Changed preference whether to retain rare alleles to false (previously true).
Improved handling of Tassel Preferences: Preference changes should be persisted when executing GUI and set only temporarily from Command Line Flags. Also getting preferences should use stored values when executing GUI. And should use default values (if not temporarily set) when executing from Command Line.
Formatting only
Those tests just need to happen in the opposite order so that it doesn't try to retrieve a value from a nonexistent site. New code is while (validSite && !polybits.fastGet(nextSite)) -Jason
Partial reversion of the HDF5Mutable caching the previous system
Fixed bug…  boolean validSite = true; to boolean validSite = nextSite < nsites; -Jason
Added call to fireProgress(100) to end.  Changed Button Name to "Archaeopteryx Tree"
Added call to fireProgress(100) to end
Added call to fireProgress(100)  And changed name to "Genomic Selection"
Changed Name to "Intersect Join"
Changed name to "Union Join" instead of "U Join"
Added call to fireProgress(100).  Added icon bitmap for Manhattan Display Plugin
Added call to fireProgress(100).  Added icon for QQ Plot Plugin
Changed Name to "Merge Alignments".  Added icon for Merge Alignment Plugin
Improved icon for Separate Plugin
Smaller SynonymizerPlugin icon
Changed name to "Linkage Disequilibrium"
Improved PrintHeapAction to report "Max available Heap" and to report all numbers in MB.
Changed Data, Analysis, and Results Modes to have drop down menus at the top instead of buttons.
Merge branch 'master' of ssh://git.code.sf.net/p/tassel/code