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 PeptideCollection getNonIndeterminents() {
PeptideCollection pc = new PeptideCollection();
for (PeptideHit p : peptideHits) {
if (!p.isIndeterminate()) {
pc.addPeptideHit(p);
}
}
return pc;
}
public PeptideCollection filterByProteinCoverage(int minCoverage) {
HashSet<String> proDiscard = new HashSet<String>();
for (String pName : minProteins.keySet()) {
Protein p = minProteins.get(pName);
if (p.getCoveragePercent() < minCoverage) {
proDiscard.add(pName);
}
}
PeptideCollection new_pc = new PeptideCollection();
for (PeptideHit ph : peptideHits) {
new_pc.addPeptideHit(ph.maskProtein(proDiscard));
}
new_pc.createProteinList();
return new_pc;
}
public PeptideCollection filterByPeptidePerProtein(int numPeps) {
HashSet<String> proDiscard = new HashSet<String>();
for (String pName : minProteins.keySet()) {
Protein p = minProteins.get(pName);
if (p.getNumUniquePeptides() < numPeps) {
proDiscard.add(pName);
}
}
PeptideCollection new_pc = new PeptideCollection();
for (PeptideHit ph : peptideHits) {
new_pc.addPeptideHit(ph.maskProtein(proDiscard));
}
new_pc.createProteinList();
return new_pc;
}
private DefaultMutableTreeNode getClusterTree(ExperimentPanel expPanel) {
DefaultMutableTreeNode root = new DefaultMutableTreeNode(getClusterListPanel(expPanel));
DefaultMutableTreeNode child, grandchild;
// Sort by cluster num
ArrayList<Integer> sortClusterNum = new ArrayList<Integer>();
sortClusterNum.addAll(clusters.keySet());
Collections.sort(sortClusterNum);
for (Integer i : sortClusterNum) {
PeptideCollection pc = clusters.get(i);
child = new DefaultMutableTreeNode(pc);
root.add(child);
grandchild = pc.getPeptideTree(expPanel, false);
child.add(grandchild);
grandchild = pc.getProteinTree(expPanel, false);
child.add(grandchild);
}
return root;
}
public int compareTo(PeptideCollection pc) {
int x = getNumElements();
int y = pc.getNumElements();
if (x > y) {
return -1;
}
if (x < y) {
return 1;
}
return 0;
}
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++;
}
}
}
// public PeptideCollection getCutoffCollection(double omssa, double mascot, double xtandem) {
// return getCutoffCollection(omssa, mascot, xtandem, false);
// }
public PeptideCollection getCutoffCollection(FilterSettings fs) {
PeptideCollection pc = new PeptideCollection();
for (PeptideHit p : peptideHits) {
if (fs.getUsePepProphet() && p.isPepXML()) {
if (p.getPepProphet() >= fs.getPeptideProphetCutoff()) {
pc.addPeptideHit(p);
}
} else {
switch (p.getSourceType()) {
case MASCOT:
if (fs.getUseIonIdent()) {
if (p.getIonScore() >= p.getIdent()) {
pc.addPeptideHit(p);
}
} else if (p.getExpect() <= fs.getMascotCutoff()) {
pc.addPeptideHit(p);
}
break;
case OMSSA:
if (p.getExpect() <= fs.getOmssaCutoff()) {
pc.addPeptideHit(p);
}
break;
case XTANDEM:
if (p.getExpect() <= fs.getXtandemCutoff()) {
pc.addPeptideHit(p);
}
break;
case SEQUEST:
if (p.getExpect() <= fs.getSequestCutoff()) {
pc.addPeptideHit(p);
}
break;
case PEPXML:
if (!p.CanGetPepProphet() || (p.getPepProphet() >= fs.getPeptideProphetCutoff())) {
pc.addPeptideHit(p);
}
break;
}
}
}
return pc;
}