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

[INTERNAL] addendum to [9807], fixed windows dll export prolem

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9809 6adb6e08-d915-0410-9...

2828b90fad88337e1d5b466d05130528e39a2f8d authored over 12 years ago by Chris Bielow <[email protected]>

[INTERNAL] fix for win incompatibility introduced in [9802]

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9808 6adb6e08-d915-0410-9...

70dd2f9e63ba8802e72a060ac66e6240402559e3 authored over 12 years ago by Stephan Aiche <[email protected]>

[INTERNAL] moved code from ConsensusMap header to C file

* reverted [9803]; we do not allow using namespace std in header files
* fixed formating of F...

3dd1a41f08d30e1b3034b7b504cb3d20417b3b56 authored over 12 years ago by Stephan Aiche <[email protected]>

* EOL style for TOPP and UTILS fixed

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9806 6adb6e08-d915-0410-9...

5baf2213d817fb638fdf67eee91a0a6600a27bcd authored over 12 years ago by Chris Bielow <[email protected]>

[FIX,DOC,API,PARAM,TEST] MapAlignerPoseClustering now uses constant memory instead of loading all files at the beginning

; MapAlignerPoseClustering now honours the "maximal number of peaks" parameter (ignored before) ...

39421b0866a61c7c2f7604c0bf517415981aea2b authored over 12 years ago by Chris Bielow <[email protected]>

[FIX] allocated Xerces strings are freed after parsing of each file, saving memory [FIXING-#431]

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9804 6adb6e08-d915-0410-9...

48baa288cb37db50336e7d606ac2d91ce5755142 authored over 12 years ago by Chris Bielow <[email protected]>

[INTERNAL] minor changes

not worth mentioning. its friday afternoon. :)

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

14f4516d8a17a81f27c1a1866dddf60c691a4b7b authored over 12 years ago by Immanuel Luhn <[email protected]>

[INTERNAL, FIX] Fix the += operator

After merging two consensu map with the += operator, the modifications
parameters were redundant...

4df1d5f150877851579db613210570d5217e282e authored over 12 years ago by Immanuel Luhn <[email protected]>

Additional commit to make IDFilter work again

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9801 6adb6e08-d915-0410-9...

9401a388c41fdd230eb7453771e19ea2c0723792 authored over 12 years ago by Sven Nahnsen <[email protected]>

[FIX] improved reporter ion positions to the exact masses given by AB sciex [FIXED-#430]

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9800 6adb6e08-d915-0410-...

12b067019bc2e70a5cc0b7f8449c837f7130f93b authored over 12 years ago by Chris Bielow <[email protected]>

filter peptide ids for charges

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9799 6adb6e08-d915-0410-...

69dc5e45f4d0aed4293c248ee11db95571c9008b authored over 12 years ago by Sven Nahnsen <[email protected]>

now we can also handle data that has beeen processed with TPP

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9798 6adb6e08-d915-0410-...

bc582596ef30c59453cb11264e30a74e7eaa2cd0 authored over 12 years ago by Sven Nahnsen <[email protected]>

Changes s.t. TOPP Tools can be applied to chromatograms

distinguish "real" peak data and "chromatogram" peak data, pass peak
data to the TOPPTool and th...

dfb206964ea1c87a350101a6ccc3289cbdf9e573 authored over 12 years ago by Hannes Roest <[email protected]>

** amend 9795, allow to find non-exact matches

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9796 6adb6e08-d915-0410-9...

2706f0b415d48173c89005b5d58d61065d189875 authored over 12 years ago by Hannes Roest <[email protected]>

[TOPPView] get the combo box to work for chromatograms

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9795 6adb6e08-d915-0410-9...

ef49a2d72aace275768989b062f4363d8b90641d authored over 12 years ago by Hannes Roest <[email protected]>

**cleanup: fxn to check for chromatogram type

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9794 6adb6e08-d915-0410-9...

c4eab0d71807954d3fdfdeb068820d644b758c5c authored over 12 years ago by Hannes Roest <[email protected]>

[INTERNAL] moved transformation related methods out of MapAlignerBase in preparation of the break-up of the MapAligner code

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9791 6adb6e08-d915-0410-9...

e6388a05c09647089928c6271507df3de91f4725 authored over 12 years ago by Stephan Aiche <[email protected]>

** fix error, only add one peak to chromatogram instead of all

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9790 6adb6e08-d915-0410-9...

18dddc8d29214e7fcb34664376b175b2ce31bfdb authored over 12 years ago by Hannes Roest <[email protected]>

corrected cvs in MzQuantML, added first IDMapper support for writeout

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9789 6adb6e08-d915-0410-9...

39031079869b2230ab92aea7278890a4cb8fa50d authored over 12 years ago by Mathias Walzer <[email protected]>

updated some cvs for MzQuantML and improved ratio handling

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9788 6adb6e08-d915-0410-9...

65acad69319a195d268eae4c191c9e373cd143ad authored over 12 years ago by Mathias Walzer <[email protected]>

Resolved MzQuantML readin software name/version bug. Removed some typos and indentations and so forth.

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9787 6adb6e08-d915-0410-9...

b53a1a5636a1903d5cce841f7964111964ef9c7d authored over 12 years ago by Mathias Walzer <[email protected]>

changed CVs for Quantification modifications according to PSI-MOD

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9786 6adb6e08-d915-0410-9...

3debe27fc47f2238bd5abe53dd98659b04dc9b23 authored over 12 years ago by Mathias Walzer <[email protected]>

changed CVs for Quantification modifications according to PSI-MOD

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9785 6adb6e08-d915-0410-9...

ba8d8740df8fc3e839b2cd0066c0099d21ec119e authored over 12 years ago by Mathias Walzer <[email protected]>

fixed weird bug in MzQuantML writeto function - ratio handling is smoother now

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9783 6adb6e08-d915-0410-9...

d95f01e246f5608f50cf5e89cc5a0949e6fcfacf authored over 12 years ago by Mathias Walzer <[email protected]>

changed MzQuantML writeout of ratios - not done

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9782 6adb6e08-d915-0410-9...

30176b63a54b92b1c4acd48be702ea1ab9aa9a98 authored over 12 years ago by Mathias Walzer <[email protected]>

Added ConsensusFeature::Ratio code to SILACAnalyzer

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9780 6adb6e08-d915-0410-9...

7ef9209520f5794134b206bbdd8d8ea65e5d6446 authored over 12 years ago by Mathias Walzer <[email protected]>

Added slim struct for ratios in ConsensusFeature. Will replace metainfo store of ratios. According additional code in quantification tools and MzQuantML write out pending

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9779 6adb6e08-d915-0410-9...

474564793af369ec38ecd2e350ba7a68a350b2e1 authored over 12 years ago by Mathias Walzer <[email protected]>

IDMapper would not work like that right now (but soon) with MzQuantML - so just commented out mzq functionality

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9776 6adb6e08-d915-0410-9...

321ce9e7bcd684853580306bee69af17a60d5a38 authored over 12 years ago by Mathias Walzer <[email protected]>

MzQuantML kind of works - jumbles around some data still lots of todos

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9775 6adb6e08-d915-0410-9...

e266835c07dc140c6357206fc3766610dbb4749e authored over 12 years ago by Mathias Walzer <[email protected]>

MzQuantML read in code near complete - CVhandling and ID missing yet

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9774 6adb6e08-d915-0410-9...

5505598eddc00dda2332003157ed7da3a09c73f3 authored over 12 years ago by Mathias Walzer <[email protected]>

mzquantml writeout adapted completely to new schema, should produce almost valid files (except cv parts :( )

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9771 6adb6e08-d915-0410-9...

5350f4d3cac5a38e9aad9cbe1ea47d34f9002429 authored over 12 years ago by Mathias Walzer <[email protected]>

adapted cases in respect to recent schema change for MzQuantML writeout

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9770 6adb6e08-d915-0410-9...

28d2524b4cfe0ca9001a1d5bbe857292218899a1 authored over 12 years ago by Mathias Walzer <[email protected]>

[FIX-#386] fixed randomly occuring bug in LogStream d'tor by not letting global instances delete their own buf

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9769 6adb6e08-d915-0410-9...

cef43d4da30d55c72248d2157721240f1bd2bbda authored over 12 years ago by Stephan Aiche <[email protected]>

added little more bits to mzQuantML read in code

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9768 6adb6e08-d915-0410-9...

1cec2138a46d8f6516c400d0ffc2bd735aed7e31 authored over 12 years ago by Mathias Walzer <[email protected]>

* fixed parsing bug introduced in [9766]

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9767 6adb6e08-d915-0410-9...

7f05de52b654be99acc185ce0b9532da93e5eddf authored over 12 years ago by Chris Bielow <[email protected]>

** PREPS for new MapAlignment

** added FeatureFileOptions (to control if ConvexHulls and Subordinates are loaded during Feature...

7ade00a94da394b04f613a08dc06b9d5211f5700 authored over 12 years ago by Chris Bielow <[email protected]>

** fixed test error introduced in [9757]

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9765 6adb6e08-d915-0410-9...

5876907813f1122ecaf06d2d8db38e51762c297b authored over 12 years ago by Chris Bielow <[email protected]>

fixed precision bug in TOPPView

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9764 6adb6e08-d915-0410-9...

e7c148fb342b1983253aafc4e0c5c4f1cc82507e authored over 12 years ago by Timo Sachsenberg <[email protected]>

[FIX] fixed error introduced in [9758]; reformated code

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9763 6adb6e08-d915-0410-9...

600c816ae78506263cadf042921e5be98539ba96 authored over 12 years ago by Stephan Aiche <[email protected]>

added first bits of code for MzQuantML read in, changed some CVs in write out

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9762 6adb6e08-d915-0410-9...

5bdec2e76e05cd5a9ef8da819120ba6613deaf07 authored over 12 years ago by Mathias Walzer <[email protected]>

** minor

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9760 6adb6e08-d915-0410-9...

777c47ba5ea06ba749a5710699d97332f06436aa authored over 12 years ago by Chris Bielow <[email protected]>

** typo fix

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9759 6adb6e08-d915-0410-9...

f5b4a6f7c1983dfdeb4bc1db808b7f18b6d18d3e authored over 12 years ago by Chris Bielow <[email protected]>

** removed some more pow()'s

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9758 6adb6e08-d915-0410-9...

95ffcf2af8633b40fe9f55b53f8790ed6b83d5c3 authored over 12 years ago by Chris Bielow <[email protected]>

** doubled speed of StablePairFinder

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9757 6adb6e08-d915-0410-9...

c8629298950f390b26f0795cc3bb3d259304c8a7 authored over 12 years ago by Chris Bielow <[email protected]>

[FIX] fixed error in dmg package creation

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9756 6adb6e08-d915-0410-9...

be77fdc2b4652363fe70a6e7a317789ed39710fd authored over 12 years ago by Stephan Aiche <[email protected]>

** added output filetype for TOPPAS output nodes

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9755 6adb6e08-d915-0410-9...

62b8bc425698202076af6ed1ead943d6b55eba1e authored over 12 years ago by Chris Bielow <[email protected]>

added flag to filter modified peptides

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9754 6adb6e08-d915-0410-9...

f6789829996813cc5085febeb74ac87b408732f6 authored over 12 years ago by Timo Sachsenberg <[email protected]>

added mzQuantML capability to iTRAQAnalyzer - initial commit

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9752 6adb6e08-d915-0410-9...

24e314dc5aeb39c220cced97cd6db7dbb25a5226 authored over 12 years ago by Mathias Walzer <[email protected]>

** changed some X!TandemAdapter parameters to more sensible defaults

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9751 6adb6e08-d915-0410-9...

47ad0dd9095581bf4549d30d05964f2d5c46a7d7 authored over 12 years ago by Chris Bielow <[email protected]>

added AnalysisSummary support to MzQuantMLHandler

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9750 6adb6e08-d915-0410-9...

0888ac057a80a933730122c49204eee17836e39b authored over 12 years ago by Mathias Walzer <[email protected]>

** improved docu for ITRAQAnalyzer

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9749 6adb6e08-d915-0410-9...

c7e25beb2b87fbb7a0c1a1a87c8a913573ebedfa authored over 12 years ago by Chris Bielow <[email protected]>

** TOPPAS: fixed resume-bug (hard TOPPAS crash when changing the I/O mapping of an edge and clicking "resume" on sink node <-- this should not have worked and the earliest resume node should be the source node of the edge)

** TOPPAS: clicking resume now sets the pipeline status to "running"

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

302a9e393c14b12af86def3e048458e4b24e6352 authored over 12 years ago by Chris Bielow <[email protected]>

** fixed bad bug, preventing picked ground truth from simulator be to be valid (especially for charge>1)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9747 6adb6e08-d915-0410-9...

c5aadb2d871f772b971ab8317e63ae2bcccbbf54 authored over 12 years ago by Chris Bielow <[email protected]>

** removed useless codeline from FalseDiscoveryRate (decoy peptides are already added inside the FDR algorithm, and the insert() here was a null operation anyways)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9746 6adb6e08-d915-0410-9...

a3e1486b48239d9b96f32bef8c48ccd93bb6ba3c authored over 12 years ago by Chris Bielow <[email protected]>

[FIX] corrected test error introduced [9743]

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9745 6adb6e08-d915-0410-9...

10aad74670db4ec87ebe62d4329ab95ddec8d191 authored over 12 years ago by Stephan Aiche <[email protected]>

fixed dataprocessing and rawfile writeout bug in mzquantmlhandler, improved SILACAnalyzer fileoutput

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9744 6adb6e08-d915-0410-9...

72e4f593f093c2af78cdd3bb480687fb49b78c9c authored over 12 years ago by Mathias Walzer <[email protected]>

** Simulator: added MS2 spectra to picked ground truth; added more meta information to MSe spectra (sequence and intensity)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9743 6adb6e08-d915-0410-...

ddbc0ad5c7ae857ba3a20a171ae3c27533e6fcb1 authored over 12 years ago by Chris Bielow <[email protected]>

** fixed bug in FileFilter -remove_meta (did filter the exact opposite -- somewhat)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9742 6adb6e08-d915-0410-9...

2f0d511c077aa0eb161a4c263f9d70e7f350205e authored over 12 years ago by Chris Bielow <[email protected]>

added SILACAnalyzer mzquantml writeout and improved some mzq handler parts

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9741 6adb6e08-d915-0410-9...

faf395a77b8da74988d0e6ea6efac56418a49be1 authored over 12 years ago by Mathias Walzer <[email protected]>

added MSQuantifications as superclass for Quantifications experiments capsuling ConsensusMaps and FeatureMaps and main target for MzQuantML store and load(next todo) also adapted MzQuantMLHandler to new schema

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9738 6adb6e08-d915-0410-9...

426d554a0824e1db0f3078e5c29c685fd92bfbe6 authored over 12 years ago by Mathias Walzer <[email protected]>

** fixed #423

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9737 6adb6e08-d915-0410-9...

70696bd709e85583a2b09c321d1bb7498d96e200 authored over 12 years ago by Chris Bielow <[email protected]>

test cases for mzTab export

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9736 6adb6e08-d915-0410-9...

2a510f13f255189faf8eded7011a15cc118d285b authored over 12 years ago by Timo Sachsenberg <[email protected]>

some preparations for testing

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9735 6adb6e08-d915-0410-9...

a8da5011c5eab2e7b428deb9a7af510fd8606026 authored over 12 years ago by Timo Sachsenberg <[email protected]>

direct integration of mzTab export into ProteinQuantifier

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9734 6adb6e08-d915-0410-9...

18ccacbce509d5ae07409843bfb229a3ebc4e520 authored over 12 years ago by Timo Sachsenberg <[email protected]>

[FIX] fixed test errors introduced in [9727]

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9731 6adb6e08-d915-0410-9...

d39ca01bb177e81464f5f1c9785dff9822ffee52 authored over 12 years ago by Stephan Aiche <[email protected]>

fixed newly introduced bug in QTClusterFinder

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9729 6adb6e08-d915-0410-9...

5f22c410db8f01e22b8cf23e41c4f9680dc61f0d authored over 12 years ago by Timo Sachsenberg <[email protected]>

** some cleaning up

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9727 6adb6e08-d915-0410-9...

51a791ed936737415c7343b2bda9b26ac86c9b0c authored over 12 years ago by Chris Bielow <[email protected]>

another fabs!=abs error

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9726 6adb6e08-d915-0410-9...

3f78fc751a99d2aab83749fd414c8c193a448fb9 authored over 12 years ago by Timo Sachsenberg <[email protected]>

fixed another fabs!=abs bug

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9725 6adb6e08-d915-0410-9...

80dffb21c5394a7f26e49a8184b4a96802a35af4 authored over 12 years ago by Timo Sachsenberg <[email protected]>

fixed abs!=fabs bug

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9724 6adb6e08-d915-0410-...

913657795dc0c837a2d0a484e7467972a70ef767 authored over 12 years ago by Timo Sachsenberg <[email protected]>

value passing by reference

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9723 6adb6e08-d915-0410-9...

2cf8670787123f5b0c9b0335bbaaea368a490b20 authored over 12 years ago by Timo Sachsenberg <[email protected]>

** append 9673, forgot to set dirty flag to false

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9720 6adb6e08-d915-0410-9...

f42053baa8daa606aaf9ea41124fae5b0365b151 authored over 12 years ago by Hannes Roest <[email protected]>

allow featureXML to also show progress when loading

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9719 6adb6e08-d915-0410-9...

dca907594e1963e2bb6ac6c3efbc0ddf9505ec94 authored over 12 years ago by Hannes Roest <[email protected]>

stopped LogStream from caching empty lines

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9714 6adb6e08-d915-0410-9...

d4de0d8177a33eaa1ba8b306e374374bdafa4cd3 authored over 12 years ago by Stephan Aiche <[email protected]>

** reserve space when loading feature maps (small time improvement - ~ 3% Windows, 10% Linux)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9712 6adb6e08-d915-0410-9...

852700b6ef8f4fc6cdfc0e7a3c7f5d9cab950937 authored over 12 years ago by Chris Bielow <[email protected]>

** added time measurement for every TOPP tool per default (written to CMD line at the very end)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9711 6adb6e08-d915-0410-9...

dc0308023124d9438507e7ee416692e2436ee520 authored over 12 years ago by Chris Bielow <[email protected]>

forgot one file

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9706 6adb6e08-d915-0410-9...

0140eab4831ba7d96c0afd566252ad324fbff0b7 authored over 12 years ago by Timo Sachsenberg <[email protected]>

mz error filtering added to idfilter

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9705 6adb6e08-d915-0410-...

8f1dc1103e72251b0df53df08d7e517bec3f22a8 authored over 12 years ago by Timo Sachsenberg <[email protected]>

** made SequenceCoverageCalculator compatible to TOPPAS

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9703 6adb6e08-d915-0410-9...

cd4f9f6ff2fe23caf6a8383213477d5ef36ef9d9 authored over 12 years ago by Chris Bielow <[email protected]>

also copy the TargetList cv terms, add tests

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9700 6adb6e08-d915-0410-9...

98052100f5ca5f4854e58d8dd4ecb36ac987843a authored over 12 years ago by Hannes Roest <[email protected]>

some refactoring of MzTabExporter

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9699 6adb6e08-d915-0410-...

3d7cba1bba887f02d8db1b48d5d5d1a02de70564 authored over 12 years ago by Timo Sachsenberg <[email protected]>

allow FileMerger to merge TraML files, add tests for this

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9698 6adb6e08-d915-0410-9...

1e822fab35b6b1f6d8f57277dbf2a9ef6b87efd8 authored over 12 years ago by Hannes Roest <[email protected]>

fix bug when adding CV term

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9697 6adb6e08-d915-0410-9...

8324304dd2b7bb93fabd8016bab4ff74be9d1845 authored over 12 years ago by Hannes Roest <[email protected]>

remove preprocessor statement that was for testing only

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9696 6adb6e08-d915-0410-9...

4b0bf8e27b19a982a3d752304119bf879c66b633 authored over 12 years ago by Hannes Roest <[email protected]>

** speed improvement for PepXMLFile

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9694 6adb6e08-d915-0410-9...

b4e5db9970a4b730aee5df079d481dbf0a6da801 authored over 12 years ago by Chris Bielow <[email protected]>

** formatting

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9692 6adb6e08-d915-0410-9...

445f3424b1f9d1d7137a335fcd1beef71b206908 authored over 12 years ago by Chris Bielow <[email protected]>

Add output-files for ProteinQuantifier tests.

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9689 6adb6e08-d915-0410-...

da199453382747d5348fc326a5807eac0f90fc65 authored over 12 years ago by Immanuel Luhn <[email protected]>

** minor parse error message improvement

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9687 6adb6e08-d915-0410-9...

448bfcf972009a31e412661541d579677d13f547 authored over 12 years ago by Chris Bielow <[email protected]>

** prevented FileInfo from crashing on emtpy idXML

** added testcase

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9686 6a...

384464c8eef45e00b64e57df1286df0691873b92 authored over 12 years ago by Chris Bielow <[email protected]>

first mzq validator version

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9685 6adb6e08-d915-0410-9...

ecfbb6303771746197cb18b4554c5f238678cfa8 authored over 12 years ago by Mathias Walzer <[email protected]>

** removed excessive std::endl in FileInfo (replaced with faster "\n")

** closed open streams in FileInfo (this bug did not show due to endl's)

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

7c3ce5b610dbfc4936df2e891ce3e123d404c979 authored over 12 years ago by Chris Bielow <[email protected]>

redirected cdash submissions to new cdash server cdash.openms.de

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9680 6adb6e08-d915-0410-9...

c275f2822e0689db7f847b6119b80811626264b6 authored over 12 years ago by Stephan Aiche <[email protected]>

add tests for MapRTTransformer on chromatograms

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9678 6adb6e08-d915-0410-9...

432dcccac923387851ba164064cc344caac0fe20 authored over 12 years ago by Hannes Roest <[email protected]>

MapRTTransform: also transform chromatograms

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9677 6adb6e08-d915-0410-9...

df94666d63b4fd842e2b11240e4957d2faa6112b authored over 12 years ago by Hannes Roest <[email protected]>

** added prepending of Decoy string to DecoyDatabase.C (fixing #421)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9676 6adb6e08-d915-0410-9...

522d436373c6f6f0bf3d3a45367cb26d7818091f authored over 12 years ago by Chris Bielow <[email protected]>

** fixed docu of PeptideIndexer

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9675 6adb6e08-d915-0410-9...

f1351572479a0a65da3f247c6a79843d53a7c04b authored over 12 years ago by Chris Bielow <[email protected]>

allow fast access to proteins and peptides in TargetedExperiment

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9673 6adb6e08-d915-0410-9...

ed579220caf58f260345a58080202da60c075390 authored over 12 years ago by Hannes Roest <[email protected]>

changes in Transition class due to the changes in the data model of TraML 1.0.0

- product is now a separate struct, thus the product attributes are not
stored in ReactionMoni...

49064745b29eb2a1cc6829ae531935ee55d201ba authored over 12 years ago by Hannes Roest <[email protected]>

avoid ambiguous call of log

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@9669 6adb6e08-d915-0410-...

2df809b3ca3c39517036ebb9561593f345f5e196 authored over 12 years ago by Immanuel Luhn <[email protected]>

Latest version of ProteinQuantifier and FileMerger to compute triple

SILAC-ratios, respectively merge consensusXML-files.
Moreover, tests for both TOOP tools are adde...

34cd70f437b01a7cc4267c1a3f80ef194a138966 authored over 12 years ago by Immanuel Luhn <[email protected]>