private DefaultMutableTreeNode ProListToEquivTree(ArrayList<Protein> proList, String name) {
DefaultMutableTreeNode root, child;
int size = 0;
PeptideProteinNameSet pps = ProteinListToPPNSet(proList);
root = new DefaultMutableTreeNode(pps);
HashSet<String> usedProteins = new HashSet<String>();
for (Protein p : proList) {
if (!usedProteins.contains(p.getName())) {
if (p.getEquivalent().size() > 0) {
ArrayList<Protein> equivList = new ArrayList<Protein>();
equivList.add(p);
equivList.addAll(p.getEquivalent());
PeptideProteinNameSet ppsEquiv = ProteinListToPPNSet(equivList);
ppsEquiv.setName(p.getName() + " Group (" + equivList.size() + ")");
child = new DefaultMutableTreeNode(ppsEquiv);
size++;
for (Protein ps : equivList) {
child.add(new DefaultMutableTreeNode(ps));
usedProteins.add(ps.getName());
}
root.add(child);
} else {
root.add(new DefaultMutableTreeNode(p));
usedProteins.add(p.getName());
size++;
}
}
}
pps.setName(name + " (" + size + ")");
return root;
}
private PeptideProteinNameSet ProteinListToPPNSet(ArrayList<Protein> proteins) {
Set<String> protNames = new HashSet<String>();
Set<String> pepNames = new HashSet<String>();
for (Protein p : proteins) {
protNames.add(p.getName());
pepNames.addAll(p.getPeptides());
}
PeptideProteinNameSet pps = new PeptideProteinNameSet();
pps.setPeptides(pepNames);
pps.setProteins(protNames);
return pps;
}
private DefaultMutableTreeNode getPeptideTree(ExperimentPanel expPanel, boolean useListPanel) {
DefaultMutableTreeNode root;
if (useListPanel) {
root = new DefaultMutableTreeNode(getPeptideListPanel(expPanel));
} else {
PeptideProteinNameSet pps = getPeptideProteinNameSet();
pps.setName("Peptides (" + pps.getPeptides().size() + ")");
root = new DefaultMutableTreeNode(pps);
}
DefaultMutableTreeNode child;
ArrayList<Peptide> sortPeptides = new ArrayList<Peptide>();
sortPeptides.addAll(minPeptides.values());
Collections.sort(sortPeptides);
for (Peptide pg : sortPeptides) {
// child = pg.getTree();
child = new DefaultMutableTreeNode(pg);
root.add(child);
}
return root;
}
private DefaultMutableTreeNode getProteinTree(ExperimentPanel expPanel, boolean useListPanel) {
DefaultMutableTreeNode root;
if (useListPanel) {
ProteinListPanel plp = getProteinListPanel(expPanel);
root = new DefaultMutableTreeNode(plp);
} else {
PeptideProteinNameSet pps = getPeptideProteinNameSet();
pps.setName("Proteins (" + pps.getProteins().size() + ")");
root = new DefaultMutableTreeNode(pps);
}
DefaultMutableTreeNode child;
ArrayList<Protein> sortProteins = new ArrayList<Protein>();
sortProteins.addAll(minProteins.values());
Collections.sort(sortProteins);
for (Protein prot : sortProteins) {
// child = prot.getTree(expPanel);
child = new DefaultMutableTreeNode(prot);
root.add(child);
}
return root;
}
private DefaultMutableTreeNode getParsimonyTree(ExperimentPanel expPanel) {
DefaultMutableTreeNode root = new DefaultMutableTreeNode(getParsimonyListPanel(expPanel));
DefaultMutableTreeNode child;
// Discrete
PeptideProteinNameSet pps = ProteinListToPPNSet(getDiscretes());
pps.setName("Discrete (" + getDiscretes().size() + ")");
child = new DefaultMutableTreeNode(pps);
for (Protein p : getDiscretes()) {
child.add(new DefaultMutableTreeNode(p));
}
root.add(child);
// Differentiable
pps = ProteinListToPPNSet(getDifferentiables());
pps.setName("Differentiable (" + getDifferentiables().size() + ")");
child = new DefaultMutableTreeNode(pps);
for (Protein p : getDifferentiables()) {
child.add(new DefaultMutableTreeNode(p));
}
root.add(child);
// Superset
child = ProListToEquivTree(getSupersets(), "Superset");
root.add(child);
// Subsumable
child = ProListToEquivTree(getSubsumables(), "Subsumable");
root.add(child);
// Subset
child = ProListToEquivTree(getSubsets(), "Subset");
root.add(child);
// Equivalent
child = ProListToEquivTree(getEquivalents(), "Equivalent");
root.add(child);
return root;
}
private PeptideProteinNameSet getPeptideProteinNameSet() {
PeptideProteinNameSet pps = new PeptideProteinNameSet();
pps.setPeptides(minPeptides.keySet());
pps.setProteins(minProteins.keySet());
return pps;
}