/**
* 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;
}
public void appendProteins(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> psms = new ArrayList<IdentifiedPSM>(pps);
Collections.sort(psms);
out.append(protein);
for (IdentifiedPSM psm : psms) {
out.append("\t");
IPolypeptide unModified = psm.getPeptide(); // .getUnModified();
out.append(unModified.toString());
out.append("\t");
out.append(psm.getId());
}
out.append("\n");
}
} catch (Exception e) {
throw new RuntimeException(e);
}
}
protected void writePeptide(IPolypeptide pp, List<KeyValueObject<String, String>> holder) {
long numberFragments = getAndIncrementFragmentIndex();
String str = pp.toString();
holder.add(new KeyValueObject<String, String>(str, pp.toString()));
}
public void setDecoy(boolean isso) {
if (m_Peptide == null) return;
if (m_Peptide.isDecoy() == isso) return;
if (isso) m_Peptide = m_Peptide.asDecoy();
}
public boolean isDecoy() {
if (m_Peptide != null) return m_Peptide.isDecoy();
else return false;
}