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 void setPeptideId(final String pPeptideId) {
if (m_Peptide != null || m_PeptideId != null)
throw new IllegalStateException("Cannot reset peptide"); // ToDo change
m_PeptideId = pPeptideId;
IMainData main = getMainData();
if (main != null) {
// RawPeptideScan rawScan = main.getRawScan(getId());
// pMeasured = rawScan;
ITaxonomy taxonomy = main.getTaxonomy();
if (taxonomy != null) {
String peptideId = getPeptideId();
m_Peptide = taxonomy.getPeptideById(peptideId);
if (m_Peptide == null)
m_Peptide = Polypeptide.fromString(peptideId); // key may be all we need
}
} else {
m_Peptide = Polypeptide.fromString(getPeptideId());
}
if (m_Peptide != null) {
IPeptideDigester digester = PeptideBondDigester.getDefaultDigester();
int missedCleavages = digester.probableNumberMissedCleavages(m_Peptide);
((Polypeptide) m_Peptide).setMissedCleavages(missedCleavages);
}
}
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);
}
/** finish handling and set up the enclosed object Usually called when the end tag is seen */
@Override
public void finishProcessing() {
IMeasuredSpectrum pMeasured = null;
final double pScore = getScore();
final double pHyperScore = getHyperScore();
final double rawScore = getRawScore();
IonTypeScorer scorer = getIonScore();
IProteinPosition[] containedInProteins = m_Positions.toArray(IProteinPosition.EMPTY_ARRAY);
((Polypeptide) m_Peptide).setContainedInProteins(containedInProteins);
SpectralMatch scan =
new SpectralMatch(m_Peptide, pMeasured, pScore, pHyperScore, rawScore, scorer, null);
if (m_Usage != null) scan.getUsage().addTo(m_Usage);
setElementObject(scan);
}