MS annotation + Merge: Add special peaks to the table

[Rene Ranzinger]

A preference is needed to allow creating special peaks (m/z values in the MS2 whose intensities need to be extracted from the mzXML file. For each annotation in the MS1 overview one column for each special peak is added.

Special peaks should also be included in the merge report but should hidden by default.

[dbrentw]

Initial commit in SVN revision 4866

[Rene Ranzinger]

Summary of the discussion with Mindy today:

• Remove the special peak upload from the MS upload
• Special peaks becomes a optional function that the user can invoke similar to the filters in MS annotation
• Preferences allow to create a named set of special peaks per MS level (e.g. for N-Glycans, for O-glycans for peptides)
• The dialog for the optional "apply special peaks" function will look similar to the last page in the MS wizard except a drop down that allows to pick the set on top (drop down default value can be controlled by preferences as well)
• When special peaks are applied they are persisted in the data structure (so they become accessible for merge)
• It is possible to reapply special peaks in case user decides to choose a different configuration (will overwrite old special peaks)

[dbrentw]

First edition of the new version is ready for initial testing. SVN revision 1690