added missing include

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11489 6adb6e08-d915-0410-941f-83917bcadc18
[DOC] improve documentation

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11493 6adb6e08-d915-0410-941f-83917bcadc18
[FEATURE,DOC,INTERNAL] OpenSwath::Scoring add functions

- rename methods in scoring
- add documentation
- add new functions for RootMeanSquareDeviation and SpectralAngle
- ensure that scores are set to zero before scoring

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11494 6adb6e08-d915-0410-941f-83917bcadc18
[TEST] add test for OpenSwathAnalyzer with trafoXML

- we have not tested using a trafoXML file so far, do this before
  refactoring

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11495 6adb6e08-d915-0410-941f-83917bcadc18
[INTERNAL] MRMFeatureFinderScoring refactoring

Rework how the scoring is done:

- Use simple struct to hold scoring
- Create class SwathScorer to call actual scoring functions
- Improve documentation
- remove RT map and compute reference map in seperate method

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11496 6adb6e08-d915-0410-941f-83917bcadc18
[INTERNAL] MRMFeatureFinderScoring simplify

- remove ITransitionGroup from FeatureFinder (not necessary any more)
  and all other classes using it

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11497 6adb6e08-d915-0410-941f-83917bcadc18
[FEATURE] add option to detect and remove overlapping peaks during the peakpicking process

- add removeOverlappingPeaks_ which checks for overlapping peaks and
  corrects them
- allow adjacent Features (change how overlapping features are
  calculated): now adjacent features are specifically allowed (e.g.
  those that share either right or left border)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11498 6adb6e08-d915-0410-941f-83917bcadc18
[INTERNAL] extract class PeakPickerMRM

- extract the MRM PeakPicker and leave as standalone class

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11499 6adb6e08-d915-0410-941f-83917bcadc18
[FEATURE] add minimal peak width to peak picker

- peaks below the minimal width are not reported upon

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11500 6adb6e08-d915-0410-941f-83917bcadc18
[FEATURE] do consistency check in MRMTransitionGroupPicker

check that the right and left borders of all peaks found are consistent
(to notice shoulders and non-coeluting peak shapes already at this
stage).

- add parameter to recalculate peaks

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11501 6adb6e08-d915-0410-941f-83917bcadc18
[TEST] add test for PeakPickerMRM

add to test

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11502 6adb6e08-d915-0410-941f-83917bcadc18
[INTERNAL] remove smoothed chromatogram from interface of PeakPickerMRM

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11503 6adb6e08-d915-0410-941f-83917bcadc18
[BUILD] allow build system to compile with crawdad

Crawdad is a chromatographic peak picker from the MacCoss lab. This
patch allows to link OpenMS against the Crawdid library when compiling
with the following cmake options:

-DCrawdad_DIR=/path/to/Crawdad/ -DWITH_CRAWDAD=TRUE

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11504 6adb6e08-d915-0410-941f-83917bcadc18
[FEATURE] allow Crawdad peak picking in OpenMS using PeakPickerMRM

- if OpenMS was compiled with Crawdad support, this option can be chosen
  for MRM peak picking

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11505 6adb6e08-d915-0410-941f-83917bcadc18
[FEATURE] PeakPickerMRM add new picking method

- add "corrected" method which uses the smoothed chromatogram to pick
- ignore peak width when less than zero
- move method for crawdad
- replace exception with error messagen and sensible handling

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11506 6adb6e08-d915-0410-941f-83917bcadc18
[FIX] fix peak calculation in MRM PeakPicking

- adapt peak calculation to how PeakPickerHiRes defines the peak. This
  assumes that at least 3 points are part of the peak.
- this may break how legacy code worked if no peak_width was specified

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11507 6adb6e08-d915-0410-941f-83917bcadc18
[FEATURE] add method to compute peak quality to MRMTransitionGroupPicker

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11508 6adb6e08-d915-0410-941f-83917bcadc18
[FEATURE] add the MRMTransitionGroupPicker TOPP tool

[TEST] add test for MRMTransitionGroupPicker

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11509 6adb6e08-d915-0410-941f-83917bcadc18
DOC for params

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11510 6adb6e08-d915-0410-941f-83917bcadc18
[FIX] fix compiler warnings

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11515 6adb6e08-d915-0410-941f-83917bcadc18