public void createProteinList() {
minProteins = new HashMap<String, Protein>();
for (Peptide pg : minPeptides.values()) {
String pepName = pg.getSequence();
for (String protName : pg.getProteins()) {
if (minProteins.containsKey(protName)) {
Protein prot = minProteins.get(protName);
prot.addPeptide(pepName);
} else {
Protein prot = new Protein();
prot.setName(protName);
prot.addPeptide(pepName);
prot.setCluster(cluster_num);
minProteins.put(protName, prot);
}
}
}
for (Protein p : minProteins.values()) {
ProteinInfo pInfo = new ProteinInfo();
pInfo.setName(p.getName());
pInfo.setDescription(p.getDescription());
pInfo.setLength(p.getLength());
MassSieveFrame.addProtein(pInfo);
}
}
public void updateParsimony() {
for (Protein prot : minProteins.values()) {
for (String pepName : prot.getPeptides()) {
Peptide pep = minPeptides.get(pepName);
prot.addAssociatedProteins(pep.getProteins());
}
}
for (Protein prot : minProteins.values()) {
prot.updateParsimony(minProteins);
}
for (Protein prot : minProteins.values()) {
prot.computeParsimonyType();
}
}
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 updateProteins(HashMap<String, Protein> mainProteins) {
minProteins = new HashMap<String, Protein>();
for (Peptide pg : minPeptides.values()) {
String pepName = pg.getSequence();
for (String protName : pg.getProteins()) {
if (minProteins.containsKey(protName)) {
Protein prot = minProteins.get(protName);
prot.addPeptide(pepName);
} else {
Protein prot = mainProteins.get(protName);
minProteins.put(protName, prot);
}
}
}
for (Peptide pg : minPeptides.values()) {
pg.updateProteins(minProteins);
}
for (Protein p : minProteins.values()) {
p.updatePeptides(minPeptides);
}
}
