/** * 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; }