[FIX] removed unnecessary if(test_mode_) code from FileMerger, FileConverter, and PrecursorMassCorrector as we can handle the file location in the TOPP test using FuzzyDiff's -whitelist

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11425 6adb6e08-d915-0410-941f-83917bcadc18
[FIX] fixed false slot connection of TOPP tool exec in TOPPView

The slot must be created before the start method is called. used to be after.


git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11426 6adb6e08-d915-0410-941f-83917bcadc18
[INTERNAL,FIX-517] removed not implemented functions from API

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11427 6adb6e08-d915-0410-941f-83917bcadc18
[BUILD-#552] add pyOpenMS to the default target (if it is enabled)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11428 6adb6e08-d915-0410-941f-83917bcadc18
[NOP] fix typos in CMAKE files

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11429 6adb6e08-d915-0410-941f-83917bcadc18
[INTERNAL,FIX-#517] move pick function to header

- since it is a templated function, it should reside in the header file

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11430 6adb6e08-d915-0410-941f-83917bcadc18
[NOP] change licence statement to BSD in GUI

- remove old licence from ./source

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11431 6adb6e08-d915-0410-941f-83917bcadc18
[FIX-#553] fixed TOPPView's Apply TOPP tool functionality

 * TOPPView now uses the File::findExecutable method to find the correct TOPP executable 
 * QProcess::FailedToStart error is correctly handled by TOPPViewBase::runTOPPTool_
 * improved error output if the process fails to start

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11432 6adb6e08-d915-0410-941f-83917bcadc18
[FIX] Added upper bound for mass trace length as a parameter for mass trace detection

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11433 6adb6e08-d915-0410-941f-83917bcadc18
[FIX-#549,BUILD,PARAM,TEST,DOC] more general solution for extracting RTs from Mascot XML files based on regular expressions, with tests and improved documentation

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11434 6adb6e08-d915-0410-941f-83917bcadc18
[REVERT] revert 11434

patch breaks build on all test machines

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11435 6adb6e08-d915-0410-941f-83917bcadc18
[REVERT] revert 11435, un-revert 11434 (contrib needs to be rebuilt\!)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11436 6adb6e08-d915-0410-941f-83917bcadc18
[BUILD] extended search names for libsvm for upcoming changes of contrib libsvm

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11437 6adb6e08-d915-0410-941f-83917bcadc18
[FIX-XXX] Decrease memory footprint of FeatureLinkerUnlabeled

apply the same improvements made to MapAlignerPoseClustering in r9805
also to FeatureLinkerUnlabeled:

- instead of loading all maps into memory at once, only those two that
  are actually needed are loaded
- only implemented for FeatureMaps (ConsensusMaps are still loaded into
  memory first)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11438 6adb6e08-d915-0410-941f-83917bcadc18
[INTERNAL] Provide the same reserve interface for Spectra/Chromatograms

- The user can now specify in which vector he wants to reserve space
- calling reserve() on the MSExperiment is now deprecated

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11439 6adb6e08-d915-0410-941f-83917bcadc18
[INTERNAL] separate MzML Handler writeTo into individual functions

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11440 6adb6e08-d915-0410-941f-83917bcadc18
[INTERNAL] CachedMzML

- allow inheritance
- const-correctness for writeSpectrum_

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11441 6adb6e08-d915-0410-941f-83917bcadc18
[FEATURE] allow MassTraceExtractor to write out full MassTraces into consensusXML

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11444 6adb6e08-d915-0410-941f-83917bcadc18
[TEST] set regex parameter in .ini file to avoid CMake warning (reported by Hannes)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11446 6adb6e08-d915-0410-941f-83917bcadc18
[BUILD] made boost's search for static-only libs optional to support linking against shared libs on windows systems

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11447 6adb6e08-d915-0410-941f-83917bcadc18