these examples are describing the “old” biojava way. In the latest svn they still work, but are labeled as deprecated and that the org.biojavax interface should be used instead. Would be good to update this example –Andreas 10:57, 30 April 2008 (UTC)
Update Cookbook to use biojavax
Many of the examples in the cookbook use deprecated classes. As a n00b, I am finding documentation of updated classes is lacking.