private List<ClusterDendogram> clusterIsolateList(
IsolateSimilarityMatrix similarityMatrix, List<Isolate> isolates, Cluster.distType type) {
// represent fecal samples
List<ClusterDendogram> clusterB = new ArrayList<ClusterDendogram>();
// represent fecal samples
List<ClusterDendogram> clusterF = new ArrayList<ClusterDendogram>();
// represent immediate (after) samples
List<ClusterDendogram> clusterI = new ArrayList<ClusterDendogram>();
// represent later samples
List<ClusterDendogram> clusterL = new ArrayList<ClusterDendogram>();
List<ClusterDendogram> clusterD = new ArrayList<ClusterDendogram>();
// clusters resulting from clustering the above clusters will be placed in
// clusters and this will prevent me from having to refactor the rest of this
// method.
List<ClusterDendogram> clusters = new ArrayList<ClusterDendogram>();
for (Isolate sample : isolates) {
Cluster newCluster = new Cluster(similarityMatrix, sample);
Dendogram newDendogram = new DendogramLeaf(sample);
switch (sample.getSampleMethod()) {
case FECAL:
clusterF.add(new ClusterDendogram(newCluster, newDendogram));
break;
case IMM:
clusterI.add(new ClusterDendogram(newCluster, newDendogram));
break;
case LATER:
clusterL.add(new ClusterDendogram(newCluster, newDendogram));
break;
case DEEP:
clusterD.add(new ClusterDendogram(newCluster, newDendogram));
break;
case BEFORE:
clusterB.add(new ClusterDendogram(newCluster, newDendogram));
break;
default:
System.err.println("serious error here");
break;
}
}
// System.out.printf("clusterList size: %d\n", clusters.size());
// cluster within each group
clusterF = clusterGroup(clusterF, type);
clusterI = clusterGroup(clusterI, type);
clusterL = clusterGroup(clusterL, type);
clusterD = clusterGroup(clusterD, type);
clusterB = clusterGroup(clusterB, type);
// cluster each group together:
// F and I together first since they are the closest in time
// F_I and L next since they are the next closest in time
// was going to use "clusterAcrossGroup" but there seemed to be a lot of
// logical traps such as where to put clusters that are combined and all of
// the problems that followed from that
clusters.addAll(clusterF);
clusters.addAll(clusterD);
clusters = clusterGroup(clusters, type);
clusters.addAll(clusterI);
clusters = clusterGroup(clusters, type);
clusters.addAll(clusterL);
clusters = clusterGroup(clusters, type);
clusters.addAll(clusterB);
clusters = clusterGroup(clusters, type);
// clusters within all the day's clusters
// based on the above clusterGroup call this would likely be repetitive
// clusters = clusterGroup(clusters, type);
return clusters;
}
