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

* fixed LogStream test

* clearCache now is public to enable a controlled clearing of the log-cache
* fixed maintainer ...

9d2ff92a690548744165bdb8559fcbf2b263fb1d authored over 13 years ago by Stephan Aiche <[email protected]>

** fixed bug in Lorentzian peak shape

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7865 6adb6e08-d915-0410-9...

78bfce937f5f129511d4a2b8e151c8c2187bd438 authored over 13 years ago by Chris Bielow <[email protected]>

Added OpenMP flag to test executables for linking

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7864 6adb6e08-d915-0410-9...

263af52028daa0cbfb4182028b7b2630a2c25996 authored over 13 years ago by Chris Bielow <[email protected]>

** fixed a lot of tests

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7863 6adb6e08-d915-0410-9...

b013f784e7fb44f2330461010c7b3beb2f158eae authored over 13 years ago by Chris Bielow <[email protected]>

fixed problems introduced by additional statistics in FileInfo

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7859 6adb6e08-d915-0410-...

80872bc9c4a5878b60e047a85ad69c0d337e9a6b authored over 13 years ago by Oliver Kohlbacher <[email protected]>

fixed a few warnings, coding style violations and the TextExporter test

broken after the introduction of features widths

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

54b8394a8092a4cc789acef40befe9072f7f161f authored over 13 years ago by Oliver Kohlbacher <[email protected]>

fix for ticket 222 ('IDMapper should support mapping charge-matched entities only') - no tests yet

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7857 6adb6e08-d915-0410-9...

23dc880177fc2dcea8acb3ae17611d5df7bd33a6 authored over 13 years ago by Hendrik Weisser <[email protected]>

** sim: RT distortion model fixed once and for all

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7856 6adb6e08-d915-0410-9...

377cdbd904b714acbebbc81787dbf3033d97ad68 authored over 13 years ago by Chris Bielow <[email protected]>

** some defaults changed for sim

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7855 6adb6e08-d915-0410-9...

fef4a0415d147bcba053f2e89fa66d358a404ed7 authored over 13 years ago by Chris Bielow <[email protected]>

** fixed TOPPAS example pipelines such that they run out of the box

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7854 6adb6e08-d915-0410-9...

fe22abd3abc265ee25bed7c14c5a637165c352d3 authored over 13 years ago by Chris Bielow <[email protected]>

Fixed a few warnings under Darwin/64/gcc4.2.1.

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7853 6adb6e08-d915-0410-9...

0260e73e7564c2bcbbbeb99e66d6ac855c6e6e2a authored over 13 years ago by Oliver Kohlbacher <[email protected]>

RTSim now tries to resample the variance a few times before it skipps the peptide

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7852 6adb6e08-d915-0410-9...

dc7c66e315ad71975cd122f469d1e6b819db9874 authored over 13 years ago by Stephan Aiche <[email protected]>

** silenced warning in BaseLabeler

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7851 6adb6e08-d915-0410-9...

100efb4e8658ffea66625277ca23d9f8ea551090 authored over 13 years ago by Chris Bielow <[email protected]>

** updated tutorial (FASTA content still missing)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7850 6adb6e08-d915-0410-...

2de0ee83c7264e53e7211010623ff6a64ed6f75b authored over 13 years ago by Chris Bielow <[email protected]>

** fixed Sim bug, when aligning data to grid

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7849 6adb6e08-d915-0410-9...

916766ae503a2d482388aca2a833f5aaa4e36434 authored over 13 years ago by Chris Bielow <[email protected]>

** fixed EGH bug causing segfault

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7848 6adb6e08-d915-0410-9...

dd60891a6b57cc33e404505f129bb6912ff3b0ea authored over 13 years ago by Chris Bielow <[email protected]>

** fixed some warnings

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7844 6adb6e08-d915-0410-9...

84b9f4ab97b95a996facee1458b2682792286b4c authored over 13 years ago by Chris Bielow <[email protected]>

Cosmetic changes

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7843 6adb6e08-d915-0410-9...

a18ef6d2a946d8dfe9463a2cf07d50e9a919af68 authored over 13 years ago by Oliver Kohlbacher <[email protected]>

** some docu for IsotopeModels

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7840 6adb6e08-d915-0410-9...

101d04d30473ec7adc51b1a8a3144a73e1fbc65b authored over 13 years ago by Chris Bielow <[email protected]>

** fixed small bug in Decharger (peptide id's are doubled)

** logger for decharger
** some docu

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

66ee12bfb097276b7d3486f9fd490c738fc02dc2 authored over 13 years ago by Chris Bielow <[email protected]>

** merged Sim branch back to HEAD

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7837 6adb6e08-d915-0410-9...

18d95245f8a5a93331c1449bdc1e5e15b6f6be68 authored over 13 years ago by Chris Bielow <[email protected]>

** new skewness

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Sim2@7836 6adb6e08-d915...

dc6b27e6dce8766883fe17bf379c3dcc45e920aa authored over 13 years ago by Chris Bielow <[email protected]>

** new EGH default for skewness

** fixed Convex Hull cutting

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

c7cc19ad813b0bba4281a73f80b8e4312306d21f authored over 13 years ago by Chris Bielow <[email protected]>

** fixed #253

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7834 6adb6e08-d915-0410-9...

9458024bffe98496db7d821afe8aefb27873ac7c authored over 13 years ago by Chris Bielow <[email protected]>

** fixed template type ambiguity in FF wavelet

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7833 6adb6e08-d915-0410-9...

10d30b1ffa2cdc0bd708235b9a59418764a76c0f authored over 13 years ago by Chris Bielow <[email protected]>

* fixed OMSSA Version problem with gcc compilers

* fixed ConsensusID test (removed setMinInt for parameter removed in [7824] )
* fixed Copyright...

17ce7dde8da8125d21fcbd5dd96726a5e0225ff7 authored over 13 years ago by Stephan Aiche <[email protected]>

* clang compiler is now also detected in CMakeLists.txt

* fixed some clang warnings

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

572b7e944ee2ed1291a340f2bfe5897a2b66aeb9 authored over 13 years ago by Stephan Aiche <[email protected]>

** EGH parameter rename

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Sim2@7830 6adb6e08-d915...

32326a9eab00c3e7be5e5fed8b86c5ac920491c2 authored over 13 years ago by Chris Bielow <[email protected]>

fixed egh parameter bug: meta value check was not adapted after renaming meta value

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Sim2@7829 6adb6e08-d915...

f3696758a4bc691ad0278f85193a349d3b39c8cd authored over 13 years ago by Stephan Aiche <[email protected]>

** do not store 0 intensity peaks in simulated maps

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Sim2@7828 6adb6e08-d915...

74afd2e98b62f8f9e9c83a09457702e84c6bca82 authored over 13 years ago by Chris Bielow <[email protected]>

** sampling of raw points does now depend on FWHM, i.e. resolution

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Sim2@7827 6adb6e08-d915...

ca7c929fd01be5b88e87107a5d9d4eb39d5658e2 authored over 13 years ago by Chris Bielow <[email protected]>

code clean-up; intensity correction for iso_wave

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7826 6adb6e08-d915-0410-9...

4deb7d53c9f10a2b6065389ae1f8429c6559bb8d authored over 13 years ago by Rene Hussong <[email protected]>

** fixed [252]

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7825 6adb6e08-d915-0410-9...

37da347a86d685a8f3e39b80b607d4076dd39902 authored over 13 years ago by Chris Bielow <[email protected]>

deleted parameter w/o function minimal_number_of_engines

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7824 6adb6e08-d915-0410-9...

e62846a9abc80a7ff61620aad0d0a58572fd7d20 authored over 13 years ago by Sven Nahnsen <[email protected]>

changed spectraidentificationview precusor window view to 100 Th

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7820 6adb6e08-d915-0410-9...

a2fccd927916efe2f2ea97214fac8f6cd08c9db7 authored over 13 years ago by Timo Sachsenberg <[email protected]>

fixed small focus bug in TOPPViewOpenDialog

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7819 6adb6e08-d915-0410-9...

e4bdf6bdc8649d7fd5b580f41d2af6dffa7e727a authored over 13 years ago by Timo Sachsenberg <[email protected]>

fixed a mall bug that yielded an empty statistics line if there

were no features in a slice

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

caeeee9588617d953e6bd22d99ebc97c3876537c authored almost 14 years ago by Oliver Kohlbacher <[email protected]>

- Added width to Features (BaseFeature, in fact). Nasty hacks still included in

a few places: featureXML can't really store it, so I am making use of userParams
and a few ...

a2c523ac8db6418610dd583574860e5728ecfa98 authored almost 14 years ago by Oliver Kohlbacher <[email protected]>

** alignment integrated into SpectraMerger (todo: reference spectrum (e.g. by RT))

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7815 6adb6e08-d915-0410-9...

117ad4d4ccbbba76dea799d2e9305797a2a98f1a authored almost 14 years ago by Chris Bielow <[email protected]>

** added todo

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7812 6adb6e08-d915-0410-9...

3514525cf0e7fab2b935cb93723097a46cb39b9f authored almost 14 years ago by Chris Bielow <[email protected]>

** fixed minor bug in SpectrumAlignment (reuse does not clear result) + minor speed improvement + better test

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7811 6adb6e08-d915-0410-...

45d9b5812d53c889538c23ea3b3a8b14ddd6c004 authored almost 14 years ago by Chris Bielow <[email protected]>

addition to last commit: removing TrafoInverter (use 'MapAligner -type apply_given_trafo -invert' instead)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7810 6adb6e08-d915-0410-9...

20879d3739461ced38ab3a5ddc7a23768b9a2335 authored almost 14 years ago by Hendrik Weisser <[email protected]>

RT alignment (etc.): separating data generation from modeling of transformations

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7809 6adb6e08-d915-0410-9...

0ac5df9b67e366f29ca14074ba0c881af3cd92e6 authored almost 14 years ago by Hendrik Weisser <[email protected]>

** fixes for TPP ProteinProphet wrapper

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7804 6adb6e08-d915-0410-9...

f25b3fc715d51a2afe42031f838ed930da4e063a authored almost 14 years ago by Chris Bielow <[email protected]>

** corrected wrong merge

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7802 6adb6e08-d915-0410-9...

51b840971c5a631404e0986b8a97c381feea0b1d authored almost 14 years ago by Chris Bielow <[email protected]>

** some refinements to GenericWrapper

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7801 6adb6e08-d915-0410-9...

7af0b055ad04e502a927eec9c8fabc5963885595 authored almost 14 years ago by Chris Bielow <[email protected]>

** added "workingdirectory" tag to ttd files (required for windows version of TPP -argghhh)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7800 6adb6e08-d915-0410-9...

82c9849aa2878140d1a0756ddba13cdf4cac4112 authored almost 14 years ago by Chris Bielow <[email protected]>

** copyright (part 2)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7798 6adb6e08-d915-0410-9...

e8234ed1399e2a31713a3f94b57a67ea84d02547 authored almost 14 years ago by Chris Bielow <[email protected]>

** changed copyright to 2011 (part1)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7797 6adb6e08-d915-0410-9...

5871d4bb9e96b7398bba026061245d10be1f62fd authored almost 14 years ago by Chris Bielow <[email protected]>

** added citation

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7796 6adb6e08-d915-0410-9...

026ebe6666367780f73cdc08f0b155d393ba4ad9 authored almost 14 years ago by Chris Bielow <[email protected]>

** removed confusing < and > characters from ttd template

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7795 6adb6e08-d915-0410-9...

97436f73ad8bc70da114c6ff3799ede61c14b9e8 authored almost 14 years ago by Chris Bielow <[email protected]>

** enabled refinement flag in XTandemAdapter (fixing #251)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7794 6adb6e08-d915-0410-9...

9527bc6b36dcd3db311d56467b6d569a8929dbc0 authored almost 14 years ago by Chris Bielow <[email protected]>

erased "const_" from GenericWrapper.C line 339 to fix build problems under Mac OS 10.6.6

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7793 6adb6e08-d915-0410-9...

ccdeef94c1f16a70d5fe644a95ed4657a42a86fe authored almost 14 years ago by hp-23 <[email protected]>

fixed a typo ('Idenifier' vs. 'Identifier')

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Sim2@7791 6adb6e08-d91...

07694054100211509b581ee7905edabe0f2f2577 authored almost 14 years ago by Oliver Kohlbacher <[email protected]>

fixed some clang warnings and errors

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7786 6adb6e08-d915-0410-9...

4ea2d4c08546da513c9e1cad5ad224ad62488c98 authored almost 14 years ago by Stephan Aiche <[email protected]>

** disabled warning about variadic macros

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7785 6adb6e08-d915-0410-9...

cee1cbc927cdc0f561a86a5131710bbeafbe76b2 authored almost 14 years ago by Chris Bielow <[email protected]>

** hopefully fixed last OMP issue with LogStream & added test

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7784 6adb6e08-d915-0410-9...

f571c7ee3dff5f8d980b7d4c370f6e0f853eae52 authored almost 14 years ago by Chris Bielow <[email protected]>

** logger OpenMP bug removed

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7783 6adb6e08-d915-0410-9...

46c4e53fed8ef6eee4b780d3e47a334edb725833 authored almost 14 years ago by Chris Bielow <[email protected]>

** larger critical section for logger

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Sim2@7782 6adb6e08-d915...

a3d0a0dc6ded4cbe868ec27cb0175896e51156eb authored almost 14 years ago by Chris Bielow <[email protected]>

** reverted LogStream change from [7576]

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7781 6adb6e08-d915-0410-9...

6254612104e3008f102d62cbe93ceb7fccdf886e authored almost 14 years ago by Chris Bielow <[email protected]>

* performance improvement by skipping major part of LogStreamBuf::sync if no output streams are attached

* LogStream is now-cache omp thread-safe

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

bcf2b59390d7812fbe0b9a68b191b01663510f94 authored almost 14 years ago by Stephan Aiche <[email protected]>

** fixed bug in GenericWrapper (file forwarding)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7779 6adb6e08-d915-0410-9...

1e4935d5795c06dc76bbdc51ceb03daea908e2b7 authored almost 14 years ago by Chris Bielow <[email protected]>

** some more info text for external tools

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7778 6adb6e08-d915-0410-9...

365602b8c1a9bc2b2ae5e787983889275966884c authored almost 14 years ago by Chris Bielow <[email protected]>

** new Folder to hold third party libs

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7775 6adb6e08-d915-0410-9...

1da1acb2fb5d0fe931c94058701805101d9fdb4d authored almost 14 years ago by Chris Bielow <[email protected]>

** fixed bug #249

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7774 6adb6e08-d915-0410-9...

6c7ca500765de55099363d301fac2af7669380c3 authored almost 14 years ago by Chris Bielow <[email protected]>

** fixed small bug in GenericWrapper (pre copy)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7773 6adb6e08-d915-0410-9...

388d0d04c53e78eaf53569186206c70437938457 authored almost 14 years ago by Chris Bielow <[email protected]>

** GenericWrapper can now deal with external tools who write files in-place

** added TPP's RefreshParser (experimental)

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

d7e06872a2c83d34849d1cf91cf250200457d63c authored almost 14 years ago by Chris Bielow <[email protected]>

** minor

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7771 6adb6e08-d915-0410-9...

b3dd1568d8560b9390b795d5348aee2c2a42bf57 authored almost 14 years ago by Chris Bielow <[email protected]>

** GenericWrapper now supports two or more file forwardings

** bugfix in GenericWrapper.C (when #mappings>=10)
** TPP's ProteinProphet supported (experimenta...

adddd400cb550be6f08370372ee8138e4b404d27 authored almost 14 years ago by Chris Bielow <[email protected]>

** minor improvement when writing param XML

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7769 6adb6e08-d915-0410-9...

2da4087ed6e8741fdc3550123c0081ceb657460f authored almost 14 years ago by Chris Bielow <[email protected]>

** added missing typenames

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7768 6adb6e08-d915-0410-9...

3ffcbb6a3f595229383885c332b981e05d0c55a4 authored almost 14 years ago by Chris Bielow <[email protected]>

** SpectraMerger speed improved

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7767 6adb6e08-d915-0410-9...

4f7d858394661e4cb84efddecbd338378b84a622 authored almost 14 years ago by Chris Bielow <[email protected]>

** some spectra merge fixes

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7766 6adb6e08-d915-0410-9...

f5cc0aac1c653bef5a8747254e0becd511533bd8 authored almost 14 years ago by Chris Bielow <[email protected]>

** added missing include

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7765 6adb6e08-d915-0410-9...

6168a2769f04e4a1eea5542552936fec821e6da9 authored almost 14 years ago by Chris Bielow <[email protected]>

minor: missed one change in last commit

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7764 6adb6e08-d915-0410-9...

3e3dc33aedf32ad3b5ea4b30aa9f3a33605f464c authored almost 14 years ago by Timo Sachsenberg <[email protected]>

** quick fix of bug #248

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7763 6adb6e08-d915-0410-9...

9375a186a33c9c9fb97e47ea77f8282792c1e4ef authored almost 14 years ago by Chris Bielow <[email protected]>

fixed bug #246

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7762 6adb6e08-d915-0410-9...

0366417ad847acf3deb228b7d333ca05dc8f8813 authored almost 14 years ago by Timo Sachsenberg <[email protected]>

added convenience accessors for individual rows and columns in a matrix

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Sim2@7761 6adb6e08-d91...

0d1a4b355700ee7e178cf089d2c47e59d14a866f authored almost 14 years ago by Oliver Kohlbacher <[email protected]>

** small lorentz improve ...

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Sim2@7760 6adb6e08-d915...

8e0bf25f3cfb93b33f5c03642bd53e1293645a42 authored almost 14 years ago by Chris Bielow <[email protected]>

** removed confusing RT param (saving run-time memory)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Sim2@7759 6adb6e08-d915...

c1e61e413912d628de87b4072da9394f46468a61 authored almost 14 years ago by Chris Bielow <[email protected]>

** merged contrib requirements from trunk to sim branch

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Sim2@7758 6adb6e08-d915...

63d1bbad84df24f48a1a2189af0287f2691e8efa authored almost 14 years ago by Chris Bielow <[email protected]>

** fixed two tests

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7757 6adb6e08-d915-0410-9...

5174e2bf72b4439e4a25505bce711b0590dc824f authored almost 14 years ago by Chris Bielow <[email protected]>

** fixed template weirdness (VS2005 complains for unknown reason)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7756 6adb6e08-d915-0410-9...

581c5a0a6929dce7aa86f0f9e310ae6bedb31518 authored almost 14 years ago by Chris Bielow <[email protected]>

** PeptideIndexer reworked completely (can now deal with ambiguous AA & better stats and error checking)

** adapted to new seqan version (see contrib)
** PeptideIndexer tests

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

e3d3b8be7337cdbdda25cb2ff1d05c9298371e45 authored almost 14 years ago by Chris Bielow <[email protected]>

default mapping in 2D mz->y_axis

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7751 6adb6e08-d915-0410-9...

6c68eb1699be832106377a05dfe00eded23bf5fc authored almost 14 years ago by Timo Sachsenberg <[email protected]>

** last fixes for clang++ compiler (only warnings left) [new contrib required for clang -- available tomorrow]

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7749 6adb6e08-d915-0410-9...

1da9c2bf1b9e7747cbffe8c8663090c23e881d66 authored almost 14 years ago by Chris Bielow <[email protected]>

added missing test and some test updates

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Sim2@7748 6adb6e08-d915...

19f46f86b051c368227e7d9178ad5b8498f3630a authored almost 14 years ago by Stephan Aiche <[email protected]>

* lorentzian variation of EGH RT profile shape parameters (tau and sigma)

* some documentation updates to appease the checker

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

7204cd36259a9cd8173b280b86b0390a46a77ded authored almost 14 years ago by Stephan Aiche <[email protected]>

tandem ms changes.

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Sim2@7746 6adb6e08-d91...

6a7938c2cae12a7adb2ce7f3a28d2b1561377319 authored almost 14 years ago by Sandro Andreotti <[email protected]>

TOPPAS/TOPPView integration: opening of generated files in embedded mode

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7745 6adb6e08-d915-0410-9...

da7ddf305d000b5eccc61a3f65c78a568875ad2e authored almost 14 years ago by Timo Sachsenberg <[email protected]>

** fixed model_fitter test

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Sim2@7744 6adb6e08-d915...

6db13116be506ca76feb468ad3d7661c4191add3 authored almost 14 years ago by Chris Bielow <[email protected]>

** fix of BAD bug in SparseVector, (indirectly) found by clang++ compiler

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7743 6adb6e08-d915-0410-9...

be4bc2b1cde15af587d7a5976ea70f761ff4c397 authored almost 14 years ago by Chris Bielow <[email protected]>

** significant speedup of IsotopeModel calculation

** added Lorentzian shaped peaks
** scaling also for 1D signals

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

3c85e6a0f17de424d283d75d99b1cff6d1520a00 authored almost 14 years ago by Chris Bielow <[email protected]>

fixed problem with too big signals

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Sim2@7741 6adb6e08-d915...

9931430b9c2e7ef25d912c53a385194747082b41 authored almost 14 years ago by Stephan Aiche <[email protected]>

TOPPView/TOPPAS integration: inclusion of pipelines works now

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7740 6adb6e08-d915-0410-9...

697beaea1f6d47828b014471a9b8752ea00f5211 authored almost 14 years ago by Timo Sachsenberg <[email protected]>

more work on TOPPView/TOPPAS integration

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7739 6adb6e08-d915-0410-9...

64af7ee22c2bfa6dab6b1a33efcaa8ad81d4cedf authored almost 14 years ago by Timo Sachsenberg <[email protected]>

** check file extension to warn users if they used the wrong suffix when loading an XML file

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7738 6adb6e08-d915-0410-9...

ad75b52d270bc68bcdd378340ef82eddc64223d9 authored almost 14 years ago by Chris Bielow <[email protected]>

fixed SpectraMerger

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7715 6adb6e08-d915-0410-9...

cb0128cfc299c4e779dc66ddc4a9f7676989fef2 authored almost 14 years ago by Chris Bielow <[email protected]>

** enabled merging by Precursor in SpectraMerger

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@7714 6adb6e08-d915-0410-9...

1304c9dc53505db2561bc4fb4b108cf59007d2fa authored almost 14 years ago by Chris Bielow <[email protected]>

** fixed bug in ClusterAnalyzer, preventing reconstruction of thresholded clusterings

** added const-ness to clustering to ease usage

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

f8fc7f8fef744305e6a23c84953b81ee6023c074 authored almost 14 years ago by Chris Bielow <[email protected]>