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);
}