Replace TaxonRefference array which was used only to get its length with TaxonReferenceLength field.
Replace Hashtable usage with HashMap, because it is not synchronized, hence is faster.
Get rid of ugly ,,((Integer) taxa2Ref.get(new Integer(someIntegerValue))).intValue()'' constructs.
Use Taxon.getNumber() method instead of directly accessing legacy Taxon.number field which value is never set by any part of Mesquite.