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 losses.
Further simplify getMatchForIon with helper function for computing ionMz with neutralloss.
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.
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.
Don't calculate internal ion neutral loss.
Implement MH whole sequence ions.
Add git svn documentation.