import jalview.viewmodel.AlignmentViewport;
/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
+ * This class implements distance calculations used in constructing a Neighbour
+ * Joining tree
*/
public class NJTree extends TreeBuilder
{
{
super(av, sm, scoreParameters);
}
- // private long _lycount = 0, _lylimit = 0;
/**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * {@inheritDoc}
*/
@Override
- protected
- double findMinDistance()
+ protected double findMinDistance()
{
double min = Double.MAX_VALUE;
}
/**
- * DOCUMENT ME!
- *
- * @param tmpi
- * DOCUMENT ME!
- * @param tmpj
- * DOCUMENT ME!
- * @param dist
- * DOCUMENT ME!
+ * {@inheritDoc}
*/
@Override
- protected
- void findNewDistances(SequenceNode tmpi, SequenceNode tmpj, double dist)
+ protected void findNewDistances(SequenceNode nodei, SequenceNode nodej,
+ double dist)
{
+ nodei.dist = ((dist + ri) - rj) / 2;
+ nodej.dist = (dist - nodei.dist);
- tmpi.dist = ((dist + ri) - rj) / 2;
- tmpj.dist = (dist - tmpi.dist);
-
- if (tmpi.dist < 0)
+ if (nodei.dist < 0)
{
- tmpi.dist = 0;
+ nodei.dist = 0;
}
- if (tmpj.dist < 0)
+ if (nodej.dist < 0)
{
- tmpj.dist = 0;
+ nodej.dist = 0;
}
}
-
-
/**
* Calculates and saves the distance between the combination of cluster(i) and
* cluster(j) and all other clusters. The new distance to cluster k is