support for multiple variants at same slice location
updated to latest jillion
minor code cleanup
removed old jillion jar
1. bug fixes for ProtienSequenceBuilder insert(String)
made creation of trace archive not static
now using try-with-resource blocks
code clean up and attempt to make these tests pass on Windows.
made unknown amino acid 3 letter code actually 3 letters...
bug fixes for Exonerate parser
added constructor that takes "this" so we don't always have to pass the ".class" version.
Added Frames for reverse direction. changed frames from 0, 1, 2 to 1,2,3 and -1,-2,-3. Added lots of helper methods. OrfFinder now finds in all 6 frames by default and can do either direction only if asked.