doc:changed some of the layout

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11813 6adb6e08-d915-0410-941f-83917bcadc18
doc:closed tag

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11814 6adb6e08-d915-0410-941f-83917bcadc18
doc:small fix in formatting

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11815 6adb6e08-d915-0410-941f-83917bcadc18
[NOP] explicite use of costly AASequence constructor in tests (preparation for some refactoring)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11816 6adb6e08-d915-0410-941f-83917bcadc18
[NOP] prevent implicit and costly conversions by making AASequence(String) etc. explicit

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11817 6adb6e08-d915-0410-941f-83917bcadc18
[NOP] style fixes

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11818 6adb6e08-d915-0410-941f-83917bcadc18
[BUILD] enabled explicit single value constructor test

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11819 6adb6e08-d915-0410-941f-83917bcadc18
[FEATURE,IO,TEST,DOC] added option to merge only new IDs into an existing file

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11820 6adb6e08-d915-0410-941f-83917bcadc18
qcml:changed xslt schema to work with previous changes

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11821 6adb6e08-d915-0410-941f-83917bcadc18
qcml:changed xslt code uglily to make output look good

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11822 6adb6e08-d915-0410-941f-83917bcadc18
qcml:cv ID is now capitalized like in XML schema

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11823 6adb6e08-d915-0410-941f-83917bcadc18
[NOP] coding style fixes

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11824 6adb6e08-d915-0410-941f-83917bcadc18
[FEATURE,API] allow extraction of asymmetrical and individual RT windows for ChromatogramExtractor

- instead of passing only a target RT and an extraction_window (for all
  chromatograms), now for each chromatogram a start and end RT can be
  specified. This allows for asymmetrical and individual RT extraction
  windows for each extraction coordinate.

- The parameter rt_extraction_window is removed from calls to the new
  interface of extractChromatograms
- each ChromatogramExtractorAlgorithm::ExtractionCoordinate now posesses
  an rt_start and rt_end member (instead of just an rt member)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11825 6adb6e08-d915-0410-941f-83917bcadc18
[FEATURE,PARAM] added option to adapt RT window based on presence of IDs

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11827 6adb6e08-d915-0410-941f-83917bcadc18
[FIX,TEST] fixed 'IDRipper_3' tests (partly broken in r11820, partly useless before), thanks to Stephan for the notice

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11830 6adb6e08-d915-0410-941f-83917bcadc18
[FIX] typo

- Crawdad, not Crowdad

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11831 6adb6e08-d915-0410-941f-83917bcadc18
[FEATURE] add MS Numpress class with test to OpenMS

- add MSNumpress from https://github.com/fickludd/ms-numpress to
  MATH/MISC (unmodified except header guard and include)
- add class MSNumpressCoder providing an interface similar to the Base64
  allowing for decoding and encoding data
- extract method decodeSingleString in Base64

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11832 6adb6e08-d915-0410-941f-83917bcadc18
[FEATURE] allow mzMLHandler to read numpress arrays

- add the decompression of float arrays using the MSNumpressCoder
- additionally parse the CV terms MS:1002312, MS:1002313 and MS:1002314

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11833 6adb6e08-d915-0410-941f-83917bcadc18
[FEATURE] Extend PeakFileOptions to store MSNumpress config object

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11834 6adb6e08-d915-0410-941f-83917bcadc18
[FEATURE] allow MzMLHandler to write numpress arrays

- try to write the arrays using MSNumpressCoder
- if it fails, use the regular functions to write base64 (uncompressed)
  arrays

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11835 6adb6e08-d915-0410-941f-83917bcadc18