Add unit tests (using qunit) to test aminoacid.js, peptide.js, and ion.js.
Refactor _seqMassMono and _seqMassAvg to use common base function.
Refactor _addResidueModMasses to reduce looping, simplify logic.
Refactor to simplify and reuse n versus c term subsequence logic.
Refactor neutral loss handling in getMatchForIon to handle cases more uniformly and utilize resuable helper functions.
Implement optional calculation and display of internal ions as available in msproduct (part of ProteinProspector). The "Internal" checkbox can be enabled by setting `showInternalIonOption` to `true`. Rework slicing to allow an optional startIndex - this can be used for describing internal ions. Add fully general getSeqMass to Peptide class.
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`.
Implement MH whole sequence ions.
Add git svn documentation.