[FIX] added template argument to IMSDataConsumer to support all mzml load operations

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11579 6adb6e08-d915-0410-941f-83917bcadc18
[FIX] addendum to [11579]

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11585 6adb6e08-d915-0410-941f-83917bcadc18
[FIX] fix MSData consumers

- set default template argument for IMSDataConsumer
- use MSExperiment for MzMLFile::transform
- add setExperimentalSettings to MSDataTransformingConsumer.h
- remove erroneous const from Map in MzMLFile::transform

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11589 6adb6e08-d915-0410-941f-83917bcadc18
[FIX] bugfix and minor improvements

- bugfix in PeakPickerMRM when dealing with empty chromatograms
- minor improvements in QTClusterFinder (pre-increment)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11590 6adb6e08-d915-0410-941f-83917bcadc18
[FEATURE] allow minimal quality threshold in PeakPicker

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11591 6adb6e08-d915-0410-941f-83917bcadc18
[FEATURE] use shared_ptr in SpectrumAccessOpenMS

Previously, a full MSExperiment was transferred to the Handler class and
ownership was not completely transferred.

For clear transfership of ownership, use boost::shared_ptr in
SpectrumAccessOpenMS.

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11592 6adb6e08-d915-0410-941f-83917bcadc18
[FEATURE] add option to also add cached meta value directly

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11593 6adb6e08-d915-0410-941f-83917bcadc18
[FEATURE] Add CachedConsumer

The new class allows to consume Spectra/Chromatograms and cache them
directly to disk. It implements the IMSDataConsumer.h Interface.

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11594 6adb6e08-d915-0410-941f-83917bcadc18
[NOP] whitespace changes in comments

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11629 6adb6e08-d915-0410-941f-83917bcadc18
[FIX] allow better control of PPHiRes parameters

- allow to set the SignalToNoise parameters
- allow to set the max spacing parameter

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11630 6adb6e08-d915-0410-941f-83917bcadc18
[FIX] extend MSDataWritingConsumer to chromatograms

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11631 6adb6e08-d915-0410-941f-83917bcadc18
missing usage of boost shared pointer

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11632 6adb6e08-d915-0410-941f-83917bcadc18
[FEATURE] PeakPickerIterative

- new PeakPicker for high-res TOF data

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11634 6adb6e08-d915-0410-941f-83917bcadc18
[TEST] add test data for PeakPickerIterative

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11635 6adb6e08-d915-0410-941f-83917bcadc18
[FEATURE-#581] ability to write indexedmzML

- getWriteIndex and setWriteIndex in PeakFileOptions control whether a
  mzML or indexedmzML is written
- a vector of (ids,offsets) stores the binary offsets during writing
- the additional tags are written in writeHeader_ and writeFooter_
- default behavior is still regular mzML

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11636 6adb6e08-d915-0410-941f-83917bcadc18
[TEST] indexedmzML test, FileFilter option

- FileFilter can now write indexedmzML or mzML
- test for both behaviors is added

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11637 6adb6e08-d915-0410-941f-83917bcadc18
[FEATURE-#592] Lazy loading for indexedmzML

implements lazy loading of indexedmzML using the IndexedMzMLFile class.

- IndexedMzMLFile allows to parse an indexedmzML file and access
  individual spectra and chromatogram without loading them into memory
- IndexedMzMLDecoder parses a indexedmzML and retrieves the binary
  offsets
- MzMLSpectrumDecoder decodes strings with single <spectrum> and
  <chromatogram> tags

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11652 6adb6e08-d915-0410-941f-83917bcadc18
Merged release branch into trunk 11472:11703

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11707 6adb6e08-d915-0410-941f-83917bcadc18
[BUILD,FIX] Trunk compiles again from merge [11708]

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11709 6adb6e08-d915-0410-941f-83917bcadc18
[FIX] fixed small bug in jumping window mower

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11711 6adb6e08-d915-0410-941f-83917bcadc18