[FEATURE] Adding new TOPP tool IsobaricAnalyzer for analysis of ms2 labeled experiments.

 * all analysis steps (channel extraction, isotope correction) are now independent of the
   quantitation method (itraq4plex, tmt6plex)
 * lots of refactoring, restructuring, etc. w.r.t. to the old implementation
 * added some more tests to the individual classes/methods

Merge branch 'isobaricanalyzer'



git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11264 6adb6e08-d915-0410-941f-83917bcadc18
[FIX,NOP] fixed some cpplint and cppcheck warnings

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11265 6adb6e08-d915-0410-941f-83917bcadc18
[FIX] fixed some compiler warnings in TESTs 

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11266 6adb6e08-d915-0410-941f-83917bcadc18
[FEATURE,NOP] added intensity based filtering options to the IsobaricChannelExtractor

 * allow filtering based on precursor/reporter intensity
 * default settings correspond to the original implementation in ITRAQChannelExtractor

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11267 6adb6e08-d915-0410-941f-83917bcadc18
[BUILD] fix checker script

- when typedefs were in the pxd file, it would fail to identify the
  correct class -> fix

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11268 6adb6e08-d915-0410-941f-83917bcadc18
[DOC] pyOpenMS Manual.tex updated

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11269 6adb6e08-d915-0410-941f-83917bcadc18
[BUILD] update ignore list

- various small changes
- more docu on the reported error

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11270 6adb6e08-d915-0410-941f-83917bcadc18
[FIX] pyOpenMS: fix DataFilters

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11271 6adb6e08-d915-0410-941f-83917bcadc18
[FIX] pyOpenMS: fix ProteinResolver

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11272 6adb6e08-d915-0410-941f-83917bcadc18
[FIX] pyOpenMS: fix ItraqConstants

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11273 6adb6e08-d915-0410-941f-83917bcadc18
[FIX] pyOpenMS: fix PeakIndex

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11274 6adb6e08-d915-0410-941f-83917bcadc18
[FIX] pyOpenMS: fix OptimizePeakDeconvolution

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11275 6adb6e08-d915-0410-941f-83917bcadc18
[BUILD] Feature: PythonExtensionChecker now writes cdash xml file

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11276 6adb6e08-d915-0410-941f-83917bcadc18
[BUILD] Feature: allow 1:n mappings

allow 1:n mappings between C++ .h files and .pxd files -> one .h file
might contain multiple classes and thus multiple .pxd files could map to
the same C++ header file.

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11277 6adb6e08-d915-0410-941f-83917bcadc18
[FEATURE] FileFilter now supports filtering of MS/MS spectra by their collision energy and the width of the isolation window

 * added the corresponding predicates to RangeUtils
 * added TOPP tests 

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11278 6adb6e08-d915-0410-941f-83917bcadc18
[FIX-#535,VISUAL] Fall back to Spectra only

If an input file contains spectra and chromatograms, display only
spectra but output a warning to the LOG about the extra chromatograms.

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11279 6adb6e08-d915-0410-941f-83917bcadc18
[FIX] addendum to [11042] fixing compile issues on win-xp 32bit systems

 * added missing openmp include 

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11281 6adb6e08-d915-0410-941f-83917bcadc18
[FIX] fixed minor error in mzXML::writeTo()
 
 * empty spectra in mzXML get the xsi:nil attribute which should have the value "true", but got the value "1"

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11282 6adb6e08-d915-0410-941f-83917bcadc18
[FEATURE] * print command line of TOPP tool when debug mode is enabled

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11284 6adb6e08-d915-0410-941f-83917bcadc18
[FIX] fixed warnings introduced in [11264]

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11285 6adb6e08-d915-0410-941f-83917bcadc18