sdata.addOperation(CigarArray.M, end - start + 1);
this.seqData = new AlignmentView(sdata, start);
}
-
+// System.err.println("Made seqData");// dbg
if (!(type.equals("NJ")))
{
type = "AV";
distance = findDistances(this.seqData
.getSequenceStrings(Comparison.GapChars.charAt(0)));
-
+// System.err.println("Made distances");// dbg
makeLeaves();
-
+// System.err.println("Made leaves");// dbg
+
noClus = cluster.size();
cluster();
+// System.err.println("Made clusters");// dbg
+
}
/**
public void reCount(SequenceNode node)
{
ycount = 0;
+ _lycount=0;
+// _lylimit = this.node.size();
_reCount(node);
}
-
+ private long _lycount=0,_lylimit=0;
/**
* DOCUMENT ME!
*
*/
public void _reCount(SequenceNode node)
{
+// if (_lycount<_lylimit)
+// {
+// System.err.println("Warning: depth of _recount greater than number of nodes.");
+// }
if (node == null)
{
return;
}
+ _lycount++;
if ((node.left() != null) && (node.right() != null))
{
+
_reCount((SequenceNode) node.left());
_reCount((SequenceNode) node.right());
((SequenceNode) node).count = 1;
((SequenceNode) node).ycount = ycount++;
}
+ _lycount--;
}
/**