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

[FEATURE] integrated qcustomplot widget with permission of the author into OpenMS

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10839 6adb6e08-d915-0410-...

34fb0fb599acd87e4e7d5acf52a356cfd7c1c3c6 authored over 11 years ago by Timo Sachsenberg <[email protected]>

changed the built-in stylesheet of QCExporter

(border="0" renders nonexisting table attachments invisible).

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

fff510a1ca94e5b8f9ad22108afdacd2d0c66298 authored over 11 years ago by Oliver Kohlbacher <[email protected]>

[FIX] mime.types now also gets copied while generating the required folder structure for KNIME; for compatibility we will also keep the old file

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10.1@10834 6ad...

dc60853655c701cd5fabb3fbe80407d0d028d8f3 authored over 11 years ago by Stephan Aiche <[email protected]>

[FIX] added mime.types file required by latest version of gkn

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10.1@10833 6ad...

b12f23fd6bf3db4f394be2d876a010aef6f5cbba authored over 11 years ago by Stephan Aiche <[email protected]>

made QCExporter be able to export any QP Attachment table, added some more docu

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10.1@10832 6ad...

4bd2fb9b7fa2c7e7587c4bd47504533704bea96d authored over 11 years ago by Mathias Walzer <[email protected]>

[FIX] fixed win32 compile error introduced in [10496]

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10831 6adb6e08-d915-0410-...

b0872004f1fc8f74e7dccd370dadd13cb8057390 authored over 11 years ago by Stephan Aiche <[email protected]>

QCEmbedder now has parameter set/run if no qc file given and table should be attached to set

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10.1@10830 6ad...

6c28153b76157b5fd9598dc2abe24765043319ba authored over 11 years ago by Mathias Walzer <[email protected]>

QCEmbedder can now create a new qc file if none given - added as run so far.

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10.1@10829 6ad...

e9c807f31299e5ce675dc390df465b3b94319ddf authored over 11 years ago by Mathias Walzer <[email protected]>

QCEmbedder can now introduce QP in topleven run/set, if not yet contained to attach something to.

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10.1@10828 6ad...

851b83e6f52249d709c3273d8890c32ed07d6613 authored over 11 years ago by Mathias Walzer <[email protected]>

fixed glitch that kept Attachments from being attached to sets

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10.1@10827 6ad...

e68751ce735b521b259b0a9e91b8c621fa06889d authored over 11 years ago by Mathias Walzer <[email protected]>

[TEST] fix headers of testfiles

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10826 6adb6e08-d915-0410-...

a120876972686268f539baf273c721a462a30c24 authored over 11 years ago by Hannes Roest <[email protected]>

made -plot optional for QCEmbedder

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10.1@10823 6ad...

709493d75ad9c77e62dd4e5682eee8d0f7996562 authored over 11 years ago by Mathias Walzer <[email protected]>

removed old MS1/MS2 options that bloated qcml files and were redundant

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10.1@10822 6ad...

7cd6cd2149d4c49072aebb47f0b459858776c17b authored over 11 years ago by Mathias Walzer <[email protected]>

[NOP] set OpenMS version to 1.10.1

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10.1@10820 6ad...

78ad6e4c033a3b7e61c67c8e77b684b193026107 authored over 11 years ago by Stephan Aiche <[email protected]>

[NOP] created 1.10.1 branch

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10.1@10819 6ad...

90a2ed2aff61233ff9493c608ac8a24bc58adcfc authored over 11 years ago by Stephan Aiche <[email protected]>

[FIX-#518] fix various segfaults when loading empty chromatograms into TOPPView

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10806 6adb6e08-d915-0410-...

c5f360a1a3c0552544f153e65a846f216d131fe3 authored over 11 years ago by Hannes Roest <[email protected]>

[TEST] fix test files after merge

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10805 6adb6e08-d915-0410-...

44e4cf86689bd5d3d4ae08e0e63f4d0da101ebbf authored over 11 years ago by Hannes Roest <[email protected]>

[NOP] remove unnecessary cout command

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10804 6adb6e08-d915-0410-...

166cd6dbe2efe7de78c5505865201235298625ba authored over 11 years ago by Hannes Roest <[email protected]>

Merged release branch into trunk 10369:10800

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10801 6adb6e08-d915-0410-...

7a7d32dd45d5b3b955b6b165df1343612241c8b4 authored over 11 years ago by Timo Sachsenberg <[email protected]>

[FIX] fixed TOPPAS open containing folder for input/tool/output nodes on mac osx

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10796 6adb6...

b48c4a875f190bad126cd346b8b0e48dcb0b0e0b authored over 11 years ago by Stephan Aiche <[email protected]>

[DOC] added publication reference

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10795 6adb6...

09944a1dfbf6134f0298589fc3ed9d74f21c51a2 authored over 11 years ago by Hendrik Weisser <[email protected]>

[FIX] fixed TOPPAS: Open in TOPPView on mac osx

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10794 6adb6...

a01182af6e04fe2ed705293689717ebb46ed33d2 authored over 11 years ago by Stephan Aiche <[email protected]>

[NOP] promoted some tools/utils to official (fixes issue with tool/util categories in KNIME)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10790 6adb6...

f7fa9c4a998d57fcf2ca485eb6e11d3fbbcbba6f authored over 11 years ago by Timo Sachsenberg <[email protected]>

[FIX] mzMLHandler did not escape cv-param values correctly

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10789 6adb6...

e1b395785571f1ab9ac0180ab37278657b54db1c authored over 11 years ago by Stephan Aiche <[email protected]>

[FIX] fixed error in KNIME config files for lnx and mac

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10788 6adb6...

8e4cf145cbfc3991ad70a9588f1e3f87235cbcdd authored over 11 years ago by Stephan Aiche <[email protected]>

[NOP] small changes to documentation

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10785 6adb6...

4f394ba2eb38f0052aab9d2e761abab899c21b94 authored over 11 years ago by Timo Sachsenberg <[email protected]>

[DOC] some more upates and fixes for the mac build documentation

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10784 6adb6...

ef440f82fedca2c09be2504fc46197572a05ab1a authored over 11 years ago by Stephan Aiche <[email protected]>

[DOC] updated mac build/install instructions

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10783 6adb6...

e638fe7b134b029b0b879cb82dfb90f0163fcd70 authored over 11 years ago by Stephan Aiche <[email protected]>

[FIX-#514] fixed UTILS category and docurl issue

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10782 6adb6...

16569bc8b8726bdde9fb243e8c3f58e8647cfce0 authored over 11 years ago by Stephan Aiche <[email protected]>

[FIX,NOP] fixed some warnings, checker errors, and formatting issues

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10781 6adb6...

a9c0eadaf9611b3864b321d5a9f259dc14e1d4b2 authored over 11 years ago by Stephan Aiche <[email protected]>

[FIX-#515] fix segfaults during parallel executiontr

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10780 6adb6...

80fab912c95a0ea60d4ca8d84017337559fbfa24 authored over 11 years ago by Hannes Roest <[email protected]>

[FIX] deprecation of sequest out dirs

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10779 6adb6...

91889e137c158a4e550aca0f68b862499f15d294 authored over 11 years ago by Timo Sachsenberg <[email protected]>

[NOP] added more about KNIME in CHANGELOG and adapted date as well as some fixed tests

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10778 6adb6...

2f2bd634db39357019d9d25464de4fa172e977b4 authored over 11 years ago by Timo Sachsenberg <[email protected]>

[FIX] Added category "Utilities" to all UTILs for nicer KNIME integration

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10777 6adb...

24f0ff8f4a7006ac4ade1733e2cea0d29e1899ac authored over 11 years ago by Johannes Veit <[email protected]>

[TEST] added tests for UTILS -write_ini to avoid bugs like r10773

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10776 6adb6...

942f5d5c43994d8f3deb3c21e004a0f8a7e66e4f authored over 11 years ago by Chris Bielow <[email protected]>

[DOC] added paper ref to ConsensusID and fixed some typos

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10775 6adb6...

e6223d2f8f026dabd7bdb63a52badf0d30c7d2b0 authored over 11 years ago by Chris Bielow <[email protected]>

[NOP] added some changelog entries

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10774 6adb6...

6cabe9be1f84f21ce74de0b96919a50a355c353b authored over 11 years ago by Timo Sachsenberg <[email protected]>

[FIX] QApplication error introduced in r10755

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10773 6adb6...

9470ddac696b4f6a46278cb1f078397859f8389f authored over 11 years ago by Chris Bielow <[email protected]>

[TEST] Fixed a typo in MassTrace_test.

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10772 6adb6...

f50391775e4221ff2422c22cc31496608ee40f83 authored over 11 years ago by Erhan Kenar <[email protected]>

[FEATURE,TEST] Added more robust peak area calculation method for mass traces and corresponding unit tests. Fixed follow-up errors in FeatureFinderMetabo-related unit tests.

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10771 6adb6...

01825c18ca04b62e6b4f1114cbea3fc726d5479a authored over 11 years ago by Erhan Kenar <[email protected]>

[FIX] of checker warnings

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10770 6adb6...

294482e8d24c8e1dcbdd791e123df28067034f4a authored over 11 years ago by Chris Bielow <[email protected]>

[TEST,FIX] Added several missing tests for MassTrace kernel class. Fixed some issues in MassTrace and related classes. Resolved checker.php and coding style issues.

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10769 6adb6...

1847c847e115356a30e25565d2c4aa6653a95afa authored over 11 years ago by Erhan Kenar <[email protected]>

[FIX-#513] Commented out the functionality of smartFileNames_() (not mature enough for the 1.10 release)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10768 6adb...

2545b77efd363f6df73d359142fa402b63958347 authored over 11 years ago by Johannes Veit <[email protected]>

[FIX] fixed cppcheck and checker warnings; added ParamXMLFile::writeXMLToStream test

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10767 6adb6...

fb9a2c9b0f3686600e50db711b787e5cd3086116 authored over 11 years ago by Stephan Aiche <[email protected]>

[NOP] updated the license shipped with the KNIME plugin to be Eclipse installer conform

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10763 6adb6...

82ba6a2a907217931e5ed454869e9440b6c170e2 authored over 11 years ago by Stephan Aiche <[email protected]>

[FIX-#512] fixed #512; implemented getSizeOnly/setSizeOnly methods

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10762 6adb6...

183d379a071c0f6dd563cc819770b09ffd6b6d68 authored over 11 years ago by Stephan Aiche <[email protected]>

[FIX] fixed the other half of [10755]

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10761 6adb6...

de15b5c2edfc7dc085036e35a8492ed82cae5f9b authored over 11 years ago by Stephan Aiche <[email protected]>

[FIX] removed several warnings

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10760 6adb6...

235f784bb60db0aa44da6de82c8809a4ca0c7404 authored over 11 years ago by Stephan Aiche <[email protected]>

[TEST] Fixed missing tests for ElutionPeakDetection_test (errors from checker.php)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10759 6adb6...

c6151adace28584e3052d367378adea07aff7273 authored over 11 years ago by Erhan Kenar <[email protected]>

[FIX,FEATURE] Several fixes improving robustness of MassTraceExtractor and FeatureFinderMetabo tools. Added improved isotope ratio model for better feature assembly. Overhauled version for OpenMS 1.10 release.

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10758 6adb6...

f3a4a8b6a96ef7d0a699af3e7065e3a9572d2cb7 authored over 11 years ago by Erhan Kenar <[email protected]>

[TEST] added MyriMAtch test

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10757 6adb6...

4f4ee99a909c7b03d7d46d1441b33c6eb3673a82 authored over 11 years ago by Timo Sachsenberg <[email protected]>

[DOC,NOP] info when using redundant FileFilter options

* optimization during sort by preallocation

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

ae0c04f1f3d81f3c76d31b3f254fc90209c3a086 authored over 11 years ago by Chris Bielow <[email protected]>

fixed a few warnings (OSX) due to missing const cast

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10755 6adb...

7bfbe406ac49ce04e31ceaf0e978182b2179d9ba authored over 11 years ago by Oliver Kohlbacher <[email protected]>

[FIX] spectra list not updated anymore if identification data was loaded

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10753 6adb6...

0d14c73caca10422488b7b17c34e6234a041d6ee authored over 11 years ago by Timo Sachsenberg <[email protected]>

[FIX] fixed compile warning

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10752 6adb6...

b860435ec5dc4f3bb144bb4c56cd4ebf39b93696 authored over 11 years ago by Timo Sachsenberg <[email protected]>

[TESTING] added XTandem test

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10751 6adb6...

2a89ee9a5a7a195f1519ffb6ff6e262e14afbdfa authored over 11 years ago by Timo Sachsenberg <[email protected]>

[FIX] small fix for the TOPP bash profile; we now check if ~/.profile exists before we include it

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10750 6adb6...

0edddaaa6735958acee54e6f6e0589ab18b20e17 authored over 11 years ago by Stephan Aiche <[email protected]>

[FIX] fixed failing INIUpdater test

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10749 6adb6...

9bcc5226713530df7224fb4ef9e4bff5fc572c20 authored over 11 years ago by Timo Sachsenberg <[email protected]>

[FEATURE] added advanced parameter to change isotopic abundancies for metabolic labeling experiments (default disabled)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10748 6adb6...

4040eb23603c6fe6cfd8eb18f43cecb9ae4aad72 authored over 11 years ago by Timo Sachsenberg <[email protected]>

[FEATURE] improved runtime of StablePairFinder when it uses identifications

* reimplemented the StablePairFinder::compatibleIDs_ method
* 1st test show speed up of ~ 60%
...

e1f256c34ef7ade5c44f467561297528174ead77 authored over 11 years ago by Stephan Aiche <[email protected]>

[FIX] broken tests

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10744 6adb6...

e3ebbe3a6b9e948964090949123bd021d36bb8f7 authored over 11 years ago by Chris Bielow <[email protected]>

[DOC] for FeatureFinderUnlabled (warning for long runtime for 'use_identifications')

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10743 6adb6...

5d5bf45c6dd1c2454eb383f13e67ef9a43d49f85 authored over 11 years ago by Chris Bielow <[email protected]>

[FIX] StopWatch test for linux fixed

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10742 6adb6...

de761b60f3ef45f1182121401fc14ea869e466b6 authored over 11 years ago by Chris Bielow <[email protected]>

[FIX]

* no more negative/wrong stopwatch measurements (on Windows) due to small datatype
* removed su...

9b0b873448afe0d5c457f64e6c746629f44de363 authored over 11 years ago by Chris Bielow <[email protected]>

[FIX] fixed test failing because of new parameter

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10740 6adb6...

23bf9db59285acf452aa4ec2f58e4d7b7931ed6e authored over 11 years ago by Timo Sachsenberg <[email protected]>

[FIX-#511] Fixed temp dir creation & deletion also for ExecutePipeline (for the TOPPAS fix, see r10681, r10682, r10734)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10739 6adb...

05a87a53780c8fcb65050f172798ff8bca4ec900 authored over 11 years ago by Johannes Veit <[email protected]>

[NOP,FIX] fixed some cpplint errors

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10738 6adb6...

702b2b1eee2eb20ab87f37233a4ac606b00fa259 authored over 11 years ago by Stephan Aiche <[email protected]>

[PARAM] added max_isotopes to FeatureFinderCentroided as parameter for metablic labeling experiments

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10737 6adb6...

d7d58eff68dce35c59102bd88582a3937a6a06c7 authored over 11 years ago by Timo Sachsenberg <[email protected]>

[DOC] FeatureLinker docu fixed

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10736 6adb6...

716f6623defdca7e4e6916bff75119b04a3b49d2 authored over 11 years ago by Chris Bielow <[email protected]>

[NOP] reduced verbosity of tools if not in debug mode

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10735 6adb6...

ee7683d09f81a9c774c2140538438ccac59ed51a authored over 11 years ago by Timo Sachsenberg <[email protected]>

[FIX] TOPPAS bug: TOPPAS tmp directory was deleted by ~TOPPASScene(). Moved this to ~TOPPASBase().

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10734 6adb...

12d48c177e71754026e53b0f68234357cdaea6fc authored over 11 years ago by Johannes Veit <[email protected]>

[FIX] less stringent E-value threshold for OMSSA hits (avoid premature filtering by OMSSA)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10733 6adb6...

47f0739ab2581a3ceb617074a5112a5c848075e9 authored over 11 years ago by Chris Bielow <[email protected]>

[NOP,FIX] fix for the knime windows package

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10732 6adb6...

bb45eddf5bc3dc23ac663cacec376aae96c8bf17 authored over 11 years ago by Stephan Aiche <[email protected]>

[DOC] nicer formatting of command line -- no splitting of small words

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10731 6adb6...

a5a9a901132973639ba3c5625fe730d241addd74 authored over 11 years ago by Chris Bielow <[email protected]>

[DOC] better error message for failing FASTA file parse

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10730 6adb6...

50f79b6fddac3cdae1e45789568b7d53f6436346 authored over 11 years ago by Chris Bielow <[email protected]>

[DOC] more words on FDR

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10729 6adb6...

1c5d7dfaa852e3d72bfa349f48a09e0772add06b authored over 11 years ago by Chris Bielow <[email protected]>

[FIX] ModificationsDB returns cleared result vectors which only contain the actual results and not part of the old input

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10728 6adb6...

ffe607149b090ba0d2e7af4c00c25913fb9c3218 authored over 11 years ago by Chris Bielow <[email protected]>

[DOC] fixed references, and some formatting

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10727 6adb6...

23e491e396edbfe2333528b10d56e2a776e257a1 authored over 11 years ago by Chris Bielow <[email protected]>

[DOC] made decoy annotation of PeptideIndexer and FalseDiscoveryRate more clear (hopefully)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10726 6adb6...

c0eba9b93c4b5cc0cdc40644e4494b0a47c8ec6b authored over 11 years ago by Chris Bielow <[email protected]>

[FIX] accidently changed mac instead of win ini in [10724]; reverterd [10724] and applied the changes to the correct file

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10725 6adb6...

252f8eaac3f886b06e83dd40141b8746dce689b9 authored over 11 years ago by Stephan Aiche <[email protected]>

[FIX] fixed knime bundle problem on windows

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10724 6adb6...

d55f6a07b3fdbf1b2acc57d7daacb89864582c55 authored over 11 years ago by Stephan Aiche <[email protected]>

[FIX,BUILD] fixed the generation of the OpenMS version information for the KNIME package for older cmake versions

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10723 6adb6...

33af6938bf10dc206d8d53e858767c9b1fba5de6 authored over 11 years ago by Stephan Aiche <[email protected]>

[FIX]corrected/replaced R scripts for qc plots, added default run name behaviour in QC tools if none given

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10722 6adb6...

3520937e752b3db4e450b09232b94eb62c959a81 authored over 11 years ago by Mathias Walzer <[email protected]>

[GUI,FEATURE-#509] implemented handling of QEvent::FileOpen for QApplicationTOPP to enable handling of odoc event on mac osx.

See #509 for details

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

d9c459043950e6ead09f60f9c8f6c8d0677cafdf authored over 11 years ago by Stephan Aiche <[email protected]>

[BUILD,GUI] added application specific templates for mac osx gui apps (${appname}.plist.in) including file associations

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10720 6adb6...

0a94ba5d2918d328955bb2dc1866522a1a862270 authored over 11 years ago by Stephan Aiche <[email protected]>

[TEST] some test dependency fixes

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10719 6adb6...

9414ca1ceb8aa69eda560251154c6786ae6811c4 authored over 11 years ago by Stephan Aiche <[email protected]>

[NOP] minor speedup of spectra list in TOPPView

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10718 6adb6...

d8922f809b7f790862c6bb9eb84c7ced950a6087 authored over 11 years ago by Timo Sachsenberg <[email protected]>

[NOP] minor cleanup of SpectraViewWidget

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10717 6adb6...

bdb1ab7dfc55ac5512c9d530d4f66a6ee73f8780 authored over 11 years ago by Timo Sachsenberg <[email protected]>

[FIX] allow storing TOPPAS pipeline when edges are either green OR YELLOW

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10716 6adb6...

3c05a3a4816c98df7e4692b71191d3a08997d1d1 authored over 11 years ago by Chris Bielow <[email protected]>

[NOP] code move and comments

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10715 6adb6...

2e2dd9ce1b75c02834db6a2b0840ee53460d3363 authored over 11 years ago by Hannes Roest <[email protected]>

[FIX-#508] FIX add columns for uniprot id and fragment ch/nr/type, add tests

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10714 6adb6...

c19b95b5228c765e32bb674d7f54f004364d613c authored over 11 years ago by Hannes Roest <[email protected]>

[FIX-#508] allow free columns for TSV

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10713 6adb6...

e32712f72e77d15c7af628fc3a8173441448ae40 authored over 11 years ago by Hannes Roest <[email protected]>

[FIX] Added external csv embedding, corrected a R script.

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10712 6adb6...

7680927c62681c9851e580ada3395bd4c030cc6b authored over 11 years ago by Mathias Walzer <[email protected]>

[FIX-#473] change in/out types again to csv

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10711 6adb6...

af874a63ea05ffc765c3363479f94d9092b71211 authored over 11 years ago by Hannes Roest <[email protected]>

[FIX] remove all instances of addText() from TOPPBase, since it allowed for misleading documentation of parameters on the command line.

This documentation is however lost in the INI file, thus parameter names might not be explanatory...

c715eb583806563095d7104d4b18b37c94ad8422 authored over 11 years ago by Chris Bielow <[email protected]>

[FEATURE] Param:update() now allows to match old parameters if the name of the leaf-node is unique (i.e. the path is allowed to change).

Useful when introducing new subsections and just moving parameters within the param tree

git-sv...

60b49e2d81b5d5907c39a01e4da0c884eb8008d8 authored over 11 years ago by Chris Bielow <[email protected]>

[BUILD] implemented knime payload packaging on lnx systems; needs further testing

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10708 6adb6...

6a31dab5bdb8eba5c9a52d1d57421c0e1452d900 authored over 11 years ago by Stephan Aiche <[email protected]>

[FIX-#507,BUILD,DOC] adapted [10704] to support also windows, removed obsolete doc_prepare

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10707 6adb6...

30a6979ec3eee38231e22add41c57a3af87710e9 authored over 11 years ago by Stephan Aiche <[email protected]>

[FIX] ConvertTSVToTraML/ConvertTraMLToTSV: fixed i/o format declaration bug introduced in [10454], TransitionTSVReader: added exception for non-UniMod modifications

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10706 6adb6...

ec7cf64761028ad9bb68893b977075320eeb1d67 authored over 11 years ago by George Rosenberger <[email protected]>

[NOP] removed some redundant information

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10@10705 6adb6...

bfb6ca4b3d498514564eee2b1cf853d8a22e4347 authored over 11 years ago by Timo Sachsenberg <[email protected]>