import jalview.datamodel.SequenceNode;
import jalview.viewmodel.AlignmentViewport;
+/**
+ * This class implements distance calculations used in constructing a Average
+ * Distance tree (also known as UPGMA)
+ */
public class AverageDistanceTree extends TreeBuilder
{
/**
}
/**
- * Returns the minimum distance between two clusters, and also sets the
- * indices of the clusters in fields mini and minj
- *
- * @return DOCUMENT ME!
+ * {@inheritDoc}
*/
@Override
protected double findMinDistance()
}
/**
- * DOCUMENT ME!
- *
- * @param tmpi
- * DOCUMENT ME!
- * @param tmpj
- * DOCUMENT ME!
- * @param dist
- * DOCUMENT ME!
+ * {@inheritDoc}
*/
@Override
- protected void findNewDistances(SequenceNode tmpi, SequenceNode tmpj,
+ protected void findNewDistances(SequenceNode nodei, SequenceNode nodej,
double dist)
{
double ih = 0;
double jh = 0;
- SequenceNode sni = tmpi;
- SequenceNode snj = tmpj;
+ SequenceNode sni = nodei;
+ SequenceNode snj = nodej;
while (sni != null)
{
snj = (SequenceNode) snj.left();
}
- tmpi.dist = ((dist / 2) - ih);
- tmpj.dist = ((dist / 2) - jh);
+ nodei.dist = ((dist / 2) - ih);
+ nodej.dist = ((dist / 2) - jh);
}
}