import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.SimilarityParamsI;
import jalview.datamodel.AlignmentView;
+import jalview.datamodel.BinaryNode;
import jalview.datamodel.CigarArray;
import jalview.datamodel.SeqCigar;
import jalview.datamodel.SequenceI;
protected double rj;
- SequenceNode maxdist;
+ BinaryNode maxdist;
- SequenceNode top;
+ BinaryNode top;
double maxDistValue;
*
* @return DOCUMENT ME!
*/
- double findHeight(SequenceNode nd)
+ double findHeight(BinaryNode nd)
{
if (nd == null)
{
if ((nd.left() == null) && (nd.right() == null))
{
- nd.height = ((SequenceNode) nd.parent()).height + nd.dist;
+ nd.height = ((BinaryNode) nd.parent()).height + nd.dist;
if (nd.height > maxheight)
{
{
if (nd.parent() != null)
{
- nd.height = ((SequenceNode) nd.parent()).height + nd.dist;
+ nd.height = ((BinaryNode) nd.parent()).height + nd.dist;
}
else
{
nd.height = (float) 0.0;
}
- maxheight = findHeight((SequenceNode) (nd.left()));
- maxheight = findHeight((SequenceNode) (nd.right()));
+ maxheight = findHeight((BinaryNode) (nd.left()));
+ maxheight = findHeight((BinaryNode) (nd.right()));
}
return maxheight;
* @param nd
* DOCUMENT ME!
*/
- void reCount(SequenceNode nd)
+ void reCount(BinaryNode nd)
{
ycount = 0;
// _lycount = 0;
* @param nd
* DOCUMENT ME!
*/
- void _reCount(SequenceNode nd)
+ void _reCount(BinaryNode nd)
{
// if (_lycount<_lylimit)
// {
if ((nd.left() != null) && (nd.right() != null))
{
- _reCount((SequenceNode) nd.left());
- _reCount((SequenceNode) nd.right());
+ _reCount(nd.left());
+ _reCount((BinaryNode) nd.right());
- SequenceNode l = (SequenceNode) nd.left();
- SequenceNode r = (SequenceNode) nd.right();
+ BinaryNode l = nd.left();
+ BinaryNode r = nd.right();
nd.count = l.count + r.count;
nd.ycount = (l.ycount + r.ycount) / 2;
*
* @return DOCUMENT ME!
*/
- public SequenceNode getTopNode()
+ public BinaryNode getTopNode()
{
return top;
}
*
* @param nd
*/
- void findMaxDist(SequenceNode nd)
+ void findMaxDist(BinaryNode nd)
{
if (nd == null)
{
}
else
{
- findMaxDist((SequenceNode) nd.left());
- findMaxDist((SequenceNode) nd.right());
+ findMaxDist((BinaryNode) nd.left());
+ findMaxDist((BinaryNode) nd.right());
}
}
sn.setLeft((node.elementAt(i)));
sn.setRight((node.elementAt(j)));
- SequenceNode tmpi = (node.elementAt(i));
- SequenceNode tmpj = (node.elementAt(j));
+ BinaryNode tmpi = (node.elementAt(i));
+ BinaryNode tmpj = (node.elementAt(j));
findNewDistances(tmpi, tmpj, dist);
* Computes and stores new distances for nodei and nodej, given the previous
* distance between them
*/
- protected abstract void findNewDistances(SequenceNode nodei,
- SequenceNode nodej, double previousDistance);
+ protected abstract void findNewDistances(BinaryNode nodei,
+ BinaryNode nodej, double previousDistance);
/**
* Calculates and saves the distance between the combination of cluster(i) and