Refined Buneman Trees

implementing an algorithm with a high time and space complexity. However,
by implementing the algorithm in Java and integrating it into JSplits as a plugin,
the author has been handed a free user interface that fits perfectly with
this algorithm. Also, this method can hopefully become an integrated part in
future releases of JSplits which is easily and freely available, thereby contributing
something valueable to the field of tree reconstruction.
JSplits plug-ins fall into categories based on input and output. The refined
Buneman tree algorithm will take a distance matrix as input and return a compatible
set of splits, which can then be visualised in JSplits. Other methods
might take a set of aligned nucleotide sequences and return tree structures. A
full list of the extensive set of implemented methods and possible types of new
methods can be found in the JSplits source code documentation, which is probably
available upon request from Dr. Huson. At the time of writing it is not
publicly available.
The general way of creating a JSplits plug-in consists of two steps:
• Implementing an interface from the catalogue of possible interfaces available
in JSplits
• Placing the implementing file correctly in the JSplits directory structure,
which is grouped by input type
The JSplits application will automatically detect the presence of implemented
methods and create drop-down menu options for them. So the plug-in
facility is very easy to use indeed, and the author experienced no problems with
it at all.
The author did experience a few problems with the classes used in JSplits.
For some odd reason, the taxa list and input distance data is given in arrays
with offset 1 instead of the traditional offset 0 used in most other computer
science contexts - particularly in the Java programming language. But in spite
of this minor quirk, the author has been very satisfied working with JSplits.
11.4 The Distances2Splits interface
In JSplits terminology, the refined Buneman tree algorithm falls in the category
distances-to-splits algorithm, and Dr. Huson pointed out that the author should
implement his work as a Java class implementing the Distances2Splits interface
found in JSplits. That interface looks like this:
package splits.algorithms.distances;
interface Distances2Splits extends DistancesTransform
{
boolean isApplicable(Taxa taxa, Distances d);
}
Splits apply(Taxa taxa, Distances d) throws Exception;
70