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

[INTERNAL] OpenMS : Refactor OpenSwathConfidenceScoring into OpenMS library

OpenMSKernel changed

-merged with:

added missing OPENMS_DLL annotation

OpenMSKernel changed

...

9f1d6732e61815f35097f0f708005ec02be78d8c authored over 11 years ago by Hannes Roest <[email protected]>

fixed missing OpenSwathAlgo lib declaration in setup.py

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11083 6adb6e08-d915-0410-...

bad56c9e13a38beb30579d5b959c72d31ae2e950 authored over 11 years ago by Hannes Roest <[email protected]>

added support for CVTermList

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11082 6adb6e08-d915-0410-...

439e9ca2ba2ab69428d1eccb11977d8864ba0222 authored over 11 years ago by Hannes Roest <[email protected]>

[FEATURE] add ChromatogramExtractor

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11081 6adb6e08-d915-0410-...

24277be4f5b4894f3a5bf755cd72e80718971ac0 authored over 11 years ago by Hannes Roest <[email protected]>

wrapped LightTargetedExperiment

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11080 6adb6e08-d915-0410-...

e6fe1512f19ccf130716bf2f15c4e98ebfc7c70d authored over 11 years ago by Hannes Roest <[email protected]>

unittest cleanup

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11079 6adb6e08-d915-0410-...

500661589090bfcfba4052ef7d35a6854b75b488 authored over 11 years ago by Hannes Roest <[email protected]>

cleanup integration test

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11078 6adb6e08-d915-0410-...

f0cde0926a000701968f511fdb2c6cb2aba7c5b1 authored over 11 years ago by Hannes Roest <[email protected]>

cleanup

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11077 6adb6e08-d915-0410-...

5aeddc95f26bbbc09dbb90055c64f11535a579fb authored over 11 years ago by Hannes Roest <[email protected]>

add two pyTOPP tools

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11076 6adb6e08-d915-0410-...

73b84134e90a951591b5bb25bb4d05e36799d70f authored over 11 years ago by Hannes Roest <[email protected]>

[FEATURE] add MSChromatogram and extend MSExperiment

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11075 6adb6e08-d915-0410-...

7e43495b5efd25b45bd2cb7bab09c5f4dd03d18e authored over 11 years ago by Hannes Roest <[email protected]>

pyOpenMS: more classes wrapped + cleanup

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11074 6adb6e08-d915-0410-...

b0791a7036f35fa08463227b1c1896420308e839 authored over 11 years ago by Hannes Roest <[email protected]>

[DOC] write up how to wrap new classes

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11073 6adb6e08-d915-0410-...

794e1dca5757cf7cd3d4a961d2e3f99ad703ed87 authored over 11 years ago by Hannes Roest <[email protected]>

[FEATURE] wrap MRMRTNormalizer with tests

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11072 6adb6e08-d915-0410-...

c770e77490acf92fa49f45e6f125a47bb4e0fde4 authored over 11 years ago by Hannes Roest <[email protected]>

[INTERNAL] add direct methods for pyOpenMS, catch error

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11071 6adb6e08-d915-0410-...

5c103daba4e7088dc5fb36cf3e33bed8dd0bf876 authored over 11 years ago by Hannes Roest <[email protected]>

[FEATURE] wrap CVTerm and CVTermList (not all functions supported)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11070 6adb6e08-d915-0410-...

eb96a49b9dc7880f9ba858234a9fb0a3e0ce50e5 authored over 11 years ago by Hannes Roest <[email protected]>

[FEATURE] wrap MRMFeatureFinderScoring

OpenMSKernel changed

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@110...

bd0fe4982d72d07fde5fe63cf8a2ebf7195b247d authored over 11 years ago by Hannes Roest <[email protected]>

[TEST] added tests for pepxml and idxml in separate files

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11068 6adb6e08-d915-0410-...

b3b64beb413ab7efa4bbf5a005e66ab164c5ed83 authored over 11 years ago by Hannes Roest <[email protected]>

[FEATURE] wrapped TargetedExperiment

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11067 6adb6e08-d915-0410-...

36d014f245442c422380239c48f64a4f5928ec48 authored over 11 years ago by Hannes Roest <[email protected]>

first try: wrap PepXML class

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11066 6adb6e08-d915-0410-...

959ac8b41cc1351983c7a33b5ae8833547af0be2 authored over 11 years ago by Hannes Roest <[email protected]>

fixed typo in README

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11065 6adb6e08-d915-0410-...

9bdef60746fe669bf3747551c4b900ead857f3b6 authored over 11 years ago by Hannes Roest <[email protected]>

fixed iterator bug for MSSpectrum

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11064 6adb6e08-d915-0410-...

e026f33fa4cd2b377d1b0c30ff8169a3ad832ea1 authored over 11 years ago by Hannes Roest <[email protected]>

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11063 6adb6e08-d915-0410-941f-83917bcadc18

5d35c82fbc45bcfdd7bae2a8368358924ef85de8 authored over 11 years ago by Hannes Roest <[email protected]>

fixed build issue on linux

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11062 6adb6e08-d915-0410-...

9f4ef11ec6043d85f809b65ee72fd3a5cb98858c authored over 11 years ago by Hannes Roest <[email protected]>

got pyopenms working on win 7

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11061 6adb6e08-d915-0410-...

b232500d1cb8679ae9dac96bfb2e0f6e847cb00f authored over 11 years ago by Hannes Roest <[email protected]>

[FIX] add const in kernel

OpenMSKernel changed

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@110...

afc73b39b9487b94b396adc5b97a7945dcd4fc63 authored over 11 years ago by Hannes Roest <[email protected]>

tried fix for msvc++ 9

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11059 6adb6e08-d915-0410-...

e657069859be2f4ade8c9652260f9d016730db31 authored over 11 years ago by Hannes Roest <[email protected]>

added tests, added build of pyTOPP tools

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11058 6adb6e08-d915-0410-...

20573fc8804921ae351d0a4a2e5194f85103cc61 authored over 11 years ago by Hannes Roest <[email protected]>

fixed type issue

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11057 6adb6e08-d915-0410-...

ea6a21cd1f4182a569fa08d78c946b7fb10544b9 authored over 11 years ago by Hannes Roest <[email protected]>

fix for pyopenms build

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11056 6adb6e08-d915-0410-...

21df1c88f1231f4be6100fe0ed52b53e78f62e5f authored over 11 years ago by Hannes Roest <[email protected]>

fixed corrupt cmake file for make target 'targets'

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11055 6adb6e08-d915-0410-...

f625d038779fdc5c9f5d7a37a3d0da231c261f04 authored over 11 years ago by Hannes Roest <[email protected]>

[FIX] OPENMS_DLLAPI template switch

OpenMSKernel changed

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@110...

a575d41a182086207c079f0270a1ac1da7cc3472 authored over 11 years ago by Hannes Roest <[email protected]>

fixed run_nose.py

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11053 6adb6e08-d915-0410-...

2199c6192acfe4eaba93eba9f70e3cebc06f341d authored over 11 years ago by Hannes Roest <[email protected]>

[INTERNAL] add functions / constructors necessary for pyOpenMS

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11052 6adb6e08-d915-0410-...

048b95c4e5402b293475407dbbb9303bd5130d33 authored over 11 years ago by Hannes Roest <[email protected]>

added pyTOPP/IDMapper.py

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11051 6adb6e08-d915-0410-...

7ab2799788343d30ee715dfac403dee607f95bf5 authored over 11 years ago by Hannes Roest <[email protected]>

pyTOPP/FeatureLinkerUnlabeledQT.py finished

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11050 6adb6e08-d915-0410-...

2fdd390e3c13f7973954ef3604830e1934e420b9 authored over 11 years ago by Hannes Roest <[email protected]>

[INTERNAL] add functions / constructors necessary for pyOpenMS

OpenMSKernel changed

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@110...

248209274e9c82f90a8a29329c006478153222bc authored over 11 years ago by Hannes Roest <[email protected]>

build system part

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11048 6adb6e08-d915-0410-...

4e3d6f97cc50faaa01e4d5736b1edffb651155cb authored over 11 years ago by Hannes Roest <[email protected]>

add more features

split 10786: pyOpenMS part

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

444256776e9ff4ea66ad40142cf1a58c7f51cf1b authored over 11 years ago by Hannes Roest <[email protected]>

added pxds/ Filoptions

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11046 6adb6e08-d915-0410-...

361b8ee45724a159979dabd64a247738f6a6bccf authored over 11 years ago by Hannes Roest <[email protected]>

file cleanup

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11045 6adb6e08-d915-0410-...

8c1d3e548ec39809d19f4179a11bba0c84d11152 authored over 11 years ago by Hannes Roest <[email protected]>

add pyOpenMS code

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11044 6adb6e08-d915-0410-...

b5ddd10bd3245e83528be52cd7f52ffdbe8a72e1 authored over 11 years ago by Hannes Roest <[email protected]>

[DOCU] fix typos

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11043 6adb6e08-d915-0410-...

7f90cdd9268323fc4496b9e1560257754018341f authored over 11 years ago by Hannes Roest <[email protected]>

[FIX, FEATURE] * cleanup of MascotGenericFile yielding ~10% performance increase while parsing

* OpenMP support for MGF-reading to increase speed (up to factor of 4x), since on Windows VS2012...

efa9d5a720616e142a2758b41cb0d6cf1330c505 authored over 11 years ago by Chris Bielow <[email protected]>

[FEATURE,TEST,FIX] FileInfo now prints some basic information on peptide modifications in idXML files

* Chromatogram information pushed into library to avoid redundancies

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

f3796b8c4311e168d0fd1bc71301650110a6b23a authored over 11 years ago by Chris Bielow <[email protected]>

[FIX, TEST] removed whitespaces to fix mzTab test

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11040 6adb6e08-d915-0410-...

a93347ea3e5fd4d4d51cb160826bfa928b8097c0 authored over 11 years ago by Timo Sachsenberg <[email protected]>

[TEST] improved mzTab test

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11039 6adb6e08-d915-0410-...

414b0483ae2e6a9b0eda2fb7df3971abcba2bf38 authored over 11 years ago by Stephan Aiche <[email protected]>

[FEATURE] switched to boost::lexical_cast for String::toDouble() and String::toFloat()

Switching to boost::lexical_cast improves run time up to 3-fold when parsing mgf
files. Other pa...

3a14243022798a5ef30de6a3cfcca85421d94f65 authored over 11 years ago by Stephan Aiche <[email protected]>

[FIX] fixed problematic version handling/check of mzML handler

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11037 6adb6e08-d915-0410-...

07a523594e31882a5a835fb8946ae2768fa67677 authored over 11 years ago by Stephan Aiche <[email protected]>

[FIX,TEST] fixed MRMDecoy test that created data in the source tree

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11036 6adb6e08-d915-0410-...

e43995978557a3828f625bb1703f59a61cc81b14 authored over 11 years ago by Stephan Aiche <[email protected]>

[FIX,TEST] fixed test dependency for TOPP_NoiseFilterGaussian_1_out1

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11035 6adb6e08-d915-0410-...

58a50e341eff9fd4ced1507e960f41753d9431b2 authored over 11 years ago by Stephan Aiche <[email protected]>

[FIX] improve memory footprint of OMMSAAdapter by holding experiment data only as long as required

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11034 6adb6e08-d915-0410-...

4abc63880fd3ab5a7b90c789da0904a540e891e9 authored over 11 years ago by Chris Bielow <[email protected]>

[IO, DOC, FEATURE] * DecoyDatabase can now handle an arbitrary number of input files (not just a single FASTA file plus contaminant). This makes it easier to create target-decoy databases from multiple fasta files (e.g. if the sample contains multiple species, e.g. CElegans, EColi plus contaminants).

This is a sensible way to go since DB-Adapters support only a single input file and for OMSSA its...

f6e4d62bcd148cb8bc752362ce087937f9f0a1f2 authored over 11 years ago by Chris Bielow <[email protected]>

[FEATURE] * added progress bar when storing MGF files

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10990 6adb6e08-d915-0410-...

5486009e9e2c30d41f55a2820dc4d0c636d97fcb authored over 11 years ago by Chris Bielow <[email protected]>

[FIX/FEATURE] * make MSExperiment a little more fail-safe/verbose in debug mode

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10989 6adb6e08-d915-0410-...

ce728ad9eb27e1c8462057afded59d3c8d5f3ee4 authored over 11 years ago by Chris Bielow <[email protected]>

[FIX] * avoid TOPPView crash when jumping to area without any data (using Ctrl-g)

* fix warning in TOPPBase

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

edb0a0eac2240c756c6bef036e5873b10c84ea5c authored over 11 years ago by Chris Bielow <[email protected]>

[FIX] merged r10983 into Release branch

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10.1@10986 6ad...

40f9007031873daeef3d531bc66e82ff0636a30f authored over 11 years ago by Chris Bielow <[email protected]>

[FEATURE,FIX] allow disconnected input nodes which contain non-existing files (e.g. only valid on other systems with different mount points); this allows easy switching between two sets of input nodes - one set for each system. Once connected, the files need to be present obviously

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10984 6adb6e08-d915-0410-...

a7828bac2e2aee09a9dfe3d8791f4f392d91cabb authored over 11 years ago by Chris Bielow <[email protected]>

[FIX] EICExtractor now sorts MSExperiment before quant, since AreaIterator depends on sorted spectra

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10983 6adb6e08-d915-0410-...

91075f493cfc04461396b9d9290d09abfb8240d0 authored over 11 years ago by Chris Bielow <[email protected]>

[NOP] minor optimization (if at all)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10982 6adb6e08-d915-0410-...

d1454033b12d44b0759de150a974a34ea77fa8b2 authored over 11 years ago by Chris Bielow <[email protected]>

[FIX] removed duplicated code and cleaned input/output parameters for ProteinResolver

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10981 6adb6e08-d915-0410-...

048e6458527019f1e65e759764fd2212589bc858 authored over 11 years ago by Chris Bielow <[email protected]>

[FEATURE] Added optional m/z scoring function to FeatureFindingMetabo class.

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10979 6adb6e08-d915-0410-...

15e4800e84af1881db2e61de2e7f67f3d811d67b authored over 11 years ago by Erhan Kenar <[email protected]>

[FORMAT] full support for localization scores in MzTab modifications

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10978 6adb6e08-d915-0410-...

68aae4ea5a15adb8569e4a1943ea39525aa8cb38 authored over 11 years ago by Timo Sachsenberg <[email protected]>

[NOP] removed quotes for consistency reasons

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10977 6adb6e08-d915-0410-...

d0f338170b4069cc23d1e8cab006f606a8dcbc7f authored over 11 years ago by Timo Sachsenberg <[email protected]>

[FORMAT,TEST] added optional column support in mzTab

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10976 6adb6e08-d915-0410-...

d9bc27857f54099ff861ceb1cf3cefcd12ddf439 authored over 11 years ago by Timo Sachsenberg <[email protected]>

[DOC,FIX] fixed parameter unique description in ID filter

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10974 6adb6e08-d915-0410-...

7fc66862f4b15c78984746d147c732850b2656dc authored over 11 years ago by Timo Sachsenberg <[email protected]>

[DOC] better predecessor/successor tools for ProteinResolver

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10972 6adb6e08-d915-0410-...

9bfa75962bc1a87ac067ae7b9e5cb380a3b87aec authored over 11 years ago by Chris Bielow <[email protected]>

[DOCU] fixed spelling and formatting for ProteinResolver

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10970 6adb6e08-d915-0410-...

98ab9771b59b7c5d3fd5d3026ae84e6393295c47 authored over 11 years ago by Chris Bielow <[email protected]>

[FORMAT] yet another round of mzTab changes integrated into the parser and writer

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10969 6adb6e08-d915-0410-...

8826dcd19b5878f886ff37c2d389257f8c8f29a8 authored over 11 years ago by Timo Sachsenberg <[email protected]>

[FIX] fixed segfault in MSSim-Raw introduced with debugging code in [10566]

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10967 6adb6e08-d915-0410-...

5def031a1cc58df48e848ceeaf8a43efc38b6939 authored over 11 years ago by Stephan Aiche <[email protected]>

[FORMAT] more mzTab sepcific fixes

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10966 6adb6e08-d915-0410-...

95932627c5b389305abca3283dd27f66259ec948 authored over 11 years ago by Timo Sachsenberg <[email protected]>

[FIX, FORMAT] some minor bug fixes to mzTab

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10965 6adb6e08-d915-0410-...

632aa8d9223840a8757022c926c0c9981840b751 authored over 11 years ago by Timo Sachsenberg <[email protected]>

[FORMAT,TEST] added mzTab tests and fixed some bugs

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10964 6adb6e08-d915-0410-...

c80fe15f75226f6e0b6af3070cab1c476fbf452a authored over 11 years ago by Timo Sachsenberg <[email protected]>

[FORMAT] initial mzTab reading methods

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10961 6adb6e08-d915-0410-...

0fca68a48ab4d039e8f910e1b3df512d3a066b60 authored over 11 years ago by Timo Sachsenberg <[email protected]>

[FORMAT] MzTab format update to 1.0RC3

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10956 6adb6e08-d915-0410-...

1546331c824c1820435a7257e43fc20a58fb68d2 authored over 11 years ago by Timo Sachsenberg <[email protected]>

[FIX] another fix for the class generator; generated uncompilable code

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10937 6adb6e08-d915-0410-...

38f8739f2460373ad97d1264d3b0e1938c3f5917 authored over 11 years ago by Stephan Aiche <[email protected]>

[BUILD,FIX] small fix to create_class script

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10936 6adb6e08-d915-0410-...

061293cc7cd367e6042d5422e0d5e916cb4fd062 authored over 11 years ago by Stephan Aiche <[email protected]>

[BUILD] added script to add new classes based on templates, including the corresponding registration in the sources.cmake files

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10935 6adb6e08-d915-0410-...

c4eda80b8a6bc01143ddd73857d8da07ba600d07 authored over 11 years ago by Stephan Aiche <[email protected]>

[FIX] Adding missing isotope model MetaboliteIsoModelNoised5 to repository

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10934 6adb6e08-d915-0410-...

a9946676e33718e63a3952d1d283194bb73ed564 authored over 11 years ago by Erhan Kenar <[email protected]>

[TEST] Fixed failing FeatureFinderMetabo tests.

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10932 6adb6e08-d915-0410-...

1753cacf800f0353bd9b8bd0f58f289c2945d700 authored over 11 years ago by Erhan Kenar <[email protected]>

remove arbitrary check that chromatogram needs to have a certain type to be displayed

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10930 6adb6e08-d915-0410-...

8a1cde6cc5ad4bb9b5d39516d219c288062e26d4 authored over 11 years ago by Hannes Roest <[email protected]>

[FIX] CSV to TraML: add check for required for TSV column header

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10924 6adb6e08-d915-0410-...

ce66e94be2b2ffe3d3be7ddc2858ce0517d1eb0a authored over 11 years ago by Hannes Roest <[email protected]>

[FIX] fix CSV to TraML with more error checking

allow the unimod id to be empty
ensure that the header has the same length as each row

git-svn-...

5c19ed698962ea0a7952fa850def49344c4ae56d authored over 11 years ago by Hannes Roest <[email protected]>

[FIX-#523] fixed opening of www.openms.de and doc urls

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10916 6adb6e08-d915-0410-...

3556e3b9b96f5ba448cedd3e3710c96f42927f72 authored over 11 years ago by Stephan Aiche <[email protected]>

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10915 6adb6e08-d915-0410-...

b2e88efae142d66f02f93e3b1ae6c5497c01eab0 authored over 11 years ago by Stephan Aiche <[email protected]>

[FEATURE-#522,FIX] TOPPBase now also accepts command line parameters for the parameters in subsections. --helphelp prints out the parameters accordingly.

* this commit also fixes the compile error introduced in [10911]
* added tests for the CLI par...

4beb6edacff84bf28e2049dd9633addef17808e6 authored over 11 years ago by Stephan Aiche <[email protected]>

[FIX] Removed AccurateMassSearch tool from cmake sources. For now...

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10913 6adb6e08-d915-0410-...

15e419570826b9f2dbc87ccc483662b6d8fb0df9 authored over 11 years ago by Erhan Kenar <[email protected]>

[FIX,FEATURE] Simplified m/z scoring function (FeatureFindingMetabo). Added new metabolite isotope model with 5% RMS error on isotopic abundances. Users can choose between 2% or 5% RMS error model via parameter.

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10912 6adb6e08-d915-0410-...

b6d620a1a885416192db46c88ec0504fc958ed95 authored over 11 years ago by Erhan Kenar <[email protected]>

[FIX] fixed bug in Param::merge leading to an exception when merging certain constellations

* also fixed a warning in MassTrace c'tor

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

528d92fbfeb07882284c5dbcda45bf483f71087c authored over 11 years ago by Stephan Aiche <[email protected]>

[DOC,INTERNAL] fixed Author and Maintainer, some doc for breakString()

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10910 6adb6e08-d915-0410-...

8e2a4bfb4ca0726c99e06a3ca0bae9ae96a30fa7 authored over 11 years ago by Chris Bielow <[email protected]>

[FIX] fixed win compile issue (missing OPENMS_DLLAPI) introduced in [10899]

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10908 6adb6e08-d915-0410-...

289d296560a6531f0b2ddc93d01ce10af50f9ea0 authored over 11 years ago by Stephan Aiche <[email protected]>

[INTERNAL,API] moved Param::parseCommandLine used by TOPPBase to TOPPBase

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10906 6adb6e08-d915-0410-...

7a207ba4390eddee4f0d87efa271bf26cb49616d authored over 11 years ago by Stephan Aiche <[email protected]>

[FIX] proper zoom stack handling for mouse wheel zoom on 1D Canvas

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10.1@10905 6ad...

6dd36ecdd8790676a85c333de91986602ed6f8da authored over 11 years ago by Timo Sachsenberg <[email protected]>

[FIX] fixed some lnx compile issues introduced in [10899]

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10900 6adb6e08-d915-0410-...

edc2f6d8f865a14e5442538b95aacfb67d9cc962 authored over 11 years ago by Stephan Aiche <[email protected]>

[INTERNAL] more refactoring of TOPPBase; extracted some util classes and functions; created tests and updated cmd output

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10899 6adb6e08-d915-0410-...

514b664d13ca670249e1a9e457b7b46c2a9b2b2a authored over 11 years ago by Stephan Aiche <[email protected]>

[INTERNAL] small refactoring in TOPPBase

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10897 6adb6e08-d915-0410-...

8ac2f101a7f236ce433aef1baf72a6f0468ff94c authored over 11 years ago by Stephan Aiche <[email protected]>

[FIX] removed QCustomPlot library because of symbol collision with libsvm on windows

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10846 6adb6e08-d915-0410-...

88b8c2a9b37ed19d9f1f1e6a4de43ad2f5d74460 authored over 11 years ago by Timo Sachsenberg <[email protected]>

[RESOURCE,INTERNAL] updated OpenMS head revision to 1.11

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@10845 6adb6e08-d915-0410-...

8a050f3489cc0c6cda7af8bb3010d82da6846ef0 authored over 11 years ago by Stephan Aiche <[email protected]>

[FIX] fix recently introduced wrong parameter naming bug for RNPxl

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10.1@10843 6ad...

3ccdf8ac5ac4c9218b9ab08dfd91b5f65d9ae23b authored over 11 years ago by Timo Sachsenberg <[email protected]>

[FIX] propagate fasta parameter to ini file in RNPxl to remove source of error

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10.1@10841 6ad...

1ab78b5db28ff6bba806161b3da68a4f7acf9a78 authored over 11 years ago by Timo Sachsenberg <[email protected]>

[FIX] removed non-functional elements from TOPPView preferences dialog

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.10.1@10840 6ad...

8156724209fe21ddae9ca2839b367f2c86822d8b authored over 11 years ago by Timo Sachsenberg <[email protected]>