public void appendPeptides(Appendable out) {
try {
List<String> proteins = new ArrayList<String>(proteinToHits.keySet());
Collections.sort(proteins);
for (String protein : proteins) {
Set<IdentifiedPSM> pps = proteinToHits.get(protein);
List<IdentifiedPSM> peptides = new ArrayList<IdentifiedPSM>(pps);
Collections.sort(peptides);
for (IdentifiedPSM psm : peptides) {
Polypeptide peptide = (Polypeptide) psm.getPeptide(); // .getUnModified();
out.append(peptide.toString());
out.append("\t");
out.append(psm.getId());
out.append("\t");
out.append(protein);
out.append("\t");
String rt = String.format("%11.3f", peptide.getRetentionTime()).trim();
out.append(rt);
out.append("\n");
}
}
} catch (Exception e) {
throw new RuntimeException(e);
}
}
public static IdentifiedPSM processPeptide(final String line, double retentionTime, String id) {
String peptide = XMLUtil.extractAttribute(line, "peptide");
if (peptide == null) throw new IllegalArgumentException("bad line " + line);
Polypeptide polypeptide = Polypeptide.fromString(peptide);
polypeptide.setRetentionTime(retentionTime);
return new IdentifiedPSM(id, polypeptide);
}