Create top-level package tdg09 and move all packages there.
Analyse - new main class for running analysis, replacing MainAvHu09
Options - the container for command line options, used by JCommander
SiteAnalyser - implements Callable, run by Analyse for each site
CoreUtils - replaces FileUtils
PhyloAlignment - change scope of getNumberOfActiveAminoAcids
TreeNodeLabeler - can now be called programatically.
New libraries for updated version of tdg09
wip
Analyse - show command-line usage, collect results for later processing, perform lrt and fdr correction, output table of results, output conserved locations
Result & Model - objects storing results of site analysis, add YAML for output
Options - add descriptions to parameters
SiteAnalyser, PhyloAlignment - suppress all output, make heterogenous model agnostic (not flu specific)
CoreUtils - added a getDoubleComparator utility method that returns a double comparator on a particular field in a particular object
YAML encoding library
CoreUtils - moved to tdg.Utils
Analyse - use CompletionService so we can collect results out-of-order, print full results ordered by site, left-pad some output so it looks prettier
Utils - doubleComparator uses generic-fied class so it can be used a bit more cleanly
Constants - increase the tolerance so things converge
Analyse - insert line-breaks into labelled tree output but ask YAML to collapse newlines when reading
Model is inner class of Result
Analyse - shuffle around results
SiteAnalyser - remove old code
PhyloAlignment - remove old code and replace Vector with List
TreeNodeLabeler - clean up
Get YAML output into a form that can be read by R
Some minor refactoring, added start of new README.md
Move README to README.md.
Don't check in testing code!
Add new README and tutorial.
Add example plot produced using R
British spelling…?
Add example R code, full packaged binary and updated build.xml file.