*/
public class NJTree
{
+ public static final String AVERAGE_DISTANCE = "AV";
+
+ public static final String NEIGHBOUR_JOINING = "NJ";
+
Vector<Cluster> cluster;
SequenceI[] sequence;
this.seqData = new AlignmentView(sdata, start);
}
// System.err.println("Made seqData");// dbg
- if (!(type.equals("NJ")))
+ if (!(type.equals(NEIGHBOUR_JOINING)))
{
- type = "AV";
+ type = AVERAGE_DISTANCE;
}
if (sm == null && !(pwtype.equals("PID")))
{
while (noClus > 2)
{
- if (type.equals("NJ"))
+ if (type.equals(NEIGHBOUR_JOINING))
{
findMinNJDistance();
}
ri = findr(i, j);
rj = findr(j, i);
- if (type.equals("NJ"))
+ if (type.equals(NEIGHBOUR_JOINING))
{
findClusterNJDistance(i, j);
}
SequenceNode tmpi = (node.elementAt(i));
SequenceNode tmpj = (node.elementAt(j));
- if (type.equals("NJ"))
+ if (type.equals(NEIGHBOUR_JOINING))
{
findNewNJDistances(tmpi, tmpj, dist);
}