[FIX] fixed windows compile errors introduced with MSNumpress

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11841 6adb6e08-d915-0410-941f-83917bcadc18
[FIX] * TOPPAS: allow number of input files to downstream nodes to be derived from collect-nodes

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11842 6adb6e08-d915-0410-941f-83917bcadc18
[FIX] fixed std::pow ambiguity error in MSNumpressCoder_test

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11843 6adb6e08-d915-0410-941f-83917bcadc18
[FIX,BUILD,NOP] fixed some cmake 2.8.12 warnings

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11844 6adb6e08-d915-0410-941f-83917bcadc18
[FEATURE] directory support for GenericWrapper (via a file within this directory)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11845 6adb6e08-d915-0410-941f-83917bcadc18
[FIX, FEATURE] 
 * cleanup of projection drawing in TOPPAS
 * allow projections to show absolute or relative intensities (switch via context menu)
 * also allow switch between sticks and area (context menu of 1D canvas)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11846 6adb6e08-d915-0410-941f-83917bcadc18
[FEATURE] improving capabilities of EICExtractor (autoRT, add meta information)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11847 6adb6e08-d915-0410-941f-83917bcadc18
[FIX] remove unnecessary headers from MSNumpress

- stdint.h is not available with MSVS2008 and apparently not necessary
  in the code. None of the typdefs found in stdint.h are found in the
  code, it should be safe to delete the include.
- stdio is not used, vector is already declared in the .h file,
  stdexcept is also not used

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11848 6adb6e08-d915-0410-941f-83917bcadc18
[FEATURE] add two more output columns to EICExtractor (theoretical RT and m/z)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11849 6adb6e08-d915-0410-941f-83917bcadc18
[FIX,TEST] hopefully fixed 'IDRipper_3' tests (thanks to Hannes for the notice)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11850 6adb6e08-d915-0410-941f-83917bcadc18
[FIX] attempt to fix compile error on older Visual Studio versions (untested)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11851 6adb6e08-d915-0410-941f-83917bcadc18
[FIX] removed non-existing PP-Rapid from ToolHandler - to avoid crashing TOPPDocumenter

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11852 6adb6e08-d915-0410-941f-83917bcadc18
[FIX] TOPPDocumenter now checks for tools presence before executing them (better error message)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11853 6adb6e08-d915-0410-941f-83917bcadc18
[FIX] bugfix, extra space

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11854 6adb6e08-d915-0410-941f-83917bcadc18
[FEATURE] add decoy member to light transition experiment

- store whether a transition is target or decoy

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11855 6adb6e08-d915-0410-941f-83917bcadc18
[INTERNAL] refactor method in DataAccessHelper

- extract convertTargetedPeptide method to convert a single peptide

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11856 6adb6e08-d915-0410-941f-83917bcadc18
[FEATURE] directly read TSV to LightTargetedExperiment

- can now read a TSV file and directly output a LightTargetedExperiment
  (without the need to first convert to TargetedExperiment and then to
  LightTargetedExperiment)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11857 6adb6e08-d915-0410-941f-83917bcadc18
[INTERNAL] add assertions and pre/post conditions to the code

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11858 6adb6e08-d915-0410-941f-83917bcadc18
[API,IOFORMAT] allow to control whether to use DIA scores

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11859 6adb6e08-d915-0410-941f-83917bcadc18
[FIX] performance fix if S/N is set to zero

- do not compute SignalToNoise if it is set to zero

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11860 6adb6e08-d915-0410-941f-83917bcadc18