added ProgressListener argument to Argument parse() method. Created GCRunMutator function to mutate 5 G or C repeats, in the process of implementing. Tried to improve Dictionary efficiency. Need to further improve reading and usage speeds of GappedKmer.
improved chiptools Kmer data class to no longer store a list of rows with all entries but rather only the fwd sequence. updated some chiptools argument classes to comply with ProgressListener argument in the parse() method. Need to fix memory overflow when saving very large data objects.
updated JProbeGUI frame to revalidate whole frame when new components are added. This should fix bug on macs where the components aren't painted until the window is resized.
Added apache commons-io library for BoundedInputStream. Improved input of large gapped kmers somewhat by using string.intern(). Import/export/save/load now handle all throwables in order to gracefully deal with out of memory errors. FunctionThread in function plugin also handles all throwables.
updated Muate method to only check overlap with the binding sites, not the binding sites and binding barrier region, but prevents mutations in the binding barrier as well.