[FEATURE] enable LOG_DEBUG for TOPPAS by --debug flag

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11866 6adb6e08-d915-0410-941f-83917bcadc18
[FIX] * cleanup of TOPPASToolVertex
 * re-enabled filename heuristic

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11867 6adb6e08-d915-0410-941f-83917bcadc18
[NOP] space/formatting

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11868 6adb6e08-d915-0410-941f-83917bcadc18
[INTERNAL] optimize performance of mzXMLHandler if FillData is false

- if the raw spectral data should not be appended to the spectra list,
  we can skip several steps in the mzXMLHandler

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11869 6adb6e08-d915-0410-941f-83917bcadc18
[INTERNAL,API] refactoring in ChromatogramExtractor

- add createPeptideReferenceMap_ function for easy lookup of peptides
- add typedef in TargetedExperiment
- move prepare function in ChromExtractor, make templated

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11870 6adb6e08-d915-0410-941f-83917bcadc18
[TEST] fix test after r11857

- OpenSwathDataAccessHelper::convertTargetedPeptide is now used to
  determine the output peptide sequence
- the output is now always in UniMod identifiers (and not in human
  understandable identifiers like "Phospho")

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11871 6adb6e08-d915-0410-941f-83917bcadc18
[TEST] fix test after r11854

the extra space was there from the beginning, now it is removed

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11872 6adb6e08-d915-0410-941f-83917bcadc18
wf FIRST COMIT +++++ =====

wf second commit

mini change

bugfix: use correct inversion

[FIX] bugfix for Segfault

handle error smarter

[FIX] add output file

switch for file caching

amend

switch to shared pointers as well

add option to cache files

code move

[DOC] fix docu

extract fxn

extract fxn

cleanup

Default Parameters

rename param

pass params through

progress logger

[FIX] fix prev commit

add OSW workflow

undo stupid
TRIAL DUMMY add comments about speed
TRIAL dUMMY == add comments about speed
added data reduction step

- Add iterative Peakpicker as data reduction step
[NOP]
[FIX] clear meta data
[INTERNAL] switch to new Chromatogram Extractor interface
cleanup, use shared prep function
new fxn
fix: changes the parameter!

minor improvements
Switch to new chrom extractor interface
[FEATURE] read TraML and csv transition files
[FEATURE] add TSV output to OpenSwathWorkflow

make out_tsv optional

add additional meta values

fix