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);
}
}
/**
* this is what a Mapper does
*
* @param keyin
* @param valuein
* @return iterator over mapped key values
*/
@Nonnull
@Override
public Iterable<KeyValueObject<String, String>> mapValues(
@Nonnull final String annotation, @Nonnull final String sequence) {
List<KeyValueObject<String, String>> holder = new ArrayList<KeyValueObject<String, String>>();
IPeptideDigester digester = getDigester();
IProtein prot = Protein.getProtein(annotation, annotation, sequence, null);
// do a boolean for a peptide belonging to a decoy protein, but use the public isDecoy
// boolean/method in Protein class
boolean isDecoy = prot.isDecoy();
IPolypeptide[] pps = digester.digest(prot);
PeptideModification[] modifications1 = getModifications();
for (int i = 0; i < pps.length; i++) {
IPolypeptide pp = pps[i];
if (!pp.isValid()) continue;
// hadoop write intermediate seq finder
writePeptide(pp, holder);
// if(isDecoy)
// continue; // skip the rest of the loop
// if it is decoy, don't add modifications to it
if (!isDecoy || isGenerateDecoysForModifiedPeptides()) {
// generate modified peptides and add to the output
IModifiedPeptide[] modifications =
ModifiedPolypeptide.buildModifications(pp, modifications1);
for (int m = 0; m < modifications.length; m++) {
IModifiedPeptide modification = modifications[m];
writePeptide(modification, holder);
}
}
}
boolean semiTryptic = digester.isSemiTryptic();
if (semiTryptic) {
IPolypeptide[] semipps = digester.addSemiCleavages(prot);
for (int j = 0; j < semipps.length; j++) {
IPolypeptide semipp = semipps[j];
if (!semipp.isValid()) continue;
writePeptide(semipp, holder);
IModifiedPeptide[] modifications =
ModifiedPolypeptide.buildModifications(semipp, modifications1);
for (int k = 0; k < modifications.length; k++) {
IModifiedPeptide modification = modifications[k];
writePeptide(modification, holder);
}
}
}
return holder;
}