private void addLinkedMembers(PeptideCollection cluster, Integer clustNum, Peptide pg) {
for (String proName : pg.getProteins()) {
Protein pro = minProteins.get(proName);
pro.setCluster(clustNum);
for (String pepName : pro.getPeptides()) {
Peptide subPg = minPeptides.get(pepName);
if (subPg.getCluster() == -1) {
subPg.setCluster(clustNum);
cluster.addPeptideGroup(subPg);
addLinkedMembers(cluster, clustNum, subPg);
}
}
}
}
public void updateClusters() {
clusters = new HashMap<Integer, PeptideCollection>();
for (Peptide pg : minPeptides.values()) {
pg.setCluster(-1);
}
int cluster_num = 1;
for (Peptide pg : minPeptides.values()) {
if (pg.getCluster() == -1) {
PeptideCollection newCluster = new PeptideCollection();
newCluster.setClusterNum(cluster_num);
pg.setCluster(cluster_num);
newCluster.addPeptideGroup(pg);
addLinkedMembers(newCluster, cluster_num, pg);
newCluster.updateProteins(minProteins);
newCluster.updateParsimony();
clusters.put(cluster_num, newCluster);
cluster_num++;
}
}
int equivGroup = 0;
HashSet<String> usedProteins = new HashSet<String>();
ArrayList<Protein> equivOrder = new ArrayList<Protein>();
equivOrder.addAll(getCountables());
equivOrder.addAll(getSubsets());
equivOrder.addAll(getSubsumables());
for (Protein p : equivOrder) {
if (!usedProteins.contains(p.getName())) {
p.setEquivalentGroup(equivGroup);
usedProteins.add(p.getName());
for (Protein ps : p.getEquivalent()) {
ps.setEquivalentGroup(equivGroup);
usedProteins.add(ps.getName());
}
equivGroup++;
}
}
}