Refactor neutral loss handling in getMatchForIon to handle cases more uniformly and utilize resuable helper functions.
Allow building a table of internal ions as available in msproduct (part of ProteinProspector). Rework slicing to allow an optional startIndex. This can be used for describing internal ions. Add fully general getSeqMass to Peptide class.
Initial implementation of displaying internal ions over the spectrum.
Don't calculate internal ion neutral loss.
Implement table showing all ions under consideration (current table doesn't display neutral loss for instance) sorted by m/z. This is optional and may be enabled by setting the option `showAllTable` to `true`.
Separate annotating internal ions and showing table into two separate options. Disable table by default.
Implement MH whole sequence ions.
Add git svn documentation.