public ArrayList<String> getClusterIDs(int clusterNum) {
ArrayList<String> clusterSeqs = new ArrayList<String>();
for (int i = 0; i < seqList.size(); i++) {
if (cluster[i] == clusterNum) clusterSeqs.add(seqList.get(i));
}
return clusterSeqs;
}
public int getClusterSize(int clusterNum) {
int count = 0;
for (int i = 0; i < seqList.size(); i++) {
if (cluster[i] == clusterNum) count++;
}
return count;
}
public void buildClusterer(ArrayList<String> seqDB, double[][] sm) {
seqList = seqDB;
this.setSimMatrix(sm);
Attribute seqString = new Attribute("sequence", (FastVector) null);
FastVector attrInfo = new FastVector();
attrInfo.addElement(seqString);
Instances data = new Instances("data", attrInfo, 0);
for (int i = 0; i < seqList.size(); i++) {
Instance currentInst = new Instance(1);
currentInst.setDataset(data);
currentInst.setValue(0, seqList.get(i));
data.add(currentInst);
}
try {
buildClusterer(data);
} catch (Exception e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}