/*
* Bottom up hierarchical clustering
*/
private static HashSet<Cluster> findClusters(Collection<Point3d> points, double threshold) {
HashSet<Cluster> clusters = new HashSet<>(points.size() * 2);
for (Point3d p : points) {
Cluster candidate = new Cluster();
candidate.add(p);
for (Point3d p2 : points) {
if (p != p2 && p.distance(p2) <= threshold) {
candidate.add(p2);
}
}
Iterator<Cluster> iter = clusters.iterator();
while (iter.hasNext()) {
Cluster c = iter.next();
for (Point3d p2 : candidate) {
if (c.contains(p2)) { // Se os clusters C e candidate se intersectam, fundi-los
candidate.addAll(c);
iter.remove();
break;
}
}
}
clusters.add(candidate);
}
return clusters;
}
/** Generate the hierarchical cluster and display it as a denogram in the graph */
public TreeNode makeTree(ClutoSolution cs) {
int[] tsize = cs.getTreeCounts();
int[][] ftree = cs.getForwardTree();
int nnrows = tsize.length;
int nrows = cs.getMatrix().getRowCount();
// for (int i = 0; i < nnrows-1; i++) {
// String s = "ftree" + "\t" + i + "\t" + ftree[i][0] + "\t" + ftree[i][1] + "\t" + tsize[i];
// System.out.println(s);
// }
Cluster[] ca = new Cluster[nnrows];
for (int i = 0; i < nnrows - 1; i++) {
if (!true) {
String s = "ftree" + "\t" + i + "\t" + ftree[i][0] + "\t" + ftree[i][1] + "\t" + tsize[i];
System.out.println(s);
}
Cluster cn = i < nrows ? (Cluster) new RowCluster(tm, i, null) : new CompositeCluster();
cn.setSimilarity(Math.abs(tsize[i]));
ca[i] = cn;
if (ftree[i][0] > -1) {
cn.add(ca[ftree[i][0]]);
}
if (ftree[i][0] > -1) {
cn.add(ca[ftree[i][1]]);
}
rootNode = cn;
}
return rootNode;
}
@Test
public void testBacked() {
Cluster<Integer, Integer> c = new BackedClusterImpl<Integer, Integer>(graph);
Graph<Integer, Integer> inducedGraph = c.getInducedGraph();
assertEquals(0, inducedGraph.getEdgeCount());
assertEquals(0, c.size());
c.add(0);
c.add(1);
assertEquals(2, c.size());
assertEquals(1, inducedGraph.getEdgeCount());
}
/**
* Create partitions from an input tree - recursive so will be called by many nodes, beginning
* with root but with calculations actually beginning on leaves.
*
* @param partitions Partitions in the form of entries in the hash table
* @param curInterestPercentage Current percentage of interest that we want splits to occur above
* to view in the network later
*/
private ArrayList<Cluster> constructClusters(
LinkedList<HashEntry> partitions, double curInterestPercentage) {
ArrayList<Cluster> clusters = new ArrayList<Cluster>();
// Thresholds for the current run of the cluster builder (c.f. the threshold for the partitions
// list).
double curInterestThreshold = (double) (noOfTrees * (curInterestPercentage / 100.0d));
int majInterestThreshold = (int) (noOfTrees * (50.0 / 100.0d));
for (Iterator<HashEntry> it = partitions.iterator(); it.hasNext(); ) {
HashEntry entry = it.next();
// Checks if this partition is still above threshold... partition.
// If not: remove it - O(1).
if ((double) entry.count <= curInterestThreshold) {
// correct the isMajority flag to now refer to majority not if of interest or not..
if (entry.count <= majInterestThreshold) {
entry.isMajority = false;
}
it.remove();
continue;
}
// Constructs clusters (list of TreeNode's for each set bit) from each partition.
if ((double) entry.count > curInterestThreshold) {
Cluster cluster = new Cluster();
if (entry.count > majInterestThreshold) {
cluster.isMajority = true;
}
cluster.aboveSplit = entry.partition;
cluster.noOfOccurrences = entry.count;
cluster.edgeLength = entry.edgeLengthsSum / entry.count;
for (int i = 0; i < entry.partition.size(); i++) {
if (entry.partition.get(i)) {
TreeNode node = new TreeNode(taxa.getName(i));
node.edgeLength = leafEdgeLengths[i] / noOfTrees;
cluster.add(node);
}
}
clusters.add(cluster);
}
}
// Sort by number of taxa.
// TODO: This might obviously be optimized a bit, e.g. with a PriorityQueue. - Eiriksson
Collections.sort(clusters);
return clusters;
}