public Graph toGraph() {
Table edgeTable = new Table();
Table nodeTable = new Table();
HashMap<String, Integer> unique = new HashMap<String, Integer>();
edgeTable.addColumn("Node1", int.class);
edgeTable.addColumn("Node2", int.class);
nodeTable.addColumn("key", int.class);
nodeTable.addColumn("name", String.class);
nodeTable.addColumn("type", String.class);
nodeTable.addColumn("indeterminate", int.class);
int idx = 0;
for (Protein prot : minProteins.values()) {
int row = nodeTable.addRow();
unique.put(prot.getName(), idx);
nodeTable.setInt(row, "key", idx++);
nodeTable.setString(row, "name", prot.getName());
nodeTable.setString(row, "type", "protein");
nodeTable.setInt(row, "indeterminate", 0);
}
for (Peptide pep : minPeptides.values()) {
int row = nodeTable.addRow();
unique.put(pep.getSequence(), idx);
nodeTable.setInt(row, "key", idx++);
nodeTable.setString(row, "name", pep.getSequence());
nodeTable.setString(row, "type", "peptide");
if (pep.getIndeterminateType() == PeptideIndeterminacyType.NONE) {
nodeTable.setInt(row, "indeterminate", 0);
} else {
nodeTable.setInt(row, "indeterminate", 1);
}
}
for (Protein prot : minProteins.values()) {
int id1 = unique.get(prot.getName());
for (String pep : prot.getPeptides()) {
int id2 = unique.get(pep);
int row = edgeTable.addRow();
edgeTable.setInt(row, "Node1", id1);
edgeTable.setInt(row, "Node2", id2);
}
}
Graph g = new Graph(nodeTable, edgeTable, false, "key", "Node1", "Node2");
// System.err.println(g.getEdgeCount());
return g;
}
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 PeptideCollection getPepXML() {
PeptideCollection new_pc = new PeptideCollection();
for (Peptide pg : minPeptides.values()) {
if (pg.containsPepXML()) {
new_pc.minPeptides.put(pg.getSequence(), pg);
}
}
return new_pc;
}
public void addPeptideGroup(Peptide pg) {
String key = pg.getSequence();
if (minPeptides.containsKey(key)) {
System.out.print("This PeptideCollection already contains " + key);
System.out.println(" are you sure this is what you want?");
} else {
minPeptides.put(key, pg);
}
}
public PeptideCollection getPeptidesByHits(int numHits) {
PeptideCollection new_pc = new PeptideCollection();
for (Peptide pg : minPeptides.values()) {
if (pg.getNumPeptideHits() >= numHits) {
new_pc.minPeptides.put(pg.getSequence(), pg);
}
}
new_pc.updatePeptideHits();
return new_pc;
}
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);
}
}
