import jalview.datamodel.SeqCigar;
import jalview.datamodel.SequenceI;
import jalview.datamodel.SequenceNode;
-import jalview.math.MatrixI;
import jalview.viewmodel.AlignmentViewport;
import java.util.BitSet;
import java.util.Vector;
-public abstract class TreeBuilder
+public abstract class TreeBuilder extends TreeEngine
{
public static final String AVERAGE_DISTANCE = "AV";
public static final String NEIGHBOUR_JOINING = "NJ";
- protected Vector<BitSet> clusters;
-
protected SequenceI[] sequences;
public AlignmentView seqData;
- protected BitSet done;
-
- protected int noseqs;
-
- int noClus;
-
- protected MatrixI distances;
-
- protected int mini;
-
- protected int minj;
-
- protected double ri;
-
- protected double rj;
-
- BinaryNode maxdist;
-
- BinaryNode top;
-
- double maxDistValue;
-
- double maxheight;
-
- int ycount;
-
- Vector<SequenceNode> node;
-
private AlignmentView seqStrings;
/**
}
/**
- * DOCUMENT ME!
- *
- * @param nd
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- double findHeight(BinaryNode nd)
- {
- if (nd == null)
- {
- return maxheight;
- }
-
- if ((nd.left() == null) && (nd.right() == null))
- {
- nd.height = ((BinaryNode) nd.parent()).height + nd.dist;
-
- if (nd.height > maxheight)
- {
- return nd.height;
- }
- else
- {
- return maxheight;
- }
- }
- else
- {
- if (nd.parent() != null)
- {
- nd.height = ((BinaryNode) nd.parent()).height + nd.dist;
- }
- else
- {
- maxheight = 0;
- nd.height = (float) 0.0;
- }
-
- maxheight = findHeight((BinaryNode) (nd.left()));
- maxheight = findHeight((BinaryNode) (nd.right()));
- }
-
- return maxheight;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param nd
- * DOCUMENT ME!
- */
- void reCount(BinaryNode nd)
- {
- ycount = 0;
- // _lycount = 0;
- // _lylimit = this.node.size();
- _reCount(nd);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param nd
- * DOCUMENT ME!
- */
- void _reCount(BinaryNode nd)
- {
- // if (_lycount<_lylimit)
- // {
- // System.err.println("Warning: depth of _recount greater than number of
- // nodes.");
- // }
- if (nd == null)
- {
- return;
- }
- // _lycount++;
-
- if ((nd.left() != null) && (nd.right() != null))
- {
-
- _reCount(nd.left());
- _reCount((BinaryNode) nd.right());
-
- BinaryNode l = nd.left();
- BinaryNode r = nd.right();
-
- nd.count = l.count + r.count;
- nd.ycount = (l.ycount + r.ycount) / 2;
- }
- else
- {
- nd.count = 1;
- nd.ycount = ycount++;
- }
- // _lycount--;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public BinaryNode getTopNode()
- {
- return top;
- }
-
- /**
*
* @return true if tree has real distances
*/
}
/**
- * Form clusters by grouping sub-clusters, starting from one sequence per
- * cluster, and finishing when only two clusters remain
- */
- void cluster()
- {
- while (noClus > 2)
- {
- findMinDistance();
-
- joinClusters(mini, minj);
-
- noClus--;
- }
-
- int rightChild = done.nextClearBit(0);
- int leftChild = done.nextClearBit(rightChild + 1);
-
- joinClusters(leftChild, rightChild);
- top = (node.elementAt(leftChild));
-
- reCount(top);
- findHeight(top);
- findMaxDist(top);
- }
-
- /**
- * Returns the minimum distance between two clusters, and also sets the
- * indices of the clusters in fields mini and minj
- *
- * @return
- */
- protected abstract double findMinDistance();
-
- /**
* Calculates the tree using the given score model and parameters, and the
* configured tree type
* <p>
cluster();
}
- /**
- * Finds the node, at or below the given node, with the maximum distance, and
- * saves the node and the distance value
- *
- * @param nd
- */
- void findMaxDist(BinaryNode nd)
- {
- if (nd == null)
- {
- return;
- }
-
- if ((nd.left() == null) && (nd.right() == null))
- {
- double dist = nd.dist;
-
- if (dist > maxDistValue)
- {
- maxdist = nd;
- maxDistValue = dist;
- }
- }
- else
- {
- findMaxDist((BinaryNode) nd.left());
- findMaxDist((BinaryNode) nd.right());
- }
- }
-
- /**
- * Calculates and returns r, whatever that is
- *
- * @param i
- * @param j
- *
- * @return
- */
- protected double findr(int i, int j)
- {
- double tmp = 1;
-
- for (int k = 0; k < noseqs; k++)
- {
- if ((k != i) && (k != j) && (!done.get(k)))
- {
- tmp = tmp + distances.getValue(i, k);
- }
- }
-
- if (noClus > 2)
- {
- tmp = tmp / (noClus - 2);
- }
-
- return tmp;
- }
-
protected void init(AlignmentView seqView, int start, int end)
{
- this.node = new Vector<SequenceNode>();
+ this.node = new Vector<BinaryNode>();
if (seqView != null)
{
this.seqData = seqView;
}
/**
- * Merges cluster(j) to cluster(i) and recalculates cluster and node distances
- *
- * @param i
- * @param j
- */
- void joinClusters(final int i, final int j)
- {
- double dist = distances.getValue(i, j);
-
- ri = findr(i, j);
- rj = findr(j, i);
-
- findClusterDistance(i, j);
-
- SequenceNode sn = new SequenceNode();
-
- sn.setLeft((node.elementAt(i)));
- sn.setRight((node.elementAt(j)));
-
- BinaryNode tmpi = (node.elementAt(i));
- BinaryNode tmpj = (node.elementAt(j));
-
- findNewDistances(tmpi, tmpj, dist);
-
- tmpi.setParent(sn);
- tmpj.setParent(sn);
-
- node.setElementAt(sn, i);
-
- /*
- * move the members of cluster(j) to cluster(i)
- * and mark cluster j as out of the game
- */
- clusters.get(i).or(clusters.get(j));
- clusters.get(j).clear();
- done.set(j);
- }
-
- /*
- * Computes and stores new distances for nodei and nodej, given the previous
- * distance between them
- */
- protected abstract void findNewDistances(BinaryNode nodei,
- BinaryNode nodej, double previousDistance);
-
- /**
- * Calculates and saves the distance between the combination of cluster(i) and
- * cluster(j) and all other clusters. The form of the calculation depends on
- * the tree clustering method being used.
- *
- * @param i
- * @param j
- */
- protected abstract void findClusterDistance(int i, int j);
-
- /**
* Start by making a cluster for each individual sequence
*/
void makeLeaves()
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