years ago by Chris Bielow <[email protected]>

[FEATURE] added new normalization methods to ConsensusMapNormalizer

* 'median' performs median correction
* 'quantile' performs quantile normalization (or an approx...

9e9f4b9982c56c74ca8ae851ed779f6d8da76b82 authored about 12 years ago by Johannes Veit <[email protected]>

* fixed a lot of TOPPAS signal/slot issues e.g.

- deleting a vertex or editing parameters of tools did not lead to changed workflow (marked wi...

f17130aad87beddf17d778a1227a283cedd5eabd authored about 12 years ago by Chris Bielow <[email protected]>

Fixed compile error of MassTrace_test (changes in constructor broke the test)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9915 6adb6e08-d915-0410-9...

e634dd2d76d02fd00afd020e11f94bc05de70a28 authored about 12 years ago by Erhan Kenar <[email protected]>

[INTERNAL] fixed compile error for earlier versions of Qt (4.5) introduced yesterday

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9914 6adb6e08-d915-0410-9...

dd49428d2424159cee4467c771f8b8801be1caa4 authored about 12 years ago by Chris Bielow <[email protected]>

[FIX] processes actively running in TOPPAS are now shown correctly with yellow light (before all processes ENQUEUED where shown)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9913 6adb6e08-d915-0410-9...

b78b4ab0ed17ce86f7883dac56af3bb503594620 authored about 12 years ago by Chris Bielow <[email protected]>

[DOC] * fixed some documentation errors, extended doc for IDPep

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9912 6adb6e08-d915-0410-9...

e09c2558b8e56770de21870c8498454e43dec3b9 authored about 12 years ago by Chris Bielow <[email protected]>

[FEATURE,TEST] added TMT-6plex support

* iTRAQ-Quant classes in ANALYSIS/QUANTITATION support now TMT-6plex
* added TOPP-tool TMTAnal...

c85ecc54e001a7309f53bdd493bdcbbf8eb9f0d8 authored about 12 years ago by Stephan Aiche <[email protected]>

[INTERNAL] updated uncrustify.cfg to remove tabs/spaces before preprocessor macros

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9910 6adb6e08-d915-0410-9...

20329961d2a483eb472e78aa28d3f7ae8dafe07c authored about 12 years ago by Stephan Aiche <[email protected]>

[INTERNAL] removed listing of qt detail information from cmake configure screen

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9909 6adb6e08-d915-0410-9...

ce9ed28c667dda812ca06184bbf9d61262f3c2db authored about 12 years ago by Stephan Aiche <[email protected]>

[INTERNAL, TOPPVIEW] speedup scrolling through many chromatograms

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9908 6adb6e08-d915-0410-9...

c9cc4cf4fb2cb8fac25e5df3031c87e8f6077acc authored about 12 years ago by Hannes Roest <[email protected]>

[INTERNAL] remove unused fields in Transition

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9907 6adb6e08-d915-0410-9...

e1325acb18a7b641fe67e1b8d4934c75d37e150c authored about 12 years ago by Hannes Roest <[email protected]>

[INTERNAL] Slight modifications

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9906 6adb6e08-d915-0410-...

6b8598ef3131d656ff322159fbe23fd8b3d776f9 authored about 12 years ago by Immanuel Luhn <[email protected]>

[FEATURE, DOC]

* allow TOPPAS to open empty (0-byte) files -- very convenient to create new workflows
* fixed ...

84be1b401950e1a9d436938c9ab872048aea429f authored about 12 years ago by Chris Bielow <[email protected]>

[INTERNAL] * fixed some output streams and flushing

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9904 6adb6e08-d915-0410-9...

927f07692244b64f2a4374fa284dbad1e2844fe1 authored about 12 years ago by Chris Bielow <[email protected]>

[FIX, FEATURE, IO, DOC]

* fixed #441
* added max_length parameter to filter for long peptides

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

eee48ed4bc0c56e088845cd7c375925ec983c24f authored about 12 years ago by Chris Bielow <[email protected]>

[FIX] fixed #440 ('ineffective hashing if m/z tolerance is in ppm')

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9902 6adb6e08-d915-0410-9...

5453dac8be88d4c45df2645a11412a06b27f5b2c authored about 12 years ago by Hendrik Weisser <[email protected]>

[FIX] dont allow | as separator between ID and description in FASTA files

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9901 6adb6e08-d915-0410-9...

9c82d19f6bba804bd7d98743c3834a83977c4594 authored about 12 years ago by Chris Bielow <[email protected]>

[FEATURE,FIX,PARAM] * fixed #439

* PeptideIndexer will gracefully complain (exit>0) if no decoy proteins where mapped (which hints...

09e72459d073bfad8b32440cb2df88c93a85bb80 authored about 12 years ago by Chris Bielow <[email protected]>

[DOC] minor confusing typo in IDFilter

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9898 6adb6e08-d915-0410-9...

40b4b90e2ceecd6771d11dea8aa0135b5cafd8ce authored about 12 years ago by Chris Bielow <[email protected]>

[FIX] amendmend to [9893]

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9897 6adb6e08-d915-0410-9...

a272b9884bfd870fb14ddd995f587bf6e423130a authored about 12 years ago by Chris Bielow <[email protected]>

Fixed bug due to compilation error of MassTraceExtractor.

M source/APPLICATIONS/TOPP/MassTraceExtractor.C

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

d387c54977379c10c74aa22f42711be5ce532cef authored about 12 years ago by Erhan Kenar <[email protected]>

[FIX] fixed tests failing since [9886]

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9895 6adb6e08-d915-0410-9...

ad6bc99985147d43fb78e8edbee716b8e6bc76fe authored about 12 years ago by Stephan Aiche <[email protected]>

Major functionality overhaul of FeatureFinderMetabo and preparation for publication.

M source/KERNEL/MassTrace.C
M source/FILTERING/DATAREDUCTION/ElutionPeakDetection.C
M s...

190385f0fdb42211e3921307e29f8202b1f5b40d authored about 12 years ago by Erhan Kenar <[email protected]>

[FIX] minor formatting of file suffix types in TOPPAS node

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9893 6adb6e08-d915-0410-9...

6e5397e539d1a0b9c625b5e96a329aafc021c7f1 authored about 12 years ago by Chris Bielow <[email protected]>

[FIX] another fix for ID processing

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9892 6adb6e08-d915-0410-9...

074fdf89d9448a6fc6116f96398fbf928ab3bc38 authored about 12 years ago by Alexandra Zerck <[email protected]>

[FIX] fixed ID processing

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9891 6adb6e08-d915-0410-9...

61ec2380d9551759898c63ced9c4d6c1d84783ea authored about 12 years ago by Alexandra Zerck <[email protected]>

[TEST,FIX] fixed r9888

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9889 6adb6e08-d915-0410-9...

4dd46ef31a2ace366cf877f99dce177e9905160c authored over 12 years ago by Alexandra Zerck <[email protected]>

[TEST,FIX] enhanced tests and fixed checker errors

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9888 6adb6e08-d915-0410-9...

44bc731f9c549e9301d4de9d1145c194b07df1d5 authored over 12 years ago by Alexandra Zerck <[email protected]>

[FIX, DOC] * fixed #435

* made ConsensusID robust (exit gracefully) against missing RT/MZ in idXML

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

fbefce665f009bd60c89b19e8ab107f3f5a1e74e authored over 12 years ago by Chris Bielow <[email protected]>

[DOC] minor typo

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9886 6adb6e08-d915-0410-9...

b9df3412ff3df75b75c14d624702e4fbadf86920 authored over 12 years ago by Chris Bielow <[email protected]>

[FIX] OMSSAAdapter&Co: improved error messages (and made sure they are written to console by flush before app crashes).

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9885 6adb6e08-d915-0410-9...

c919579d5252c3da424cdb7ba9719ea24c3c3e7a authored over 12 years ago by Chris Bielow <[email protected]>

[DOC] added "%" before "OpenMS" to avoid reference to namespace

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9884 6adb6e08-d915-0410-9...

cac44e7bb4375cca4ca3252c20cfcb11257813e3 authored over 12 years ago by Chris Bielow <[email protected]>

[DOC] extended windows compile instructions

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9883 6adb6e08-d915-0410-9...

a5096ec95e56c4dd8437136930a790ff81ce55dd authored over 12 years ago by Chris Bielow <[email protected]>

[TEST,FIX] enhanced test

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9882 6adb6e08-d915-0410-9...

bc054e8416c807e22e0ea09bd2b1b437e0d1f067 authored over 12 years ago by Alexandra Zerck <[email protected]>

[FIX] fixed for protein based lp

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9881 6adb6e08-d915-0410-9...

11c75414add7bebfff1062bb030eefb637f834d2 authored over 12 years ago by Alexandra Zerck <[email protected]>

[FIX] fixed for featurexml output

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9880 6adb6e08-d915-0410-9...

44238f50b69b3d0d4d78cf70554d7ecfaf950ca0 authored over 12 years ago by Alexandra Zerck <[email protected]>

[TEST,FIX] fixed some stuff from checker

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9879 6adb6e08-d915-0410-9...

02085d17767dca6911030b385aaa5f86876d30f3 authored over 12 years ago by Alexandra Zerck <[email protected]>

addition to r9877

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9878 6adb6e08-d915-0410-9...

6a53f913606cf67960151b71c1c36186a4913811 authored over 12 years ago by Alexandra Zerck <[email protected]>

[TEST,FIX] removed bug in mass ranges calculation, changed parameter names in preprocessing

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9877 6adb6e08-d915-0410-9...

5dfec4e8b467fc17a605cab68af5057dafea0cae authored over 12 years ago by Alexandra Zerck <[email protected]>

[FEATURE,TEST] added iterative precursor ion selection with LPs

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9876 6adb6e08-d915-0410-9...

07538193bae26ae5055d497d9e7d5e9f587cbc79 authored over 12 years ago by Alexandra Zerck <[email protected]>

[TEST,FIX] fixed r9874

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9875 6adb6e08-d915-0410-9...

872d537e3b407252f170a0de6a6330c2593c5275 authored over 12 years ago by Alexandra Zerck <[email protected]>

[TEST,FIX] fixed IDRipper prep test by adding file_origin to to whitelist

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9874 6adb6e08-d915-0410-9...

c0ed7ea4916aa4c887f7f6245b34e4ae5032e365 authored over 12 years ago by Stephan Aiche <[email protected]>

[NOP,FIX] fixed code style warnings in ANALYSIS/TARGETED

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9873 6adb6e08-d915-0410-9...

0b52891b2bb04abd1f8ab4bfe2c2c81fa2279e49 authored over 12 years ago by Stephan Aiche <[email protected]>

[FIX] FileFilter produced unparsable output when concatenating string metadata \n FileFilter concatenated (whysoever) stringmetadata of spectra in one userparamelement without escaping the quotes. Fixed in writeUserParam function so writing invalid userparams will not be possible.

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9872 6adb6e08-d915-0410-9...

484ded6b36a5c355386b1326244dd5b2f1b9d9ba authored over 12 years ago by Mathias Walzer <[email protected]>

[INTERNAL, FEATURE, TEST] Remodeling of ProteinResolver, introduction of

quantitative experimental design.

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

c48a8b175dc4a98c1a944d4bb71992b2de23a5d7 authored over 12 years ago by Immanuel Luhn <[email protected]>

[TEST] IDRipper

Included test to show that IDMerger works properly.
IDMerger merges two file -> test correctness...

b4a551b2f840e45f434d9126505bd71729facee9 authored over 12 years ago by Immanuel Luhn <[email protected]>

[FIX] compiler warning in ReactionMonitoringTransition c'tor

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9869 6adb6e08-d915-0410-9...

3a163bd0972edac1be9c5717deadedb6b96e11cc authored over 12 years ago by Stephan Aiche <[email protected]>

[BUG] Old file name in IDRipper test

Changed old file name to new file name

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

17e1a3cf859bfa729e91cacecdb8215c664c17b3 authored over 12 years ago by Immanuel Luhn <[email protected]>

[DOC] minor fix for ImageCreator

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9866 6adb6e08-d915-0410-9...

9dced87241e88b206ef2f6a69207736f6a26bbfd authored over 12 years ago by Chris Bielow <[email protected]>

[FIX] fixed failing TraMLFile_test; fixed code formating issues in some related classes

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9865 6adb6e08-d915-0410-9...

b3582b3c83e3a02ddfd2094c50ab94e512efda0f authored over 12 years ago by Stephan Aiche <[email protected]>

[FIX] addendum to [9854]; ini style sheet was only copied for doc target but not for doc_*

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9864 6adb6e08-d915-0410-9...

d277b6a64ee878efebf38d56f68bf2c2625a82b8 authored over 12 years ago by Stephan Aiche <[email protected]>

[DOC,COMMENT,TEST,INTERNAL,TEST] IDRipper update

Example for doxygen documentation.
Changes in source documentation.
Simplification of source cod...

40fd73987409545068c6d2a119946a0cd46b449b authored over 12 years ago by Immanuel Luhn <[email protected]>

* addendum to r9861

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9862 6adb6e08-d915-0410-9...

d0e328252027fea704f2001206f499ad70566e79 authored over 12 years ago by Chris Bielow <[email protected]>

[INTERNAL,DOC] minor changes to TOPPDocumenter.C for nicer formatting (can still be improved)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9861 6adb6e08-d915-0410-9...

4bce82599586c7451f3bb125cace6ebf599aaef9 authored over 12 years ago by Chris Bielow <[email protected]>

[TEST,FIX] Fix test after commit 9851

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9860 6adb6e08-d915-0410-9...

e52c77d1bd2bf276b1f124aec0636730ab7c45ee authored over 12 years ago by Hannes Roest <[email protected]>

[INTERNAL] fixed minor issues when finding boost

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9858 6adb6e08-d915-0410-9...

0a83a40878723dcb297d086f3732f6d19564721e authored over 12 years ago by Chris Bielow <[email protected]>

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9855 6adb6e08-d915-0410-941f-83917bcadc18

0701a61675967723b554a9102608cdc9fc1a336a authored over 12 years ago by Chris Bielow <[email protected]>

* added html version of INI files to Documentation; include in TOPP/UTILS still todo

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9854 6adb6e08-d915-0410-9...

f709d0e1686d156f978e16aca58c9a867ef79b2d authored over 12 years ago by Chris Bielow <[email protected]>

[INTERNAL] xlst doc changed

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9852 6adb6e08-d915-0410-9...

2da8b9710557b2ce3b3b34a91d3d3a1c82210a30 authored over 12 years ago by Chris Bielow <[email protected]>

[FEATURE] store re-occuring attributes of TraML more efficiently

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9851 6adb6e08-d915-0410-9...

605e4971e0d54cb40b5e44ddaa307a591619a97a authored over 12 years ago by Hannes Roest <[email protected]>

[FIX] also show progress of writing TraML files

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9850 6adb6e08-d915-0410-9...

fee35f180588bea59701cb8d8f9d0a5418db1e20 authored over 12 years ago by Hannes Roest <[email protected]>

[FIX] also show progress of writing out chromatograms

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9849 6adb6e08-d915-0410-9...

9a307404445b5ecc96984db5688b9912aed9c75a authored over 12 years ago by Hannes Roest <[email protected]>

[FEATURE,API,TEST] First version of IDRipper

IDRipper rips idXML-files into several idXML-files according to the
annotated file origin of the...

c75ca5fa955488127c9c2f199e9597dfe015354b authored over 12 years ago by Immanuel Luhn <[email protected]>

[INTERNAL, TEST] Remodeling of ProteinResolver

Moved functional code from the TOPP class ProteinResolver to a helper
class ProteinResolver, whi...

018bf4e42c2baa16c3ba9df1e1c4576b2db89d39 authored over 12 years ago by Immanuel Luhn <[email protected]>

[FIX] fixed compile error introduced with [9845]

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9846 6adb6e08-d915-0410-...

3e625a792d3bb969a4e91ada445d532dae02b719 authored over 12 years ago by Immanuel Luhn <[email protected]>

[FIX] fixed windows compile error introduced with [9842]

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9845 6adb6e08-d915-0410-9...

92963e08030097ef57762ba2be156fcc7a34010f authored over 12 years ago by Stephan Aiche <[email protected]>

[FIX] fix for MapAlignerPoseClustering problem under Windows (cannot load vcomp[d].dll)

* see http://blogs.msdn.com/b/kangsu/archive/2005/10/24/484462.aspx for details

git-svn-id: ht...

59207bcd48bf012b79e75117886e57b20c707432 authored over 12 years ago by Stephan Aiche <[email protected]>

[FIX] adopted files to code changes introduced in [9815]

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9843 6adb6e08-d915-0410-9...

5aeca73237e2b2f5f9a60ff7521513c1fe53d0e4 authored over 12 years ago by Stephan Aiche <[email protected]>

[FIX] fixed error produced when MapAlignerIdentification was applied to FeatureMaps (introduced in [9585])

* moved code from MapAlignerBase.h to MapAlignerIdentification and refactored it

git-svn-id: h...

534ac69c42dfc0b87c1e088a65e435e10ef389ca authored over 12 years ago by Stephan Aiche <[email protected]>

[API] added alignMaps() method to MapAlignmentAlgorithmIdentification interface

* this method was originally alignFeatureOrConsensusMaps_; just moved it to the public interfac...

99951f5d723c1299f65f51120d79bd862ac257f4 authored over 12 years ago by Stephan Aiche <[email protected]>

[FIX] Ticket 433 - write out dataProcessing of Chromatograms

For chromatograms, the dataProcessing vector was not stored in the mzML
file (but it was read in...

fcccf56f5e6bbf6c0278586a5e63404ec22b2378 authored over 12 years ago by Hannes Roest <[email protected]>

[TEST] fixed PSLPFormulation test

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9839 6adb6e08-d915-0410-9...

090309eeb16ef7db839c901325a0de385c5107ac authored over 12 years ago by Alexandra Zerck <[email protected]>

[FEATURE] added inclusion list creation with ILPs for feature maps and protein lists

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9838 6adb6e08-d915-0410-9...

eb4b4307c958d4aa912ab76c9f7792dc68e7b370 authored over 12 years ago by Alexandra Zerck <[email protected]>

[INTERNAL,TEST] added functionality to LPWrapper

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9837 6adb6e08-d915-0410-9...

9a539aaa773c1c7cc2c4d9d17cb79142a5337e81 authored over 12 years ago by Alexandra Zerck <[email protected]>

[INTERNAL,FIX] resolved compile errors of OpenMS for VS2012

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9835 6adb6e08-d915-0410-9...

8fab204fb9a2d4d5d0bf9f8d985342a29960c740 authored over 12 years ago by Chris Bielow <[email protected]>

[INTERNAL] changes to the build system to enable building of custom boost libraries under windows

[DOC] new build instructions for Qt under Windows, making the build much faster

git-svn-id: http...

017e2d9d6d502bacc37e42aea0e35f50d93e8b69 authored over 12 years ago by Chris Bielow <[email protected]>

[INTERNAL] amend 9832, add a complete replace

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9833 6adb6e08-d915-0410-9...

35eabb259501ed2be3cb7385117a19f6e1614786 authored over 12 years ago by Hannes Roest <[email protected]>

[INTERNAL] add an option to replace a CV Term in a CVTermList

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9832 6adb6e08-d915-0410-9...

613b1eb03a41f8752910dd40493c0f14f8f63ff0 authored over 12 years ago by Hannes Roest <[email protected]>

[INTERNAL] fix for MyriMatchAdapter (more than 6 var mods allowed now)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9825 6adb6e08-d915-0410-9...

8a06c88bb43fd484bd6d625aeebb23986b244ef8 authored over 12 years ago by Chris Bielow <[email protected]>

[DOC,INTERNAL] added Myrimatch page to TOPP documentation; fixed page name

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9824 6adb6e08-d915-0410-9...

1e2e3d9e2da186a0a4356578eb959ce0fc6c015c authored over 12 years ago by Chris Bielow <[email protected]>

[FEATURE] added MyriMatch adapter from branch "IDAdapter" with minor changes

[INTERNAL] mzXML and MzDataHandlers now support MSNSPECTRUM (will be inferred from scan type etc ...

37a8cea7d12d7f402c90f97e6f7814769a10c6ae authored over 12 years ago by Chris Bielow <[email protected]>

[INTERNAL] fixed issue with OPENMS_DLLAPI, introduced in r9808

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9822 6adb6e08-d915-0410-9...

5cc48c02b5409a449cd03b16b5a5ec721e6eb7af authored over 12 years ago by Chris Bielow <[email protected]>

[FEATURE] first version of ProteinResolver which is based on IsoformResolver -- second attempt

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9821 6adb6e08-d915-0410-9...

3aaa3dfe22f379f6ef120bfae3c38d1b39784e1f authored over 12 years ago by David Wojnar <[email protected]>

[INTERNAL] reverse merged incomplete commit r9818

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9820 6adb6e08-d915-0410-9...

e02b2a2107a9ebf7ce27d36cf8b248014618f06d authored over 12 years ago by Chris Bielow <[email protected]>

also add the NativeID to the title of MGF files to make later matching easier

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9819 6adb6e08-d915-0410-9...

b9cbb987525206178b9d7b8fa4c7ccddf1e20ddd authored over 12 years ago by Hannes Roest <[email protected]>

[FEATURE] first version of ProteinResolver which is based on IsoformResolver

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9818 6adb6e08-d915-0410-9...

49b8b92f861eadd2c7f0737ca1eae2494925bdf8 authored over 12 years ago by David Wojnar <[email protected]>

[TEST] add explanatory testcase to LinearResampler

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9816 6adb6e08-d915-0410-9...

7c9fa0fd4767b33d388059c38a491eaef220719f authored over 12 years ago by Hannes Roest <[email protected]>

[PARAM] renamed UserParam reflect convention in FalseDiscoveryRate

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9815 6adb6e08-d915-0410-9...

7c1d5cb188d38e64fcf8565faade55e6bc32aa87 authored over 12 years ago by Timo Sachsenberg <[email protected]>

[FIX,TEST] fixed data processing info problem in SILACAnalyzer introduced in [9744]

* SILACAnalyzer tried to add the processing info by hand and not with the TOPPBase functionalit...

bea16978c53fe8a065a47f1f6e5a4c1758a288ab authored over 12 years ago by Stephan Aiche <[email protected]>

[INTERNAL] SILACAnalyzer_negativ.consensusXML fixed

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9813 6adb6e08-d915-0410-9...

3b3c4bdc3cde77af6efa90d9d92b62cf5f4e8469 authored over 12 years ago by Chris Bielow <[email protected]>

[TEST] updated test data for INIUpdater tests to correct test errors introduced in [9775] and [9757]

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9812 6adb6e08-d915-0410-9...

2cee1f3c85c908d961916b35b359cbee97e1eacb authored over 12 years ago by Stephan Aiche <[email protected]>

[INTERNAL] fix for OMP in MapAlignerPoseClustering

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9811 6adb6e08-d915-0410-9...

839028f74a4e43e8296b89dcfee2a90cf240e7bb authored over 12 years ago by Chris Bielow <[email protected]>