containReduce that performs the
containing match part of the basic operations
you'll need to do to reconstruct the genome. The class
you'll check out is
ShotgunReconstruct.java and accessible here.
The basic idea is to remove any string that is completely contained in
another string, leaving the other strings in the ArrayList
passed to the method. You'll want to look at the ArrayList
API to see if there are useful methods to help in this process, and
you'll need methods from the String class as well.
After completing containReduce you should implement methods
that will perform the other matching operations. If two strings overlap,
you'll need to remove them, create a new string that represents their
merge, and add this string to the collection of strands. In this
discussion you're using strings, in Part II you'll use a class
that represents strands, not a String object.
Owen L. Astrachan
Last modified: Thu Oct 14 23:51:28 EDT 2004