/**
* 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;
}
@SuppressWarnings({"UnusedParameters", "UnusedAssignment"})
protected boolean handleSearchHit(
String[] lines,
double retentionTime,
boolean onlyUniquePeptides,
ISpectrumDataFilter... filters) {
//noinspection UnnecessaryLocalVariable,UnusedDeclaration,UnusedAssignment
Double expectedValue = null;
//noinspection UnnecessaryLocalVariable,UnusedDeclaration,UnusedAssignment
Double hyperScoreValue = null;
int index = 0;
String line = lines[index++]; // handle first line
while (!line.contains("<search_hit")) {
line = lines[index++];
if (index >= lines.length) return false;
}
String id = scan_id;
if ("".equals(id)) throw new UnsupportedOperationException("Fix This"); // ToDo
boolean trueHit = !line.contains("protein=\"DECOY_");
boolean processSpectrum = parseHitValue(line) <= 2;
//noinspection UnnecessaryLocalVariable,UnusedDeclaration,UnusedAssignment
boolean isUnique = true;
//noinspection UnnecessaryLocalVariable,UnusedDeclaration,UnusedAssignment
boolean isModified = false;
if (!line.contains("hit_rank=\"1\"")) return false;
IdentifiedPSM peptide = processPeptide(line, retentionTime, id);
IProtein protein = null;
for (; index < lines.length; index++) {
line = lines[index];
if (line.contains("</search_hit")) break; // we are done
if (line.contains(" modified_peptide="))
peptide = processModifiedPeptide(line, retentionTime, id);
if (line.contains("<alternative_protein")) {
isUnique = false;
if (onlyUniquePeptides) processSpectrum = false; // only process unique hits
}
if (line.contains("<search_score name=\"hyperscore\" value=\"")) {
hyperScoreValue = parseValue(line);
}
if (line.contains("<search_score name=\"expect\" value=\"")) {
expectedValue = parseValue(line);
}
if (line.contains("protein=\"DECOY_")) { // another protein
if (trueHit) processSpectrum = false; // one decoy one not
}
if (line.contains("<alternative_protein")) { // another protein
if (!trueHit && !line.contains("protein=\"DECOY_")) // we start as decoy and fit to a real
processSpectrum = false; // one decoy one not
}
if (line.contains("protein_descr=\"")) {
protein = processProtein(line);
}
}
if (processSpectrum) {
@SuppressWarnings("ConstantConditions")
String idP = protein.getId();
if (id.contains("DECOY")) return false;
Set<IdentifiedPSM> pps = proteinToHits.get(idP);
if (pps == null) {
pps = new HashSet<IdentifiedPSM>();
proteinToHits.put(idP, pps);
}
pps.add(peptide);
return true; // processed
}
return false; // unprocessed
}