don't call addChild in storeNodes
Mark as 'filthy' all nodes whose underlying taxa set has been changed by the operator
Add a (default) interface method to get tree nodes in post-order
Clear possibly marked nodes status upon restore
set taxon set input when tree is labeled
update comment to reflect code
Add command line option to control startup printouts verbosity
cosmetic: join exceptions code
print startup messages via Log.print*
Fix off by one bug.
Cosmetic: new style loops
print startup messages via Log.print*
add a tree operator flag (mark clades) to enable/disable full marking of internal nodes as filthy. Under full marking, a node is filthy if its clade (tips set) has been changed by the operator
add a tree operator flag (mark clades) to enable/disable full marking of internal nodes as filthy. Under full marking, a node is filthy if its clade (tips set) has been changed by the operator
print startup messages via Log.print*
cache post-order traversal for re-use by multiple callers in one posterior calculation, and other speedups for large trees
fix condition for adding the taxa and fix tree parse test
spelling error
Print via Log.* to allow user control
Add scale-all-independently with indicators functionality